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-055404
(783 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 ... 133 2e-31
Alignment gi|NP_872355.1| major histocompatibility complex, class II, DQ ... 112 6e-30
Alignment gi|XP_949921.1| PREDICTED: similar to HLA class II histocompati... 97 1e-24
Alignment gi|NP_068818.4| major histocompatibility complex, class II, DR ... 91 2e-22
Alignment gi|NP_002115.1| major histocompatibility complex, class II, DR ... 100 1e-21
Alignment gi|NP_002116.2| major histocompatibility complex, class II, DR ... 100 1e-21
Alignment gi|XP_945926.1| PREDICTED: similar to HLA class II histocompati... 98 9e-21
Alignment gi|NP_002111.1| major histocompatibility complex, class II, DO ... 82 1e-19
Alignment gi|NP_072049.2| major histocompatibility complex, class II, DR ... 82 1e-18
Alignment gi|XP_949915.1| PREDICTED: similar to HLA class II histocompati... 89 3e-18
>ref|NP_002114.2| major histocompatibility complex, class II, DQ beta 1 precursor
[Homo sapiens]
Length = 261
Score = 133 bits (334), Expect = 2e-31
Identities = 99/255 (38%), Positives = 131/255 (51%), Gaps = 12/255 (4%)
Frame = +1
Query: 55 LSGMEGLLLP*GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAV 234
+S + L +P GL A + +ML L P++EGR SP D YQF C+F N + VR V
Sbjct: 1 MSWKKALRIPGGLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRL-V 59
Query: 235 TDSSTCLDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEE 414
+ S ++ VR EFRAVT LG P A Y + Q D LE A +D VC+H YQ+E
Sbjct: 60 SRSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLEL 119
Query: 415 RTTLPRAVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSR------IGLL*Y-- 570
RTTL R V P VT+S S +AL HH+L VC+ TDF P + V+ R G++
Sbjct: 120 RTTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPL 179
Query: 571 ----SWRCDLSSYSELRLYLGRARDA*HDSPPVRCLHVPRAALCLQIPILLYCRAQSDSA 738
W + E+ G V HV + LQ PI + RAQS+SA
Sbjct: 180 IRNGDWTFQILVMLEMTPQRG----------DVYTCHVEHPS--LQSPITVEWRAQSESA 227
Query: 739 LSIILSAVWGFLLVL 783
S +LS + GF+L L
Sbjct: 228 QSKMLSGIGGFVLGL 242
>ref|NP_872355.1| major histocompatibility complex, class II, DQ beta 2 [Homo
sapiens]
Length = 231
Score = 112 bits (279), Expect(2) = 6e-30
Identities = 70/166 (42%), Positives = 91/166 (54%)
Frame = +1
Query: 55 LSGMEGLLLP*GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAV 234
+S L +P G W AA+ VMLV L P++E R P D QF C+F N + VR V
Sbjct: 1 MSWKMALQIPGGFWAAAVTVMLVMLSTPVAEARDFPKDFLVQFKGMCYFTNGTERVR-GV 59
Query: 235 TDSSTCLDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEE 414
+++ R EF+AVT LGR + + DFLE A +D VC+H Y+ E
Sbjct: 60 ARYIYNREEYGRFDSDVGEFQAVTELGRSIEDW-NNYKDFLEQERAAVDKVCRHNYEAEL 118
Query: 415 RTTLPRAVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSR 552
RTTL R V P VT+S S +AL HH+L VC+ TDF P + VQ R
Sbjct: 119 RTTLQRQVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVQWFR 164
Score = 37.4 bits (85), Expect(2) = 6e-30
Identities = 19/46 (41%), Positives = 29/46 (63%)
Frame = +2
Query: 566 DTAGGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRSP 703
+TAG V++ L N D T +LVM ++ D+YTC V+H + +SP
Sbjct: 169 ETAGVVSTSLIRNGDWTFQILVMLEITPQRGDIYTCQVEHPSLQSP 214
>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 = 96.7 bits (239), Expect(2) = 1e-24
Identities = 64/162 (39%), Positives = 85/162 (52%)
Frame = +1
Query: 73 LLLP*GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTC 252
L LP G AAL V L+ L +P++ + Q ECHFFN + VR
Sbjct: 4 LKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGIYN- 62
Query: 253 LDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPR 432
+++VR E+RAVT LGRP A + Q DFLE AE+D VC+H Y + E T+ R
Sbjct: 63 QEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTVQR 122
Query: 433 AVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG 558
V P VTV + Q L HH+L VC+ + F P + V+ R G
Sbjct: 123 RVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNG 164
Score = 35.0 bits (79), Expect(2) = 1e-24
Identities = 23/57 (40%), Positives = 32/57 (56%)
Frame = +2
Query: 566 DTAGGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRSPSCCTVELSQTL 736
+ AG V++ L N D T LVM + + +VYTC V+H + SP TVE S+ L
Sbjct: 167 EKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVMSP--LTVEWSEQL 221
>ref|NP_068818.4| major histocompatibility complex, class II, DR beta 4 precursor
[Homo sapiens]
Length = 266
Score = 90.9 bits (224), Expect(2) = 2e-22
Identities = 60/162 (37%), Positives = 82/162 (50%)
Frame = +1
Query: 73 LLLP*GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTC 252
L LP G AAL V L L +P++ + Q ECHF N + V +
Sbjct: 4 LKLPGGSCMAALTVTLTVLSSPLALAGDTQPRFLEQAKCECHFLNGTERVWNLIRYIYN- 62
Query: 253 LDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPR 432
+++ R + E++AVT LGRPDA Y + Q D LE AE+D C++ Y + E T+ R
Sbjct: 63 QEEYARYNSDLGEYQAVTELGRPDAEYWNSQKDLLERRRAEVDTYCRYNYGVVESFTVQR 122
Query: 433 AVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG 558
V P VTV S Q L HH+L VC+ F P + V+ R G
Sbjct: 123 RVQPKVTVYPSKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNG 164
Score = 33.1 bits (74), Expect(2) = 2e-22
Identities = 25/67 (37%), Positives = 34/67 (50%)
Frame = +2
Query: 566 DTAGGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRSPSCCTVELSQTLP*A 745
+ AG V++ L N D T LVM + + +VYTC V+H + SP TV+ S A
Sbjct: 167 EKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSMMSP--LTVQWSARSESA 224
Query: 746 SY*ALSG 766
LSG
Sbjct: 225 QSKMLSG 231
>ref|NP_002115.1| major histocompatibility complex, class II, DR beta 1 precursor
[Homo sapiens]
Length = 266
Score = 100 bits (250), Expect = 1e-21
Identities = 83/252 (32%), Positives = 112/252 (44%), Gaps = 15/252 (5%)
Frame = +1
Query: 73 LLLP*GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTC 252
L LP G AL V L+ L +P++ + +Q ECHFFN + VR C
Sbjct: 4 LKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVRLL----ERC 59
Query: 253 L---DDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTT 423
+ ++ VR E+RAVT LGRPDA Y + Q D LE A +D C+H Y + E T
Sbjct: 60 IYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFT 119
Query: 424 LPRAVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG------------LL* 567
+ R V P VTV S Q L HH+L VC+ + F P + V+ R G +
Sbjct: 120 VQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQN 179
Query: 568 YSWRCDLSSYSELRLYLGRARDA*HDSPPVRCLHVPRAALCLQIPILLYCRAQSDSALSI 747
W E G + P V P+ + RA+S+SA S
Sbjct: 180 GDWTFQTLVMLETVPRSGEVYTCQVEHPSVTS------------PLTVEWRARSESAQSK 227
Query: 748 ILSAVWGFLLVL 783
+LS V GF+L L
Sbjct: 228 MLSGVGGFVLGL 239
>ref|NP_002116.2| major histocompatibility complex, class II, DR beta 5 precursor
[Homo sapiens]
Length = 266
Score = 100 bits (250), Expect = 1e-21
Identities = 85/249 (34%), Positives = 112/249 (44%), Gaps = 12/249 (4%)
Frame = +1
Query: 73 LLLP*GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTC 252
L LP G + A L V L+ L +P++ + Q ECHFFN + VR D
Sbjct: 4 LKLPGGSYMAKLTVTLMVLSSPLALAGDTRPRFLQQDKYECHFFNGTERVRFLHRDIYNQ 63
Query: 253 LDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPR 432
+D +R E+RAVT LGRPDA Y + Q DFLE A +D C+H Y + E T+ R
Sbjct: 64 EED-LRFDSDVGEYRAVTELGRPDAEYWNSQKDFLEDRRAAVDTYCRHNYGVGESFTVQR 122
Query: 433 AVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSR-----------IGLL*Y-SW 576
V P VTV + Q L HH+L VC+ F P + V+ R GL+ W
Sbjct: 123 RVEPKVTVYPARTQTLQHHNLLVCSVNGFYPGSIEVRWFRNSQEEKAGVVSTGLIQNGDW 182
Query: 577 RCDLSSYSELRLYLGRARDA*HDSPPVRCLHVPRAALCLQIPILLYCRAQSDSALSIILS 756
E G + P V P+ + RAQS+SA S +LS
Sbjct: 183 TFQTLVMLETVPRSGEVYTCQVEHPSVTS------------PLTVEWRAQSESAQSKMLS 230
Query: 757 AVWGFLLVL 783
V GF+L L
Sbjct: 231 GVGGFVLGL 239
>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 = 97.8 bits (242), Expect = 9e-21
Identities = 83/249 (33%), Positives = 112/249 (44%), Gaps = 12/249 (4%)
Frame = +1
Query: 73 LLLP*GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTC 252
L LP G AAL V L+ L +P++ + Q ECHFFN + VR
Sbjct: 4 LKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGIYN- 62
Query: 253 LDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPR 432
+++VR E+RAVT LGRP A + Q DFLE AE+D VC+H Y + E T+ R
Sbjct: 63 QEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTVQR 122
Query: 433 AVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG------------LL*YSW 576
V P VTV + Q L HH+L VC+ + F P + V+ R G + W
Sbjct: 123 RVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDW 182
Query: 577 RCDLSSYSELRLYLGRARDA*HDSPPVRCLHVPRAALCLQIPILLYCRAQSDSALSIILS 756
E G + P V P+ + RA+S+SA S +LS
Sbjct: 183 TFQTLVMLETVPRSGEVYTCQVEHPSV------------MSPLTVEWRARSESAQSKMLS 230
Query: 757 AVWGFLLVL 783
V GF+L L
Sbjct: 231 GVGGFVLGL 239
>ref|NP_002111.1| major histocompatibility complex, class II, DO beta precursor [Homo
sapiens]
Length = 273
Score = 82.0 bits (201), Expect(2) = 1e-19
Identities = 50/144 (34%), Positives = 74/144 (51%)
Frame = +1
Query: 94 WTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTCLDDHVRC 273
W AL V L L + M++G SP D Q +C+F N + V+ V L+++VR
Sbjct: 8 WVVALLVNLTRLDSSMTQGTDSPEDFVIQAKADCYFTNGTEKVQFVVRFIFN-LEEYVRF 66
Query: 274 SRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPRAVLPHVT 453
F A+T LG+PDA + ++D LE + +D VC+H Y++ T+ R V P VT
Sbjct: 67 DSDVGMFVALTKLGQPDAEQWNSRLDLLERSRQAVDGVCRHNYRLGAPFTVGRKVQPEVT 126
Query: 454 VSRSNEQALYHHHLSVCAATDFCP 525
V L+ H+L C+ T F P
Sbjct: 127 VYPERTPLLHQHNLLHCSVTGFYP 150
Score = 32.3 bits (72), Expect(2) = 1e-19
Identities = 19/46 (41%), Positives = 26/46 (56%)
Frame = +2
Query: 566 DTAGGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRSP 703
+ AG +++ N D T +VM +M L VYTCLV HS+ SP
Sbjct: 164 ERAGVMSTGPIRNGDWTFQTVVMLEMTPELGHVYTCLVDHSSLLSP 209
>ref|NP_072049.2| major histocompatibility complex, class II, DR beta 3 precursor
[Homo sapiens]
Length = 266
Score = 81.6 bits (200), Expect(2) = 1e-18
Identities = 59/163 (36%), Positives = 81/163 (49%), Gaps = 1/163 (0%)
Frame = +1
Query: 73 LLLP*GLWTAALCVMLVALGAPMS-EGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSST 249
L LP G AAL V L+ L + ++ G P + + ECHFFN + VR
Sbjct: 4 LKLPGGSSLAALTVTLMVLSSRLAFAGDTRPRFLELR-KSECHFFNGTERVRYLDRYFHN 62
Query: 250 CLDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLP 429
++ +R E+RAVT LGRP A + Q D LE +D C+H Y + E T+
Sbjct: 63 -QEEFLRFDSDVGEYRAVTELGRPVAESWNSQKDLLEQKRGRVDNYCRHNYGVGESFTVQ 121
Query: 430 RAVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG 558
R V P VTV + Q L HH+L VC+ + F P + V+ R G
Sbjct: 122 RRVHPQVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNG 164
Score = 29.6 bits (65), Expect(2) = 1e-18
Identities = 17/45 (37%), Positives = 25/45 (55%)
Frame = +2
Query: 566 DTAGGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRS 700
+ AG V++ L N D T LVM + + +VYTC V+H + S
Sbjct: 167 EKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTS 211
>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 = 89.4 bits (220), Expect = 3e-18
Identities = 71/210 (33%), Positives = 95/210 (45%), Gaps = 12/210 (5%)
Frame = +1
Query: 190 ECHFFNLNDIVRCAVTDSSTCLDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTL 369
ECHFFN + VR +++VR E+RAVT LGRP A + Q DFLE
Sbjct: 61 ECHFFNGTERVRYLHRGIYN-QEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRR 119
Query: 370 AELDPVCKHRYQIEERTTLPRAVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCS 549
AE+D VC+H Y + E T+ R V P VTV + Q L HH+L VC+ + F P + V+
Sbjct: 120 AEVDTVCRHNYGVGESFTVQRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWF 179
Query: 550 RIG------------LL*YSWRCDLSSYSELRLYLGRARDA*HDSPPVRCLHVPRAALCL 693
R G + W E G + P V
Sbjct: 180 RNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV------------ 227
Query: 694 QIPILLYCRAQSDSALSIILSAVWGFLLVL 783
P+ + RA+S+SA S +LS V GF+L L
Sbjct: 228 MSPLTVEWRARSESAQSKMLSGVGGFVLGL 257
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: 33,659,514
Number of Sequences: 39411
Number of extensions: 942660
Number of successful extensions: 4521
Number of sequences better than 1.0e-05: 10
Number of HSP's better than 0.0 without gapping: 3616
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): 4493
length of database: 17,774,539
effective HSP length: 100
effective length of database: 13,833,439
effective search space used: 2213350240
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-055404
(783 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 ... 111 7e-25
Alignment gi|NP_034512.1| histocompatibility 2, class II antigen E beta [... 87 4e-20
Alignment gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ... 77 4e-18
Alignment gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/... 71 3e-16
>ref|NP_996988.1| histocompatibility 2, class II antigen A, beta 1 [Mus musculus]
Length = 265
Score = 111 bits (278), Expect = 7e-25
Identities = 87/242 (35%), Positives = 119/242 (49%), Gaps = 13/242 (5%)
Frame = +1
Query: 91 LWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTCLDDHVR 270
L +A V+L+ L +P +EG S YQF EC+F N +R VT +++VR
Sbjct: 8 LLLSAAVVVLMVLSSPGTEGGDSERHFVYQFMGECYFTNGTQRIRY-VTRYIYNREEYVR 66
Query: 271 CSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQ-IEERTTLPRAVLPH 447
E RAVT LGRPDA Y + Q + LE T AELD VC+H Y+ E T+L R P+
Sbjct: 67 YDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSLRRLEQPN 126
Query: 448 VTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG------------LL*YSWRCDLS 591
V +S S +AL HH+ VC+ TDF PT + V+ R G + W +
Sbjct: 127 VVISLSRTEALNHHNTLVCSVTDFYPTQIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVL 186
Query: 592 SYSELRLYLGRARDA*HDSPPVRCLHVPRAALCLQIPILLYCRAQSDSALSIILSAVWGF 771
E+ G V HV + L+ PI + RAQS+SA S +LS + G
Sbjct: 187 VMLEMTPRRGE----------VYTCHVEHPS--LKSPITVEWRAQSESAWSKMLSGIGGC 234
Query: 772 LL 777
+L
Sbjct: 235 VL 236
>ref|NP_034512.1| histocompatibility 2, class II antigen E beta [Mus musculus]
Length = 264
Score = 87.4 bits (215), Expect(2) = 4e-20
Identities = 58/154 (37%), Positives = 83/154 (53%), Gaps = 1/154 (0%)
Frame = +1
Query: 100 AALCVMLVALGAPMSEGRYS-PLDVPYQFGDECHFFNLNDIVRCAVTDSSTCLDDHVRCS 276
AA+ ++L L P++ R S P + Y ECHF+N VR L++++R
Sbjct: 11 AAVILLLTVLSPPVALVRDSRPWFLEY-CKSECHFYNGTQRVRFLKRYFYN-LEENLRFD 68
Query: 277 RYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPRAVLPHVTV 456
EFRAVT LGRPDA + Q + L+ A +D C+H Y+I + +PR V P VTV
Sbjct: 69 SDVGEFRAVTELGRPDAENWNSQPEILDEKRAAVDTYCRHNYEIFDNFLVPRRVEPTVTV 128
Query: 457 SRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG 558
+ Q L HH+L VC+ +DF P + V+ R G
Sbjct: 129 YPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNG 162
Score = 29.3 bits (64), Expect(2) = 4e-20
Identities = 16/46 (34%), Positives = 24/46 (52%)
Frame = +2
Query: 566 DTAGGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRSP 703
+ G V++ L N D T LVM + + +VYTC V+H + P
Sbjct: 165 EKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDP 210
>ref|NP_034519.2| histocompatibility 2, O region beta locus [Mus musculus]
Length = 271
Score = 77.0 bits (188), Expect(2) = 4e-18
Identities = 51/155 (32%), Positives = 79/155 (50%)
Frame = +1
Query: 94 WTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTCLDDHVRC 273
W AL V L+ L + M EGR SP + Q +C+F N + V V L++++
Sbjct: 8 WVVALLVNLMRLDSFMIEGRDSPENFVIQAKADCYFTNGTEKVHLLVRFIFN-LEEYLHF 66
Query: 274 SRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPRAVLPHVT 453
F A+T LG PDA + ++D LE + A ++ VC+ +Y++ T+ R V P VT
Sbjct: 67 DSDLGMFVALTELGEPDADQWNKRLDLLETSRAAVNMVCRQKYKLGAPFTVERNVPPEVT 126
Query: 454 VSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG 558
V L H+L +C+ T F P ++V+ R G
Sbjct: 127 VYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNG 161
Score = 32.7 bits (73), Expect(2) = 4e-18
Identities = 17/46 (36%), Positives = 26/46 (56%)
Frame = +2
Query: 566 DTAGGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRSP 703
+ +G +++ L N D T VM +MI L D+Y+CLV+H P
Sbjct: 164 ERSGVMSTGLVRNGDWTFQTTVMLEMIPELGDIYSCLVEHPGLLRP 209
>ref|NP_001029150.1| H-2 class II histocompatibility antigen E-a/k beta-2 [Mus musculus]
Length = 287
Score = 71.2 bits (173), Expect(2) = 3e-16
Identities = 56/165 (33%), Positives = 79/165 (47%)
Frame = +1
Query: 64 MEGLLLP*GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDS 243
M L LP GL AA+ + L+ L P+ R Q ECH+FN + V +VT
Sbjct: 1 MVSLWLPRGLCVAAVILSLMMLTPPVILVRDPRPRFLEQLKAECHYFNGKERV-WSVTRF 59
Query: 244 STCLDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTT 423
++ R + +F AVT LGRP Y + Q D L+ A +D C++ Y + +
Sbjct: 60 IYNQEEFARFNSDFGKFLAVTELGRPIVEYLNTQKDMLDNYRASVDR-CRNNYDLVDIFM 118
Query: 424 LPRAVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG 558
L P VTV + Q L HH+L VC+ DF P + V+ R G
Sbjct: 119 LNLKAEPKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNG 163
Score = 32.3 bits (72), Expect(2) = 3e-16
Identities = 18/46 (39%), Positives = 26/46 (56%)
Frame = +2
Query: 566 DTAGGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRSP 703
+ G V++ L N D T LVM +M+ +VYTC V+H + SP
Sbjct: 166 EKTGVVSTGLIQNRDWTYQTLVMLEMVPRGGEVYTCQVEHPSLTSP 211
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: 39,721,620
Number of Sequences: 45328
Number of extensions: 1055993
Number of successful extensions: 4573
Number of sequences better than 1.0e-05: 4
Number of HSP's better than 0.0 without gapping: 3756
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): 4552
length of database: 21,768,885
effective HSP length: 101
effective length of database: 17,190,757
effective search space used: 2733330363
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)