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= 20060611S-038855 (685 letters) Database: RefSeqSP 1040 sequences; 434,620 total letters Searching...done ***** No hits found ****** 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: 634,612 Number of Sequences: 1040 Number of extensions: 15214 Number of successful extensions: 46 Number of sequences better than 1.0e-05: 0 Number of HSP's better than 0.0 without gapping: 44 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): 46 length of database: 434,620 effective HSP length: 74 effective length of database: 357,660 effective search space used: 54721980 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 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= 20060611S-038855 (685 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] 190 1e-48 Alignment gi|NP_001012694.1| major histocompatibility complex, class II, ... 185 2e-47 Alignment gi|NP_001012698.2| major histocompatibility complex, class II, ... 142 2e-34 Alignment gi|NP_001012697.1| major histocompatibility complex, class II, ... 141 4e-34 Alignment gi|NP_001013618.1| major histocompatibility complex, class II, ... 128 3e-30 Alignment gi|XP_582099.2| PREDICTED: similar to major histocompatibility ... 124 5e-29 Alignment gi|XP_876139.1| PREDICTED: similar to H-2 class II histocompati... 93 2e-19 >ref|NP_001029840.2| MHC class II antigen [Bos taurus] Length = 261 Score = 190 bits (482), Expect = 1e-48 Identities = 96/156 (61%), Positives = 113/156 (72%) Frame = +3 Query: 51 MSGMVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVA 230 MSGMVAL +PRGLWTA V V LV+L P AEGRDSP+DFVVQFKG CYF NGT+RVR V Sbjct: 1 MSGMVALWIPRGLWTAVVMVTLVMLSTPGAEGRDSPKDFVVQFKGLCYFTNGTERVRYVT 60 Query: 231 RYIYNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEG 410 RYIYNQEE++RFDSD +RA+TPLGRP+A WNSQ D + R DT C+H++ + Sbjct: 61 RYIYNQEEYVRFDSDWDLYRALTPLGRPDAEYWNSQKDFLEQTRAEADTVCRHNYQAELI 120 Query: 411 TDPASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518 T RV+P+V ISPS +AL H NLL C DFY Sbjct: 121 TS-LQRRVEPTVTISPSRTEALNHHNLLVCSVTDFY 155 >ref|NP_001012694.1| major histocompatibility complex, class II, DQ beta [Bos taurus] Length = 261 Score = 185 bits (470), Expect = 2e-47 Identities = 95/156 (60%), Positives = 111/156 (71%) Frame = +3 Query: 51 MSGMVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVA 230 MSGMVALR+PRGLWTAAV V L VL P AEGRDSPQD VV F G+CYF NGT+RVR V Sbjct: 1 MSGMVALRIPRGLWTAAVMVTLAVLSTPGAEGRDSPQDTVVHFMGQCYFTNGTERVRYVT 60 Query: 231 RYIYNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEG 410 RYIYNQEE +DSDVGE+RAVT LGR A WNSQ D+ + R LDT C+H++ ++ Sbjct: 61 RYIYNQEETAYYDSDVGEYRAVTQLGRTLAEYWNSQKDILEQTRAELDTVCRHNYQLEVI 120 Query: 411 TDPASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518 T +V+P+V IS S +AL H NLL C DFY Sbjct: 121 TS-LQRQVEPTVTISLSRTEALNHHNLLVCSVTDFY 155 >ref|NP_001012698.2| major histocompatibility complex, class II, DRB3 [Bos taurus] Length = 266 Score = 142 bits (359), Expect = 2e-34 Identities = 74/155 (47%), Positives = 99/155 (63%), Gaps = 2/155 (1%) Frame = +3 Query: 60 MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239 MV L G W AA+ VML+VL P+A R+ F+ +KGEC+F+NGT+RVR + R+ Sbjct: 1 MVCLYFSGGSWMAALIVMLMVLCPPLAWAREIQPHFLEYYKGECHFFNGTERVRFLDRHF 60 Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419 YN EE +RFDSD GEFRAVT LGRP A WNSQ D + KR +D C+H++ G + Sbjct: 61 YNGEEFVRFDSDWGEFRAVTELGRPAAEHWNSQKDFLEQKRAEVDRVCRHNY---GGVES 117 Query: 420 ASV--RVQPSVNISPSAADALRHRNLLCCRGDDFY 518 +V RV+P+V + P+ L+H NLL C + FY Sbjct: 118 FTVQRRVEPTVTVYPAKTQPLQHHNLLVCSVNGFY 152 >ref|NP_001012697.1| major histocompatibility complex, class II, DY beta [Bos taurus] Length = 259 Score = 141 bits (356), Expect = 4e-34 Identities = 79/152 (51%), Positives = 98/152 (64%), Gaps = 2/152 (1%) Frame = +3 Query: 75 LPRGLWTAAVTVMLV--VLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYIYNQ 248 +PR T A VM V VL P A RD+P++FV QFKG CYF NGT+ VRLVAR IYN+ Sbjct: 5 IPRNPGTVAGMVMAVFLVLRIPEAHCRDAPKNFVYQFKGMCYFTNGTEHVRLVARQIYNK 64 Query: 249 EEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDPASV 428 EE L FDSD+GEF AVT LGR A WN+Q D+ R +DT C+H++ G Sbjct: 65 EEILHFDSDLGEFVAVTELGRVCAEIWNTQKDLLAEFRAYVDTLCRHNYKETAGF-TVQR 123 Query: 429 RVQPSVNISPSAADALRHRNLLCCRGDDFYLR 524 RV+P+V +SP++ +AL H NLL C DFY R Sbjct: 124 RVEPTVTVSPASTEALNHHNLLVCSVTDFYPR 155 >ref|NP_001013618.1| major histocompatibility complex, class II, DO beta [Bos taurus] Length = 271 Score = 128 bits (322), Expect = 3e-30 Identities = 64/145 (44%), Positives = 90/145 (62%), Gaps = 2/145 (1%) Frame = +3 Query: 90 WTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYIYNQEEHLRFD 269 W + L A V +GRDSP+DFV Q K +CYF NGT++VR V R+I+N E++ RFD Sbjct: 8 WVVTFLSTALRLDASVTQGRDSPEDFVTQAKADCYFTNGTEKVRFVVRFIFNLEDYARFD 67 Query: 270 SDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDPASV--RVQPS 443 SD+G F A+T LG+P+A WN++ D+ R +D C+ ++++ P +V RVQP Sbjct: 68 SDLGMFVALTELGKPDAERWNNRPDILARSRASVDMLCRRNYYLGA---PFTVGRRVQPE 124 Query: 444 VNISPSAADALRHRNLLCCRGDDFY 518 V + P AL+HRNLL C FY Sbjct: 125 VTVYPEKTPALQHRNLLLCLVTGFY 149 >ref|XP_582099.2| PREDICTED: similar to major histocompatibility complex, class II, DR beta 5 precursor [Bos taurus] Length = 255 Score = 124 bits (312), Expect = 5e-29 Identities = 64/141 (45%), Positives = 89/141 (63%) Frame = +3 Query: 96 AAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYIYNQEEHLRFDSD 275 AA+ V+L+VL P + R++ F+ QFKGEC F NG +R+R ARYIYN +E + FDSD Sbjct: 2 AALAVLLMVLSLPFSWARETQPHFIHQFKGECRFSNGLERMRFFARYIYNTQEDVHFDSD 61 Query: 276 VGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDPASVRVQPSVNIS 455 VGEF A+T LGR +A WN Q D + R +DT C+ S++ G+ RV+P+V + Sbjct: 62 VGEFTALTELGRLDAEYWNQQKDFMEQMRAKVDTLCR-SNYQGIGSFLRQRRVEPTVTVY 120 Query: 456 PSAADALRHRNLLCCRGDDFY 518 P+ L+H NLL C + FY Sbjct: 121 PAKTQPLQHHNLLVCSVNGFY 141 >ref|XP_876139.1| PREDICTED: similar to H-2 class II histocompatibility antigen, I-E beta chain precursor [Bos taurus] Length = 269 Score = 93.2 bits (230), Expect = 2e-19 Identities = 50/117 (42%), Positives = 67/117 (57%) Frame = +3 Query: 168 VVQFKGECYFYNGTQRVRLVARYIYNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDV 347 +VQ K EC+F NGTQ+VR + RYIYN+EE ++FDS VGE+RA T +GRP A WN Sbjct: 1 MVQGKSECHFSNGTQQVRFLDRYIYNREEQVQFDSLVGEYRARTEMGRPAAERWNRWPQA 60 Query: 348 PDHKRV*LDTPCKHSHHIKEGTDPASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518 R + C ++ + RVQP+V + P + L H NLL C + FY Sbjct: 61 LQRARAAVHAYCASNYEF-FASRTVQRRVQPTVTVYPVKSRPLWHHNLLVCSVNGFY 116 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: 23,671,325 Number of Sequences: 33508 Number of extensions: 579046 Number of successful extensions: 1809 Number of sequences better than 1.0e-05: 7 Number of HSP's better than 0.0 without gapping: 1667 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): 1798 length of database: 16,112,626 effective HSP length: 98 effective length of database: 12,828,842 effective search space used: 1654920618 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= 20060611S-038855 (685 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 ... 180 8e-46 Alignment gi|NP_872355.1| major histocompatibility complex, class II, DQ ... 171 7e-43 Alignment gi|NP_002115.1| major histocompatibility complex, class II, DR ... 151 4e-37 Alignment gi|XP_945926.1| PREDICTED: similar to HLA class II histocompati... 149 2e-36 Alignment gi|XP_949921.1| PREDICTED: similar to HLA class II histocompati... 149 2e-36 Alignment gi|NP_002116.2| major histocompatibility complex, class II, DR ... 149 2e-36 Alignment gi|NP_002112.3| major histocompatibility complex, class II, DP ... 143 1e-34 Alignment gi|NP_068818.4| major histocompatibility complex, class II, DR ... 142 2e-34 Alignment gi|NP_072049.2| major histocompatibility complex, class II, DR ... 142 2e-34 Alignment gi|NP_002111.1| major histocompatibility complex, class II, DO ... 126 1e-29 >ref|NP_002114.2| major histocompatibility complex, class II, DQ beta 1 precursor [Homo sapiens] Length = 261 Score = 180 bits (457), Expect = 8e-46 Identities = 93/156 (59%), Positives = 112/156 (71%) Frame = +3 Query: 51 MSGMVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVA 230 MS ALR+P GL A VT+ML +L PVAEGRDSP+DFV QFKG CYF NGT+RVRLV+ Sbjct: 1 MSWKKALRIPGGLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVS 60 Query: 231 RYIYNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEG 410 R IYN+EE +RFDSDVGEFRAVT LG P A WNSQ D+ + KR +D C+H++ ++ Sbjct: 61 RSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELR 120 Query: 411 TDPASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518 T RV+P+V ISPS +AL H NLL C DFY Sbjct: 121 T-TLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFY 155 >ref|NP_872355.1| major histocompatibility complex, class II, DQ beta 2 [Homo sapiens] Length = 231 Score = 171 bits (432), Expect = 7e-43 Identities = 88/156 (56%), Positives = 110/156 (70%) Frame = +3 Query: 51 MSGMVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVA 230 MS +AL++P G W AAVTVMLV+L PVAE RD P+DF+VQFKG CYF NGT+RVR VA Sbjct: 1 MSWKMALQIPGGFWAAAVTVMLVMLSTPVAEARDFPKDFLVQFKGMCYFTNGTERVRGVA 60 Query: 231 RYIYNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEG 410 RYIYN+EE+ RFDSDVGEF+AVT LGR WN+ D + +R +D C+H++ + Sbjct: 61 RYIYNREEYGRFDSDVGEFQAVTELGR-SIEDWNNYKDFLEQERAAVDKVCRHNYEAELR 119 Query: 411 TDPASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518 T +V+P+V ISPS +AL H NLL C DFY Sbjct: 120 T-TLQRQVEPTVTISPSRTEALNHHNLLVCSVTDFY 154 >ref|NP_002115.1| major histocompatibility complex, class II, DR beta 1 precursor [Homo sapiens] Length = 266 Score = 151 bits (382), Expect = 4e-37 Identities = 77/153 (50%), Positives = 103/153 (67%) Frame = +3 Query: 60 MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239 MV L+LP G A+TV L+VL +P+A D+ F+ Q K EC+F+NGT+RVRL+ R I Sbjct: 1 MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVRLLERCI 60 Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419 YNQEE +RFDSDVGE+RAVT LGRP+A WNSQ D+ + +R +DT C+H++ + E + Sbjct: 61 YNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGE-SFT 119 Query: 420 ASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518 RV+P V + PS L+H NLL C FY Sbjct: 120 VQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFY 152 >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 = 149 bits (376), Expect = 2e-36 Identities = 77/153 (50%), Positives = 102/153 (66%) Frame = +3 Query: 60 MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239 MV L+LP G AA+TV L+VL +P+A D+ F+ Q K EC+F+NGT+RVR + R I Sbjct: 1 MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60 Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419 YNQEE++RFDSDVGE+RAVT LGRP A SWNSQ D + +R +DT C+H++ + E + Sbjct: 61 YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGE-SFT 119 Query: 420 ASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518 RV P V + P+ L+H NLL C FY Sbjct: 120 VQRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFY 152 >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 = 149 bits (376), Expect = 2e-36 Identities = 77/153 (50%), Positives = 102/153 (66%) Frame = +3 Query: 60 MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239 MV L+LP G AA+TV L+VL +P+A D+ F+ Q K EC+F+NGT+RVR + R I Sbjct: 1 MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60 Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419 YNQEE++RFDSDVGE+RAVT LGRP A SWNSQ D + +R +DT C+H++ + E + Sbjct: 61 YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGE-SFT 119 Query: 420 ASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518 RV P V + P+ L+H NLL C FY Sbjct: 120 VQRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFY 152 >ref|NP_002116.2| major histocompatibility complex, class II, DR beta 5 precursor [Homo sapiens] Length = 266 Score = 149 bits (376), Expect = 2e-36 Identities = 76/153 (49%), Positives = 103/153 (67%) Frame = +3 Query: 60 MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239 MV L+LP G + A +TV L+VL +P+A D+ F+ Q K EC+F+NGT+RVR + R I Sbjct: 1 MVCLKLPGGSYMAKLTVTLMVLSSPLALAGDTRPRFLQQDKYECHFFNGTERVRFLHRDI 60 Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419 YNQEE LRFDSDVGE+RAVT LGRP+A WNSQ D + +R +DT C+H++ + E + Sbjct: 61 YNQEEDLRFDSDVGEYRAVTELGRPDAEYWNSQKDFLEDRRAAVDTYCRHNYGVGE-SFT 119 Query: 420 ASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518 RV+P V + P+ L+H NLL C + FY Sbjct: 120 VQRRVEPKVTVYPARTQTLQHHNLLVCSVNGFY 152 >ref|NP_002112.3| major histocompatibility complex, class II, DP beta 1 precursor [Homo sapiens] Length = 258 Score = 143 bits (361), Expect = 1e-34 Identities = 75/153 (49%), Positives = 99/153 (64%) Frame = +3 Query: 60 MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239 M+ L++ T A+T +L+VL V +GR +P++++ Q + ECY +NGTQR + RYI Sbjct: 1 MMVLQVSAAPRTVALTALLMVLLTSVVQGRATPENYLFQGRQECYAFNGTQR--FLERYI 58 Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419 YN+EE RFDSDVGEFRAVT LGRP A WNSQ D+ + KR D C+H++ + G Sbjct: 59 YNREEFARFDSDVGEFRAVTELGRPAAEYWNSQKDILEEKRAVPDRMCRHNYEL-GGPMT 117 Query: 420 ASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518 RVQP VN+SPS L+H NLL C DFY Sbjct: 118 LQRRVQPRVNVSPSKKGPLQHHNLLVCHVTDFY 150 >ref|NP_068818.4| major histocompatibility complex, class II, DR beta 4 precursor [Homo sapiens] Length = 266 Score = 142 bits (359), Expect = 2e-34 Identities = 73/153 (47%), Positives = 102/153 (66%) Frame = +3 Query: 60 MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239 MV L+LP G AA+TV L VL +P+A D+ F+ Q K EC+F NGT+RV + RYI Sbjct: 1 MVCLKLPGGSCMAALTVTLTVLSSPLALAGDTQPRFLEQAKCECHFLNGTERVWNLIRYI 60 Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419 YNQEE+ R++SD+GE++AVT LGRP+A WNSQ D+ + +R +DT C++++ + E + Sbjct: 61 YNQEEYARYNSDLGEYQAVTELGRPDAEYWNSQKDLLERRRAEVDTYCRYNYGVVE-SFT 119 Query: 420 ASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518 RVQP V + PS L+H NLL C + FY Sbjct: 120 VQRRVQPKVTVYPSKTQPLQHHNLLVCSVNGFY 152 >ref|NP_072049.2| major histocompatibility complex, class II, DR beta 3 precursor [Homo sapiens] Length = 266 Score = 142 bits (359), Expect = 2e-34 Identities = 75/153 (49%), Positives = 99/153 (64%) Frame = +3 Query: 60 MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239 MV L+LP G AA+TV L+VL + +A D+ F+ K EC+F+NGT+RVR + RY Sbjct: 1 MVCLKLPGGSSLAALTVTLMVLSSRLAFAGDTRPRFLELRKSECHFFNGTERVRYLDRYF 60 Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419 +NQEE LRFDSDVGE+RAVT LGRP A SWNSQ D+ + KR +D C+H++ + E + Sbjct: 61 HNQEEFLRFDSDVGEYRAVTELGRPVAESWNSQKDLLEQKRGRVDNYCRHNYGVGE-SFT 119 Query: 420 ASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518 RV P V + P+ L+H NLL C FY Sbjct: 120 VQRRVHPQVTVYPAKTQPLQHHNLLVCSVSGFY 152 >ref|NP_002111.1| major histocompatibility complex, class II, DO beta precursor [Homo sapiens] Length = 273 Score = 126 bits (317), Expect = 1e-29 Identities = 63/145 (43%), Positives = 91/145 (62%), Gaps = 2/145 (1%) Frame = +3 Query: 90 WTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYIYNQEEHLRFD 269 W A+ V L L + + +G DSP+DFV+Q K +CYF NGT++V+ V R+I+N EE++RFD Sbjct: 8 WVVALLVNLTRLDSSMTQGTDSPEDFVIQAKADCYFTNGTEKVQFVVRFIFNLEEYVRFD 67 Query: 270 SDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDPASV--RVQPS 443 SDVG F A+T LG+P+A WNS+ D+ + R +D C+H++ + P +V +VQP Sbjct: 68 SDVGMFVALTKLGQPDAEQWNSRLDLLERSRQAVDGVCRHNYRLGA---PFTVGRKVQPE 124 Query: 444 VNISPSAADALRHRNLLCCRGDDFY 518 V + P L NLL C FY Sbjct: 125 VTVYPERTPLLHQHNLLHCSVTGFY 149 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: 26,864,919 Number of Sequences: 39411 Number of extensions: 676289 Number of successful extensions: 2538 Number of sequences better than 1.0e-05: 10 Number of HSP's better than 0.0 without gapping: 2288 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): 2519 length of database: 17,774,539 effective HSP length: 98 effective length of database: 13,912,261 effective search space used: 1794681669 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= 20060611S-038855 (685 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 ... 153 1e-37 Alignment gi|NP_034512.1| histocompatibility 2, class II antigen E beta [... 151 5e-37 Alignment gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/... 119 3e-27 Alignment gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ... 116 2e-26 >ref|NP_996988.1| histocompatibility 2, class II antigen A, beta 1 [Mus musculus] Length = 265 Score = 153 bits (387), Expect = 1e-37 Identities = 81/152 (53%), Positives = 103/152 (67%) Frame = +3 Query: 63 VALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYIY 242 +AL++P L +AAV V+L+VL +P EG DS + FV QF GECYF NGTQR+R V RYIY Sbjct: 1 MALQIPSLLLSAAV-VVLMVLSSPGTEGGDSERHFVYQFMGECYFTNGTQRIRYVTRYIY 59 Query: 243 NQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDPA 422 N+EE++R+DSDVGE RAVT LGRP+A WNSQ ++ + R LDT C+H++ E Sbjct: 60 NREEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSL 119 Query: 423 SVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518 QP+V IS S +AL H N L C DFY Sbjct: 120 RRLEQPNVVISLSRTEALNHHNTLVCSVTDFY 151 >ref|NP_034512.1| histocompatibility 2, class II antigen E beta [Mus musculus] Length = 264 Score = 151 bits (382), Expect = 5e-37 Identities = 79/148 (53%), Positives = 98/148 (66%) Frame = +3 Query: 75 LPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYIYNQEE 254 LPR AAV ++L VL PVA RDS F+ K EC+FYNGTQRVR + RY YN EE Sbjct: 4 LPRVPCVAAVILLLTVLSPPVALVRDSRPWFLEYCKSECHFYNGTQRVRFLKRYFYNLEE 63 Query: 255 HLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDPASVRV 434 +LRFDSDVGEFRAVT LGRP+A +WNSQ ++ D KR +DT C+H++ I + RV Sbjct: 64 NLRFDSDVGEFRAVTELGRPDAENWNSQPEILDEKRAAVDTYCRHNYEIFDNF-LVPRRV 122 Query: 435 QPSVNISPSAADALRHRNLLCCRGDDFY 518 +P+V + P+ L H NLL C DFY Sbjct: 123 EPTVTVYPTKTQPLEHHNLLVCSVSDFY 150 >ref|NP_001029150.1| H-2 class II histocompatibility antigen E-a/k beta-2 [Mus musculus] Length = 287 Score = 119 bits (298), Expect = 3e-27 Identities = 66/153 (43%), Positives = 94/153 (61%) Frame = +3 Query: 60 MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239 MV+L LPRGL AAV + L++L PV RD F+ Q K EC+++NG +RV V R+I Sbjct: 1 MVSLWLPRGLCVAAVILSLMMLTPPVILVRDPRPRFLEQLKAECHYFNGKERVWSVTRFI 60 Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419 YNQEE RF+SD G+F AVT LGRP N+Q D+ D+ R +D C++++ + + Sbjct: 61 YNQEEFARFNSDFGKFLAVTELGRPIVEYLNTQKDMLDNYRASVDR-CRNNYDLVD-IFM 118 Query: 420 ASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518 +++ +P V + P+ L H NLL C DFY Sbjct: 119 LNLKAEPKVTVYPAKTQPLEHHNLLVCSVIDFY 151 >ref|NP_034519.2| histocompatibility 2, O region beta locus [Mus musculus] Length = 271 Score = 116 bits (290), Expect = 2e-26 Identities = 60/148 (40%), Positives = 88/148 (59%), Gaps = 2/148 (1%) Frame = +3 Query: 81 RGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYIYNQEEHL 260 R W A+ V L+ L + + EGRDSP++FV+Q K +CYF NGT++V L+ R+I+N EE+L Sbjct: 5 RAPWVVALLVNLMRLDSFMIEGRDSPENFVIQAKADCYFTNGTEKVHLLVRFIFNLEEYL 64 Query: 261 RFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDPASV--RV 434 FDSD+G F A+T LG P+A WN + D+ + R ++ C+ + + P +V V Sbjct: 65 HFDSDLGMFVALTELGEPDADQWNKRLDLLETSRAAVNMVCRQKYKLGA---PFTVERNV 121 Query: 435 QPSVNISPSAADALRHRNLLCCRGDDFY 518 P V + P L+ NLL C FY Sbjct: 122 PPEVTVYPERTPLLQQHNLLLCSVTGFY 149 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: 31,860,424 Number of Sequences: 45328 Number of extensions: 776930 Number of successful extensions: 2794 Number of sequences better than 1.0e-05: 4 Number of HSP's better than 0.0 without gapping: 2318 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): 2779 length of database: 21,768,885 effective HSP length: 100 effective length of database: 17,236,085 effective search space used: 2188982795 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= 20060611S-038855 (685 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... 190 9e-49 Alignment gi|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis fami... 148 5e-36 Alignment gi|XP_861384.1| PREDICTED: similar to HLA class II histocompati... 128 4e-30 Alignment gi|XP_850395.1| PREDICTED: similar to HLA class II histocompati... 128 4e-30 >ref|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Canis familiaris] Length = 269 Score = 190 bits (483), Expect = 9e-49 Identities = 95/156 (60%), Positives = 113/156 (72%) Frame = +3 Query: 51 MSGMVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVA 230 MSG + L +PRG WTAAV ++LVVL PVAEGRDSPQDFV Q+K ECYF NGT+RVRL+ Sbjct: 1 MSGKMTLCIPRGFWTAAVMMILVVLSIPVAEGRDSPQDFVFQYKAECYFTNGTERVRLLT 60 Query: 231 RYIYNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEG 410 +YIYN+EE +RFDSDVGEFRAVT LGRP+A WN Q D D R LDT C+H++ +E Sbjct: 61 KYIYNREEFVRFDSDVGEFRAVTELGRPDAEYWNRQKDEMDRVRAELDTVCRHNYGREEL 120 Query: 411 TDPASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518 T RV+P+V I PS + L H NLL C DFY Sbjct: 121 T-TLQRRVEPTVTIFPSKTEVLNHHNLLVCSVTDFY 155 >ref|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis familiaris] Length = 266 Score = 148 bits (373), Expect = 5e-36 Identities = 74/153 (48%), Positives = 100/153 (65%) Frame = +3 Query: 60 MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239 MV L G W A+ ++L+VL P A RD+P F+ K ECYF NGT+RVR V RYI Sbjct: 1 MVCLCFLGGSWMTALMLILMVLNPPFAWARDTPPHFLEVAKSECYFTNGTERVRFVERYI 60 Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419 +N+EE +RFDSDVGEFRAVT LGRP A SWN Q ++ + +R +DT C+H++ + E + Sbjct: 61 HNREEFVRFDSDVGEFRAVTELGRPVAESWNGQKEILEQERATVDTYCRHNYGVIE-SFT 119 Query: 420 ASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518 RV+P+V + P+ L+H NLL C + FY Sbjct: 120 VQRRVEPTVTVYPTKTQTLQHHNLLVCSVNGFY 152 >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 = 128 bits (322), Expect = 4e-30 Identities = 62/145 (42%), Positives = 92/145 (63%), Gaps = 2/145 (1%) Frame = +3 Query: 90 WTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYIYNQEEHLRFD 269 W A+ V + L + + +GRDSP+DFV+Q K +CYF NGT++V+ V R+I+N EE+ RFD Sbjct: 8 WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67 Query: 270 SDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDPASV--RVQPS 443 S VG F A+T LG+P+A WNSQ + + R +D C+H++ + P +V +VQP Sbjct: 68 SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGA---PFTVGRKVQPE 124 Query: 444 VNISPSAADALRHRNLLCCRGDDFY 518 V + P +++H NLL C FY Sbjct: 125 VTVYPERTPSMQHHNLLLCSVTGFY 149 >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 = 128 bits (322), Expect = 4e-30 Identities = 62/145 (42%), Positives = 92/145 (63%), Gaps = 2/145 (1%) Frame = +3 Query: 90 WTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYIYNQEEHLRFD 269 W A+ V + L + + +GRDSP+DFV+Q K +CYF NGT++V+ V R+I+N EE+ RFD Sbjct: 8 WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67 Query: 270 SDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDPASV--RVQPS 443 S VG F A+T LG+P+A WNSQ + + R +D C+H++ + P +V +VQP Sbjct: 68 SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGA---PFTVGRKVQPE 124 Query: 444 VNISPSAADALRHRNLLCCRGDDFY 518 V + P +++H NLL C FY Sbjct: 125 VTVYPERTPSMQHHNLLLCSVTGFY 149 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: 27,714,776 Number of Sequences: 33732 Number of extensions: 675472 Number of successful extensions: 2302 Number of sequences better than 1.0e-05: 4 Number of HSP's better than 0.0 without gapping: 2116 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): 2296 length of database: 19,266,565 effective HSP length: 99 effective length of database: 15,927,097 effective search space used: 2038668416 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)