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_0086_F05
(1216 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] 405 e-113
Alignment gi|NP_001012694.1| major histocompatibility complex, class II, ... 389 e-108
Alignment gi|NP_001012698.2| major histocompatibility complex, class II, ... 298 4e-81
Alignment gi|NP_001012697.1| major histocompatibility complex, class II, ... 297 1e-80
Alignment gi|XP_582099.2| PREDICTED: similar to major histocompatibility ... 269 3e-72
Alignment gi|NP_001013618.1| major histocompatibility complex, class II, ... 267 1e-71
Alignment gi|XP_876139.1| PREDICTED: similar to H-2 class II histocompati... 241 1e-63
Alignment gi|XP_874766.1| PREDICTED: similar to HLA class II histocompati... 156 4e-38
Alignment gi|NP_001029503.1| hypothetical protein LOC508800 [Bos taurus] 72 1e-12
Alignment gi|NP_001035571.1| major histocompatibility complex, class II, ... 72 1e-12
>ref|NP_001029840.2| MHC class II antigen [Bos taurus]
Length = 261
Score = 405 bits (1042), Expect = e-113
Identities = 198/261 (75%), Positives = 218/261 (83%)
Frame = +3
Query: 54 MSGMVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVT 233
MSGMVAL +PRGLWTA + V LV+L P AEGRDSP+DFVVQFKG CYF NGT+RVR VT
Sbjct: 1 MSGMVALWIPRGLWTAVVMVTLVMLSTPGAEGRDSPKDFVVQFKGLCYFTNGTERVRYVT 60
Query: 234 RFIYNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEG 413
R+IYNQEEY RFDSD YRA+TPLGRPDA+YWNSQKD LEQTRAE DTVC+HNYQ E
Sbjct: 61 RYIYNQEEYVRFDSDWDLYRALTPLGRPDAEYWNSQKDFLEQTRAEADTVCRHNYQAELI 120
Query: 414 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 593
T+LQRRV+PTVTISPS+ EALNHHNLLVC+VTDFYPSQ+KV+WFRN +EETAGVVSTPLI
Sbjct: 121 TSLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPSQIKVRWFRNDREETAGVVSTPLI 180
Query: 594 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 773
RNGDWT+Q+LVMLEM QRGDVYTC VEH SLQSPI+VEWRAQSESAQSKMLS
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPIMVEWRAQSESAQSKMLSGVGGFVL 240
Query: 774 XXXXXXXXXXXHHRSQKGLVR 836
HHRSQKGL+R
Sbjct: 241 GLIFLGLGLIIHHRSQKGLMR 261
>ref|NP_001012694.1| major histocompatibility complex, class II, DQ beta [Bos taurus]
Length = 261
Score = 389 bits (998), Expect = e-108
Identities = 192/260 (73%), Positives = 214/260 (82%)
Frame = +3
Query: 54 MSGMVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVT 233
MSGMVALR+PRGLWTAA+ V L VL P AEGRDSPQD VV F G+CYF NGT+RVR VT
Sbjct: 1 MSGMVALRIPRGLWTAAVMVTLAVLSTPGAEGRDSPQDTVVHFMGQCYFTNGTERVRYVT 60
Query: 234 RFIYNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEG 413
R+IYNQEE A +DSDVGEYRAVT LGR A+YWNSQKDILEQTRAELDTVC+HNYQ+E
Sbjct: 61 RYIYNQEETAYYDSDVGEYRAVTQLGRTLAEYWNSQKDILEQTRAELDTVCRHNYQLEVI 120
Query: 414 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 593
T+LQR+V+PTVTIS S+ EALNHHNLLVC+VTDFYP Q+KV+WF+NG+EETAG+VSTPLI
Sbjct: 121 TSLQRQVEPTVTISLSRTEALNHHNLLVCSVTDFYPGQIKVRWFQNGKEETAGIVSTPLI 180
Query: 594 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 773
RNGDWT+Q+LVMLEM +RGDVYTC VEH SLQSPI VEWRAQSESAQSKMLS
Sbjct: 181 RNGDWTFQILVMLEMTPKRGDVYTCHVEHPSLQSPISVEWRAQSESAQSKMLSGVGGFVL 240
Query: 774 XXXXXXXXXXXHHRSQKGLV 833
RSQKGLV
Sbjct: 241 GLIFLGLGLIVRRRSQKGLV 260
>ref|NP_001012698.2| major histocompatibility complex, class II, DRB3 [Bos taurus]
Length = 266
Score = 298 bits (764), Expect = 4e-81
Identities = 145/255 (56%), Positives = 180/255 (70%)
Frame = +3
Query: 63 MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFI 242
MV L G W AAL VML+VL P+A R+ F+ +KGEC+FFNGT+RVR + R
Sbjct: 1 MVCLYFSGGSWMAALIVMLMVLCPPLAWAREIQPHFLEYYKGECHFFNGTERVRFLDRHF 60
Query: 243 YNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTL 422
YN EE+ RFDSD GE+RAVT LGRP A++WNSQKD LEQ RAE+D VC+HNY E T+
Sbjct: 61 YNGEEFVRFDSDWGEFRAVTELGRPAAEHWNSQKDFLEQKRAEVDRVCRHNYGGVESFTV 120
Query: 423 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 602
QRRV+PTVT+ P+K + L HHNLLVC+V FYP ++V+WFRNG EE AGV+ST LI+NG
Sbjct: 121 QRRVEPTVTVYPAKTQPLQHHNLLVCSVNGFYPGHIEVRWFRNGHEEEAGVISTGLIQNG 180
Query: 603 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 782
DWT+Q +VMLE Q G+VYTC+V+H SPI VEWRA+S+SAQSKM+S
Sbjct: 181 DWTFQTMVMLETVPQSGEVYTCQVDHPKRTSPITVEWRARSDSAQSKMMSGVGGFVLGLL 240
Query: 783 XXXXXXXXHHRSQKG 827
+ R+QKG
Sbjct: 241 FLAVGLFIYFRNQKG 255
>ref|NP_001012697.1| major histocompatibility complex, class II, DY beta [Bos taurus]
Length = 259
Score = 297 bits (760), Expect = 1e-80
Identities = 149/227 (65%), Positives = 175/227 (77%), Gaps = 2/227 (0%)
Frame = +3
Query: 78 LPRGLWTAALTVMLV--VLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFIYNQ 251
+PR T A VM V VL P A RD+P++FV QFKG CYF NGT+ VRLV R IYN+
Sbjct: 5 IPRNPGTVAGMVMAVFLVLRIPEAHCRDAPKNFVYQFKGMCYFTNGTEHVRLVARQIYNK 64
Query: 252 EEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTLQRR 431
EE FDSD+GE+ AVT LGR A+ WN+QKD+L + RA +DT+C+HNY+ G T+QRR
Sbjct: 65 EEILHFDSDLGEFVAVTELGRVCAEIWNTQKDLLAEFRAYVDTLCRHNYKETAGFTVQRR 124
Query: 432 VQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWT 611
V+PTVT+SP+ EALNHHNLLVC+VTDFYP QVKV+WFRN QE+TAGV TPL +NGDWT
Sbjct: 125 VEPTVTVSPASTEALNHHNLLVCSVTDFYPRQVKVKWFRNQQEQTAGVGFTPLTQNGDWT 184
Query: 612 YQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 752
YQ+ VMLE Q GDVY C V+H SLQSPI VEWRAQSESAQSKM S
Sbjct: 185 YQIHVMLETVPQLGDVYVCHVDHPSLQSPITVEWRAQSESAQSKMQS 231
>ref|XP_582099.2| PREDICTED: similar to major histocompatibility complex, class II,
DR beta 5 precursor [Bos taurus]
Length = 255
Score = 269 bits (688), Expect = 3e-72
Identities = 130/243 (53%), Positives = 167/243 (68%)
Frame = +3
Query: 99 AALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFIYNQEEYARFDSD 278
AAL V+L+VL P + R++ F+ QFKGEC F NG +R+R R+IYN +E FDSD
Sbjct: 2 AALAVLLMVLSLPFSWARETQPHFIHQFKGECRFSNGLERMRFFARYIYNTQEDVHFDSD 61
Query: 279 VGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISP 458
VGE+ A+T LGR DA+YWN QKD +EQ RA++DT+C+ NYQ QRRV+PTVT+ P
Sbjct: 62 VGEFTALTELGRLDAEYWNQQKDFMEQMRAKVDTLCRSNYQGIGSFLRQRRVEPTVTVYP 121
Query: 459 SKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEM 638
+K + L HHNLLVC+V FYP ++V+WF N EE AGV+ST LI+NGDWT+Q +VMLE
Sbjct: 122 AKTQPLQHHNLLVCSVNGFYPGHIEVRWFWNSHEEEAGVISTGLIQNGDWTFQTMVMLET 181
Query: 639 NLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXXXXXXXXXXHHRS 818
Q G+VYTC+VEH S SP+ VEWRAQS+SAQ K++S H RS
Sbjct: 182 VPQSGEVYTCQVEHPSRTSPLTVEWRAQSDSAQRKLMSGIGGFVLGLLFLGVGLFIHLRS 241
Query: 819 QKG 827
+KG
Sbjct: 242 KKG 244
>ref|NP_001013618.1| major histocompatibility complex, class II, DO beta [Bos taurus]
Length = 271
Score = 267 bits (683), Expect = 1e-71
Identities = 128/247 (51%), Positives = 165/247 (66%)
Frame = +3
Query: 93 WTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFIYNQEEYARFD 272
W + L A V +GRDSP+DFV Q K +CYF NGT++VR V RFI+N E+YARFD
Sbjct: 8 WVVTFLSTALRLDASVTQGRDSPEDFVTQAKADCYFTNGTEKVRFVVRFIFNLEDYARFD 67
Query: 273 SDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTI 452
SD+G + A+T LG+PDA+ WN++ DIL ++RA +D +C+ NY + T+ RRVQP VT+
Sbjct: 68 SDLGMFVALTELGKPDAERWNNRPDILARSRASVDMLCRRNYYLGAPFTVGRRVQPEVTV 127
Query: 453 SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVML 632
P K AL H NLL+C VT FYP +KV WFRNGQE+ G++ST LIRNGDWT+Q+ VML
Sbjct: 128 YPEKTPALQHRNLLLCLVTGFYPGDIKVTWFRNGQEQREGIMSTGLIRNGDWTFQMTVML 187
Query: 633 EMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXXXXXXXXXXHH 812
M + G+VYTC V+H SL SP+ VEWRAQSE + K+LS H
Sbjct: 188 AMTPELGEVYTCLVDHPSLLSPVSVEWRAQSEYSWRKILSGAAAFLVGLVFFLVEIVVHI 247
Query: 813 RSQKGLV 833
R+ KG V
Sbjct: 248 RAWKGRV 254
>ref|XP_876139.1| PREDICTED: similar to H-2 class II histocompatibility antigen, I-E
beta chain precursor [Bos taurus]
Length = 269
Score = 241 bits (614), Expect = 1e-63
Identities = 115/194 (59%), Positives = 142/194 (73%)
Frame = +3
Query: 171 VVQFKGECYFFNGTQRVRLVTRFIYNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDI 350
+VQ K EC+F NGTQ+VR + R+IYN+EE +FDS VGEYRA T +GRP A+ WN
Sbjct: 1 MVQGKSECHFSNGTQQVRFLDRYIYNREEQVQFDSLVGEYRARTEMGRPAAERWNRWPQA 60
Query: 351 LEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQV 530
L++ RA + C NY+ T+QRRVQPTVT+ P K+ L HHNLLVC+V FYP +
Sbjct: 61 LQRARAAVHAYCASNYEFFASRTVQRRVQPTVTVYPVKSRPLWHHNLLVCSVNGFYPGHI 120
Query: 531 KVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVE 710
+V+WFRNGQEE AGVVST LI NGDWT+Q++VMLE+ Q G+VY C VEH S SP+ VE
Sbjct: 121 EVRWFRNGQEEEAGVVSTGLIPNGDWTFQIMVMLEIVPQGGEVYACHVEHPSRTSPVTVE 180
Query: 711 WRAQSESAQSKMLS 752
WRAQ ES+Q KMLS
Sbjct: 181 WRAQDESSQEKMLS 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 = 156 bits (394), Expect = 4e-38
Identities = 74/137 (54%), Positives = 97/137 (70%)
Frame = +3
Query: 417 TLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIR 596
TLQ++V+PTVT+ P+K + L H++LLVC+V FY V+V+WF GQEE AGV+ST LI+
Sbjct: 90 TLQKKVEPTVTVYPAKTQPLQHNHLLVCSVNGFYLGHVEVRWFWKGQEEEAGVISTGLIQ 149
Query: 597 NGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXX 776
NGDWT++ +VMLE LQ G+VYTC++EH S +SPI EWRAQS+SAQSKM+S
Sbjct: 150 NGDWTFETIVMLETVLQSGEVYTCQLEHPSWRSPIAEEWRAQSDSAQSKMMSGTGGFALG 209
Query: 777 XXXXXXXXXXHHRSQKG 827
H R+QKG
Sbjct: 210 LLFLVVGLFTHFRNQKG 226
>ref|NP_001029503.1| hypothetical protein LOC508800 [Bos taurus]
Length = 299
Score = 71.6 bits (174), Expect = 1e-12
Identities = 44/169 (26%), Positives = 81/169 (47%), Gaps = 5/169 (2%)
Frame = +3
Query: 237 FIYNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCK---HNYQIE 407
+ Y+ +++ +FD ++ + + P + W ++ +++ +A L+ C Y
Sbjct: 134 YAYDGQDFIKFDKEIPAWVPLDPAAQNTKRKWEAEAVYVQRAKAYLEEECPGMLRRYLPY 193
Query: 408 EGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTP 587
T L R+ P+V+++ A H L C DFYP + + W R G + A
Sbjct: 194 SRTHLDRQESPSVSVTGHAAPG--HKRTLKCLAYDFYPRSIGLHWTRAGDAQEAES-GGD 250
Query: 588 LIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW--RAQSE 728
++ +G+ TYQ V++ + + Y+C VEH SL P+ V W R Q+E
Sbjct: 251 VLPSGNGTYQSWVVVGVPPEDQAPYSCHVEHRSLTRPLTVPWDPRQQAE 299
>ref|NP_001035571.1| major histocompatibility complex, class II, DM beta-chain,
expressed [Bos taurus]
Length = 262
Score = 71.6 bits (174), Expect = 1e-12
Identities = 47/157 (29%), Positives = 70/157 (44%), Gaps = 1/157 (0%)
Frame = +3
Query: 285 EYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISPSK 464
E+ + L R + + N+ ++++ L H T + R PTV ++ +
Sbjct: 65 EFGVLNGLARYLSQFLNNNSYLIQRLSNGLQNCAAHTQPFWSSLTHRTR-PPTVQVAKTT 123
Query: 465 AEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIR-NGDWTYQVLVMLEMN 641
+L C V FYP+ V + W RNGQE + +I+ NGDWTYQ + L
Sbjct: 124 PFNTRESVMLACYVWGFYPADVAITWRRNGQEVLPHGRAWRIIQPNGDWTYQTVSHLATT 183
Query: 642 LQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 752
GD YTC VEH IL +W AQ+ +S
Sbjct: 184 PSFGDTYTCVVEHIGAPELILQDWTPGLLPAQTVKVS 220
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: 43,019,489
Number of Sequences: 33508
Number of extensions: 1172198
Number of successful extensions: 4934
Number of sequences better than 1.0e-05: 10
Number of HSP's better than 0.0 without gapping: 4170
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): 4881
length of database: 16,112,626
effective HSP length: 104
effective length of database: 12,627,794
effective search space used: 3788338200
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_0086_F05
(1216 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... 308 7e-84
Alignment gi|XP_850395.1| PREDICTED: similar to HLA class II histocompati... 280 2e-75
Alignment gi|XP_861384.1| PREDICTED: similar to HLA class II histocompati... 267 2e-71
Alignment gi|XP_849737.1| PREDICTED: similar to HLA class II histocompati... 70 4e-12
Alignment gi|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris] 70 4e-12
Alignment gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati... 69 9e-12
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... 60 3e-09
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 (993), Expect = e-107
Identities = 185/258 (71%), Positives = 212/258 (82%)
Frame = +3
Query: 54 MSGMVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVT 233
MSG + L +PRG WTAA+ ++LVVL PVAEGRDSPQDFV Q+K ECYF NGT+RVRL+T
Sbjct: 1 MSGKMTLCIPRGFWTAAVMMILVVLSIPVAEGRDSPQDFVFQYKAECYFTNGTERVRLLT 60
Query: 234 RFIYNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEG 413
++IYN+EE+ RFDSDVGE+RAVT LGRPDA+YWN QKD +++ RAELDTVC+HNY EE
Sbjct: 61 KYIYNREEFVRFDSDVGEFRAVTELGRPDAEYWNRQKDEMDRVRAELDTVCRHNYGREEL 120
Query: 414 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 593
TTLQRRV+PTVTI PSK E LNHHNLLVC+VTDFYP Q+KV+WFRN QE+TAGVVSTPLI
Sbjct: 121 TTLQRRVEPTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLI 180
Query: 594 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 773
RNGDWT+Q+LVMLEM QRGDVYTC VEH+SLQSPI V+WRAQSESAQSKMLS
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHASLQSPITVQWRAQSESAQSKMLSGIGGFVL 240
Query: 774 XXXXXXXXXXXHHRSQKG 827
HRSQKG
Sbjct: 241 GLIFLGLGLIIRHRSQKG 258
>ref|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis familiaris]
Length = 266
Score = 308 bits (789), Expect = 7e-84
Identities = 150/255 (58%), Positives = 184/255 (72%)
Frame = +3
Query: 63 MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFI 242
MV L G W AL ++L+VL P A RD+P F+ K ECYF NGT+RVR V R+I
Sbjct: 1 MVCLCFLGGSWMTALMLILMVLNPPFAWARDTPPHFLEVAKSECYFTNGTERVRFVERYI 60
Query: 243 YNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTL 422
+N+EE+ RFDSDVGE+RAVT LGRP A+ WN QK+ILEQ RA +DT C+HNY + E T+
Sbjct: 61 HNREEFVRFDSDVGEFRAVTELGRPVAESWNGQKEILEQERATVDTYCRHNYGVIESFTV 120
Query: 423 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 602
QRRV+PTVT+ P+K + L HHNLLVC+V FYP ++V+W RNGQEE AGVVST LIRNG
Sbjct: 121 QRRVEPTVTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNG 180
Query: 603 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 782
DWT+Q+LVMLE+ Q G+VYTC+VEH SL SP+ VEWRAQS+SAQSKMLS
Sbjct: 181 DWTFQILVMLEIVPQSGEVYTCQVEHPSLTSPVTVEWRAQSDSAQSKMLSGIGGFVLGLL 240
Query: 783 XXXXXXXXHHRSQKG 827
+ 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 = 280 bits (717), Expect = 2e-75
Identities = 132/247 (53%), Positives = 172/247 (69%)
Frame = +3
Query: 93 WTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFIYNQEEYARFD 272
W AL V + L + + +GRDSP+DFV+Q K +CYF NGT++V+ V RFI+N EEYARFD
Sbjct: 8 WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67
Query: 273 SDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTI 452
S VG + A+T LG+PDA+ WNSQ ILE++RA +D +C+HNY++ T+ R+VQP VT+
Sbjct: 68 SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTV 127
Query: 453 SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVML 632
P + ++ HHNLL+C+VT FYP +K++WFRNGQEE GV+ST LIRNGDWT+Q +VML
Sbjct: 128 YPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVML 187
Query: 633 EMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXXXXXXXXXXHH 812
EM + GDVYTC V H SL SP+ VEWRAQS + KMLS
Sbjct: 188 EMTPELGDVYTCLVNHPSLLSPVSVEWRAQSTYSWRKMLSGIAAFLLGLIFLLVGTVICL 247
Query: 813 RSQKGLV 833
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 = 267 bits (682), Expect = 2e-71
Identities = 119/207 (57%), Positives = 157/207 (75%)
Frame = +3
Query: 93 WTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFIYNQEEYARFD 272
W AL V + L + + +GRDSP+DFV+Q K +CYF NGT++V+ V RFI+N EEYARFD
Sbjct: 8 WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67
Query: 273 SDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTI 452
S VG + A+T LG+PDA+ WNSQ ILE++RA +D +C+HNY++ T+ R+VQP VT+
Sbjct: 68 SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTV 127
Query: 453 SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVML 632
P + ++ HHNLL+C+VT FYP +K++WFRNGQEE GV+ST LIRNGDWT+Q +VML
Sbjct: 128 YPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVML 187
Query: 633 EMNLQRGDVYTCRVEHSSLQSPILVEW 713
EM + GDVYTC V H SL SP+ VEW
Sbjct: 188 EMTPELGDVYTCLVNHPSLLSPVSVEW 214
>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 = 70.1 bits (170), Expect = 4e-12
Identities = 43/144 (29%), Positives = 64/144 (44%), Gaps = 1/144 (0%)
Frame = +3
Query: 285 EYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISPSK 464
E+ + L +DY N Q+ + ++ L H Q G+ R PTV ++ S
Sbjct: 65 EFGTLNVLANYLSDYLNQQEYLHQRLSNGLQDCATHT-QSFWGSLTHRTRPPTVQVAKST 123
Query: 465 AEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIR-NGDWTYQVLVMLEMN 641
+L C V FYP+ V + W +NGQ + + + + NGDWTYQ + L
Sbjct: 124 PFNTKESVMLACYVWGFYPADVTISWRKNGQPVPSHSSALNMAQPNGDWTYQTVSHLATT 183
Query: 642 LQRGDVYTCRVEHSSLQSPILVEW 713
D YTC VEH P+ +W
Sbjct: 184 PSYEDTYTCVVEHIGAPEPVCEDW 207
>ref|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris]
Length = 254
Score = 70.1 bits (170), Expect = 4e-12
Identities = 60/217 (27%), Positives = 85/217 (39%)
Frame = +3
Query: 63 MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFI 242
M L P+ W A+ V++ A D +F+ F G+ F ++ V R
Sbjct: 14 MAFLMGPQESW--AVKEEHVIIQAEFYLTPDPSGEFMFDFDGDEIFHVDMEKKETVWRL- 70
Query: 243 YNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTL 422
EE+ RF S + A L D +A LDT+ K + T
Sbjct: 71 ---EEFGRFAS----FEAQGALANIAVD------------KANLDTMIKRSNH-----TP 106
Query: 423 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 602
V P VT+ + L N+L+C + F P + V W RNG T GV T +
Sbjct: 107 NTNVPPEVTVLSNTPVELGEPNILICFIDKFSPPVINVTWLRNGNPVTTGVSETIFLPRE 166
Query: 603 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 713
D ++ L DVY C+VEH L P+L W
Sbjct: 167 DHLFRKFHYLPFLPSAEDVYDCKVEHWGLDEPLLKHW 203
>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 = +3
Query: 363 RAELDTVCKHNYQIE--EGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKV 536
+A LD + + + + GT L + P V + P L N+L+C V + +P + +
Sbjct: 63 KAHLDVLVERSNRTRAINGTHLSSPLPPRVAVLPKFRVELGQPNVLICIVDNIFPPVINI 122
Query: 537 QWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWR 716
W RNGQ + GV T D ++ L D+Y C+VEH L+ P+L W
Sbjct: 123 TWLRNGQIISEGVAQTSFYSQPDHLFRKFCYLTFVPSAEDMYDCKVEHWGLEEPLLRHWE 182
Query: 717 AQ 722
Q
Sbjct: 183 PQ 184
>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 = +3
Query: 438 PTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQ 617
P VT+ L N L+C V + +P + V W +N T GV T GD ++
Sbjct: 113 PEVTVFSKSPVMLGQPNTLICLVDNIFPPVINVTWLKNRHSVTEGVSETSFFAKGDHSFS 172
Query: 618 VLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKM 746
+ 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 = 60.5 bits (145), Expect = 3e-09
Identities = 46/168 (27%), Positives = 81/168 (48%), Gaps = 8/168 (4%)
Frame = +3
Query: 234 RFIYNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQ--IE 407
R+ Y+ + F+ ++ + P W +++ +++ +A L+ C Q +E
Sbjct: 136 RYAYDGRNFIEFNKEIPAWVPQDPAALNTKKKWEAEEVYVQRAKAYLEEECPVMLQRYLE 195
Query: 408 EGTT-LQRRVQPTVTI-SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFR--NGQEETAGV 575
G T L R+ P+V+I S E + L C V+ FYP ++ + W + + QE +G
Sbjct: 196 YGKTYLDRQEPPSVSITSHGTPEGIQ---TLKCWVSGFYPQEIDLHWIQADDTQETKSGG 252
Query: 576 VSTPLIRNGDWTYQVLVMLEMNLQ--RGDVYTCRVEHSSLQSPILVEW 713
P +G+ TYQ V++ + Q Y+C V+HSSL P+ V W
Sbjct: 253 ALLP---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 = +3
Query: 420 LQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRN 599
LQR+V+P +S + H L VC V+ FYP V V W R G++E G + + ++ N
Sbjct: 199 LQRKVRPEAWLSAGSSPGPGHLRL-VCHVSGFYPKPVWVSWMR-GEQEQQGTLYSDILPN 256
Query: 600 GDWTYQVLVMLEMNLQRGDVYTCRVEHSSL 689
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: 50,425,244
Number of Sequences: 33732
Number of extensions: 1374385
Number of successful extensions: 6218
Number of sequences better than 1.0e-05: 10
Number of HSP's better than 0.0 without gapping: 4990
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): 6173
length of database: 19,266,565
effective HSP length: 105
effective length of database: 15,724,705
effective search space used: 4701686795
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_0086_F05
(1216 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] 74 9e-15
Alignment gi|NP_998996.1| CD1 antigen [Sus scrofa] 63 2e-11
Alignment gi|NP_999362.2| neonatal Fc receptor FcRn [Sus scrofa] 62 2e-11
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 = 73.6 bits (179), Expect = 9e-15
Identities = 49/179 (27%), Positives = 79/179 (44%), Gaps = 5/179 (2%)
Frame = +3
Query: 192 CYFFNGTQRVRLVTRFIYNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAE 371
CY + +R ++F Y+ +Y + D+ + AV + W ++ + EQ+RA
Sbjct: 122 CYVARDGRLLRGYSQFAYDGADYIVLNEDLRSWTAVGMAAQITRRKWE-EETVAEQSRAY 180
Query: 372 LDTVCK---HNYQIEEGTTLQRRVQPT--VTISPSKAEALNHHNLLVCAVTDFYPSQVKV 536
L+ C H Y TLQR P VT PS + L C FYP ++ +
Sbjct: 181 LEVACVQSLHRYLANGKETLQRSDPPKTHVTRHPSSDNKVT----LRCWALGFYPKEISL 236
Query: 537 QWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 713
W + GQ+++ V +GD T++ L + YTC V+H LQ P+ + W
Sbjct: 237 TWQQEGQDQSQDVEVVETRPSGDGTFRKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRW 295
>ref|NP_998996.1| CD1 antigen [Sus scrofa]
Length = 339
Score = 62.8 bits (151), Expect = 2e-11
Identities = 57/194 (29%), Positives = 86/194 (44%), Gaps = 8/194 (4%)
Frame = +3
Query: 168 FVVQFKGECYFFNGTQRVRLVTRFIYNQEEYARFDSDVGEYRAVTPLGRPDADY----WN 335
F VQ G C ++G V V R Y ++A F ++ +P G A +N
Sbjct: 112 FDVQIAGGCDLYHGETSVGFV-RIAYQGSDFASFQNNSW---LPSPKGGTRAQLVCKLFN 167
Query: 336 SQKDILEQTRAELDTVCKHNYQ--IEEGTT-LQRRVQPTVTISPSKAEALNHHNLLVCAV 506
+ LE L C ++ G LQR+V+P +S S H +LVC V
Sbjct: 168 LYQGTLEIIHKLLSDTCPRFVLGLLDAGKADLQRQVRPEAWLS-SGPNPSPGHLMLVCHV 226
Query: 507 TDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSS 686
+ FYP + V W R+ QE+ G ++ N D T+ + V L++ +CRV+HSS
Sbjct: 227 SGFYPKPIWVMWMRDEQEQ-PGTQQGDILPNADGTWYLRVTLDVAAGEASGLSCRVKHSS 285
Query: 687 L-QSPILVEWRAQS 725
L I++ W S
Sbjct: 286 LGGQDIILYWEQHS 299
>ref|NP_999362.2| neonatal Fc receptor FcRn [Sus scrofa]
Length = 356
Score = 62.4 bits (150), Expect = 2e-11
Identities = 43/172 (25%), Positives = 78/172 (45%), Gaps = 3/172 (1%)
Frame = +3
Query: 228 VTRFIYNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNY--Q 401
V F N EE+ +FD+ +G + P R W + D + + + L C H
Sbjct: 130 VATFALNGEEFMKFDTKLGTWDGEWPEARTIGSKWMQEPDAVNKEKTFLLYSCPHRLLGH 189
Query: 402 IEEGT-TLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVV 578
+E G L+ + P++ + A ++L C FYP ++++++ RNG AG
Sbjct: 190 LERGRGNLEWKEPPSMRMKARPGTAPG-FSVLTCIAFSFYPPELQLRFLRNGL--AAGSG 246
Query: 579 STPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESA 734
+ + NGD ++ L + Y C V+H+ L P+ VE + ++S+
Sbjct: 247 ESDIGPNGDGSFHAWSSLTVKSGDEHHYCCVVQHAGLAQPLTVELESPAKSS 298
>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 = +3
Query: 456 PSKAEALNHH-------NLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTY 614
P K + + H N L C V+ F+P Q+++ +NG++ A + L + DW++
Sbjct: 24 PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAE--QSDLSFSKDWSF 81
Query: 615 QVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 713
+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 = +3
Query: 435 QPTVTISPSKAEALNHHNLLV-CAVTDFYPSQVKVQWFRNGQEETAG-VVSTPLIRNGDW 608
+P V P AE L+ + V C V FYP + V+W NGQ E G +TP ++ D
Sbjct: 370 EPQVYTLPPPAEELSRSKVTVTCLVIGFYPPDIHVEWKSNGQPEPEGNYRTTPPQQDVDG 429
Query: 609 T---YQVLVMLEMNLQRGDVYTCRVEHSSLQS 695
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: 1,144,510
Number of Sequences: 1040
Number of extensions: 29853
Number of successful extensions: 121
Number of sequences better than 1.0e-05: 5
Number of HSP's better than 0.0 without gapping: 105
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): 116
length of database: 434,620
effective HSP length: 79
effective length of database: 352,460
effective search space used: 114549500
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_0086_F05
(1216 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 ... 380 e-105
Alignment gi|NP_872355.1| major histocompatibility complex, class II, DQ ... 335 4e-92
Alignment gi|NP_002115.1| major histocompatibility complex, class II, DR ... 317 2e-86
Alignment gi|XP_945926.1| PREDICTED: similar to HLA class II histocompati... 308 5e-84
Alignment gi|NP_068818.4| major histocompatibility complex, class II, DR ... 307 1e-83
Alignment gi|NP_002116.2| major histocompatibility complex, class II, DR ... 307 1e-83
Alignment gi|NP_002112.3| major histocompatibility complex, class II, DP ... 305 4e-83
Alignment gi|NP_072049.2| major histocompatibility complex, class II, DR ... 295 5e-80
Alignment gi|XP_949921.1| PREDICTED: similar to HLA class II histocompati... 286 2e-77
Alignment gi|XP_949915.1| PREDICTED: similar to HLA class II histocompati... 282 5e-76
>ref|NP_002114.2| major histocompatibility complex, class II, DQ beta 1 precursor
[Homo sapiens]
Length = 261
Score = 380 bits (977), Expect = e-105
Identities = 188/260 (72%), Positives = 211/260 (81%)
Frame = +3
Query: 54 MSGMVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVT 233
MS ALR+P GL A +T+ML +L PVAEGRDSP+DFV QFKG CYF NGT+RVRLV+
Sbjct: 1 MSWKKALRIPGGLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVS 60
Query: 234 RFIYNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEG 413
R IYN+EE RFDSDVGE+RAVT LG P A+YWNSQKDILE+ RA +D VC+HNYQ+E
Sbjct: 61 RSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELR 120
Query: 414 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 593
TTLQRRV+PTVTISPS+ EALNHHNLLVC+VTDFYP+Q+KV+WFRN QEETAGVVSTPLI
Sbjct: 121 TTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLI 180
Query: 594 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 773
RNGDWT+Q+LVMLEM QRGDVYTC VEH SLQSPI VEWRAQSESAQSKMLS
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVL 240
Query: 774 XXXXXXXXXXXHHRSQKGLV 833
HHRSQKGL+
Sbjct: 241 GLIFLGLGLIIHHRSQKGLL 260
>ref|NP_872355.1| major histocompatibility complex, class II, DQ beta 2 [Homo
sapiens]
Length = 231
Score = 335 bits (860), Expect = 4e-92
Identities = 160/221 (72%), Positives = 187/221 (84%)
Frame = +3
Query: 54 MSGMVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVT 233
MS +AL++P G W AA+TVMLV+L PVAE RD P+DF+VQFKG CYF NGT+RVR V
Sbjct: 1 MSWKMALQIPGGFWAAAVTVMLVMLSTPVAEARDFPKDFLVQFKGMCYFTNGTERVRGVA 60
Query: 234 RFIYNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEG 413
R+IYN+EEY RFDSDVGE++AVT LGR D WN+ KD LEQ RA +D VC+HNY+ E
Sbjct: 61 RYIYNREEYGRFDSDVGEFQAVTELGRSIED-WNNYKDFLEQERAAVDKVCRHNYEAELR 119
Query: 414 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 593
TTLQR+V+PTVTISPS+ EALNHHNLLVC+VTDFYP+Q+KVQWFRN QEETAGVVST LI
Sbjct: 120 TTLQRQVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVQWFRNDQEETAGVVSTSLI 179
Query: 594 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWR 716
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 = 317 bits (811), Expect = 2e-86
Identities = 156/255 (61%), Positives = 189/255 (74%)
Frame = +3
Query: 63 MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFI 242
MV L+LP G ALTV L+VL +P+A D+ F+ Q K EC+FFNGT+RVRL+ R I
Sbjct: 1 MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVRLLERCI 60
Query: 243 YNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTL 422
YNQEE RFDSDVGEYRAVT LGRPDA+YWNSQKD+LEQ RA +DT C+HNY + E T+
Sbjct: 61 YNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTV 120
Query: 423 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 602
QRRV+P VT+ PSK + L HHNLLVC+V+ FYP ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 603 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 782
DWT+Q LVMLE + G+VYTC+VEH S+ SP+ VEWRA+SESAQSKMLS
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSESAQSKMLSGVGGFVLGLL 240
Query: 783 XXXXXXXXHHRSQKG 827
+ 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 = 154/255 (60%), Positives = 187/255 (73%)
Frame = +3
Query: 63 MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFI 242
MV L+LP G AALTV L+VL +P+A D+ F+ Q K EC+FFNGT+RVR + R I
Sbjct: 1 MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60
Query: 243 YNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTL 422
YNQEE RFDSDVGEYRAVT LGRP A+ WNSQKD LE+ RAE+DTVC+HNY + E T+
Sbjct: 61 YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120
Query: 423 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 602
QRRV P VT+ P+K + L HHNLLVC+V+ FYP ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 603 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 782
DWT+Q LVMLE + G+VYTC+VEH S+ SP+ VEWRA+SESAQSKMLS
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEWRARSESAQSKMLSGVGGFVLGLL 240
Query: 783 XXXXXXXXHHRSQKG 827
+ R+QKG
Sbjct: 241 FLGAGLFIYFRNQKG 255
>ref|NP_068818.4| major histocompatibility complex, class II, DR beta 4 precursor
[Homo sapiens]
Length = 266
Score = 307 bits (787), Expect = 1e-83
Identities = 150/255 (58%), Positives = 188/255 (73%)
Frame = +3
Query: 63 MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFI 242
MV L+LP G AALTV L VL +P+A D+ F+ Q K EC+F NGT+RV + R+I
Sbjct: 1 MVCLKLPGGSCMAALTVTLTVLSSPLALAGDTQPRFLEQAKCECHFLNGTERVWNLIRYI 60
Query: 243 YNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTL 422
YNQEEYAR++SD+GEY+AVT LGRPDA+YWNSQKD+LE+ RAE+DT C++NY + E T+
Sbjct: 61 YNQEEYARYNSDLGEYQAVTELGRPDAEYWNSQKDLLERRRAEVDTYCRYNYGVVESFTV 120
Query: 423 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 602
QRRVQP VT+ PSK + L HHNLLVC+V FYP ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVQPKVTVYPSKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 603 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 782
DWT+Q LVMLE + G+VYTC+VEH S+ SP+ V+W A+SESAQSKMLS
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSMMSPLTVQWSARSESAQSKMLSGVGGFVLGLL 240
Query: 783 XXXXXXXXHHRSQKG 827
+ R+QKG
Sbjct: 241 FLGTGLFIYFRNQKG 255
>ref|NP_002116.2| major histocompatibility complex, class II, DR beta 5 precursor
[Homo sapiens]
Length = 266
Score = 307 bits (786), Expect = 1e-83
Identities = 151/255 (59%), Positives = 185/255 (72%)
Frame = +3
Query: 63 MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFI 242
MV L+LP G + A LTV L+VL +P+A D+ F+ Q K EC+FFNGT+RVR + R I
Sbjct: 1 MVCLKLPGGSYMAKLTVTLMVLSSPLALAGDTRPRFLQQDKYECHFFNGTERVRFLHRDI 60
Query: 243 YNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTL 422
YNQEE RFDSDVGEYRAVT LGRPDA+YWNSQKD LE RA +DT C+HNY + E T+
Sbjct: 61 YNQEEDLRFDSDVGEYRAVTELGRPDAEYWNSQKDFLEDRRAAVDTYCRHNYGVGESFTV 120
Query: 423 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 602
QRRV+P VT+ P++ + L HHNLLVC+V FYP ++V+WFRN QEE AGVVST LI+NG
Sbjct: 121 QRRVEPKVTVYPARTQTLQHHNLLVCSVNGFYPGSIEVRWFRNSQEEKAGVVSTGLIQNG 180
Query: 603 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 782
DWT+Q LVMLE + G+VYTC+VEH S+ SP+ VEWRAQSESAQSKMLS
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRAQSESAQSKMLSGVGGFVLGLL 240
Query: 783 XXXXXXXXHHRSQKG 827
+ ++QKG
Sbjct: 241 FLGAGLFIYFKNQKG 255
>ref|NP_002112.3| major histocompatibility complex, class II, DP beta 1 precursor
[Homo sapiens]
Length = 258
Score = 305 bits (782), Expect = 4e-83
Identities = 150/254 (59%), Positives = 188/254 (74%)
Frame = +3
Query: 63 MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFI 242
M+ L++ T ALT +L+VL V +GR +P++++ Q + ECY FNGTQR + R+I
Sbjct: 1 MMVLQVSAAPRTVALTALLMVLLTSVVQGRATPENYLFQGRQECYAFNGTQR--FLERYI 58
Query: 243 YNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTL 422
YN+EE+ARFDSDVGE+RAVT LGRP A+YWNSQKDILE+ RA D +C+HNY++ TL
Sbjct: 59 YNREEFARFDSDVGEFRAVTELGRPAAEYWNSQKDILEEKRAVPDRMCRHNYELGGPMTL 118
Query: 423 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 602
QRRVQP V +SPSK L HHNLLVC VTDFYP ++V+WF NGQEETAGVVST LIRNG
Sbjct: 119 QRRVQPRVNVSPSKKGPLQHHNLLVCHVTDFYPGSIQVRWFLNGQEETAGVVSTNLIRNG 178
Query: 603 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 782
DWT+Q+LVMLEM Q+GDVYTC+VEH+SL SP+ VEW+AQS+SA+SK L+
Sbjct: 179 DWTFQILVMLEMTPQQGDVYTCQVEHTSLDSPVTVEWKAQSDSARSKTLTGAGGFVLGLI 238
Query: 783 XXXXXXXXHHRSQK 824
H RS+K
Sbjct: 239 ICGVGIFMHRRSKK 252
>ref|NP_072049.2| major histocompatibility complex, class II, DR beta 3 precursor
[Homo sapiens]
Length = 266
Score = 295 bits (755), Expect = 5e-80
Identities = 146/255 (57%), Positives = 182/255 (71%)
Frame = +3
Query: 63 MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFI 242
MV L+LP G AALTV L+VL + +A D+ F+ K EC+FFNGT+RVR + R+
Sbjct: 1 MVCLKLPGGSSLAALTVTLMVLSSRLAFAGDTRPRFLELRKSECHFFNGTERVRYLDRYF 60
Query: 243 YNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTL 422
+NQEE+ RFDSDVGEYRAVT LGRP A+ WNSQKD+LEQ R +D C+HNY + E T+
Sbjct: 61 HNQEEFLRFDSDVGEYRAVTELGRPVAESWNSQKDLLEQKRGRVDNYCRHNYGVGESFTV 120
Query: 423 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 602
QRRV P VT+ P+K + L HHNLLVC+V+ FYP ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVHPQVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 603 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 782
DWT+Q LVMLE + G+VYTC+VEH S+ S + VEWRA+SESAQSKMLS
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSALTVEWRARSESAQSKMLSGVGGFVLGLL 240
Query: 783 XXXXXXXXHHRSQKG 827
+ 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 = 286 bits (733), Expect = 2e-77
Identities = 139/220 (63%), Positives = 169/220 (76%)
Frame = +3
Query: 63 MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFI 242
MV L+LP G AALTV L+VL +P+A D+ F+ Q K EC+FFNGT+RVR + R I
Sbjct: 1 MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60
Query: 243 YNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTL 422
YNQEE RFDSDVGEYRAVT LGRP A+ WNSQKD LE+ RAE+DTVC+HNY + E T+
Sbjct: 61 YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120
Query: 423 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 602
QRRV P VT+ P+K + L HHNLLVC+V+ FYP ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 603 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQ 722
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 = 282 bits (721), Expect = 5e-76
Identities = 137/220 (62%), Positives = 165/220 (75%)
Frame = +3
Query: 168 FVVQFKGECYFFNGTQRVRLVTRFIYNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKD 347
F+ Q K EC+FFNGT+RVR + R IYNQEE RFDSDVGEYRAVT LGRP A+ WNSQKD
Sbjct: 54 FLKQDKFECHFFNGTERVRYLHRGIYNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKD 113
Query: 348 ILEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQ 527
LE+ RAE+DTVC+HNY + E T+QRRV P VT+ P+K + L HHNLLVC+V+ FYP
Sbjct: 114 FLERRRAEVDTVCRHNYGVGESFTVQRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGS 173
Query: 528 VKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILV 707
++V+WFRNGQEE AGVVST LI+NGDWT+Q LVMLE + G+VYTC+VEH S+ SP+ V
Sbjct: 174 IEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTV 233
Query: 708 EWRAQSESAQSKMLSXXXXXXXXXXXXXXXXXXHHRSQKG 827
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: 48,964,829
Number of Sequences: 39411
Number of extensions: 1377078
Number of successful extensions: 6261
Number of sequences better than 1.0e-05: 10
Number of HSP's better than 0.0 without gapping: 4925
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): 6193
length of database: 17,774,539
effective HSP length: 104
effective length of database: 13,675,795
effective search space used: 4102738500
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_0086_F05
(1216 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 ... 334 1e-91
Alignment gi|NP_034512.1| histocompatibility 2, class II antigen E beta [... 290 3e-78
Alignment gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/... 266 3e-71
Alignment gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ... 254 1e-67
Alignment gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ... 78 2e-14
Alignment gi|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus ... 77 4e-14
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_034511.2| histocompatibility 2, class II antigen E alpha ... 65 2e-10
Alignment gi|XP_908790.2| PREDICTED: similar to histocompatibility 2, Q r... 64 3e-10
>ref|NP_996988.1| histocompatibility 2, class II antigen A, beta 1 [Mus musculus]
Length = 265
Score = 334 bits (857), Expect = 1e-91
Identities = 169/255 (66%), Positives = 199/255 (78%), Gaps = 1/255 (0%)
Frame = +3
Query: 66 VALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFIY 245
+AL++P L +AA+ V+L+VL +P EG DS + FV QF GECYF NGTQR+R VTR+IY
Sbjct: 1 MALQIPSLLLSAAV-VVLMVLSSPGTEGGDSERHFVYQFMGECYFTNGTQRIRYVTRYIY 59
Query: 246 NQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQ-IEEGTTL 422
N+EEY R+DSDVGE+RAVT LGRPDA+YWNSQ +ILE+TRAELDTVC+HNY+ E T+L
Sbjct: 60 NREEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSL 119
Query: 423 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 602
+R QP V IS S+ EALNHHN LVC+VTDFYP+Q+KV+WFRNGQEET GV ST LIRNG
Sbjct: 120 RRLEQPNVVISLSRTEALNHHNTLVCSVTDFYPTQIKVRWFRNGQEETVGVSSTQLIRNG 179
Query: 603 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 782
DWT+QVLVMLEM +RG+VYTC VEH SL+SPI VEWRAQSESA SKMLS
Sbjct: 180 DWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRAQSESAWSKMLSGIGGCVLGVI 239
Query: 783 XXXXXXXXHHRSQKG 827
HRSQKG
Sbjct: 240 FLGLGLFIRHRSQKG 254
>ref|NP_034512.1| histocompatibility 2, class II antigen E beta [Mus musculus]
Length = 264
Score = 290 bits (741), Expect = 3e-78
Identities = 140/250 (56%), Positives = 178/250 (71%)
Frame = +3
Query: 78 LPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFIYNQEE 257
LPR AA+ ++L VL PVA RDS F+ K EC+F+NGTQRVR + R+ YN EE
Sbjct: 4 LPRVPCVAAVILLLTVLSPPVALVRDSRPWFLEYCKSECHFYNGTQRVRFLKRYFYNLEE 63
Query: 258 YARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTLQRRVQ 437
RFDSDVGE+RAVT LGRPDA+ WNSQ +IL++ RA +DT C+HNY+I + + RRV+
Sbjct: 64 NLRFDSDVGEFRAVTELGRPDAENWNSQPEILDEKRAAVDTYCRHNYEIFDNFLVPRRVE 123
Query: 438 PTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQ 617
PTVT+ P+K + L HHNLLVC+V+DFYP ++V+WFRNG+EE G+VST L+RNGDWT+Q
Sbjct: 124 PTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQ 183
Query: 618 VLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXXXXXXX 797
LVMLE Q G+VYTC+VEH SL P+ VEW+AQS SAQ+KMLS
Sbjct: 184 TLVMLETVPQSGEVYTCQVEHPSLTDPVTVEWKAQSTSAQNKMLSGVGGFVLGLLFLRAG 243
Query: 798 XXXHHRSQKG 827
+ 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 = 266 bits (680), Expect = 3e-71
Identities = 131/230 (56%), Positives = 171/230 (74%)
Frame = +3
Query: 63 MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFI 242
MV+L LPRGL AA+ + L++L PV RD F+ Q K EC++FNG +RV VTRFI
Sbjct: 1 MVSLWLPRGLCVAAVILSLMMLTPPVILVRDPRPRFLEQLKAECHYFNGKERVWSVTRFI 60
Query: 243 YNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTL 422
YNQEE+ARF+SD G++ AVT LGRP +Y N+QKD+L+ RA +D C++NY + + L
Sbjct: 61 YNQEEFARFNSDFGKFLAVTELGRPIVEYLNTQKDMLDNYRASVDR-CRNNYDLVDIFML 119
Query: 423 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 602
+ +P VT+ P+K + L HHNLLVC+V DFYP ++V+WFRNG+EE GVVST LI+N
Sbjct: 120 NLKAEPKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNR 179
Query: 603 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 752
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 = 254 bits (649), Expect = 1e-67
Identities = 121/250 (48%), Positives = 163/250 (65%)
Frame = +3
Query: 84 RGLWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFIYNQEEYA 263
R W AL V L+ L + + EGRDSP++FV+Q K +CYF NGT++V L+ RFI+N EEY
Sbjct: 5 RAPWVVALLVNLMRLDSFMIEGRDSPENFVIQAKADCYFTNGTEKVHLLVRFIFNLEEYL 64
Query: 264 RFDSDVGEYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTLQRRVQPT 443
FDSD+G + A+T LG PDAD WN + D+LE +RA ++ VC+ Y++ T++R V P
Sbjct: 65 HFDSDLGMFVALTELGEPDADQWNKRLDLLETSRAAVNMVCRQKYKLGAPFTVERNVPPE 124
Query: 444 VTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVL 623
VT+ P + L HNLL+C+VT FYP + V+WFRNGQEE +GV+ST L+RNGDWT+Q
Sbjct: 125 VTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVRNGDWTFQTT 184
Query: 624 VMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXXXXXXXXX 803
VMLEM + GD+Y+C VEH L P+ V W AQSE + K+LS
Sbjct: 185 VMLEMIPELGDIYSCLVEHPGLLRPVSVAWMAQSEYSWKKILSGAAVFLLGLIVFLVGVV 244
Query: 804 XHHRSQKGLV 833
H ++QK V
Sbjct: 245 IHLKAQKASV 254
>ref|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus musculus]
Length = 261
Score = 78.2 bits (191), Expect = 2e-14
Identities = 59/221 (26%), Positives = 92/221 (41%), Gaps = 13/221 (5%)
Frame = +3
Query: 90 LWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFIYNQEEYARF 269
LW L + L +GA FV + C + +N++ A +
Sbjct: 4 LWLLLLVLSLHCMGAG---------GFVAHVESTCVLNDAGTPQDFTYCVSFNKDLLACW 54
Query: 270 DSDVG-----EYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTLQRRV 434
D DVG E+ ++ L ++ N Q+ ++ + + L H + T + R
Sbjct: 55 DPDVGKIVPCEFGVLSRLAEIISNILNEQESLIHRLQNGLQDCATHTQPFWDVLTHRTRA 114
Query: 435 QPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQ--------EETAGVVSTPL 590
P+V ++ + +L C V FYP+ V + W +NGQ E+TA
Sbjct: 115 -PSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQP----- 168
Query: 591 IRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 713
NGDWTYQ + L + GDVYTC V+HS PI +W
Sbjct: 169 --NGDWTYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDW 207
>ref|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus musculus]
Length = 261
Score = 77.0 bits (188), Expect = 4e-14
Identities = 59/221 (26%), Positives = 90/221 (40%), Gaps = 13/221 (5%)
Frame = +3
Query: 90 LWTAALTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFFNGTQRVRLVTRFIYNQEEYARF 269
LW L + L +GA FV + C + +N++ A +
Sbjct: 4 LWLLLLVLSLDCMGAG---------GFVAHVESTCVLDDAGTPQDFTYCVSFNKDLLACW 54
Query: 270 DSDVG-----EYRAVTPLGRPDADYWNSQKDILEQTRAELDTVCKHNYQIEEGTTLQRRV 434
D DVG E+ + P + N ++ +L++ + L H T + R
Sbjct: 55 DPDVGKIVPCEFGVLYPWAENFSRILNKEESLLQRLQNGLLDCASHTQPFWNALTHRTRA 114
Query: 435 QPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQ--------EETAGVVSTPL 590
P+V ++ + +L C V FYP+ V + W +NGQ E+TA
Sbjct: 115 -PSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQP----- 168
Query: 591 IRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 713
NGDWTYQ + L + GDVYTC V+HS PI +W
Sbjct: 169 --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 = +3
Query: 381 VCKHNYQI---EEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRN 551
V KHN + +T P T+ P L N L+C V + +P + + W RN
Sbjct: 92 VVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRN 151
Query: 552 GQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSES 731
+ GV T N D+++ L L D+Y C+VEH L+ P+L W + +
Sbjct: 152 SKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEPEIPA 211
Query: 732 AQSKM 746
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 = +3
Query: 432 VQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWT 611
V P VT+ P L N+L+C V D +P + V W RN Q T GV T +
Sbjct: 111 VPPRVTVLPKTRVELGKPNVLICIVDDIFPPVINVTWLRNSQPITKGVAQTSFYSQPNHR 170
Query: 612 YQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQ 722
++ L DVY C+VEH L +P+L W Q
Sbjct: 171 FRKFHYLTFVPSAEDVYDCKVEHWGLDTPLLQHWEPQ 207
>ref|NP_034511.2| histocompatibility 2, class II antigen E alpha [Mus musculus]
Length = 255
Score = 64.7 bits (156), Expect = 2e-10
Identities = 49/193 (25%), Positives = 76/193 (39%)
Frame = +3
Query: 153 DSPQDFVVQFKGECYFFNGTQRVRLVTRFIYNQEEYARFDSDVGEYRAVTPLGRPDADYW 332
D +F+ F G+ F ++ + R EE+A+F S + A L D
Sbjct: 42 DKRGEFMFDFDGDEIFHVDIEKSETIWRL----EEFAKFAS----FEAQGALANIAVD-- 91
Query: 333 NSQKDILEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTD 512
+A LD + + + T V P VT+ L N+L+C +
Sbjct: 92 ----------KANLDVMKERS-----NNTPDANVAPEVTVLSRSPVNLGEPNILICFIDK 136
Query: 513 FYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQ 692
F P V V WFRNG+ T GV T + D ++ L D Y C V+H L+
Sbjct: 137 FSPPVVNVTWFRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLE 196
Query: 693 SPILVEWRAQSES 731
P+ W + ++
Sbjct: 197 EPLRKHWEFEEKT 209
>ref|XP_908790.2| PREDICTED: similar to histocompatibility 2, Q region locus 6
isoform 2 [Mus musculus]
Length = 465
Score = 63.9 bits (154), Expect = 3e-10
Identities = 46/185 (24%), Positives = 75/185 (40%), Gaps = 5/185 (2%)
Frame = +3
Query: 174 VQFKGECYFFNGTQRVRLVTRFIYNQEEYARFDSDVGEYRAVTPLGRPDADYWNSQKDIL 353
+Q+ C + + +R +F Y +Y + D+ + A + W Q I
Sbjct: 232 LQWMYGCDVGSDERLLRGYLQFAYEGRDYIALNEDLKTWTAADMAAQITLHKWE-QAGIA 290
Query: 354 EQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISPSKAEALNHHN-----LLVCAVTDFY 518
E+ RA L+ C + + LQ R + + P KA +H L C FY
Sbjct: 291 ERDRAYLEGACVQSLR----RYLQLRKETLLCTDPPKAHVTHHPRSYGAVTLRCWALGFY 346
Query: 519 PSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSP 698
P+ + + W NG+E T + GD T+Q + + L + YTC V H L P
Sbjct: 347 PADITLTWQLNGEELTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCHVNHEGLPEP 406
Query: 699 ILVEW 713
+ + W
Sbjct: 407 LTLRW 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: 57,894,713
Number of Sequences: 45328
Number of extensions: 1570117
Number of successful extensions: 6610
Number of sequences better than 1.0e-05: 10
Number of HSP's better than 0.0 without gapping: 5309
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): 6549
length of database: 21,768,885
effective HSP length: 106
effective length of database: 16,964,117
effective search space used: 5055306866
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)