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-065393
(1113 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] 54 7e-09
Alignment gi|NP_999362.2| neonatal Fc receptor FcRn [Sus scrofa] 47 8e-07
Alignment gi|NP_998996.1| CD1 antigen [Sus scrofa] 47 1e-06
Alignment gi|NP_999143.1| beta 2-microglobulin [Sus scrofa] 44 7e-06
>ref|NP_998933.1| swine leukocyte antigen 7 [Sus scrofa]
Length = 401
Score = 53.9 bits (128), Expect = 7e-09
Identities = 37/147 (25%), Positives = 64/147 (43%), Gaps = 5/147 (3%)
Frame = +2
Query: 293 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYC---RHNYRISDT 463
Y+G + + + D+ + AV + + W + + EQ RA ++ C H Y +
Sbjct: 139 YDGADYIVLNEDLRSWTAVGMAAQITRRKWEE-ETVAEQSRAYLEVACVQSLHRYLANGK 197
Query: 464 FLVPRRAEPT--VTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTG 637
+ R P VT +P+ + L C GFYP + + W + GQ+++ V
Sbjct: 198 ETLQRSDPPKTHVTRHPSSDNKVT----LRCWALGFYPKEISLTWQQEGQDQSQDVEVVE 253
Query: 638 LIPNGDWTFQTMVMLETVPQSGEVYSC 718
P+GD TF+ L P + Y+C
Sbjct: 254 TRPSGDGTFRKWAALVVPPGEEQSYTC 280
>ref|NP_999362.2| neonatal Fc receptor FcRn [Sus scrofa]
Length = 356
Score = 47.0 bits (110), Expect = 8e-07
Identities = 39/145 (26%), Positives = 60/145 (41%), Gaps = 4/145 (2%)
Frame = +2
Query: 296 NGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVP 475
NGEE ++FD+ +G + R W D + + + + C H R+
Sbjct: 136 NGEEFMKFDTKLGTWDGEWPEARTIGSKWMQEPDAVNKEKTFLLYSCPH--RLLGHLERG 193
Query: 476 RR----AEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLI 643
R EP A+ ++L C FYP +++R+ RNG AAG + +
Sbjct: 194 RGNLEWKEPPSMRMKARPGTAPGFSVLTCIAFSFYPPELQLRFLRNGL--AAGSGESDIG 251
Query: 644 PNGDWTFQTMVMLETVPQSGEVYSC 718
PNGD +F L TV E + C
Sbjct: 252 PNGDGSFHAWSSL-TVKSGDEHHYC 275
>ref|NP_998996.1| CD1 antigen [Sus scrofa]
Length = 339
Score = 46.6 bits (109), Expect = 1e-06
Identities = 24/66 (36%), Positives = 33/66 (50%)
Frame = +2
Query: 521 PLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLETVPQS 700
P H +LVC V+GFYP + V W R+ QE+ G ++PN D T+ V L+
Sbjct: 215 PSPGHLMLVCHVSGFYPKPIWVMWMRDEQEQ-PGTQQGDILPNADGTWYLRVTLDVAAGE 273
Query: 701 GEVYSC 718
SC
Sbjct: 274 ASGLSC 279
>ref|NP_999143.1| beta 2-microglobulin [Sus scrofa]
Length = 118
Score = 43.9 bits (102), Expect = 7e-06
Identities = 25/77 (32%), Positives = 36/77 (46%)
Frame = +2
Query: 488 PTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQ 667
P V VY N L C V+GF+P +E+ +NG E + L + DW+F
Sbjct: 25 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNG--EKMNAEQSDLSFSKDWSFY 82
Query: 668 TMVMLETVPQSGEVYSC 718
+V E P + + YSC
Sbjct: 83 LLVHTEFTPNAVDQYSC 99
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: 1,078,477
Number of Sequences: 1040
Number of extensions: 27618
Number of successful extensions: 93
Number of sequences better than 1.0e-05: 4
Number of HSP's better than 0.0 without gapping: 80
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): 89
length of database: 434,620
effective HSP length: 78
effective length of database: 353,500
effective search space used: 103222000
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-065393
(1113 letters)
Database: RefSeqBP
33,508 sequences; 16,112,626 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001012698.2| major histocompatibility complex, class II, ... 306 2e-83
Alignment gi|XP_582099.2| PREDICTED: similar to major histocompatibility ... 257 1e-68
Alignment gi|NP_001012694.1| major histocompatibility complex, class II, ... 240 2e-63
Alignment gi|NP_001029840.2| MHC class II antigen [Bos taurus] 237 1e-62
Alignment gi|XP_876139.1| PREDICTED: similar to H-2 class II histocompati... 226 2e-59
Alignment gi|NP_001012697.1| major histocompatibility complex, class II, ... 211 6e-55
Alignment gi|NP_001013618.1| major histocompatibility complex, class II, ... 204 1e-52
Alignment gi|XP_874766.1| PREDICTED: similar to HLA class II histocompati... 154 2e-37
Alignment gi|NP_001035571.1| major histocompatibility complex, class II, ... 67 2e-11
Alignment gi|NP_001012399.1| hemochromatosis [Bos taurus] 57 3e-08
>ref|NP_001012698.2| major histocompatibility complex, class II, DRB3 [Bos taurus]
Length = 266
Score = 306 bits (783), Expect = 2e-83
Identities = 148/202 (73%), Positives = 162/202 (80%)
Frame = +2
Query: 113 MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHY 292
M+ L FS G WMAAL VML+VL PPLA AR+ P NGTERVR LDRH+
Sbjct: 1 MVCLYFSGGSWMAALIVMLMVLCPPLAWAREIQPHFLEYYKGECHFFNGTERVRFLDRHF 60
Query: 293 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLV 472
YNGEE +RFDSD GE+RAVTELGRP A+ WNS+KD LEQ+RAEVD CRHNY ++F V
Sbjct: 61 YNGEEFVRFDSDWGEFRAVTELGRPAAEHWNSQKDFLEQKRAEVDRVCRHNYGGVESFTV 120
Query: 473 PRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 652
RR EPTVTVYPAKTQPLQHHNLLVCSV GFYPGH+EVRWFRNG EE AGV+STGLI NG
Sbjct: 121 QRRVEPTVTVYPAKTQPLQHHNLLVCSVNGFYPGHIEVRWFRNGHEEEAGVISTGLIQNG 180
Query: 653 DWTFQTMVMLETVPQSGEVYSC 718
DWTFQTMVMLETVPQSGEVY+C
Sbjct: 181 DWTFQTMVMLETVPQSGEVYTC 202
>ref|XP_582099.2| PREDICTED: similar to major histocompatibility complex, class II,
DR beta 5 precursor [Bos taurus]
Length = 255
Score = 257 bits (657), Expect = 1e-68
Identities = 129/207 (62%), Positives = 151/207 (72%), Gaps = 4/207 (1%)
Frame = +2
Query: 146 MAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILRFDS 325
MAAL V+L+VLS P + AR+T P NG ER+R R+ YN +E + FDS
Sbjct: 1 MAALAVLLMVLSLPFSWARETQPHFIHQFKGECRFSNGLERMRFFARYIYNTQEDVHFDS 60
Query: 326 DVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTVTVY 505
DVGE+ A+TELGR +A+ WN +KD +EQ RA+VDT CR NY+ +FL RR EPTVTVY
Sbjct: 61 DVGEFTALTELGRLDAEYWNQQKDFMEQMRAKVDTLCRSNYQGIGSFLRQRRVEPTVTVY 120
Query: 506 PAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLE 685
PAKTQPLQHHNLLVCSV GFYPGH+EVRWF N EE AGV+STGLI NGDWTFQTMVMLE
Sbjct: 121 PAKTQPLQHHNLLVCSVNGFYPGHIEVRWFWNSHEEEAGVISTGLIQNGDWTFQTMVMLE 180
Query: 686 TVPQSGEVYSC----PSANRPPELKCR 754
TVPQSGEVY+C PS P ++ R
Sbjct: 181 TVPQSGEVYTCQVEHPSRTSPLTVEWR 207
>ref|NP_001012694.1| major histocompatibility complex, class II, DQ beta [Bos taurus]
Length = 261
Score = 240 bits (612), Expect = 2e-63
Identities = 121/220 (55%), Positives = 150/220 (68%), Gaps = 4/220 (1%)
Frame = +2
Query: 107 SSMLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDR 286
S M+ L RG W AA+ V L VLS P A RD+P NGTERVR + R
Sbjct: 2 SGMVALRIPRGLWTAAVMVTLAVLSTPGAEGRDSPQDTVVHFMGQCYFTNGTERVRYVTR 61
Query: 287 HYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTF 466
+ YN EE +DSDVGEYRAVT+LGR A+ WNS+KDILEQ RAE+DT CRHNY++
Sbjct: 62 YIYNQEETAYYDSDVGEYRAVTQLGRTLAEYWNSQKDILEQTRAELDTVCRHNYQLEVIT 121
Query: 467 LVPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIP 646
+ R+ EPTVT+ ++T+ L HHNLLVCSVT FYPG ++VRWF+NG+EE AG+VST LI
Sbjct: 122 SLQRQVEPTVTISLSRTEALNHHNLLVCSVTDFYPGQIKVRWFQNGKEETAGIVSTPLIR 181
Query: 647 NGDWTFQTMVMLETVPQSGEVYSC----PSANRPPELKCR 754
NGDWTFQ +VMLE P+ G+VY+C PS P ++ R
Sbjct: 182 NGDWTFQILVMLEMTPKRGDVYTCHVEHPSLQSPISVEWR 221
>ref|NP_001029840.2| MHC class II antigen [Bos taurus]
Length = 261
Score = 237 bits (605), Expect = 1e-62
Identities = 120/214 (56%), Positives = 143/214 (66%), Gaps = 4/214 (1%)
Frame = +2
Query: 107 SSMLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDR 286
S M+ L RG W A + V LV+LS P A RD+P NGTERVR + R
Sbjct: 2 SGMVALWIPRGLWTAVVMVTLVMLSTPGAEGRDSPKDFVVQFKGLCYFTNGTERVRYVTR 61
Query: 287 HYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTF 466
+ YN EE +RFDSD YRA+T LGRP+A+ WNS+KD LEQ RAE DT CRHNY+
Sbjct: 62 YIYNQEEYVRFDSDWDLYRALTPLGRPDAEYWNSQKDFLEQTRAEADTVCRHNYQAELIT 121
Query: 467 LVPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIP 646
+ RR EPTVT+ P++T+ L HHNLLVCSVT FYP ++VRWFRN +EE AGVVST LI
Sbjct: 122 SLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPSQIKVRWFRNDREETAGVVSTPLIR 181
Query: 647 NGDWTFQTMVMLETVPQSGEVYSC----PSANRP 736
NGDWTFQ +VMLE PQ G+VY+C PS P
Sbjct: 182 NGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSP 215
>ref|XP_876139.1| PREDICTED: similar to H-2 class II histocompatibility antigen, I-E
beta chain precursor [Bos taurus]
Length = 269
Score = 226 bits (576), Expect = 2e-59
Identities = 110/171 (64%), Positives = 127/171 (74%), Gaps = 4/171 (2%)
Frame = +2
Query: 254 NGTERVRLLDRHYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTY 433
NGT++VR LDR+ YN EE ++FDS VGEYRA TE+GRP A+ WN L++ RA V Y
Sbjct: 12 NGTQQVRFLDRYIYNREEQVQFDSLVGEYRARTEMGRPAAERWNRWPQALQRARAAVHAY 71
Query: 434 CRHNYRISDTFLVPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEE 613
C NY + V RR +PTVTVYP K++PL HHNLLVCSV GFYPGH+EVRWFRNGQEE
Sbjct: 72 CASNYEFFASRTVQRRVQPTVTVYPVKSRPLWHHNLLVCSVNGFYPGHIEVRWFRNGQEE 131
Query: 614 AAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYSC----PSANRPPELKCR 754
AGVVSTGLIPNGDWTFQ MVMLE VPQ GEVY+C PS P ++ R
Sbjct: 132 EAGVVSTGLIPNGDWTFQIMVMLEIVPQGGEVYACHVEHPSRTSPVTVEWR 182
>ref|NP_001012697.1| major histocompatibility complex, class II, DY beta [Bos taurus]
Length = 259
Score = 211 bits (538), Expect = 6e-55
Identities = 112/201 (55%), Positives = 132/201 (65%), Gaps = 4/201 (1%)
Frame = +2
Query: 164 MLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILRFDSDVGEYR 343
+ +VL P A RD P NGTE VRL+ R YN EEIL FDSD+GE+
Sbjct: 19 VFLVLRIPEAHCRDAPKNFVYQFKGMCYFTNGTEHVRLVARQIYNKEEILHFDSDLGEFV 78
Query: 344 AVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTVTVYPAKTQP 523
AVTELGR A+ WN++KD+L + RA VDT CRHNY+ + F V RR EPTVTV PA T+
Sbjct: 79 AVTELGRVCAEIWNTQKDLLAEFRAYVDTLCRHNYKETAGFTVQRRVEPTVTVSPASTEA 138
Query: 524 LQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLETVPQSG 703
L HHNLLVCSVT FYP V+V+WFRN QE+ AGV T L NGDWT+Q VMLETVPQ G
Sbjct: 139 LNHHNLLVCSVTDFYPRQVKVKWFRNQQEQTAGVGFTPLTQNGDWTYQIHVMLETVPQLG 198
Query: 704 EVYSC----PSANRPPELKCR 754
+VY C PS P ++ R
Sbjct: 199 DVYVCHVDHPSLQSPITVEWR 219
>ref|NP_001013618.1| major histocompatibility complex, class II, DO beta [Bos taurus]
Length = 271
Score = 204 bits (519), Expect = 1e-52
Identities = 101/208 (48%), Positives = 129/208 (62%), Gaps = 4/208 (1%)
Frame = +2
Query: 143 WMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILRFD 322
W+ + L + RD+P NGTE+VR + R +N E+ RFD
Sbjct: 8 WVVTFLSTALRLDASVTQGRDSPEDFVTQAKADCYFTNGTEKVRFVVRFIFNLEDYARFD 67
Query: 323 SDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTVTV 502
SD+G + A+TELG+P+A+ WN+R DIL + RA VD CR NY + F V RR +P VTV
Sbjct: 68 SDLGMFVALTELGKPDAERWNNRPDILARSRASVDMLCRRNYYLGAPFTVGRRVQPEVTV 127
Query: 503 YPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVML 682
YP KT LQH NLL+C VTGFYPG ++V WFRNGQE+ G++STGLI NGDWTFQ VML
Sbjct: 128 YPEKTPALQHRNLLLCLVTGFYPGDIKVTWFRNGQEQREGIMSTGLIRNGDWTFQMTVML 187
Query: 683 ETVPQSGEVYSC----PSANRPPELKCR 754
P+ GEVY+C PS P ++ R
Sbjct: 188 AMTPELGEVYTCLVDHPSLLSPVSVEWR 215
>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 = 154 bits (388), Expect = 2e-37
Identities = 100/218 (45%), Positives = 123/218 (56%), Gaps = 2/218 (0%)
Frame = +2
Query: 71 LPAPFTHCPLLFSSMLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXX 250
L +PF P LF+S + L FS+G WMAAL VM+ LSP L AR+T
Sbjct: 2 LSSPF---PFLFASTVCLYFSKGSWMAALLVMMG-LSPLLTWARETQ------------- 44
Query: 251 XNGTERVRLLDRHYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDT 430
Y + DS + A++ G+P A + D
Sbjct: 45 --------------YKRTPWVVIDSQIS---AISH-GKPCALNGYRECD----------- 75
Query: 431 YCRH--NYRISDTFLVPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNG 604
C H + + + ++ EPTVTVYPAKTQPLQH++LLVCSV GFY GHVEVRWF G
Sbjct: 76 GCFHPIGLKANRDITLQKKVEPTVTVYPAKTQPLQHNHLLVCSVNGFYLGHVEVRWFWKG 135
Query: 605 QEEAAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYSC 718
QEE AGV+STGLI NGDWTF+T+VMLETV QSGEVY+C
Sbjct: 136 QEEEAGVISTGLIQNGDWTFETIVMLETVLQSGEVYTC 173
>ref|NP_001035571.1| major histocompatibility complex, class II, DM beta-chain,
expressed [Bos taurus]
Length = 262
Score = 67.4 bits (163), Expect = 2e-11
Identities = 39/87 (44%), Positives = 47/87 (54%), Gaps = 3/87 (3%)
Frame = +2
Query: 467 LVPRRAEPTVTVYPAKTQPLQHHN--LLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGL 640
L R PTV V AKT P +L C V GFYP V + W RNGQE + +
Sbjct: 108 LTHRTRPPTVQV--AKTTPFNTRESVMLACYVWGFYPADVAITWRRNGQEVLPHGRAWRI 165
Query: 641 I-PNGDWTFQTMVMLETVPQSGEVYSC 718
I PNGDWT+QT+ L T P G+ Y+C
Sbjct: 166 IQPNGDWTYQTVSHLATTPSFGDTYTC 192
>ref|NP_001012399.1| hemochromatosis [Bos taurus]
Length = 356
Score = 57.0 bits (136), Expect = 3e-08
Identities = 40/149 (26%), Positives = 68/149 (45%), Gaps = 4/149 (2%)
Frame = +2
Query: 284 RHYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNY-RISD 460
++ Y+G++ L F + ++RA + +W K +Q RA +D C + +
Sbjct: 145 KYGYDGQDHLEFRPETLDWRAAEPRAQVTKLEWEVNKIRAKQNRAYLDRDCPEQLLHLLE 204
Query: 461 TFLVP--RRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQE-EAAGVVS 631
P ++ P V V T L L C FYP ++ +RW ++ Q +A +
Sbjct: 205 LGRGPLEQQVPPLVKVTHHVTSSL---TTLRCRALNFYPQNITIRWLKDKQFLDAKEIKP 261
Query: 632 TGLIPNGDWTFQTMVMLETVPQSGEVYSC 718
++PNGD T+Q V L +P + YSC
Sbjct: 262 EDVLPNGDGTYQAWVALAMLPGEEQRYSC 290
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: 40,769,968
Number of Sequences: 33508
Number of extensions: 1104515
Number of successful extensions: 3711
Number of sequences better than 1.0e-05: 10
Number of HSP's better than 0.0 without gapping: 3308
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): 3687
length of database: 16,112,626
effective HSP length: 103
effective length of database: 12,661,302
effective search space used: 3380567634
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-065393
(1113 letters)
Database: RefSeqCP
33,732 sequences; 19,266,565 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis fami... 296 3e-80
Alignment gi|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Ca... 257 1e-68
Alignment gi|XP_850395.1| PREDICTED: similar to HLA class II histocompati... 221 8e-58
Alignment gi|XP_861384.1| PREDICTED: similar to HLA class II histocompati... 221 1e-57
Alignment gi|XP_849737.1| PREDICTED: similar to HLA class II histocompati... 62 1e-09
Alignment gi|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris] 55 9e-08
Alignment gi|XP_855624.1| PREDICTED: MHC class Ib [Canis familiaris] 53 5e-07
Alignment gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati... 51 2e-06
Alignment gi|NP_001018646.1| MHC class Ib [Canis familiaris] 50 3e-06
Alignment gi|NP_001011726.1| MHC class II DLA DQalpha chain [Canis famili... 50 5e-06
>ref|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis familiaris]
Length = 266
Score = 296 bits (757), Expect = 3e-80
Identities = 143/218 (65%), Positives = 165/218 (75%), Gaps = 4/218 (1%)
Frame = +2
Query: 113 MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHY 292
M+ LCF G WM AL ++L+VL+PP A ARDTPP NGTERVR ++R+
Sbjct: 1 MVCLCFLGGSWMTALMLILMVLNPPFAWARDTPPHFLEVAKSECYFTNGTERVRFVERYI 60
Query: 293 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLV 472
+N EE +RFDSDVGE+RAVTELGRP A+ WN +K+ILEQ RA VDTYCRHNY + ++F V
Sbjct: 61 HNREEFVRFDSDVGEFRAVTELGRPVAESWNGQKEILEQERATVDTYCRHNYGVIESFTV 120
Query: 473 PRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 652
RR EPTVTVYP KTQ LQHHNLLVCSV GFYPGH+EVRW RNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVEPTVTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNG 180
Query: 653 DWTFQTMVMLETVPQSGEVYSC----PSANRPPELKCR 754
DWTFQ +VMLE VPQSGEVY+C PS P ++ R
Sbjct: 181 DWTFQILVMLEIVPQSGEVYTCQVEHPSLTSPVTVEWR 218
>ref|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Canis familiaris]
Length = 269
Score = 257 bits (657), Expect = 1e-68
Identities = 122/204 (59%), Positives = 151/204 (74%)
Frame = +2
Query: 107 SSMLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDR 286
S + LC RGFW AA+ ++LVVLS P+A RD+P NGTERVRLL +
Sbjct: 2 SGKMTLCIPRGFWTAAVMMILVVLSIPVAEGRDSPQDFVFQYKAECYFTNGTERVRLLTK 61
Query: 287 HYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTF 466
+ YN EE +RFDSDVGE+RAVTELGRP+A+ WN +KD +++ RAE+DT CRHNY +
Sbjct: 62 YIYNREEFVRFDSDVGEFRAVTELGRPDAEYWNRQKDEMDRVRAELDTVCRHNYGREELT 121
Query: 467 LVPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIP 646
+ RR EPTVT++P+KT+ L HHNLLVCSVT FYPG ++VRWFRN QE+ AGVVST LI
Sbjct: 122 TLQRRVEPTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLIR 181
Query: 647 NGDWTFQTMVMLETVPQSGEVYSC 718
NGDWTFQ +VMLE PQ G+VY+C
Sbjct: 182 NGDWTFQILVMLEMTPQRGDVYTC 205
>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 = 221 bits (564), Expect = 8e-58
Identities = 108/208 (51%), Positives = 138/208 (66%), Gaps = 4/208 (1%)
Frame = +2
Query: 143 WMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILRFD 322
WM AL V + L + RD+P NGTE+V+ + R +N EE RFD
Sbjct: 8 WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67
Query: 323 SDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTVTV 502
S VG + A+TELG+P+A+ WNS+ ILE+ RA VD CRHNY + F V R+ +P VTV
Sbjct: 68 SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTV 127
Query: 503 YPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVML 682
YP +T +QHHNLL+CSVTGFYPG ++++WFRNGQEE GV+STGLI NGDWTFQTMVML
Sbjct: 128 YPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVML 187
Query: 683 ETVPQSGEVYSC----PSANRPPELKCR 754
E P+ G+VY+C PS P ++ R
Sbjct: 188 EMTPELGDVYTCLVNHPSLLSPVSVEWR 215
>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 = 221 bits (563), Expect = 1e-57
Identities = 104/192 (54%), Positives = 132/192 (68%)
Frame = +2
Query: 143 WMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILRFD 322
WM AL V + L + RD+P NGTE+V+ + R +N EE RFD
Sbjct: 8 WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67
Query: 323 SDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTVTV 502
S VG + A+TELG+P+A+ WNS+ ILE+ RA VD CRHNY + F V R+ +P VTV
Sbjct: 68 SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTV 127
Query: 503 YPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVML 682
YP +T +QHHNLL+CSVTGFYPG ++++WFRNGQEE GV+STGLI NGDWTFQTMVML
Sbjct: 128 YPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVML 187
Query: 683 ETVPQSGEVYSC 718
E P+ G+VY+C
Sbjct: 188 EMTPELGDVYTC 199
>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 = 61.6 bits (148), Expect = 1e-09
Identities = 36/115 (31%), Positives = 56/115 (48%), Gaps = 1/115 (0%)
Frame = +2
Query: 377 DWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTVTVYPAKTQPLQHHNLLVCSV 556
D+ ++++ L QR + C + + L R PTV V + + +L C V
Sbjct: 78 DYLNQQEYLHQRLSNGLQDCATHTQSFWGSLTHRTRPPTVQVAKSTPFNTKESVMLACYV 137
Query: 557 TGFYPGHVEVRWFRNGQEEAAGVVSTGLI-PNGDWTFQTMVMLETVPQSGEVYSC 718
GFYP V + W +NGQ + + + PNGDWT+QT+ L T P + Y+C
Sbjct: 138 WGFYPADVTISWRKNGQPVPSHSSALNMAQPNGDWTYQTVSHLATTPSYEDTYTC 192
>ref|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris]
Length = 254
Score = 55.5 bits (132), Expect = 9e-08
Identities = 38/143 (26%), Positives = 60/143 (41%), Gaps = 1/143 (0%)
Frame = +2
Query: 293 YNGEEILRFDSDVGE-YRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFL 469
++G+EI D + E + E GR + + + +A +DT + + +T
Sbjct: 51 FDGDEIFHVDMEKKETVWRLEEFGRFASFEAQGALANIAVDKANLDTMIKRSNHTPNT-- 108
Query: 470 VPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPN 649
P VTV L N+L+C + F P + V W RNG GV T +P
Sbjct: 109 ---NVPPEVTVLSNTPVELGEPNILICFIDKFSPPVINVTWLRNGNPVTTGVSETIFLPR 165
Query: 650 GDWTFQTMVMLETVPQSGEVYSC 718
D F+ L +P + +VY C
Sbjct: 166 EDHLFRKFHYLPFLPSAEDVYDC 188
>ref|XP_855624.1| PREDICTED: MHC class Ib [Canis familiaris]
Length = 381
Score = 53.1 bits (126), Expect = 5e-07
Identities = 46/185 (24%), Positives = 78/185 (42%), Gaps = 9/185 (4%)
Frame = +2
Query: 269 VRLLDRHYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNS------RKDILEQRRAEVDT 430
+R RH Y+G + + D+ + + + + W++ RK+ LE R E
Sbjct: 140 LRGYQRHAYDGLDYITLSEDLRSWIVEDPVAQITRRKWDAATVAENRKNFLEGRCLE--W 197
Query: 431 YCRHNYRISDTFLVPRRAEPTVTVYPAKTQPLQHHNL-LVCSVTGFYPGHVEVRWFRNGQ 607
RH +T +RA+P T +P+ H + L C GFYP + + W R+G+
Sbjct: 198 LRRHLENGRETL---QRADPPKT--SVTRRPISEHEVTLKCWALGFYPAEITLTWQRDGE 252
Query: 608 EEAAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYSCPSANR--PPELKCRW*HSKQASS 781
++ P GD TFQ + + Y+C ++ P + RW Q S+
Sbjct: 253 DQTQDTELVETRPGGDGTFQKWAAVVVPSGEEQRYTCHILHKSLPKPITLRWEPPPQ-ST 311
Query: 782 VPASS 796
+P S
Sbjct: 312 IPIVS 316
>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 = 51.2 bits (121), Expect = 2e-06
Identities = 25/77 (32%), Positives = 35/77 (45%)
Frame = +2
Query: 488 PTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQ 667
P V V P L N+L+C V +P + + W RNGQ + GV T D F+
Sbjct: 90 PRVAVLPKFRVELGQPNVLICIVDNIFPPVINITWLRNGQIISEGVAQTSFYSQPDHLFR 149
Query: 668 TMVMLETVPQSGEVYSC 718
L VP + ++Y C
Sbjct: 150 KFCYLTFVPSAEDMYDC 166
>ref|NP_001018646.1| MHC class Ib [Canis familiaris]
Length = 381
Score = 50.4 bits (119), Expect = 3e-06
Identities = 39/157 (24%), Positives = 66/157 (42%), Gaps = 7/157 (4%)
Frame = +2
Query: 269 VRLLDRHYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNS------RKDILEQRRAEVDT 430
+R RH Y+G + + D+ + + + + W++ RK+ LE R E
Sbjct: 140 LRGYQRHAYDGLDYITLSEDLRSWIVEDPVAQITRRKWDAATVAENRKNFLEGRCLE--W 197
Query: 431 YCRHNYRISDTFLVPRRAEPTVTVYPAKTQPLQHHNL-LVCSVTGFYPGHVEVRWFRNGQ 607
RH +T +RA+P T +P+ H + L C GFYP + + W R+G+
Sbjct: 198 LRRHLENGRETL---QRADPPKT--SVTRRPISEHEVTLKCWALGFYPAEITLTWQRDGE 252
Query: 608 EEAAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYSC 718
++ P GD TFQ + + Y+C
Sbjct: 253 DQTQDTELVETRPGGDGTFQKWAAVVVPSGEEQRYTC 289
>ref|NP_001011726.1| MHC class II DLA DQalpha chain [Canis familiaris]
Length = 255
Score = 49.7 bits (117), Expect = 5e-06
Identities = 23/77 (29%), Positives = 34/77 (44%)
Frame = +2
Query: 488 PTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQ 667
P VTV+ L N L+C V +P + V W +N GV T GD +F
Sbjct: 113 PEVTVFSKSPVMLGQPNTLICLVDNIFPPVINVTWLKNRHSVTEGVSETSFFAKGDHSFS 172
Query: 668 TMVMLETVPQSGEVYSC 718
+ L +P + ++Y C
Sbjct: 173 KISYLTFLPSAEDIYDC 189
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: 47,850,150
Number of Sequences: 33732
Number of extensions: 1293485
Number of successful extensions: 4460
Number of sequences better than 1.0e-05: 10
Number of HSP's better than 0.0 without gapping: 3865
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): 4451
length of database: 19,266,565
effective HSP length: 104
effective length of database: 15,758,437
effective search space used: 4191744242
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-065393
(1113 letters)
Database: RefSeqHP
39,411 sequences; 17,774,539 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_002115.1| major histocompatibility complex, class II, DR ... 294 1e-79
Alignment gi|XP_949921.1| PREDICTED: similar to HLA class II histocompati... 288 4e-78
Alignment gi|XP_945926.1| PREDICTED: similar to HLA class II histocompati... 288 6e-78
Alignment gi|NP_072049.2| major histocompatibility complex, class II, DR ... 286 2e-77
Alignment gi|NP_002116.2| major histocompatibility complex, class II, DR ... 286 3e-77
Alignment gi|NP_068818.4| major histocompatibility complex, class II, DR ... 279 4e-75
Alignment gi|XP_949915.1| PREDICTED: similar to HLA class II histocompati... 262 4e-70
Alignment gi|NP_002114.2| major histocompatibility complex, class II, DQ ... 238 9e-63
Alignment gi|NP_872355.1| major histocompatibility complex, class II, DQ ... 236 3e-62
Alignment gi|NP_002112.3| major histocompatibility complex, class II, DP ... 223 2e-58
>ref|NP_002115.1| major histocompatibility complex, class II, DR beta 1 precursor
[Homo sapiens]
Length = 266
Score = 294 bits (752), Expect = 1e-79
Identities = 149/218 (68%), Positives = 168/218 (77%), Gaps = 4/218 (1%)
Frame = +2
Query: 113 MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHY 292
M+ L G M ALTV L+VLS PLALA DT P NGTERVRLL+R
Sbjct: 1 MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVRLLERCI 60
Query: 293 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLV 472
YN EE +RFDSDVGEYRAVTELGRP+A+ WNS+KD+LEQRRA VDTYCRHNY + ++F V
Sbjct: 61 YNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTV 120
Query: 473 PRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 652
RR EP VTVYP+KTQPLQHHNLLVCSV+GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 653 DWTFQTMVMLETVPQSGEVYSC----PSANRPPELKCR 754
DWTFQT+VMLETVP+SGEVY+C PS P ++ R
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWR 218
>ref|XP_949921.1| PREDICTED: similar to HLA class II histocompatibility antigen,
DRB1-9 beta chain precursor (MHC class I antigen DRB1*9)
(DR-9) (DR9) isoform 3 [Homo sapiens]
Length = 325
Score = 288 bits (738), Expect = 4e-78
Identities = 154/241 (63%), Positives = 172/241 (71%), Gaps = 4/241 (1%)
Frame = +2
Query: 113 MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHY 292
M+ L G MAALTV L+VLS PLALA DT P NGTERVR L R
Sbjct: 1 MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60
Query: 293 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLV 472
YN EE +RFDSDVGEYRAVTELGRP A+ WNS+KD LE+RRAEVDT CRHNY + ++F V
Sbjct: 61 YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120
Query: 473 PRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 652
RR P VTVYPAKTQPLQHHNLLVCSV+GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 653 DWTFQTMVMLETVPQSGEVYSC----PSANRPPELKCRW*HSKQASSVPASSQHEKAPAM 820
DWTFQT+VMLETVP+SGEVY+C PS P L W S+Q S S +K +
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSP--LTVEW--SEQLSDFINFSPTKKGTVL 236
Query: 821 L 823
+
Sbjct: 237 I 237
>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 = 288 bits (737), Expect = 6e-78
Identities = 148/218 (67%), Positives = 164/218 (75%), Gaps = 4/218 (1%)
Frame = +2
Query: 113 MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHY 292
M+ L G MAALTV L+VLS PLALA DT P NGTERVR L R
Sbjct: 1 MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60
Query: 293 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLV 472
YN EE +RFDSDVGEYRAVTELGRP A+ WNS+KD LE+RRAEVDT CRHNY + ++F V
Sbjct: 61 YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120
Query: 473 PRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 652
RR P VTVYPAKTQPLQHHNLLVCSV+GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 653 DWTFQTMVMLETVPQSGEVYSC----PSANRPPELKCR 754
DWTFQT+VMLETVP+SGEVY+C PS P ++ R
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEWR 218
>ref|NP_072049.2| major histocompatibility complex, class II, DR beta 3 precursor
[Homo sapiens]
Length = 266
Score = 286 bits (732), Expect = 2e-77
Identities = 140/202 (69%), Positives = 158/202 (78%)
Frame = +2
Query: 113 MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHY 292
M+ L G +AALTV L+VLS LA A DT P NGTERVR LDR++
Sbjct: 1 MVCLKLPGGSSLAALTVTLMVLSSRLAFAGDTRPRFLELRKSECHFFNGTERVRYLDRYF 60
Query: 293 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLV 472
+N EE LRFDSDVGEYRAVTELGRP A+ WNS+KD+LEQ+R VD YCRHNY + ++F V
Sbjct: 61 HNQEEFLRFDSDVGEYRAVTELGRPVAESWNSQKDLLEQKRGRVDNYCRHNYGVGESFTV 120
Query: 473 PRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 652
RR P VTVYPAKTQPLQHHNLLVCSV+GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVHPQVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 653 DWTFQTMVMLETVPQSGEVYSC 718
DWTFQT+VMLETVP+SGEVY+C
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTC 202
>ref|NP_002116.2| major histocompatibility complex, class II, DR beta 5 precursor
[Homo sapiens]
Length = 266
Score = 286 bits (731), Expect = 3e-77
Identities = 146/218 (66%), Positives = 162/218 (74%), Gaps = 4/218 (1%)
Frame = +2
Query: 113 MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHY 292
M+ L G +MA LTV L+VLS PLALA DT P NGTERVR L R
Sbjct: 1 MVCLKLPGGSYMAKLTVTLMVLSSPLALAGDTRPRFLQQDKYECHFFNGTERVRFLHRDI 60
Query: 293 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLV 472
YN EE LRFDSDVGEYRAVTELGRP+A+ WNS+KD LE RRA VDTYCRHNY + ++F V
Sbjct: 61 YNQEEDLRFDSDVGEYRAVTELGRPDAEYWNSQKDFLEDRRAAVDTYCRHNYGVGESFTV 120
Query: 473 PRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 652
RR EP VTVYPA+TQ LQHHNLLVCSV GFYPG +EVRWFRN QEE AGVVSTGLI NG
Sbjct: 121 QRRVEPKVTVYPARTQTLQHHNLLVCSVNGFYPGSIEVRWFRNSQEEKAGVVSTGLIQNG 180
Query: 653 DWTFQTMVMLETVPQSGEVYSC----PSANRPPELKCR 754
DWTFQT+VMLETVP+SGEVY+C PS P ++ R
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWR 218
>ref|NP_068818.4| major histocompatibility complex, class II, DR beta 4 precursor
[Homo sapiens]
Length = 266
Score = 279 bits (713), Expect = 4e-75
Identities = 138/202 (68%), Positives = 159/202 (78%)
Frame = +2
Query: 113 MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHY 292
M+ L G MAALTV L VLS PLALA DT P NGTERV L R+
Sbjct: 1 MVCLKLPGGSCMAALTVTLTVLSSPLALAGDTQPRFLEQAKCECHFLNGTERVWNLIRYI 60
Query: 293 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLV 472
YN EE R++SD+GEY+AVTELGRP+A+ WNS+KD+LE+RRAEVDTYCR+NY + ++F V
Sbjct: 61 YNQEEYARYNSDLGEYQAVTELGRPDAEYWNSQKDLLERRRAEVDTYCRYNYGVVESFTV 120
Query: 473 PRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 652
RR +P VTVYP+KTQPLQHHNLLVCSV GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVQPKVTVYPSKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180
Query: 653 DWTFQTMVMLETVPQSGEVYSC 718
DWTFQT+VMLETVP+SGEVY+C
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTC 202
>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 = 262 bits (669), Expect = 4e-70
Identities = 127/171 (74%), Positives = 141/171 (82%), Gaps = 4/171 (2%)
Frame = +2
Query: 254 NGTERVRLLDRHYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTY 433
NGTERVR L R YN EE +RFDSDVGEYRAVTELGRP A+ WNS+KD LE+RRAEVDT
Sbjct: 66 NGTERVRYLHRGIYNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTV 125
Query: 434 CRHNYRISDTFLVPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEE 613
CRHNY + ++F V RR P VTVYPAKTQPLQHHNLLVCSV+GFYPG +EVRWFRNGQEE
Sbjct: 126 CRHNYGVGESFTVQRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEE 185
Query: 614 AAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYSC----PSANRPPELKCR 754
AGVVSTGLI NGDWTFQT+VMLETVP+SGEVY+C PS P ++ R
Sbjct: 186 KAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEWR 236
>ref|NP_002114.2| major histocompatibility complex, class II, DQ beta 1 precursor
[Homo sapiens]
Length = 261
Score = 238 bits (606), Expect = 9e-63
Identities = 120/210 (57%), Positives = 146/210 (69%), Gaps = 4/210 (1%)
Frame = +2
Query: 137 GFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILR 316
G A +T+ML +LS P+A RD+P NGTERVRL+ R YN EEI+R
Sbjct: 12 GLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVR 71
Query: 317 FDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTV 496
FDSDVGE+RAVT LG P A+ WNS+KDILE++RA VD CRHNY++ + RR EPTV
Sbjct: 72 FDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTV 131
Query: 497 TVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMV 676
T+ P++T+ L HHNLLVCSVT FYP ++VRWFRN QEE AGVVST LI NGDWTFQ +V
Sbjct: 132 TISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILV 191
Query: 677 MLETVPQSGEVYSC----PSANRPPELKCR 754
MLE PQ G+VY+C PS P ++ R
Sbjct: 192 MLEMTPQRGDVYTCHVEHPSLQSPITVEWR 221
>ref|NP_872355.1| major histocompatibility complex, class II, DQ beta 2 [Homo
sapiens]
Length = 231
Score = 236 bits (601), Expect = 3e-62
Identities = 120/210 (57%), Positives = 144/210 (68%), Gaps = 4/210 (1%)
Frame = +2
Query: 137 GFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILR 316
GFW AA+TVMLV+LS P+A ARD P NGTERVR + R+ YN EE R
Sbjct: 12 GFWAAAVTVMLVMLSTPVAEARDFPKDFLVQFKGMCYFTNGTERVRGVARYIYNREEYGR 71
Query: 317 FDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTV 496
FDSDVGE++AVTELGR +DWN+ KD LEQ RA VD CRHNY + R+ EPTV
Sbjct: 72 FDSDVGEFQAVTELGR-SIEDWNNYKDFLEQERAAVDKVCRHNYEAELRTTLQRQVEPTV 130
Query: 497 TVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMV 676
T+ P++T+ L HHNLLVCSVT FYP ++V+WFRN QEE AGVVST LI NGDWTFQ +V
Sbjct: 131 TISPSRTEALNHHNLLVCSVTDFYPAQIKVQWFRNDQEETAGVVSTSLIRNGDWTFQILV 190
Query: 677 MLETVPQSGEVYSC----PSANRPPELKCR 754
MLE PQ G++Y+C PS P ++ R
Sbjct: 191 MLEITPQRGDIYTCQVEHPSLQSPITVEWR 220
>ref|NP_002112.3| major histocompatibility complex, class II, DP beta 1 precursor
[Homo sapiens]
Length = 258
Score = 223 bits (569), Expect = 2e-58
Identities = 110/189 (58%), Positives = 130/189 (68%)
Frame = +2
Query: 152 ALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILRFDSDV 331
ALT +L+VL + R TP NGT+R L+R+ YN EE RFDSDV
Sbjct: 14 ALTALLMVLLTSVVQGRATPENYLFQGRQECYAFNGTQR--FLERYIYNREEFARFDSDV 71
Query: 332 GEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTVTVYPA 511
GE+RAVTELGRP A+ WNS+KDILE++RA D CRHNY + + RR +P V V P+
Sbjct: 72 GEFRAVTELGRPAAEYWNSQKDILEEKRAVPDRMCRHNYELGGPMTLQRRVQPRVNVSPS 131
Query: 512 KTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLETV 691
K PLQHHNLLVC VT FYPG ++VRWF NGQEE AGVVST LI NGDWTFQ +VMLE
Sbjct: 132 KKGPLQHHNLLVCHVTDFYPGSIQVRWFLNGQEETAGVVSTNLIRNGDWTFQILVMLEMT 191
Query: 692 PQSGEVYSC 718
PQ G+VY+C
Sbjct: 192 PQQGDVYTC 200
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: 46,489,524
Number of Sequences: 39411
Number of extensions: 1299422
Number of successful extensions: 5054
Number of sequences better than 1.0e-05: 10
Number of HSP's better than 0.0 without gapping: 4157
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): 4988
length of database: 17,774,539
effective HSP length: 103
effective length of database: 13,715,206
effective search space used: 3661960002
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-065393
(1113 letters)
Database: RefSeqMP
45,328 sequences; 21,768,885 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_034512.1| histocompatibility 2, class II antigen E beta [... 285 6e-77
Alignment gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/... 227 1e-59
Alignment gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ... 213 3e-55
Alignment gi|NP_996988.1| histocompatibility 2, class II antigen A, beta ... 210 2e-54
Alignment gi|NP_032235.1| histocompatibility-2 complex class 1-like [Mus ... 65 1e-10
Alignment gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ... 64 2e-10
Alignment gi|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus ... 60 4e-09
Alignment gi|NP_034508.2| histocompatibility 2, class II antigen A, alpha... 56 8e-08
Alignment gi|NP_032232.1| histocompatibility 2, O region alpha locus [Mus... 54 2e-07
Alignment gi|NP_034511.2| histocompatibility 2, class II antigen E alpha ... 53 5e-07
>ref|NP_034512.1| histocompatibility 2, class II antigen E beta [Mus musculus]
Length = 264
Score = 285 bits (729), Expect = 6e-77
Identities = 132/191 (69%), Positives = 159/191 (83%)
Frame = +2
Query: 146 MAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILRFDS 325
+AA+ ++L VLSPP+AL RD+ P NGT+RVR L R++YN EE LRFDS
Sbjct: 10 VAAVILLLTVLSPPVALVRDSRPWFLEYCKSECHFYNGTQRVRFLKRYFYNLEENLRFDS 69
Query: 326 DVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTVTVY 505
DVGE+RAVTELGRP+A++WNS+ +IL+++RA VDTYCRHNY I D FLVPRR EPTVTVY
Sbjct: 70 DVGEFRAVTELGRPDAENWNSQPEILDEKRAAVDTYCRHNYEIFDNFLVPRRVEPTVTVY 129
Query: 506 PAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLE 685
P KTQPL+HHNLLVCSV+ FYPG++EVRWFRNG+EE G+VSTGL+ NGDWTFQT+VMLE
Sbjct: 130 PTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLE 189
Query: 686 TVPQSGEVYSC 718
TVPQSGEVY+C
Sbjct: 190 TVPQSGEVYTC 200
>ref|NP_001029150.1| H-2 class II histocompatibility antigen E-a/k beta-2 [Mus musculus]
Length = 287
Score = 227 bits (579), Expect = 1e-59
Identities = 117/218 (53%), Positives = 148/218 (67%), Gaps = 4/218 (1%)
Frame = +2
Query: 113 MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHY 292
M+ L RG +AA+ + L++L+PP+ L RD P NG ERV + R
Sbjct: 1 MVSLWLPRGLCVAAVILSLMMLTPPVILVRDPRPRFLEQLKAECHYFNGKERVWSVTRFI 60
Query: 293 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLV 472
YN EE RF+SD G++ AVTELGRP + N++KD+L+ RA VD CR+NY + D F++
Sbjct: 61 YNQEEFARFNSDFGKFLAVTELGRPIVEYLNTQKDMLDNYRASVDR-CRNNYDLVDIFML 119
Query: 473 PRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 652
+AEP VTVYPAKTQPL+HHNLLVCSV FYPG +EVRWFRNG+EE GVVSTGLI N
Sbjct: 120 NLKAEPKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNR 179
Query: 653 DWTFQTMVMLETVPQSGEVYSC----PSANRPPELKCR 754
DWT+QT+VMLE VP+ GEVY+C PS P ++ R
Sbjct: 180 DWTYQTLVMLEMVPRGGEVYTCQVEHPSLTSPVTVEWR 217
>ref|NP_034519.2| histocompatibility 2, O region beta locus [Mus musculus]
Length = 271
Score = 213 bits (542), Expect = 3e-55
Identities = 103/195 (52%), Positives = 128/195 (65%)
Frame = +2
Query: 134 RGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEIL 313
R W+ AL V L+ L + RD+P NGTE+V LL R +N EE L
Sbjct: 5 RAPWVVALLVNLMRLDSFMIEGRDSPENFVIQAKADCYFTNGTEKVHLLVRFIFNLEEYL 64
Query: 314 RFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPT 493
FDSD+G + A+TELG P+A WN R D+LE RA V+ CR Y++ F V R P
Sbjct: 65 HFDSDLGMFVALTELGEPDADQWNKRLDLLETSRAAVNMVCRQKYKLGAPFTVERNVPPE 124
Query: 494 VTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTM 673
VTVYP +T LQ HNLL+CSVTGFYPG + V+WFRNGQEE +GV+STGL+ NGDWTFQT
Sbjct: 125 VTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVRNGDWTFQTT 184
Query: 674 VMLETVPQSGEVYSC 718
VMLE +P+ G++YSC
Sbjct: 185 VMLEMIPELGDIYSC 199
>ref|NP_996988.1| histocompatibility 2, class II antigen A, beta 1 [Mus musculus]
Length = 265
Score = 210 bits (535), Expect = 2e-54
Identities = 108/208 (51%), Positives = 138/208 (66%), Gaps = 5/208 (2%)
Frame = +2
Query: 146 MAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILRFDS 325
++A V+L+VLS P D+ NGT+R+R + R+ YN EE +R+DS
Sbjct: 10 LSAAVVVLMVLSSPGTEGGDSERHFVYQFMGECYFTNGTQRIRYVTRYIYNREEYVRYDS 69
Query: 326 DVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAE-PTVTV 502
DVGE+RAVTELGRP+A+ WNS+ +ILE+ RAE+DT CRHNY +T RR E P V +
Sbjct: 70 DVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSLRRLEQPNVVI 129
Query: 503 YPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVML 682
++T+ L HHN LVCSVT FYP ++VRWFRNGQEE GV ST LI NGDWTFQ +VML
Sbjct: 130 SLSRTEALNHHNTLVCSVTDFYPTQIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVML 189
Query: 683 ETVPQSGEVYSC----PSANRPPELKCR 754
E P+ GEVY+C PS P ++ R
Sbjct: 190 EMTPRRGEVYTCHVEHPSLKSPITVEWR 217
>ref|NP_032235.1| histocompatibility-2 complex class 1-like [Mus musculus]
Length = 341
Score = 65.1 bits (157), Expect = 1e-10
Identities = 41/150 (27%), Positives = 71/150 (47%), Gaps = 5/150 (3%)
Frame = +2
Query: 284 RHYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYC-----RHNY 448
++ Y+G++ + F+ D + A+ + + W + L+ ++ ++ C R
Sbjct: 129 QYAYDGQDFIIFNKDTLSWLAMDYVAHITKQAWEANLHELQYQKNWLEEECIAWLKRFLE 188
Query: 449 RISDTFLVPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVV 628
DT + R P V +T P C GFYP + + W +NG+E A V
Sbjct: 189 YGRDT--LERTEHPVVRTTRKETFP--GITTFFCRAHGFYPPEISMTWMKNGEEIAQEVD 244
Query: 629 STGLIPNGDWTFQTMVMLETVPQSGEVYSC 718
G++P+GD T+QT + + PQS +VYSC
Sbjct: 245 YGGVLPSGDGTYQTWLSVNLDPQSNDVYSC 274
>ref|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus musculus]
Length = 261
Score = 64.3 bits (155), Expect = 2e-10
Identities = 45/151 (29%), Positives = 70/151 (46%), Gaps = 9/151 (5%)
Frame = +2
Query: 293 YNGEEILRFDSDVG-----EYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRIS 457
+N + + +D DVG E+ ++ L + N ++ ++ + + + H
Sbjct: 46 FNKDLLACWDPDVGKIVPCEFGVLSRLAEIISNILNEQESLIHRLQNGLQDCATHTQPFW 105
Query: 458 DTFLVPRRAEPTVTVYPAKTQPLQHHN--LLVCSVTGFYPGHVEVRWFRNGQ--EEAAGV 625
D L R P+V V A+T P +L C V GFYP V + W +NGQ +
Sbjct: 106 DV-LTHRTRAPSVRV--AQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNK 162
Query: 626 VSTGLIPNGDWTFQTMVMLETVPQSGEVYSC 718
T PNGDWT+QT+ L P G+VY+C
Sbjct: 163 EKTAQ-PNGDWTYQTVSYLALTPSYGDVYTC 192
>ref|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus musculus]
Length = 261
Score = 60.1 bits (144), Expect = 4e-09
Identities = 48/151 (31%), Positives = 73/151 (48%), Gaps = 9/151 (5%)
Frame = +2
Query: 293 YNGEEILRFDSDVGEYRAVTELG--RPEAKDWN---SRKDILEQRRAEVDTYCRHNYRIS 457
+N + + +D DVG+ E G P A++++ ++++ L QR C + +
Sbjct: 46 FNKDLLACWDPDVGKI-VPCEFGVLYPWAENFSRILNKEESLLQRLQNGLLDCASHTQPF 104
Query: 458 DTFLVPRRAEPTVTVYPAKTQPLQHHN--LLVCSVTGFYPGHVEVRWFRNGQ--EEAAGV 625
L R P+V V A+T P +L C V GFYP V + W +NGQ +
Sbjct: 105 WNALTHRTRAPSVRV--AQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNK 162
Query: 626 VSTGLIPNGDWTFQTMVMLETVPQSGEVYSC 718
T PNGDWT+QT+ L P G+VY+C
Sbjct: 163 EKTAQ-PNGDWTYQTVSYLALTPSYGDVYTC 192
>ref|NP_034508.2| histocompatibility 2, class II antigen A, alpha [Mus musculus]
Length = 256
Score = 55.8 bits (133), Expect = 8e-08
Identities = 24/77 (31%), Positives = 36/77 (46%)
Frame = +2
Query: 488 PTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQ 667
P TV+P L N L+C V +P + + W RN + A GV T N D++F
Sbjct: 114 PQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFH 173
Query: 668 TMVMLETVPQSGEVYSC 718
+ L +P ++Y C
Sbjct: 174 KLSYLTFIPSDDDIYDC 190
>ref|NP_032232.1| histocompatibility 2, O region alpha locus [Mus musculus]
Length = 250
Score = 54.3 bits (129), Expect = 2e-07
Identities = 40/145 (27%), Positives = 58/145 (40%), Gaps = 1/145 (0%)
Frame = +2
Query: 287 HYYNGEEILRFDSDVGEYR-AVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDT 463
H ++GE+I D E + E G D+ S + +A +D + R
Sbjct: 50 HEFDGEQIFSVDLKNEEVVWRLPEFGDFAHSDFQSGLMSISMIKAHLDILVERSNRTRAV 109
Query: 464 FLVPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLI 643
+ PR VTV P L N+L+C V +P + V W RN Q GV T
Sbjct: 110 SVPPR-----VTVLPKTRVELGKPNVLICIVDDIFPPVINVTWLRNSQPITKGVAQTSFY 164
Query: 644 PNGDWTFQTMVMLETVPQSGEVYSC 718
+ F+ L VP + +VY C
Sbjct: 165 SQPNHRFRKFHYLTFVPSAEDVYDC 189
>ref|NP_034511.2| histocompatibility 2, class II antigen E alpha [Mus musculus]
Length = 255
Score = 53.1 bits (126), Expect = 5e-07
Identities = 27/77 (35%), Positives = 36/77 (46%)
Frame = +2
Query: 488 PTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQ 667
P VTV L N+L+C + F P V V WFRNG+ GV T +P D F+
Sbjct: 112 PEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWFRNGRPVTEGVSETVFLPRDDHLFR 171
Query: 668 TMVMLETVPQSGEVYSC 718
L +P + + Y C
Sbjct: 172 KFHYLTFLPSTDDFYDC 188
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: 54,585,054
Number of Sequences: 45328
Number of extensions: 1459906
Number of successful extensions: 5137
Number of sequences better than 1.0e-05: 10
Number of HSP's better than 0.0 without gapping: 4360
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): 5115
length of database: 21,768,885
effective HSP length: 105
effective length of database: 17,009,445
effective search space used: 4507502925
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)