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-014077
(1157 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_850803.1| PREDICTED: similar to HLA class II histocompati... 313 2e-85
Alignment gi|NP_001011726.1| major histocompatibility complex, class II, ... 273 3e-73
Alignment gi|NP_001011723.1| MHC class II DR alpha chain [Canis lupus fam... 252 5e-67
Alignment gi|XP_532104.2| PREDICTED: similar to HLA class II histocompati... 161 1e-39
Alignment gi|NP_001041564.1| major histocompatibility complex, class II, ... 75 2e-13
Alignment gi|NP_001014403.1| major histocompatibility complex, class II, ... 74 2e-13
Alignment gi|NP_001014768.1| DLA class II histocompatibility antigen, DR-... 74 3e-13
Alignment gi|NP_001041592.1| major histocompatibility complex, class II, ... 69 8e-12
Alignment gi|XP_535458.1| PREDICTED: similar to beta-2-microglobulin prec... 62 1e-09
Alignment gi|XP_850148.1| PREDICTED: similar to beta-2-microglobulin prec... 62 1e-09
>ref|XP_850803.1| PREDICTED: similar to HLA class II histocompatibility antigen, DO
alpha chain precursor (MHC class II antigen DOA) (MHC DZ
alpha) (MHC DN-alpha) isoform 11 [Canis familiaris].
Length = 227
Score = 313 bits (802), Expect = 2e-85
Identities = 149/194 (76%), Positives = 162/194 (83%), Gaps = 7/194 (3%)
Frame = +1
Query: 169 MGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPEFSNFADFDPQNGLRGIA 348
MGSYGPAFYQSY SGQF ++FDGEQLFSV+LKKR+AVWRLPEF N A FDPQNGL IA
Sbjct: 1 MGSYGPAFYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEFGNLAHFDPQNGLASIA 60
Query: 349 LIRAHLDVLVERSNHTRATN-------VPPRVTVLPKSPVALGQPNVLICIVDNIFPPVI 507
+I+AHLDVLVERSN TRA N +PPRV VLPK V LGQPNVLICIVDNIFPPVI
Sbjct: 61 VIKAHLDVLVERSNRTRAINGTHLSSPLPPRVAVLPKFRVELGQPNVLICIVDNIFPPVI 120
Query: 508 NITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTH 687
NITWL NGQ ++EGV QTSFY+QPDH FRKF YLTFVPSA D YDCKVEHWGL+EPL H
Sbjct: 121 NITWLRNGQIISEGVAQTSFYSQPDHLFRKFCYLTFVPSAEDMYDCKVEHWGLEEPLLRH 180
Query: 688 WEPQVTMPLPDTTE 729
WEPQV +P+PDT E
Sbjct: 181 WEPQVPIPVPDTIE 194
>ref|NP_001011726.1| major histocompatibility complex, class II, DQ alpha [Canis lupus
familiaris].
Length = 255
Score = 273 bits (697), Expect = 3e-73
Identities = 125/205 (60%), Positives = 155/205 (75%)
Frame = +1
Query: 115 ILMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLP 294
IL ++SP I ADH+ +YG YQSY SGQ+T++FDG++ F VDL+K+E VWRLP
Sbjct: 13 ILTIMMSPSGGEEIVADHVANYGINVYQSYGPSGQYTHEFDGDEEFYVDLEKKETVWRLP 72
Query: 295 EFSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLI 474
FS F FDPQ LR +A+I+ +L+++ +RSN T ATN P VTV KSPV LGQPN LI
Sbjct: 73 VFSTFRSFDPQGALRNLAIIKQNLNIMTKRSNQTAATNEVPEVTVFSKSPVMLGQPNTLI 132
Query: 475 CIVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVE 654
C+VDNIFPPVIN+TWL N +VTEGV++TSF+A+ DHSF K YLTF+PSA D YDCKVE
Sbjct: 133 CLVDNIFPPVINVTWLKNRHSVTEGVSETSFFAKGDHSFSKISYLTFLPSAEDIYDCKVE 192
Query: 655 HWGLDEPLFTHWEPQVTMPLPDTTE 729
HWGLDEPL HWEP+V P+ + TE
Sbjct: 193 HWGLDEPLLKHWEPEVPTPMSELTE 217
>ref|NP_001011723.1| MHC class II DR alpha chain [Canis lupus familiaris].
Length = 254
Score = 252 bits (643), Expect = 5e-67
Identities = 115/205 (56%), Positives = 149/205 (72%)
Frame = +1
Query: 115 ILMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLP 294
I+ L+ PQ++ A+K +H+ FY + D SG+F +DFDG+++F VD++K+E VWRL
Sbjct: 13 IMAFLMGPQESWAVKEEHV-IIQAEFYLTPDPSGEFMFDFDGDEIFHVDMEKKETVWRLE 71
Query: 295 EFSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLI 474
EF FA F+ Q L IA+ +A+LD +++RSNHT TNVPP VTVL +PV LG+PN+LI
Sbjct: 72 EFGRFASFEAQGALANIAVDKANLDTMIKRSNHTPNTNVPPEVTVLSNTPVELGEPNILI 131
Query: 475 CIVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVE 654
C +D PPVIN+TWL NG VT GV++T F + DH FRKFHYL F+PSA D YDCKVE
Sbjct: 132 CFIDKFSPPVINVTWLRNGNPVTTGVSETIFLPREDHLFRKFHYLPFLPSAEDVYDCKVE 191
Query: 655 HWGLDEPLFTHWEPQVTMPLPDTTE 729
HWGLDEPL HWE + PLP+TTE
Sbjct: 192 HWGLDEPLLKHWEFEPPTPLPETTE 216
>ref|XP_532104.2| PREDICTED: similar to HLA class II histocompatibility antigen, DO
alpha chain precursor (MHC class II antigen DOA) (MHC DZ
alpha) (MHC DN-alpha) isoform 10 [Canis familiaris].
Length = 142
Score = 161 bits (407), Expect = 1e-39
Identities = 76/98 (77%), Positives = 85/98 (86%)
Frame = +1
Query: 121 MTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPEF 300
M+LLSP + GAI+ADHMGSYGPAFYQSY SGQF ++FDGEQLFSV+LKKR+AVWRLPEF
Sbjct: 1 MSLLSPHETGAIEADHMGSYGPAFYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEF 60
Query: 301 SNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVP 414
N A FDPQNGL IA+I+AHLDVLVERSN TRA N P
Sbjct: 61 GNLAHFDPQNGLASIAVIKAHLDVLVERSNRTRAINEP 98
>ref|NP_001041564.1| major histocompatibility complex, class II, DM alpha [Canis lupus
familiaris].
Length = 170
Score = 74.7 bits (182), Expect = 2e-13
Identities = 43/126 (34%), Positives = 62/126 (49%), Gaps = 1/126 (0%)
Frame = +1
Query: 337 RGIALIRA-HLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLICIVDNIFPPVINI 513
+G AL+R HL L+ S A P V V P+ G+PN+L+C + N+FPP + +
Sbjct: 13 QGAALLRLLHLLWLLPYSR--TAPEGFPMVDVFTLKPLEFGKPNMLVCFISNLFPPTLTV 70
Query: 514 TWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWE 693
W H+ V EG+ T A SF+ F YL F P+ D + C V H + +W
Sbjct: 71 NWWHHLDPV-EGIGPTFVSAVDGFSFQAFSYLNFTPAPSDLFSCVVTHEIDNYTAIAYWV 129
Query: 694 PQVTMP 711
P +P
Sbjct: 130 PHDALP 135
>ref|NP_001014403.1| major histocompatibility complex, class II, DQ beta 1 [Canis lupus
familiaris].
Length = 269
Score = 74.3 bits (181), Expect = 2e-13
Identities = 41/122 (33%), Positives = 53/122 (43%), Gaps = 6/122 (4%)
Frame = +1
Query: 352 IRAHLDVLVERSNHTRAT------NVPPRVTVLPKSPVALGQPNVLICIVDNIFPPVINI 513
+RA LD + R N+ R V P VT+ P L N+L+C V + +P I +
Sbjct: 103 VRAELDTVC-RHNYGREELTTLQRRVEPTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKV 161
Query: 514 TWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWE 693
W N Q T GV T D +F+ L P GD Y C VEH L P+ W
Sbjct: 162 RWFRNDQEQTAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHASLQSPITVQWR 221
Query: 694 PQ 699
Q
Sbjct: 222 AQ 223
>ref|NP_001014768.1| DLA class II histocompatibility antigen, DR-1 beta chain precursor
[Canis lupus familiaris].
Length = 266
Score = 73.6 bits (179), Expect = 3e-13
Identities = 36/97 (37%), Positives = 47/97 (48%)
Frame = +1
Query: 409 VPPRVTVLPKSPVALGQPNVLICIVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHS 588
V P VTV P L N+L+C V+ +P I + WL NGQ GV T D +
Sbjct: 124 VEPTVTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNGDWT 183
Query: 589 FRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWEPQ 699
F+ L VP +G+ Y C+VEH L P+ W Q
Sbjct: 184 FQILVMLEIVPQSGEVYTCQVEHPSLTSPVTVEWRAQ 220
>ref|NP_001041592.1| major histocompatibility complex, class II, DO beta [Canis lupus
familiaris].
Length = 270
Score = 68.9 bits (167), Expect = 8e-12
Identities = 40/122 (32%), Positives = 52/122 (42%), Gaps = 5/122 (4%)
Frame = +1
Query: 355 RAHLDVLVERSNH-----TRATNVPPRVTVLPKSPVALGQPNVLICIVDNIFPPVINITW 519
RA +D+L + T V P VTV P+ ++ N+L+C V +P I I W
Sbjct: 98 RASVDLLCRHNYELGAPFTVGRKVQPEVTVYPERTPSMQHHNLLLCSVTGFYPGDIKIKW 157
Query: 520 LHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWEPQ 699
NGQ GV T D +F+ L P GD Y C V H L P+ W Q
Sbjct: 158 FRNGQEERVGVMSTGLIRNGDWTFQTMVMLEMTPELGDVYTCLVNHPSLLSPVSVEWRAQ 217
Query: 700 VT 705
T
Sbjct: 218 ST 219
>ref|XP_535458.1| PREDICTED: similar to beta-2-microglobulin precursor isoform 2
[Canis familiaris].
Length = 125
Score = 62.0 bits (149), Expect = 1e-09
Identities = 33/98 (33%), Positives = 46/98 (46%)
Frame = +1
Query: 400 ATNVPPRVTVLPKSPVALGQPNVLICIVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQP 579
A PP++ V + P G+PN L C V PP I I L NG+ + T SF
Sbjct: 27 AVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSF--SK 84
Query: 580 DHSFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWE 693
D +F + F P+ D + C+V+H L EP W+
Sbjct: 85 DWTFYLLVHTEFTPNEQDEFSCRVKHVTLSEPQIVKWD 122
>ref|XP_850148.1| PREDICTED: similar to beta-2-microglobulin precursor isoform 3
[Canis familiaris].
Length = 125
Score = 62.0 bits (149), Expect = 1e-09
Identities = 33/98 (33%), Positives = 46/98 (46%)
Frame = +1
Query: 400 ATNVPPRVTVLPKSPVALGQPNVLICIVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQP 579
A PP++ V + P G+PN L C V PP I I L NG+ + T SF
Sbjct: 27 AVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSF--SK 84
Query: 580 DHSFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWE 693
D +F + F P+ D + C+V+H L EP W+
Sbjct: 85 DWTFYLLVHTEFTPNEQDEFSCRVKHVTLSEPQIVKWD 122
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: 49,060,478
Number of extensions: 1480234
Number of successful extensions: 7761
Number of sequences better than 1.0e-05: 12
Number of HSP's gapped: 7664
Number of HSP's successfully gapped: 12
Length of query: 385
Length of database: 18,874,504
Length adjustment: 105
Effective length of query: 280
Effective length of database: 15,374,224
Effective search space: 4304782720
Effective search space used: 4304782720
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-014077
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-014077
(1157 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_001192849.1| HLA class II histocompatibility antigen, DO ... 351 8e-97
Alignment gi|XP_002697222.1| PREDICTED: MHC class II antigen-like [Bos ta... 351 8e-97
Alignment gi|XP_002702869.1| PREDICTED: MHC class II antigen-like [Bos ta... 333 1e-91
Alignment gi|NP_001012693.1| major histocompatibility complex, class II, ... 260 2e-69
Alignment gi|NP_001012696.1| major histocompatibility complex, class II, ... 258 7e-69
Alignment gi|NP_001012699.1| major histocompatibility complex, class II, ... 248 6e-66
Alignment gi|XP_002702914.1| PREDICTED: BOLA-DQA2 protein-like [Bos tauru... 246 4e-65
Alignment gi|NP_001013619.3| major histocompatibility complex, class II, ... 244 1e-64
Alignment gi|NP_001012695.1| major histocompatibility complex, class II, ... 236 2e-62
Alignment gi|NP_001073045.1| major histocompatibility complex, class II, ... 232 4e-61
>ref|NP_001192849.1| HLA class II histocompatibility antigen, DO alpha chain [Bos
taurus].
Length = 250
Score = 351 bits (900), Expect = 8e-97
Identities = 167/203 (82%), Positives = 178/203 (87%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
LMTLLS Q+ GAIKADHMGSYGPAFYQSYDG+GQFTYDFDGEQLFSVDLKKREAVWRLPE
Sbjct: 14 LMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSVDLKKREAVWRLPE 73
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
F NFA FDPQ+GL IA+I+AHL+ LV+RSN TRA NV PRV VLPKS V LG+PNVLIC
Sbjct: 74 FGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNVSPRVAVLPKSHVQLGEPNVLIC 133
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
IVD IFPPVINITWL NG VT+GVTQ+SFYAQPDH FRKFHYLTFVP DFYDCKVEH
Sbjct: 134 IVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTFVPLVDDFYDCKVEH 193
Query: 658 WGLDEPLFTHWEPQVTMPLPDTT 726
WGLD+PLF HWEPQV LPDTT
Sbjct: 194 WGLDQPLFQHWEPQVPTALPDTT 216
>ref|XP_002697222.1| PREDICTED: MHC class II antigen-like [Bos taurus].
Length = 250
Score = 351 bits (900), Expect = 8e-97
Identities = 167/203 (82%), Positives = 178/203 (87%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
LMTLLS Q+ GAIKADHMGSYGPAFYQSYDG+GQFTYDFDGEQLFSVDLKKREAVWRLPE
Sbjct: 14 LMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSVDLKKREAVWRLPE 73
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
F NFA FDPQ+GL IA+I+AHL+ LV+RSN TRA NV PRV VLPKS V LG+PNVLIC
Sbjct: 74 FGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNVSPRVAVLPKSHVQLGEPNVLIC 133
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
IVD IFPPVINITWL NG VT+GVTQ+SFYAQPDH FRKFHYLTFVP DFYDCKVEH
Sbjct: 134 IVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTFVPLVDDFYDCKVEH 193
Query: 658 WGLDEPLFTHWEPQVTMPLPDTT 726
WGLD+PLF HWEPQV LPDTT
Sbjct: 194 WGLDQPLFQHWEPQVPTALPDTT 216
>ref|XP_002702869.1| PREDICTED: MHC class II antigen-like [Bos taurus].
Length = 224
Score = 333 bits (855), Expect = 1e-91
Identities = 158/191 (82%), Positives = 169/191 (88%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
LMTLLS Q+ GAIKADHMGSYGPAFYQSYDG+GQFTYDFDGEQLFSVDLKKREAVWRLPE
Sbjct: 14 LMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSVDLKKREAVWRLPE 73
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
F NFA FDPQ+GL IA+I+AHL+ LV+RSN TRA NV PRV VLPKS V LG+PNVLIC
Sbjct: 74 FGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNVSPRVAVLPKSHVQLGEPNVLIC 133
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
IVD IFPPVINITWL NG VT+GVTQ+SFYAQPDH FRKFHYLTFVP DFYDCKVEH
Sbjct: 134 IVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTFVPLVDDFYDCKVEH 193
Query: 658 WGLDEPLFTHW 690
WGLD+PLF HW
Sbjct: 194 WGLDQPLFQHW 204
>ref|NP_001012693.1| major histocompatibility complex, class II, DQ alpha 5 [Bos
taurus].
Length = 255
Score = 260 bits (664), Expect = 2e-69
Identities = 121/204 (59%), Positives = 148/204 (72%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
L T++SP I ADH+G YG + YQSY SGQ+T++FDG++ F VDL+K+E W+LP
Sbjct: 14 LTTMMSPSGGEDIVADHVGIYGISIYQSYGPSGQYTHEFDGDEQFYVDLEKKETAWQLPL 73
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
FS FDPQ LR IA+++ H+D L + SN T ATN P VTV KSPV LGQPN LIC
Sbjct: 74 FSRMLSFDPQLALRNIAIMKLHVDFLTKFSNSTAATNKVPEVTVFSKSPVMLGQPNTLIC 133
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
VDNIFPPVINITWL NG +VTEGV++TSF + D+SF K YL F+PS D YDCKVEH
Sbjct: 134 HVDNIFPPVINITWLRNGHSVTEGVSETSFLIRSDYSFLKIKYLAFLPSDDDIYDCKVEH 193
Query: 658 WGLDEPLFTHWEPQVTMPLPDTTE 729
WGLDEPL HWEP++ P+ + TE
Sbjct: 194 WGLDEPLLKHWEPEIPAPMSELTE 217
>ref|NP_001012696.1| major histocompatibility complex, class II, DY alpha [Bos taurus].
Length = 253
Score = 258 bits (659), Expect = 7e-69
Identities = 117/204 (57%), Positives = 149/204 (73%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
L T++SP I ADH+G+YG YQ+Y SGQFT++FDG++LF VDL K+E VWRLPE
Sbjct: 12 LATMMSPYGGEDIVADHVGTYGTNVYQTYGASGQFTFEFDGDELFYVDLGKKETVWRLPE 71
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
FSN F+ Q+ LR I + + +LD+L++ S+ T AT+ P V V PKS V LG PN LIC
Sbjct: 72 FSNITKFEVQSALRNIVMSKRNLDILIKNSSFTPATSEIPEVAVFPKSSVVLGIPNTLIC 131
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
VDNIFPPVINITW +NG V EG+ +T+FY + DHSF KF YLTF+P+ DFYDC+VEH
Sbjct: 132 QVDNIFPPVINITWFYNGHFVAEGIAETTFYPKSDHSFLKFSYLTFLPTNEDFYDCRVEH 191
Query: 658 WGLDEPLFTHWEPQVTMPLPDTTE 729
WGL+EPL HWEP++ P + TE
Sbjct: 192 WGLEEPLVKHWEPEIPTPTSELTE 215
>ref|NP_001012699.1| major histocompatibility complex, class II, DQ alpha 2 [Bos
taurus].
Length = 268
Score = 248 bits (634), Expect = 6e-66
Identities = 120/191 (62%), Positives = 137/191 (71%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
L T++S I ADH+GSYG YQS+ SGQ+T +FDG+++F VDL K+E VWRLP
Sbjct: 14 LTTMMSSSGGEDIVADHVGSYGTEIYQSHGPSGQYTQEFDGDEMFYVDLGKKETVWRLPM 73
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
FS FA FDPQ L IA + +LDVL +RSN T N P VTV KSPV LGQPN LIC
Sbjct: 74 FSQFAGFDPQAALSEIATAKHNLDVLTKRSNFTPVINEVPEVTVFSKSPVMLGQPNTLIC 133
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
VDNIFPPVINITWL NG VTEGV++TSF + DHSF K YLTF+PS D YDCKVEH
Sbjct: 134 HVDNIFPPVINITWLKNGHAVTEGVSETSFLPKDDHSFLKIGYLTFLPSDNDIYDCKVEH 193
Query: 658 WGLDEPLFTHW 690
WGLDEPL HW
Sbjct: 194 WGLDEPLLKHW 204
>ref|XP_002702914.1| PREDICTED: BOLA-DQA2 protein-like [Bos taurus].
Length = 254
Score = 246 bits (627), Expect = 4e-65
Identities = 119/204 (58%), Positives = 146/204 (71%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
L T++SP I ADH+GSYG QS+ S Q+T +FDG++LF VDL+K+E VWRLP
Sbjct: 14 LTTMMSPCGGEDIVADHVGSYGTVISQSHGPSDQYTQEFDGDKLFYVDLEKKETVWRLPM 73
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
FS FA FDPQ LR IA+ + +L+++++ SN A N P VTV KSP+ LGQPN LIC
Sbjct: 74 FSQFASFDPQAILRNIAISKHNLNIMIKYSNFIPAINEVPEVTVFSKSPMVLGQPNTLIC 133
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
+DN FPPVINITWL NG VTEGV++TSF + DHSF K YLTF+PS D YDCKVEH
Sbjct: 134 HMDN-FPPVINITWLKNGHAVTEGVSETSFLPKDDHSFLKIGYLTFLPSDDDVYDCKVEH 192
Query: 658 WGLDEPLFTHWEPQVTMPLPDTTE 729
W LDEPL HWEP+V P+ + TE
Sbjct: 193 WSLDEPLLKHWEPEVPAPMSELTE 216
>ref|NP_001013619.3| major histocompatibility complex, class II, DQ alpha, type 1 [Bos
taurus].
Length = 255
Score = 244 bits (622), Expect = 1e-64
Identities = 117/204 (57%), Positives = 142/204 (69%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
L T+ S I ADH+G+YG FYQS+ SGQ+ ++FDG++LF VDL K+E VW+LP
Sbjct: 14 LTTMTSLCGGEDIVADHIGTYGADFYQSHGPSGQYIHEFDGDELFYVDLGKKETVWQLPM 73
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
F F+ Q+ L IA + LDVL +RSN T N P VTV KSP+ LGQPN LIC
Sbjct: 74 FGELTSFEAQDALNEIAKAKHTLDVLTKRSNFTPVINEVPEVTVFSKSPMMLGQPNTLIC 133
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
VDNIFPPVINITWL NG VTEGV++TSF + D+SF K YLTF+PS D YDCKVEH
Sbjct: 134 HVDNIFPPVINITWLRNGHAVTEGVSETSFLPKSDYSFLKIGYLTFLPSDDDVYDCKVEH 193
Query: 658 WGLDEPLFTHWEPQVTMPLPDTTE 729
WGLDEPL HWEP++ P+ + TE
Sbjct: 194 WGLDEPLLKHWEPEIPAPMSELTE 217
>ref|NP_001012695.1| major histocompatibility complex, class II, DR alpha [Bos taurus].
Length = 253
Score = 236 bits (603), Expect = 2e-62
Identities = 107/204 (52%), Positives = 147/204 (72%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
+ L+ Q++ AIK +H+ FY + S +F +DFDG+++F VD+ K+E VWRLPE
Sbjct: 13 ITVLIGLQESWAIKENHV-IIQAEFYLKPEESAEFMFDFDGDEIFHVDMGKKETVWRLPE 71
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
F +FA F+ Q L +A+++A+LD++++RSN+T TNVPP VT+LP PV LG+PN LIC
Sbjct: 72 FGHFASFEAQGALANMAVMKANLDIMIKRSNNTPNTNVPPEVTLLPNKPVELGEPNTLIC 131
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
+D PPVI++TWL NG+ VT+GV+QT F + DH FRKFHYL F+P+ D YDCKVEH
Sbjct: 132 FIDKFSPPVISVTWLRNGKPVTDGVSQTVFLPRNDHLFRKFHYLPFLPTTEDVYDCKVEH 191
Query: 658 WGLDEPLFTHWEPQVTMPLPDTTE 729
GL+EPL HWE + PLP+TTE
Sbjct: 192 LGLNEPLLKHWEYEAPAPLPETTE 215
>ref|NP_001073045.1| major histocompatibility complex, class II, DQ alpha, type 3 [Bos
taurus].
Length = 254
Score = 232 bits (592), Expect = 4e-61
Identities = 115/204 (56%), Positives = 138/204 (67%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
L T+ S I ADH+G+YG FYQS+ SGQ+ + FDG++ F VDL+K EAVWRLP
Sbjct: 14 LTTMTSLCGGEDIVADHVGTYGTDFYQSHGPSGQYIHQFDGDEEFYVDLEKEEAVWRLPM 73
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
F F PQ LR IA+ + +LDVL + N T N P VTV KSPV L QPN LIC
Sbjct: 74 FDKLR-FHPQGALRNIAIAKHNLDVLTKLYNFTPVINEVPEVTVFSKSPVMLSQPNTLIC 132
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
VDNIFPPVINITWL NG +VTE V++TSF + D+S+ K YL F PS D YDCKVEH
Sbjct: 133 HVDNIFPPVINITWLRNGHSVTEHVSETSFLLRSDYSYLKISYLPFRPSDDDVYDCKVEH 192
Query: 658 WGLDEPLFTHWEPQVTMPLPDTTE 729
WGLDEPL HWEP++ P+ + TE
Sbjct: 193 WGLDEPLLKHWEPEIPAPMSELTE 216
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: 46,932,249
Number of extensions: 1443062
Number of successful extensions: 7771
Number of sequences better than 1.0e-05: 53
Number of HSP's gapped: 7684
Number of HSP's successfully gapped: 54
Length of query: 385
Length of database: 17,681,374
Length adjustment: 104
Effective length of query: 281
Effective length of database: 14,240,222
Effective search space: 4001502382
Effective search space used: 4001502382
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-014077
(1157 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_001172072.1| src-like-adapter [Sus scrofa]. 432 e-121
Alignment gi|NP_001123696.1| SLA class II histocompatibility antigen, DQ ... 260 1e-69
Alignment gi|NP_001107534.2| SLA class II histocompatibility antigen, DQ ... 250 9e-67
Alignment gi|NP_001107178.1| MHC class II DR-alpha [Sus scrofa]. 244 5e-65
Alignment gi|NP_001004039.1| SLA-DM alpha chain [Sus scrofa]. 92 7e-19
Alignment gi|NP_001107177.1| major histocompatibility complex, class II, ... 92 7e-19
Alignment gi|XP_003128397.1| PREDICTED: DLA class II histocompatibility a... 73 3e-13
Alignment gi|XP_003128376.1| PREDICTED: HLA class II histocompatibility a... 73 3e-13
Alignment gi|NP_001107536.2| MHC class II, DO beta [Sus scrofa]. 73 3e-13
Alignment gi|XP_003128372.1| PREDICTED: DLA class II histocompatibility a... 72 4e-13
>ref|NP_001172072.1| src-like-adapter [Sus scrofa].
Length = 250
Score = 432 bits (1112), Expect = e-121
Identities = 205/205 (100%), Positives = 205/205 (100%)
Frame = +1
Query: 115 ILMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLP 294
ILMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLP
Sbjct: 13 ILMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLP 72
Query: 295 EFSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLI 474
EFSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLI
Sbjct: 73 EFSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLI 132
Query: 475 CIVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVE 654
CIVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVE
Sbjct: 133 CIVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVE 192
Query: 655 HWGLDEPLFTHWEPQVTMPLPDTTE 729
HWGLDEPLFTHWEPQVTMPLPDTTE
Sbjct: 193 HWGLDEPLFTHWEPQVTMPLPDTTE 217
>ref|NP_001123696.1| SLA class II histocompatibility antigen, DQ haplotype D alpha chain
precursor [Sus scrofa].
Length = 255
Score = 260 bits (664), Expect = 1e-69
Identities = 119/192 (61%), Positives = 146/192 (76%)
Frame = +1
Query: 154 IKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPEFSNFADFDPQNG 333
I ADH+ SYG YQSY SG +T++FDG++ F VDL+K+E VW+LP FS F FDPQ
Sbjct: 26 IAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYVDLEKKETVWQLPLFSKFTSFDPQGA 85
Query: 334 LRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLICIVDNIFPPVINI 513
LR IA + +L++L++RSN+T A N P VTV PKSPV LGQPN LIC VDNIFPPVINI
Sbjct: 86 LRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINI 145
Query: 514 TWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWE 693
TWL NG +VTEG ++TSF ++ DHSF K YLTF+PS DFYDCKVEHWGLD+PL HWE
Sbjct: 146 TWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 205
Query: 694 PQVTMPLPDTTE 729
P++ P+ + TE
Sbjct: 206 PEIPAPMSELTE 217
>ref|NP_001107534.2| SLA class II histocompatibility antigen, DQ haplotype C alpha chain
precursor [Sus scrofa].
Length = 254
Score = 250 bits (639), Expect = 9e-67
Identities = 119/204 (58%), Positives = 149/204 (73%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
L T++S I ADH+ SYG YQSY SG FT++FDG++ F VDL+K+E VWRLP
Sbjct: 14 LTTVMSACGGEDIAADHVASYGLNVYQSYGPSGYFTHEFDGDEEFYVDLEKKETVWRLPL 73
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
FS F FDPQ LR IA ++ +L+++ +RSN+T A N P VTV KSPV LGQPN LIC
Sbjct: 74 FSEFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNQVPEVTVFSKSPVILGQPNTLIC 133
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
VD+IFPPVINITWL NG +V +G ++TSF ++ DHSF K YLTF+PS DFYDCKVEH
Sbjct: 134 HVDSIFPPVINITWLKNGHSV-KGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEH 192
Query: 658 WGLDEPLFTHWEPQVTMPLPDTTE 729
WGLD+PL HWEP++ P+ + TE
Sbjct: 193 WGLDKPLLKHWEPEIPAPMSELTE 216
>ref|NP_001107178.1| MHC class II DR-alpha [Sus scrofa].
Length = 252
Score = 244 bits (624), Expect = 5e-65
Identities = 112/204 (54%), Positives = 149/204 (73%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
++T+L+ QK+ AI +H+ FY S D SG+F +DFDG+++F VD++KRE VWRL E
Sbjct: 12 VITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEE 70
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
F +FA F+ Q L IA+ +A+L++L++RSN+T TNVPP VTVL PV LG+PN+LIC
Sbjct: 71 FGHFASFEAQGALANIAVDKANLEILIKRSNNTPNTNVPPEVTVLSDKPVELGEPNILIC 130
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
+D PPV+N+TWL NG VT GV++T F + DH FRKFHYL F+PS D YDC+VEH
Sbjct: 131 FIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEH 190
Query: 658 WGLDEPLFTHWEPQVTMPLPDTTE 729
WGLD+PL HWE + PLP+TTE
Sbjct: 191 WGLDKPLLKHWEFEAQTPLPETTE 214
>ref|NP_001004039.1| SLA-DM alpha chain [Sus scrofa].
Length = 260
Score = 91.7 bits (226), Expect = 7e-19
Identities = 53/165 (32%), Positives = 79/165 (47%), Gaps = 5/165 (3%)
Frame = +1
Query: 232 FDGEQLFSVDLKKREAVWRLPEFSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNV 411
+DG+QLFS + + V RLPEF+++A I + ++E+ +
Sbjct: 63 YDGDQLFSFNFSQNIRVPRLPEFADWAH--QIEDTPAIFFDKGFCREMIEKVGPLFEGKI 120
Query: 412 P-----PRVTVLPKSPVALGQPNVLICIVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQ 576
P P V P+ G+PN L+C V N+FPP + +TW H+ V EG+ T A
Sbjct: 121 PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSAT 179
Query: 577 PDHSFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWEPQVTMP 711
D SF+ F YL F P+ D + C V H ++W PQ +P
Sbjct: 180 DDLSFQAFSYLNFTPTPSDLFSCVVTHELDGYVAISYWVPQNALP 224
>ref|NP_001107177.1| major histocompatibility complex, class II, DO alpha [Sus scrofa].
Length = 260
Score = 91.7 bits (226), Expect = 7e-19
Identities = 53/165 (32%), Positives = 79/165 (47%), Gaps = 5/165 (3%)
Frame = +1
Query: 232 FDGEQLFSVDLKKREAVWRLPEFSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNV 411
+DG+QLFS + + V RLPEF+++A I + ++E+ +
Sbjct: 63 YDGDQLFSFNFSQNIRVPRLPEFADWAH--QIEDTPAIFFDKGFCREMIEKVGPLFEGKI 120
Query: 412 P-----PRVTVLPKSPVALGQPNVLICIVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQ 576
P P V P+ G+PN L+C V N+FPP + +TW H+ V EG+ T A
Sbjct: 121 PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSAT 179
Query: 577 PDHSFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWEPQVTMP 711
D SF+ F YL F P+ D + C V H ++W PQ +P
Sbjct: 180 DDLSFQAFSYLNFTPTPSDLFSCVVTHELDGYVAISYWVPQNALP 224
>ref|XP_003128397.1| PREDICTED: DLA class II histocompatibility antigen, DR-1 beta
chain-like [Sus scrofa].
Length = 321
Score = 73.2 bits (178), Expect = 3e-13
Identities = 41/122 (33%), Positives = 55/122 (45%), Gaps = 6/122 (4%)
Frame = +1
Query: 352 IRAHLDVLVERSNH------TRATNVPPRVTVLPKSPVALGQPNVLICIVDNIFPPVINI 513
+RA +D RSN+ T V P VTV P L N+L+C V +P + +
Sbjct: 100 VRAAVDTFC-RSNYEFFESCTVQRRVKPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEV 158
Query: 514 TWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWE 693
W NGQ GV T D +F+ L VP +G+ Y C+VEH L P+ W
Sbjct: 159 RWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWR 218
Query: 694 PQ 699
Q
Sbjct: 219 AQ 220
>ref|XP_003128376.1| PREDICTED: HLA class II histocompatibility antigen, DO beta
chain-like [Sus scrofa].
Length = 277
Score = 72.8 bits (177), Expect = 3e-13
Identities = 43/120 (35%), Positives = 54/120 (45%), Gaps = 5/120 (4%)
Frame = +1
Query: 355 RAHLDVLVERSNHTRAT-----NVPPRVTVLPKSPVALGQPNVLICIVDNIFPPVINITW 519
RA +DVL R+ A V P VTV P+ +L N+L+C V +P I I W
Sbjct: 111 RASVDVLCRRNYWLGAPLTVERKVQPEVTVHPERTPSLQLRNLLLCSVTGFYPGAIEIRW 170
Query: 520 LHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWEPQ 699
NGQ EGV T D +F+ L P GD Y C V+H L P+ W Q
Sbjct: 171 FRNGQEQREGVLATGLVRNGDWTFQTVVMLEMTPELGDVYTCLVDHPSLLSPVSVEWRAQ 230
>ref|NP_001107536.2| MHC class II, DO beta [Sus scrofa].
Length = 277
Score = 72.8 bits (177), Expect = 3e-13
Identities = 43/120 (35%), Positives = 54/120 (45%), Gaps = 5/120 (4%)
Frame = +1
Query: 355 RAHLDVLVERSNHTRAT-----NVPPRVTVLPKSPVALGQPNVLICIVDNIFPPVINITW 519
RA +DVL R+ A V P VTV P+ +L N+L+C V +P I I W
Sbjct: 111 RASVDVLCRRNYWLGAPLTVERKVQPEVTVHPERTPSLQLRNLLLCSVTGFYPGAIEIRW 170
Query: 520 LHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWEPQ 699
NGQ EGV T D +F+ L P GD Y C V+H L P+ W Q
Sbjct: 171 FRNGQEQREGVLATGLIRNGDWTFQTVVMLEMTPELGDVYTCLVDHPSLLSPVSVEWRAQ 230
>ref|XP_003128372.1| PREDICTED: DLA class II histocompatibility antigen, DR-1 beta
chain-like [Sus scrofa].
Length = 261
Score = 72.4 bits (176), Expect = 4e-13
Identities = 34/94 (36%), Positives = 45/94 (47%)
Frame = +1
Query: 409 VPPRVTVLPKSPVALGQPNVLICIVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHS 588
V PRVTV P L N+L+C V +P + + W NGQ GV T D +
Sbjct: 119 VKPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWT 178
Query: 589 FRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHW 690
F+ L VP +G+ Y C+VEH L P+ W
Sbjct: 179 FQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 212
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: 30,526,130
Number of extensions: 957241
Number of successful extensions: 4997
Number of sequences better than 1.0e-05: 27
Number of HSP's gapped: 4942
Number of HSP's successfully gapped: 27
Length of query: 385
Length of database: 11,343,932
Length adjustment: 101
Effective length of query: 284
Effective length of database: 8,829,335
Effective search space: 2507531140
Effective search space used: 2507531140
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-014077
(1157 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_032232.2| histocompatibility 2, O region alpha locus [Mus... 326 2e-89
Alignment gi|NP_034508.2| histocompatibility 2, class II antigen A, alpha... 257 1e-68
Alignment gi|NP_034511.2| histocompatibility 2, class II antigen E alpha ... 237 1e-62
Alignment gi|NP_034516.3| class II histocompatibility antigen, M alpha ch... 88 1e-17
Alignment gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ... 79 9e-15
Alignment gi|NP_034512.2| H-2 class II histocompatibility antigen, I-E be... 72 8e-13
Alignment gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ... 69 9e-12
Alignment gi|NP_001029150.1| histocompatibility 2, class II antigen E bet... 68 1e-11
Alignment gi|NP_996988.2| histocompatibility 2, class II antigen A, beta ... 67 2e-11
Alignment gi|XP_003086107.1| PREDICTED: class II histocompatibility antig... 67 3e-11
>ref|NP_032232.2| histocompatibility 2, O region alpha locus [Mus musculus].
Length = 250
Score = 326 bits (835), Expect = 2e-89
Identities = 151/203 (74%), Positives = 171/203 (84%)
Frame = +1
Query: 121 MTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPEF 300
M+ LSP+ AIKADHMGSYGPAFYQSYD SGQFT++FDGEQ+FSVDLK E VWRLPEF
Sbjct: 15 MSFLSPRGVRAIKADHMGSYGPAFYQSYDASGQFTHEFDGEQIFSVDLKNEEVVWRLPEF 74
Query: 301 SNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLICI 480
+FA D Q+GL I++I+AHLD+LVERSN TRA +VPPRVTVLPK+ V LG+PNVLICI
Sbjct: 75 GDFAHSDFQSGLMSISMIKAHLDILVERSNRTRAVSVPPRVTVLPKTRVELGKPNVLICI 134
Query: 481 VDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEHW 660
VD+IFPPVIN+TWL N Q +T+GV QTSFY+QP+H FRKFHYLTFVPSA D YDCKVEHW
Sbjct: 135 VDDIFPPVINVTWLRNSQPITKGVAQTSFYSQPNHRFRKFHYLTFVPSAEDVYDCKVEHW 194
Query: 661 GLDEPLFTHWEPQVTMPLPDTTE 729
GLD PL HWEPQV P PDT E
Sbjct: 195 GLDTPLLQHWEPQVLTPPPDTIE 217
>ref|NP_034508.2| histocompatibility 2, class II antigen A, alpha precursor [Mus
musculus].
Length = 256
Score = 257 bits (657), Expect = 1e-68
Identities = 115/192 (59%), Positives = 145/192 (75%)
Frame = +1
Query: 154 IKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPEFSNFADFDPQNG 333
I+ADH+G+YG + YQS GQ+T++FDG++LF VDL K+E VW LPEF A FDPQ G
Sbjct: 27 IEADHVGTYGISVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFGQLASFDPQGG 86
Query: 334 LRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLICIVDNIFPPVINI 513
L+ IA+++ +L VL +RSN T ATN P+ TV PKSPV LGQPN LIC VDNIFPPVINI
Sbjct: 87 LQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINI 146
Query: 514 TWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWE 693
TWL N ++V +GV +TSF+ D+SF K YLTF+PS D YDCKVEHWGL+EP+ HWE
Sbjct: 147 TWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWE 206
Query: 694 PQVTMPLPDTTE 729
P++ P+ + TE
Sbjct: 207 PEIPAPMSELTE 218
>ref|NP_034511.2| histocompatibility 2, class II antigen E alpha precursor [Mus
musculus].
Length = 255
Score = 237 bits (604), Expect = 1e-62
Identities = 110/204 (53%), Positives = 145/204 (71%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
+ L+S QK+ AIK +H FY D G+F +DFDG+++F VD++K E +WRL E
Sbjct: 14 IAVLMSSQKSWAIKEEHT-IIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEE 72
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
F+ FA F+ Q L IA+ +A+LDV+ ERSN+T NV P VTVL +SPV LG+PN+LIC
Sbjct: 73 FAKFASFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPNILIC 132
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
+D PPV+N+TW NG+ VTEGV++T F + DH FRKFHYLTF+PS DFYDC+V+H
Sbjct: 133 FIDKFSPPVVNVTWFRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDH 192
Query: 658 WGLDEPLFTHWEPQVTMPLPDTTE 729
WGL+EPL HWE + LP+TTE
Sbjct: 193 WGLEEPLRKHWEFEEKTLLPETTE 216
>ref|NP_034516.3| class II histocompatibility antigen, M alpha chain precursor [Mus
musculus].
Length = 261
Score = 88.2 bits (217), Expect = 1e-17
Identities = 51/166 (30%), Positives = 78/166 (46%), Gaps = 6/166 (3%)
Frame = +1
Query: 232 FDGEQLFSVDLKKREAVWRLPEFSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNV 411
+D ++LFS D + V RLP+F+ +A Q IA ++ ++L+ + +
Sbjct: 63 YDEDELFSFDFSQNTRVPRLPDFAEWAQ--GQGDASAIAFDKSFCEMLMREVSPKLEGQI 120
Query: 412 P-----PRVTVLPKSPVALGQPNVLICIVDNIFPPVINITW-LHNGQTVTEGVTQTSFYA 573
P P V P+ G+PN L+C + N+FPP + + W LH+ EG + TS A
Sbjct: 121 PVSRGLPVAEVFTLKPLEFGKPNTLVCFISNLFPPTLTVNWQLHSAP--VEGASPTSISA 178
Query: 574 QPDHSFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWEPQVTMP 711
+F+ F YL F P D Y C V H +W PQ +P
Sbjct: 179 VDGLTFQAFSYLNFTPEPFDLYSCTVTHEIDRYTAIAYWVPQNALP 224
>ref|NP_034519.2| histocompatibility 2, O region beta locus [Mus musculus].
Length = 271
Score = 78.6 bits (192), Expect = 9e-15
Identities = 39/98 (39%), Positives = 49/98 (50%)
Frame = +1
Query: 406 NVPPRVTVLPKSPVALGQPNVLICIVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDH 585
NVPP VTV P+ L Q N+L+C V +P I++ W NGQ GV T D
Sbjct: 120 NVPPEVTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVRNGDW 179
Query: 586 SFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWEPQ 699
+F+ L +P GD Y C VEH GL P+ W Q
Sbjct: 180 TFQTTVMLEMIPELGDIYSCLVEHPGLLRPVSVAWMAQ 217
>ref|NP_034512.2| H-2 class II histocompatibility antigen, I-E beta chain precursor
[Mus musculus].
Length = 264
Score = 72.0 bits (175), Expect = 8e-13
Identities = 34/99 (34%), Positives = 49/99 (49%)
Frame = +1
Query: 409 VPPRVTVLPKSPVALGQPNVLICIVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHS 588
V P VTV P L N+L+C V + +P I + W NG+ G+ T D +
Sbjct: 122 VEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWT 181
Query: 589 FRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWEPQVT 705
F+ L VP +G+ Y C+VEH L +P+ W+ Q T
Sbjct: 182 FQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEWKAQST 220
>ref|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus musculus].
Length = 261
Score = 68.6 bits (166), Expect = 9e-12
Identities = 47/127 (37%), Positives = 61/127 (48%), Gaps = 3/127 (2%)
Frame = +1
Query: 325 QNGLRGIAL-IRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLICIVDNIFPP 501
QNGL+ A + DVL R TRA P V V +P +P +L C V +P
Sbjct: 91 QNGLQDCATHTQPFWDVLTHR---TRA----PSVRVAQTTPFNTREPVMLACYVWGFYPA 143
Query: 502 VINITWLHNGQTVTEGVTQTSFYAQP--DHSFRKFHYLTFVPSAGDFYDCKVEHWGLDEP 675
+ ITW+ NGQ V + AQP D +++ YL PS GD Y C V+H G EP
Sbjct: 144 DVTITWMKNGQLVPSHSNKEKT-AQPNGDWTYQTVSYLALTPSYGDVYTCVVQHSGTSEP 202
Query: 676 LFTHWEP 696
+ W P
Sbjct: 203 IRGDWTP 209
>ref|NP_001029150.1| histocompatibility 2, class II antigen E beta2 [Mus musculus].
Length = 287
Score = 68.2 bits (165), Expect = 1e-11
Identities = 32/97 (32%), Positives = 46/97 (47%)
Frame = +1
Query: 415 PRVTVLPKSPVALGQPNVLICIVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFR 594
P+VTV P L N+L+C V + +P I + W NG+ GV T D +++
Sbjct: 125 PKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNRDWTYQ 184
Query: 595 KFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWEPQVT 705
L VP G+ Y C+VEH L P+ W + T
Sbjct: 185 TLVMLEMVPRGGEVYTCQVEHPSLTSPVTVEWRARST 221
>ref|NP_996988.2| histocompatibility 2, class II antigen A, beta 1 precursor [Mus
musculus].
Length = 265
Score = 67.4 bits (163), Expect = 2e-11
Identities = 38/121 (31%), Positives = 51/121 (42%), Gaps = 6/121 (4%)
Frame = +1
Query: 355 RAHLDVLVERS-----NHTRATNVP-PRVTVLPKSPVALGQPNVLICIVDNIFPPVINIT 516
RA LD + + HT + P V + AL N L+C V + +P I +
Sbjct: 99 RAELDTVCRHNYEGPETHTSLRRLEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVR 158
Query: 517 WLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWEP 696
W NGQ T GV+ T D +F+ L P G+ Y C VEH L P+ W
Sbjct: 159 WFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRA 218
Query: 697 Q 699
Q
Sbjct: 219 Q 219
>ref|XP_003086107.1| PREDICTED: class II histocompatibility antigen, M beta 1 chain-like
[Mus musculus].
Length = 261
Score = 67.0 bits (162), Expect = 3e-11
Identities = 36/97 (37%), Positives = 48/97 (49%), Gaps = 2/97 (2%)
Frame = +1
Query: 412 PPRVTVLPKSPVALGQPNVLICIVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQP--DH 585
PP V V +P +P +L C V +P + ITW+ NGQ V + AQP D
Sbjct: 114 PPSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKT-AQPNGDW 172
Query: 586 SFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWEP 696
+++ YL PS GD Y C V+H G EP+ W P
Sbjct: 173 TYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDWTP 209
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: 40,265,334
Number of extensions: 1188351
Number of successful extensions: 5967
Number of sequences better than 1.0e-05: 21
Number of HSP's gapped: 5897
Number of HSP's successfully gapped: 21
Length of query: 385
Length of database: 15,617,559
Length adjustment: 103
Effective length of query: 282
Effective length of database: 12,523,851
Effective search space: 3531725982
Effective search space used: 3531725982
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 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-014077
(1157 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_002110.1| HLA class II histocompatibility antigen, DO alp... 347 2e-95
Alignment gi|NP_002113.2| HLA class II histocompatibility antigen, DQ alp... 261 1e-69
Alignment gi|XP_003120319.1| PREDICTED: HLA class II histocompatibility a... 259 3e-69
Alignment gi|XP_003120317.1| PREDICTED: HLA class II histocompatibility a... 259 3e-69
Alignment gi|XP_003119375.1| PREDICTED: HLA class II histocompatibility a... 259 4e-69
Alignment gi|XP_003119374.1| PREDICTED: HLA class II histocompatibility a... 259 4e-69
Alignment gi|NP_064440.1| HLA class II histocompatibility antigen, DQ alp... 256 2e-68
Alignment gi|XP_003120318.1| PREDICTED: HLA class II histocompatibility a... 254 8e-68
Alignment gi|XP_003119376.1| PREDICTED: HLA class II histocompatibility a... 254 1e-67
Alignment gi|NP_001229454.1| HLA class II histocompatibility antigen, DP ... 254 1e-67
>ref|NP_002110.1| HLA class II histocompatibility antigen, DO alpha chain precursor
[Homo sapiens].
Length = 250
Score = 347 bits (889), Expect = 2e-95
Identities = 165/204 (80%), Positives = 176/204 (86%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
LMTLLSPQ+AGA KADHMGSYGPAFYQSY SGQFT++FD EQLFSVDLKK EAVWRLPE
Sbjct: 14 LMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPE 73
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
F +FA FDPQ GL GIA I+AHLD+LVERSN +RA NVPPRVTVLPKS V LGQPN+LIC
Sbjct: 74 FGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILIC 133
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
IVDNIFPPVINITWL NGQTVTEGV QTSFY+QPDH FRKFHYL FVPSA D YDC+VEH
Sbjct: 134 IVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEH 193
Query: 658 WGLDEPLFTHWEPQVTMPLPDTTE 729
WGLD PL HWE QV +P PD E
Sbjct: 194 WGLDAPLLRHWELQVPIPPPDAME 217
>ref|NP_002113.2| HLA class II histocompatibility antigen, DQ alpha 1 chain precursor
[Homo sapiens].
Length = 255
Score = 261 bits (666), Expect = 1e-69
Identities = 118/204 (57%), Positives = 152/204 (74%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
L T++SP I ADH+ S G YQ Y SGQ+T++FDG++ F VDL+++E WR PE
Sbjct: 14 LTTVMSPCGGEDIVADHVASCGVNLYQFYGPSGQYTHEFDGDEQFYVDLERKETAWRWPE 73
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
FS F FDPQ LR +A+ + +L+++++R N T ATN P VTV KSPV LGQPN LIC
Sbjct: 74 FSKFGGFDPQGALRNMAVAKHNLNIMIKRYNSTAATNEVPEVTVFSKSPVTLGQPNTLIC 133
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
+VDNIFPPV+NITWL NGQ+VTEGV++TSF ++ DHSF K YLTF+PSA + YDCKVEH
Sbjct: 134 LVDNIFPPVVNITWLSNGQSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEH 193
Query: 658 WGLDEPLFTHWEPQVTMPLPDTTE 729
WGLD+PL HWEP++ P+ + TE
Sbjct: 194 WGLDQPLLKHWEPEIPAPMSELTE 217
>ref|XP_003120319.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 3 [Homo sapiens].
Length = 254
Score = 259 bits (662), Expect = 3e-69
Identities = 121/204 (59%), Positives = 153/204 (75%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
L T++SP I ADH+ SYG YQSY SGQFT++FDG++ F VDL+++E VW+LP
Sbjct: 14 LTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQFTHEFDGDEEFYVDLERKETVWKLPL 73
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
F FDPQ L IA+++ +L++L++RSN T ATN P VTV KSPV LGQPN LIC
Sbjct: 74 FHRLR-FDPQFALTNIAVLKHNLNILIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLIC 132
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
+VDNIFPPV+NITWL NG +VTEGV++TSF ++ DHSF K YLTF+PSA + YDCKVEH
Sbjct: 133 LVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEH 192
Query: 658 WGLDEPLFTHWEPQVTMPLPDTTE 729
WGLDEPL HWEP++ P+ + TE
Sbjct: 193 WGLDEPLLKHWEPEIPAPMSELTE 216
>ref|XP_003120317.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 1 [Homo sapiens].
Length = 254
Score = 259 bits (662), Expect = 3e-69
Identities = 121/204 (59%), Positives = 153/204 (75%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
L T++SP I ADH+ SYG YQSY SGQFT++FDG++ F VDL+++E VW+LP
Sbjct: 14 LTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQFTHEFDGDEEFYVDLERKETVWKLPL 73
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
F FDPQ L IA+++ +L++L++RSN T ATN P VTV KSPV LGQPN LIC
Sbjct: 74 FHRLR-FDPQFALTNIAVLKHNLNILIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLIC 132
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
+VDNIFPPV+NITWL NG +VTEGV++TSF ++ DHSF K YLTF+PSA + YDCKVEH
Sbjct: 133 LVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEH 192
Query: 658 WGLDEPLFTHWEPQVTMPLPDTTE 729
WGLDEPL HWEP++ P+ + TE
Sbjct: 193 WGLDEPLLKHWEPEIPAPMSELTE 216
>ref|XP_003119375.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 2 [Homo sapiens].
Length = 255
Score = 259 bits (661), Expect = 4e-69
Identities = 118/204 (57%), Positives = 153/204 (75%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
L T++SP I ADH+ SYG YQSY SGQ++++FDG++ F VDL+++E VW+LP
Sbjct: 14 LTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPL 73
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
F F FDPQ L IA+++ +L+++++RSN T ATN P VTV KSPV LGQPN LIC
Sbjct: 74 FRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLIC 133
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
+VDNIFPPV+NITWL NG +VTEGV++TSF ++ DHSF K YLTF+PS + YDCKVEH
Sbjct: 134 LVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEH 193
Query: 658 WGLDEPLFTHWEPQVTMPLPDTTE 729
WGLDEPL HWEP++ P+ + TE
Sbjct: 194 WGLDEPLLKHWEPEIPTPMSELTE 217
>ref|XP_003119374.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 1 [Homo sapiens].
Length = 255
Score = 259 bits (661), Expect = 4e-69
Identities = 118/204 (57%), Positives = 153/204 (75%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
L T++SP I ADH+ SYG YQSY SGQ++++FDG++ F VDL+++E VW+LP
Sbjct: 14 LTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPL 73
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
F F FDPQ L IA+++ +L+++++RSN T ATN P VTV KSPV LGQPN LIC
Sbjct: 74 FRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLIC 133
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
+VDNIFPPV+NITWL NG +VTEGV++TSF ++ DHSF K YLTF+PS + YDCKVEH
Sbjct: 134 LVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEH 193
Query: 658 WGLDEPLFTHWEPQVTMPLPDTTE 729
WGLDEPL HWEP++ P+ + TE
Sbjct: 194 WGLDEPLLKHWEPEIPTPMSELTE 217
>ref|NP_064440.1| HLA class II histocompatibility antigen, DQ alpha 2 chain precursor
[Homo sapiens].
Length = 255
Score = 256 bits (655), Expect = 2e-68
Identities = 118/204 (57%), Positives = 151/204 (74%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
L ++SP I ADH+ SYG FYQS+ SGQ+T++FDG++ F VDL+ +E VW+LP
Sbjct: 14 LTAVMSPCGGEDIVADHVASYGVNFYQSHGPSGQYTHEFDGDEEFYVDLETKETVWQLPM 73
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
FS F FDPQ+ LR +A+ + L+ ++ +SN T ATN P VTV K PV LGQPN LIC
Sbjct: 74 FSKFISFDPQSALRNMAVGKHTLEFMMRQSNSTAATNEVPEVTVFSKFPVTLGQPNTLIC 133
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
+VDNIFPPV+NITWL NG +VTEGV++TSF ++ DHSF K YLTF+PSA + YDCKVEH
Sbjct: 134 LVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEH 193
Query: 658 WGLDEPLFTHWEPQVTMPLPDTTE 729
WGLDEPL HWEP++ P+ + TE
Sbjct: 194 WGLDEPLLKHWEPEIPAPMSELTE 217
>ref|XP_003120318.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 2 [Homo sapiens].
Length = 249
Score = 254 bits (650), Expect = 8e-68
Identities = 120/204 (58%), Positives = 152/204 (74%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
L T++SP ADH+ SYG YQSY SGQFT++FDG++ F VDL+++E VW+LP
Sbjct: 14 LTTVMSP-----CGADHVASYGVNLYQSYGPSGQFTHEFDGDEEFYVDLERKETVWKLPL 68
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
F FDPQ L IA+++ +L++L++RSN T ATN P VTV KSPV LGQPN LIC
Sbjct: 69 FHRLR-FDPQFALTNIAVLKHNLNILIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLIC 127
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
+VDNIFPPV+NITWL NG +VTEGV++TSF ++ DHSF K YLTF+PSA + YDCKVEH
Sbjct: 128 LVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEH 187
Query: 658 WGLDEPLFTHWEPQVTMPLPDTTE 729
WGLDEPL HWEP++ P+ + TE
Sbjct: 188 WGLDEPLLKHWEPEIPAPMSELTE 211
>ref|XP_003119376.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 3 [Homo sapiens].
Length = 250
Score = 254 bits (649), Expect = 1e-67
Identities = 117/204 (57%), Positives = 152/204 (74%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
L T++SP ADH+ SYG YQSY SGQ++++FDG++ F VDL+++E VW+LP
Sbjct: 14 LTTVMSP-----CGADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPL 68
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
F F FDPQ L IA+++ +L+++++RSN T ATN P VTV KSPV LGQPN LIC
Sbjct: 69 FRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLIC 128
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
+VDNIFPPV+NITWL NG +VTEGV++TSF ++ DHSF K YLTF+PS + YDCKVEH
Sbjct: 129 LVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEH 188
Query: 658 WGLDEPLFTHWEPQVTMPLPDTTE 729
WGLDEPL HWEP++ P+ + TE
Sbjct: 189 WGLDEPLLKHWEPEIPTPMSELTE 212
>ref|NP_001229454.1| HLA class II histocompatibility antigen, DP alpha 1 chain precursor
[Homo sapiens].
Length = 260
Score = 254 bits (649), Expect = 1e-67
Identities = 117/204 (57%), Positives = 151/204 (74%)
Frame = +1
Query: 118 LMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPE 297
L LLS + AGAIKADH+ +Y AF Q++ +G+F ++FD +++F VDL K+E VW L E
Sbjct: 20 LAFLLSLRGAGAIKADHVSTYA-AFVQTHRPTGEFMFEFDEDEMFYVDLDKKETVWHLEE 78
Query: 298 FSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPKSPVALGQPNVLIC 477
F F+ Q GL IA++ +L+ L++RSNHT+ATN PP VTV PK PV LGQPN LIC
Sbjct: 79 FGQAFSFEAQGGLANIAILNNNLNTLIQRSNHTQATNDPPEVTVFPKEPVELGQPNTLIC 138
Query: 478 IVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEH 657
+D FPPV+N+TWL NG+ VTEGV ++ F + D+SF KFHYLTFVPSA DFYDC+VEH
Sbjct: 139 HIDKFFPPVLNVTWLCNGELVTEGVAESLFLPRTDYSFHKFHYLTFVPSAEDFYDCRVEH 198
Query: 658 WGLDEPLFTHWEPQVTMPLPDTTE 729
WGLD+PL HWE Q + +P+TTE
Sbjct: 199 WGLDQPLLKHWEAQEPIQMPETTE 222
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: 47,944,339
Number of extensions: 1442233
Number of successful extensions: 7540
Number of sequences better than 1.0e-05: 43
Number of HSP's gapped: 7458
Number of HSP's successfully gapped: 43
Length of query: 385
Length of database: 18,297,164
Length adjustment: 104
Effective length of query: 281
Effective length of database: 14,868,908
Effective search space: 4178163148
Effective search space used: 4178163148
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-014077
(1157 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_Chr07 553 e-155
>Sscrofa_Chr07
|| Length = 134764511
Score = 553 bits (279), Expect = e-155
Identities = 282/283 (99%)
Strand = Plus / Minus
Query: 409 gtgcctccaagggtgaccgtcctccccaagtcccctgtggcgctgggccagcccaacgtc 468
|||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||
Sbjct: 29547343 gtgcctccaagggtgaccatcctccccaagtcccctgtggcgctgggccagcccaacgtc 29547284
Query: 469 ctcatctgcatcgtggacaacatcttcccccctgtcatcaatatcacttggctgcacaac 528
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29547283 ctcatctgcatcgtggacaacatcttcccccctgtcatcaatatcacttggctgcacaac 29547224
Query: 529 ggccagacggtcaccgagggggtgacccagaccagcttctatgcccagcccgaccactcg 588
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29547223 ggccagacggtcaccgagggggtgacccagaccagcttctatgcccagcccgaccactcg 29547164
Query: 589 ttccggaagttccactacctgaccttcgtgccctcggcaggcgacttctatgactgcaaa 648
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29547163 ttccggaagttccactacctgaccttcgtgccctcggcaggcgacttctatgactgcaaa 29547104
Query: 649 gtggagcactggggcctggacgagccgctctttacgcactggg 691
|||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29547103 gtggagcactggggcctggacgagccgctctttacgcactggg 29547061
Score = 496 bits (250), Expect = e-137
Identities = 250/250 (100%)
Strand = Plus / Minus
Query: 160 gctgaccacatgggctcctatggaccagccttctaccagtcctatgacggctcgggtcag 219
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29548025 gctgaccacatgggctcctatggaccagccttctaccagtcctatgacggctcgggtcag 29547966
Query: 220 ttcacctacgatttcgatggggagcagctcttctccgtggacctgaagaagagggaggct 279
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29547965 ttcacctacgatttcgatggggagcagctcttctccgtggacctgaagaagagggaggct 29547906
Query: 280 gtgtggcgtctgcctgaattcagcaacttcgccgactttgacccgcagaatgggctgaga 339
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29547905 gtgtggcgtctgcctgaattcagcaacttcgccgactttgacccgcagaatgggctgaga 29547846
Query: 340 ggcattgcactgatcagagcccatctggatgtcttggtggagcgctccaaccataccaga 399
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29547845 ggcattgcactgatcagagcccatctggatgtcttggtggagcgctccaaccataccaga 29547786
Query: 400 gccaccaatg 409
||||||||||
Sbjct: 29547785 gccaccaatg 29547776
Score = 285 bits (144), Expect = 3e-74
Identities = 156/160 (97%)
Strand = Plus / Minus
Query: 826 aggtaatgatccttctgagaggctgggatgtgagagagaccctccgccccagcttcctcg 885
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29546623 aggtaatgatccttctgagaggctgggatgtgagagagaccctccgccccagcttcctcg 29546564
Query: 886 caagtttctgacagcccggaatacttggctccaccatccaccaagtgcatcccggcagag 945
|||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Sbjct: 29546563 caagtttctgacagcccggaatacttggctccaccatccaccaagtgcatcctggcagag 29546504
Query: 946 ctgcctttcagtggcatcaacctgtaacctaaacccctcc 985
|||||||||||||||||||||||||| |||| || |||||
Sbjct: 29546503 ctgcctttcagtggcatcaacctgtagcctagacgcctcc 29546464
Score = 276 bits (139), Expect = 3e-71
Identities = 139/139 (100%)
Strand = Plus / Minus
Query: 691 gagccccaggtgactatgccgctgccagacaccacagagaccctggtctgtgccctcggc 750
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29546985 gagccccaggtgactatgccgctgccagacaccacagagaccctggtctgtgccctcggc 29546926
Query: 751 ctggcgcttggcctggtgggcttcctcgtgggcgtcacccttatcatcacaggcagacgc 810
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29546925 ctggcgcttggcctggtgggcttcctcgtgggcgtcacccttatcatcacaggcagacgc 29546866
Query: 811 cggtccagctcccccaggt 829
|||||||||||||||||||
Sbjct: 29546865 cggtccagctcccccaggt 29546847
Score = 276 bits (139), Expect = 3e-71
Identities = 153/160 (95%)
Strand = Plus / Minus
Query: 1 ctttgctttcttcctttacccgnnnnnnngcaacgcacacaccaaccaagacttatttgg 60
|||||||||||||||||||||| |||||||||||||||||||||||||||||||
Sbjct: 29549315 ctttgctttcttcctttacccgcccccccgcaacgcacacaccaaccaagacttatttgg 29549256
Query: 61 ttaaaacaccagagggccatggtcctccatggggggctggtcctgggactccacatcttg 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29549255 ttaaaacaccagagggccatggtcctccatggggggctggtcctgggactccacatcttg 29549196
Query: 121 atgaccctcctgagtccccagaaagctggggccatcaagg 160
||||||||||||||||||||||||||||||||||||||||
Sbjct: 29549195 atgaccctcctgagtccccagaaagctggggccatcaagg 29549156
Score = 63.9 bits (32), Expect = 2e-07
Identities = 32/32 (100%)
Strand = Plus / Plus
Query: 637 tatgactgcaaagtggagcactggggcctgga 668
||||||||||||||||||||||||||||||||
Sbjct: 29169707 tatgactgcaaagtggagcactggggcctgga 29169738
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: 26,017,873
Number of extensions: 117
Number of successful extensions: 117
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 116
Number of HSP's successfully gapped: 6
Length of query: 1157
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 1136
Effective length of database: 2,808,413,156
Effective search space: 3190357345216
Effective search space used: 3190357345216
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)