Search to RefSeqBP
BLASTX 2.2.10 [Oct-19-2004]
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= LVR01_0002_B02
(1220 letters)
Database: RefSeqBP
33,508 sequences; 16,112,626 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001029840.2| MHC class II antigen [Bos taurus] 387 e-107
Alignment gi|NP_001012694.1| major histocompatibility complex, class II, ... 378 e-105
Alignment gi|NP_001012697.1| major histocompatibility complex, class II, ... 297 1e-80
Alignment gi|NP_001012698.2| major histocompatibility complex, class II, ... 288 6e-78
Alignment gi|XP_582099.2| PREDICTED: similar to major histocompatibility ... 258 7e-69
Alignment gi|NP_001013618.1| major histocompatibility complex, class II, ... 255 6e-68
Alignment gi|XP_876139.1| PREDICTED: similar to H-2 class II histocompati... 240 2e-63
Alignment gi|XP_874766.1| PREDICTED: similar to HLA class II histocompati... 153 3e-37
Alignment gi|NP_001029503.1| hypothetical protein LOC508800 [Bos taurus] 75 1e-13
Alignment gi|NP_001012399.1| hemochromatosis [Bos taurus] 71 2e-12
>ref|NP_001029840.2| MHC class II antigen [Bos taurus]
Length = 261
Score = 387 bits (994), Expect = e-107
Identities = 191/261 (73%), Positives = 212/261 (81%)
Frame = +2
Query: 53 MSGMVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVA 232
MSGMVAL +PRGLWTA V + LV+L P AEGRDSP+DFV QFK CYF NGT+RVR V
Sbjct: 1 MSGMVALWIPRGLWTAVVMVTLVMLSTPGAEGRDSPKDFVVQFKGLCYFTNGTERVRYVT 60
Query: 233 RYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEG 412
RYIYNQEE +RFDSD YRA+TPLGRP+A+ WN QKD LEQTRAE DTVC+HNYQ E
Sbjct: 61 RYIYNQEEYVRFDSDWDLYRALTPLGRPDAEYWNSQKDFLEQTRAEADTVCRHNYQAELI 120
Query: 413 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 592
T+LQRRV+PTVTISPS+ EALNHHNLLVC+VTDFYPSQ+KV+WFRN +EETAGVVSTPLI
Sbjct: 121 TSLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPSQIKVRWFRNDREETAGVVSTPLI 180
Query: 593 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 772
RNGDWT+Q+LVMLEM QRGDVYTC VEH SLQSPI+VEWRAQSESAQSKMLS
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPIMVEWRAQSESAQSKMLSGVGGFVL 240
Query: 773 XXXXXXXXXXXRHRSQKGLVR 835
HRSQKGL+R
Sbjct: 241 GLIFLGLGLIIHHRSQKGLMR 261
>ref|NP_001012694.1| major histocompatibility complex, class II, DQ beta [Bos taurus]
Length = 261
Score = 378 bits (971), Expect = e-105
Identities = 187/260 (71%), Positives = 209/260 (80%)
Frame = +2
Query: 53 MSGMVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVA 232
MSGMVALR+PRGLWTAAV + L VL P AEGRDSPQD V F +CYF NGT+RVR V
Sbjct: 1 MSGMVALRIPRGLWTAAVMVTLAVLSTPGAEGRDSPQDTVVHFMGQCYFTNGTERVRYVT 60
Query: 233 RYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEG 412
RYIYNQEE +DSDVGEYRAVT LGR A+ WN QKD+LEQTRAELDTVC+HNYQ+E
Sbjct: 61 RYIYNQEETAYYDSDVGEYRAVTQLGRTLAEYWNSQKDILEQTRAELDTVCRHNYQLEVI 120
Query: 413 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 592
T+LQR+V+PTVTIS S+ EALNHHNLLVC+VTDFYP Q+KV+WF+NG+EETAG+VSTPLI
Sbjct: 121 TSLQRQVEPTVTISLSRTEALNHHNLLVCSVTDFYPGQIKVRWFQNGKEETAGIVSTPLI 180
Query: 593 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 772
RNGDWT+Q+LVMLEM +RGDVYTC VEH SLQSPI VEWRAQSESAQSKMLS
Sbjct: 181 RNGDWTFQILVMLEMTPKRGDVYTCHVEHPSLQSPISVEWRAQSESAQSKMLSGVGGFVL 240
Query: 773 XXXXXXXXXXXRHRSQKGLV 832
R RSQKGLV
Sbjct: 241 GLIFLGLGLIVRRRSQKGLV 260
>ref|NP_001012697.1| major histocompatibility complex, class II, DY beta [Bos taurus]
Length = 259
Score = 297 bits (761), Expect = 1e-80
Identities = 149/227 (65%), Positives = 177/227 (77%), Gaps = 2/227 (0%)
Frame = +2
Query: 77 LPRGLWTAAVTMMLV--VLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYIYNQ 250
+PR T A +M V VL P A RD+P++FV+QFK CYF NGT+ VRLVAR IYN+
Sbjct: 5 IPRNPGTVAGMVMAVFLVLRIPEAHCRDAPKNFVYQFKGMCYFTNGTEHVRLVARQIYNK 64
Query: 251 EELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRR 430
EE+L FDSD+GE+ AVT LGR A+ WN QKD+L + RA +DT+C+HNY+ G T+QRR
Sbjct: 65 EEILHFDSDLGEFVAVTELGRVCAEIWNTQKDLLAEFRAYVDTLCRHNYKETAGFTVQRR 124
Query: 431 VQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWT 610
V+PTVT+SP+ EALNHHNLLVC+VTDFYP QVKV+WFRN QE+TAGV TPL +NGDWT
Sbjct: 125 VEPTVTVSPASTEALNHHNLLVCSVTDFYPRQVKVKWFRNQQEQTAGVGFTPLTQNGDWT 184
Query: 611 YQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 751
YQ+ VMLE Q GDVY C V+H SLQSPI VEWRAQSESAQSKM S
Sbjct: 185 YQIHVMLETVPQLGDVYVCHVDHPSLQSPITVEWRAQSESAQSKMQS 231
>ref|NP_001012698.2| major histocompatibility complex, class II, DRB3 [Bos taurus]
Length = 266
Score = 288 bits (737), Expect = 6e-78
Identities = 141/255 (55%), Positives = 177/255 (69%)
Frame = +2
Query: 62 MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
MV L G W AA+ +ML+VL P+A R+ F+ +K EC+FFNGT+RVR + R+
Sbjct: 1 MVCLYFSGGSWMAALIVMLMVLCPPLAWAREIQPHFLEYYKGECHFFNGTERVRFLDRHF 60
Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
YN EE +RFDSD GE+RAVT LGRP A+ WN QKD LEQ RAE+D VC+HNY E T+
Sbjct: 61 YNGEEFVRFDSDWGEFRAVTELGRPAAEHWNSQKDFLEQKRAEVDRVCRHNYGGVESFTV 120
Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
QRRV+PTVT+ P+K + L HHNLLVC+V FYP ++V+WFRNG EE AGV+ST LI+NG
Sbjct: 121 QRRVEPTVTVYPAKTQPLQHHNLLVCSVNGFYPGHIEVRWFRNGHEEEAGVISTGLIQNG 180
Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 781
DWT+Q +VMLE Q G+VYTC+V+H SPI VEWRA+S+SAQSKM+S
Sbjct: 181 DWTFQTMVMLETVPQSGEVYTCQVDHPKRTSPITVEWRARSDSAQSKMMSGVGGFVLGLL 240
Query: 782 XXXXXXXXRHRSQKG 826
R+QKG
Sbjct: 241 FLAVGLFIYFRNQKG 255
>ref|XP_582099.2| PREDICTED: similar to major histocompatibility complex, class II,
DR beta 5 precursor [Bos taurus]
Length = 255
Score = 258 bits (659), Expect = 7e-69
Identities = 122/218 (55%), Positives = 161/218 (73%)
Frame = +2
Query: 98 AAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYIYNQEELLRFDSD 277
AA+ ++L+VL P + R++ F+ QFK EC F NG +R+R ARYIYN +E + FDSD
Sbjct: 2 AALAVLLMVLSLPFSWARETQPHFIHQFKGECRFSNGLERMRFFARYIYNTQEDVHFDSD 61
Query: 278 VGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISP 457
VGE+ A+T LGR +A+ WN QKD +EQ RA++DT+C+ NYQ QRRV+PTVT+ P
Sbjct: 62 VGEFTALTELGRLDAEYWNQQKDFMEQMRAKVDTLCRSNYQGIGSFLRQRRVEPTVTVYP 121
Query: 458 SKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEM 637
+K + L HHNLLVC+V FYP ++V+WF N EE AGV+ST LI+NGDWT+Q +VMLE
Sbjct: 122 AKTQPLQHHNLLVCSVNGFYPGHIEVRWFWNSHEEEAGVISTGLIQNGDWTFQTMVMLET 181
Query: 638 NLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 751
Q G+VYTC+VEH S SP+ VEWRAQS+SAQ K++S
Sbjct: 182 VPQSGEVYTCQVEHPSRTSPLTVEWRAQSDSAQRKLMS 219
>ref|NP_001013618.1| major histocompatibility complex, class II, DO beta [Bos taurus]
Length = 271
Score = 255 bits (651), Expect = 6e-68
Identities = 118/220 (53%), Positives = 156/220 (70%)
Frame = +2
Query: 92 WTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYIYNQEELLRFD 271
W + L A V +GRDSP+DFV Q K +CYF NGT++VR V R+I+N E+ RFD
Sbjct: 8 WVVTFLSTALRLDASVTQGRDSPEDFVTQAKADCYFTNGTEKVRFVVRFIFNLEDYARFD 67
Query: 272 SDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTI 451
SD+G + A+T LG+P+A+ WN + D+L ++RA +D +C+ NY + T+ RRVQP VT+
Sbjct: 68 SDLGMFVALTELGKPDAERWNNRPDILARSRASVDMLCRRNYYLGAPFTVGRRVQPEVTV 127
Query: 452 SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVML 631
P K AL H NLL+C VT FYP +KV WFRNGQE+ G++ST LIRNGDWT+Q+ VML
Sbjct: 128 YPEKTPALQHRNLLLCLVTGFYPGDIKVTWFRNGQEQREGIMSTGLIRNGDWTFQMTVML 187
Query: 632 EMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 751
M + G+VYTC V+H SL SP+ VEWRAQSE + K+LS
Sbjct: 188 AMTPELGEVYTCLVDHPSLLSPVSVEWRAQSEYSWRKILS 227
>ref|XP_876139.1| PREDICTED: similar to H-2 class II histocompatibility antigen, I-E
beta chain precursor [Bos taurus]
Length = 269
Score = 240 bits (612), Expect = 2e-63
Identities = 115/192 (59%), Positives = 141/192 (73%)
Frame = +2
Query: 176 QFKFECYFFNGTQRVRLVARYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLE 355
Q K EC+F NGTQ+VR + RYIYN+EE ++FDS VGEYRA T +GRP A+ WN L+
Sbjct: 3 QGKSECHFSNGTQQVRFLDRYIYNREEQVQFDSLVGEYRARTEMGRPAAERWNRWPQALQ 62
Query: 356 QTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKV 535
+ RA + C NY+ T+QRRVQPTVT+ P K+ L HHNLLVC+V FYP ++V
Sbjct: 63 RARAAVHAYCASNYEFFASRTVQRRVQPTVTVYPVKSRPLWHHNLLVCSVNGFYPGHIEV 122
Query: 536 QWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWR 715
+WFRNGQEE AGVVST LI NGDWT+Q++VMLE+ Q G+VY C VEH S SP+ VEWR
Sbjct: 123 RWFRNGQEEEAGVVSTGLIPNGDWTFQIMVMLEIVPQGGEVYACHVEHPSRTSPVTVEWR 182
Query: 716 AQSESAQSKMLS 751
AQ ES+Q KMLS
Sbjct: 183 AQDESSQEKMLS 194
>ref|XP_874766.1| PREDICTED: similar to HLA class II histocompatibility antigen,
DRB1-7 beta chain precursor (MHC class I antigen DRB1*7)
(DR-7) (DR7) [Bos taurus]
Length = 347
Score = 153 bits (386), Expect = 3e-37
Identities = 73/137 (53%), Positives = 96/137 (70%)
Frame = +2
Query: 416 TLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIR 595
TLQ++V+PTVT+ P+K + L H++LLVC+V FY V+V+WF GQEE AGV+ST LI+
Sbjct: 90 TLQKKVEPTVTVYPAKTQPLQHNHLLVCSVNGFYLGHVEVRWFWKGQEEEAGVISTGLIQ 149
Query: 596 NGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXX 775
NGDWT++ +VMLE LQ G+VYTC++EH S +SPI EWRAQS+SAQSKM+S
Sbjct: 150 NGDWTFETIVMLETVLQSGEVYTCQLEHPSWRSPIAEEWRAQSDSAQSKMMSGTGGFALG 209
Query: 776 XXXXXXXXXXRHRSQKG 826
R+QKG
Sbjct: 210 LLFLVVGLFTHFRNQKG 226
>ref|NP_001029503.1| hypothetical protein LOC508800 [Bos taurus]
Length = 299
Score = 74.7 bits (182), Expect = 1e-13
Identities = 51/198 (25%), Positives = 87/198 (43%), Gaps = 5/198 (2%)
Frame = +2
Query: 149 RDSPQDFVFQFKFECYFFNGTQRVRLVARYIYNQEELLRFDSDVGEYRAVTPLGRPEADS 328
+D FQ F C N Y Y+ ++ ++FD ++ + + P +
Sbjct: 106 KDREGSHTFQGAFGCELRNNESSGAFWG-YAYDGQDFIKFDKEIPAWVPLDPAAQNTKRK 164
Query: 329 WNGQKDVLEQTRAELDTVCK---HNYQIEEGTTLQRRVQPTVTISPSKAEALNHHNLLVC 499
W + +++ +A L+ C Y T L R+ P+V+++ A H L C
Sbjct: 165 WEAEAVYVQRAKAYLEEECPGMLRRYLPYSRTHLDRQESPSVSVTGHAAPG--HKRTLKC 222
Query: 500 AVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEH 679
DFYP + + W R G + A ++ +G+ TYQ V++ + + Y+C VEH
Sbjct: 223 LAYDFYPRSIGLHWTRAGDAQEAES-GGDVLPSGNGTYQSWVVVGVPPEDQAPYSCHVEH 281
Query: 680 SSLQSPILVEW--RAQSE 727
SL P+ V W R Q+E
Sbjct: 282 RSLTRPLTVPWDPRQQAE 299
>ref|NP_001012399.1| hemochromatosis [Bos taurus]
Length = 356
Score = 71.2 bits (173), Expect = 2e-12
Identities = 47/165 (28%), Positives = 76/165 (46%), Gaps = 5/165 (3%)
Frame = +2
Query: 233 RYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCK----HNYQ 400
+Y Y+ ++ L F + ++RA P + W K +Q RA LD C H +
Sbjct: 145 KYGYDGQDHLEFRPETLDWRAAEPRAQVTKLEWEVNKIRAKQNRAYLDRDCPEQLLHLLE 204
Query: 401 IEEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVS 580
+ G L+++V P V ++ +L L C +FYP + ++W ++ Q A +
Sbjct: 205 LGRGP-LEQQVPPLVKVTHHVTSSLT---TLRCRALNFYPQNITIRWLKDKQFLDAKEIK 260
Query: 581 TP-LIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 712
++ NGD TYQ V L M Y+C+VEH L P+ W
Sbjct: 261 PEDVLPNGDGTYQAWVALAMLPGEEQRYSCQVEHPGLDQPLTATW 305
Database: RefSeqBP
Posted date: Aug 1, 2006 7:14 PM
Number of letters in database: 16,112,626
Number of sequences in database: 33,508
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 Hits to DB: 41,725,578
Number of Sequences: 33508
Number of extensions: 1103339
Number of successful extensions: 4608
Number of sequences better than 1.0e-05: 10
Number of HSP's better than 0.0 without gapping: 3964
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 4564
length of database: 16,112,626
effective HSP length: 104
effective length of database: 12,627,794
effective search space used: 3813593788
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
Search to RefSeqCP
BLASTX 2.2.10 [Oct-19-2004]
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= LVR01_0002_B02
(1220 letters)
Database: RefSeqCP
33,732 sequences; 19,266,565 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Ca... 387 e-107
Alignment gi|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis fami... 310 2e-84
Alignment gi|XP_850395.1| PREDICTED: similar to HLA class II histocompati... 266 3e-71
Alignment gi|XP_861384.1| PREDICTED: similar to HLA class II histocompati... 253 3e-67
Alignment gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati... 69 9e-12
Alignment gi|XP_849737.1| PREDICTED: similar to HLA class II histocompati... 68 2e-11
Alignment gi|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris] 67 3e-11
Alignment gi|NP_001011726.1| MHC class II DLA DQalpha chain [Canis famili... 65 2e-10
Alignment gi|XP_536867.2| PREDICTED: similar to Zinc-alpha-2-glycoprotein... 65 2e-10
Alignment gi|XP_853335.1| PREDICTED: similar to T-cell surface glycoprote... 59 7e-09
>ref|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Canis familiaris]
Length = 269
Score = 387 bits (994), Expect = e-107
Identities = 187/258 (72%), Positives = 212/258 (82%)
Frame = +2
Query: 53 MSGMVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVA 232
MSG + L +PRG WTAAV M+LVVL PVAEGRDSPQDFVFQ+K ECYF NGT+RVRL+
Sbjct: 1 MSGKMTLCIPRGFWTAAVMMILVVLSIPVAEGRDSPQDFVFQYKAECYFTNGTERVRLLT 60
Query: 233 RYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEG 412
+YIYN+EE +RFDSDVGE+RAVT LGRP+A+ WN QKD +++ RAELDTVC+HNY EE
Sbjct: 61 KYIYNREEFVRFDSDVGEFRAVTELGRPDAEYWNRQKDEMDRVRAELDTVCRHNYGREEL 120
Query: 413 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 592
TTLQRRV+PTVTI PSK E LNHHNLLVC+VTDFYP Q+KV+WFRN QE+TAGVVSTPLI
Sbjct: 121 TTLQRRVEPTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLI 180
Query: 593 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 772
RNGDWT+Q+LVMLEM QRGDVYTC VEH+SLQSPI V+WRAQSESAQSKMLS
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHASLQSPITVQWRAQSESAQSKMLSGIGGFVL 240
Query: 773 XXXXXXXXXXXRHRSQKG 826
RHRSQKG
Sbjct: 241 GLIFLGLGLIIRHRSQKG 258
>ref|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis familiaris]
Length = 266
Score = 310 bits (794), Expect = 2e-84
Identities = 151/255 (59%), Positives = 185/255 (72%)
Frame = +2
Query: 62 MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
MV L G W A+ ++L+VL P A RD+P F+ K ECYF NGT+RVR V RYI
Sbjct: 1 MVCLCFLGGSWMTALMLILMVLNPPFAWARDTPPHFLEVAKSECYFTNGTERVRFVERYI 60
Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
+N+EE +RFDSDVGE+RAVT LGRP A+SWNGQK++LEQ RA +DT C+HNY + E T+
Sbjct: 61 HNREEFVRFDSDVGEFRAVTELGRPVAESWNGQKEILEQERATVDTYCRHNYGVIESFTV 120
Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
QRRV+PTVT+ P+K + L HHNLLVC+V FYP ++V+W RNGQEE AGVVST LIRNG
Sbjct: 121 QRRVEPTVTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNG 180
Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 781
DWT+Q+LVMLE+ Q G+VYTC+VEH SL SP+ VEWRAQS+SAQSKMLS
Sbjct: 181 DWTFQILVMLEIVPQSGEVYTCQVEHPSLTSPVTVEWRAQSDSAQSKMLSGIGGFVLGLL 240
Query: 782 XXXXXXXXRHRSQKG 826
R+QKG
Sbjct: 241 FLAVGLFIYFRNQKG 255
>ref|XP_850395.1| PREDICTED: similar to HLA class II histocompatibility antigen, DO
beta chain precursor (MHC class II antigen DOB) isoform
1 [Canis familiaris]
Length = 270
Score = 266 bits (680), Expect = 3e-71
Identities = 124/247 (50%), Positives = 168/247 (68%)
Frame = +2
Query: 92 WTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYIYNQEELLRFD 271
W A+ + + L + + +GRDSP+DFV Q K +CYF NGT++V+ V R+I+N EE RFD
Sbjct: 8 WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67
Query: 272 SDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTI 451
S VG + A+T LG+P+A+ WN Q +LE++RA +D +C+HNY++ T+ R+VQP VT+
Sbjct: 68 SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTV 127
Query: 452 SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVML 631
P + ++ HHNLL+C+VT FYP +K++WFRNGQEE GV+ST LIRNGDWT+Q +VML
Sbjct: 128 YPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVML 187
Query: 632 EMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXXXXXXXXXXRH 811
EM + GDVYTC V H SL SP+ VEWRAQS + KMLS
Sbjct: 188 EMTPELGDVYTCLVNHPSLLSPVSVEWRAQSTYSWRKMLSGIAAFLLGLIFLLVGTVICL 247
Query: 812 RSQKGLV 832
R+QKG V
Sbjct: 248 RAQKGYV 254
>ref|XP_861384.1| PREDICTED: similar to HLA class II histocompatibility antigen, DO
beta chain precursor (MHC class II antigen DOB) isoform
2 [Canis familiaris]
Length = 228
Score = 253 bits (645), Expect = 3e-67
Identities = 111/207 (53%), Positives = 153/207 (73%)
Frame = +2
Query: 92 WTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYIYNQEELLRFD 271
W A+ + + L + + +GRDSP+DFV Q K +CYF NGT++V+ V R+I+N EE RFD
Sbjct: 8 WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67
Query: 272 SDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTI 451
S VG + A+T LG+P+A+ WN Q +LE++RA +D +C+HNY++ T+ R+VQP VT+
Sbjct: 68 SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTV 127
Query: 452 SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVML 631
P + ++ HHNLL+C+VT FYP +K++WFRNGQEE GV+ST LIRNGDWT+Q +VML
Sbjct: 128 YPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVML 187
Query: 632 EMNLQRGDVYTCRVEHSSLQSPILVEW 712
EM + GDVYTC V H SL SP+ VEW
Sbjct: 188 EMTPELGDVYTCLVNHPSLLSPVSVEW 214
>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 = 68.9 bits (167), Expect = 9e-12
Identities = 36/122 (29%), Positives = 56/122 (45%), Gaps = 2/122 (1%)
Frame = +2
Query: 362 RAELDTVCKHNYQIE--EGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKV 535
+A LD + + + + GT L + P V + P L N+L+C V + +P + +
Sbjct: 63 KAHLDVLVERSNRTRAINGTHLSSPLPPRVAVLPKFRVELGQPNVLICIVDNIFPPVINI 122
Query: 536 QWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWR 715
W RNGQ + GV T D ++ L D+Y C+VEH L+ P+L W
Sbjct: 123 TWLRNGQIISEGVAQTSFYSQPDHLFRKFCYLTFVPSAEDMYDCKVEHWGLEEPLLRHWE 182
Query: 716 AQ 721
Q
Sbjct: 183 PQ 184
>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 = 67.8 bits (164), Expect = 2e-11
Identities = 47/163 (28%), Positives = 72/163 (44%), Gaps = 6/163 (3%)
Frame = +2
Query: 242 YNQEELLRFDSDVG-----EYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIE 406
+N++ L +D D E+ + L +D N Q++ L Q + C + Q
Sbjct: 46 FNKDLLTCWDPDEAKMVPYEFGTLNVLANYLSDYLN-QQEYLHQRLSNGLQDCATHTQSF 104
Query: 407 EGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTP 586
G+ R PTV ++ S +L C V FYP+ V + W +NGQ + +
Sbjct: 105 WGSLTHRTRPPTVQVAKSTPFNTKESVMLACYVWGFYPADVTISWRKNGQPVPSHSSALN 164
Query: 587 LIR-NGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 712
+ + NGDWTYQ + L D YTC VEH P+ +W
Sbjct: 165 MAQPNGDWTYQTVSHLATTPSYEDTYTCVVEHIGAPEPVCEDW 207
>ref|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris]
Length = 254
Score = 67.4 bits (163), Expect = 3e-11
Identities = 38/117 (32%), Positives = 52/117 (44%)
Frame = +2
Query: 362 RAELDTVCKHNYQIEEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQW 541
+A LDT+ K + T V P VT+ + L N+L+C + F P + V W
Sbjct: 92 KANLDTMIKRSNH-----TPNTNVPPEVTVLSNTPVELGEPNILICFIDKFSPPVINVTW 146
Query: 542 FRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 712
RNG T GV T + D ++ L DVY C+VEH L P+L W
Sbjct: 147 LRNGNPVTTGVSETIFLPREDHLFRKFHYLPFLPSAEDVYDCKVEHWGLDEPLLKHW 203
>ref|NP_001011726.1| MHC class II DLA DQalpha chain [Canis familiaris]
Length = 255
Score = 64.7 bits (156), Expect = 2e-10
Identities = 30/103 (29%), Positives = 46/103 (44%)
Frame = +2
Query: 437 PTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQ 616
P VT+ L N L+C V + +P + V W +N T GV T GD ++
Sbjct: 113 PEVTVFSKSPVMLGQPNTLICLVDNIFPPVINVTWLKNRHSVTEGVSETSFFAKGDHSFS 172
Query: 617 VLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKM 745
+ L D+Y C+VEH L P+L W + + S++
Sbjct: 173 KISYLTFLPSAEDIYDCKVEHWGLDEPLLKHWEPEVPTPMSEL 215
>ref|XP_536867.2| PREDICTED: similar to Zinc-alpha-2-glycoprotein precursor
(Zn-alpha-2-glycoprotein) (Zn-alpha-2-GP) [Canis
familiaris]
Length = 315
Score = 64.7 bits (156), Expect = 2e-10
Identities = 60/230 (26%), Positives = 99/230 (43%), Gaps = 8/230 (3%)
Frame = +2
Query: 47 SIMSGMVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRL 226
S M G+ L A + +V L + +D FQ F C N +
Sbjct: 75 SQMEGIEDWEKESKLQKAREDIFMVTLKDIMEYYKDKEGSHTFQGMFGCELQNN-KNSGA 133
Query: 227 VARYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQ-- 400
RY Y+ + F+ ++ + P W ++ +++ +A L+ C Q
Sbjct: 134 FWRYAYDGRNFIEFNKEIPAWVPQDPAALNTKKKWEAEEVYVQRAKAYLEEECPVMLQRY 193
Query: 401 IEEGTT-LQRRVQPTVTI-SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFR--NGQEETA 568
+E G T L R+ P+V+I S E + L C V+ FYP ++ + W + + QE +
Sbjct: 194 LEYGKTYLDRQEPPSVSITSHGTPEGIQ---TLKCWVSGFYPQEIDLHWIQADDTQETKS 250
Query: 569 GVVSTPLIRNGDWTYQVLVMLEMNLQ--RGDVYTCRVEHSSLQSPILVEW 712
G P +G+ TYQ V++ + Q Y+C V+HSSL P+ V W
Sbjct: 251 GGALLP---SGNNTYQAWVVMSASPQDLASFSYSCLVKHSSLSQPLTVLW 297
>ref|XP_853335.1| PREDICTED: similar to T-cell surface glycoprotein CD1a precursor
(CD1a antigen) (T-cell surface antigen T6/Leu-6) (hTa1
thymocyte antigen) [Canis familiaris]
Length = 357
Score = 59.3 bits (142), Expect = 7e-09
Identities = 33/90 (36%), Positives = 50/90 (55%)
Frame = +2
Query: 419 LQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRN 598
LQR+V+P +S + H L VC V+ FYP V V W R G++E G + + ++ N
Sbjct: 199 LQRKVRPEAWLSAGSSPGPGHLRL-VCHVSGFYPKPVWVSWMR-GEQEQQGTLYSDILPN 256
Query: 599 GDWTYQVLVMLEMNLQRGDVYTCRVEHSSL 688
D T+ + V L++ + +CRV HSSL
Sbjct: 257 TDGTWYLQVSLDVKSKEAAGLSCRVRHSSL 286
Database: RefSeqCP
Posted date: Aug 1, 2006 9:25 PM
Number of letters in database: 19,266,565
Number of sequences in database: 33,732
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 Hits to DB: 48,909,197
Number of Sequences: 33732
Number of extensions: 1290257
Number of successful extensions: 5756
Number of sequences better than 1.0e-05: 10
Number of HSP's better than 0.0 without gapping: 4767
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 5724
length of database: 19,266,565
effective HSP length: 105
effective length of database: 15,724,705
effective search space used: 4733136205
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
Search to RefSeqHP
BLASTX 2.2.10 [Oct-19-2004]
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= LVR01_0002_B02
(1220 letters)
Database: RefSeqHP
39,411 sequences; 17,774,539 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_002114.2| major histocompatibility complex, class II, DQ ... 374 e-103
Alignment gi|NP_872355.1| major histocompatibility complex, class II, DQ ... 328 7e-90
Alignment gi|NP_002115.1| major histocompatibility complex, class II, DR ... 311 7e-85
Alignment gi|XP_945926.1| PREDICTED: similar to HLA class II histocompati... 308 5e-84
Alignment gi|NP_002116.2| major histocompatibility complex, class II, DR ... 300 2e-81
Alignment gi|NP_002112.3| major histocompatibility complex, class II, DP ... 298 8e-81
Alignment gi|NP_068818.4| major histocompatibility complex, class II, DR ... 293 2e-79
Alignment gi|NP_072049.2| major histocompatibility complex, class II, DR ... 293 3e-79
Alignment gi|XP_949921.1| PREDICTED: similar to HLA class II histocompati... 288 7e-78
Alignment gi|XP_949915.1| PREDICTED: similar to HLA class II histocompati... 284 9e-77
>ref|NP_002114.2| major histocompatibility complex, class II, DQ beta 1 precursor
[Homo sapiens]
Length = 261
Score = 374 bits (959), Expect = e-103
Identities = 184/260 (70%), Positives = 210/260 (80%)
Frame = +2
Query: 53 MSGMVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVA 232
MS ALR+P GL A VT+ML +L PVAEGRDSP+DFV+QFK CYF NGT+RVRLV+
Sbjct: 1 MSWKKALRIPGGLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVS 60
Query: 233 RYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEG 412
R IYN+EE++RFDSDVGE+RAVT LG P A+ WN QKD+LE+ RA +D VC+HNYQ+E
Sbjct: 61 RSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELR 120
Query: 413 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 592
TTLQRRV+PTVTISPS+ EALNHHNLLVC+VTDFYP+Q+KV+WFRN QEETAGVVSTPLI
Sbjct: 121 TTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLI 180
Query: 593 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 772
RNGDWT+Q+LVMLEM QRGDVYTC VEH SLQSPI VEWRAQSESAQSKMLS
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVL 240
Query: 773 XXXXXXXXXXXRHRSQKGLV 832
HRSQKGL+
Sbjct: 241 GLIFLGLGLIIHHRSQKGLL 260
>ref|NP_872355.1| major histocompatibility complex, class II, DQ beta 2 [Homo
sapiens]
Length = 231
Score = 328 bits (840), Expect = 7e-90
Identities = 159/221 (71%), Positives = 184/221 (83%)
Frame = +2
Query: 53 MSGMVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVA 232
MS +AL++P G W AAVT+MLV+L PVAE RD P+DF+ QFK CYF NGT+RVR VA
Sbjct: 1 MSWKMALQIPGGFWAAAVTVMLVMLSTPVAEARDFPKDFLVQFKGMCYFTNGTERVRGVA 60
Query: 233 RYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEG 412
RYIYN+EE RFDSDVGE++AVT LGR D WN KD LEQ RA +D VC+HNY+ E
Sbjct: 61 RYIYNREEYGRFDSDVGEFQAVTELGRSIED-WNNYKDFLEQERAAVDKVCRHNYEAELR 119
Query: 413 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 592
TTLQR+V+PTVTISPS+ EALNHHNLLVC+VTDFYP+Q+KVQWFRN QEETAGVVST LI
Sbjct: 120 TTLQRQVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVQWFRNDQEETAGVVSTSLI 179
Query: 593 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWR 715
RNGDWT+Q+LVMLE+ QRGD+YTC+VEH SLQSPI VEWR
Sbjct: 180 RNGDWTFQILVMLEITPQRGDIYTCQVEHPSLQSPITVEWR 220
>ref|NP_002115.1| major histocompatibility complex, class II, DR beta 1 precursor
[Homo sapiens]
Length = 266
Score = 311 bits (797), Expect = 7e-85
Identities = 152/255 (59%), Positives = 189/255 (74%)
Frame = +2
Query: 62 MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
MV L+LP G A+T+ L+VL +P+A D+ F++Q KFEC+FFNGT+RVRL+ R I
Sbjct: 1 MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVRLLERCI 60
Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
YNQEE +RFDSDVGEYRAVT LGRP+A+ WN QKD+LEQ RA +DT C+HNY + E T+
Sbjct: 61 YNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTV 120
Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
QRRV+P VT+ PSK + L HHNLLVC+V+ FYP ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 781
DWT+Q LVMLE + G+VYTC+VEH S+ SP+ VEWRA+SESAQSKMLS
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSESAQSKMLSGVGGFVLGLL 240
Query: 782 XXXXXXXXRHRSQKG 826
R+QKG
Sbjct: 241 FLGAGLFIYFRNQKG 255
>ref|XP_945926.1| PREDICTED: similar to HLA class II histocompatibility antigen,
DRB1-9 beta chain precursor (MHC class I antigen DRB1*9)
(DR-9) (DR9) isoform 1 [Homo sapiens]
Length = 266
Score = 308 bits (790), Expect = 5e-84
Identities = 153/255 (60%), Positives = 188/255 (73%)
Frame = +2
Query: 62 MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
MV L+LP G AA+T+ L+VL +P+A D+ F+ Q KFEC+FFNGT+RVR + R I
Sbjct: 1 MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60
Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
YNQEE +RFDSDVGEYRAVT LGRP A+SWN QKD LE+ RAE+DTVC+HNY + E T+
Sbjct: 61 YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120
Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
QRRV P VT+ P+K + L HHNLLVC+V+ FYP ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 781
DWT+Q LVMLE + G+VYTC+VEH S+ SP+ VEWRA+SESAQSKMLS
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEWRARSESAQSKMLSGVGGFVLGLL 240
Query: 782 XXXXXXXXRHRSQKG 826
R+QKG
Sbjct: 241 FLGAGLFIYFRNQKG 255
>ref|NP_002116.2| major histocompatibility complex, class II, DR beta 5 precursor
[Homo sapiens]
Length = 266
Score = 300 bits (768), Expect = 2e-81
Identities = 144/230 (62%), Positives = 179/230 (77%)
Frame = +2
Query: 62 MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
MV L+LP G + A +T+ L+VL +P+A D+ F+ Q K+EC+FFNGT+RVR + R I
Sbjct: 1 MVCLKLPGGSYMAKLTVTLMVLSSPLALAGDTRPRFLQQDKYECHFFNGTERVRFLHRDI 60
Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
YNQEE LRFDSDVGEYRAVT LGRP+A+ WN QKD LE RA +DT C+HNY + E T+
Sbjct: 61 YNQEEDLRFDSDVGEYRAVTELGRPDAEYWNSQKDFLEDRRAAVDTYCRHNYGVGESFTV 120
Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
QRRV+P VT+ P++ + L HHNLLVC+V FYP ++V+WFRN QEE AGVVST LI+NG
Sbjct: 121 QRRVEPKVTVYPARTQTLQHHNLLVCSVNGFYPGSIEVRWFRNSQEEKAGVVSTGLIQNG 180
Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 751
DWT+Q LVMLE + G+VYTC+VEH S+ SP+ VEWRAQSESAQSKMLS
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRAQSESAQSKMLS 230
>ref|NP_002112.3| major histocompatibility complex, class II, DP beta 1 precursor
[Homo sapiens]
Length = 258
Score = 298 bits (762), Expect = 8e-81
Identities = 143/230 (62%), Positives = 180/230 (78%)
Frame = +2
Query: 62 MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
M+ L++ T A+T +L+VL V +GR +P++++FQ + ECY FNGTQR + RYI
Sbjct: 1 MMVLQVSAAPRTVALTALLMVLLTSVVQGRATPENYLFQGRQECYAFNGTQR--FLERYI 58
Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
YN+EE RFDSDVGE+RAVT LGRP A+ WN QKD+LE+ RA D +C+HNY++ TL
Sbjct: 59 YNREEFARFDSDVGEFRAVTELGRPAAEYWNSQKDILEEKRAVPDRMCRHNYELGGPMTL 118
Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
QRRVQP V +SPSK L HHNLLVC VTDFYP ++V+WF NGQEETAGVVST LIRNG
Sbjct: 119 QRRVQPRVNVSPSKKGPLQHHNLLVCHVTDFYPGSIQVRWFLNGQEETAGVVSTNLIRNG 178
Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 751
DWT+Q+LVMLEM Q+GDVYTC+VEH+SL SP+ VEW+AQS+SA+SK L+
Sbjct: 179 DWTFQILVMLEMTPQQGDVYTCQVEHTSLDSPVTVEWKAQSDSARSKTLT 228
>ref|NP_068818.4| major histocompatibility complex, class II, DR beta 4 precursor
[Homo sapiens]
Length = 266
Score = 293 bits (750), Expect = 2e-79
Identities = 144/255 (56%), Positives = 183/255 (71%)
Frame = +2
Query: 62 MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
MV L+LP G AA+T+ L VL +P+A D+ F+ Q K EC+F NGT+RV + RYI
Sbjct: 1 MVCLKLPGGSCMAALTVTLTVLSSPLALAGDTQPRFLEQAKCECHFLNGTERVWNLIRYI 60
Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
YNQEE R++SD+GEY+AVT LGRP+A+ WN QKD+LE+ RAE+DT C++NY + E T+
Sbjct: 61 YNQEEYARYNSDLGEYQAVTELGRPDAEYWNSQKDLLERRRAEVDTYCRYNYGVVESFTV 120
Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
QRRVQP VT+ PSK + L HHNLLVC+V FYP ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVQPKVTVYPSKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 781
DWT+Q LVMLE + G+VYTC+VEH S+ SP+ V+W A+SESAQSKMLS
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSMMSPLTVQWSARSESAQSKMLSGVGGFVLGLL 240
Query: 782 XXXXXXXXRHRSQKG 826
R+QKG
Sbjct: 241 FLGTGLFIYFRNQKG 255
>ref|NP_072049.2| major histocompatibility complex, class II, DR beta 3 precursor
[Homo sapiens]
Length = 266
Score = 293 bits (749), Expect = 3e-79
Identities = 146/255 (57%), Positives = 181/255 (70%)
Frame = +2
Query: 62 MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
MV L+LP G AA+T+ L+VL + +A D+ F+ K EC+FFNGT+RVR + RY
Sbjct: 1 MVCLKLPGGSSLAALTVTLMVLSSRLAFAGDTRPRFLELRKSECHFFNGTERVRYLDRYF 60
Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
+NQEE LRFDSDVGEYRAVT LGRP A+SWN QKD+LEQ R +D C+HNY + E T+
Sbjct: 61 HNQEEFLRFDSDVGEYRAVTELGRPVAESWNSQKDLLEQKRGRVDNYCRHNYGVGESFTV 120
Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
QRRV P VT+ P+K + L HHNLLVC+V+ FYP ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVHPQVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 781
DWT+Q LVMLE + G+VYTC+VEH S+ S + VEWRA+SESAQSKMLS
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSALTVEWRARSESAQSKMLSGVGGFVLGLL 240
Query: 782 XXXXXXXXRHRSQKG 826
R+QKG
Sbjct: 241 FLGAGLFIYFRNQKG 255
>ref|XP_949921.1| PREDICTED: similar to HLA class II histocompatibility antigen,
DRB1-9 beta chain precursor (MHC class I antigen DRB1*9)
(DR-9) (DR9) isoform 3 [Homo sapiens]
Length = 325
Score = 288 bits (737), Expect = 7e-78
Identities = 138/220 (62%), Positives = 171/220 (77%)
Frame = +2
Query: 62 MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
MV L+LP G AA+T+ L+VL +P+A D+ F+ Q KFEC+FFNGT+RVR + R I
Sbjct: 1 MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60
Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
YNQEE +RFDSDVGEYRAVT LGRP A+SWN QKD LE+ RAE+DTVC+HNY + E T+
Sbjct: 61 YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120
Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
QRRV P VT+ P+K + L HHNLLVC+V+ FYP ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQ 721
DWT+Q LVMLE + G+VYTC+VEH S+ SP+ VEW Q
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEWSEQ 220
>ref|XP_949915.1| PREDICTED: similar to HLA class II histocompatibility antigen,
DRB1-9 beta chain precursor (MHC class I antigen DRB1*9)
(DR-9) (DR9) isoform 2 [Homo sapiens]
Length = 284
Score = 284 bits (727), Expect = 9e-77
Identities = 138/220 (62%), Positives = 166/220 (75%)
Frame = +2
Query: 167 FVFQFKFECYFFNGTQRVRLVARYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKD 346
F+ Q KFEC+FFNGT+RVR + R IYNQEE +RFDSDVGEYRAVT LGRP A+SWN QKD
Sbjct: 54 FLKQDKFECHFFNGTERVRYLHRGIYNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKD 113
Query: 347 VLEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQ 526
LE+ RAE+DTVC+HNY + E T+QRRV P VT+ P+K + L HHNLLVC+V+ FYP
Sbjct: 114 FLERRRAEVDTVCRHNYGVGESFTVQRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGS 173
Query: 527 VKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILV 706
++V+WFRNGQEE AGVVST LI+NGDWT+Q LVMLE + G+VYTC+VEH S+ SP+ V
Sbjct: 174 IEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTV 233
Query: 707 EWRAQSESAQSKMLSXXXXXXXXXXXXXXXXXXRHRSQKG 826
EWRA+SESAQSKMLS R+QKG
Sbjct: 234 EWRARSESAQSKMLSGVGGFVLGLLFLGAGLFIYFRNQKG 273
Database: RefSeqHP
Posted date: Aug 2, 2006 12:57 AM
Number of letters in database: 17,774,539
Number of sequences in database: 39,411
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 Hits to DB: 47,502,071
Number of Sequences: 39411
Number of extensions: 1299103
Number of successful extensions: 5795
Number of sequences better than 1.0e-05: 10
Number of HSP's better than 0.0 without gapping: 4645
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 5745
length of database: 17,774,539
effective HSP length: 104
effective length of database: 13,675,795
effective search space used: 4130090090
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
Search to RefSeqSP
BLASTX 2.2.10 [Oct-19-2004]
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= LVR01_0002_B02
(1220 letters)
Database: RefSeqSP
1040 sequences; 434,620 total letters
Searching...done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_998933.1| swine leukocyte antigen 7 [Sus scrofa] 73 2e-14
Alignment gi|NP_999362.2| neonatal Fc receptor FcRn [Sus scrofa] 63 1e-11
Alignment gi|NP_998996.1| CD1 antigen [Sus scrofa] 58 5e-10
Alignment gi|NP_999143.1| beta 2-microglobulin [Sus scrofa] 56 2e-09
Alignment gi|NP_998993.1| IgG heavy chain [Sus scrofa] 46 2e-06
>ref|NP_998933.1| swine leukocyte antigen 7 [Sus scrofa]
Length = 401
Score = 72.8 bits (177), Expect = 2e-14
Identities = 49/185 (26%), Positives = 82/185 (44%), Gaps = 5/185 (2%)
Frame = +2
Query: 173 FQFKFECYFFNGTQRVRLVARYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVL 352
+Q+ CY + +R +++ Y+ + + + D+ + AV + W ++ V
Sbjct: 116 YQWLCGCYVARDGRLLRGYSQFAYDGADYIVLNEDLRSWTAVGMAAQITRRKWE-EETVA 174
Query: 353 EQTRAELDTVCK---HNYQIEEGTTLQRRVQPT--VTISPSKAEALNHHNLLVCAVTDFY 517
EQ+RA L+ C H Y TLQR P VT PS + L C FY
Sbjct: 175 EQSRAYLEVACVQSLHRYLANGKETLQRSDPPKTHVTRHPSSDNKVT----LRCWALGFY 230
Query: 518 PSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSP 697
P ++ + W + GQ+++ V +GD T++ L + YTC V+H LQ P
Sbjct: 231 PKEISLTWQQEGQDQSQDVEVVETRPSGDGTFRKWAALVVPPGEEQSYTCHVQHEGLQEP 290
Query: 698 ILVEW 712
+ + W
Sbjct: 291 LTLRW 295
>ref|NP_999362.2| neonatal Fc receptor FcRn [Sus scrofa]
Length = 356
Score = 63.2 bits (152), Expect = 1e-11
Identities = 43/172 (25%), Positives = 79/172 (45%), Gaps = 3/172 (1%)
Frame = +2
Query: 227 VARYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNY--Q 400
VA + N EE ++FD+ +G + P R W + D + + + L C H
Sbjct: 130 VATFALNGEEFMKFDTKLGTWDGEWPEARTIGSKWMQEPDAVNKEKTFLLYSCPHRLLGH 189
Query: 401 IEEGT-TLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVV 577
+E G L+ + P++ + A ++L C FYP ++++++ RNG AG
Sbjct: 190 LERGRGNLEWKEPPSMRMKARPGTAPGF-SVLTCIAFSFYPPELQLRFLRNGL--AAGSG 246
Query: 578 STPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESA 733
+ + NGD ++ L + Y C V+H+ L P+ VE + ++S+
Sbjct: 247 ESDIGPNGDGSFHAWSSLTVKSGDEHHYCCVVQHAGLAQPLTVELESPAKSS 298
>ref|NP_998996.1| CD1 antigen [Sus scrofa]
Length = 339
Score = 57.8 bits (138), Expect = 5e-10
Identities = 36/103 (34%), Positives = 54/103 (52%), Gaps = 1/103 (0%)
Frame = +2
Query: 419 LQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRN 598
LQR+V+P +S S H +LVC V+ FYP + V W R+ QE+ G ++ N
Sbjct: 199 LQRQVRPEAWLS-SGPNPSPGHLMLVCHVSGFYPKPIWVMWMRDEQEQ-PGTQQGDILPN 256
Query: 599 GDWTYQVLVMLEMNLQRGDVYTCRVEHSSL-QSPILVEWRAQS 724
D T+ + V L++ +CRV+HSSL I++ W S
Sbjct: 257 ADGTWYLRVTLDVAAGEASGLSCRVKHSSLGGQDIILYWEQHS 299
>ref|NP_999143.1| beta 2-microglobulin [Sus scrofa]
Length = 118
Score = 56.2 bits (134), Expect = 2e-09
Identities = 29/93 (31%), Positives = 49/93 (52%), Gaps = 7/93 (7%)
Frame = +2
Query: 455 PSKAEALNHH-------NLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTY 613
P K + + H N L C V+ F+P Q+++ +NG++ A + L + DW++
Sbjct: 24 PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAE--QSDLSFSKDWSF 81
Query: 614 QVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 712
+LV E D Y+CRV+H +L P +V+W
Sbjct: 82 YLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKW 114
>ref|NP_998993.1| IgG heavy chain [Sus scrofa]
Length = 474
Score = 46.2 bits (108), Expect = 2e-06
Identities = 30/92 (32%), Positives = 44/92 (47%), Gaps = 5/92 (5%)
Frame = +2
Query: 434 QPTVTISPSKAEALNHHNLLV-CAVTDFYPSQVKVQWFRNGQEETAG-VVSTPLIRNGDW 607
+P V P AE L+ + V C V FYP + V+W NGQ E G +TP ++ D
Sbjct: 370 EPQVYTLPPPAEELSRSKVTVTCLVIGFYPPDIHVEWKSNGQPEPEGNYRTTPPQQDVDG 429
Query: 608 T---YQVLVMLEMNLQRGDVYTCRVEHSSLQS 694
T Y L + + G+ + C V H +L +
Sbjct: 430 TFFLYSKLAVDKARWDHGETFECAVMHEALHN 461
Database: RefSeqSP
Posted date: Aug 1, 2006 7:14 PM
Number of letters in database: 434,620
Number of sequences in database: 1040
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 Hits to DB: 1,104,957
Number of Sequences: 1040
Number of extensions: 27728
Number of successful extensions: 110
Number of sequences better than 1.0e-05: 5
Number of HSP's better than 0.0 without gapping: 96
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 108
length of database: 434,620
effective HSP length: 79
effective length of database: 352,460
effective search space used: 115254420
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
Search to RefSeqMP
BLASTX 2.2.10 [Oct-19-2004]
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= LVR01_0002_B02
(1220 letters)
Database: RefSeqMP
45,328 sequences; 21,768,885 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_996988.1| histocompatibility 2, class II antigen A, beta ... 324 1e-88
Alignment gi|NP_034512.1| histocompatibility 2, class II antigen E beta [... 289 4e-78
Alignment gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/... 256 4e-68
Alignment gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ... 244 2e-64
Alignment gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ... 75 1e-13
Alignment gi|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus ... 75 1e-13
Alignment gi|NP_034508.2| histocompatibility 2, class II antigen A, alpha... 70 4e-12
Alignment gi|NP_032232.1| histocompatibility 2, O region alpha locus [Mus... 68 2e-11
Alignment gi|NP_032235.1| histocompatibility-2 complex class 1-like [Mus ... 64 4e-10
Alignment gi|XP_908790.2| PREDICTED: similar to histocompatibility 2, Q r... 63 5e-10
>ref|NP_996988.1| histocompatibility 2, class II antigen A, beta 1 [Mus musculus]
Length = 265
Score = 324 bits (831), Expect = 1e-88
Identities = 164/255 (64%), Positives = 197/255 (77%), Gaps = 1/255 (0%)
Frame = +2
Query: 65 VALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYIY 244
+AL++P L +AAV ++L+VL +P EG DS + FV+QF ECYF NGTQR+R V RYIY
Sbjct: 1 MALQIPSLLLSAAV-VVLMVLSSPGTEGGDSERHFVYQFMGECYFTNGTQRIRYVTRYIY 59
Query: 245 NQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQ-IEEGTTL 421
N+EE +R+DSDVGE+RAVT LGRP+A+ WN Q ++LE+TRAELDTVC+HNY+ E T+L
Sbjct: 60 NREEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSL 119
Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
+R QP V IS S+ EALNHHN LVC+VTDFYP+Q+KV+WFRNGQEET GV ST LIRNG
Sbjct: 120 RRLEQPNVVISLSRTEALNHHNTLVCSVTDFYPTQIKVRWFRNGQEETVGVSSTQLIRNG 179
Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 781
DWT+QVLVMLEM +RG+VYTC VEH SL+SPI VEWRAQSESA SKMLS
Sbjct: 180 DWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRAQSESAWSKMLSGIGGCVLGVI 239
Query: 782 XXXXXXXXRHRSQKG 826
RHRSQKG
Sbjct: 240 FLGLGLFIRHRSQKG 254
>ref|NP_034512.1| histocompatibility 2, class II antigen E beta [Mus musculus]
Length = 264
Score = 289 bits (740), Expect = 4e-78
Identities = 140/250 (56%), Positives = 178/250 (71%)
Frame = +2
Query: 77 LPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYIYNQEE 256
LPR AAV ++L VL PVA RDS F+ K EC+F+NGTQRVR + RY YN EE
Sbjct: 4 LPRVPCVAAVILLLTVLSPPVALVRDSRPWFLEYCKSECHFYNGTQRVRFLKRYFYNLEE 63
Query: 257 LLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRRVQ 436
LRFDSDVGE+RAVT LGRP+A++WN Q ++L++ RA +DT C+HNY+I + + RRV+
Sbjct: 64 NLRFDSDVGEFRAVTELGRPDAENWNSQPEILDEKRAAVDTYCRHNYEIFDNFLVPRRVE 123
Query: 437 PTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQ 616
PTVT+ P+K + L HHNLLVC+V+DFYP ++V+WFRNG+EE G+VST L+RNGDWT+Q
Sbjct: 124 PTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQ 183
Query: 617 VLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXXXXXXX 796
LVMLE Q G+VYTC+VEH SL P+ VEW+AQS SAQ+KMLS
Sbjct: 184 TLVMLETVPQSGEVYTCQVEHPSLTDPVTVEWKAQSTSAQNKMLSGVGGFVLGLLFLRAG 243
Query: 797 XXXRHRSQKG 826
R+QKG
Sbjct: 244 LFIYFRNQKG 253
>ref|NP_001029150.1| H-2 class II histocompatibility antigen E-a/k beta-2 [Mus musculus]
Length = 287
Score = 256 bits (653), Expect = 4e-68
Identities = 128/230 (55%), Positives = 166/230 (72%)
Frame = +2
Query: 62 MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
MV+L LPRGL AAV + L++L PV RD F+ Q K EC++FNG +RV V R+I
Sbjct: 1 MVSLWLPRGLCVAAVILSLMMLTPPVILVRDPRPRFLEQLKAECHYFNGKERVWSVTRFI 60
Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
YNQEE RF+SD G++ AVT LGRP + N QKD+L+ RA +D C++NY + + L
Sbjct: 61 YNQEEFARFNSDFGKFLAVTELGRPIVEYLNTQKDMLDNYRASVDR-CRNNYDLVDIFML 119
Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
+ +P VT+ P+K + L HHNLLVC+V DFYP ++V+WFRNG+EE GVVST LI+N
Sbjct: 120 NLKAEPKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNR 179
Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 751
DWTYQ LVMLEM + G+VYTC+VEH SL SP+ VEWRA+S SAQ+K+LS
Sbjct: 180 DWTYQTLVMLEMVPRGGEVYTCQVEHPSLTSPVTVEWRARSTSAQNKLLS 229
>ref|NP_034519.2| histocompatibility 2, O region beta locus [Mus musculus]
Length = 271
Score = 244 bits (622), Expect = 2e-64
Identities = 113/223 (50%), Positives = 156/223 (69%)
Frame = +2
Query: 83 RGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYIYNQEELL 262
R W A+ + L+ L + + EGRDSP++FV Q K +CYF NGT++V L+ R+I+N EE L
Sbjct: 5 RAPWVVALLVNLMRLDSFMIEGRDSPENFVIQAKADCYFTNGTEKVHLLVRFIFNLEEYL 64
Query: 263 RFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRRVQPT 442
FDSD+G + A+T LG P+AD WN + D+LE +RA ++ VC+ Y++ T++R V P
Sbjct: 65 HFDSDLGMFVALTELGEPDADQWNKRLDLLETSRAAVNMVCRQKYKLGAPFTVERNVPPE 124
Query: 443 VTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVL 622
VT+ P + L HNLL+C+VT FYP + V+WFRNGQEE +GV+ST L+RNGDWT+Q
Sbjct: 125 VTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVRNGDWTFQTT 184
Query: 623 VMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 751
VMLEM + GD+Y+C VEH L P+ V W AQSE + K+LS
Sbjct: 185 VMLEMIPELGDIYSCLVEHPGLLRPVSVAWMAQSEYSWKKILS 227
>ref|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus musculus]
Length = 261
Score = 75.5 bits (184), Expect = 1e-13
Identities = 50/170 (29%), Positives = 79/170 (46%), Gaps = 13/170 (7%)
Frame = +2
Query: 242 YNQEELLRFDSDVG-----EYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIE 406
+N++ L +D DVG E+ ++ L ++ N Q+ ++ + + L H
Sbjct: 46 FNKDLLACWDPDVGKIVPCEFGVLSRLAEIISNILNEQESLIHRLQNGLQDCATHTQPFW 105
Query: 407 EGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQ--------EE 562
+ T + R P+V ++ + +L C V FYP+ V + W +NGQ E+
Sbjct: 106 DVLTHRTRA-PSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEK 164
Query: 563 TAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 712
TA NGDWTYQ + L + GDVYTC V+HS PI +W
Sbjct: 165 TAQP-------NGDWTYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDW 207
>ref|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus musculus]
Length = 261
Score = 75.1 bits (183), Expect = 1e-13
Identities = 61/231 (26%), Positives = 93/231 (40%), Gaps = 23/231 (9%)
Frame = +2
Query: 89 LWTAAVTMMLVVLGAP----------VAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARY 238
LW + + L +GA V + +PQDF + F
Sbjct: 4 LWLLLLVLSLDCMGAGGFVAHVESTCVLDDAGTPQDFTYCVSF----------------- 46
Query: 239 IYNQEELLRFDSDVG-----EYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQI 403
N++ L +D DVG E+ + P + N ++ +L++ + L H
Sbjct: 47 --NKDLLACWDPDVGKIVPCEFGVLYPWAENFSRILNKEESLLQRLQNGLLDCASHTQPF 104
Query: 404 EEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQ--------E 559
T + R P+V ++ + +L C V FYP+ V + W +NGQ E
Sbjct: 105 WNALTHRTRA-PSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKE 163
Query: 560 ETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 712
+TA NGDWTYQ + L + GDVYTC V+HS PI +W
Sbjct: 164 KTAQP-------NGDWTYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDW 207
>ref|NP_034508.2| histocompatibility 2, class II antigen A, alpha [Mus musculus]
Length = 256
Score = 70.1 bits (170), Expect = 4e-12
Identities = 35/125 (28%), Positives = 55/125 (44%), Gaps = 3/125 (2%)
Frame = +2
Query: 380 VCKHNYQI---EEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRN 550
V KHN + +T P T+ P L N L+C V + +P + + W RN
Sbjct: 92 VVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRN 151
Query: 551 GQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSES 730
+ GV T N D+++ L L D+Y C+VEH L+ P+L W + +
Sbjct: 152 SKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEPEIPA 211
Query: 731 AQSKM 745
S++
Sbjct: 212 PMSEL 216
>ref|NP_032232.1| histocompatibility 2, O region alpha locus [Mus musculus]
Length = 250
Score = 68.2 bits (165), Expect = 2e-11
Identities = 34/97 (35%), Positives = 45/97 (46%)
Frame = +2
Query: 431 VQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWT 610
V P VT+ P L N+L+C V D +P + V W RN Q T GV T +
Sbjct: 111 VPPRVTVLPKTRVELGKPNVLICIVDDIFPPVINVTWLRNSQPITKGVAQTSFYSQPNHR 170
Query: 611 YQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQ 721
++ L DVY C+VEH L +P+L W Q
Sbjct: 171 FRKFHYLTFVPSAEDVYDCKVEHWGLDTPLLQHWEPQ 207
>ref|NP_032235.1| histocompatibility-2 complex class 1-like [Mus musculus]
Length = 341
Score = 63.5 bits (153), Expect = 4e-10
Identities = 40/156 (25%), Positives = 71/156 (45%), Gaps = 3/156 (1%)
Frame = +2
Query: 233 RYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQ--IE 406
+Y Y+ ++ + F+ D + A+ + +W L+ + L+ C + +E
Sbjct: 129 QYAYDGQDFIIFNKDTLSWLAMDYVAHITKQAWEANLHELQYQKNWLEEECIAWLKRFLE 188
Query: 407 EGT-TLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVST 583
G TL+R P V + + E C FYP ++ + W +NG+E V
Sbjct: 189 YGRDTLERTEHPVVRTT--RKETFPGITTFFCRAHGFYPPEISMTWMKNGEEIAQEVDYG 246
Query: 584 PLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQ 691
++ +GD TYQ + + ++ Q DVY+C VEH Q
Sbjct: 247 GVLPSGDGTYQTWLSVNLDPQSNDVYSCHVEHCGRQ 282
>ref|XP_908790.2| PREDICTED: similar to histocompatibility 2, Q region locus 6
isoform 2 [Mus musculus]
Length = 465
Score = 63.2 bits (152), Expect = 5e-10
Identities = 43/184 (23%), Positives = 75/184 (40%), Gaps = 5/184 (2%)
Frame = +2
Query: 176 QFKFECYFFNGTQRVRLVARYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLE 355
Q+ + C + + +R ++ Y + + + D+ + A + W Q + E
Sbjct: 233 QWMYGCDVGSDERLLRGYLQFAYEGRDYIALNEDLKTWTAADMAAQITLHKWE-QAGIAE 291
Query: 356 QTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISPSKAEALNHHN-----LLVCAVTDFYP 520
+ RA L+ C + + LQ R + + P KA +H L C FYP
Sbjct: 292 RDRAYLEGACVQSLR----RYLQLRKETLLCTDPPKAHVTHHPRSYGAVTLRCWALGFYP 347
Query: 521 SQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPI 700
+ + + W NG+E T + GD T+Q + + L + YTC V H L P+
Sbjct: 348 ADITLTWQLNGEELTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCHVNHEGLPEPL 407
Query: 701 LVEW 712
+ W
Sbjct: 408 TLRW 411
Database: RefSeqMP
Posted date: Aug 2, 2006 12:58 AM
Number of letters in database: 21,768,885
Number of sequences in database: 45,328
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 Hits to DB: 56,050,254
Number of Sequences: 45328
Number of extensions: 1474320
Number of successful extensions: 6156
Number of sequences better than 1.0e-05: 10
Number of HSP's better than 0.0 without gapping: 5030
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 6094
length of database: 21,768,885
effective HSP length: 106
effective length of database: 16,964,117
effective search space used: 5089235100
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)