Animal-Genome cDNA LVR01_0002_B02


Search to RefSeqBP

BLASTX 2.2.10 [Oct-19-2004]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= LVR01_0002_B02
         (1220 letters)

Database: RefSeqBP 
           33,508 sequences; 16,112,626 total letters

Searching..................................................done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001029840.2| MHC class II antigen [Bos taurus]                 387   e-107
Alignment   gi|NP_001012694.1| major histocompatibility complex, class II, ...   378   e-105
Alignment   gi|NP_001012697.1| major histocompatibility complex, class II, ...   297   1e-80
Alignment   gi|NP_001012698.2| major histocompatibility complex, class II, ...   288   6e-78
Alignment   gi|XP_582099.2| PREDICTED: similar to major histocompatibility ...   258   7e-69
Alignment   gi|NP_001013618.1| major histocompatibility complex, class II, ...   255   6e-68
Alignment   gi|XP_876139.1| PREDICTED: similar to H-2 class II histocompati...   240   2e-63
Alignment   gi|XP_874766.1| PREDICTED: similar to HLA class II histocompati...   153   3e-37
Alignment   gi|NP_001029503.1| hypothetical protein LOC508800 [Bos taurus]        75   1e-13
Alignment   gi|NP_001012399.1| hemochromatosis [Bos taurus]                       71   2e-12

>ref|NP_001029840.2| MHC class II antigen [Bos taurus]
          Length = 261

 Score =  387 bits (994), Expect = e-107
 Identities = 191/261 (73%), Positives = 212/261 (81%)
 Frame = +2

Query: 53  MSGMVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVA 232
           MSGMVAL +PRGLWTA V + LV+L  P AEGRDSP+DFV QFK  CYF NGT+RVR V 
Sbjct: 1   MSGMVALWIPRGLWTAVVMVTLVMLSTPGAEGRDSPKDFVVQFKGLCYFTNGTERVRYVT 60

Query: 233 RYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEG 412
           RYIYNQEE +RFDSD   YRA+TPLGRP+A+ WN QKD LEQTRAE DTVC+HNYQ E  
Sbjct: 61  RYIYNQEEYVRFDSDWDLYRALTPLGRPDAEYWNSQKDFLEQTRAEADTVCRHNYQAELI 120

Query: 413 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 592
           T+LQRRV+PTVTISPS+ EALNHHNLLVC+VTDFYPSQ+KV+WFRN +EETAGVVSTPLI
Sbjct: 121 TSLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPSQIKVRWFRNDREETAGVVSTPLI 180

Query: 593 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 772
           RNGDWT+Q+LVMLEM  QRGDVYTC VEH SLQSPI+VEWRAQSESAQSKMLS       
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPIMVEWRAQSESAQSKMLSGVGGFVL 240

Query: 773 XXXXXXXXXXXRHRSQKGLVR 835
                       HRSQKGL+R
Sbjct: 241 GLIFLGLGLIIHHRSQKGLMR 261


>ref|NP_001012694.1| major histocompatibility complex, class II, DQ beta [Bos taurus]
          Length = 261

 Score =  378 bits (971), Expect = e-105
 Identities = 187/260 (71%), Positives = 209/260 (80%)
 Frame = +2

Query: 53  MSGMVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVA 232
           MSGMVALR+PRGLWTAAV + L VL  P AEGRDSPQD V  F  +CYF NGT+RVR V 
Sbjct: 1   MSGMVALRIPRGLWTAAVMVTLAVLSTPGAEGRDSPQDTVVHFMGQCYFTNGTERVRYVT 60

Query: 233 RYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEG 412
           RYIYNQEE   +DSDVGEYRAVT LGR  A+ WN QKD+LEQTRAELDTVC+HNYQ+E  
Sbjct: 61  RYIYNQEETAYYDSDVGEYRAVTQLGRTLAEYWNSQKDILEQTRAELDTVCRHNYQLEVI 120

Query: 413 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 592
           T+LQR+V+PTVTIS S+ EALNHHNLLVC+VTDFYP Q+KV+WF+NG+EETAG+VSTPLI
Sbjct: 121 TSLQRQVEPTVTISLSRTEALNHHNLLVCSVTDFYPGQIKVRWFQNGKEETAGIVSTPLI 180

Query: 593 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 772
           RNGDWT+Q+LVMLEM  +RGDVYTC VEH SLQSPI VEWRAQSESAQSKMLS       
Sbjct: 181 RNGDWTFQILVMLEMTPKRGDVYTCHVEHPSLQSPISVEWRAQSESAQSKMLSGVGGFVL 240

Query: 773 XXXXXXXXXXXRHRSQKGLV 832
                      R RSQKGLV
Sbjct: 241 GLIFLGLGLIVRRRSQKGLV 260


>ref|NP_001012697.1| major histocompatibility complex, class II, DY beta [Bos taurus]
          Length = 259

 Score =  297 bits (761), Expect = 1e-80
 Identities = 149/227 (65%), Positives = 177/227 (77%), Gaps = 2/227 (0%)
 Frame = +2

Query: 77  LPRGLWTAAVTMMLV--VLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYIYNQ 250
           +PR   T A  +M V  VL  P A  RD+P++FV+QFK  CYF NGT+ VRLVAR IYN+
Sbjct: 5   IPRNPGTVAGMVMAVFLVLRIPEAHCRDAPKNFVYQFKGMCYFTNGTEHVRLVARQIYNK 64

Query: 251 EELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRR 430
           EE+L FDSD+GE+ AVT LGR  A+ WN QKD+L + RA +DT+C+HNY+   G T+QRR
Sbjct: 65  EEILHFDSDLGEFVAVTELGRVCAEIWNTQKDLLAEFRAYVDTLCRHNYKETAGFTVQRR 124

Query: 431 VQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWT 610
           V+PTVT+SP+  EALNHHNLLVC+VTDFYP QVKV+WFRN QE+TAGV  TPL +NGDWT
Sbjct: 125 VEPTVTVSPASTEALNHHNLLVCSVTDFYPRQVKVKWFRNQQEQTAGVGFTPLTQNGDWT 184

Query: 611 YQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 751
           YQ+ VMLE   Q GDVY C V+H SLQSPI VEWRAQSESAQSKM S
Sbjct: 185 YQIHVMLETVPQLGDVYVCHVDHPSLQSPITVEWRAQSESAQSKMQS 231


>ref|NP_001012698.2| major histocompatibility complex, class II, DRB3 [Bos taurus]
          Length = 266

 Score =  288 bits (737), Expect = 6e-78
 Identities = 141/255 (55%), Positives = 177/255 (69%)
 Frame = +2

Query: 62  MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
           MV L    G W AA+ +ML+VL  P+A  R+    F+  +K EC+FFNGT+RVR + R+ 
Sbjct: 1   MVCLYFSGGSWMAALIVMLMVLCPPLAWAREIQPHFLEYYKGECHFFNGTERVRFLDRHF 60

Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
           YN EE +RFDSD GE+RAVT LGRP A+ WN QKD LEQ RAE+D VC+HNY   E  T+
Sbjct: 61  YNGEEFVRFDSDWGEFRAVTELGRPAAEHWNSQKDFLEQKRAEVDRVCRHNYGGVESFTV 120

Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
           QRRV+PTVT+ P+K + L HHNLLVC+V  FYP  ++V+WFRNG EE AGV+ST LI+NG
Sbjct: 121 QRRVEPTVTVYPAKTQPLQHHNLLVCSVNGFYPGHIEVRWFRNGHEEEAGVISTGLIQNG 180

Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 781
           DWT+Q +VMLE   Q G+VYTC+V+H    SPI VEWRA+S+SAQSKM+S          
Sbjct: 181 DWTFQTMVMLETVPQSGEVYTCQVDHPKRTSPITVEWRARSDSAQSKMMSGVGGFVLGLL 240

Query: 782 XXXXXXXXRHRSQKG 826
                     R+QKG
Sbjct: 241 FLAVGLFIYFRNQKG 255


>ref|XP_582099.2| PREDICTED: similar to major histocompatibility complex, class II,
           DR beta 5 precursor [Bos taurus]
          Length = 255

 Score =  258 bits (659), Expect = 7e-69
 Identities = 122/218 (55%), Positives = 161/218 (73%)
 Frame = +2

Query: 98  AAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYIYNQEELLRFDSD 277
           AA+ ++L+VL  P +  R++   F+ QFK EC F NG +R+R  ARYIYN +E + FDSD
Sbjct: 2   AALAVLLMVLSLPFSWARETQPHFIHQFKGECRFSNGLERMRFFARYIYNTQEDVHFDSD 61

Query: 278 VGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISP 457
           VGE+ A+T LGR +A+ WN QKD +EQ RA++DT+C+ NYQ       QRRV+PTVT+ P
Sbjct: 62  VGEFTALTELGRLDAEYWNQQKDFMEQMRAKVDTLCRSNYQGIGSFLRQRRVEPTVTVYP 121

Query: 458 SKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEM 637
           +K + L HHNLLVC+V  FYP  ++V+WF N  EE AGV+ST LI+NGDWT+Q +VMLE 
Sbjct: 122 AKTQPLQHHNLLVCSVNGFYPGHIEVRWFWNSHEEEAGVISTGLIQNGDWTFQTMVMLET 181

Query: 638 NLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 751
             Q G+VYTC+VEH S  SP+ VEWRAQS+SAQ K++S
Sbjct: 182 VPQSGEVYTCQVEHPSRTSPLTVEWRAQSDSAQRKLMS 219


>ref|NP_001013618.1| major histocompatibility complex, class II, DO beta [Bos taurus]
          Length = 271

 Score =  255 bits (651), Expect = 6e-68
 Identities = 118/220 (53%), Positives = 156/220 (70%)
 Frame = +2

Query: 92  WTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYIYNQEELLRFD 271
           W        + L A V +GRDSP+DFV Q K +CYF NGT++VR V R+I+N E+  RFD
Sbjct: 8   WVVTFLSTALRLDASVTQGRDSPEDFVTQAKADCYFTNGTEKVRFVVRFIFNLEDYARFD 67

Query: 272 SDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTI 451
           SD+G + A+T LG+P+A+ WN + D+L ++RA +D +C+ NY +    T+ RRVQP VT+
Sbjct: 68  SDLGMFVALTELGKPDAERWNNRPDILARSRASVDMLCRRNYYLGAPFTVGRRVQPEVTV 127

Query: 452 SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVML 631
            P K  AL H NLL+C VT FYP  +KV WFRNGQE+  G++ST LIRNGDWT+Q+ VML
Sbjct: 128 YPEKTPALQHRNLLLCLVTGFYPGDIKVTWFRNGQEQREGIMSTGLIRNGDWTFQMTVML 187

Query: 632 EMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 751
            M  + G+VYTC V+H SL SP+ VEWRAQSE +  K+LS
Sbjct: 188 AMTPELGEVYTCLVDHPSLLSPVSVEWRAQSEYSWRKILS 227


>ref|XP_876139.1| PREDICTED: similar to H-2 class II histocompatibility antigen, I-E
           beta chain precursor [Bos taurus]
          Length = 269

 Score =  240 bits (612), Expect = 2e-63
 Identities = 115/192 (59%), Positives = 141/192 (73%)
 Frame = +2

Query: 176 QFKFECYFFNGTQRVRLVARYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLE 355
           Q K EC+F NGTQ+VR + RYIYN+EE ++FDS VGEYRA T +GRP A+ WN     L+
Sbjct: 3   QGKSECHFSNGTQQVRFLDRYIYNREEQVQFDSLVGEYRARTEMGRPAAERWNRWPQALQ 62

Query: 356 QTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKV 535
           + RA +   C  NY+     T+QRRVQPTVT+ P K+  L HHNLLVC+V  FYP  ++V
Sbjct: 63  RARAAVHAYCASNYEFFASRTVQRRVQPTVTVYPVKSRPLWHHNLLVCSVNGFYPGHIEV 122

Query: 536 QWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWR 715
           +WFRNGQEE AGVVST LI NGDWT+Q++VMLE+  Q G+VY C VEH S  SP+ VEWR
Sbjct: 123 RWFRNGQEEEAGVVSTGLIPNGDWTFQIMVMLEIVPQGGEVYACHVEHPSRTSPVTVEWR 182

Query: 716 AQSESAQSKMLS 751
           AQ ES+Q KMLS
Sbjct: 183 AQDESSQEKMLS 194


>ref|XP_874766.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DRB1-7 beta chain precursor (MHC class I antigen DRB1*7)
           (DR-7) (DR7) [Bos taurus]
          Length = 347

 Score =  153 bits (386), Expect = 3e-37
 Identities = 73/137 (53%), Positives = 96/137 (70%)
 Frame = +2

Query: 416 TLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIR 595
           TLQ++V+PTVT+ P+K + L H++LLVC+V  FY   V+V+WF  GQEE AGV+ST LI+
Sbjct: 90  TLQKKVEPTVTVYPAKTQPLQHNHLLVCSVNGFYLGHVEVRWFWKGQEEEAGVISTGLIQ 149

Query: 596 NGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXX 775
           NGDWT++ +VMLE  LQ G+VYTC++EH S +SPI  EWRAQS+SAQSKM+S        
Sbjct: 150 NGDWTFETIVMLETVLQSGEVYTCQLEHPSWRSPIAEEWRAQSDSAQSKMMSGTGGFALG 209

Query: 776 XXXXXXXXXXRHRSQKG 826
                       R+QKG
Sbjct: 210 LLFLVVGLFTHFRNQKG 226


>ref|NP_001029503.1| hypothetical protein LOC508800 [Bos taurus]
          Length = 299

 Score = 74.7 bits (182), Expect = 1e-13
 Identities = 51/198 (25%), Positives = 87/198 (43%), Gaps = 5/198 (2%)
 Frame = +2

Query: 149 RDSPQDFVFQFKFECYFFNGTQRVRLVARYIYNQEELLRFDSDVGEYRAVTPLGRPEADS 328
           +D      FQ  F C   N          Y Y+ ++ ++FD ++  +  + P  +     
Sbjct: 106 KDREGSHTFQGAFGCELRNNESSGAFWG-YAYDGQDFIKFDKEIPAWVPLDPAAQNTKRK 164

Query: 329 WNGQKDVLEQTRAELDTVCK---HNYQIEEGTTLQRRVQPTVTISPSKAEALNHHNLLVC 499
           W  +   +++ +A L+  C      Y     T L R+  P+V+++   A    H   L C
Sbjct: 165 WEAEAVYVQRAKAYLEEECPGMLRRYLPYSRTHLDRQESPSVSVTGHAAPG--HKRTLKC 222

Query: 500 AVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEH 679
              DFYP  + + W R G  + A      ++ +G+ TYQ  V++ +  +    Y+C VEH
Sbjct: 223 LAYDFYPRSIGLHWTRAGDAQEAES-GGDVLPSGNGTYQSWVVVGVPPEDQAPYSCHVEH 281

Query: 680 SSLQSPILVEW--RAQSE 727
            SL  P+ V W  R Q+E
Sbjct: 282 RSLTRPLTVPWDPRQQAE 299


>ref|NP_001012399.1| hemochromatosis [Bos taurus]
          Length = 356

 Score = 71.2 bits (173), Expect = 2e-12
 Identities = 47/165 (28%), Positives = 76/165 (46%), Gaps = 5/165 (3%)
 Frame = +2

Query: 233 RYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCK----HNYQ 400
           +Y Y+ ++ L F  +  ++RA  P  +     W   K   +Q RA LD  C     H  +
Sbjct: 145 KYGYDGQDHLEFRPETLDWRAAEPRAQVTKLEWEVNKIRAKQNRAYLDRDCPEQLLHLLE 204

Query: 401 IEEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVS 580
           +  G  L+++V P V ++     +L     L C   +FYP  + ++W ++ Q   A  + 
Sbjct: 205 LGRGP-LEQQVPPLVKVTHHVTSSLT---TLRCRALNFYPQNITIRWLKDKQFLDAKEIK 260

Query: 581 TP-LIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 712
              ++ NGD TYQ  V L M       Y+C+VEH  L  P+   W
Sbjct: 261 PEDVLPNGDGTYQAWVALAMLPGEEQRYSCQVEHPGLDQPLTATW 305


  Database: RefSeqBP
    Posted date:  Aug 1, 2006  7:14 PM
  Number of letters in database: 16,112,626
  Number of sequences in database:  33,508
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 41,725,578
Number of Sequences: 33508
Number of extensions: 1103339
Number of successful extensions: 4608
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 3964
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 4564
length of database: 16,112,626
effective HSP length: 104
effective length of database: 12,627,794
effective search space used: 3813593788
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqCP

BLASTX 2.2.10 [Oct-19-2004]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= LVR01_0002_B02
         (1220 letters)

Database: RefSeqCP 
           33,732 sequences; 19,266,565 total letters

Searching..................................................done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Ca...   387   e-107
Alignment   gi|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis fami...   310   2e-84
Alignment   gi|XP_850395.1| PREDICTED: similar to HLA class II histocompati...   266   3e-71
Alignment   gi|XP_861384.1| PREDICTED: similar to HLA class II histocompati...   253   3e-67
Alignment   gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati...    69   9e-12
Alignment   gi|XP_849737.1| PREDICTED: similar to HLA class II histocompati...    68   2e-11
Alignment   gi|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris]     67   3e-11
Alignment   gi|NP_001011726.1| MHC class II DLA DQalpha chain [Canis famili...    65   2e-10
Alignment   gi|XP_536867.2| PREDICTED: similar to Zinc-alpha-2-glycoprotein...    65   2e-10
Alignment   gi|XP_853335.1| PREDICTED: similar to T-cell surface glycoprote...    59   7e-09

>ref|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Canis familiaris]
          Length = 269

 Score =  387 bits (994), Expect = e-107
 Identities = 187/258 (72%), Positives = 212/258 (82%)
 Frame = +2

Query: 53  MSGMVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVA 232
           MSG + L +PRG WTAAV M+LVVL  PVAEGRDSPQDFVFQ+K ECYF NGT+RVRL+ 
Sbjct: 1   MSGKMTLCIPRGFWTAAVMMILVVLSIPVAEGRDSPQDFVFQYKAECYFTNGTERVRLLT 60

Query: 233 RYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEG 412
           +YIYN+EE +RFDSDVGE+RAVT LGRP+A+ WN QKD +++ RAELDTVC+HNY  EE 
Sbjct: 61  KYIYNREEFVRFDSDVGEFRAVTELGRPDAEYWNRQKDEMDRVRAELDTVCRHNYGREEL 120

Query: 413 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 592
           TTLQRRV+PTVTI PSK E LNHHNLLVC+VTDFYP Q+KV+WFRN QE+TAGVVSTPLI
Sbjct: 121 TTLQRRVEPTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLI 180

Query: 593 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 772
           RNGDWT+Q+LVMLEM  QRGDVYTC VEH+SLQSPI V+WRAQSESAQSKMLS       
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHASLQSPITVQWRAQSESAQSKMLSGIGGFVL 240

Query: 773 XXXXXXXXXXXRHRSQKG 826
                      RHRSQKG
Sbjct: 241 GLIFLGLGLIIRHRSQKG 258


>ref|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis familiaris]
          Length = 266

 Score =  310 bits (794), Expect = 2e-84
 Identities = 151/255 (59%), Positives = 185/255 (72%)
 Frame = +2

Query: 62  MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
           MV L    G W  A+ ++L+VL  P A  RD+P  F+   K ECYF NGT+RVR V RYI
Sbjct: 1   MVCLCFLGGSWMTALMLILMVLNPPFAWARDTPPHFLEVAKSECYFTNGTERVRFVERYI 60

Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
           +N+EE +RFDSDVGE+RAVT LGRP A+SWNGQK++LEQ RA +DT C+HNY + E  T+
Sbjct: 61  HNREEFVRFDSDVGEFRAVTELGRPVAESWNGQKEILEQERATVDTYCRHNYGVIESFTV 120

Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
           QRRV+PTVT+ P+K + L HHNLLVC+V  FYP  ++V+W RNGQEE AGVVST LIRNG
Sbjct: 121 QRRVEPTVTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNG 180

Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 781
           DWT+Q+LVMLE+  Q G+VYTC+VEH SL SP+ VEWRAQS+SAQSKMLS          
Sbjct: 181 DWTFQILVMLEIVPQSGEVYTCQVEHPSLTSPVTVEWRAQSDSAQSKMLSGIGGFVLGLL 240

Query: 782 XXXXXXXXRHRSQKG 826
                     R+QKG
Sbjct: 241 FLAVGLFIYFRNQKG 255


>ref|XP_850395.1| PREDICTED: similar to HLA class II histocompatibility antigen, DO
           beta chain precursor (MHC class II antigen DOB) isoform
           1 [Canis familiaris]
          Length = 270

 Score =  266 bits (680), Expect = 3e-71
 Identities = 124/247 (50%), Positives = 168/247 (68%)
 Frame = +2

Query: 92  WTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYIYNQEELLRFD 271
           W  A+ + +  L + + +GRDSP+DFV Q K +CYF NGT++V+ V R+I+N EE  RFD
Sbjct: 8   WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67

Query: 272 SDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTI 451
           S VG + A+T LG+P+A+ WN Q  +LE++RA +D +C+HNY++    T+ R+VQP VT+
Sbjct: 68  SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTV 127

Query: 452 SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVML 631
            P +  ++ HHNLL+C+VT FYP  +K++WFRNGQEE  GV+ST LIRNGDWT+Q +VML
Sbjct: 128 YPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVML 187

Query: 632 EMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXXXXXXXXXXRH 811
           EM  + GDVYTC V H SL SP+ VEWRAQS  +  KMLS                    
Sbjct: 188 EMTPELGDVYTCLVNHPSLLSPVSVEWRAQSTYSWRKMLSGIAAFLLGLIFLLVGTVICL 247

Query: 812 RSQKGLV 832
           R+QKG V
Sbjct: 248 RAQKGYV 254


>ref|XP_861384.1| PREDICTED: similar to HLA class II histocompatibility antigen, DO
           beta chain precursor (MHC class II antigen DOB) isoform
           2 [Canis familiaris]
          Length = 228

 Score =  253 bits (645), Expect = 3e-67
 Identities = 111/207 (53%), Positives = 153/207 (73%)
 Frame = +2

Query: 92  WTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYIYNQEELLRFD 271
           W  A+ + +  L + + +GRDSP+DFV Q K +CYF NGT++V+ V R+I+N EE  RFD
Sbjct: 8   WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67

Query: 272 SDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTI 451
           S VG + A+T LG+P+A+ WN Q  +LE++RA +D +C+HNY++    T+ R+VQP VT+
Sbjct: 68  SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTV 127

Query: 452 SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVML 631
            P +  ++ HHNLL+C+VT FYP  +K++WFRNGQEE  GV+ST LIRNGDWT+Q +VML
Sbjct: 128 YPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVML 187

Query: 632 EMNLQRGDVYTCRVEHSSLQSPILVEW 712
           EM  + GDVYTC V H SL SP+ VEW
Sbjct: 188 EMTPELGDVYTCLVNHPSLLSPVSVEW 214


>ref|XP_850803.1| PREDICTED: similar to HLA class II histocompatibility antigen, DO
           alpha chain precursor (MHC class II antigen DOA) (MHC DZ
           alpha) (MHC DN-alpha) isoform 11 [Canis familiaris]
          Length = 227

 Score = 68.9 bits (167), Expect = 9e-12
 Identities = 36/122 (29%), Positives = 56/122 (45%), Gaps = 2/122 (1%)
 Frame = +2

Query: 362 RAELDTVCKHNYQIE--EGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKV 535
           +A LD + + + +     GT L   + P V + P     L   N+L+C V + +P  + +
Sbjct: 63  KAHLDVLVERSNRTRAINGTHLSSPLPPRVAVLPKFRVELGQPNVLICIVDNIFPPVINI 122

Query: 536 QWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWR 715
            W RNGQ  + GV  T      D  ++    L       D+Y C+VEH  L+ P+L  W 
Sbjct: 123 TWLRNGQIISEGVAQTSFYSQPDHLFRKFCYLTFVPSAEDMYDCKVEHWGLEEPLLRHWE 182

Query: 716 AQ 721
            Q
Sbjct: 183 PQ 184


>ref|XP_849737.1| PREDICTED: similar to HLA class II histocompatibility antigen, DM
           beta chain precursor (MHC class II antigen DMB) [Canis
           familiaris]
          Length = 263

 Score = 67.8 bits (164), Expect = 2e-11
 Identities = 47/163 (28%), Positives = 72/163 (44%), Gaps = 6/163 (3%)
 Frame = +2

Query: 242 YNQEELLRFDSDVG-----EYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIE 406
           +N++ L  +D D       E+  +  L    +D  N Q++ L Q  +     C  + Q  
Sbjct: 46  FNKDLLTCWDPDEAKMVPYEFGTLNVLANYLSDYLN-QQEYLHQRLSNGLQDCATHTQSF 104

Query: 407 EGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTP 586
            G+   R   PTV ++ S         +L C V  FYP+ V + W +NGQ   +   +  
Sbjct: 105 WGSLTHRTRPPTVQVAKSTPFNTKESVMLACYVWGFYPADVTISWRKNGQPVPSHSSALN 164

Query: 587 LIR-NGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 712
           + + NGDWTYQ +  L       D YTC VEH     P+  +W
Sbjct: 165 MAQPNGDWTYQTVSHLATTPSYEDTYTCVVEHIGAPEPVCEDW 207


>ref|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris]
          Length = 254

 Score = 67.4 bits (163), Expect = 3e-11
 Identities = 38/117 (32%), Positives = 52/117 (44%)
 Frame = +2

Query: 362 RAELDTVCKHNYQIEEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQW 541
           +A LDT+ K +       T    V P VT+  +    L   N+L+C +  F P  + V W
Sbjct: 92  KANLDTMIKRSNH-----TPNTNVPPEVTVLSNTPVELGEPNILICFIDKFSPPVINVTW 146

Query: 542 FRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 712
            RNG   T GV  T  +   D  ++    L       DVY C+VEH  L  P+L  W
Sbjct: 147 LRNGNPVTTGVSETIFLPREDHLFRKFHYLPFLPSAEDVYDCKVEHWGLDEPLLKHW 203


>ref|NP_001011726.1| MHC class II DLA DQalpha chain [Canis familiaris]
          Length = 255

 Score = 64.7 bits (156), Expect = 2e-10
 Identities = 30/103 (29%), Positives = 46/103 (44%)
 Frame = +2

Query: 437 PTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQ 616
           P VT+       L   N L+C V + +P  + V W +N    T GV  T     GD ++ 
Sbjct: 113 PEVTVFSKSPVMLGQPNTLICLVDNIFPPVINVTWLKNRHSVTEGVSETSFFAKGDHSFS 172

Query: 617 VLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKM 745
            +  L       D+Y C+VEH  L  P+L  W  +  +  S++
Sbjct: 173 KISYLTFLPSAEDIYDCKVEHWGLDEPLLKHWEPEVPTPMSEL 215


>ref|XP_536867.2| PREDICTED: similar to Zinc-alpha-2-glycoprotein precursor
           (Zn-alpha-2-glycoprotein) (Zn-alpha-2-GP) [Canis
           familiaris]
          Length = 315

 Score = 64.7 bits (156), Expect = 2e-10
 Identities = 60/230 (26%), Positives = 99/230 (43%), Gaps = 8/230 (3%)
 Frame = +2

Query: 47  SIMSGMVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRL 226
           S M G+        L  A   + +V L   +   +D      FQ  F C   N  +    
Sbjct: 75  SQMEGIEDWEKESKLQKAREDIFMVTLKDIMEYYKDKEGSHTFQGMFGCELQNN-KNSGA 133

Query: 227 VARYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQ-- 400
             RY Y+    + F+ ++  +    P        W  ++  +++ +A L+  C    Q  
Sbjct: 134 FWRYAYDGRNFIEFNKEIPAWVPQDPAALNTKKKWEAEEVYVQRAKAYLEEECPVMLQRY 193

Query: 401 IEEGTT-LQRRVQPTVTI-SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFR--NGQEETA 568
           +E G T L R+  P+V+I S    E +     L C V+ FYP ++ + W +  + QE  +
Sbjct: 194 LEYGKTYLDRQEPPSVSITSHGTPEGIQ---TLKCWVSGFYPQEIDLHWIQADDTQETKS 250

Query: 569 GVVSTPLIRNGDWTYQVLVMLEMNLQ--RGDVYTCRVEHSSLQSPILVEW 712
           G    P   +G+ TYQ  V++  + Q      Y+C V+HSSL  P+ V W
Sbjct: 251 GGALLP---SGNNTYQAWVVMSASPQDLASFSYSCLVKHSSLSQPLTVLW 297


>ref|XP_853335.1| PREDICTED: similar to T-cell surface glycoprotein CD1a precursor
           (CD1a antigen) (T-cell surface antigen T6/Leu-6) (hTa1
           thymocyte antigen) [Canis familiaris]
          Length = 357

 Score = 59.3 bits (142), Expect = 7e-09
 Identities = 33/90 (36%), Positives = 50/90 (55%)
 Frame = +2

Query: 419 LQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRN 598
           LQR+V+P   +S   +    H  L VC V+ FYP  V V W R G++E  G + + ++ N
Sbjct: 199 LQRKVRPEAWLSAGSSPGPGHLRL-VCHVSGFYPKPVWVSWMR-GEQEQQGTLYSDILPN 256

Query: 599 GDWTYQVLVMLEMNLQRGDVYTCRVEHSSL 688
            D T+ + V L++  +     +CRV HSSL
Sbjct: 257 TDGTWYLQVSLDVKSKEAAGLSCRVRHSSL 286


  Database: RefSeqCP
    Posted date:  Aug 1, 2006  9:25 PM
  Number of letters in database: 19,266,565
  Number of sequences in database:  33,732
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 48,909,197
Number of Sequences: 33732
Number of extensions: 1290257
Number of successful extensions: 5756
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 4767
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 5724
length of database: 19,266,565
effective HSP length: 105
effective length of database: 15,724,705
effective search space used: 4733136205
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqHP

BLASTX 2.2.10 [Oct-19-2004]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= LVR01_0002_B02
         (1220 letters)

Database: RefSeqHP 
           39,411 sequences; 17,774,539 total letters

Searching..................................................done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_002114.2| major histocompatibility complex, class II, DQ ...   374   e-103
Alignment   gi|NP_872355.1| major histocompatibility complex, class II, DQ ...   328   7e-90
Alignment   gi|NP_002115.1| major histocompatibility complex, class II, DR ...   311   7e-85
Alignment   gi|XP_945926.1| PREDICTED: similar to HLA class II histocompati...   308   5e-84
Alignment   gi|NP_002116.2| major histocompatibility complex, class II, DR ...   300   2e-81
Alignment   gi|NP_002112.3| major histocompatibility complex, class II, DP ...   298   8e-81
Alignment   gi|NP_068818.4| major histocompatibility complex, class II, DR ...   293   2e-79
Alignment   gi|NP_072049.2| major histocompatibility complex, class II, DR ...   293   3e-79
Alignment   gi|XP_949921.1| PREDICTED: similar to HLA class II histocompati...   288   7e-78
Alignment   gi|XP_949915.1| PREDICTED: similar to HLA class II histocompati...   284   9e-77

>ref|NP_002114.2| major histocompatibility complex, class II, DQ beta 1 precursor
           [Homo sapiens]
          Length = 261

 Score =  374 bits (959), Expect = e-103
 Identities = 184/260 (70%), Positives = 210/260 (80%)
 Frame = +2

Query: 53  MSGMVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVA 232
           MS   ALR+P GL  A VT+ML +L  PVAEGRDSP+DFV+QFK  CYF NGT+RVRLV+
Sbjct: 1   MSWKKALRIPGGLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVS 60

Query: 233 RYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEG 412
           R IYN+EE++RFDSDVGE+RAVT LG P A+ WN QKD+LE+ RA +D VC+HNYQ+E  
Sbjct: 61  RSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELR 120

Query: 413 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 592
           TTLQRRV+PTVTISPS+ EALNHHNLLVC+VTDFYP+Q+KV+WFRN QEETAGVVSTPLI
Sbjct: 121 TTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLI 180

Query: 593 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 772
           RNGDWT+Q+LVMLEM  QRGDVYTC VEH SLQSPI VEWRAQSESAQSKMLS       
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVL 240

Query: 773 XXXXXXXXXXXRHRSQKGLV 832
                       HRSQKGL+
Sbjct: 241 GLIFLGLGLIIHHRSQKGLL 260


>ref|NP_872355.1| major histocompatibility complex, class II, DQ beta 2 [Homo
           sapiens]
          Length = 231

 Score =  328 bits (840), Expect = 7e-90
 Identities = 159/221 (71%), Positives = 184/221 (83%)
 Frame = +2

Query: 53  MSGMVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVA 232
           MS  +AL++P G W AAVT+MLV+L  PVAE RD P+DF+ QFK  CYF NGT+RVR VA
Sbjct: 1   MSWKMALQIPGGFWAAAVTVMLVMLSTPVAEARDFPKDFLVQFKGMCYFTNGTERVRGVA 60

Query: 233 RYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEG 412
           RYIYN+EE  RFDSDVGE++AVT LGR   D WN  KD LEQ RA +D VC+HNY+ E  
Sbjct: 61  RYIYNREEYGRFDSDVGEFQAVTELGRSIED-WNNYKDFLEQERAAVDKVCRHNYEAELR 119

Query: 413 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 592
           TTLQR+V+PTVTISPS+ EALNHHNLLVC+VTDFYP+Q+KVQWFRN QEETAGVVST LI
Sbjct: 120 TTLQRQVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVQWFRNDQEETAGVVSTSLI 179

Query: 593 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWR 715
           RNGDWT+Q+LVMLE+  QRGD+YTC+VEH SLQSPI VEWR
Sbjct: 180 RNGDWTFQILVMLEITPQRGDIYTCQVEHPSLQSPITVEWR 220


>ref|NP_002115.1| major histocompatibility complex, class II, DR beta 1 precursor
           [Homo sapiens]
          Length = 266

 Score =  311 bits (797), Expect = 7e-85
 Identities = 152/255 (59%), Positives = 189/255 (74%)
 Frame = +2

Query: 62  MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
           MV L+LP G    A+T+ L+VL +P+A   D+   F++Q KFEC+FFNGT+RVRL+ R I
Sbjct: 1   MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVRLLERCI 60

Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
           YNQEE +RFDSDVGEYRAVT LGRP+A+ WN QKD+LEQ RA +DT C+HNY + E  T+
Sbjct: 61  YNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTV 120

Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
           QRRV+P VT+ PSK + L HHNLLVC+V+ FYP  ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 781
           DWT+Q LVMLE   + G+VYTC+VEH S+ SP+ VEWRA+SESAQSKMLS          
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSESAQSKMLSGVGGFVLGLL 240

Query: 782 XXXXXXXXRHRSQKG 826
                     R+QKG
Sbjct: 241 FLGAGLFIYFRNQKG 255


>ref|XP_945926.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DRB1-9 beta chain precursor (MHC class I antigen DRB1*9)
           (DR-9) (DR9) isoform 1 [Homo sapiens]
          Length = 266

 Score =  308 bits (790), Expect = 5e-84
 Identities = 153/255 (60%), Positives = 188/255 (73%)
 Frame = +2

Query: 62  MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
           MV L+LP G   AA+T+ L+VL +P+A   D+   F+ Q KFEC+FFNGT+RVR + R I
Sbjct: 1   MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60

Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
           YNQEE +RFDSDVGEYRAVT LGRP A+SWN QKD LE+ RAE+DTVC+HNY + E  T+
Sbjct: 61  YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120

Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
           QRRV P VT+ P+K + L HHNLLVC+V+ FYP  ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 781
           DWT+Q LVMLE   + G+VYTC+VEH S+ SP+ VEWRA+SESAQSKMLS          
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEWRARSESAQSKMLSGVGGFVLGLL 240

Query: 782 XXXXXXXXRHRSQKG 826
                     R+QKG
Sbjct: 241 FLGAGLFIYFRNQKG 255


>ref|NP_002116.2| major histocompatibility complex, class II, DR beta 5 precursor
           [Homo sapiens]
          Length = 266

 Score =  300 bits (768), Expect = 2e-81
 Identities = 144/230 (62%), Positives = 179/230 (77%)
 Frame = +2

Query: 62  MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
           MV L+LP G + A +T+ L+VL +P+A   D+   F+ Q K+EC+FFNGT+RVR + R I
Sbjct: 1   MVCLKLPGGSYMAKLTVTLMVLSSPLALAGDTRPRFLQQDKYECHFFNGTERVRFLHRDI 60

Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
           YNQEE LRFDSDVGEYRAVT LGRP+A+ WN QKD LE  RA +DT C+HNY + E  T+
Sbjct: 61  YNQEEDLRFDSDVGEYRAVTELGRPDAEYWNSQKDFLEDRRAAVDTYCRHNYGVGESFTV 120

Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
           QRRV+P VT+ P++ + L HHNLLVC+V  FYP  ++V+WFRN QEE AGVVST LI+NG
Sbjct: 121 QRRVEPKVTVYPARTQTLQHHNLLVCSVNGFYPGSIEVRWFRNSQEEKAGVVSTGLIQNG 180

Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 751
           DWT+Q LVMLE   + G+VYTC+VEH S+ SP+ VEWRAQSESAQSKMLS
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRAQSESAQSKMLS 230


>ref|NP_002112.3| major histocompatibility complex, class II, DP beta 1 precursor
           [Homo sapiens]
          Length = 258

 Score =  298 bits (762), Expect = 8e-81
 Identities = 143/230 (62%), Positives = 180/230 (78%)
 Frame = +2

Query: 62  MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
           M+ L++     T A+T +L+VL   V +GR +P++++FQ + ECY FNGTQR   + RYI
Sbjct: 1   MMVLQVSAAPRTVALTALLMVLLTSVVQGRATPENYLFQGRQECYAFNGTQR--FLERYI 58

Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
           YN+EE  RFDSDVGE+RAVT LGRP A+ WN QKD+LE+ RA  D +C+HNY++    TL
Sbjct: 59  YNREEFARFDSDVGEFRAVTELGRPAAEYWNSQKDILEEKRAVPDRMCRHNYELGGPMTL 118

Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
           QRRVQP V +SPSK   L HHNLLVC VTDFYP  ++V+WF NGQEETAGVVST LIRNG
Sbjct: 119 QRRVQPRVNVSPSKKGPLQHHNLLVCHVTDFYPGSIQVRWFLNGQEETAGVVSTNLIRNG 178

Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 751
           DWT+Q+LVMLEM  Q+GDVYTC+VEH+SL SP+ VEW+AQS+SA+SK L+
Sbjct: 179 DWTFQILVMLEMTPQQGDVYTCQVEHTSLDSPVTVEWKAQSDSARSKTLT 228


>ref|NP_068818.4| major histocompatibility complex, class II, DR beta 4 precursor
           [Homo sapiens]
          Length = 266

 Score =  293 bits (750), Expect = 2e-79
 Identities = 144/255 (56%), Positives = 183/255 (71%)
 Frame = +2

Query: 62  MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
           MV L+LP G   AA+T+ L VL +P+A   D+   F+ Q K EC+F NGT+RV  + RYI
Sbjct: 1   MVCLKLPGGSCMAALTVTLTVLSSPLALAGDTQPRFLEQAKCECHFLNGTERVWNLIRYI 60

Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
           YNQEE  R++SD+GEY+AVT LGRP+A+ WN QKD+LE+ RAE+DT C++NY + E  T+
Sbjct: 61  YNQEEYARYNSDLGEYQAVTELGRPDAEYWNSQKDLLERRRAEVDTYCRYNYGVVESFTV 120

Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
           QRRVQP VT+ PSK + L HHNLLVC+V  FYP  ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVQPKVTVYPSKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 781
           DWT+Q LVMLE   + G+VYTC+VEH S+ SP+ V+W A+SESAQSKMLS          
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSMMSPLTVQWSARSESAQSKMLSGVGGFVLGLL 240

Query: 782 XXXXXXXXRHRSQKG 826
                     R+QKG
Sbjct: 241 FLGTGLFIYFRNQKG 255


>ref|NP_072049.2| major histocompatibility complex, class II, DR beta 3 precursor
           [Homo sapiens]
          Length = 266

 Score =  293 bits (749), Expect = 3e-79
 Identities = 146/255 (57%), Positives = 181/255 (70%)
 Frame = +2

Query: 62  MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
           MV L+LP G   AA+T+ L+VL + +A   D+   F+   K EC+FFNGT+RVR + RY 
Sbjct: 1   MVCLKLPGGSSLAALTVTLMVLSSRLAFAGDTRPRFLELRKSECHFFNGTERVRYLDRYF 60

Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
           +NQEE LRFDSDVGEYRAVT LGRP A+SWN QKD+LEQ R  +D  C+HNY + E  T+
Sbjct: 61  HNQEEFLRFDSDVGEYRAVTELGRPVAESWNSQKDLLEQKRGRVDNYCRHNYGVGESFTV 120

Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
           QRRV P VT+ P+K + L HHNLLVC+V+ FYP  ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVHPQVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 781
           DWT+Q LVMLE   + G+VYTC+VEH S+ S + VEWRA+SESAQSKMLS          
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSALTVEWRARSESAQSKMLSGVGGFVLGLL 240

Query: 782 XXXXXXXXRHRSQKG 826
                     R+QKG
Sbjct: 241 FLGAGLFIYFRNQKG 255


>ref|XP_949921.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DRB1-9 beta chain precursor (MHC class I antigen DRB1*9)
           (DR-9) (DR9) isoform 3 [Homo sapiens]
          Length = 325

 Score =  288 bits (737), Expect = 7e-78
 Identities = 138/220 (62%), Positives = 171/220 (77%)
 Frame = +2

Query: 62  MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
           MV L+LP G   AA+T+ L+VL +P+A   D+   F+ Q KFEC+FFNGT+RVR + R I
Sbjct: 1   MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60

Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
           YNQEE +RFDSDVGEYRAVT LGRP A+SWN QKD LE+ RAE+DTVC+HNY + E  T+
Sbjct: 61  YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120

Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
           QRRV P VT+ P+K + L HHNLLVC+V+ FYP  ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQ 721
           DWT+Q LVMLE   + G+VYTC+VEH S+ SP+ VEW  Q
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEWSEQ 220


>ref|XP_949915.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DRB1-9 beta chain precursor (MHC class I antigen DRB1*9)
           (DR-9) (DR9) isoform 2 [Homo sapiens]
          Length = 284

 Score =  284 bits (727), Expect = 9e-77
 Identities = 138/220 (62%), Positives = 166/220 (75%)
 Frame = +2

Query: 167 FVFQFKFECYFFNGTQRVRLVARYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKD 346
           F+ Q KFEC+FFNGT+RVR + R IYNQEE +RFDSDVGEYRAVT LGRP A+SWN QKD
Sbjct: 54  FLKQDKFECHFFNGTERVRYLHRGIYNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKD 113

Query: 347 VLEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQ 526
            LE+ RAE+DTVC+HNY + E  T+QRRV P VT+ P+K + L HHNLLVC+V+ FYP  
Sbjct: 114 FLERRRAEVDTVCRHNYGVGESFTVQRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGS 173

Query: 527 VKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILV 706
           ++V+WFRNGQEE AGVVST LI+NGDWT+Q LVMLE   + G+VYTC+VEH S+ SP+ V
Sbjct: 174 IEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTV 233

Query: 707 EWRAQSESAQSKMLSXXXXXXXXXXXXXXXXXXRHRSQKG 826
           EWRA+SESAQSKMLS                    R+QKG
Sbjct: 234 EWRARSESAQSKMLSGVGGFVLGLLFLGAGLFIYFRNQKG 273


  Database: RefSeqHP
    Posted date:  Aug 2, 2006 12:57 AM
  Number of letters in database: 17,774,539
  Number of sequences in database:  39,411
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 47,502,071
Number of Sequences: 39411
Number of extensions: 1299103
Number of successful extensions: 5795
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 4645
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 5745
length of database: 17,774,539
effective HSP length: 104
effective length of database: 13,675,795
effective search space used: 4130090090
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqSP

BLASTX 2.2.10 [Oct-19-2004]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= LVR01_0002_B02
         (1220 letters)

Database: RefSeqSP 
           1040 sequences; 434,620 total letters

Searching...done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_998933.1| swine leukocyte antigen 7 [Sus scrofa]                73   2e-14
Alignment   gi|NP_999362.2| neonatal Fc receptor FcRn [Sus scrofa]                63   1e-11
Alignment   gi|NP_998996.1| CD1 antigen [Sus scrofa]                              58   5e-10
Alignment   gi|NP_999143.1| beta 2-microglobulin [Sus scrofa]                     56   2e-09
Alignment   gi|NP_998993.1| IgG heavy chain [Sus scrofa]                          46   2e-06

>ref|NP_998933.1| swine leukocyte antigen 7 [Sus scrofa]
          Length = 401

 Score = 72.8 bits (177), Expect = 2e-14
 Identities = 49/185 (26%), Positives = 82/185 (44%), Gaps = 5/185 (2%)
 Frame = +2

Query: 173 FQFKFECYFFNGTQRVRLVARYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVL 352
           +Q+   CY     + +R  +++ Y+  + +  + D+  + AV    +     W  ++ V 
Sbjct: 116 YQWLCGCYVARDGRLLRGYSQFAYDGADYIVLNEDLRSWTAVGMAAQITRRKWE-EETVA 174

Query: 353 EQTRAELDTVCK---HNYQIEEGTTLQRRVQPT--VTISPSKAEALNHHNLLVCAVTDFY 517
           EQ+RA L+  C    H Y      TLQR   P   VT  PS    +     L C    FY
Sbjct: 175 EQSRAYLEVACVQSLHRYLANGKETLQRSDPPKTHVTRHPSSDNKVT----LRCWALGFY 230

Query: 518 PSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSP 697
           P ++ + W + GQ+++  V       +GD T++    L +       YTC V+H  LQ P
Sbjct: 231 PKEISLTWQQEGQDQSQDVEVVETRPSGDGTFRKWAALVVPPGEEQSYTCHVQHEGLQEP 290

Query: 698 ILVEW 712
           + + W
Sbjct: 291 LTLRW 295


>ref|NP_999362.2| neonatal Fc receptor FcRn [Sus scrofa]
          Length = 356

 Score = 63.2 bits (152), Expect = 1e-11
 Identities = 43/172 (25%), Positives = 79/172 (45%), Gaps = 3/172 (1%)
 Frame = +2

Query: 227 VARYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNY--Q 400
           VA +  N EE ++FD+ +G +    P  R     W  + D + + +  L   C H     
Sbjct: 130 VATFALNGEEFMKFDTKLGTWDGEWPEARTIGSKWMQEPDAVNKEKTFLLYSCPHRLLGH 189

Query: 401 IEEGT-TLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVV 577
           +E G   L+ +  P++ +      A    ++L C    FYP ++++++ RNG    AG  
Sbjct: 190 LERGRGNLEWKEPPSMRMKARPGTAPGF-SVLTCIAFSFYPPELQLRFLRNGL--AAGSG 246

Query: 578 STPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESA 733
            + +  NGD ++     L +       Y C V+H+ L  P+ VE  + ++S+
Sbjct: 247 ESDIGPNGDGSFHAWSSLTVKSGDEHHYCCVVQHAGLAQPLTVELESPAKSS 298


>ref|NP_998996.1| CD1 antigen [Sus scrofa]
          Length = 339

 Score = 57.8 bits (138), Expect = 5e-10
 Identities = 36/103 (34%), Positives = 54/103 (52%), Gaps = 1/103 (0%)
 Frame = +2

Query: 419 LQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRN 598
           LQR+V+P   +S S       H +LVC V+ FYP  + V W R+ QE+  G     ++ N
Sbjct: 199 LQRQVRPEAWLS-SGPNPSPGHLMLVCHVSGFYPKPIWVMWMRDEQEQ-PGTQQGDILPN 256

Query: 599 GDWTYQVLVMLEMNLQRGDVYTCRVEHSSL-QSPILVEWRAQS 724
            D T+ + V L++        +CRV+HSSL    I++ W   S
Sbjct: 257 ADGTWYLRVTLDVAAGEASGLSCRVKHSSLGGQDIILYWEQHS 299


>ref|NP_999143.1| beta 2-microglobulin [Sus scrofa]
          Length = 118

 Score = 56.2 bits (134), Expect = 2e-09
 Identities = 29/93 (31%), Positives = 49/93 (52%), Gaps = 7/93 (7%)
 Frame = +2

Query: 455 PSKAEALNHH-------NLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTY 613
           P K +  + H       N L C V+ F+P Q+++   +NG++  A    + L  + DW++
Sbjct: 24  PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAE--QSDLSFSKDWSF 81

Query: 614 QVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 712
            +LV  E      D Y+CRV+H +L  P +V+W
Sbjct: 82  YLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKW 114


>ref|NP_998993.1| IgG heavy chain [Sus scrofa]
          Length = 474

 Score = 46.2 bits (108), Expect = 2e-06
 Identities = 30/92 (32%), Positives = 44/92 (47%), Gaps = 5/92 (5%)
 Frame = +2

Query: 434 QPTVTISPSKAEALNHHNLLV-CAVTDFYPSQVKVQWFRNGQEETAG-VVSTPLIRNGDW 607
           +P V   P  AE L+   + V C V  FYP  + V+W  NGQ E  G   +TP  ++ D 
Sbjct: 370 EPQVYTLPPPAEELSRSKVTVTCLVIGFYPPDIHVEWKSNGQPEPEGNYRTTPPQQDVDG 429

Query: 608 T---YQVLVMLEMNLQRGDVYTCRVEHSSLQS 694
           T   Y  L + +     G+ + C V H +L +
Sbjct: 430 TFFLYSKLAVDKARWDHGETFECAVMHEALHN 461


  Database: RefSeqSP
    Posted date:  Aug 1, 2006  7:14 PM
  Number of letters in database: 434,620
  Number of sequences in database:  1040
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,104,957
Number of Sequences: 1040
Number of extensions: 27728
Number of successful extensions: 110
Number of sequences better than 1.0e-05: 5
Number of HSP's better than  0.0 without gapping: 96
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 108
length of database: 434,620
effective HSP length: 79
effective length of database: 352,460
effective search space used: 115254420
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqMP

BLASTX 2.2.10 [Oct-19-2004]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= LVR01_0002_B02
         (1220 letters)

Database: RefSeqMP 
           45,328 sequences; 21,768,885 total letters

Searching..................................................done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_996988.1| histocompatibility 2, class II antigen A, beta ...   324   1e-88
Alignment   gi|NP_034512.1| histocompatibility 2, class II antigen E beta [...   289   4e-78
Alignment   gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/...   256   4e-68
Alignment   gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ...   244   2e-64
Alignment   gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ...    75   1e-13
Alignment   gi|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus ...    75   1e-13
Alignment   gi|NP_034508.2| histocompatibility 2, class II antigen A, alpha...    70   4e-12
Alignment   gi|NP_032232.1| histocompatibility 2, O region alpha locus [Mus...    68   2e-11
Alignment   gi|NP_032235.1| histocompatibility-2 complex class 1-like [Mus ...    64   4e-10
Alignment   gi|XP_908790.2| PREDICTED: similar to histocompatibility 2, Q r...    63   5e-10

>ref|NP_996988.1| histocompatibility 2, class II antigen A, beta 1 [Mus musculus]
          Length = 265

 Score =  324 bits (831), Expect = 1e-88
 Identities = 164/255 (64%), Positives = 197/255 (77%), Gaps = 1/255 (0%)
 Frame = +2

Query: 65  VALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYIY 244
           +AL++P  L +AAV ++L+VL +P  EG DS + FV+QF  ECYF NGTQR+R V RYIY
Sbjct: 1   MALQIPSLLLSAAV-VVLMVLSSPGTEGGDSERHFVYQFMGECYFTNGTQRIRYVTRYIY 59

Query: 245 NQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQ-IEEGTTL 421
           N+EE +R+DSDVGE+RAVT LGRP+A+ WN Q ++LE+TRAELDTVC+HNY+  E  T+L
Sbjct: 60  NREEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSL 119

Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
           +R  QP V IS S+ EALNHHN LVC+VTDFYP+Q+KV+WFRNGQEET GV ST LIRNG
Sbjct: 120 RRLEQPNVVISLSRTEALNHHNTLVCSVTDFYPTQIKVRWFRNGQEETVGVSSTQLIRNG 179

Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 781
           DWT+QVLVMLEM  +RG+VYTC VEH SL+SPI VEWRAQSESA SKMLS          
Sbjct: 180 DWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRAQSESAWSKMLSGIGGCVLGVI 239

Query: 782 XXXXXXXXRHRSQKG 826
                   RHRSQKG
Sbjct: 240 FLGLGLFIRHRSQKG 254


>ref|NP_034512.1| histocompatibility 2, class II antigen E beta [Mus musculus]
          Length = 264

 Score =  289 bits (740), Expect = 4e-78
 Identities = 140/250 (56%), Positives = 178/250 (71%)
 Frame = +2

Query: 77  LPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYIYNQEE 256
           LPR    AAV ++L VL  PVA  RDS   F+   K EC+F+NGTQRVR + RY YN EE
Sbjct: 4   LPRVPCVAAVILLLTVLSPPVALVRDSRPWFLEYCKSECHFYNGTQRVRFLKRYFYNLEE 63

Query: 257 LLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRRVQ 436
            LRFDSDVGE+RAVT LGRP+A++WN Q ++L++ RA +DT C+HNY+I +   + RRV+
Sbjct: 64  NLRFDSDVGEFRAVTELGRPDAENWNSQPEILDEKRAAVDTYCRHNYEIFDNFLVPRRVE 123

Query: 437 PTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQ 616
           PTVT+ P+K + L HHNLLVC+V+DFYP  ++V+WFRNG+EE  G+VST L+RNGDWT+Q
Sbjct: 124 PTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQ 183

Query: 617 VLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXXXXXXX 796
            LVMLE   Q G+VYTC+VEH SL  P+ VEW+AQS SAQ+KMLS               
Sbjct: 184 TLVMLETVPQSGEVYTCQVEHPSLTDPVTVEWKAQSTSAQNKMLSGVGGFVLGLLFLRAG 243

Query: 797 XXXRHRSQKG 826
                R+QKG
Sbjct: 244 LFIYFRNQKG 253


>ref|NP_001029150.1| H-2 class II histocompatibility antigen E-a/k beta-2 [Mus musculus]
          Length = 287

 Score =  256 bits (653), Expect = 4e-68
 Identities = 128/230 (55%), Positives = 166/230 (72%)
 Frame = +2

Query: 62  MVALRLPRGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYI 241
           MV+L LPRGL  AAV + L++L  PV   RD    F+ Q K EC++FNG +RV  V R+I
Sbjct: 1   MVSLWLPRGLCVAAVILSLMMLTPPVILVRDPRPRFLEQLKAECHYFNGKERVWSVTRFI 60

Query: 242 YNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 421
           YNQEE  RF+SD G++ AVT LGRP  +  N QKD+L+  RA +D  C++NY + +   L
Sbjct: 61  YNQEEFARFNSDFGKFLAVTELGRPIVEYLNTQKDMLDNYRASVDR-CRNNYDLVDIFML 119

Query: 422 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 601
             + +P VT+ P+K + L HHNLLVC+V DFYP  ++V+WFRNG+EE  GVVST LI+N 
Sbjct: 120 NLKAEPKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNR 179

Query: 602 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 751
           DWTYQ LVMLEM  + G+VYTC+VEH SL SP+ VEWRA+S SAQ+K+LS
Sbjct: 180 DWTYQTLVMLEMVPRGGEVYTCQVEHPSLTSPVTVEWRARSTSAQNKLLS 229


>ref|NP_034519.2| histocompatibility 2, O region beta locus [Mus musculus]
          Length = 271

 Score =  244 bits (622), Expect = 2e-64
 Identities = 113/223 (50%), Positives = 156/223 (69%)
 Frame = +2

Query: 83  RGLWTAAVTMMLVVLGAPVAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARYIYNQEELL 262
           R  W  A+ + L+ L + + EGRDSP++FV Q K +CYF NGT++V L+ R+I+N EE L
Sbjct: 5   RAPWVVALLVNLMRLDSFMIEGRDSPENFVIQAKADCYFTNGTEKVHLLVRFIFNLEEYL 64

Query: 263 RFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRRVQPT 442
            FDSD+G + A+T LG P+AD WN + D+LE +RA ++ VC+  Y++    T++R V P 
Sbjct: 65  HFDSDLGMFVALTELGEPDADQWNKRLDLLETSRAAVNMVCRQKYKLGAPFTVERNVPPE 124

Query: 443 VTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVL 622
           VT+ P +   L  HNLL+C+VT FYP  + V+WFRNGQEE +GV+ST L+RNGDWT+Q  
Sbjct: 125 VTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVRNGDWTFQTT 184

Query: 623 VMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 751
           VMLEM  + GD+Y+C VEH  L  P+ V W AQSE +  K+LS
Sbjct: 185 VMLEMIPELGDIYSCLVEHPGLLRPVSVAWMAQSEYSWKKILS 227


>ref|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus musculus]
          Length = 261

 Score = 75.5 bits (184), Expect = 1e-13
 Identities = 50/170 (29%), Positives = 79/170 (46%), Gaps = 13/170 (7%)
 Frame = +2

Query: 242 YNQEELLRFDSDVG-----EYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQIE 406
           +N++ L  +D DVG     E+  ++ L    ++  N Q+ ++ + +  L     H     
Sbjct: 46  FNKDLLACWDPDVGKIVPCEFGVLSRLAEIISNILNEQESLIHRLQNGLQDCATHTQPFW 105

Query: 407 EGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQ--------EE 562
           +  T + R  P+V ++ +         +L C V  FYP+ V + W +NGQ        E+
Sbjct: 106 DVLTHRTRA-PSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEK 164

Query: 563 TAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 712
           TA         NGDWTYQ +  L +    GDVYTC V+HS    PI  +W
Sbjct: 165 TAQP-------NGDWTYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDW 207


>ref|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus musculus]
          Length = 261

 Score = 75.1 bits (183), Expect = 1e-13
 Identities = 61/231 (26%), Positives = 93/231 (40%), Gaps = 23/231 (9%)
 Frame = +2

Query: 89  LWTAAVTMMLVVLGAP----------VAEGRDSPQDFVFQFKFECYFFNGTQRVRLVARY 238
           LW   + + L  +GA           V +   +PQDF +   F                 
Sbjct: 4   LWLLLLVLSLDCMGAGGFVAHVESTCVLDDAGTPQDFTYCVSF----------------- 46

Query: 239 IYNQEELLRFDSDVG-----EYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQI 403
             N++ L  +D DVG     E+  + P     +   N ++ +L++ +  L     H    
Sbjct: 47  --NKDLLACWDPDVGKIVPCEFGVLYPWAENFSRILNKEESLLQRLQNGLLDCASHTQPF 104

Query: 404 EEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQ--------E 559
               T + R  P+V ++ +         +L C V  FYP+ V + W +NGQ        E
Sbjct: 105 WNALTHRTRA-PSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKE 163

Query: 560 ETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 712
           +TA         NGDWTYQ +  L +    GDVYTC V+HS    PI  +W
Sbjct: 164 KTAQP-------NGDWTYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDW 207


>ref|NP_034508.2| histocompatibility 2, class II antigen A, alpha [Mus musculus]
          Length = 256

 Score = 70.1 bits (170), Expect = 4e-12
 Identities = 35/125 (28%), Positives = 55/125 (44%), Gaps = 3/125 (2%)
 Frame = +2

Query: 380 VCKHNYQI---EEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRN 550
           V KHN  +      +T      P  T+ P     L   N L+C V + +P  + + W RN
Sbjct: 92  VVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRN 151

Query: 551 GQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSES 730
            +    GV  T    N D+++  L  L       D+Y C+VEH  L+ P+L  W  +  +
Sbjct: 152 SKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEPEIPA 211

Query: 731 AQSKM 745
             S++
Sbjct: 212 PMSEL 216


>ref|NP_032232.1| histocompatibility 2, O region alpha locus [Mus musculus]
          Length = 250

 Score = 68.2 bits (165), Expect = 2e-11
 Identities = 34/97 (35%), Positives = 45/97 (46%)
 Frame = +2

Query: 431 VQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWT 610
           V P VT+ P     L   N+L+C V D +P  + V W RN Q  T GV  T      +  
Sbjct: 111 VPPRVTVLPKTRVELGKPNVLICIVDDIFPPVINVTWLRNSQPITKGVAQTSFYSQPNHR 170

Query: 611 YQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQ 721
           ++    L       DVY C+VEH  L +P+L  W  Q
Sbjct: 171 FRKFHYLTFVPSAEDVYDCKVEHWGLDTPLLQHWEPQ 207


>ref|NP_032235.1| histocompatibility-2 complex class 1-like [Mus musculus]
          Length = 341

 Score = 63.5 bits (153), Expect = 4e-10
 Identities = 40/156 (25%), Positives = 71/156 (45%), Gaps = 3/156 (1%)
 Frame = +2

Query: 233 RYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLEQTRAELDTVCKHNYQ--IE 406
           +Y Y+ ++ + F+ D   + A+  +      +W      L+  +  L+  C    +  +E
Sbjct: 129 QYAYDGQDFIIFNKDTLSWLAMDYVAHITKQAWEANLHELQYQKNWLEEECIAWLKRFLE 188

Query: 407 EGT-TLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVST 583
            G  TL+R   P V  +  + E         C    FYP ++ + W +NG+E    V   
Sbjct: 189 YGRDTLERTEHPVVRTT--RKETFPGITTFFCRAHGFYPPEISMTWMKNGEEIAQEVDYG 246

Query: 584 PLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQ 691
            ++ +GD TYQ  + + ++ Q  DVY+C VEH   Q
Sbjct: 247 GVLPSGDGTYQTWLSVNLDPQSNDVYSCHVEHCGRQ 282


>ref|XP_908790.2| PREDICTED: similar to histocompatibility 2, Q region locus 6
           isoform 2 [Mus musculus]
          Length = 465

 Score = 63.2 bits (152), Expect = 5e-10
 Identities = 43/184 (23%), Positives = 75/184 (40%), Gaps = 5/184 (2%)
 Frame = +2

Query: 176 QFKFECYFFNGTQRVRLVARYIYNQEELLRFDSDVGEYRAVTPLGRPEADSWNGQKDVLE 355
           Q+ + C   +  + +R   ++ Y   + +  + D+  + A     +     W  Q  + E
Sbjct: 233 QWMYGCDVGSDERLLRGYLQFAYEGRDYIALNEDLKTWTAADMAAQITLHKWE-QAGIAE 291

Query: 356 QTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISPSKAEALNHHN-----LLVCAVTDFYP 520
           + RA L+  C  + +      LQ R +  +   P KA   +H        L C    FYP
Sbjct: 292 RDRAYLEGACVQSLR----RYLQLRKETLLCTDPPKAHVTHHPRSYGAVTLRCWALGFYP 347

Query: 521 SQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPI 700
           + + + W  NG+E T  +        GD T+Q    + + L +   YTC V H  L  P+
Sbjct: 348 ADITLTWQLNGEELTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCHVNHEGLPEPL 407

Query: 701 LVEW 712
            + W
Sbjct: 408 TLRW 411


  Database: RefSeqMP
    Posted date:  Aug 2, 2006 12:58 AM
  Number of letters in database: 21,768,885
  Number of sequences in database:  45,328
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 56,050,254
Number of Sequences: 45328
Number of extensions: 1474320
Number of successful extensions: 6156
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 5030
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 6094
length of database: 21,768,885
effective HSP length: 106
effective length of database: 16,964,117
effective search space used: 5089235100
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)