Search to RefSeqBP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-012820
(1104 letters)
Database: RefSeq49_BP.fasta
33,088 sequences; 17,681,374 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001014861.1| oxysterols receptor LXR-alpha [Bos taurus]. 465 e-136
Alignment gi|NP_001014883.1| oxysterols receptor LXR-beta [Bos taurus]. 267 7e-76
Alignment gi|NP_001029880.1| bile acid receptor [Bos taurus]. 140 2e-33
Alignment gi|XP_002698801.1| PREDICTED: thyroid hormone receptor, beta (e... 111 1e-25
Alignment gi|NP_001124228.1| retinoic acid receptor, gamma [Bos taurus]. 104 4e-24
Alignment gi|XP_001255422.2| PREDICTED: thyroid hormone receptor, beta (e... 107 1e-23
Alignment gi|NP_001161404.1| vitamin D3 receptor [Bos taurus]. 104 1e-22
Alignment gi|NP_001073236.1| nuclear receptor subfamily 1 group I member ... 101 1e-21
Alignment gi|NP_001014942.2| retinoic acid receptor, alpha [Bos taurus]. 99 7e-21
Alignment gi|NP_001161372.1| photoreceptor-specific nuclear receptor [Bos... 99 7e-21
>ref|NP_001014861.1| oxysterols receptor LXR-alpha [Bos taurus].
Length = 447
Score = 465 bits (1197), Expect(2) = e-136
Identities = 231/272 (84%), Positives = 235/272 (86%)
Frame = +3
Query: 231 MSLWVEAPVPDVSPDSAVELWEXXXXXXXXXXXXXXXCILREESSTPQSAGGASRVGLDA 410
MSLW+EAPVPDVSPDSAVELWE CILREESSTPQSAG SR+GL+A
Sbjct: 1 MSLWLEAPVPDVSPDSAVELWEPDAQDASSQPLGSSKCILREESSTPQSAGDTSRMGLEA 60
Query: 411 TESTALLPGVEASPESTELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG 590
E TALLPGVEA PESTELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG
Sbjct: 61 PEPTALLPGVEAPPESTELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG 120
Query: 591 FFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLK 770
FFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKK+K
Sbjct: 121 FFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKMK 180
Query: 771 RQEEEQAQATSVPPRAXXXXXXXXXXXXXXXGMIEKLVAAQQQCNRRSFSDQLRVTPWPM 950
RQEEEQAQATS PPRA GMIEKLVAAQQ CNRRSFSDQLRVTPWPM
Sbjct: 181 RQEEEQAQATSAPPRASSPPQVLPQLSPEQLGMIEKLVAAQQLCNRRSFSDQLRVTPWPM 240
Query: 951 APDPQSREARQQRFAHFTELAIVSVQEIVDFA 1046
APDPQSREARQQRFAHFTELAIVSVQEIVDFA
Sbjct: 241 APDPQSREARQQRFAHFTELAIVSVQEIVDFA 272
Score = 39.3 bits (90), Expect(2) = e-136
Identities = 19/21 (90%), Positives = 19/21 (90%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F KQL GFLQLSREDQIALLK
Sbjct: 271 FAKQLPGFLQLSREDQIALLK 291
>ref|NP_001014883.1| oxysterols receptor LXR-beta [Bos taurus].
Length = 498
Score = 267 bits (682), Expect(2) = 7e-76
Identities = 142/262 (54%), Positives = 173/262 (66%), Gaps = 34/262 (12%)
Frame = +3
Query: 363 STPQSAGGASRVGLD-----ATESTALLPGVEASP-----ESTELRPQKRKKGPAPKMLG 512
STP S+ G G + A G +++ ++ E +KRKKGPAPKMLG
Sbjct: 19 STPSSSPGGKEDGPEPCPGGADPDVPSTDGADSASVVVILDTAEEPERKRKKGPAPKMLG 78
Query: 513 NELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKG--ARYVCHSGGHCPMDTYMRRKCQE 686
+ELC VCGD ASGFHYNVLSCEGCKGFFRRSVI+G RY C GG C MD +MRRKCQ+
Sbjct: 79 DELCQVCGDTASGFHYNVLSCEGCKGFFRRSVIRGGAGRYACRGGGTCQMDAFMRRKCQQ 138
Query: 687 CRLRKCRQAGMREECVLSEEQIRLKKLKRQEEEQAQ---------ATSVPPRAXXXXXXX 839
CRLRKC++AGMRE+CVLS+EQIR KK+++Q+++Q Q ++S P
Sbjct: 139 CRLRKCKEAGMREQCVLSKEQIRKKKIRKQQQQQQQQSSPTGPGVSSSSPASGPGASPGG 198
Query: 840 XXXXXXXXG-------------MIEKLVAAQQQCNRRSFSDQLRVTPWPMAPDPQSREAR 980
G MI++LVAAQ QCN+RSFSDQ +VTPWP+ DPQSR+AR
Sbjct: 199 SDGGGQGSGEGEGVQLTAAQELMIQQLVAAQLQCNKRSFSDQPKVTPWPLGADPQSRDAR 258
Query: 981 QQRFAHFTELAIVSVQEIVDFA 1046
QQRFAHFTELAI+SVQEIVDFA
Sbjct: 259 QQRFAHFTELAIISVQEIVDFA 280
Score = 36.6 bits (83), Expect(2) = 7e-76
Identities = 17/21 (80%), Positives = 18/21 (85%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F KQ+ GFLQL REDQIALLK
Sbjct: 279 FAKQVPGFLQLGREDQIALLK 299
>ref|NP_001029880.1| bile acid receptor [Bos taurus].
Length = 482
Score = 140 bits (354), Expect = 2e-33
Identities = 60/99 (60%), Positives = 79/99 (79%)
Frame = +3
Query: 495 APKMLGNELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGARYVCHSGGHCPMDTYMRR 674
A ++ G+ELC VCGD+ASG+HYN L+CEGCKGFFRRS+ K A Y C +GG+C MD YMRR
Sbjct: 128 AGRIKGDELCVVCGDRASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCVMDMYMRR 187
Query: 675 KCQECRLRKCRQAGMREECVLSEEQIRLKKLKRQEEEQA 791
KCQECRLRKC++ GM EC+L+E Q + K+L++ ++ A
Sbjct: 188 KCQECRLRKCKEMGMLAECLLTEIQCKSKRLRKNVKQHA 226
>ref|XP_002698801.1| PREDICTED: thyroid hormone receptor, beta (erythroblastic leukemia
viral (v-erb-a) oncogene homolog 2, avian) [Bos taurus].
Length = 520
Score = 111 bits (277), Expect(2) = 1e-25
Identities = 66/218 (30%), Positives = 109/218 (50%), Gaps = 9/218 (4%)
Frame = +3
Query: 441 EASPESTELRPQKRK-KGPAPKMLG-NELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIK 614
+++P + + +++K KG P L +ELC VCGDKA+G+HY ++CEGCKGFFRR++ K
Sbjct: 137 QSAPSAQTFQTEEKKCKGYIPSYLDKDELCVVCGDKATGYHYRCITCEGCKGFFRRTIQK 196
Query: 615 GAR--YVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSE-EQIRLKKLKRQEEE 785
Y C G C +D R +CQECR +KC GM + VL + +++ +KL + E
Sbjct: 197 NLHPSYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLAKRKLIEENRE 256
Query: 786 QAQATSVPPRAXXXXXXXXXXXXXXXGMIEKLVAAQQQCN----RRSFSDQLRVTPWPMA 953
+ + + + E VA Q + +R F + + P+
Sbjct: 257 KRRREELQRSMGHKPEPTDQEWELIKTVTEAHVATNAQGSHWKQKRKFLPE-DIGQAPIV 315
Query: 954 PDPQSREARQQRFAHFTELAIVSVQEIVDFANSXQASC 1067
P+ + + F+HFT++ ++ +VDFA C
Sbjct: 316 NAPEGGKVDLEAFSHFTKIITPAITRVVDFAKKLPMFC 353
Score = 24.3 bits (51), Expect(2) = 1e-25
Identities = 12/21 (57%), Positives = 14/21 (66%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F K+L F +L EDQI LLK
Sbjct: 345 FAKKLPMFCELPCEDQIILLK 365
>ref|NP_001124228.1| retinoic acid receptor, gamma [Bos taurus].
Length = 458
Score = 104 bits (259), Expect(2) = 4e-24
Identities = 65/215 (30%), Positives = 104/215 (48%), Gaps = 1/215 (0%)
Frame = +3
Query: 405 DATESTALLPGVEASPESTELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGC 584
D + A L S S E+ P P P++ + C VC DK+SG+HY V SCEGC
Sbjct: 53 DLPKEMASLSVETQSTSSEEMVPSSPSPPPPPRVY--KPCFVCNDKSSGYHYGVSSCEGC 110
Query: 585 KGFFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKK 764
KGFFRRS+ K Y CH +C ++ R +CQ CRL+KC + GM +E V ++ + K+
Sbjct: 111 KGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKEAVRNDRNKKKKE 170
Query: 765 LKRQEEEQAQATSVPPRAXXXXXXXXXXXXXXXGMIEKLVAAQQQCNRRSFSDQLRVTPW 944
+K EE + + P+ +E+L+ + ++ +F ++ +
Sbjct: 171 VK--EEGSLDSYELSPQ------------------LEELITKVSKAHQETFPSLCQLGKY 210
Query: 945 PMAPDPQSR-EARQQRFAHFTELAIVSVQEIVDFA 1046
R + + F+ELA + +IV+FA
Sbjct: 211 TTNSSADHRVQLDLGLWDKFSELATKCIIKIVEFA 245
Score = 26.2 bits (56), Expect(2) = 4e-24
Identities = 13/21 (61%), Positives = 14/21 (66%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F K+L GF LS DQI LLK
Sbjct: 244 FAKRLPGFTGLSIADQITLLK 264
>ref|XP_001255422.2| PREDICTED: thyroid hormone receptor, beta (erythroblastic leukemia
viral (v-erb-a) oncogene homolog 2, avian), partial [Bos
taurus].
Length = 328
Score = 107 bits (268), Expect = 1e-23
Identities = 61/195 (31%), Positives = 96/195 (49%), Gaps = 7/195 (3%)
Frame = +3
Query: 513 NELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAR--YVCHSGGHCPMDTYMRRKCQE 686
+ELC VCGDKA+G+HY ++CEGCKGFFRR++ K Y C G C +D R +CQE
Sbjct: 9 DELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQE 68
Query: 687 CRLRKCRQAGMREECVLSE-EQIRLKKLKRQEEEQAQATSVPPRAXXXXXXXXXXXXXXX 863
CR +KC GM + VL + +++ +KL + E+ + +
Sbjct: 69 CRFKKCIYVGMATDLVLDDSKRLAKRKLIEENREKRRREELQRSMGHKPEPTDQEWELIK 128
Query: 864 GMIEKLVAAQQQCN----RRSFSDQLRVTPWPMAPDPQSREARQQRFAHFTELAIVSVQE 1031
+ E VA Q + +R F + + P+ P+ + + F+HFT++ ++
Sbjct: 129 TVTEAHVATNAQGSHWKQKRKFLPE-DIGQAPIVNAPEGGKVDLEAFSHFTKIITPAITR 187
Query: 1032 IVDFANSXQASCSSA 1076
+VDFA C A
Sbjct: 188 VVDFAKKLPMFCEMA 202
>ref|NP_001161404.1| vitamin D3 receptor [Bos taurus].
Length = 426
Score = 104 bits (260), Expect = 1e-22
Identities = 45/92 (48%), Positives = 66/92 (71%), Gaps = 3/92 (3%)
Frame = +3
Query: 519 LCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLR 698
+C VCGD+A+GFH+N ++CEGCKGFFRRS+ + A + C G C + RR CQ CRL+
Sbjct: 23 ICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLK 82
Query: 699 KCRQAGMREECVLSEEQIRLKK---LKRQEEE 785
+C GM +E +L++E+++ K+ LKR+EEE
Sbjct: 83 RCIDIGMMKEFILTDEEVQRKREMILKRKEEE 114
>ref|NP_001073236.1| nuclear receptor subfamily 1 group I member 3 [Bos taurus].
Length = 348
Score = 101 bits (251), Expect = 1e-21
Identities = 44/95 (46%), Positives = 65/95 (68%)
Frame = +3
Query: 522 CSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRK 701
C+VCGD+A+G+H++ L+CEGCKGFFRR+V K C G C ++ RR C CRL+K
Sbjct: 11 CAVCGDRATGYHFHALTCEGCKGFFRRTVNKSTSLTCPFAGSCEVNKAQRRHCPACRLQK 70
Query: 702 CRQAGMREECVLSEEQIRLKKLKRQEEEQAQATSV 806
C AGM+++ +LS E + L++ RQ + +AQ S+
Sbjct: 71 CLDAGMKKDMILSTEALALRR-ARQAQRRAQQGSM 104
>ref|NP_001014942.2| retinoic acid receptor, alpha [Bos taurus].
Length = 462
Score = 99.0 bits (245), Expect = 7e-21
Identities = 46/111 (41%), Positives = 67/111 (60%)
Frame = +3
Query: 447 SPESTELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGARY 626
S S E+ P P P++ + C VC DK+SG+HY V +CEGCKGFFRRS+ K Y
Sbjct: 65 SSSSEEIVPSPPSPPPLPRIY--KPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVY 122
Query: 627 VCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLKRQE 779
CH +C ++ R +CQ CRL+KC + GM +E V ++ + K++ + E
Sbjct: 123 TCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKKKKEVPKPE 173
>ref|NP_001161372.1| photoreceptor-specific nuclear receptor [Bos taurus].
Length = 411
Score = 99.0 bits (245), Expect = 7e-21
Identities = 54/145 (37%), Positives = 80/145 (55%), Gaps = 8/145 (5%)
Frame = +3
Query: 402 LDATESTALLPGVEASPESTELRPQKRKKGPAPKMLGNEL-CSVCGDKASGFHYNVLSCE 578
+ + + A+ V AS + + P + G P +G L C VCGD +SG HY + +C
Sbjct: 1 MSSNVAAAVPAAVSASRKES---PGRWGLGEEPTGVGPSLQCRVCGDSSSGKHYGIYACN 57
Query: 579 GCKGFFRRSVIKGARYVCHSG-GHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEE--- 746
GC GFF+RSV + Y C G G CP+D R +CQ CRL+KC QAGM ++ V +E
Sbjct: 58 GCSGFFKRSVRRRLIYRCQVGAGMCPVDKAHRNQCQACRLKKCLQAGMNQDAVQNERQPR 117
Query: 747 ---QIRLKKLKRQEEEQAQATSVPP 812
Q+R+ ++ + E + Q + PP
Sbjct: 118 STAQVRMDSVESETEPRLQPLATPP 142
Database: RefSeq49_BP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 17,681,374
Number of sequences in database: 33,088
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33088
Number of Hits to DB: 52,155,242
Number of extensions: 1908472
Number of successful extensions: 14655
Number of sequences better than 1.0e-05: 67
Number of HSP's gapped: 14214
Number of HSP's successfully gapped: 72
Length of query: 368
Length of database: 17,681,374
Length adjustment: 104
Effective length of query: 264
Effective length of database: 14,240,222
Effective search space: 3759418608
Effective search space used: 3759418608
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 35 (18.1 bits)
Animal-Genome cDNA 20110601C-012820
Search to RefSeqCP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-012820
(1104 letters)
Database: RefSeq49_CP.fasta
33,336 sequences; 18,874,504 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|XP_540745.1| PREDICTED: similar to Oxysterols receptor LXR-a... 447 e-130
Alignment gi|XP_851316.1| PREDICTED: similar to Oxysterols receptor LXR-b... 276 1e-78
Alignment gi|XP_863477.1| PREDICTED: similar to Oxysterols receptor LXR-b... 254 5e-72
Alignment gi|XP_848688.1| PREDICTED: similar to nuclear receptor subfamil... 137 2e-32
Alignment gi|XP_866622.1| PREDICTED: similar to Bile acid receptor (Farne... 137 2e-32
Alignment gi|XP_852959.1| PREDICTED: similar to nuclear receptor subfamil... 137 2e-32
Alignment gi|XP_862690.1| PREDICTED: similar to thyroid hormone receptor,... 110 2e-25
Alignment gi|XP_542762.1| PREDICTED: similar to Thyroid hormone receptor ... 110 2e-25
Alignment gi|XP_862616.1| PREDICTED: similar to thyroid hormone receptor,... 110 3e-25
Alignment gi|XP_862596.1| PREDICTED: similar to thyroid hormone receptor,... 109 5e-25
>ref|XP_540745.1| PREDICTED: similar to Oxysterols receptor LXR-alpha (Liver X receptor
alpha) (Nuclear orphan receptor LXR-alpha) [Canis
familiaris].
Length = 447
Score = 447 bits (1149), Expect(2) = e-130
Identities = 220/272 (80%), Positives = 226/272 (83%)
Frame = +3
Query: 231 MSLWVEAPVPDVSPDSAVELWEXXXXXXXXXXXXXXXCILREESSTPQSAGGASRVGLDA 410
MSLW+EAPVPD SPDSA ELWE CIL EE+ TPQSAGG+ GL A
Sbjct: 1 MSLWLEAPVPDASPDSAAELWEPDTQDASSQALGGNDCILGEEAGTPQSAGGSLGAGLQA 60
Query: 411 TESTALLPGVEASPESTELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG 590
E T LLPGV+ PES ELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG
Sbjct: 61 AEPTVLLPGVDTPPESAELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG 120
Query: 591 FFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLK 770
FFRRSVIKGA YVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLK
Sbjct: 121 FFRRSVIKGAHYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLK 180
Query: 771 RQEEEQAQATSVPPRAXXXXXXXXXXXXXXXGMIEKLVAAQQQCNRRSFSDQLRVTPWPM 950
RQEEEQAQATS+PPR GMIEKLVAAQQQCNRRSFSD+LRVTPWPM
Sbjct: 181 RQEEEQAQATSMPPRVSSPPQVLPQLSPEQRGMIEKLVAAQQQCNRRSFSDRLRVTPWPM 240
Query: 951 APDPQSREARQQRFAHFTELAIVSVQEIVDFA 1046
APDPQSREARQQRFAHFTELAIVSVQEIVDFA
Sbjct: 241 APDPQSREARQQRFAHFTELAIVSVQEIVDFA 272
Score = 39.3 bits (90), Expect(2) = e-130
Identities = 19/21 (90%), Positives = 19/21 (90%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F KQL GFLQLSREDQIALLK
Sbjct: 271 FAKQLPGFLQLSREDQIALLK 291
>ref|XP_851316.1| PREDICTED: similar to Oxysterols receptor LXR-beta (Liver X receptor
beta) (Nuclear orphan receptor LXR-beta)
(Ubiquitously-expressed nuclear receptor) (Nuclear
receptor NER) isoform 1 [Canis familiaris].
Length = 455
Score = 276 bits (706), Expect(2) = 1e-78
Identities = 136/220 (61%), Positives = 160/220 (72%), Gaps = 21/220 (9%)
Frame = +3
Query: 450 PESTELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGA--R 623
P+ E +KRKKGPAPKMLG+ELC VCGDKASGFHYNVLSCEGCKGFFRRSV++G R
Sbjct: 61 PDPAEEPERKRKKGPAPKMLGHELCRVCGDKASGFHYNVLSCEGCKGFFRRSVVRGGARR 120
Query: 624 YVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLKRQEEEQAQATS 803
Y C GG C MD +MRRKCQ+CRLRKC++AGMRE+CVLSEEQIR KK+++Q+++Q Q +
Sbjct: 121 YACRGGGTCQMDAFMRRKCQQCRLRKCKEAGMREQCVLSEEQIRKKKIRKQQQQQQQQSP 180
Query: 804 VPPRAXXXXXXXXXXXXXXXG-------------------MIEKLVAAQQQCNRRSFSDQ 926
V P G MI++LVAAQ QCN+RSFSDQ
Sbjct: 181 VGPMGSSTACGPGASPGGSDGGGQGSGEGEGIQLTAAQELMIQQLVAAQLQCNKRSFSDQ 240
Query: 927 LRVTPWPMAPDPQSREARQQRFAHFTELAIVSVQEIVDFA 1046
+VTPWP+ DPQSR+ARQQRFAHFTELAI+SVQEIVDFA
Sbjct: 241 PKVTPWPLGADPQSRDARQQRFAHFTELAIISVQEIVDFA 280
Score = 36.6 bits (83), Expect(2) = 1e-78
Identities = 17/21 (80%), Positives = 18/21 (85%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F KQ+ GFLQL REDQIALLK
Sbjct: 279 FAKQVPGFLQLGREDQIALLK 299
>ref|XP_863477.1| PREDICTED: similar to Oxysterols receptor LXR-beta (Liver X receptor
beta) (Nuclear orphan receptor LXR-beta)
(Ubiquitously-expressed nuclear receptor) (Nuclear
receptor NER) isoform 2 [Canis familiaris].
Length = 377
Score = 254 bits (649), Expect(2) = 5e-72
Identities = 125/202 (61%), Positives = 147/202 (72%), Gaps = 21/202 (10%)
Frame = +3
Query: 504 MLGNELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGA--RYVCHSGGHCPMDTYMRRK 677
MLG+ELC VCGDKASGFHYNVLSCEGCKGFFRRSV++G RY C GG C MD +MRRK
Sbjct: 1 MLGHELCRVCGDKASGFHYNVLSCEGCKGFFRRSVVRGGARRYACRGGGTCQMDAFMRRK 60
Query: 678 CQECRLRKCRQAGMREECVLSEEQIRLKKLKRQEEEQAQATSVPPRAXXXXXXXXXXXXX 857
CQ+CRLRKC++AGMRE+CVLSEEQIR KK+++Q+++Q Q + V P
Sbjct: 61 CQQCRLRKCKEAGMREQCVLSEEQIRKKKIRKQQQQQQQQSPVGPMGSSTACGPGASPGG 120
Query: 858 XXG-------------------MIEKLVAAQQQCNRRSFSDQLRVTPWPMAPDPQSREAR 980
G MI++LVAAQ QCN+RSFSDQ +VTPWP+ DPQSR+AR
Sbjct: 121 SDGGGQGSGEGEGIQLTAAQELMIQQLVAAQLQCNKRSFSDQPKVTPWPLGADPQSRDAR 180
Query: 981 QQRFAHFTELAIVSVQEIVDFA 1046
QQRFAHFTELAI+SVQEIVDFA
Sbjct: 181 QQRFAHFTELAIISVQEIVDFA 202
Score = 36.6 bits (83), Expect(2) = 5e-72
Identities = 17/21 (80%), Positives = 18/21 (85%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F KQ+ GFLQL REDQIALLK
Sbjct: 201 FAKQVPGFLQLGREDQIALLK 221
>ref|XP_848688.1| PREDICTED: similar to nuclear receptor subfamily 1, group H, member
5 isoform 1 [Canis familiaris].
Length = 490
Score = 137 bits (345), Expect = 2e-32
Identities = 58/91 (63%), Positives = 73/91 (80%)
Frame = +3
Query: 516 ELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRL 695
ELC VCGDKASG+HYN L+CEGCKGFFRRS+ K A Y C +GGHC MD YMRRKCQECRL
Sbjct: 119 ELCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYHCKNGGHCEMDMYMRRKCQECRL 178
Query: 696 RKCRQAGMREECVLSEEQIRLKKLKRQEEEQ 788
+KC+ GM EC+L+E Q + K+L++ +++
Sbjct: 179 KKCKAVGMLAECLLTEIQCKSKRLRKNFKQK 209
>ref|XP_866622.1| PREDICTED: similar to Bile acid receptor (Farnesoid X-activated
receptor) (Farnesol receptor HRR-1) (Retinoid X
receptor-interacting protein 14) (RXR-interacting
protein 14) isoform 2 [Canis familiaris].
Length = 455
Score = 137 bits (344), Expect = 2e-32
Identities = 62/111 (55%), Positives = 81/111 (72%), Gaps = 4/111 (3%)
Frame = +3
Query: 480 RKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGARYVCHSGGHCPMD 659
R A ++ G+ELC VCGD+ASG+HYN L+CEGCKGFFRRS+ K A Y C +GG+C MD
Sbjct: 92 RMGASAGRIKGDELCVVCGDRASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCVMD 151
Query: 660 TYMRRKCQECRLRKCRQAGMREEC----VLSEEQIRLKKLKRQEEEQAQAT 800
YMRRKCQECRLRKC++ GM EC +L+E Q + K+L++ ++ A T
Sbjct: 152 MYMRRKCQECRLRKCKEMGMLAECMYTGLLTEIQCKSKRLRKNVKQHADQT 202
>ref|XP_852959.1| PREDICTED: similar to nuclear receptor subfamily 1, group H, member
4 isoform 1 [Canis familiaris].
Length = 472
Score = 137 bits (344), Expect = 2e-32
Identities = 62/111 (55%), Positives = 81/111 (72%), Gaps = 4/111 (3%)
Frame = +3
Query: 480 RKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGARYVCHSGGHCPMD 659
R A ++ G+ELC VCGD+ASG+HYN L+CEGCKGFFRRS+ K A Y C +GG+C MD
Sbjct: 109 RMGASAGRIKGDELCVVCGDRASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCVMD 168
Query: 660 TYMRRKCQECRLRKCRQAGMREEC----VLSEEQIRLKKLKRQEEEQAQAT 800
YMRRKCQECRLRKC++ GM EC +L+E Q + K+L++ ++ A T
Sbjct: 169 MYMRRKCQECRLRKCKEMGMLAECMYTGLLTEIQCKSKRLRKNVKQHADQT 219
>ref|XP_862690.1| PREDICTED: similar to thyroid hormone receptor, beta isoform 10
[Canis familiaris].
Length = 467
Score = 110 bits (276), Expect(2) = 2e-25
Identities = 65/206 (31%), Positives = 102/206 (49%), Gaps = 8/206 (3%)
Frame = +3
Query: 474 QKRKKGPAPKMLG-NELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAR--YVCHSGG 644
+K+ KG P L +ELC VCGDKA+G+HY ++CEGCKGFFRR++ K Y C G
Sbjct: 96 EKKCKGYIPSYLDKDELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEG 155
Query: 645 HCPMDTYMRRKCQECRLRKCRQAGMREECVLSE-EQIRLKKLKRQEEEQAQATSVPPRAX 821
C +D R +CQECR +KC GM + VL + +++ +KL + E+ + +
Sbjct: 156 KCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLAKRKLIEENREKRRREELQKSIG 215
Query: 822 XXXXXXXXXXXXXXGMIEKLVAAQQQCN----RRSFSDQLRVTPWPMAPDPQSREARQQR 989
+ E VA Q + +R F + + P+ P+ + +
Sbjct: 216 HKPEPTDEEWELIKTVTEAHVATNAQGSHWKQKRKFLPE-DIGQAPIVNAPEGGKVDLEA 274
Query: 990 FAHFTELAIVSVQEIVDFANSXQASC 1067
F+HFT++ ++ +VDFA C
Sbjct: 275 FSHFTKIITPAITRVVDFAKKLPMFC 300
Score = 24.3 bits (51), Expect(2) = 2e-25
Identities = 12/21 (57%), Positives = 14/21 (66%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F K+L F +L EDQI LLK
Sbjct: 292 FAKKLPMFCELPCEDQIILLK 312
>ref|XP_542762.1| PREDICTED: similar to Thyroid hormone receptor beta-2 isoform 1
[Canis familiaris].
Length = 476
Score = 110 bits (275), Expect(2) = 2e-25
Identities = 65/203 (32%), Positives = 100/203 (49%), Gaps = 8/203 (3%)
Frame = +3
Query: 483 KKGPAPKMLG-NELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAR--YVCHSGGHCP 653
KKG P L +ELC VCGDKA+G+HY ++CEGCKGFFRR++ K Y C G C
Sbjct: 108 KKGYIPSYLDKDELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCV 167
Query: 654 MDTYMRRKCQECRLRKCRQAGMREECVLSE-EQIRLKKLKRQEEEQAQATSVPPRAXXXX 830
+D R +CQECR +KC GM + VL + +++ +KL + E+ + +
Sbjct: 168 IDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLAKRKLIEENREKRRREELQKSIGHKP 227
Query: 831 XXXXXXXXXXXGMIEKLVAAQQQCN----RRSFSDQLRVTPWPMAPDPQSREARQQRFAH 998
+ E VA Q + +R F + + P+ P+ + + F+H
Sbjct: 228 EPTDEEWELIKTVTEAHVATNAQGSHWKQKRKFLPE-DIGQAPIVNAPEGGKVDLEAFSH 286
Query: 999 FTELAIVSVQEIVDFANSXQASC 1067
FT++ ++ +VDFA C
Sbjct: 287 FTKIITPAITRVVDFAKKLPMFC 309
Score = 24.3 bits (51), Expect(2) = 2e-25
Identities = 12/21 (57%), Positives = 14/21 (66%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F K+L F +L EDQI LLK
Sbjct: 301 FAKKLPMFCELPCEDQIILLK 321
>ref|XP_862616.1| PREDICTED: similar to thyroid hormone receptor, beta isoform 8 [Canis
familiaris].
Length = 476
Score = 110 bits (274), Expect(2) = 3e-25
Identities = 68/214 (31%), Positives = 104/214 (48%), Gaps = 16/214 (7%)
Frame = +3
Query: 474 QKRKKGPAPKMLG-NELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAR--YVCHSGG 644
+K+ KG P L +ELC VCGDKA+G+HY ++CEGCKGFFRR++ K Y C G
Sbjct: 96 EKKCKGYIPSYLDKDELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEG 155
Query: 645 HCPMDTYMRRKCQECRLRKCRQAGMREECVLSE-EQIRLKKLKRQEEEQAQATSVPPRAX 821
C +D R +CQECR +KC GM + VL + +++ +KL + E+ + +
Sbjct: 156 KCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLAKRKLIEENREKRRREELQKSIG 215
Query: 822 XXXXXXXXXXXXXXGMIEKLVAAQQQCN----RRSF--SDQLRVTP------WPMAPDPQ 965
+ E VA Q + +R F S L +T P+ P+
Sbjct: 216 HKPEPTDEEWELIKTVTEAHVATNAQGSHWKQKRKFLVSTSLTITKPEDIGQAPIVNAPE 275
Query: 966 SREARQQRFAHFTELAIVSVQEIVDFANSXQASC 1067
+ + F+HFT++ ++ +VDFA C
Sbjct: 276 GGKVDLEAFSHFTKIITPAITRVVDFAKKLPMFC 309
Score = 24.3 bits (51), Expect(2) = 3e-25
Identities = 12/21 (57%), Positives = 14/21 (66%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F K+L F +L EDQI LLK
Sbjct: 301 FAKKLPMFCELPCEDQIILLK 321
>ref|XP_862596.1| PREDICTED: similar to thyroid hormone receptor, beta isoform 7 [Canis
familiaris].
Length = 476
Score = 109 bits (272), Expect(2) = 5e-25
Identities = 66/214 (30%), Positives = 103/214 (48%), Gaps = 16/214 (7%)
Frame = +3
Query: 474 QKRKKGPAPKMLG-NELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAR--YVCHSGG 644
+K+ KG P L +ELC VCGDKA+G+HY ++CEGCKGFFRR++ K Y C G
Sbjct: 96 EKKCKGYIPSYLDKDELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEG 155
Query: 645 HCPMDTYMRRKCQECRLRKCRQAGMREECVLSE-EQIRLKKLKRQEEEQAQATSVPPRAX 821
C +D R +CQECR +KC GM + VL + +++ +KL + E+ + +
Sbjct: 156 KCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLAKRKLIEENREKRRREELQKSIG 215
Query: 822 XXXXXXXXXXXXXXGMIEKLVAAQQQCN----RRSF--------SDQLRVTPWPMAPDPQ 965
+ E VA Q + +R F + Q + P+ P+
Sbjct: 216 HKPEPTDEEWELIKTVTEAHVATNAQGSHWKQKRKFLAAPHSKSAKQEDIGQAPIVNAPE 275
Query: 966 SREARQQRFAHFTELAIVSVQEIVDFANSXQASC 1067
+ + F+HFT++ ++ +VDFA C
Sbjct: 276 GGKVDLEAFSHFTKIITPAITRVVDFAKKLPMFC 309
Score = 24.3 bits (51), Expect(2) = 5e-25
Identities = 12/21 (57%), Positives = 14/21 (66%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F K+L F +L EDQI LLK
Sbjct: 301 FAKKLPMFCELPCEDQIILLK 321
Database: RefSeq49_CP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 18,874,504
Number of sequences in database: 33,336
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33336
Number of Hits to DB: 54,308,276
Number of extensions: 1961716
Number of successful extensions: 15785
Number of sequences better than 1.0e-05: 151
Number of HSP's gapped: 15244
Number of HSP's successfully gapped: 168
Length of query: 368
Length of database: 18,874,504
Length adjustment: 104
Effective length of query: 264
Effective length of database: 15,407,560
Effective search space: 4067595840
Effective search space used: 4067595840
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 35 (18.1 bits)
Search to RefSeqSP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-012820
(1104 letters)
Database: RefSeq49_SP.fasta
24,897 sequences; 11,343,932 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001095284.1| oxysterols receptor LXR-alpha [Sus scrofa]. 484 e-142
Alignment gi|XP_003127410.1| PREDICTED: oxysterols receptor LXR-beta-like... 268 2e-76
Alignment gi|XP_001928835.2| PREDICTED: bile acid receptor [Sus scrofa]. 136 2e-32
Alignment gi|XP_001928500.3| PREDICTED: thyroid hormone receptor beta [Su... 112 3e-26
Alignment gi|XP_001924421.2| PREDICTED: retinoic acid receptor gamma [Sus... 104 2e-24
Alignment gi|NP_001033094.1| nuclear receptor subfamily 1 group I member ... 106 3e-23
Alignment gi|NP_001090883.1| vitamin D3 receptor [Sus scrofa]. 104 8e-23
Alignment gi|NP_001033085.1| constitutive androstane receptor [Sus scrofa]. 102 4e-22
Alignment gi|NP_001177175.1| retinoic acid receptor RXR-beta [Sus scrofa]. 100 1e-21
Alignment gi|XP_001926863.2| PREDICTED: retinoic acid receptor beta isofo... 100 1e-21
>ref|NP_001095284.1| oxysterols receptor LXR-alpha [Sus scrofa].
Length = 447
Score = 484 bits (1247), Expect(2) = e-142
Identities = 242/272 (88%), Positives = 242/272 (88%)
Frame = +3
Query: 231 MSLWVEAPVPDVSPDSAVELWEXXXXXXXXXXXXXXXCILREESSTPQSAGGASRVGLDA 410
MSLWVEAPVPDVSPDSAVELWE CILREESSTPQSAGGASRVGLDA
Sbjct: 1 MSLWVEAPVPDVSPDSAVELWESDAQDASSQSLGSSSCILREESSTPQSAGGASRVGLDA 60
Query: 411 TESTALLPGVEASPESTELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG 590
TESTALLPGVEASPESTELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG
Sbjct: 61 TESTALLPGVEASPESTELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG 120
Query: 591 FFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLK 770
FFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLK
Sbjct: 121 FFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLK 180
Query: 771 RQEEEQAQATSVPPRAXXXXXXXXXXXXXXXGMIEKLVAAQQQCNRRSFSDQLRVTPWPM 950
RQEEEQAQATSVPPRA GMIEKLVAAQQQCNRRSFSDQLRVTPWPM
Sbjct: 181 RQEEEQAQATSVPPRASSPPQVLPQLSPEQLGMIEKLVAAQQQCNRRSFSDQLRVTPWPM 240
Query: 951 APDPQSREARQQRFAHFTELAIVSVQEIVDFA 1046
APDPQSREARQQRFAHFTELAIVSVQEIVDFA
Sbjct: 241 APDPQSREARQQRFAHFTELAIVSVQEIVDFA 272
Score = 39.3 bits (90), Expect(2) = e-142
Identities = 19/21 (90%), Positives = 19/21 (90%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F KQL GFLQLSREDQIALLK
Sbjct: 271 FAKQLPGFLQLSREDQIALLK 291
>ref|XP_003127410.1| PREDICTED: oxysterols receptor LXR-beta-like isoform 2 [Sus scrofa].
Length = 467
Score = 268 bits (685), Expect(2) = 2e-76
Identities = 146/250 (58%), Positives = 170/250 (68%), Gaps = 27/250 (10%)
Frame = +3
Query: 378 AGGASRVGLDATEST--ALLPGVEASPESTELRPQKRKKGPAPKMLGNELCSVCGDKASG 551
AG AS VG A T +L E PE +KRKKGPAPKMLG+ELC VCGD ASG
Sbjct: 52 AGSASVVGEMAPRHTDWVILDPAE-EPE------RKRKKGPAPKMLGDELCQVCGDTASG 104
Query: 552 FHYNVLSCEGCKGFFRRSVIKG--ARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMRE 725
FHYNVLSCEGCKGFFRRSVI+G RY C GG C MD +MRRKCQ+CRLRKC++AGMRE
Sbjct: 105 FHYNVLSCEGCKGFFRRSVIRGGAGRYACRGGGTCQMDAFMRRKCQQCRLRKCKEAGMRE 164
Query: 726 ECVLSEEQIRLKKLKRQEEEQAQATSVPPRAXXXXXXXXXXXXXXXG------------- 866
+CVLS+EQIR KK+++Q+++Q Q +S P A G
Sbjct: 165 QCVLSKEQIRKKKIRKQQQQQQQQSS--PTAPGVSSGSASGPGASPGGSDGGGQGSGEGE 222
Query: 867 ----------MIEKLVAAQQQCNRRSFSDQLRVTPWPMAPDPQSREARQQRFAHFTELAI 1016
MI++LVAAQ QCN+RSFSDQ +VTPWP+ DPQSR+ARQQRFAHFTELAI
Sbjct: 223 GIQLTAAQELMIQQLVAAQLQCNKRSFSDQPKVTPWPLGADPQSRDARQQRFAHFTELAI 282
Query: 1017 VSVQEIVDFA 1046
+SVQEIVDFA
Sbjct: 283 ISVQEIVDFA 292
Score = 36.6 bits (83), Expect(2) = 2e-76
Identities = 17/21 (80%), Positives = 18/21 (85%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F KQ+ GFLQL REDQIALLK
Sbjct: 291 FAKQVPGFLQLGREDQIALLK 311
>ref|XP_001928835.2| PREDICTED: bile acid receptor [Sus scrofa].
Length = 512
Score = 136 bits (342), Expect = 2e-32
Identities = 63/124 (50%), Positives = 84/124 (67%), Gaps = 4/124 (3%)
Frame = +3
Query: 441 EASPESTELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGA 620
EA + + R ++ G+ELC VCGD+ASG+HYN L+CEGCKGFFRRS+ K A
Sbjct: 136 EAGEVEIPVTKKTRLGASTGRIKGDELCVVCGDRASGYHYNALTCEGCKGFFRRSITKNA 195
Query: 621 RYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREEC----VLSEEQIRLKKLKRQEEEQ 788
Y C +GG+C MD YMRRKCQECRLRKC++ GM EC +L+E Q + K+L++ ++
Sbjct: 196 VYKCKNGGNCVMDMYMRRKCQECRLRKCKEMGMLAECMYTGLLTEIQCKSKRLRKNVKQH 255
Query: 789 AQAT 800
A T
Sbjct: 256 ADQT 259
>ref|XP_001928500.3| PREDICTED: thyroid hormone receptor beta [Sus scrofa].
Length = 461
Score = 112 bits (281), Expect(2) = 3e-26
Identities = 76/252 (30%), Positives = 122/252 (48%), Gaps = 12/252 (4%)
Frame = +3
Query: 348 LREESSTP---QSAGGASRVGLDATE-STALLPGVEASPESTELRPQKRKKGPAPKMLG- 512
L+ E S+P Q+ +S + LD + + +PG + T +K+ KG P L
Sbjct: 49 LKNEQSSPHLIQATWTSSILHLDHDDVNDQSVPGAQ-----TFQTEEKKCKGYIPSYLDK 103
Query: 513 NELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAR--YVCHSGGHCPMDTYMRRKCQE 686
+ELC VCGDKA+G+HY ++CEGCKGFFRR++ K Y C G C +D R +CQE
Sbjct: 104 DELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYACKYEGKCVIDKVTRNQCQE 163
Query: 687 CRLRKCRQAGMREECVLSE-EQIRLKKLKRQEEEQAQATSVPPRAXXXXXXXXXXXXXXX 863
CR +KC GM + VL + +++ +KL + E+ + +
Sbjct: 164 CRFKKCIYVGMATDLVLDDSKRLAKRKLIEENREKRRREELQRSIGHKPEPTDQEWELIK 223
Query: 864 GMIEKLVAAQQQCN----RRSFSDQLRVTPWPMAPDPQSREARQQRFAHFTELAIVSVQE 1031
+ E VA Q + +R F + + P+ P+ + + F+HFT++ ++
Sbjct: 224 TVTEAHVATNAQGSHWKQKRKFLPE-DIGQAPIVNAPEGGKVDLEAFSHFTKIITPAITR 282
Query: 1032 IVDFANSXQASC 1067
+VDFA C
Sbjct: 283 VVDFAKKLPMFC 294
Score = 24.3 bits (51), Expect(2) = 3e-26
Identities = 12/21 (57%), Positives = 14/21 (66%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F K+L F +L EDQI LLK
Sbjct: 286 FAKKLPMFCELPCEDQIILLK 306
>ref|XP_001924421.2| PREDICTED: retinoic acid receptor gamma [Sus scrofa].
Length = 429
Score = 104 bits (259), Expect(2) = 2e-24
Identities = 65/207 (31%), Positives = 103/207 (49%), Gaps = 2/207 (0%)
Frame = +3
Query: 432 PGVEA-SPESTELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKGFFRRSV 608
P VE S S E+ P P P++ + C VC DK+SG+HY V SCEGCKGFFRRS+
Sbjct: 32 PPVETQSTSSEEMVPSSPSPPPPPRVY--KPCFVCNDKSSGYHYGVSSCEGCKGFFRRSI 89
Query: 609 IKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLKRQEEEQ 788
K Y CH +C ++ R +CQ CRL+KC + GM +E V ++ + K++K EE
Sbjct: 90 QKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKEAVRNDRNKKKKEVK--EEGS 147
Query: 789 AQATSVPPRAXXXXXXXXXXXXXXXGMIEKLVAAQQQCNRRSFSDQLRVTPWPMAPDPQS 968
+ + P+ +E+L+ + ++ +F ++ +
Sbjct: 148 LDSYELSPQ------------------LEELITKVSKAHQETFPSLCQLGKYTTNSSADH 189
Query: 969 R-EARQQRFAHFTELAIVSVQEIVDFA 1046
R + + F+ELA + +IV+FA
Sbjct: 190 RVQLDLGLWDKFSELATKCIIKIVEFA 216
Score = 26.2 bits (56), Expect(2) = 2e-24
Identities = 13/21 (61%), Positives = 14/21 (66%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F K+L GF LS DQI LLK
Sbjct: 215 FAKRLPGFTGLSIADQITLLK 235
>ref|NP_001033094.1| nuclear receptor subfamily 1 group I member 2 [Sus scrofa].
Length = 421
Score = 106 bits (264), Expect = 3e-23
Identities = 46/104 (44%), Positives = 72/104 (69%), Gaps = 1/104 (0%)
Frame = +3
Query: 510 GNELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGARYVC-HSGGHCPMDTYMRRKCQE 686
G ++C VCGDKA+G+H+NV++CEGCKGFFRR++ + AR C G C + RR+CQ
Sbjct: 23 GPQICRVCGDKATGYHFNVMTCEGCKGFFRRAIKRNARPRCLFRKGACEITRKTRRQCQA 82
Query: 687 CRLRKCRQAGMREECVLSEEQIRLKKLKRQEEEQAQATSVPPRA 818
CRLRKC ++GMR+E ++S+ + ++ + +++ Q + PP A
Sbjct: 83 CRLRKCLESGMRKEMIMSDAAVEQRRALIRRKKREQIGAQPPGA 126
>ref|NP_001090883.1| vitamin D3 receptor [Sus scrofa].
Length = 427
Score = 104 bits (260), Expect = 8e-23
Identities = 45/92 (48%), Positives = 66/92 (71%), Gaps = 3/92 (3%)
Frame = +3
Query: 519 LCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLR 698
+C VCGD+A+GFH+N ++CEGCKGFFRRS+ + A + C G C + RR CQ CRL+
Sbjct: 23 ICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLK 82
Query: 699 KCRQAGMREECVLSEEQIRLKK---LKRQEEE 785
+C GM +E +L++E+++ K+ LKR+EEE
Sbjct: 83 RCVDIGMMKEFILTDEEVQRKREMILKRKEEE 114
>ref|NP_001033085.1| constitutive androstane receptor [Sus scrofa].
Length = 348
Score = 102 bits (254), Expect = 4e-22
Identities = 44/95 (46%), Positives = 66/95 (69%)
Frame = +3
Query: 522 CSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRK 701
C+VCGD+A+G+H++ L+CEGCKGFFRR+V K +C G C ++ RR C CRL+K
Sbjct: 11 CAVCGDRATGYHFHALTCEGCKGFFRRTVNKSTSLICPFAGSCKVNKAQRRHCPACRLQK 70
Query: 702 CRQAGMREECVLSEEQIRLKKLKRQEEEQAQATSV 806
C AGM+++ +LS E + L++ RQ + +AQ S+
Sbjct: 71 CLDAGMKKDMILSAEVLALRR-ARQVQRRAQQASL 104
>ref|NP_001177175.1| retinoic acid receptor RXR-beta [Sus scrofa].
Length = 532
Score = 100 bits (249), Expect = 1e-21
Identities = 51/133 (38%), Positives = 65/133 (48%), Gaps = 6/133 (4%)
Frame = +3
Query: 369 PQSAGGASRVGLDATESTALLPGVEASPESTELRPQKRKKG------PAPKMLGNELCSV 530
P G + V ST LPG + P P +G P G LC++
Sbjct: 147 PAPPGFSGPVSSPQINSTVSLPGGGSGPPEDVKPPVLGVRGLHCPPPPGGPGAGKRLCAI 206
Query: 531 CGDKASGFHYNVLSCEGCKGFFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQ 710
CGD++SG HY V SCEGCKGFF+R++ K Y C C +D R +CQ CR +KC
Sbjct: 207 CGDRSSGKHYGVYSCEGCKGFFKRTIRKDLTYSCRDNKDCTVDKRQRNRCQYCRYQKCLA 266
Query: 711 AGMREECVLSEEQ 749
GM+ E V E Q
Sbjct: 267 TGMKREAVQEERQ 279
>ref|XP_001926863.2| PREDICTED: retinoic acid receptor beta isoform 1 [Sus scrofa].
Length = 448
Score = 100 bits (249), Expect = 1e-21
Identities = 48/111 (43%), Positives = 67/111 (60%)
Frame = +3
Query: 447 SPESTELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGARY 626
S S EL P P P++ + C VC DK+SG+HY V +CEGCKGFFRRS+ K Y
Sbjct: 58 STSSEELVPSPPSPLPPPRVY--KPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMIY 115
Query: 627 VCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLKRQE 779
CH +C ++ R +CQ CRL+KC + GM +E V ++ + K+ +QE
Sbjct: 116 TCHRDKNCVINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKKKKEPSKQE 166
Database: RefSeq49_SP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 11,343,932
Number of sequences in database: 24,897
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24897
Number of Hits to DB: 33,818,547
Number of extensions: 1241973
Number of successful extensions: 9877
Number of sequences better than 1.0e-05: 47
Number of HSP's gapped: 9412
Number of HSP's successfully gapped: 52
Length of query: 368
Length of database: 11,343,932
Length adjustment: 100
Effective length of query: 268
Effective length of database: 8,854,232
Effective search space: 2372934176
Effective search space used: 2372934176
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Search to RefSeqMP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-012820
(1104 letters)
Database: RefSeq49_MP.fasta
30,036 sequences; 15,617,559 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001171201.1| oxysterols receptor LXR-alpha [Mus musculus]. 431 e-126
Alignment gi|NP_038867.2| oxysterols receptor LXR-alpha [Mus musculus]. 431 e-126
Alignment gi|NP_033499.1| oxysterols receptor LXR-beta [Mus musculus]. 265 2e-75
Alignment gi|NP_033134.2| bile acid receptor isoform 3 [Mus musculus]. 144 9e-35
Alignment gi|NP_941060.2| nuclear receptor subfamily 1, group H, member 5... 140 1e-33
Alignment gi|NP_963913.2| nuclear receptor subfamily 1, group H, member 5... 140 1e-33
Alignment gi|NP_001157172.1| bile acid receptor isoform 1 [Mus musculus]. 139 5e-33
Alignment gi|NP_001156976.1| bile acid receptor isoform 2 [Mus musculus]. 139 5e-33
Alignment gi|NP_033406.1| thyroid hormone receptor beta isoform 2 [Mus mu... 115 8e-27
Alignment gi|NP_001106888.1| thyroid hormone receptor beta isoform 1 [Mus... 110 2e-25
>ref|NP_001171201.1| oxysterols receptor LXR-alpha [Mus musculus].
Length = 445
Score = 431 bits (1109), Expect(2) = e-126
Identities = 216/272 (79%), Positives = 225/272 (82%)
Frame = +3
Query: 231 MSLWVEAPVPDVSPDSAVELWEXXXXXXXXXXXXXXXCILREESSTPQSAGGASRVGLDA 410
MSLW+EA +PDVSPDSA ELW+ CILREE+ PQS G A +GL++
Sbjct: 1 MSLWLEASMPDVSPDSATELWKTEPQDAGDQGGNT--CILREEARMPQSTGVALGIGLES 58
Query: 411 TESTALLPGVEASPESTELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG 590
E TALLP E PE TELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG
Sbjct: 59 AEPTALLPRAETLPEPTELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG 118
Query: 591 FFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLK 770
FFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLK
Sbjct: 119 FFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLK 178
Query: 771 RQEEEQAQATSVPPRAXXXXXXXXXXXXXXXGMIEKLVAAQQQCNRRSFSDQLRVTPWPM 950
RQEEEQAQATSV PR GMIEKLVAAQQQCNRRSFSD+LRVTPWP+
Sbjct: 179 RQEEEQAQATSVSPRVSSPPQVLPQLSPEQLGMIEKLVAAQQQCNRRSFSDRLRVTPWPI 238
Query: 951 APDPQSREARQQRFAHFTELAIVSVQEIVDFA 1046
APDPQSREARQQRFAHFTELAIVSVQEIVDFA
Sbjct: 239 APDPQSREARQQRFAHFTELAIVSVQEIVDFA 270
Score = 39.3 bits (90), Expect(2) = e-126
Identities = 19/21 (90%), Positives = 19/21 (90%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F KQL GFLQLSREDQIALLK
Sbjct: 269 FAKQLPGFLQLSREDQIALLK 289
>ref|NP_038867.2| oxysterols receptor LXR-alpha [Mus musculus].
Length = 445
Score = 431 bits (1109), Expect(2) = e-126
Identities = 216/272 (79%), Positives = 225/272 (82%)
Frame = +3
Query: 231 MSLWVEAPVPDVSPDSAVELWEXXXXXXXXXXXXXXXCILREESSTPQSAGGASRVGLDA 410
MSLW+EA +PDVSPDSA ELW+ CILREE+ PQS G A +GL++
Sbjct: 1 MSLWLEASMPDVSPDSATELWKTEPQDAGDQGGNT--CILREEARMPQSTGVALGIGLES 58
Query: 411 TESTALLPGVEASPESTELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG 590
E TALLP E PE TELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG
Sbjct: 59 AEPTALLPRAETLPEPTELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG 118
Query: 591 FFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLK 770
FFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLK
Sbjct: 119 FFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLK 178
Query: 771 RQEEEQAQATSVPPRAXXXXXXXXXXXXXXXGMIEKLVAAQQQCNRRSFSDQLRVTPWPM 950
RQEEEQAQATSV PR GMIEKLVAAQQQCNRRSFSD+LRVTPWP+
Sbjct: 179 RQEEEQAQATSVSPRVSSPPQVLPQLSPEQLGMIEKLVAAQQQCNRRSFSDRLRVTPWPI 238
Query: 951 APDPQSREARQQRFAHFTELAIVSVQEIVDFA 1046
APDPQSREARQQRFAHFTELAIVSVQEIVDFA
Sbjct: 239 APDPQSREARQQRFAHFTELAIVSVQEIVDFA 270
Score = 39.3 bits (90), Expect(2) = e-126
Identities = 19/21 (90%), Positives = 19/21 (90%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F KQL GFLQLSREDQIALLK
Sbjct: 269 FAKQLPGFLQLSREDQIALLK 289
>ref|NP_033499.1| oxysterols receptor LXR-beta [Mus musculus].
Length = 446
Score = 265 bits (677), Expect(2) = 2e-75
Identities = 140/262 (53%), Positives = 165/262 (62%), Gaps = 35/262 (13%)
Frame = +3
Query: 366 TPQSAGGASRVGLDATESTALLPGVEASP----------------ESTELRPQKRKKGPA 497
TP G+ + AT T G E P E + +KRKKGPA
Sbjct: 10 TPVPGNGSPQPSTSATSPTIKEEGQETDPPPGSEGSSSAYIVVILEPEDEPERKRKKGPA 69
Query: 498 PKMLGNELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGA--RYVCHSGGHCPMDTYMR 671
PKMLG+ELC VCGDKASGFHYNVLSCEGCKGFFRRSV+ G RY C G C MD +MR
Sbjct: 70 PKMLGHELCRVCGDKASGFHYNVLSCEGCKGFFRRSVVHGGAGRYACRGSGTCQMDAFMR 129
Query: 672 RKCQECRLRKCRQAGMREECVLSEEQIRLKKLKRQEEEQAQATSVPPRAXXXXXXXXXXX 851
RKCQ CRLRKC++AGMRE+CVLSEEQIR K++++Q+++Q S P +
Sbjct: 130 RKCQLCRLRKCKEAGMREQCVLSEEQIRKKRIQKQQQQQPPPPSEPAASSSGRPAASPGT 189
Query: 852 XXXXG-----------------MIEKLVAAQQQCNRRSFSDQLRVTPWPMAPDPQSREAR 980
MI++LVAAQ QCN+RSFSDQ +VTPWP+ DPQSR+AR
Sbjct: 190 SEASSQGSGEGEGIQLTAAQELMIQQLVAAQLQCNKRSFSDQPKVTPWPLGADPQSRDAR 249
Query: 981 QQRFAHFTELAIVSVQEIVDFA 1046
QQRFAHFTELAI+SVQEIVDFA
Sbjct: 250 QQRFAHFTELAIISVQEIVDFA 271
Score = 36.6 bits (83), Expect(2) = 2e-75
Identities = 17/21 (80%), Positives = 18/21 (85%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F KQ+ GFLQL REDQIALLK
Sbjct: 270 FAKQVPGFLQLGREDQIALLK 290
>ref|NP_033134.2| bile acid receptor isoform 3 [Mus musculus].
Length = 484
Score = 144 bits (364), Expect = 9e-35
Identities = 65/126 (51%), Positives = 90/126 (71%), Gaps = 3/126 (2%)
Frame = +3
Query: 435 GVEASPESTELRPQKRKK---GPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKGFFRRS 605
G + E +E+ K+ + A ++ G+ELC VCGD+ASG+HYN L+CEGCKGFFRRS
Sbjct: 106 GYQGETEVSEMPVTKKPRMAAASAGRIKGDELCVVCGDRASGYHYNALTCEGCKGFFRRS 165
Query: 606 VIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLKRQEEE 785
+ K A Y C +GG+C MD YMRRKCQECRLRKC++ GM EC+L+E Q + K+L++ ++
Sbjct: 166 ITKNAVYKCKNGGNCVMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQCKSKRLRKNVKQ 225
Query: 786 QAQATS 803
A T+
Sbjct: 226 HADQTA 231
>ref|NP_941060.2| nuclear receptor subfamily 1, group H, member 5 isoform 1 [Mus
musculus].
Length = 505
Score = 140 bits (354), Expect = 1e-33
Identities = 72/137 (52%), Positives = 90/137 (65%), Gaps = 2/137 (1%)
Frame = +3
Query: 369 PQSAGGASRVGLDATESTALLPGVEASPESTELRPQKRKKGPAPKMLGNE--LCSVCGDK 542
PQ +GG S GLDA ES V E Q+ + + + G + LC VCGDK
Sbjct: 70 PQYSGG-SWCGLDARESGQSTYVVVHDDEDEFPGAQRCRATCSLRWKGQDDMLCMVCGDK 128
Query: 543 ASGFHYNVLSCEGCKGFFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMR 722
ASG+HYN L+CEGCKGFFRRS+ K A Y C +GGHC MD YMRRKCQECRL+KC+ GM
Sbjct: 129 ASGYHYNALTCEGCKGFFRRSITKNAVYSCKNGGHCEMDMYMRRKCQECRLKKCKAVGML 188
Query: 723 EECVLSEEQIRLKKLKR 773
EC+L+E Q + K+L++
Sbjct: 189 AECLLTEIQCKSKRLRK 205
>ref|NP_963913.2| nuclear receptor subfamily 1, group H, member 5 isoform 2 [Mus
musculus].
Length = 497
Score = 140 bits (354), Expect = 1e-33
Identities = 72/137 (52%), Positives = 90/137 (65%), Gaps = 2/137 (1%)
Frame = +3
Query: 369 PQSAGGASRVGLDATESTALLPGVEASPESTELRPQKRKKGPAPKMLGNE--LCSVCGDK 542
PQ +GG S GLDA ES V E Q+ + + + G + LC VCGDK
Sbjct: 70 PQYSGG-SWCGLDARESGQSTYVVVHDDEDEFPGAQRCRATCSLRWKGQDDMLCMVCGDK 128
Query: 543 ASGFHYNVLSCEGCKGFFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMR 722
ASG+HYN L+CEGCKGFFRRS+ K A Y C +GGHC MD YMRRKCQECRL+KC+ GM
Sbjct: 129 ASGYHYNALTCEGCKGFFRRSITKNAVYSCKNGGHCEMDMYMRRKCQECRLKKCKAVGML 188
Query: 723 EECVLSEEQIRLKKLKR 773
EC+L+E Q + K+L++
Sbjct: 189 AECLLTEIQCKSKRLRK 205
>ref|NP_001157172.1| bile acid receptor isoform 1 [Mus musculus].
Length = 488
Score = 139 bits (349), Expect = 5e-33
Identities = 65/130 (50%), Positives = 90/130 (69%), Gaps = 7/130 (5%)
Frame = +3
Query: 435 GVEASPESTELRPQKRKK---GPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKGFFRRS 605
G + E +E+ K+ + A ++ G+ELC VCGD+ASG+HYN L+CEGCKGFFRRS
Sbjct: 106 GYQGETEVSEMPVTKKPRMAAASAGRIKGDELCVVCGDRASGYHYNALTCEGCKGFFRRS 165
Query: 606 VIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREEC----VLSEEQIRLKKLKR 773
+ K A Y C +GG+C MD YMRRKCQECRLRKC++ GM EC +L+E Q + K+L++
Sbjct: 166 ITKNAVYKCKNGGNCVMDMYMRRKCQECRLRKCKEMGMLAECMYTGLLTEIQCKSKRLRK 225
Query: 774 QEEEQAQATS 803
++ A T+
Sbjct: 226 NVKQHADQTA 235
>ref|NP_001156976.1| bile acid receptor isoform 2 [Mus musculus].
Length = 474
Score = 139 bits (349), Expect = 5e-33
Identities = 65/130 (50%), Positives = 90/130 (69%), Gaps = 7/130 (5%)
Frame = +3
Query: 435 GVEASPESTELRPQKRKK---GPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKGFFRRS 605
G + E +E+ K+ + A ++ G+ELC VCGD+ASG+HYN L+CEGCKGFFRRS
Sbjct: 92 GYQGETEVSEMPVTKKPRMAAASAGRIKGDELCVVCGDRASGYHYNALTCEGCKGFFRRS 151
Query: 606 VIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREEC----VLSEEQIRLKKLKR 773
+ K A Y C +GG+C MD YMRRKCQECRLRKC++ GM EC +L+E Q + K+L++
Sbjct: 152 ITKNAVYKCKNGGNCVMDMYMRRKCQECRLRKCKEMGMLAECMYTGLLTEIQCKSKRLRK 211
Query: 774 QEEEQAQATS 803
++ A T+
Sbjct: 212 NVKQHADQTA 221
>ref|NP_033406.1| thyroid hormone receptor beta isoform 2 [Mus musculus].
Length = 475
Score = 115 bits (287), Expect(2) = 8e-27
Identities = 71/232 (30%), Positives = 112/232 (48%), Gaps = 8/232 (3%)
Frame = +3
Query: 396 VGLDATESTALLPGVEASPESTELRPQKRKKGPAPKMLG-NELCSVCGDKASGFHYNVLS 572
+ L + A LP + P+ + P +KKG P L +ELC VCGDKA+G+HY ++
Sbjct: 79 MALSQSSQPAHLPEEKPFPQ-VQSPPHSQKKGYIPSYLDKDELCVVCGDKATGYHYRCIT 137
Query: 573 CEGCKGFFRRSVIKGAR--YVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSE- 743
CEGCKGFFRR++ K Y C G C +D R +CQECR +KC GM + VL +
Sbjct: 138 CEGCKGFFRRTIQKSLHPSYSCKYEGKCIIDKVTRNQCQECRFKKCIYVGMATDLVLDDS 197
Query: 744 EQIRLKKLKRQEEEQAQATSVPPRAXXXXXXXXXXXXXXXGMIEKLVAAQQQCN----RR 911
+++ +KL + E+ + + + E VA Q + +R
Sbjct: 198 KRLAKRKLIEENREKRRREELQKSIGHKPEPTDEEWELIKTVTEAHVATNAQGSHWKQKR 257
Query: 912 SFSDQLRVTPWPMAPDPQSREARQQRFAHFTELAIVSVQEIVDFANSXQASC 1067
F + + P+ P+ + + F+HFT++ ++ +VDFA C
Sbjct: 258 KFLPE-DIGQAPIVNAPEGGKVDLEAFSHFTKIITPAITRVVDFAKKLPMFC 308
Score = 24.3 bits (51), Expect(2) = 8e-27
Identities = 12/21 (57%), Positives = 14/21 (66%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F K+L F +L EDQI LLK
Sbjct: 300 FAKKLPMFCELPCEDQIILLK 320
>ref|NP_001106888.1| thyroid hormone receptor beta isoform 1 [Mus musculus].
Length = 461
Score = 110 bits (275), Expect(2) = 2e-25
Identities = 65/206 (31%), Positives = 102/206 (49%), Gaps = 8/206 (3%)
Frame = +3
Query: 474 QKRKKGPAPKMLG-NELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAR--YVCHSGG 644
+K+ KG P L +ELC VCGDKA+G+HY ++CEGCKGFFRR++ K Y C G
Sbjct: 90 EKKCKGYIPSYLDKDELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKSLHPSYSCKYEG 149
Query: 645 HCPMDTYMRRKCQECRLRKCRQAGMREECVLSE-EQIRLKKLKRQEEEQAQATSVPPRAX 821
C +D R +CQECR +KC GM + VL + +++ +KL + E+ + +
Sbjct: 150 KCIIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLAKRKLIEENREKRRREELQKSIG 209
Query: 822 XXXXXXXXXXXXXXGMIEKLVAAQQQCN----RRSFSDQLRVTPWPMAPDPQSREARQQR 989
+ E VA Q + +R F + + P+ P+ + +
Sbjct: 210 HKPEPTDEEWELIKTVTEAHVATNAQGSHWKQKRKFLPE-DIGQAPIVNAPEGGKVDLEA 268
Query: 990 FAHFTELAIVSVQEIVDFANSXQASC 1067
F+HFT++ ++ +VDFA C
Sbjct: 269 FSHFTKIITPAITRVVDFAKKLPMFC 294
Score = 24.3 bits (51), Expect(2) = 2e-25
Identities = 12/21 (57%), Positives = 14/21 (66%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F K+L F +L EDQI LLK
Sbjct: 286 FAKKLPMFCELPCEDQIILLK 306
Database: RefSeq49_MP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 15,617,559
Number of sequences in database: 30,036
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 30036
Number of Hits to DB: 44,337,598
Number of extensions: 1544620
Number of successful extensions: 10582
Number of sequences better than 1.0e-05: 74
Number of HSP's gapped: 10218
Number of HSP's successfully gapped: 82
Length of query: 368
Length of database: 15,617,559
Length adjustment: 103
Effective length of query: 265
Effective length of database: 12,523,851
Effective search space: 3318820515
Effective search space used: 3318820515
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Search to RefSeqHP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-012820
(1104 letters)
Database: RefSeq49_HP.fasta
32,964 sequences; 18,297,164 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_005684.2| oxysterols receptor LXR-alpha isoform a [Homo s... 432 e-126
Alignment gi|NP_001123574.1| oxysterols receptor LXR-alpha isoform c [Hom... 388 e-113
Alignment gi|NP_001123573.1| oxysterols receptor LXR-alpha isoform b [Hom... 362 e-100
Alignment gi|NP_009052.3| oxysterols receptor LXR-beta [Homo sapiens]. 275 2e-78
Alignment gi|NP_001193921.1| bile acid receptor isoform 4 [Homo sapiens]. 142 4e-34
Alignment gi|NP_005114.1| bile acid receptor isoform 2 [Homo sapiens]. 142 4e-34
Alignment gi|NP_001193922.1| bile acid receptor isoform 3 [Homo sapiens]. 137 2e-32
Alignment gi|NP_001193908.1| bile acid receptor isoform 1 [Homo sapiens]. 137 2e-32
Alignment gi|NP_001193906.1| bile acid receptor isoform 1 [Homo sapiens]. 137 2e-32
Alignment gi|NP_001121649.1| thyroid hormone receptor beta [Homo sapiens]. 110 2e-25
>ref|NP_005684.2| oxysterols receptor LXR-alpha isoform a [Homo sapiens].
Length = 447
Score = 432 bits (1112), Expect(2) = e-126
Identities = 213/272 (78%), Positives = 223/272 (81%)
Frame = +3
Query: 231 MSLWVEAPVPDVSPDSAVELWEXXXXXXXXXXXXXXXCILREESSTPQSAGGASRVGLDA 410
MSLW+ APVPD+ PDSAVELW+ CILREE+ P SAGG + VGL+A
Sbjct: 1 MSLWLGAPVPDIPPDSAVELWKPGAQDASSQAQGGSSCILREEARMPHSAGGTAGVGLEA 60
Query: 411 TESTALLPGVEASPESTELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG 590
E TALL E E TE+RPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG
Sbjct: 61 AEPTALLTRAEPPSEPTEIRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG 120
Query: 591 FFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLK 770
FFRRSVIKGA Y+CHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLK
Sbjct: 121 FFRRSVIKGAHYICHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLK 180
Query: 771 RQEEEQAQATSVPPRAXXXXXXXXXXXXXXXGMIEKLVAAQQQCNRRSFSDQLRVTPWPM 950
RQEEEQA ATS+PPRA GMIEKLVAAQQQCNRRSFSD+LRVTPWPM
Sbjct: 181 RQEEEQAHATSLPPRASSPPQILPQLSPEQLGMIEKLVAAQQQCNRRSFSDRLRVTPWPM 240
Query: 951 APDPQSREARQQRFAHFTELAIVSVQEIVDFA 1046
APDP SREARQQRFAHFTELAIVSVQEIVDFA
Sbjct: 241 APDPHSREARQQRFAHFTELAIVSVQEIVDFA 272
Score = 39.3 bits (90), Expect(2) = e-126
Identities = 19/21 (90%), Positives = 19/21 (90%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F KQL GFLQLSREDQIALLK
Sbjct: 271 FAKQLPGFLQLSREDQIALLK 291
>ref|NP_001123574.1| oxysterols receptor LXR-alpha isoform c [Homo sapiens].
Length = 402
Score = 388 bits (997), Expect(2) = e-113
Identities = 190/226 (84%), Positives = 196/226 (86%)
Frame = +3
Query: 369 PQSAGGASRVGLDATESTALLPGVEASPESTELRPQKRKKGPAPKMLGNELCSVCGDKAS 548
P SAGG + VGL+A E TALL E E TE+RPQKRKKGPAPKMLGNELCSVCGDKAS
Sbjct: 2 PHSAGGTAGVGLEAAEPTALLTRAEPPSEPTEIRPQKRKKGPAPKMLGNELCSVCGDKAS 61
Query: 549 GFHYNVLSCEGCKGFFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREE 728
GFHYNVLSCEGCKGFFRRSVIKGA Y+CHSGGHCPMDTYMRRKCQECRLRKCRQAGMREE
Sbjct: 62 GFHYNVLSCEGCKGFFRRSVIKGAHYICHSGGHCPMDTYMRRKCQECRLRKCRQAGMREE 121
Query: 729 CVLSEEQIRLKKLKRQEEEQAQATSVPPRAXXXXXXXXXXXXXXXGMIEKLVAAQQQCNR 908
CVLSEEQIRLKKLKRQEEEQA ATS+PPRA GMIEKLVAAQQQCNR
Sbjct: 122 CVLSEEQIRLKKLKRQEEEQAHATSLPPRASSPPQILPQLSPEQLGMIEKLVAAQQQCNR 181
Query: 909 RSFSDQLRVTPWPMAPDPQSREARQQRFAHFTELAIVSVQEIVDFA 1046
RSFSD+LRVTPWPMAPDP SREARQQRFAHFTELAIVSVQEIVDFA
Sbjct: 182 RSFSDRLRVTPWPMAPDPHSREARQQRFAHFTELAIVSVQEIVDFA 227
Score = 39.3 bits (90), Expect(2) = e-113
Identities = 19/21 (90%), Positives = 19/21 (90%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F KQL GFLQLSREDQIALLK
Sbjct: 226 FAKQLPGFLQLSREDQIALLK 246
>ref|NP_001123573.1| oxysterols receptor LXR-alpha isoform b [Homo sapiens].
Length = 387
Score = 362 bits (928), Expect = e-100
Identities = 178/236 (75%), Positives = 188/236 (79%)
Frame = +3
Query: 231 MSLWVEAPVPDVSPDSAVELWEXXXXXXXXXXXXXXXCILREESSTPQSAGGASRVGLDA 410
MSLW+ APVPD+ PDSAVELW+ CILREE+ P SAGG + VGL+A
Sbjct: 1 MSLWLGAPVPDIPPDSAVELWKPGAQDASSQAQGGSSCILREEARMPHSAGGTAGVGLEA 60
Query: 411 TESTALLPGVEASPESTELRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG 590
E TALL E E TE+RPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG
Sbjct: 61 AEPTALLTRAEPPSEPTEIRPQKRKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKG 120
Query: 591 FFRRSVIKGARYVCHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLK 770
FFRRSVIKGA Y+CHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLK
Sbjct: 121 FFRRSVIKGAHYICHSGGHCPMDTYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLK 180
Query: 771 RQEEEQAQATSVPPRAXXXXXXXXXXXXXXXGMIEKLVAAQQQCNRRSFSDQLRVT 938
RQEEEQA ATS+PPRA GMIEKLVAAQQQCNRRSFSD+LRVT
Sbjct: 181 RQEEEQAHATSLPPRASSPPQILPQLSPEQLGMIEKLVAAQQQCNRRSFSDRLRVT 236
>ref|NP_009052.3| oxysterols receptor LXR-beta [Homo sapiens].
Length = 461
Score = 275 bits (704), Expect(2) = 2e-78
Identities = 145/259 (55%), Positives = 171/259 (66%), Gaps = 26/259 (10%)
Frame = +3
Query: 348 LREESSTPQSAGGASRV-GLDATESTALLPGVEASPESTELRPQKRKKGPAPKMLGNELC 524
++EE P G V G D S V PE R KRKKGPAPKMLG+ELC
Sbjct: 30 VKEEGPEPWPGGPDPDVPGTDEASSACSTDWVIPDPEEEPER--KRKKGPAPKMLGHELC 87
Query: 525 SVCGDKASGFHYNVLSCEGCKGFFRRSVIKGA--RYVCHSGGHCPMDTYMRRKCQECRLR 698
VCGDKASGFHYNVLSCEGCKGFFRRSV++G RY C GG C MD +MRRKCQ+CRLR
Sbjct: 88 RVCGDKASGFHYNVLSCEGCKGFFRRSVVRGGARRYACRGGGTCQMDAFMRRKCQQCRLR 147
Query: 699 KCRQAGMREECVLSEEQIRLKKLKRQEEEQAQATSVPPRAXXXXXXXXXXXXXXXG---- 866
KC++AGMRE+CVLSEEQIR KK+++Q+++++Q+ S P G
Sbjct: 148 KCKEAGMREQCVLSEEQIRKKKIRKQQQQESQSQSQSPVGPQGSSSSASGPGASPGGSEA 207
Query: 867 -------------------MIEKLVAAQQQCNRRSFSDQLRVTPWPMAPDPQSREARQQR 989
MI++LVAAQ QCN+RSFSDQ +VTPWP+ DPQSR+ARQQR
Sbjct: 208 GSQGSGEGEGVQLTAAQELMIQQLVAAQLQCNKRSFSDQPKVTPWPLGADPQSRDARQQR 267
Query: 990 FAHFTELAIVSVQEIVDFA 1046
FAHFTELAI+SVQEIVDFA
Sbjct: 268 FAHFTELAIISVQEIVDFA 286
Score = 36.6 bits (83), Expect(2) = 2e-78
Identities = 17/21 (80%), Positives = 18/21 (85%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F KQ+ GFLQL REDQIALLK
Sbjct: 285 FAKQVPGFLQLGREDQIALLK 305
>ref|NP_001193921.1| bile acid receptor isoform 4 [Homo sapiens].
Length = 482
Score = 142 bits (359), Expect = 4e-34
Identities = 62/107 (57%), Positives = 81/107 (75%)
Frame = +3
Query: 480 RKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGARYVCHSGGHCPMD 659
R A ++ G+ELC VCGD+ASG+HYN L+CEGCKGFFRRS+ K A Y C +GG+C MD
Sbjct: 123 RMGASAGRIKGDELCVVCGDRASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCVMD 182
Query: 660 TYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLKRQEEEQAQAT 800
YMRRKCQECRLRKC++ GM EC+L+E Q + K+L++ ++ A T
Sbjct: 183 MYMRRKCQECRLRKCKEMGMLAECLLTEIQCKSKRLRKNVKQHADQT 229
>ref|NP_005114.1| bile acid receptor isoform 2 [Homo sapiens].
Length = 472
Score = 142 bits (359), Expect = 4e-34
Identities = 62/107 (57%), Positives = 81/107 (75%)
Frame = +3
Query: 480 RKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGARYVCHSGGHCPMD 659
R A ++ G+ELC VCGD+ASG+HYN L+CEGCKGFFRRS+ K A Y C +GG+C MD
Sbjct: 113 RMGASAGRIKGDELCVVCGDRASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCVMD 172
Query: 660 TYMRRKCQECRLRKCRQAGMREECVLSEEQIRLKKLKRQEEEQAQAT 800
YMRRKCQECRLRKC++ GM EC+L+E Q + K+L++ ++ A T
Sbjct: 173 MYMRRKCQECRLRKCKEMGMLAECLLTEIQCKSKRLRKNVKQHADQT 219
>ref|NP_001193922.1| bile acid receptor isoform 3 [Homo sapiens].
Length = 486
Score = 137 bits (344), Expect = 2e-32
Identities = 62/111 (55%), Positives = 81/111 (72%), Gaps = 4/111 (3%)
Frame = +3
Query: 480 RKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGARYVCHSGGHCPMD 659
R A ++ G+ELC VCGD+ASG+HYN L+CEGCKGFFRRS+ K A Y C +GG+C MD
Sbjct: 123 RMGASAGRIKGDELCVVCGDRASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCVMD 182
Query: 660 TYMRRKCQECRLRKCRQAGMREEC----VLSEEQIRLKKLKRQEEEQAQAT 800
YMRRKCQECRLRKC++ GM EC +L+E Q + K+L++ ++ A T
Sbjct: 183 MYMRRKCQECRLRKCKEMGMLAECMYTGLLTEIQCKSKRLRKNVKQHADQT 233
>ref|NP_001193908.1| bile acid receptor isoform 1 [Homo sapiens].
Length = 476
Score = 137 bits (344), Expect = 2e-32
Identities = 62/111 (55%), Positives = 81/111 (72%), Gaps = 4/111 (3%)
Frame = +3
Query: 480 RKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGARYVCHSGGHCPMD 659
R A ++ G+ELC VCGD+ASG+HYN L+CEGCKGFFRRS+ K A Y C +GG+C MD
Sbjct: 113 RMGASAGRIKGDELCVVCGDRASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCVMD 172
Query: 660 TYMRRKCQECRLRKCRQAGMREEC----VLSEEQIRLKKLKRQEEEQAQAT 800
YMRRKCQECRLRKC++ GM EC +L+E Q + K+L++ ++ A T
Sbjct: 173 MYMRRKCQECRLRKCKEMGMLAECMYTGLLTEIQCKSKRLRKNVKQHADQT 223
>ref|NP_001193906.1| bile acid receptor isoform 1 [Homo sapiens].
Length = 476
Score = 137 bits (344), Expect = 2e-32
Identities = 62/111 (55%), Positives = 81/111 (72%), Gaps = 4/111 (3%)
Frame = +3
Query: 480 RKKGPAPKMLGNELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGARYVCHSGGHCPMD 659
R A ++ G+ELC VCGD+ASG+HYN L+CEGCKGFFRRS+ K A Y C +GG+C MD
Sbjct: 113 RMGASAGRIKGDELCVVCGDRASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCVMD 172
Query: 660 TYMRRKCQECRLRKCRQAGMREEC----VLSEEQIRLKKLKRQEEEQAQAT 800
YMRRKCQECRLRKC++ GM EC +L+E Q + K+L++ ++ A T
Sbjct: 173 MYMRRKCQECRLRKCKEMGMLAECMYTGLLTEIQCKSKRLRKNVKQHADQT 223
>ref|NP_001121649.1| thyroid hormone receptor beta [Homo sapiens].
Length = 461
Score = 110 bits (276), Expect(2) = 2e-25
Identities = 65/206 (31%), Positives = 102/206 (49%), Gaps = 8/206 (3%)
Frame = +3
Query: 474 QKRKKGPAPKMLG-NELCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAR--YVCHSGG 644
+K+ KG P L +ELC VCGDKA+G+HY ++CEGCKGFFRR++ K Y C G
Sbjct: 90 EKKCKGYIPSYLDKDELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEG 149
Query: 645 HCPMDTYMRRKCQECRLRKCRQAGMREECVLSE-EQIRLKKLKRQEEEQAQATSVPPRAX 821
C +D R +CQECR +KC GM + VL + +++ +KL + E+ + +
Sbjct: 150 KCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLAKRKLIEENREKRRREELQKSIG 209
Query: 822 XXXXXXXXXXXXXXGMIEKLVAAQQQCN----RRSFSDQLRVTPWPMAPDPQSREARQQR 989
+ E VA Q + +R F + + P+ P+ + +
Sbjct: 210 HKPEPTDEEWELIKTVTEAHVATNAQGSHWKQKRKFLPE-DIGQAPIVNAPEGGKVDLEA 268
Query: 990 FAHFTELAIVSVQEIVDFANSXQASC 1067
F+HFT++ ++ +VDFA C
Sbjct: 269 FSHFTKIITPAITRVVDFAKKLPMFC 294
Score = 24.3 bits (51), Expect(2) = 2e-25
Identities = 12/21 (57%), Positives = 14/21 (66%)
Frame = +2
Query: 1040 FCKQLAGFLQLSREDQIALLK 1102
F K+L F +L EDQI LLK
Sbjct: 286 FAKKLPMFCELPCEDQIILLK 306
Database: RefSeq49_HP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 18,297,164
Number of sequences in database: 32,964
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 32964
Number of Hits to DB: 53,019,731
Number of extensions: 1892156
Number of successful extensions: 14174
Number of sequences better than 1.0e-05: 145
Number of HSP's gapped: 13679
Number of HSP's successfully gapped: 160
Length of query: 368
Length of database: 18,297,164
Length adjustment: 104
Effective length of query: 264
Effective length of database: 14,868,908
Effective search space: 3925391712
Effective search space used: 3925391712
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 35 (18.1 bits)
Search to Sscrofa10_2
BLASTN 2.2.24 [Aug-08-2010]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20110601C-012820
(1104 letters)
Database: Sscrofa_10.2.fasta
4582 sequences; 2,808,509,378 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Sscrofa_Chr02 541 e-151
Sscrofa_Chr06 96 5e-17
>Sscrofa_Chr02
|| Length = 162569375
Score = 541 bits (273), Expect = e-151
Identities = 273/273 (100%)
Strand = Plus / Minus
Query: 460 cagagctccgtccacaaaagcggaaaaaggggccagcccccaaaatgctggggaatgagc 519
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16547691 cagagctccgtccacaaaagcggaaaaaggggccagcccccaaaatgctggggaatgagc 16547632
Query: 520 tgtgcagtgtgtgtggggacaaggcctccggcttccactacaacgtgctgagctgcgagg 579
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16547631 tgtgcagtgtgtgtggggacaaggcctccggcttccactacaacgtgctgagctgcgagg 16547572
Query: 580 gctgcaagggattcttccgtcgcagtgtcatcaaaggggctcgctatgtctgccacagcg 639
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16547571 gctgcaagggattcttccgtcgcagtgtcatcaaaggggctcgctatgtctgccacagcg 16547512
Query: 640 ggggccactgccccatggacacctacatgcgtcgcaagtgccaggagtgccgtcttcgca 699
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16547511 ggggccactgccccatggacacctacatgcgtcgcaagtgccaggagtgccgtcttcgca 16547452
Query: 700 agtgccgccaggcgggcatgcgagaggagtgtg 732
|||||||||||||||||||||||||||||||||
Sbjct: 16547451 agtgccgccaggcgggcatgcgagaggagtgtg 16547419
Score = 414 bits (209), Expect = e-113
Identities = 209/209 (100%)
Strand = Plus / Minus
Query: 730 gtgtcctgtcagaagaacagatccgcctgaagaaactgaagcggcaagaggaggaacagg 789
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16546678 gtgtcctgtcagaagaacagatccgcctgaagaaactgaagcggcaagaggaggaacagg 16546619
Query: 790 ctcaggccacatctgtgcccccaagggcttcctcgccgccccaagtcctgccccagctta 849
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16546618 ctcaggccacatctgtgcccccaagggcttcctcgccgccccaagtcctgccccagctta 16546559
Query: 850 gcccagagcagctgggcatgatcgagaagctggtggctgcccagcagcagtgtaacagac 909
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16546558 gcccagagcagctgggcatgatcgagaagctggtggctgcccagcagcagtgtaacagac 16546499
Query: 910 gctccttttcagaccagcttagagtcacg 938
|||||||||||||||||||||||||||||
Sbjct: 16546498 gctccttttcagaccagcttagagtcacg 16546470
Score = 385 bits (194), Expect = e-104
Identities = 194/194 (100%)
Strand = Plus / Minus
Query: 1 cggcggggaagcggccccgtgggcgggggcgaggaggccagggctccagtcggtcggctc 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16549829 cggcggggaagcggccccgtgggcgggggcgaggaggccagggctccagtcggtcggctc 16549770
Query: 61 ccggctcctggcccctctctcgctcagctccggctccctggtggcggcggacaagggact 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16549769 ccggctcctggcccctctctcgctcagctccggctccctggtggcggcggacaagggact 16549710
Query: 121 gcaccatccccctctcccagcaagggggctccagagactgcccagccaggaagtctggcg 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16549709 gcaccatccccctctcccagcaagggggctccagagactgcccagccaggaagtctggcg 16549650
Query: 181 gcctgggcgctcgg 194
||||||||||||||
Sbjct: 16549649 gcctgggcgctcgg 16549636
Score = 377 bits (190), Expect = e-102
Identities = 190/190 (100%)
Strand = Plus / Minus
Query: 273 gactctgcagtggagctgtgggagtcagatgcacaagatgcaagcagccagtctctggga 332
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16548275 gactctgcagtggagctgtgggagtcagatgcacaagatgcaagcagccagtctctggga 16548216
Query: 333 agcagcagctgcatcctcagggaggaatccagcacaccccagtctgcggggggcgcttcg 392
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16548215 agcagcagctgcatcctcagggaggaatccagcacaccccagtctgcggggggcgcttcg 16548156
Query: 393 agggtggggctggatgcaacagagtccacggccctgcttcccggggtggaggcctctcca 452
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16548155 agggtggggctggatgcaacagagtccacggccctgcttcccggggtggaggcctctcca 16548096
Query: 453 gagtccacag 462
||||||||||
Sbjct: 16548095 gagtccacag 16548086
Score = 295 bits (149), Expect = 3e-77
Identities = 164/168 (97%), Gaps = 1/168 (0%)
Strand = Plus / Minus
Query: 938 gccttggcccatggcaccagatccccagagccgggaggcccgtcagcaacgctttgccca 997
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16546364 gccttggcccatggcaccagatccccagagccgggaggcccgtcagcaacgctttgccca 16546305
Query: 998 cttcactgagctggccatcgtctctgtgcaggagatcgttgattttg-caaacagctngc 1056
||||||||||||||||||||||||||||||||||||||||||||||| ||||||||| |
Sbjct: 16546304 cttcactgagctggccatcgtctctgtgcaggagatcgttgattttgccaaacagctgcc 16546245
Query: 1057 aggcttcttgcagctcagccgggaagaccagatcgccctcctaaagac 1104
|||||||||||||||||||||||| |||||||||||||||||||||||
Sbjct: 16546244 aggcttcttgcagctcagccgggaggaccagatcgccctcctaaagac 16546197
Score = 161 bits (81), Expect = 1e-36
Identities = 81/81 (100%)
Strand = Plus / Minus
Query: 193 ggacagtcccttggtaatgtccagggctccaggaagagatgtccttgtgggtggaggccc 252
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16548880 ggacagtcccttggtaatgtccagggctccaggaagagatgtccttgtgggtggaggccc 16548821
Query: 253 ctgtgcctgatgtttctcctg 273
|||||||||||||||||||||
Sbjct: 16548820 ctgtgcctgatgtttctcctg 16548800
>Sscrofa_Chr06
|| Length = 157765593
Score = 95.6 bits (48), Expect = 5e-17
Identities = 72/80 (90%)
Strand = Plus / Plus
Query: 528 gtgtgtggggacaaggcctccggcttccactacaacgtgctgagctgcgagggctgcaag 587
||||| ||||||| ||||||||||||||||||||||||||| ||||| || |||||||||
Sbjct: 51088985 gtgtgcggggacacggcctccggcttccactacaacgtgctcagctgtgaaggctgcaag 51089044
Query: 588 ggattcttccgtcgcagtgt 607
|| |||||||| || |||||
Sbjct: 51089045 ggcttcttccggcgaagtgt 51089064
Database: Sscrofa_10.2.fasta
Posted date: Nov 16, 2011 10:34 AM
Number of letters in database: 2,808,509,378
Number of sequences in database: 4582
Lambda K H
1.37 0.711 1.31
Gapped
Lambda K H
1.37 0.711 1.31
Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Sequences: 4582
Number of Hits to DB: 30,944,948
Number of extensions: 232
Number of successful extensions: 232
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 231
Number of HSP's successfully gapped: 7
Length of query: 1104
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 1083
Effective length of database: 2,808,413,156
Effective search space: 3041511447948
Effective search space used: 3041511447948
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
X3: 50 (99.1 bits)
S1: 18 (36.2 bits)
S2: 30 (60.0 bits)