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-002406
(1300 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_001035571.1| major histocompatibility complex, class II, ... 385 e-107
Alignment gi|XP_001253929.2| PREDICTED: major histocompatibility complex,... 79 9e-15
Alignment gi|NP_001074392.1| MHC cell surface glycoprotein [Bos taurus]. 77 4e-14
Alignment gi|XP_002697362.1| PREDICTED: histocompatibility complex, class... 77 4e-14
Alignment gi|XP_582099.3| PREDICTED: histocompatibility complex, class II... 77 4e-14
Alignment gi|NP_001012694.2| major histocompatibility complex, class II, ... 75 1e-13
Alignment gi|NP_001012698.2| major histocompatibility complex, class II, ... 72 8e-13
Alignment gi|NP_001013618.1| major histocompatibility complex, class II, ... 72 1e-12
Alignment gi|NP_001029840.2| boLa class II histocompatibility antigen, DQ... 70 4e-12
Alignment gi|NP_001099086.1| non-classical MHC class I antigen [Bos tauru... 70 5e-12
>ref|NP_001035571.1| major histocompatibility complex, class II, DM beta [Bos taurus].
Length = 262
Score = 385 bits (990), Expect = e-107
Identities = 177/241 (73%), Positives = 197/241 (81%)
Frame = +3
Query: 303 FVAHVESTCLLDDEGTPQDFTYCISFNKDLLTCWDPQETRMVPCEFGALNALATYFSVYL 482
FVAHVESTC+LDD+G P+DF+YCISFNKDLLTCWDP + M+P EFG LN LA Y S +L
Sbjct: 21 FVAHVESTCVLDDDGDPKDFSYCISFNKDLLTCWDPLQASMIPREFGVLNGLARYLSQFL 80
Query: 483 NQQEKLLQRLSNGLQNCATHTQPFWKSLTHRTQPPSVQVAKTTPFNTRESVMLACYVWGF 662
N L+QRLSNGLQNCA HTQPFW SLTHRT+PP+VQVAKTTPFNTRESVMLACYVWGF
Sbjct: 81 NNNSYLIQRLSNGLQNCAAHTQPFWSSLTHRTRPPTVQVAKTTPFNTRESVMLACYVWGF 140
Query: 663 YPADVIITWRKNGQPVLPHGKAHMITQPNGDWTYQTVSHLATTPSYGDTYTCVVEHIGVP 842
YPADV ITWR+NGQ VLPHG+A I QPNGDWTYQTVSHLATTPS+GDTYTCVVEHIG P
Sbjct: 141 YPADVAITWRRNGQEVLPHGRAWRIIQPNGDWTYQTVSHLATTPSFGDTYTCVVEHIGAP 200
Query: 843 EPILQDWTSGLSPVQTVKISVSVATXXXXXXXXXXXXXXCQRSVAPGYIFLPGTTYPEGQ 1022
E ILQDWT GL P QTVK+SV++ T +R+ + GYIFLPG+TYPEGQ
Sbjct: 201 ELILQDWTPGLLPAQTVKVSVALVTLVLGLIIFVFGLHSWRRATSSGYIFLPGSTYPEGQ 260
Query: 1023 H 1025
H
Sbjct: 261 H 261
>ref|XP_001253929.2| PREDICTED: major histocompatibility complex, class II, DR beta
3-like [Bos taurus].
Length = 266
Score = 79.0 bits (193), Expect = 9e-15
Identities = 52/162 (32%), Positives = 75/162 (46%), Gaps = 6/162 (3%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFWKSLT--HRTQP-PSVQVAK 605
E+ A+ L + Y N Q+ L+R + H +S T R +P +V AK
Sbjct: 75 EYRAVTELGQRVAEYCNSQKDFLERARAAVDTYCRHNYGVGESFTVQRRVEPIVTVYPAK 134
Query: 606 TTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQ---PNGDWTYQTVS 776
T P +L C V GFYP + + W +NG +A +I+ NGDWT+QT+
Sbjct: 135 TQPLQHHN--LLVCSVNGFYPGHIEVRWFRNGH----EEEAGVISTGLIQNGDWTFQTMV 188
Query: 777 HLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
L T P G+ YTC VEH PI +W + Q+ +S
Sbjct: 189 MLETVPQSGEVYTCQVEHPSRTSPITVEWRAQSDSAQSKMMS 230
>ref|NP_001074392.1| MHC cell surface glycoprotein [Bos taurus].
Length = 261
Score = 76.6 bits (187), Expect = 4e-14
Identities = 49/162 (30%), Positives = 75/162 (46%), Gaps = 6/162 (3%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFW--KSLTHRTQPP-SVQVAK 605
E+ A+ L + Y N QE +L+R+ + H SL R +P ++ ++
Sbjct: 78 EYRAVTPLGRPSAEYWNSQEDILERVRAEVDTVCRHNYQLELITSLQRRVEPTVTISPSR 137
Query: 606 TTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQP---NGDWTYQTVS 776
T N +L C V FYP + + W +N Q A +++ P NGDWT+Q +
Sbjct: 138 TEALNHHN--LLVCSVTDFYPGQIKVRWFRNDQ----EETAGVVSTPLIRNGDWTFQILV 191
Query: 777 HLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
L TP GD YTC VEH + PI +W + Q+ +S
Sbjct: 192 MLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSESAQSKMLS 233
>ref|XP_002697362.1| PREDICTED: histocompatibility complex, class II, DR beta 2 [Bos
taurus].
Length = 365
Score = 76.6 bits (187), Expect = 4e-14
Identities = 52/162 (32%), Positives = 76/162 (46%), Gaps = 6/162 (3%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQN-CATHTQPFWKSLTHRTQPPSVQV--AK 605
EF AL L + Y NQQ+ ++++ + C ++ Q L R P+V V AK
Sbjct: 64 EFTALTELGRLDAEYWNQQKDFMEQMRAKVDTLCRSNYQGIGSFLRQRRVEPTVTVYPAK 123
Query: 606 TTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQ---PNGDWTYQTVS 776
T P +L C V GFYP + + W N +A +I+ NGDWT+QT+
Sbjct: 124 TQPLQHHN--LLVCSVNGFYPGHIEVRWFWNSH----EEEAGVISTGLIQNGDWTFQTMV 177
Query: 777 HLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
L T P G+ YTC VEH P+ +W + Q+ +S
Sbjct: 178 MLETVPQSGEVYTCQVEHPSRTSPLTVEWRAQSDSAQSKMMS 219
>ref|XP_582099.3| PREDICTED: histocompatibility complex, class II, DR beta 2 [Bos
taurus].
Length = 365
Score = 76.6 bits (187), Expect = 4e-14
Identities = 52/162 (32%), Positives = 76/162 (46%), Gaps = 6/162 (3%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQN-CATHTQPFWKSLTHRTQPPSVQV--AK 605
EF AL L + Y NQQ+ ++++ + C ++ Q L R P+V V AK
Sbjct: 64 EFTALTELGRLDAEYWNQQKDFMEQMRAKVDTLCRSNYQGIGSFLRQRRVEPTVTVYPAK 123
Query: 606 TTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQ---PNGDWTYQTVS 776
T P +L C V GFYP + + W N +A +I+ NGDWT+QT+
Sbjct: 124 TQPLQHHN--LLVCSVNGFYPGHIEVRWFWNSH----EEEAGVISTGLIQNGDWTFQTMV 177
Query: 777 HLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
L T P G+ YTC VEH P+ +W + Q+ +S
Sbjct: 178 MLETVPQSGEVYTCQVEHPSRTSPLTVEWRAQSDSAQSKMMS 219
>ref|NP_001012694.2| major histocompatibility complex, class II, DQ beta [Bos taurus].
Length = 261
Score = 75.1 bits (183), Expect = 1e-13
Identities = 47/162 (29%), Positives = 76/162 (46%), Gaps = 6/162 (3%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFW--KSLTHRTQPP-SVQVAK 605
E+ A+ L + Y N Q+ +L++ L H SL + +P ++ +++
Sbjct: 78 EYRAVTQLGRTLAEYWNSQKDILEQTRAELDTVCRHNYQLEVITSLQRQVEPTVTISLSR 137
Query: 606 TTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQP---NGDWTYQTVS 776
T N +L C V FYP + + W +NG+ A +++ P NGDWT+Q +
Sbjct: 138 TEALNHHN--LLVCSVTDFYPGQIKVRWFQNGK----EETAGIVSTPLIRNGDWTFQILV 191
Query: 777 HLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
L TP GD YTC VEH + PI +W + Q+ +S
Sbjct: 192 MLEMTPKRGDVYTCRVEHPSLQSPISVEWRAQSESAQSKMLS 233
>ref|NP_001012698.2| major histocompatibility complex, class II, DRB3 [Bos taurus].
Length = 266
Score = 72.4 bits (176), Expect = 8e-13
Identities = 51/162 (31%), Positives = 75/162 (46%), Gaps = 6/162 (3%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFWKSLT-HRTQPPSVQV--AK 605
EF A+ L + + N Q+ L++ + H +S T R P+V V AK
Sbjct: 75 EFRAVTELGRPAAEHWNSQKDFLEQKRAEVDRVCRHNYGGVESFTVQRRVEPTVTVYPAK 134
Query: 606 TTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQ---PNGDWTYQTVS 776
T P +L C V GFYP + + W +NG +A +I+ NGDWT+QT+
Sbjct: 135 TQPLQHHN--LLVCSVNGFYPGHIEVRWFRNGH----EEEAGVISTGLIQNGDWTFQTMV 188
Query: 777 HLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
L T P G+ YTC V+H PI +W + Q+ +S
Sbjct: 189 MLETVPQSGEVYTCQVDHPKRTSPITVEWRARSDSAQSKMMS 230
>ref|NP_001013618.1| major histocompatibility complex, class II, DO beta [Bos taurus].
Length = 271
Score = 72.0 bits (175), Expect = 1e-12
Identities = 36/97 (37%), Positives = 53/97 (54%)
Frame = +3
Query: 573 RTQPPSVQVAKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPNG 752
R QP + TP +++L C V GFYP D+ +TW +NGQ + + + NG
Sbjct: 120 RVQPEVTVYPEKTPALQHRNLLL-CLVTGFYPGDIKVTWFRNGQEQREGIMSTGLIR-NG 177
Query: 753 DWTYQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDW 863
DWT+Q LA TP G+ YTC+V+H + P+ +W
Sbjct: 178 DWTFQMTVMLAMTPELGEVYTCLVDHPSLLSPVSVEW 214
>ref|NP_001029840.2| boLa class II histocompatibility antigen, DQB*0101 beta chain
precursor [Bos taurus].
Length = 261
Score = 70.1 bits (170), Expect = 4e-12
Identities = 46/161 (28%), Positives = 73/161 (45%), Gaps = 6/161 (3%)
Frame = +3
Query: 438 FGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQP--FWKSLTHRTQPP-SVQVAKT 608
+ AL L + Y N Q+ L++ H SL R +P ++ ++T
Sbjct: 79 YRALTPLGRPDAEYWNSQKDFLEQTRAEADTVCRHNYQAELITSLQRRVEPTVTISPSRT 138
Query: 609 TPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQP---NGDWTYQTVSH 779
N +L C V FYP+ + + W +N + A +++ P NGDWT+Q +
Sbjct: 139 EALNHHN--LLVCSVTDFYPSQIKVRWFRNDR----EETAGVVSTPLIRNGDWTFQILVM 192
Query: 780 LATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
L TP GD YTC VEH + PI+ +W + Q+ +S
Sbjct: 193 LEMTPQRGDVYTCHVEHPSLQSPIMVEWRAQSESAQSKMLS 233
>ref|NP_001099086.1| non-classical MHC class I antigen [Bos taurus].
Length = 342
Score = 69.7 bits (169), Expect = 5e-12
Identities = 53/175 (30%), Positives = 83/175 (47%), Gaps = 3/175 (1%)
Frame = +3
Query: 372 ISFNKDLLTCWDPQET--RMVPCEFGALNALATYFSVYLNQQEKLLQR-LSNGLQNCATH 542
++ N+DL + W +T ++ ++ A A + + + KLL+R L NG
Sbjct: 145 LALNEDLRS-WTAADTAAQITKRKWEATGAAERFRNYLEGKCVKLLRRHLENG------- 196
Query: 543 TQPFWKSLTHRTQPPSVQVAKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHG 722
K R PP V P + RE V L C+ GFYP ++ +TW++NG+
Sbjct: 197 -----KDTLLRADPPMAHVTHH-PISERE-VTLRCWALGFYPEEISLTWQRNGEDQTQDM 249
Query: 723 KAHMITQPNGDWTYQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQ 887
+ + T+P+GD T+Q + LA YTC V+H G+ EP+ W G P Q
Sbjct: 250 EL-VETRPSGDGTFQKWAALAVPSGEEQRYTCRVQHEGLQEPLTLRWDKGGEPPQ 303
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: 58,620,017
Number of extensions: 1844571
Number of successful extensions: 6188
Number of sequences better than 1.0e-05: 54
Number of HSP's gapped: 6108
Number of HSP's successfully gapped: 54
Length of query: 433
Length of database: 17,681,374
Length adjustment: 105
Effective length of query: 328
Effective length of database: 14,207,134
Effective search space: 4659939952
Effective search space used: 4659939952
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 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-002406
(1300 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_849737.1| PREDICTED: similar to HLA class II histocompati... 385 e-107
Alignment gi|NP_001041592.1| major histocompatibility complex, class II, ... 74 2e-13
Alignment gi|NP_001014768.1| DLA class II histocompatibility antigen, DR-... 73 7e-13
Alignment gi|NP_001014403.1| major histocompatibility complex, class II, ... 72 9e-13
Alignment gi|NP_001014400.1| MHC class I DLA-64 [Canis lupus familiaris]. 71 3e-12
Alignment gi|NP_001014767.1| MHC class I DLA-88 [Canis lupus familiaris]. 70 6e-12
Alignment gi|NP_001014401.1| MHC class I DLA-12 [Canis lupus familiaris]. 69 1e-11
Alignment gi|NP_001011723.1| MHC class II DR alpha chain [Canis lupus fam... 69 1e-11
Alignment gi|XP_855624.1| PREDICTED: MHC class Ib [Canis familiaris]. 60 5e-09
Alignment gi|XP_535458.1| PREDICTED: similar to beta-2-microglobulin prec... 58 2e-08
>ref|XP_849737.1| PREDICTED: similar to HLA class II histocompatibility antigen, DM
beta chain precursor (MHC class II antigen DMB) [Canis
familiaris].
Length = 263
Score = 385 bits (990), Expect = e-107
Identities = 177/243 (72%), Positives = 200/243 (82%)
Frame = +3
Query: 303 FVAHVESTCLLDDEGTPQDFTYCISFNKDLLTCWDPQETRMVPCEFGALNALATYFSVYL 482
F+AHVES+CLLDD+GTP+DFTYC+SFNKDLLTCWDP E +MVP EFG LN LA Y S YL
Sbjct: 21 FIAHVESSCLLDDDGTPKDFTYCVSFNKDLLTCWDPDEAKMVPYEFGTLNVLANYLSDYL 80
Query: 483 NQQEKLLQRLSNGLQNCATHTQPFWKSLTHRTQPPSVQVAKTTPFNTRESVMLACYVWGF 662
NQQE L QRLSNGLQ+CATHTQ FW SLTHRT+PP+VQVAK+TPFNT+ESVMLACYVWGF
Sbjct: 81 NQQEYLHQRLSNGLQDCATHTQSFWGSLTHRTRPPTVQVAKSTPFNTKESVMLACYVWGF 140
Query: 663 YPADVIITWRKNGQPVLPHGKAHMITQPNGDWTYQTVSHLATTPSYGDTYTCVVEHIGVP 842
YPADV I+WRKNGQPV H A + QPNGDWTYQTVSHLATTPSY DTYTCVVEHIG P
Sbjct: 141 YPADVTISWRKNGQPVPSHSSALNMAQPNGDWTYQTVSHLATTPSYEDTYTCVVEHIGAP 200
Query: 843 EPILQDWTSGLSPVQTVKISVSVATXXXXXXXXXXXXXXCQRSVAPGYIFLPGTTYPEGQ 1022
EP+ +DWT GLSP+QTVK+SVS T +R+ + GY+FLPGT+YPEGQ
Sbjct: 201 EPVCEDWTPGLSPMQTVKVSVSGVTLGLGFIIFSLGLLSWRRAGSSGYVFLPGTSYPEGQ 260
Query: 1023 HIS 1031
H+S
Sbjct: 261 HVS 263
>ref|NP_001041592.1| major histocompatibility complex, class II, DO beta [Canis lupus
familiaris].
Length = 270
Score = 74.3 bits (181), Expect = 2e-13
Identities = 48/148 (32%), Positives = 66/148 (44%), Gaps = 6/148 (4%)
Frame = +3
Query: 438 FGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFWKSLT--HRTQPPSVQVAKTT 611
F AL L + N Q +L+R + H T + QP + T
Sbjct: 73 FVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTVYPERT 132
Query: 612 PFNTRESVMLACYVWGFYPADVIITWRKNGQP----VLPHGKAHMITQPNGDWTYQTVSH 779
P +++L C V GFYP D+ I W +NGQ V+ G NGDWT+QT+
Sbjct: 133 PSMQHHNLLL-CSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIR-----NGDWTFQTMVM 186
Query: 780 LATTPSYGDTYTCVVEHIGVPEPILQDW 863
L TP GD YTC+V H + P+ +W
Sbjct: 187 LEMTPELGDVYTCLVNHPSLLSPVSVEW 214
>ref|NP_001014768.1| DLA class II histocompatibility antigen, DR-1 beta chain precursor
[Canis lupus familiaris].
Length = 266
Score = 72.8 bits (177), Expect = 7e-13
Identities = 46/157 (29%), Positives = 70/157 (44%), Gaps = 1/157 (0%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFWKSLT-HRTQPPSVQVAKTT 611
EF A+ L + N Q+++L++ + H +S T R P+V V T
Sbjct: 75 EFRAVTELGRPVAESWNGQKEILEQERATVDTYCRHNYGVIESFTVQRRVEPTVTVYPTK 134
Query: 612 PFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPNGDWTYQTVSHLATT 791
+ +L C V GFYP + + W +NGQ G NGDWT+Q + L
Sbjct: 135 TQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEE-EAGVVSTGLIRNGDWTFQILVMLEIV 193
Query: 792 PSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
P G+ YTC VEH + P+ +W + Q+ +S
Sbjct: 194 PQSGEVYTCQVEHPSLTSPVTVEWRAQSDSAQSKMLS 230
>ref|NP_001014403.1| major histocompatibility complex, class II, DQ beta 1 [Canis lupus
familiaris].
Length = 269
Score = 72.4 bits (176), Expect = 9e-13
Identities = 49/162 (30%), Positives = 74/162 (45%), Gaps = 6/162 (3%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHT--QPFWKSLTHRTQPP-SVQVAK 605
EF A+ L + Y N+Q+ + R+ L H + +L R +P ++ +K
Sbjct: 78 EFRAVTELGRPDAEYWNRQKDEMDRVRAELDTVCRHNYGREELTTLQRRVEPTVTIFPSK 137
Query: 606 TTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQP---NGDWTYQTVS 776
T N +L C V FYP + + W +N Q A +++ P NGDWT+Q +
Sbjct: 138 TEVLNHHN--LLVCSVTDFYPGQIKVRWFRNDQ----EQTAGVVSTPLIRNGDWTFQILV 191
Query: 777 HLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
L TP GD YTC VEH + PI W + Q+ +S
Sbjct: 192 MLEMTPQRGDVYTCHVEHASLQSPITVQWRAQSESAQSKMLS 233
>ref|NP_001014400.1| MHC class I DLA-64 [Canis lupus familiaris].
Length = 361
Score = 70.9 bits (172), Expect = 3e-12
Identities = 48/154 (31%), Positives = 77/154 (50%), Gaps = 2/154 (1%)
Frame = +3
Query: 459 ATYFSVYLNQQ--EKLLQRLSNGLQNCATHTQPFWKSLTHRTQPPSVQVAKTTPFNTRES 632
A Y+ VYL + + LL+ L G K T PP + + + P + E
Sbjct: 177 AQYYRVYLQGECVQSLLKYLERG------------KETLQLTDPPKIYLTRH-PISDHE- 222
Query: 633 VMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPNGDWTYQTVSHLATTPSYGDTY 812
V L C+ GFYPA++ +TW+++G+ + + T+P GD T+Q + + Y
Sbjct: 223 VTLRCWALGFYPAEITLTWQRDGEDQTQDTEV-VDTRPAGDGTFQKWAAVVVPSGQEQRY 281
Query: 813 TCVVEHIGVPEPILQDWTSGLSPVQTVKISVSVA 914
TC V+H G+ EP+ + W SP+ T+ I VS+A
Sbjct: 282 TCHVQHEGLAEPVTRRWEP--SPLSTIVI-VSIA 312
>ref|NP_001014767.1| MHC class I DLA-88 [Canis lupus familiaris].
Length = 361
Score = 69.7 bits (169), Expect = 6e-12
Identities = 40/114 (35%), Positives = 65/114 (57%)
Frame = +3
Query: 573 RTQPPSVQVAKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPNG 752
R +PPS +V + P + E V L C+ GFYPA++ +TW+++G+ + + T+P G
Sbjct: 205 RAEPPSTRVTRH-PISDHE-VTLRCWALGFYPAEITLTWQRDGEDQTQDTEV-VDTRPAG 261
Query: 753 DWTYQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKISVSVA 914
D T+Q + + YTC V+H G+ EP+ + W SP+ T+ I VS+A
Sbjct: 262 DGTFQKWAAVVVPSGQEQRYTCHVQHEGLAEPVTRRWEP--SPLSTIVI-VSIA 312
>ref|NP_001014401.1| MHC class I DLA-12 [Canis lupus familiaris].
Length = 358
Score = 68.9 bits (167), Expect = 1e-11
Identities = 40/114 (35%), Positives = 65/114 (57%)
Frame = +3
Query: 573 RTQPPSVQVAKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPNG 752
R +PPS +V + P + E V L C+ GFYPA++ +TW+++G+ + + T+P G
Sbjct: 202 RAEPPSTRVTRH-PVSDHE-VTLRCWALGFYPAEITLTWQRDGEDQTQDTEV-VDTRPAG 258
Query: 753 DWTYQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKISVSVA 914
D T+Q + + YTC V+H G+ EP+ + W SP+ T+ I VS+A
Sbjct: 259 DGTFQKWAAVVVPSGQEQRYTCHVQHEGLVEPVTRRWEP--SPLSTIVI-VSIA 309
>ref|NP_001011723.1| MHC class II DR alpha chain [Canis lupus familiaris].
Length = 254
Score = 68.9 bits (167), Expect = 1e-11
Identities = 35/94 (37%), Positives = 48/94 (51%)
Frame = +3
Query: 582 PPSVQVAKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPNGDWT 761
PP V V TP E +L C++ F P + +TW +NG PV G + I P D
Sbjct: 111 PPEVTVLSNTPVELGEPNILICFIDKFSPPVINVTWLRNGNPVTT-GVSETIFLPREDHL 169
Query: 762 YQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDW 863
++ +L PS D Y C VEH G+ EP+L+ W
Sbjct: 170 FRKFHYLPFLPSAEDVYDCKVEHWGLDEPLLKHW 203
>ref|XP_855624.1| PREDICTED: MHC class Ib [Canis familiaris].
Length = 381
Score = 60.1 bits (144), Expect = 5e-09
Identities = 35/114 (30%), Positives = 56/114 (49%)
Frame = +3
Query: 573 RTQPPSVQVAKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPNG 752
R PP V + P + E V L C+ GFYPA++ +TW+++G+ + + T+P G
Sbjct: 211 RADPPKTSVTRR-PISEHE-VTLKCWALGFYPAEITLTWQRDGEDQTQDTEL-VETRPGG 267
Query: 753 DWTYQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKISVSVA 914
D T+Q + + YTC + H +P+PI W P T+ I +A
Sbjct: 268 DGTFQKWAAVVVPSGEEQRYTCHILHKSLPKPITLRWEP--PPQSTIPIVSIIA 319
>ref|XP_535458.1| PREDICTED: similar to beta-2-microglobulin precursor isoform 2
[Canis familiaris].
Length = 125
Score = 57.8 bits (138), Expect = 2e-08
Identities = 29/94 (30%), Positives = 47/94 (50%)
Frame = +3
Query: 582 PPSVQVAKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPNGDWT 761
PP +QV P + L CYV GF+P ++ I KNG+ + ++ DWT
Sbjct: 31 PPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSFSK---DWT 87
Query: 762 YQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDW 863
+ + H TP+ D ++C V+H+ + EP + W
Sbjct: 88 FYLLVHTEFTPNEQDEFSCRVKHVTLSEPQIVKW 121
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: 60,984,189
Number of extensions: 1894452
Number of successful extensions: 6489
Number of sequences better than 1.0e-05: 15
Number of HSP's gapped: 6459
Number of HSP's successfully gapped: 15
Length of query: 433
Length of database: 18,874,504
Length adjustment: 106
Effective length of query: 327
Effective length of database: 15,340,888
Effective search space: 5016470376
Effective search space used: 5016470376
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-002406
(1300 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_002109.2| HLA class II histocompatibility antigen, DM bet... 375 e-104
Alignment gi|NP_001230894.1| major histocompatibility complex, class II, ... 86 1e-16
Alignment gi|NP_002115.2| major histocompatibility complex, class II, DR ... 84 4e-16
Alignment gi|XP_003120321.1| PREDICTED: HLA class II histocompatibility a... 81 2e-15
Alignment gi|XP_003120323.1| PREDICTED: HLA class II histocompatibility a... 79 7e-15
Alignment gi|NP_068818.4| major histocompatibility complex, class II, DR ... 79 7e-15
Alignment gi|NP_072049.2| major histocompatibility complex, class II, DR ... 79 7e-15
Alignment gi|XP_003119341.1| PREDICTED: HLA class II histocompatibility a... 78 2e-14
Alignment gi|XP_003119340.1| PREDICTED: HLA class II histocompatibility a... 78 2e-14
Alignment gi|XP_003119339.1| PREDICTED: HLA class II histocompatibility a... 78 2e-14
>ref|NP_002109.2| HLA class II histocompatibility antigen, DM beta chain precursor
[Homo sapiens].
Length = 263
Score = 375 bits (962), Expect = e-104
Identities = 173/243 (71%), Positives = 194/243 (79%)
Frame = +3
Query: 303 FVAHVESTCLLDDEGTPQDFTYCISFNKDLLTCWDPQETRMVPCEFGALNALATYFSVYL 482
FVAHVESTCLLDD GTP+DFTYCISFNKDLLTCWDP+E +M PCEFG LN+LA S +L
Sbjct: 21 FVAHVESTCLLDDAGTPKDFTYCISFNKDLLTCWDPEENKMAPCEFGVLNSLANVLSQHL 80
Query: 483 NQQEKLLQRLSNGLQNCATHTQPFWKSLTHRTQPPSVQVAKTTPFNTRESVMLACYVWGF 662
NQ++ L+QRL NGLQNCATHTQPFW SLT+RT+PPSVQVAKTTPFNTRE VMLACYVWGF
Sbjct: 81 NQKDTLMQRLRNGLQNCATHTQPFWGSLTNRTRPPSVQVAKTTPFNTREPVMLACYVWGF 140
Query: 663 YPADVIITWRKNGQPVLPHGKAHMITQPNGDWTYQTVSHLATTPSYGDTYTCVVEHIGVP 842
YPA+V ITWRKNG+ V+PH AH QPNGDWTYQT+SHLA TPSYGDTYTCVVEH G P
Sbjct: 141 YPAEVTITWRKNGKLVMPHSSAHKTAQPNGDWTYQTLSHLALTPSYGDTYTCVVEHTGAP 200
Query: 843 EPILQDWTSGLSPVQTVKISVSVATXXXXXXXXXXXXXXCQRSVAPGYIFLPGTTYPEGQ 1022
EPIL+DWT GLSP+QT+K+SVS T +R+ Y LPG+ Y EG
Sbjct: 201 EPILRDWTPGLSPMQTLKVSVSAVTLGLGLIIFSLGVISWRRAGHSSYTPLPGSNYSEGW 260
Query: 1023 HIS 1031
HIS
Sbjct: 261 HIS 263
>ref|NP_001230894.1| major histocompatibility complex, class II, DR beta 1 precursor
[Homo sapiens].
Length = 266
Score = 85.5 bits (210), Expect = 1e-16
Identities = 56/163 (34%), Positives = 77/163 (47%), Gaps = 7/163 (4%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFWKSLT-HRTQPPSVQV--AK 605
EF A+ L + Y N Q+ LL++ + N H +S T R P V V +K
Sbjct: 75 EFRAVTELGRPDAEYWNSQKDLLEQKRGRVDNYCRHNYGVVESFTVQRRVHPKVTVYPSK 134
Query: 606 TTPFNTRESVMLACYVWGFYPADVIITWRKNGQP----VLPHGKAHMITQPNGDWTYQTV 773
T P +L C V GFYP + + W +NGQ V+ G H NGDWT+QT+
Sbjct: 135 TQPLQHHN--LLVCSVSGFYPGSIEVRWFRNGQEEKTGVVSTGLIH-----NGDWTFQTL 187
Query: 774 SHLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
L T P G+ YTC VEH V P+ +W + Q+ +S
Sbjct: 188 VMLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSESAQSKMLS 230
>ref|NP_002115.2| major histocompatibility complex, class II, DR beta 1 precursor
[Homo sapiens].
Length = 266
Score = 83.6 bits (205), Expect = 4e-16
Identities = 54/162 (33%), Positives = 77/162 (47%), Gaps = 6/162 (3%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFWKSLT--HRTQPP-SVQVAK 605
EF A+ L + Y N Q+ +L++ + H +S T R QP +V +K
Sbjct: 75 EFRAVTELGRPDAEYWNSQKDILEQARAAVDTYCRHNYGVVESFTVQRRVQPKVTVYPSK 134
Query: 606 TTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQ---PNGDWTYQTVS 776
T P +L C V GFYP + + W NGQ KA M++ NGDWT+QT+
Sbjct: 135 TQPLQHHN--LLVCSVSGFYPGSIEVRWFLNGQ----EEKAGMVSTGLIQNGDWTFQTLV 188
Query: 777 HLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
L T P G+ YTC VEH V P+ +W + Q+ +S
Sbjct: 189 MLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSESAQSKMLS 230
>ref|XP_003120321.1| PREDICTED: HLA class II histocompatibility antigen, DQ beta 1
chain-like isoform 2 [Homo sapiens].
Length = 261
Score = 80.9 bits (198), Expect = 2e-15
Identities = 49/160 (30%), Positives = 75/160 (46%), Gaps = 4/160 (2%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHT-QPFWKSLTHRTQPPSVQVAKTT 611
EF A+ L + Y N Q+ +L+R + H Q ++ R P+V ++ +
Sbjct: 78 EFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSR 137
Query: 612 PFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQP---NGDWTYQTVSHL 782
+L C V FYPA + + W +NGQ A +++ P NGDWT+Q + L
Sbjct: 138 TEALNHHNLLVCSVTDFYPAQIKVRWFRNGQ----EETAGVVSTPLIRNGDWTFQILVML 193
Query: 783 ATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
TP GD YTC VEH + PI +W + Q+ +S
Sbjct: 194 EMTPQRGDVYTCHVEHPSLQSPITVEWRAQSESAQSKMLS 233
>ref|XP_003120323.1| PREDICTED: HLA class II histocompatibility antigen, DR beta 4
chain-like [Homo sapiens].
Length = 278
Score = 79.3 bits (194), Expect = 7e-15
Identities = 52/162 (32%), Positives = 78/162 (48%), Gaps = 6/162 (3%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFWKSLT--HRTQPP-SVQVAK 605
E+ A+ L + Y N Q+ LL+R + + +S T R QP +V +K
Sbjct: 87 EYQAVTELGRPDAEYWNSQKDLLERRRAEVDTYCRYNYGVVESFTVQRRVQPKVTVYPSK 146
Query: 606 TTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQ---PNGDWTYQTVS 776
T P +L C V GFYP + + W +NGQ KA +++ NGDWT+QT+
Sbjct: 147 TQPLQHHN--LLVCSVNGFYPGSIEVRWFRNGQ----EEKAGVVSTGLIQNGDWTFQTLV 200
Query: 777 HLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
L T P G+ YTC VEH + P+ W++ Q+ +S
Sbjct: 201 MLETVPRSGEVYTCQVEHPSMMSPLTVQWSARSESAQSKMLS 242
>ref|NP_068818.4| major histocompatibility complex, class II, DR beta 4 precursor
[Homo sapiens].
Length = 266
Score = 79.3 bits (194), Expect = 7e-15
Identities = 52/162 (32%), Positives = 78/162 (48%), Gaps = 6/162 (3%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFWKSLT--HRTQPP-SVQVAK 605
E+ A+ L + Y N Q+ LL+R + + +S T R QP +V +K
Sbjct: 75 EYQAVTELGRPDAEYWNSQKDLLERRRAEVDTYCRYNYGVVESFTVQRRVQPKVTVYPSK 134
Query: 606 TTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQ---PNGDWTYQTVS 776
T P +L C V GFYP + + W +NGQ KA +++ NGDWT+QT+
Sbjct: 135 TQPLQHHN--LLVCSVNGFYPGSIEVRWFRNGQ----EEKAGVVSTGLIQNGDWTFQTLV 188
Query: 777 HLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
L T P G+ YTC VEH + P+ W++ Q+ +S
Sbjct: 189 MLETVPRSGEVYTCQVEHPSMMSPLTVQWSARSESAQSKMLS 230
>ref|NP_072049.2| major histocompatibility complex, class II, DR beta 3 precursor
[Homo sapiens].
Length = 266
Score = 79.3 bits (194), Expect = 7e-15
Identities = 53/162 (32%), Positives = 76/162 (46%), Gaps = 6/162 (3%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFWKSLT-HRTQPPSVQV--AK 605
E+ A+ L + N Q+ LL++ + N H +S T R P V V AK
Sbjct: 75 EYRAVTELGRPVAESWNSQKDLLEQKRGRVDNYCRHNYGVGESFTVQRRVHPQVTVYPAK 134
Query: 606 TTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQ---PNGDWTYQTVS 776
T P +L C V GFYP + + W +NGQ KA +++ NGDWT+QT+
Sbjct: 135 TQPLQHHN--LLVCSVSGFYPGSIEVRWFRNGQ----EEKAGVVSTGLIQNGDWTFQTLV 188
Query: 777 HLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
L T P G+ YTC VEH V + +W + Q+ +S
Sbjct: 189 MLETVPRSGEVYTCQVEHPSVTSALTVEWRARSESAQSKMLS 230
>ref|XP_003119341.1| PREDICTED: HLA class II histocompatibility antigen, DRB1-7 beta
chain-like isoform 3 [Homo sapiens].
Length = 264
Score = 78.2 bits (191), Expect = 2e-14
Identities = 52/162 (32%), Positives = 75/162 (46%), Gaps = 6/162 (3%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFWKSLT-HRTQPPSVQV--AK 605
E+ A+ L + N Q+ +L+ + H +S T R P V V AK
Sbjct: 73 EYRAVTELGRPVAESWNSQKDILEDRRGQVDTVCRHNYGVGESFTVQRRVHPEVTVYPAK 132
Query: 606 TTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQ---PNGDWTYQTVS 776
T P +L C V GFYP + + W +NGQ KA +++ NGDWT+QT+
Sbjct: 133 TQPLQHHN--LLVCSVSGFYPGSIEVRWFRNGQ----EEKAGVVSTGLIQNGDWTFQTLV 186
Query: 777 HLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
L T P G+ YTC VEH V P+ +W + Q+ +S
Sbjct: 187 MLETVPRSGEVYTCQVEHPSVMSPLTVEWRARSESAQSKMLS 228
>ref|XP_003119340.1| PREDICTED: HLA class II histocompatibility antigen, DRB1-7 beta
chain-like isoform 2 [Homo sapiens].
Length = 266
Score = 78.2 bits (191), Expect = 2e-14
Identities = 52/162 (32%), Positives = 75/162 (46%), Gaps = 6/162 (3%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFWKSLT-HRTQPPSVQV--AK 605
E+ A+ L + N Q+ +L+ + H +S T R P V V AK
Sbjct: 75 EYRAVTELGRPVAESWNSQKDILEDRRGQVDTVCRHNYGVGESFTVQRRVHPEVTVYPAK 134
Query: 606 TTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQ---PNGDWTYQTVS 776
T P +L C V GFYP + + W +NGQ KA +++ NGDWT+QT+
Sbjct: 135 TQPLQHHN--LLVCSVSGFYPGSIEVRWFRNGQ----EEKAGVVSTGLIQNGDWTFQTLV 188
Query: 777 HLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
L T P G+ YTC VEH V P+ +W + Q+ +S
Sbjct: 189 MLETVPRSGEVYTCQVEHPSVMSPLTVEWRARSESAQSKMLS 230
>ref|XP_003119339.1| PREDICTED: HLA class II histocompatibility antigen, DRB1-7 beta
chain-like isoform 1 [Homo sapiens].
Length = 266
Score = 78.2 bits (191), Expect = 2e-14
Identities = 52/162 (32%), Positives = 75/162 (46%), Gaps = 6/162 (3%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFWKSLT-HRTQPPSVQV--AK 605
E+ A+ L + N Q+ +L+ + H +S T R P V V AK
Sbjct: 75 EYRAVTELGRPVAESWNSQKDILEDRRGQVDTVCRHNYGVGESFTVQRRVHPEVTVYPAK 134
Query: 606 TTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQ---PNGDWTYQTVS 776
T P +L C V GFYP + + W +NGQ KA +++ NGDWT+QT+
Sbjct: 135 TQPLQHHN--LLVCSVSGFYPGSIEVRWFRNGQ----EEKAGVVSTGLIQNGDWTFQTLV 188
Query: 777 HLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
L T P G+ YTC VEH V P+ +W + Q+ +S
Sbjct: 189 MLETVPRSGEVYTCQVEHPSVMSPLTVEWRARSESAQSKMLS 230
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: 59,988,049
Number of extensions: 1871357
Number of successful extensions: 6953
Number of sequences better than 1.0e-05: 60
Number of HSP's gapped: 6769
Number of HSP's successfully gapped: 60
Length of query: 433
Length of database: 18,297,164
Length adjustment: 105
Effective length of query: 328
Effective length of database: 14,835,944
Effective search space: 4866189632
Effective search space used: 4866189632
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-002406
(1300 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|XP_003086107.1| PREDICTED: class II histocompatibility antig... 344 8e-95
Alignment gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ... 342 3e-94
Alignment gi|NP_034517.2| class II histocompatibility antigen, M beta 1 c... 340 2e-93
Alignment gi|NP_996988.2| histocompatibility 2, class II antigen A, beta ... 73 4e-13
Alignment gi|NP_034512.2| H-2 class II histocompatibility antigen, I-E be... 72 7e-13
Alignment gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ... 72 1e-12
Alignment gi|XP_003086980.1| PREDICTED: h-2 class I histocompatibility an... 71 2e-12
Alignment gi|XP_997416.3| PREDICTED: h-2 class I histocompatibility antig... 71 2e-12
Alignment gi|XP_003086979.1| PREDICTED: h-2 class I histocompatibility an... 71 2e-12
Alignment gi|NP_038847.1| histocompatibility 2, M region locus 3 [Mus mus... 70 4e-12
>ref|XP_003086107.1| PREDICTED: class II histocompatibility antigen, M beta 1 chain-like
[Mus musculus].
Length = 261
Score = 344 bits (883), Expect = 8e-95
Identities = 161/241 (66%), Positives = 182/241 (75%)
Frame = +3
Query: 303 FVAHVESTCLLDDEGTPQDFTYCISFNKDLLTCWDPQETRMVPCEFGALNALATYFSVYL 482
FVAHVESTC+LDD GTPQDFTYC+SFNKDLL CWDP ++VPCEFG L A FS L
Sbjct: 21 FVAHVESTCVLDDAGTPQDFTYCVSFNKDLLACWDPDVGKIVPCEFGVLYPWAENFSRIL 80
Query: 483 NQQEKLLQRLSNGLQNCATHTQPFWKSLTHRTQPPSVQVAKTTPFNTRESVMLACYVWGF 662
N++E LLQRL NGL +CA+HTQPFW +LTHRT+PPSV+VA+TTPFNTRE VMLACYVWGF
Sbjct: 81 NKEESLLQRLQNGLLDCASHTQPFWNALTHRTRPPSVRVAQTTPFNTREPVMLACYVWGF 140
Query: 663 YPADVIITWRKNGQPVLPHGKAHMITQPNGDWTYQTVSHLATTPSYGDTYTCVVEHIGVP 842
YPADV ITW KNGQ V H QPNGDWTYQTVS+LA TPSYGD YTCVV+H G
Sbjct: 141 YPADVTITWMKNGQLVPSHSNKEKTAQPNGDWTYQTVSYLALTPSYGDVYTCVVQHSGTS 200
Query: 843 EPILQDWTSGLSPVQTVKISVSVATXXXXXXXXXXXXXXCQRSVAPGYIFLPGTTYPEGQ 1022
EPI DWT GLSP+QTVK+SVS AT ++S + Y LPG+TYPEG+
Sbjct: 201 EPIRGDWTPGLSPIQTVKVSVSAATLGLGFIIFCVGFFRWRKSHSSSYTPLPGSTYPEGR 260
Query: 1023 H 1025
H
Sbjct: 261 H 261
>ref|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus musculus].
Length = 261
Score = 342 bits (878), Expect = 3e-94
Identities = 160/241 (66%), Positives = 181/241 (75%)
Frame = +3
Query: 303 FVAHVESTCLLDDEGTPQDFTYCISFNKDLLTCWDPQETRMVPCEFGALNALATYFSVYL 482
FVAHVESTC+L+D GTPQDFTYC+SFNKDLL CWDP ++VPCEFG L+ LA S L
Sbjct: 21 FVAHVESTCVLNDAGTPQDFTYCVSFNKDLLACWDPDVGKIVPCEFGVLSRLAEIISNIL 80
Query: 483 NQQEKLLQRLSNGLQNCATHTQPFWKSLTHRTQPPSVQVAKTTPFNTRESVMLACYVWGF 662
N+QE L+ RL NGLQ+CATHTQPFW LTHRT+ PSV+VA+TTPFNTRE VMLACYVWGF
Sbjct: 81 NEQESLIHRLQNGLQDCATHTQPFWDVLTHRTRAPSVRVAQTTPFNTREPVMLACYVWGF 140
Query: 663 YPADVIITWRKNGQPVLPHGKAHMITQPNGDWTYQTVSHLATTPSYGDTYTCVVEHIGVP 842
YPADV ITW KNGQ V H QPNGDWTYQTVS+LA TPSYGD YTCVV+H G
Sbjct: 141 YPADVTITWMKNGQLVPSHSNKEKTAQPNGDWTYQTVSYLALTPSYGDVYTCVVQHSGTS 200
Query: 843 EPILQDWTSGLSPVQTVKISVSVATXXXXXXXXXXXXXXCQRSVAPGYIFLPGTTYPEGQ 1022
EPI DWT GLSP+QTVK+SVS AT ++S + Y LPG+TYPEG+
Sbjct: 201 EPIRGDWTPGLSPIQTVKVSVSAATLGLGFIIFCVGFFRWRKSHSSSYTPLPGSTYPEGR 260
Query: 1023 H 1025
H
Sbjct: 261 H 261
>ref|NP_034517.2| class II histocompatibility antigen, M beta 1 chain precursor [Mus
musculus].
Length = 261
Score = 340 bits (871), Expect = 2e-93
Identities = 160/241 (66%), Positives = 180/241 (74%)
Frame = +3
Query: 303 FVAHVESTCLLDDEGTPQDFTYCISFNKDLLTCWDPQETRMVPCEFGALNALATYFSVYL 482
FVAHVESTC+LDD GTPQDFTYC+SFNKDLL CWDP ++VPCEFG L A FS L
Sbjct: 21 FVAHVESTCVLDDAGTPQDFTYCVSFNKDLLACWDPDVGKIVPCEFGVLYPWAENFSRIL 80
Query: 483 NQQEKLLQRLSNGLQNCATHTQPFWKSLTHRTQPPSVQVAKTTPFNTRESVMLACYVWGF 662
N++E LLQRL NGL +CA+HTQPFW +LTHRT+ PSV+VA+TTPFNTRE VMLACYVWGF
Sbjct: 81 NKEESLLQRLQNGLLDCASHTQPFWNALTHRTRAPSVRVAQTTPFNTREPVMLACYVWGF 140
Query: 663 YPADVIITWRKNGQPVLPHGKAHMITQPNGDWTYQTVSHLATTPSYGDTYTCVVEHIGVP 842
YPADV ITW KNGQ V H QPNGDWTYQTVS+LA TPSYGD YTCVV+H G
Sbjct: 141 YPADVTITWMKNGQLVPSHSNKEKTAQPNGDWTYQTVSYLALTPSYGDVYTCVVQHSGTS 200
Query: 843 EPILQDWTSGLSPVQTVKISVSVATXXXXXXXXXXXXXXCQRSVAPGYIFLPGTTYPEGQ 1022
EPI DWT GLSP+QTVK+SVS AT ++S + Y L G+TYPEGQ
Sbjct: 201 EPIRGDWTPGLSPIQTVKVSVSAATLGLGFIIFCVGFFRWRKSHSSSYTPLSGSTYPEGQ 260
Query: 1023 H 1025
H
Sbjct: 261 H 261
>ref|NP_996988.2| histocompatibility 2, class II antigen A, beta 1 precursor [Mus
musculus].
Length = 265
Score = 73.2 bits (178), Expect = 4e-13
Identities = 44/145 (30%), Positives = 66/145 (45%), Gaps = 2/145 (1%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQ--PFWKSLTHRTQPPSVQVAKT 608
E A+ L + Y N Q ++L+R L H P + R + P+V ++ +
Sbjct: 73 EHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSLRRLEQPNVVISLS 132
Query: 609 TPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPNGDWTYQTVSHLAT 788
L C V FYPA + + W +NGQ + + + NGDWT+Q + L
Sbjct: 133 RTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIR-NGDWTFQVLVMLEM 191
Query: 789 TPSYGDTYTCVVEHIGVPEPILQDW 863
TP G+ YTC VEH + PI +W
Sbjct: 192 TPRRGEVYTCHVEHPSLKSPITVEW 216
>ref|NP_034512.2| H-2 class II histocompatibility antigen, I-E beta chain precursor
[Mus musculus].
Length = 264
Score = 72.4 bits (176), Expect = 7e-13
Identities = 46/157 (29%), Positives = 69/157 (43%), Gaps = 1/157 (0%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFW-KSLTHRTQPPSVQVAKTT 611
EF A+ L + N Q + L++ + H K L R P+V V T
Sbjct: 73 EFRAVTELGRPDAENWNSQPEFLEQKRAEVDTVCRHNYEISDKFLVRRRVEPTVTVYPTK 132
Query: 612 PFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPNGDWTYQTVSHLATT 791
+L C V FYP ++ + W +NG+ G NGDWT+QT+ L T
Sbjct: 133 TQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKT-GIVSTGLVRNGDWTFQTLVMLETV 191
Query: 792 PSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
P G+ YTC VEH + +P+ +W + + Q +S
Sbjct: 192 PQSGEVYTCQVEHPSLTDPVTVEWKAQSTSAQNKMLS 228
>ref|NP_034519.2| histocompatibility 2, O region beta locus [Mus musculus].
Length = 271
Score = 71.6 bits (174), Expect = 1e-12
Identities = 38/98 (38%), Positives = 54/98 (55%), Gaps = 1/98 (1%)
Frame = +3
Query: 573 RTQPPSVQV-AKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPN 749
R PP V V + TP + +++L C V GFYP D+ + W +NGQ + + + N
Sbjct: 119 RNVPPEVTVYPERTPLLQQHNLLL-CSVTGFYPGDISVKWFRNGQEERSGVMSTGLVR-N 176
Query: 750 GDWTYQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDW 863
GDWT+QT L P GD Y+C+VEH G+ P+ W
Sbjct: 177 GDWTFQTTVMLEMIPELGDIYSCLVEHPGLLRPVSVAW 214
>ref|XP_003086980.1| PREDICTED: h-2 class I histocompatibility antigen, L-D alpha
chain-like [Mus musculus].
Length = 382
Score = 71.2 bits (173), Expect = 2e-12
Identities = 51/176 (28%), Positives = 77/176 (43%)
Frame = +3
Query: 372 ISFNKDLLTCWDPQETRMVPCEFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQP 551
I+ N+DL T ++ + A Y+ Y+ + + +Q L L+
Sbjct: 162 IALNEDLKTWTAKDVAALITRRKWEQDGAAEYYKAYM--EGECVQSLRRYLE-------- 211
Query: 552 FWKSLTHRTQPPSVQVAKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAH 731
K + RT PP V T + V L C+ GFYPAD+ +TW+ NG+ L
Sbjct: 212 LGKEMLLRTDPPKAHV--THHPRSEGDVTLRCWALGFYPADITLTWQLNGEE-LTQDMEL 268
Query: 732 MITQPNGDWTYQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKI 899
+ T+P GD T+Q + + YTC V H G+PEP+ W S V + I
Sbjct: 269 VETRPAGDGTFQKWAAVVVPLGKEQNYTCHVHHEGLPEPLTLRWEPPPSTVSNMVI 324
>ref|XP_997416.3| PREDICTED: h-2 class I histocompatibility antigen, L-D alpha
chain-like isoform 3 [Mus musculus].
Length = 373
Score = 71.2 bits (173), Expect = 2e-12
Identities = 51/176 (28%), Positives = 77/176 (43%)
Frame = +3
Query: 372 ISFNKDLLTCWDPQETRMVPCEFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQP 551
I+ N+DL T ++ + A Y+ Y+ + + +Q L L+
Sbjct: 153 IALNEDLKTWTAKDVAALITRRKWEQDGAAEYYKAYM--EGECVQSLRRYLE-------- 202
Query: 552 FWKSLTHRTQPPSVQVAKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAH 731
K + RT PP V T + V L C+ GFYPAD+ +TW+ NG+ L
Sbjct: 203 LGKEMLLRTDPPKAHV--THHPRSEGDVTLRCWALGFYPADITLTWQLNGEE-LTQDMEL 259
Query: 732 MITQPNGDWTYQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKI 899
+ T+P GD T+Q + + YTC V H G+PEP+ W S V + I
Sbjct: 260 VETRPAGDGTFQKWAAVVVPLGKEQNYTCHVHHEGLPEPLTLRWEPPPSTVSNMVI 315
>ref|XP_003086979.1| PREDICTED: h-2 class I histocompatibility antigen, L-D alpha
chain-like [Mus musculus].
Length = 354
Score = 71.2 bits (173), Expect = 2e-12
Identities = 51/176 (28%), Positives = 77/176 (43%)
Frame = +3
Query: 372 ISFNKDLLTCWDPQETRMVPCEFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQP 551
I+ N+DL T ++ + A Y+ Y+ + + +Q L L+
Sbjct: 134 IALNEDLKTWTAKDVAALITRRKWEQDGAAEYYKAYM--EGECVQSLRRYLE-------- 183
Query: 552 FWKSLTHRTQPPSVQVAKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAH 731
K + RT PP V T + V L C+ GFYPAD+ +TW+ NG+ L
Sbjct: 184 LGKEMLLRTDPPKAHV--THHPRSEGDVTLRCWALGFYPADITLTWQLNGEE-LTQDMEL 240
Query: 732 MITQPNGDWTYQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKI 899
+ T+P GD T+Q + + YTC V H G+PEP+ W S V + I
Sbjct: 241 VETRPAGDGTFQKWAAVVVPLGKEQNYTCHVHHEGLPEPLTLRWEPPPSTVSNMVI 296
>ref|NP_038847.1| histocompatibility 2, M region locus 3 [Mus musculus].
Length = 336
Score = 70.1 bits (170), Expect = 4e-12
Identities = 50/155 (32%), Positives = 71/155 (45%), Gaps = 2/155 (1%)
Frame = +3
Query: 459 ATYFSVYLNQQ--EKLLQRLSNGLQNCATHTQPFWKSLTHRTQPPSVQVAKTTPFNTRES 632
A YF Y+ + E L + L NG K + R PP VA +
Sbjct: 177 AEYFRAYVEGECLELLHRFLRNG------------KEILQRADPPKAHVAHHP--RPKGD 222
Query: 633 VMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPNGDWTYQTVSHLATTPSYGDTY 812
V L C+ GFYPAD+ +TW+K+ + L + T+P+GD T+Q + + Y
Sbjct: 223 VTLRCWALGFYPADITLTWQKDEED-LTQDMELVETRPSGDGTFQKWAAVVVPSGEEQRY 281
Query: 813 TCVVEHIGVPEPILQDWTSGLSPVQTVKISVSVAT 917
TC V H G+ EP+ W G S +V I V VA+
Sbjct: 282 TCYVHHEGLTEPLALKW--GRSSQSSVVIMVIVAS 314
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: 50,765,010
Number of extensions: 1556979
Number of successful extensions: 5222
Number of sequences better than 1.0e-05: 111
Number of HSP's gapped: 5087
Number of HSP's successfully gapped: 113
Length of query: 433
Length of database: 15,617,559
Length adjustment: 104
Effective length of query: 329
Effective length of database: 12,493,815
Effective search space: 4110465135
Effective search space used: 4110465135
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-002406
(1300 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_001107179.1| MHC class II, DM beta [Sus scrofa]. 501 e-142
Alignment gi|XP_003128397.1| PREDICTED: DLA class II histocompatibility a... 84 2e-16
Alignment gi|XP_003128372.1| PREDICTED: DLA class II histocompatibility a... 82 5e-16
Alignment gi|NP_001107167.1| MHC class II histocompatibility antigen SLA-... 81 1e-15
Alignment gi|NP_001107166.1| SLA class II histocompatibility antigen, DQ ... 74 2e-13
Alignment gi|XP_003128376.1| PREDICTED: HLA class II histocompatibility a... 70 3e-12
Alignment gi|XP_003356639.1| PREDICTED: patr class I histocompatibility a... 70 3e-12
Alignment gi|XP_003128290.1| PREDICTED: patr class I histocompatibility a... 70 3e-12
Alignment gi|NP_001107536.2| MHC class II, DO beta [Sus scrofa]. 70 3e-12
Alignment gi|NP_001107528.1| MHC class I antigen 5 [Sus scrofa]. 69 4e-12
>ref|NP_001107179.1| MHC class II, DM beta [Sus scrofa].
Length = 272
Score = 501 bits (1291), Expect = e-142
Identities = 241/272 (88%), Positives = 241/272 (88%)
Frame = +3
Query: 216 MPCISPEQSMSAXXXXXXXXXXXXXXXXXFVAHVESTCLLDDEGTPQDFTYCISFNKDLL 395
MPCISPEQSMSA FVAHVESTCLLDDEGTPQDFTYCISFNKDLL
Sbjct: 1 MPCISPEQSMSALLQLLLGLSLGCTGAGGFVAHVESTCLLDDEGTPQDFTYCISFNKDLL 60
Query: 396 TCWDPQETRMVPCEFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFWKSLTHR 575
TCWDPQETRMVPCEFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFWKSLTHR
Sbjct: 61 TCWDPQETRMVPCEFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFWKSLTHR 120
Query: 576 TQPPSVQVAKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPNGD 755
TQPPSVQVAKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPNGD
Sbjct: 121 TQPPSVQVAKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPNGD 180
Query: 756 WTYQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKISVSVATXXXXXX 935
WTYQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKISVSVAT
Sbjct: 181 WTYQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKISVSVATLGLGLI 240
Query: 936 XXXXXXXXCQRSVAPGYIFLPGTTYPEGQHIS 1031
CQRSVAPGYIFLPGTTYPEGQHIS
Sbjct: 241 IFSLGLLSCQRSVAPGYIFLPGTTYPEGQHIS 272
>ref|XP_003128397.1| PREDICTED: DLA class II histocompatibility antigen, DR-1 beta
chain-like [Sus scrofa].
Length = 321
Score = 84.0 bits (206), Expect = 2e-16
Identities = 54/165 (32%), Positives = 79/165 (47%), Gaps = 3/165 (1%)
Frame = +3
Query: 378 FNKDLLTCWDPQETRMVPCEFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFW 557
+N+D L +D E+ A+ + + Y N Q+ +L+R+ + F+
Sbjct: 61 YNRDELVRFDSDVG-----EYRAVTPMGQPAAKYWNSQKDILKRVRAAVDTFCRSNYEFF 115
Query: 558 KSLT-HRTQPPSVQV--AKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKA 728
+S T R P+V V AKT P +L C V GFYP V + W +NGQ G
Sbjct: 116 ESCTVQRRVKPTVTVYPAKTQPLQHHN--LLVCSVTGFYPGHVEVRWFRNGQEEAA-GVV 172
Query: 729 HMITQPNGDWTYQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDW 863
PNGDWT+QT+ L T P G+ Y+C VEH + P+ +W
Sbjct: 173 STGLIPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 217
>ref|XP_003128372.1| PREDICTED: DLA class II histocompatibility antigen, DR-1 beta
chain-like [Sus scrofa].
Length = 261
Score = 82.4 bits (202), Expect = 5e-16
Identities = 53/159 (33%), Positives = 74/159 (46%), Gaps = 3/159 (1%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQN-CATHTQPFWKSLTHRTQPPSVQV--AK 605
EF AL L + Y NQQ+ L+++ + C ++ + R P V V AK
Sbjct: 70 EFRALTELGRPDAEYWNQQKGFLEQMRTKVDTMCRSNYLGIGSLMMQRRVKPRVTVYPAK 129
Query: 606 TTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPNGDWTYQTVSHLA 785
T P +L C V GFYP V + W +NGQ G PNGDWT+QT+ L
Sbjct: 130 TQPLQHHN--LLVCSVTGFYPGHVEVRWFRNGQEEAA-GVVSTGLIPNGDWTFQTMVMLE 186
Query: 786 TTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
T P G+ Y+C VEH + P+ +W + Q +S
Sbjct: 187 TVPQSGEVYSCRVEHPSLTSPVTVEWRAWSESAQGKMLS 225
>ref|NP_001107167.1| MHC class II histocompatibility antigen SLA-DRB1 [Sus scrofa].
Length = 266
Score = 81.3 bits (199), Expect = 1e-15
Identities = 50/146 (34%), Positives = 70/146 (47%), Gaps = 3/146 (2%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFWKS-LTHRTQPPSVQV--AK 605
E+ A+ L + Y N Q+ LL+++ + H + L R P+V V AK
Sbjct: 75 EYRAVTELGRPDAKYWNSQKDLLEQMRAAVDTYCRHNYRILDTFLVPRRAEPTVTVYPAK 134
Query: 606 TTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPNGDWTYQTVSHLA 785
T P +L C V GFYP V + W +NGQ G PNGDWT+QT+ L
Sbjct: 135 TQPLQHHN--LLVCSVTGFYPGHVEVRWFRNGQEEAA-GVVSTGLIPNGDWTFQTMVMLE 191
Query: 786 TTPSYGDTYTCVVEHIGVPEPILQDW 863
T P G+ Y+C VEH + P+ +W
Sbjct: 192 TVPQSGEVYSCRVEHPSLTSPVTVEW 217
>ref|NP_001107166.1| SLA class II histocompatibility antigen, DQ haplotype C beta chain
precursor [Sus scrofa].
Length = 261
Score = 73.9 bits (180), Expect = 2e-13
Identities = 47/160 (29%), Positives = 73/160 (45%), Gaps = 4/160 (2%)
Frame = +3
Query: 435 EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFWKSLT-HRTQPPSVQVAKTT 611
EF A+ L + N Q+ +L+++ + H + T R P+V ++ +
Sbjct: 78 EFRAVTPLGRPEADSWNSQKDVLEQMRAEVDRVCKHNYQIEEGTTLQRRVQPTVTISPSK 137
Query: 612 PFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQP---NGDWTYQTVSHL 782
+L C V FYP+ V + W +NGQ A +++ P NGDWTYQ + L
Sbjct: 138 AEALNHHNLLVCAVTDFYPSQVKVQWFRNGQ----EETAGVVSTPLIRNGDWTYQVLVML 193
Query: 783 ATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 902
GD YTC VEH + PIL +W + Q+ +S
Sbjct: 194 EMNLQRGDVYTCRVEHSSLQNPILVEWRAQSESAQSKMLS 233
>ref|XP_003128376.1| PREDICTED: HLA class II histocompatibility antigen, DO beta
chain-like [Sus scrofa].
Length = 277
Score = 70.1 bits (170), Expect = 3e-12
Identities = 41/115 (35%), Positives = 58/115 (50%)
Frame = +3
Query: 570 HRTQPPSVQVAKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPN 749
H + PS+Q+ +L C V GFYP + I W +NGQ A + + N
Sbjct: 141 HPERTPSLQLRN----------LLLCSVTGFYPGAIEIRWFRNGQEQREGVLATGLVR-N 189
Query: 750 GDWTYQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKISVSVA 914
GDWT+QTV L TP GD YTC+V+H + P+ +W + S K+ + VA
Sbjct: 190 GDWTFQTVVMLEMTPELGDVYTCLVDHPSLLSPVSVEWRA-QSDCSWTKLLIGVA 243
>ref|XP_003356639.1| PREDICTED: patr class I histocompatibility antigen, A-126 alpha
chain-like [Sus scrofa].
Length = 361
Score = 69.7 bits (169), Expect = 3e-12
Identities = 38/118 (32%), Positives = 59/118 (50%)
Frame = +3
Query: 558 KSLTHRTQPPSVQVAKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMI 737
K R +PP V + + V L C+ GFYP ++ +TW++ GQ + +
Sbjct: 197 KDTLQRAEPPKTHVTRHPSSDL--GVTLRCWALGFYPKEISLTWQREGQDQSQDMEL-VE 253
Query: 738 TQPNGDWTYQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKISVSV 911
T+P+GD T+Q + L P +YTC V+H G+ EP+ W +PV V I V +
Sbjct: 254 TRPSGDGTFQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRWDPPQTPVPIVGIIVGL 311
>ref|XP_003128290.1| PREDICTED: patr class I histocompatibility antigen, A-126 alpha
chain-like [Sus scrofa].
Length = 361
Score = 69.7 bits (169), Expect = 3e-12
Identities = 38/118 (32%), Positives = 58/118 (49%)
Frame = +3
Query: 558 KSLTHRTQPPSVQVAKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMI 737
K R +PP V + + V L C+ GFYP ++ +TW++ GQ + +
Sbjct: 197 KDTLQRAEPPKTHVTRHPSSDL--GVTLRCWALGFYPKEISLTWQREGQDQSQDMEL-VE 253
Query: 738 TQPNGDWTYQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKISVSV 911
T+P+GD T+Q + L P +YTC V+H G+ EP+ W PV V I V +
Sbjct: 254 TRPSGDGTFQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRWDPAQPPVPIVGIIVGL 311
>ref|NP_001107536.2| MHC class II, DO beta [Sus scrofa].
Length = 277
Score = 69.7 bits (169), Expect = 3e-12
Identities = 41/115 (35%), Positives = 58/115 (50%)
Frame = +3
Query: 570 HRTQPPSVQVAKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPN 749
H + PS+Q+ +L C V GFYP + I W +NGQ A + + N
Sbjct: 141 HPERTPSLQLRN----------LLLCSVTGFYPGAIEIRWFRNGQEQREGVLATGLIR-N 189
Query: 750 GDWTYQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKISVSVA 914
GDWT+QTV L TP GD YTC+V+H + P+ +W + S K+ + VA
Sbjct: 190 GDWTFQTVVMLEMTPELGDVYTCLVDHPSLLSPVSVEWRA-QSDCSWTKLLIGVA 243
>ref|NP_001107528.1| MHC class I antigen 5 [Sus scrofa].
Length = 361
Score = 69.3 bits (168), Expect = 4e-12
Identities = 37/113 (32%), Positives = 58/113 (51%)
Frame = +3
Query: 573 RTQPPSVQVAKTTPFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQPNG 752
R +PP V + + V L C+ GFYP ++ +TW++ GQ + + T+P+G
Sbjct: 202 RAEPPKTHVTRHPSSDL--GVTLRCWALGFYPKEISLTWQREGQDQSQDMEL-VETRPSG 258
Query: 753 DWTYQTVSHLATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKISVSV 911
D T+Q + L P +YTC V+H G+ EP+ W +PV V I V +
Sbjct: 259 DGTFQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRWDPAQTPVPMVGIIVGL 311
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: 37,782,977
Number of extensions: 1187969
Number of successful extensions: 4019
Number of sequences better than 1.0e-05: 31
Number of HSP's gapped: 3974
Number of HSP's successfully gapped: 31
Length of query: 433
Length of database: 11,343,932
Length adjustment: 102
Effective length of query: 331
Effective length of database: 8,804,438
Effective search space: 2914268978
Effective search space used: 2914268978
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-002406
(1300 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 593 e-166
>Sscrofa_Chr07
|| Length = 134764511
Score = 593 bits (299), Expect = e-166
Identities = 299/299 (100%)
Strand = Plus / Minus
Query: 1 aattctcagtctgggacgcggattgaggcgagtttgtaagggaccagtttagtatcaaag 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29491710 aattctcagtctgggacgcggattgaggcgagtttgtaagggaccagtttagtatcaaag 29491651
Query: 61 ggcttagtagctccaaatcactcattcagagagcaccaaaggaccaggacaacaccatat 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29491650 ggcttagtagctccaaatcactcattcagagagcaccaaaggaccaggacaacaccatat 29491591
Query: 121 tcccgctcagtgtttggagatcatctatccaggctgggacttctgggggcaggcaaggac 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29491590 tcccgctcagtgtttggagatcatctatccaggctgggacttctgggggcaggcaaggac 29491531
Query: 181 ccagggcccctggaagagcgggtccaggggaccggatgccctgtatctccccggagcaga 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29491530 ccagggcccctggaagagcgggtccaggggaccggatgccctgtatctccccggagcaga 29491471
Query: 241 gcatgagtgccctcctgcagctgctcctgggcctcagcctgggctgcaccggagcaggt 299
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29491470 gcatgagtgccctcctgcagctgctcctgggcctcagcctgggctgcaccggagcaggt 29491412
Score = 565 bits (285), Expect = e-158
Identities = 285/285 (100%)
Strand = Plus / Minus
Query: 1016 aggtcagcacatttcctagaggcggagtcctgccacttccactccctgtgagaaggcaat 1075
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29486263 aggtcagcacatttcctagaggcggagtcctgccacttccactccctgtgagaaggcaat 29486204
Query: 1076 ttggtctcgtatggatgctgctgtgcccttggctgacatcctcagaccctccacagtttc 1135
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29486203 ttggtctcgtatggatgctgctgtgcccttggctgacatcctcagaccctccacagtttc 29486144
Query: 1136 ttgggtcctctggtttctctcttcagttctttaaaatttgcagttccccctatgtaaacc 1195
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29486143 ttgggtcctctggtttctctcttcagttctttaaaatttgcagttccccctatgtaaacc 29486084
Query: 1196 ttaaccacttgcgggaaccattcctgggaatattctgtgacctagttattgtacatagct 1255
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29486083 ttaaccacttgcgggaaccattcctgggaatattctgtgacctagttattgtacatagct 29486024
Query: 1256 ggagcccaaggctatgcacctgaggggaatatcatttggggagga 1300
|||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29486023 ggagcccaaggctatgcacctgaggggaatatcatttggggagga 29485979
Score = 565 bits (285), Expect = e-158
Identities = 285/285 (100%)
Strand = Plus / Minus
Query: 580 agccgccgtctgtgcaagtggccaaaaccactccttttaacacgagggagtctgtgatgc 639
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29489143 agccgccgtctgtgcaagtggccaaaaccactccttttaacacgagggagtctgtgatgc 29489084
Query: 640 tggcctgctatgtgtggggcttctatccagctgatgtgatcatcacgtggaggaagaatg 699
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29489083 tggcctgctatgtgtggggcttctatccagctgatgtgatcatcacgtggaggaagaatg 29489024
Query: 700 ggcagccagtccttcctcatggcaaggcccatatgatcacccagcccaacggagactgga 759
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29489023 ggcagccagtccttcctcatggcaaggcccatatgatcacccagcccaacggagactgga 29488964
Query: 760 cataccagaccgtctcccatttggctacaaccccctcttacggggacacctacacctgtg 819
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29488963 cataccagaccgtctcccatttggctacaaccccctcttacggggacacctacacctgtg 29488904
Query: 820 tggtggagcacattggggttcctgagcccatccttcaggactgga 864
|||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29488903 tggtggagcacattggggttcctgagcccatccttcaggactgga 29488859
Score = 563 bits (284), Expect = e-158
Identities = 284/284 (100%)
Strand = Plus / Minus
Query: 296 aggtggctttgtggcccacgtggaaagcacctgtctgttggatgatgaggggactccaca 355
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29490741 aggtggctttgtggcccacgtggaaagcacctgtctgttggatgatgaggggactccaca 29490682
Query: 356 ggatttcacgtattgcatctccttcaacaaggacttgctgacctgttgggatccccagga 415
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29490681 ggatttcacgtattgcatctccttcaacaaggacttgctgacctgttgggatccccagga 29490622
Query: 416 gacccgtatggtcccttgtgaatttggagcgctgaatgcgttggccacatatttctctgt 475
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29490621 gacccgtatggtcccttgtgaatttggagcgctgaatgcgttggccacatatttctctgt 29490562
Query: 476 ttacctcaaccagcaggaaaaactgctccagcgcttgtccaatgggctccagaactgtgc 535
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29490561 ttacctcaaccagcaggaaaaactgctccagcgcttgtccaatgggctccagaactgtgc 29490502
Query: 536 cacacacacccaacccttctggaaatcactgacccacaggacac 579
||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29490501 cacacacacccaacccttctggaaatcactgacccacaggacac 29490458
Score = 234 bits (118), Expect = 1e-58
Identities = 118/118 (100%)
Strand = Plus / Minus
Query: 865 cttctgggctgtccccagtgcagacagtgaagatttctgtgtctgtggcgactctgggcc 924
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29486911 cttctgggctgtccccagtgcagacagtgaagatttctgtgtctgtggcgactctgggcc 29486852
Query: 925 tgggcctcatcatcttctcccttggtttgctcagctgccagagatctgttgccccagg 982
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29486851 tgggcctcatcatcttctcccttggtttgctcagctgccagagatctgttgccccagg 29486794
Score = 79.8 bits (40), Expect = 3e-12
Identities = 40/40 (100%)
Strand = Plus / Minus
Query: 980 aggctacattttcctcccggggaccacttatccagaaggt 1019
||||||||||||||||||||||||||||||||||||||||
Sbjct: 29486644 aggctacattttcctcccggggaccacttatccagaaggt 29486605
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: 40,698,028
Number of extensions: 245
Number of successful extensions: 245
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 245
Number of HSP's successfully gapped: 6
Length of query: 1300
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 1279
Effective length of database: 2,808,413,156
Effective search space: 3591960426524
Effective search space used: 3591960426524
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)