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-013585
(1422 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_853445.1| PREDICTED: similar to olfactory receptor 1184 [... 63 6e-10
>ref|XP_853445.1| PREDICTED: similar to olfactory receptor 1184 [Canis familiaris].
Length = 463
Score = 63.2 bits (152), Expect = 6e-10
Identities = 31/84 (36%), Positives = 50/84 (59%)
Frame = +1
Query: 412 DMIRNLSATIEQIAEDTAESIAAQHTSLNSMARVVLDNRMALDFLRAKEGGVCAVAHDTC 591
D ++LS ++ E AES A+ + S+A+V L NR ALD L A++GG C ++ C
Sbjct: 59 DSSKDLSERLQMAIEALAESFASLQCQITSVAQVALQNRSALDLLTAEKGGTCMSFNEDC 118
Query: 592 CTYINSNGEVETQVNKVSQQATWL 663
C +IN G VET ++ +++ +L
Sbjct: 119 CYHINETGVVETNLHILAKVRLYL 142
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: 55,305,126
Number of extensions: 1433392
Number of successful extensions: 3457
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 3457
Number of HSP's successfully gapped: 1
Length of query: 474
Length of database: 18,874,504
Length adjustment: 107
Effective length of query: 367
Effective length of database: 15,307,552
Effective search space: 5617871584
Effective search space used: 5617871584
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: 36 (18.5 bits)
Animal-Genome cDNA 20110601C-013585
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-013585
(1422 letters)
Database: RefSeq49_BP.fasta
33,088 sequences; 17,681,374 total letters
Searching..................................................done
***** No hits found ******
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: 53,041,447
Number of extensions: 1391820
Number of successful extensions: 3443
Number of sequences better than 1.0e-05: 0
Number of HSP's gapped: 3443
Number of HSP's successfully gapped: 0
Length of query: 474
Length of database: 17,681,374
Length adjustment: 106
Effective length of query: 368
Effective length of database: 14,174,046
Effective search space: 5216048928
Effective search space used: 5216048928
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: 36 (18.5 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-013585
(1422 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|XP_003355074.1| PREDICTED: LOW QUALITY PROTEIN: envelope gly... 55 7e-08
Alignment gi|XP_003355073.1| PREDICTED: envelope glycoprotein-like, parti... 55 7e-08
Alignment gi|XP_003353273.1| PREDICTED: envelope glycoprotein-like [Sus s... 55 7e-08
Alignment gi|XP_001927829.1| PREDICTED: envelope glycoprotein-like [Sus s... 54 2e-07
Alignment gi|XP_003358861.1| PREDICTED: envelope glycoprotein-like [Sus s... 54 3e-07
>ref|XP_003355074.1| PREDICTED: LOW QUALITY PROTEIN: envelope glycoprotein [Sus scrofa].
Length = 657
Score = 55.5 bits (132), Expect = 7e-08
Identities = 25/75 (33%), Positives = 43/75 (57%)
Frame = +1
Query: 427 LSATIEQIAEDTAESIAAQHTSLNSMARVVLDNRMALDFLRAKEGGVCAVAHDTCCTYIN 606
L A + + ES++ SL S++ VVL NR LD L +EGG+CA + CC Y++
Sbjct: 499 LHAAMTEDLRALEESVSNLEESLTSLSEVVLQNRRGLDLLFLREGGLCAALKEECCFYVD 558
Query: 607 SNGEVETQVNKVSQQ 651
+G + ++K+ ++
Sbjct: 559 HSGAIRDSMSKLRER 573
>ref|XP_003355073.1| PREDICTED: envelope glycoprotein-like, partial [Sus scrofa].
Length = 773
Score = 55.5 bits (132), Expect = 7e-08
Identities = 25/75 (33%), Positives = 43/75 (57%)
Frame = +1
Query: 427 LSATIEQIAEDTAESIAAQHTSLNSMARVVLDNRMALDFLRAKEGGVCAVAHDTCCTYIN 606
L A + + ES++ SL S++ VVL NR LD L +EGG+CA + CC Y++
Sbjct: 301 LHAAMTEDLRALEESVSNLEESLTSLSEVVLQNRRGLDLLFLREGGLCAALKEECCFYVD 360
Query: 607 SNGEVETQVNKVSQQ 651
+G + ++K+ ++
Sbjct: 361 HSGAIRDSMSKLRER 375
>ref|XP_003353273.1| PREDICTED: envelope glycoprotein-like [Sus scrofa].
Length = 657
Score = 55.5 bits (132), Expect = 7e-08
Identities = 25/75 (33%), Positives = 43/75 (57%)
Frame = +1
Query: 427 LSATIEQIAEDTAESIAAQHTSLNSMARVVLDNRMALDFLRAKEGGVCAVAHDTCCTYIN 606
L A + + ES++ SL S++ VVL NR LD L +EGG+CA + CC Y++
Sbjct: 499 LHAAMTEDLRALEESVSNLEESLTSLSEVVLQNRRGLDLLFLREGGLCAALKEECCFYVD 558
Query: 607 SNGEVETQVNKVSQQ 651
+G + ++K+ ++
Sbjct: 559 HSGAIRDSMSKLRER 573
>ref|XP_001927829.1| PREDICTED: envelope glycoprotein-like [Sus scrofa].
Length = 657
Score = 54.3 bits (129), Expect = 2e-07
Identities = 24/75 (32%), Positives = 43/75 (57%)
Frame = +1
Query: 427 LSATIEQIAEDTAESIAAQHTSLNSMARVVLDNRMALDFLRAKEGGVCAVAHDTCCTYIN 606
L A + + E+++ SL S++ VVL NR LD L +EGG+CA + CC Y++
Sbjct: 499 LHAAMTEDLRALEEAVSNLEESLTSLSEVVLQNRRGLDLLFLREGGLCAALKEECCFYVD 558
Query: 607 SNGEVETQVNKVSQQ 651
+G + ++K+ ++
Sbjct: 559 HSGAIRDSMSKLRER 573
>ref|XP_003358861.1| PREDICTED: envelope glycoprotein-like [Sus scrofa].
Length = 437
Score = 53.5 bits (127), Expect = 3e-07
Identities = 23/78 (29%), Positives = 44/78 (56%)
Frame = +1
Query: 418 IRNLSATIEQIAEDTAESIAAQHTSLNSMARVVLDNRMALDFLRAKEGGVCAVAHDTCCT 597
+ +L + + + +S++ SL S++ VVL NR LD L KEGG+C + CC
Sbjct: 276 LSDLHRIVTEDLQALEKSVSNLEESLTSLSEVVLQNRRGLDLLFLKEGGLCVALKEECCF 335
Query: 598 YINSNGEVETQVNKVSQQ 651
Y++ +G + ++K+ ++
Sbjct: 336 YVDHSGAIRDSMSKLRER 353
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: 34,085,766
Number of extensions: 890451
Number of successful extensions: 2238
Number of sequences better than 1.0e-05: 5
Number of HSP's gapped: 2238
Number of HSP's successfully gapped: 5
Length of query: 474
Length of database: 11,343,932
Length adjustment: 103
Effective length of query: 371
Effective length of database: 8,779,541
Effective search space: 3257209711
Effective search space used: 3257209711
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 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-013585
(1422 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_775596.1| envelope glycoprotein syncytin-B [Mus musculus]. 64 2e-10
Alignment gi|NP_001013773.1| envelope glycoprotein syncytin-A [Mus muscul... 62 1e-09
Alignment gi|XP_001480260.1| PREDICTED: envelope glycoprotein [Mus muscul... 56 8e-08
Alignment gi|XP_001479230.1| PREDICTED: envelope glycoprotein [Mus muscul... 56 8e-08
Alignment gi|XP_003085406.1| PREDICTED: envelope glycoprotein [Mus muscul... 55 1e-07
Alignment gi|XP_003086761.1| PREDICTED: envelope glycoprotein [Mus muscul... 55 1e-07
Alignment gi|XP_003085378.1| PREDICTED: envelope glycoprotein-like [Mus m... 55 2e-07
Alignment gi|XP_003086946.1| PREDICTED: envelope glycoprotein-like [Mus m... 54 2e-07
>ref|NP_775596.1| envelope glycoprotein syncytin-B [Mus musculus].
Length = 618
Score = 64.3 bits (155), Expect = 2e-10
Identities = 31/91 (34%), Positives = 50/91 (54%)
Frame = +1
Query: 391 AGIYINRDMIRNLSATIEQIAEDTAESIAAQHTSLNSMARVVLDNRMALDFLRAKEGGVC 570
AG+ + + LS + + E+ A SI ++S+A VVL NR ALD + A++GG C
Sbjct: 440 AGLATSTLYFQQLSKVLSETLEEIAASITTLQNQIDSLAGVVLQNRRALDLITAEKGGTC 499
Query: 571 AVAHDTCCTYINSNGEVETQVNKVSQQATWL 663
+ CC Y+N +G V K+ ++A+ L
Sbjct: 500 LFLQEECCFYVNQSGIVRDAARKLQERASEL 530
>ref|NP_001013773.1| envelope glycoprotein syncytin-A [Mus musculus].
Length = 617
Score = 61.6 bits (148), Expect = 1e-09
Identities = 32/91 (35%), Positives = 49/91 (53%)
Frame = +1
Query: 391 AGIYINRDMIRNLSATIEQIAEDTAESIAAQHTSLNSMARVVLDNRMALDFLRAKEGGVC 570
AGI + + LS + ++ A SI + ++S+A VVL NR ALD + A+ GG C
Sbjct: 438 AGITTSTVYFQQLSKALSDSLDEIATSIISLQDQIDSLAGVVLQNRRALDLIVAERGGTC 497
Query: 571 AVAHDTCCTYINSNGEVETQVNKVSQQATWL 663
+ CC YIN +G V K+ ++A+ L
Sbjct: 498 LFLQEECCFYINQSGVVRHAARKLRERASEL 528
>ref|XP_001480260.1| PREDICTED: envelope glycoprotein [Mus musculus].
Length = 298
Score = 55.8 bits (133), Expect = 8e-08
Identities = 33/86 (38%), Positives = 44/86 (51%)
Frame = +1
Query: 394 GIYINRDMIRNLSATIEQIAEDTAESIAAQHTSLNSMARVVLDNRMALDFLRAKEGGVCA 573
GI RD + A IE+ SI A SL S++ VVL NR LD L KEGG+CA
Sbjct: 215 GIQSLRDAVNEDLAAIEK-------SIDALEKSLTSLSEVVLQNRRGLDLLFLKEGGLCA 267
Query: 574 VAHDTCCTYINSNGEVETQVNKVSQQ 651
+ CC Y + G V + K+ ++
Sbjct: 268 ALKEECCFYADHTGIVRDSMQKLRER 293
>ref|XP_001479230.1| PREDICTED: envelope glycoprotein [Mus musculus].
Length = 298
Score = 55.8 bits (133), Expect = 8e-08
Identities = 33/86 (38%), Positives = 44/86 (51%)
Frame = +1
Query: 394 GIYINRDMIRNLSATIEQIAEDTAESIAAQHTSLNSMARVVLDNRMALDFLRAKEGGVCA 573
GI RD + A IE+ SI A SL S++ VVL NR LD L KEGG+CA
Sbjct: 215 GIQSLRDAVNEDLAAIEK-------SIDALEKSLTSLSEVVLQNRRGLDLLFLKEGGLCA 267
Query: 574 VAHDTCCTYINSNGEVETQVNKVSQQ 651
+ CC Y + G V + K+ ++
Sbjct: 268 ALKEECCFYADHTGIVRDSMQKLRER 293
>ref|XP_003085406.1| PREDICTED: envelope glycoprotein [Mus musculus].
Length = 247
Score = 55.5 bits (132), Expect = 1e-07
Identities = 24/64 (37%), Positives = 37/64 (57%)
Frame = +1
Query: 430 SATIEQIAEDTAESIAAQHTSLNSMARVVLDNRMALDFLRAKEGGVCAVAHDTCCTYINS 609
S+ + ++ E++ ++S+A VVL NR LD L AKEGG+C + CC YIN
Sbjct: 176 SSQFKSNLQEMTETVLTIQKQIDSLAAVVLQNRQGLDVLSAKEGGLCLFLQEECCFYINQ 235
Query: 610 NGEV 621
+G +
Sbjct: 236 SGRI 239
>ref|XP_003086761.1| PREDICTED: envelope glycoprotein [Mus musculus].
Length = 247
Score = 55.5 bits (132), Expect = 1e-07
Identities = 24/64 (37%), Positives = 37/64 (57%)
Frame = +1
Query: 430 SATIEQIAEDTAESIAAQHTSLNSMARVVLDNRMALDFLRAKEGGVCAVAHDTCCTYINS 609
S+ + ++ E++ ++S+A VVL NR LD L AKEGG+C + CC YIN
Sbjct: 176 SSQFKSNLQEMTETVLTIQKQIDSLAAVVLQNRQGLDVLSAKEGGLCLFLQEECCFYINQ 235
Query: 610 NGEV 621
+G +
Sbjct: 236 SGRI 239
>ref|XP_003085378.1| PREDICTED: envelope glycoprotein-like [Mus musculus].
Length = 675
Score = 54.7 bits (130), Expect = 2e-07
Identities = 26/75 (34%), Positives = 42/75 (56%)
Frame = +1
Query: 427 LSATIEQIAEDTAESIAAQHTSLNSMARVVLDNRMALDFLRAKEGGVCAVAHDTCCTYIN 606
L A ++ +SI SL S++ VVL NR LD L KEGG+CA + CC Y++
Sbjct: 518 LRAAMDVDLRTIEQSITKLEESLTSLSEVVLQNRRGLDLLFLKEGGLCAALKEECCFYVD 577
Query: 607 SNGEVETQVNKVSQQ 651
+G ++ + K+ ++
Sbjct: 578 HSGVIKDSMAKLRER 592
>ref|XP_003086946.1| PREDICTED: envelope glycoprotein-like [Mus musculus].
Length = 687
Score = 54.3 bits (129), Expect = 2e-07
Identities = 27/77 (35%), Positives = 41/77 (53%)
Frame = +1
Query: 421 RNLSATIEQIAEDTAESIAAQHTSLNSMARVVLDNRMALDFLRAKEGGVCAVAHDTCCTY 600
+ L A + ++ +SI SL S++ VVL NR LD L KEGG+CA + CC Y
Sbjct: 525 QQLQAAMHDDLKEVEKSITNLEKSLTSLSEVVLQNRRGLDLLFLKEGGLCAALKEECCFY 584
Query: 601 INSNGEVETQVNKVSQQ 651
+ G V + K+ ++
Sbjct: 585 ADHTGLVRDSMAKLRER 601
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: 46,396,349
Number of extensions: 1205982
Number of successful extensions: 2963
Number of sequences better than 1.0e-05: 8
Number of HSP's gapped: 2961
Number of HSP's successfully gapped: 8
Length of query: 474
Length of database: 15,617,559
Length adjustment: 105
Effective length of query: 369
Effective length of database: 12,463,779
Effective search space: 4599134451
Effective search space used: 4599134451
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-013585
(1422 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_001177984.1| envelope glycoprotein ENVV2 [Homo sapiens]. 115 8e-26
Alignment gi|NP_689686.2| envelope glycoprotein ENVV1 [Homo sapiens]. 110 2e-24
Alignment gi|NP_001124397.1| HERV-W_7q21.2 provirus ancestral Env polypro... 85 2e-16
Alignment gi|NP_055405.3| HERV-W_7q21.2 provirus ancestral Env polyprotei... 85 2e-16
Alignment gi|NP_997465.1| HERV-FRD_6p24.1 provirus ancestral Env polyprot... 60 4e-09
Alignment gi|NP_001007254.2| HERV-R_7q21.2 provirus ancestral Env polypro... 50 4e-06
>ref|NP_001177984.1| envelope glycoprotein ENVV2 [Homo sapiens].
Length = 535
Score = 115 bits (289), Expect = 8e-26
Identities = 71/222 (31%), Positives = 112/222 (50%), Gaps = 14/222 (6%)
Frame = +1
Query: 46 WKACSSSHSWLDNIISKLPQNEQINDTTLGGVTCAPPGFVFVCG-------------IGS 186
WK S H W D+ I + C PPG+VF+CG I
Sbjct: 232 WK--SQLHKWFDSHIPRW--------------ACTPPGYVFLCGPQKNKLPFDGSPKITY 275
Query: 187 DSPTQGWAHRCLDSWQMQGSCLLGYFRTPFSVHSLQSITSHSKSNSRLKREIMARYEDNK 366
+P + C+++ Q G C +G P + +T ++ + R KR +
Sbjct: 276 STPPVANLYTCINNIQHTGECAVGLLG-PRGI----GVTIYNTTQPRQKRALGLILAGMG 330
Query: 367 GQSNLIPSAGIYINRDM-IRNLSATIEQIAEDTAESIAAQHTSLNSMARVVLDNRMALDF 543
+I G + D+ +RNLS I+ IA+ T +SI+ S++S+A VV+DNR+ALD+
Sbjct: 331 AAIGMIAPWGGFTYHDVTLRNLSRQIDNIAKSTRDSISKLKASIDSLANVVMDNRLALDY 390
Query: 544 LRAKEGGVCAVAHDTCCTYINSNGEVETQVNKVSQQATWL*D 669
L A++GGVCAV + +CC Y+N++G +E + K+ +ATWL D
Sbjct: 391 LLAEQGGVCAVINKSCCVYVNNSGAIEEDIKKIYDEATWLHD 432
>ref|NP_689686.2| envelope glycoprotein ENVV1 [Homo sapiens].
Length = 477
Score = 110 bits (276), Expect = 2e-24
Identities = 70/227 (30%), Positives = 112/227 (49%), Gaps = 14/227 (6%)
Frame = +1
Query: 46 WKACSSSHSWLDNIISKLPQNEQINDTTLGGVTCAPPGFVFVCG-------------IGS 186
WK S H W D+ I + C PPG+VF+CG I
Sbjct: 232 WK--SQLHKWFDSHIPRW--------------ACTPPGYVFLCGPQKNKLPFDGSPKITY 275
Query: 187 DSPTQGWAHRCLDSWQMQGSCLLGYFRTPFSVHSLQSITSHSKSNSRLKREIMARYEDNK 366
+P + C+++ Q G C +G P + +T ++ + R KR +
Sbjct: 276 STPPVANLYTCINNIQHTGECAVGLLG-PRGI----GVTIYNTTQPRQKRALGLILAGMG 330
Query: 367 GQSNLIPSAGIYINRDM-IRNLSATIEQIAEDTAESIAAQHTSLNSMARVVLDNRMALDF 543
+I G + D+ +RNLS I+ IA+ T +SI+ S++S+A VV++NR+ALD+
Sbjct: 331 AAIGMIAPWGGFTYHDVTLRNLSRQIDNIAKSTRDSISKLKASIDSLANVVMNNRLALDY 390
Query: 544 LRAKEGGVCAVAHDTCCTYINSNGEVETQVNKVSQQATWL*DGPKED 684
L A++GGVCAV +CC Y+N++G +E + K+ + TWL + K D
Sbjct: 391 LLAEQGGVCAVISKSCCIYVNNSGAIEEDIKKIYDEVTWLHNFGKGD 437
>ref|NP_001124397.1| HERV-W_7q21.2 provirus ancestral Env polyprotein precursor [Homo
sapiens].
Length = 538
Score = 84.7 bits (208), Expect = 2e-16
Identities = 52/170 (30%), Positives = 79/170 (46%), Gaps = 2/170 (1%)
Frame = +1
Query: 139 VTCAPPGFVFVCGIGSDSPTQGWAHRCLDSWQMQGSCLLGYFRTPFSVHSLQSITSHSKS 318
+ C P G FVCG A+RCL+ + C L + P ++++ Q + S+ S
Sbjct: 261 IVCLPSGIFFVCGTS--------AYRCLNG-SSESMCFLSFLVPPMTIYTEQDLYSYVIS 311
Query: 319 NSRLKREIMARYEDNKGQSNLIPSA--GIYINRDMIRNLSATIEQIAEDTAESIAAQHTS 492
R KR + + G + + GI + LS + E A+S+
Sbjct: 312 KPRNKRVPILPFVIGAGVLGALGTGIGGITTSTQFYYKLSQELNGDMERVADSLVTLQDQ 371
Query: 493 LNSMARVVLDNRMALDFLRAKEGGVCAVAHDTCCTYINSNGEVETQVNKV 642
LNS+A VVL NR ALD L A+ GG C + CC Y+N +G V +V ++
Sbjct: 372 LNSLAAVVLQNRRALDLLTAERGGTCLFLGEECCYYVNQSGIVTEKVKEI 421
>ref|NP_055405.3| HERV-W_7q21.2 provirus ancestral Env polyprotein precursor [Homo
sapiens].
Length = 538
Score = 84.7 bits (208), Expect = 2e-16
Identities = 52/170 (30%), Positives = 79/170 (46%), Gaps = 2/170 (1%)
Frame = +1
Query: 139 VTCAPPGFVFVCGIGSDSPTQGWAHRCLDSWQMQGSCLLGYFRTPFSVHSLQSITSHSKS 318
+ C P G FVCG A+RCL+ + C L + P ++++ Q + S+ S
Sbjct: 261 IVCLPSGIFFVCGTS--------AYRCLNG-SSESMCFLSFLVPPMTIYTEQDLYSYVIS 311
Query: 319 NSRLKREIMARYEDNKGQSNLIPSA--GIYINRDMIRNLSATIEQIAEDTAESIAAQHTS 492
R KR + + G + + GI + LS + E A+S+
Sbjct: 312 KPRNKRVPILPFVIGAGVLGALGTGIGGITTSTQFYYKLSQELNGDMERVADSLVTLQDQ 371
Query: 493 LNSMARVVLDNRMALDFLRAKEGGVCAVAHDTCCTYINSNGEVETQVNKV 642
LNS+A VVL NR ALD L A+ GG C + CC Y+N +G V +V ++
Sbjct: 372 LNSLAAVVLQNRRALDLLTAERGGTCLFLGEECCYYVNQSGIVTEKVKEI 421
>ref|NP_997465.1| HERV-FRD_6p24.1 provirus ancestral Env polyprotein [Homo sapiens].
Length = 538
Score = 60.5 bits (145), Expect = 4e-09
Identities = 51/179 (28%), Positives = 78/179 (43%), Gaps = 10/179 (5%)
Frame = +1
Query: 157 GFVFVCGIGSDSPTQGWAHRCLDSWQMQGSCLLGYFRTP--FSVHSLQSITSHSKSNSRL 330
G ++CG H+CL S G+C +GY TP F S+ NS L
Sbjct: 296 GAFYICGQS--------IHQCLPS-NWTGTCTIGYV-TPDIFIAPGNLSLPIPIYGNSPL 345
Query: 331 KR--------EIMARYEDNKGQSNLIPSAGIYINRDMIRNLSATIEQIAEDTAESIAAQH 486
R ++A G I AGI LS I + A+++
Sbjct: 346 PRVRRAIHFIPLLAGLGILAGTGTGI--AGITKASLTYSQLSKEIANNIDTMAKALTTMQ 403
Query: 487 TSLNSMARVVLDNRMALDFLRAKEGGVCAVAHDTCCTYINSNGEVETQVNKVSQQATWL 663
++S+A VVL NR LD L A +GG+C + CC ++N +G+V+ + ++ QA+ L
Sbjct: 404 EQIDSLAAVVLQNRRGLDMLTAAQGGICLALDEKCCFWVNQSGKVQDNIRQLLNQASSL 462
>ref|NP_001007254.2| HERV-R_7q21.2 provirus ancestral Env polyprotein precursor [Homo
sapiens].
Length = 604
Score = 50.4 bits (119), Expect = 4e-06
Identities = 49/191 (25%), Positives = 85/191 (44%), Gaps = 23/191 (12%)
Frame = +1
Query: 148 APPGFVFVCGIGSDSPTQGWAHRCLDSWQMQGSCLLGYFRTPFSVHSLQSITS-----HS 312
AP G ++CG A+R L + + G+C+LG R F + L+ + +
Sbjct: 413 APSGLYWICG--------PQAYRQLPA-KWSGACVLGTIRPSFFLMPLKQGEALGYPIYD 463
Query: 313 KSNSRLKREI-MARYEDNKGQSNLIPS----------------AGIYINRDMIRNLSATI 441
++ + KR I + ++DN+ I +Y+ +IR L A +
Sbjct: 464 ETKRKSKRGITIGDWKDNEWPPERIIQYYGPATWAEDGMWGYRTPVYMLNRIIR-LQAVL 522
Query: 442 EQIAEDTAESIAAQHTSLNSMARVVLDNRMALDFLRAKEGGVCAVAHDT-CCTYINSNGE 618
E I +TA ++ M V+ NR+ALD+L A+E GVC + T CC ++ G+
Sbjct: 523 EIITNETAGALNLLAQQATKMRNVIYQNRLALDYLLAQEEGVCGKFNLTNCCLELDDEGK 582
Query: 619 VETQVNKVSQQ 651
V ++ Q+
Sbjct: 583 VIKEITAKIQK 593
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: 54,398,057
Number of extensions: 1417759
Number of successful extensions: 3472
Number of sequences better than 1.0e-05: 6
Number of HSP's gapped: 3466
Number of HSP's successfully gapped: 6
Length of query: 474
Length of database: 18,297,164
Length adjustment: 106
Effective length of query: 368
Effective length of database: 14,802,980
Effective search space: 5447496640
Effective search space used: 5447496640
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: 36 (18.5 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-013585
(1422 letters)
Database: Sscrofa_10.2.fasta
4582 sequences; 2,808,509,378 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
gb|GL893011.1| Sus scrofa unplaced genomic scaffold chrU_scaffol... 2411 0.0
Sscrofa_Chr18 74 2e-10
Sscrofa_Chr08 66 6e-08
Sscrofa_Chr13 64 2e-07
Sscrofa_Chr06 64 2e-07
gb|JH118602.1| Sus scrofa unplaced genomic scaffold ChrUScaf1230 62 9e-07
Sscrofa_Chr16 62 9e-07
Sscrofa_Chr10 62 9e-07
Sscrofa_Chr09 62 9e-07
gb|GL892848.2| Sus scrofa unplaced genomic scaffold ChrUScaf733 60 4e-06
>gb|GL893011.1| Sus scrofa unplaced genomic scaffold chrU_scaffold1819
Length = 98757
Score = 2411 bits (1216), Expect = 0.0
Identities = 1379/1426 (96%), Gaps = 8/1426 (0%)
Strand = Plus / Plus
Query: 1 ttatgccagaaagtcaaacaagttggatatcatgtaaacggactgtggaaggcttgtagt 60
|||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||
Sbjct: 85996 ttatgccagaaagtcaaacaagttggatatcatgtaaatggactgtggaaggcttgtagt 86055
Query: 61 agttctcactcctggcttgacaacataatctctaaactcccccaaaatgaacaaattaat 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 86056 agttctcactcctggcttgacaacataatctctaaactcccccaaaatgaacaaattaat 86115
Query: 121 gacactaccctgggaggtgtaacttgtgctcctccgggatttgtctttgtctgtggcata 180
||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||
Sbjct: 86116 gacactaccctgggaggtgtaacttgtgctcctccaggatttgtctttgtctgtggcata 86175
Query: 181 gggagtgactcgccaacgcaaggatgggcacatcgctgcttagacagctggcaaatgcaa 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 86176 gggagtgactcgccaacgcaaggatgggcacatcgctgcttagacagctggcaaatgcaa 86235
Query: 241 gggtcatgtctactgggatattttaggacccccttctccgtgcacagcctgcagagcatc 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 86236 gggtcatgtctactgggatattttaggacccccttctccgtgcacagcctgcagagcatc 86295
Query: 301 acttcccactctaaatcaaactcccgccttaaaagagagataatggctaggtatgaggac 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 86296 acttcccactctaaatcaaactcccgccttaaaagagagataatggctaggtatgaggac 86355
Query: 361 aataaaggacaaagcaacctcataccaagtgccggaatttatatcaatagagatatgatc 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 86356 aataaaggacaaagcaacctcataccaagtgccggaatttatatcaatagagatatgatc 86415
Query: 421 cgtaacctatctgccacaattgaacaaattgctgaggacacagctgaaagtattgcagcc 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 86416 cgtaacctatctgccacaattgaacaaattgctgaggacacagctgaaagtattgcagcc 86475
Query: 481 caacacacatctttgaactccatggctcgagtggtcctggataatagaatggctcttgat 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 86476 caacacacatctttgaactccatggctcgagtggtcctggataatagaatggctcttgat 86535
Query: 541 ttcttacgggcaaaagaaggaggagtatgtgcagtggctcatgacacatgctgcacatac 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 86536 ttcttacgggcaaaagaaggaggagtatgtgcagtggctcatgacacatgctgcacatac 86595
Query: 601 atcaattccaatggagaagttgaaacccaagtaaataaagtaagtcaacaggctacctgg 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 86596 atcaattccaatggagaagttgaaacccaagtaaataaagtaagtcaacaggctacctgg 86655
Query: 661 ttataggatggacctaaagaggatatgcaccaggacttttattttcctggttgccatctg 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 86656 ttataggatggacctaaagaggatatgcaccaggacttttattttcctggttgccatctg 86715
Query: 721 gaataggggagactctttggggggtactgattcaagggtccactttgatgatcaacctct 780
||||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||
Sbjct: 86716 gaataggggggactctttggggggtactgattcaagggtccactttgatgatcatcctct 86775
Query: 781 ttgtaatgtgcttattaattttcaaatatctgtccaggtgctgtgacaaagtggtcaaaa 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 86776 ttgtaatgtgcttattaattttcaaatatctgtccaggtgctgtgacaaagtggtcaaaa 86835
Query: 841 gagagacaaatgttttcataatccaaaatactgatgttaagcctgggacttgagaattct 900
|||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Sbjct: 86836 gagagacaaatgttttcataatccaaaatactgatgttaagcctgggacttgggaattct 86895
Query: 901 ttgaaaagaagtttcaaaactttctctcctctaatcctaaagaattaacatcgcccctgt 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 86896 ttgaaaagaagtttcaaaactttctctcctctaatcctaaagaattaacatcgcccctgt 86955
Query: 961 tcagcaggaagtagccagagcggtcgtcgcccctgttccccttaggattgaggagtatgg 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 86956 tcagcaggaagtagccagagcggtcgtcgcccctgttccccttaggattgaggagtatgg 87015
Query: 1021 aagaaagggggaactgaaactgagcaggatcctgcagggccttcctggatacagtgccct 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 87016 aagaaagggggaactgaaactgagcaggatcctgcagggccttcctggatacagtgccct 87075
Query: 1081 ctgtgt-ccccacttcctgtttgta-aaaaatctttagtcccctaggcctttgcaggttc 1138
|||||| |||||||||||||||||| ||||||||||||||||||||||||||||||||||
Sbjct: 87076 ctgtgtcccccacttcctgtttgtagaaaaatctttagtcccctaggcctttgcaggttc 87135
Query: 1139 caaagagcagactcaagcagttaataattatagaagtgnnnnnnnnnntgcagaaacaaa 1198
|||||||||||||||||||||||||||||||||||||| ||||||||||||
Sbjct: 87136 caaagagcagactcaagcagttaataattatagaagtg-aaaaaaaaatgcagaaacaaa 87194
Query: 1199 gaataagcatccaggcagaaaaagtcagccataaagcagagtcacaggactcctagttcc 1258
||||| ||| || |||||| ||||||||||||||||||||||||||||||||||||
Sbjct: 87195 gaatagcaatcaagcaagaaaagttcagccataaagcagagtcacaggactcctagttcc 87254
Query: 1259 tccntcagggnatatagataacaatccgatgcattttcctggagtgtttttacggaaccc 1318
||| ||| || |||||||||||||||| ||||||||| || |||| |||||| ||| ||
Sbjct: 87255 tcc-tcaagggatatagataacaatccaatgcatttt-cttgagttgttttacagaaacc 87312
Query: 1319 aaaaccccgtgatgaaacctgcctgacaac-gccatggagaaccaaaaaagttggaacc- 1376
|| |||||||||||||||||| ||||| || |||||||||| ||| |||||||||||||
Sbjct: 87313 aagaccccgtgatgaaacctg-ctgaccacagccatggagacccagaaaagttggaacca 87371
Query: 1377 gaagagtgatgaacaaaatggccaaaatttaactttgttgcttaac 1422
|||||||||||| ||| ||||| |||| |||||||||||||||||
Sbjct: 87372 gaagagtgatgaccaagatggcagaaatataactttgttgcttaac 87417
>Sscrofa_Chr18
|| Length = 61220071
Score = 73.8 bits (37), Expect = 2e-10
Identities = 62/69 (89%), Gaps = 1/69 (1%)
Strand = Plus / Plus
Query: 987 tcgcccctgttccccttaggattgaggagtatggaag-aaagggggaactgaaactgagc 1045
||||||||||||||||||||| |||||||||| ||| |||||||| |||||||| |||
Sbjct: 28416365 tcgcccctgttccccttaggactgaggagtatcaaagaaaaggggggactgaaaccaagc 28416424
Query: 1046 aggatcctg 1054
|||||||||
Sbjct: 28416425 aggatcctg 28416433
>Sscrofa_Chr08
|| Length = 148491826
Score = 65.9 bits (33), Expect = 6e-08
Identities = 76/89 (85%), Gaps = 1/89 (1%)
Strand = Plus / Plus
Query: 1087 ccccacttcctgtttgtaaaaaatctttagtcccctaggcctttgc-aggttccaaagag 1145
||||||||| ||||| || |||| ||||| | |||||||||| | | |||||||||||
Sbjct: 144289816 ccccacttcttgtttatagaaaacatttagcctcctaggccttccctaagttccaaagag 144289875
Query: 1146 cagactcaagcagttaataattatagaag 1174
| ||||||||||||||||||||| |||||
Sbjct: 144289876 ctgactcaagcagttaataattagagaag 144289904
Score = 60.0 bits (30), Expect = 4e-06
Identities = 49/54 (90%), Gaps = 1/54 (1%)
Strand = Plus / Plus
Query: 1111 ctttagtcccctaggcctttgcag-gttccaaagagcagactcaagcagttaat 1163
||||||||||||||||||| | | |||||||||||||| ||||||||||||||
Sbjct: 117956853 ctttagtcccctaggccttcccggagttccaaagagcaggctcaagcagttaat 117956906
>Sscrofa_Chr13
|| Length = 218635234
Score = 63.9 bits (32), Expect = 2e-07
Identities = 44/47 (93%), Gaps = 1/47 (2%)
Strand = Plus / Minus
Query: 1238 agtcacaggactcctagttcctccntcagggnatatagataacaatc 1284
|||||||||||||||||||||||| | |||| |||||||||||||||
Sbjct: 14310875 agtcacaggactcctagttcctcc-tgaggggatatagataacaatc 14310830
Score = 61.9 bits (31), Expect = 9e-07
Identities = 37/39 (94%)
Strand = Plus / Plus
Query: 1138 ccaaagagcagactcaagcagttaataattatagaagtg 1176
|||||||||||||||||||||||| |||||| |||||||
Sbjct: 81141133 ccaaagagcagactcaagcagttactaattacagaagtg 81141171
>Sscrofa_Chr06
|| Length = 157765593
Score = 63.9 bits (32), Expect = 2e-07
Identities = 69/80 (86%), Gaps = 1/80 (1%)
Strand = Plus / Minus
Query: 990 cccctgttccccttaggattgaggagtatggaag-aaagggggaactgaaactgagcagg 1048
||||||||||||| ||||||||||||||| ||| |||||||| | |||| | ||||||
Sbjct: 52319371 cccctgttcccctcaggattgaggagtatcaaagaaaaggggggattgaaccccagcagg 52319312
Query: 1049 atcctgcagggccttcctgg 1068
| ||||||||||| ||||||
Sbjct: 52319311 accctgcagggccctcctgg 52319292
Score = 60.0 bits (30), Expect = 4e-06
Identities = 30/30 (100%)
Strand = Plus / Minus
Query: 1036 gaaactgagcaggatcctgcagggccttcc 1065
||||||||||||||||||||||||||||||
Sbjct: 44021033 gaaactgagcaggatcctgcagggccttcc 44021004
Score = 60.0 bits (30), Expect = 4e-06
Identities = 71/82 (86%), Gaps = 2/82 (2%)
Strand = Plus / Minus
Query: 989 gcccctgttccccttaggattgaggagtatggaag-aaag-ggggaactgaaactgagca 1046
|||||||||||||| ||||||||||||||| ||| |||| |||| ||||||||||||||
Sbjct: 103642337 gcccctgttcccctcaggattgaggagtatcaaagtaaagcgggggactgaaactgagca 103642278
Query: 1047 ggatcctgcagggccttcctgg 1068
| | |||| | ||||||||||
Sbjct: 103642277 gcaccctggcgcgccttcctgg 103642256
>gb|JH118602.1| Sus scrofa unplaced genomic scaffold ChrUScaf1230
Length = 67760
Score = 61.9 bits (31), Expect = 9e-07
Identities = 37/39 (94%)
Strand = Plus / Plus
Query: 1137 tccaaagagcagactcaagcagttaataattatagaagt 1175
||||||||||||||||||||||||| |||||| ||||||
Sbjct: 7193 tccaaagagcagactcaagcagttactaattagagaagt 7231
>Sscrofa_Chr16
|| Length = 86898991
Score = 61.9 bits (31), Expect = 9e-07
Identities = 53/59 (89%), Gaps = 1/59 (1%)
Strand = Plus / Minus
Query: 1111 ctttagtcccctaggcctttgcag-gttccaaagagcagactcaagcagttaataatta 1168
||||||| ||||||||||| | | ||||||||||||||||||||||||||| ||||||
Sbjct: 18449565 ctttagtttcctaggcctttactgagttccaaagagcagactcaagcagttactaatta 18449507
>Sscrofa_Chr10
|| Length = 79102373
Score = 61.9 bits (31), Expect = 9e-07
Identities = 37/39 (94%)
Strand = Plus / Minus
Query: 1137 tccaaagagcagactcaagcagttaataattatagaagt 1175
||||||||||||||||||||||||| |||||| ||||||
Sbjct: 65705656 tccaaagagcagactcaagcagttactaattagagaagt 65705618
>Sscrofa_Chr09
|| Length = 153670197
Score = 61.9 bits (31), Expect = 9e-07
Identities = 46/51 (90%)
Strand = Plus / Minus
Query: 1 ttatgccagaaagtcaaacaagttggatatcatgtaaacggactgtggaag 51
|||||||||| || |||||||||||||||||||||||| | ||| ||||||
Sbjct: 6226776 ttatgccagagagccaaacaagttggatatcatgtaaatgaactatggaag 6226726
Score = 61.9 bits (31), Expect = 9e-07
Identities = 49/55 (89%)
Strand = Plus / Minus
Query: 946 taacatcgcccctgttcagcaggaagtagccagagcggtcgtcgcccctgttccc 1000
||||| ||||||| |||||||||||| || |||||||||||||||||| |||||
Sbjct: 105670727 taacaacgccccttttcagcaggaagaagttagagcggtcgtcgccccttttccc 105670673
>gb|GL892848.2| Sus scrofa unplaced genomic scaffold ChrUScaf733
Length = 211489
Score = 60.0 bits (30), Expect = 4e-06
Identities = 33/34 (97%)
Strand = Plus / Minus
Query: 1135 gttccaaagagcagactcaagcagttaataatta 1168
||||||||||||||||||||||||||| ||||||
Sbjct: 79148 gttccaaagagcagactcaagcagttactaatta 79115
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: 47,807,054
Number of extensions: 1016
Number of successful extensions: 1016
Number of sequences better than 1.0e-05: 19
Number of HSP's gapped: 1007
Number of HSP's successfully gapped: 32
Length of query: 1422
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 1401
Effective length of database: 2,808,413,156
Effective search space: 3934586831556
Effective search space used: 3934586831556
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)