Animal-Genome cDNA 20060611C-000186


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= 20060611C-000186
         (1101 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]                 393   e-109
Alignment   gi|NP_001012694.1| major histocompatibility complex, class II, ...   380   e-105
Alignment   gi|NP_001012697.1| major histocompatibility complex, class II, ...   293   2e-79
Alignment   gi|NP_001012698.2| major histocompatibility complex, class II, ...   292   4e-79
Alignment   gi|XP_582099.2| PREDICTED: similar to major histocompatibility ...   266   3e-71
Alignment   gi|NP_001013618.1| major histocompatibility complex, class II, ...   254   6e-68
Alignment   gi|XP_876139.1| PREDICTED: similar to H-2 class II histocompati...   243   2e-64
Alignment   gi|XP_874766.1| PREDICTED: similar to HLA class II histocompati...   153   3e-37
Alignment   gi|NP_001012399.1| hemochromatosis [Bos taurus]                       73   5e-13
Alignment   gi|NP_001029503.1| hypothetical protein LOC508800 [Bos taurus]        72   6e-13

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

 Score =  393 bits (1010), Expect = e-109
 Identities = 193/261 (73%), Positives = 215/261 (82%)
 Frame = +2

Query: 86  MSGMVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLT 265
           MSGMVAL +PRGLWTA + V LV+L  P AEGRDSP+DFV QFK  CYF NGT+RVR +T
Sbjct: 1   MSGMVALWIPRGLWTAVVMVTLVMLSTPGAEGRDSPKDFVVQFKGLCYFTNGTERVRYVT 60

Query: 266 RYIYNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEG 445
           RYIYNQEE+VRFDS+   YRA+TPLGRPDA+YWN QKD LEQTRAE DTVC+HNYQ E  
Sbjct: 61  RYIYNQEEYVRFDSDWDLYRALTPLGRPDAEYWNSQKDFLEQTRAEADTVCRHNYQAELI 120

Query: 446 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 625
           T+LQRRV+PTVTISPS+ EALNHHNLLVC+VTDFYPSQ+KV+WFRN +EETAGVVSTPLI
Sbjct: 121 TSLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPSQIKVRWFRNDREETAGVVSTPLI 180

Query: 626 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 805
           RNGDWT+Q+LVMLEM  QRGDVYTC VEH SLQSPI+VEWRAQSESAQSKMLS       
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPIMVEWRAQSESAQSKMLSGVGGFVL 240

Query: 806 XXXXXXXXXXXRHRSQKGLVR 868
                       HRSQKGL+R
Sbjct: 241 GLIFLGLGLIIHHRSQKGLMR 261


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

 Score =  380 bits (976), Expect = e-105
 Identities = 187/260 (71%), Positives = 211/260 (81%)
 Frame = +2

Query: 86  MSGMVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLT 265
           MSGMVALR+PRGLWTAA+ V L VL  P AEGRDSPQD V  F  +CYF NGT+RVR +T
Sbjct: 1   MSGMVALRIPRGLWTAAVMVTLAVLSTPGAEGRDSPQDTVVHFMGQCYFTNGTERVRYVT 60

Query: 266 RYIYNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEG 445
           RYIYNQEE   +DS+VGEYRAVT LGR  A+YWN QKD+LEQTRAELDTVC+HNYQ+E  
Sbjct: 61  RYIYNQEETAYYDSDVGEYRAVTQLGRTLAEYWNSQKDILEQTRAELDTVCRHNYQLEVI 120

Query: 446 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 625
           T+LQR+V+PTVTIS S+ EALNHHNLLVC+VTDFYP Q+KV+WF+NG+EETAG+VSTPLI
Sbjct: 121 TSLQRQVEPTVTISLSRTEALNHHNLLVCSVTDFYPGQIKVRWFQNGKEETAGIVSTPLI 180

Query: 626 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 805
           RNGDWT+Q+LVMLEM  +RGDVYTC VEH SLQSPI VEWRAQSESAQSKMLS       
Sbjct: 181 RNGDWTFQILVMLEMTPKRGDVYTCHVEHPSLQSPISVEWRAQSESAQSKMLSGVGGFVL 240

Query: 806 XXXXXXXXXXXRHRSQKGLV 865
                      R RSQKGLV
Sbjct: 241 GLIFLGLGLIVRRRSQKGLV 260


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

 Score =  293 bits (749), Expect = 2e-79
 Identities = 147/227 (64%), Positives = 175/227 (77%), Gaps = 2/227 (0%)
 Frame = +2

Query: 110 LPRGLWTAALTVMLV--VLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRYIYNQ 283
           +PR   T A  VM V  VL  P A  RD+P++FVYQFK  CYF NGT+ VRL+ R IYN+
Sbjct: 5   IPRNPGTVAGMVMAVFLVLRIPEAHCRDAPKNFVYQFKGMCYFTNGTEHVRLVARQIYNK 64

Query: 284 EEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRR 463
           EE + FDS++GE+ AVT LGR  A+ WN QKD+L + RA +DT+C+HNY+   G T+QRR
Sbjct: 65  EEILHFDSDLGEFVAVTELGRVCAEIWNTQKDLLAEFRAYVDTLCRHNYKETAGFTVQRR 124

Query: 464 VQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWT 643
           V+PTVT+SP+  EALNHHNLLVC+VTDFYP QVKV+WFRN QE+TAGV  TPL +NGDWT
Sbjct: 125 VEPTVTVSPASTEALNHHNLLVCSVTDFYPRQVKVKWFRNQQEQTAGVGFTPLTQNGDWT 184

Query: 644 YQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 784
           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 =  292 bits (747), Expect = 4e-79
 Identities = 144/255 (56%), Positives = 178/255 (69%)
 Frame = +2

Query: 95  MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRYI 274
           MV L    G W AAL VML+VL  P+A  R+    F+  +K EC+FFNGT+RVR L R+ 
Sbjct: 1   MVCLYFSGGSWMAALIVMLMVLCPPLAWAREIQPHFLEYYKGECHFFNGTERVRFLDRHF 60

Query: 275 YNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 454
           YN EE VRFDS+ GE+RAVT LGRP A++WN QKD LEQ RAE+D VC+HNY   E  T+
Sbjct: 61  YNGEEFVRFDSDWGEFRAVTELGRPAAEHWNSQKDFLEQKRAEVDRVCRHNYGGVESFTV 120

Query: 455 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 634
           QRRV+PTVT+ P+K + L HHNLLVC+V  FYP  ++V+WFRNG EE AGV+ST LI+NG
Sbjct: 121 QRRVEPTVTVYPAKTQPLQHHNLLVCSVNGFYPGHIEVRWFRNGHEEEAGVISTGLIQNG 180

Query: 635 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 814
           DWT+Q +VMLE   Q G+VYTC+V+H    SPI VEWRA+S+SAQSKM+S          
Sbjct: 181 DWTFQTMVMLETVPQSGEVYTCQVDHPKRTSPITVEWRARSDSAQSKMMSGVGGFVLGLL 240

Query: 815 XXXXXXXXRHRSQKG 859
                     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 =  266 bits (679), Expect = 3e-71
 Identities = 125/218 (57%), Positives = 162/218 (74%)
 Frame = +2

Query: 131 AALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRYIYNQEEHVRFDSN 310
           AAL V+L+VL  P +  R++   F++QFK EC F NG +R+R   RYIYN +E V FDS+
Sbjct: 2   AALAVLLMVLSLPFSWARETQPHFIHQFKGECRFSNGLERMRFFARYIYNTQEDVHFDSD 61

Query: 311 VGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISP 490
           VGE+ A+T LGR DA+YWN QKD +EQ RA++DT+C+ NYQ       QRRV+PTVT+ P
Sbjct: 62  VGEFTALTELGRLDAEYWNQQKDFMEQMRAKVDTLCRSNYQGIGSFLRQRRVEPTVTVYP 121

Query: 491 SKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEM 670
           +K + L HHNLLVC+V  FYP  ++V+WF N  EE AGV+ST LI+NGDWT+Q +VMLE 
Sbjct: 122 AKTQPLQHHNLLVCSVNGFYPGHIEVRWFWNSHEEEAGVISTGLIQNGDWTFQTMVMLET 181

Query: 671 NLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 784
             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 =  254 bits (650), Expect = 6e-68
 Identities = 117/220 (53%), Positives = 157/220 (71%)
 Frame = +2

Query: 125 WTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRYIYNQEEHVRFD 304
           W        + L A V +GRDSP+DFV Q K +CYF NGT++VR + R+I+N E++ RFD
Sbjct: 8   WVVTFLSTALRLDASVTQGRDSPEDFVTQAKADCYFTNGTEKVRFVVRFIFNLEDYARFD 67

Query: 305 SNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTI 484
           S++G + A+T LG+PDA+ WN + D+L ++RA +D +C+ NY +    T+ RRVQP VT+
Sbjct: 68  SDLGMFVALTELGKPDAERWNNRPDILARSRASVDMLCRRNYYLGAPFTVGRRVQPEVTV 127

Query: 485 SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVML 664
            P K  AL H NLL+C VT FYP  +KV WFRNGQE+  G++ST LIRNGDWT+Q+ VML
Sbjct: 128 YPEKTPALQHRNLLLCLVTGFYPGDIKVTWFRNGQEQREGIMSTGLIRNGDWTFQMTVML 187

Query: 665 EMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 784
            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 =  243 bits (620), Expect = 2e-64
 Identities = 117/192 (60%), Positives = 141/192 (73%)
 Frame = +2

Query: 209 QFKFECYFFNGTQRVRLLTRYIYNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLE 388
           Q K EC+F NGTQ+VR L RYIYN+EE V+FDS VGEYRA T +GRP A+ WN     L+
Sbjct: 3   QGKSECHFSNGTQQVRFLDRYIYNREEQVQFDSLVGEYRARTEMGRPAAERWNRWPQALQ 62

Query: 389 QTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKV 568
           + RA +   C  NY+     T+QRRVQPTVT+ P K+  L HHNLLVC+V  FYP  ++V
Sbjct: 63  RARAAVHAYCASNYEFFASRTVQRRVQPTVTVYPVKSRPLWHHNLLVCSVNGFYPGHIEV 122

Query: 569 QWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWR 748
           +WFRNGQEE AGVVST LI NGDWT+Q++VMLE+  Q G+VY C VEH S  SP+ VEWR
Sbjct: 123 RWFRNGQEEEAGVVSTGLIPNGDWTFQIMVMLEIVPQGGEVYACHVEHPSRTSPVTVEWR 182

Query: 749 AQSESAQSKMLS 784
           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: 449 TLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIR 628
           TLQ++V+PTVT+ P+K + L H++LLVC+V  FY   V+V+WF  GQEE AGV+ST LI+
Sbjct: 90  TLQKKVEPTVTVYPAKTQPLQHNHLLVCSVNGFYLGHVEVRWFWKGQEEEAGVISTGLIQ 149

Query: 629 NGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXX 808
           NGDWT++ +VMLE  LQ G+VYTC++EH S +SPI  EWRAQS+SAQSKM+S        
Sbjct: 150 NGDWTFETIVMLETVLQSGEVYTCQLEHPSWRSPIAEEWRAQSDSAQSKMMSGTGGFALG 209

Query: 809 XXXXXXXXXXRHRSQKG 859
                       R+QKG
Sbjct: 210 LLFLVVGLFTHFRNQKG 226


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

 Score = 72.8 bits (177), Expect = 5e-13
 Identities = 47/165 (28%), Positives = 76/165 (46%), Gaps = 5/165 (3%)
 Frame = +2

Query: 266 RYIYNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCK----HNYQ 433
           +Y Y+ ++H+ F     ++RA  P  +     W   K   +Q RA LD  C     H  +
Sbjct: 145 KYGYDGQDHLEFRPETLDWRAAEPRAQVTKLEWEVNKIRAKQNRAYLDRDCPEQLLHLLE 204

Query: 434 IEEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVS 613
           +  G  L+++V P V ++     +L     L C   +FYP  + ++W ++ Q   A  + 
Sbjct: 205 LGRGP-LEQQVPPLVKVTHHVTSSLT---TLRCRALNFYPQNITIRWLKDKQFLDAKEIK 260

Query: 614 TP-LIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 745
              ++ NGD TYQ  V L M       Y+C+VEH  L  P+   W
Sbjct: 261 PEDVLPNGDGTYQAWVALAMLPGEEQRYSCQVEHPGLDQPLTATW 305


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

 Score = 72.4 bits (176), Expect = 6e-13
 Identities = 50/198 (25%), Positives = 87/198 (43%), Gaps = 5/198 (2%)
 Frame = +2

Query: 182 RDSPQDFVYQFKFECYFFNGTQRVRLLTRYIYNQEEHVRFDSNVGEYRAVTPLGRPDADY 361
           +D      +Q  F C   N  +       Y Y+ ++ ++FD  +  +  + P  +     
Sbjct: 106 KDREGSHTFQGAFGCELRNN-ESSGAFWGYAYDGQDFIKFDKEIPAWVPLDPAAQNTKRK 164

Query: 362 WNGQKDVLEQTRAELDTVCK---HNYQIEEGTTLQRRVQPTVTISPSKAEALNHHNLLVC 532
           W  +   +++ +A L+  C      Y     T L R+  P+V+++   A    H   L C
Sbjct: 165 WEAEAVYVQRAKAYLEEECPGMLRRYLPYSRTHLDRQESPSVSVTGHAAPG--HKRTLKC 222

Query: 533 AVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEH 712
              DFYP  + + W R G  + A      ++ +G+ TYQ  V++ +  +    Y+C VEH
Sbjct: 223 LAYDFYPRSIGLHWTRAGDAQEAES-GGDVLPSGNGTYQSWVVVGVPPEDQAPYSCHVEH 281

Query: 713 SSLQSPILVEW--RAQSE 760
            SL  P+ V W  R Q+E
Sbjct: 282 RSLTRPLTVPWDPRQQAE 299


  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: 38,933,739
Number of Sequences: 33508
Number of extensions: 1082592
Number of successful extensions: 4664
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 3949
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): 4616
length of database: 16,112,626
effective HSP length: 103
effective length of database: 12,661,302
effective search space used: 3329922426
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= 20060611C-000186
         (1101 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   1e-14
Alignment   gi|NP_999362.2| neonatal Fc receptor FcRn [Sus scrofa]                59   2e-10
Alignment   gi|NP_998996.1| CD1 antigen [Sus scrofa]                              58   5e-10
Alignment   gi|NP_999143.1| beta 2-microglobulin [Sus scrofa]                     56   1e-09
Alignment   gi|NP_998993.1| IgG heavy chain [Sus scrofa]                          46   1e-06

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

 Score = 73.2 bits (178), Expect = 1e-14
 Identities = 49/185 (26%), Positives = 83/185 (44%), Gaps = 5/185 (2%)
 Frame = +2

Query: 206 YQFKFECYFFNGTQRVRLLTRYIYNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVL 385
           YQ+   CY     + +R  +++ Y+  +++  + ++  + AV    +     W  ++ V 
Sbjct: 116 YQWLCGCYVARDGRLLRGYSQFAYDGADYIVLNEDLRSWTAVGMAAQITRRKWE-EETVA 174

Query: 386 EQTRAELDTVCK---HNYQIEEGTTLQRRVQPT--VTISPSKAEALNHHNLLVCAVTDFY 550
           EQ+RA L+  C    H Y      TLQR   P   VT  PS    +     L C    FY
Sbjct: 175 EQSRAYLEVACVQSLHRYLANGKETLQRSDPPKTHVTRHPSSDNKVT----LRCWALGFY 230

Query: 551 PSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSP 730
           P ++ + W + GQ+++  V       +GD T++    L +       YTC V+H  LQ P
Sbjct: 231 PKEISLTWQQEGQDQSQDVEVVETRPSGDGTFRKWAALVVPPGEEQSYTCHVQHEGLQEP 290

Query: 731 ILVEW 745
           + + W
Sbjct: 291 LTLRW 295


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

 Score = 59.3 bits (142), Expect = 2e-10
 Identities = 41/169 (24%), Positives = 77/169 (45%), Gaps = 3/169 (1%)
 Frame = +2

Query: 269 YIYNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNY--QIEE 442
           +  N EE ++FD+ +G +    P  R     W  + D + + +  L   C H     +E 
Sbjct: 133 FALNGEEFMKFDTKLGTWDGEWPEARTIGSKWMQEPDAVNKEKTFLLYSCPHRLLGHLER 192

Query: 443 GT-TLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTP 619
           G   L+ +  P++ +      A    ++L C    FYP ++++++ RNG    AG   + 
Sbjct: 193 GRGNLEWKEPPSMRMKARPGTAPGF-SVLTCIAFSFYPPELQLRFLRNGL--AAGSGESD 249

Query: 620 LIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESA 766
           +  NGD ++     L +       Y C V+H+ L  P+ VE  + ++S+
Sbjct: 250 IGPNGDGSFHAWSSLTVKSGDEHHYCCVVQHAGLAQPLTVELESPAKSS 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: 452 LQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRN 631
           LQR+V+P   +S S       H +LVC V+ FYP  + V W R+ QE+  G     ++ N
Sbjct: 199 LQRQVRPEAWLS-SGPNPSPGHLMLVCHVSGFYPKPIWVMWMRDEQEQ-PGTQQGDILPN 256

Query: 632 GDWTYQVLVMLEMNLQRGDVYTCRVEHSSL-QSPILVEWRAQS 757
            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 = 1e-09
 Identities = 29/93 (31%), Positives = 49/93 (52%), Gaps = 7/93 (7%)
 Frame = +2

Query: 488 PSKAEALNHH-------NLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTY 646
           P K +  + H       N L C V+ F+P Q+++   +NG++  A    + L  + DW++
Sbjct: 24  PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAE--QSDLSFSKDWSF 81

Query: 647 QVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 745
            +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 = 1e-06
 Identities = 30/92 (32%), Positives = 44/92 (47%), Gaps = 5/92 (5%)
 Frame = +2

Query: 467 QPTVTISPSKAEALNHHNLLV-CAVTDFYPSQVKVQWFRNGQEETAG-VVSTPLIRNGDW 640
           +P V   P  AE L+   + V C V  FYP  + V+W  NGQ E  G   +TP  ++ D 
Sbjct: 370 EPQVYTLPPPAEELSRSKVTVTCLVIGFYPPDIHVEWKSNGQPEPEGNYRTTPPQQDVDG 429

Query: 641 T---YQVLVMLEMNLQRGDVYTCRVEHSSLQS 727
           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: 1,027,841
Number of Sequences: 1040
Number of extensions: 27248
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): 107
length of database: 434,620
effective HSP length: 78
effective length of database: 353,500
effective search space used: 101808000
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= 20060611C-000186
         (1101 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 ...   373   e-103
Alignment   gi|NP_872355.1| major histocompatibility complex, class II, DQ ...   325   5e-89
Alignment   gi|NP_002115.1| major histocompatibility complex, class II, DR ...   320   2e-87
Alignment   gi|XP_945926.1| PREDICTED: similar to HLA class II histocompati...   310   1e-84
Alignment   gi|NP_002116.2| major histocompatibility complex, class II, DR ...   307   9e-84
Alignment   gi|NP_068818.4| major histocompatibility complex, class II, DR ...   301   5e-82
Alignment   gi|NP_002112.3| major histocompatibility complex, class II, DP ...   300   1e-81
Alignment   gi|NP_072049.2| major histocompatibility complex, class II, DR ...   291   9e-79
Alignment   gi|XP_949921.1| PREDICTED: similar to HLA class II histocompati...   290   1e-78
Alignment   gi|XP_949915.1| PREDICTED: similar to HLA class II histocompati...   284   1e-76

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

 Score =  373 bits (957), Expect = e-103
 Identities = 184/260 (70%), Positives = 210/260 (80%)
 Frame = +2

Query: 86  MSGMVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLT 265
           MS   ALR+P GL  A +T+ML +L  PVAEGRDSP+DFVYQFK  CYF NGT+RVRL++
Sbjct: 1   MSWKKALRIPGGLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVS 60

Query: 266 RYIYNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEG 445
           R IYN+EE VRFDS+VGE+RAVT LG P A+YWN QKD+LE+ RA +D VC+HNYQ+E  
Sbjct: 61  RSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELR 120

Query: 446 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 625
           TTLQRRV+PTVTISPS+ EALNHHNLLVC+VTDFYP+Q+KV+WFRN QEETAGVVSTPLI
Sbjct: 121 TTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLI 180

Query: 626 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 805
           RNGDWT+Q+LVMLEM  QRGDVYTC VEH SLQSPI VEWRAQSESAQSKMLS       
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVL 240

Query: 806 XXXXXXXXXXXRHRSQKGLV 865
                       HRSQKGL+
Sbjct: 241 GLIFLGLGLIIHHRSQKGLL 260


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

 Score =  325 bits (832), Expect = 5e-89
 Identities = 156/221 (70%), Positives = 184/221 (83%)
 Frame = +2

Query: 86  MSGMVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLT 265
           MS  +AL++P G W AA+TVMLV+L  PVAE RD P+DF+ QFK  CYF NGT+RVR + 
Sbjct: 1   MSWKMALQIPGGFWAAAVTVMLVMLSTPVAEARDFPKDFLVQFKGMCYFTNGTERVRGVA 60

Query: 266 RYIYNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEG 445
           RYIYN+EE+ RFDS+VGE++AVT LGR   D WN  KD LEQ RA +D VC+HNY+ E  
Sbjct: 61  RYIYNREEYGRFDSDVGEFQAVTELGRSIED-WNNYKDFLEQERAAVDKVCRHNYEAELR 119

Query: 446 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 625
           TTLQR+V+PTVTISPS+ EALNHHNLLVC+VTDFYP+Q+KVQWFRN QEETAGVVST LI
Sbjct: 120 TTLQRQVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVQWFRNDQEETAGVVSTSLI 179

Query: 626 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWR 748
           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 =  320 bits (819), Expect = 2e-87
 Identities = 157/255 (61%), Positives = 190/255 (74%)
 Frame = +2

Query: 95  MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRYI 274
           MV L+LP G    ALTV L+VL +P+A   D+   F++Q KFEC+FFNGT+RVRLL R I
Sbjct: 1   MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVRLLERCI 60

Query: 275 YNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 454
           YNQEE VRFDS+VGEYRAVT LGRPDA+YWN QKD+LEQ RA +DT C+HNY + E  T+
Sbjct: 61  YNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTV 120

Query: 455 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 634
           QRRV+P VT+ PSK + L HHNLLVC+V+ FYP  ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 635 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 814
           DWT+Q LVMLE   + G+VYTC+VEH S+ SP+ VEWRA+SESAQSKMLS          
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSESAQSKMLSGVGGFVLGLL 240

Query: 815 XXXXXXXXRHRSQKG 859
                     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 =  310 bits (795), Expect = 1e-84
 Identities = 155/255 (60%), Positives = 188/255 (73%)
 Frame = +2

Query: 95  MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRYI 274
           MV L+LP G   AALTV L+VL +P+A   D+   F+ Q KFEC+FFNGT+RVR L R I
Sbjct: 1   MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60

Query: 275 YNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 454
           YNQEE+VRFDS+VGEYRAVT LGRP A+ WN QKD LE+ RAE+DTVC+HNY + E  T+
Sbjct: 61  YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120

Query: 455 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 634
           QRRV P VT+ P+K + L HHNLLVC+V+ FYP  ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 635 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 814
           DWT+Q LVMLE   + G+VYTC+VEH S+ SP+ VEWRA+SESAQSKMLS          
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEWRARSESAQSKMLSGVGGFVLGLL 240

Query: 815 XXXXXXXXRHRSQKG 859
                     R+QKG
Sbjct: 241 FLGAGLFIYFRNQKG 255


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

 Score =  307 bits (787), Expect = 9e-84
 Identities = 147/230 (63%), Positives = 180/230 (78%)
 Frame = +2

Query: 95  MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRYI 274
           MV L+LP G + A LTV L+VL +P+A   D+   F+ Q K+EC+FFNGT+RVR L R I
Sbjct: 1   MVCLKLPGGSYMAKLTVTLMVLSSPLALAGDTRPRFLQQDKYECHFFNGTERVRFLHRDI 60

Query: 275 YNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 454
           YNQEE +RFDS+VGEYRAVT LGRPDA+YWN QKD LE  RA +DT C+HNY + E  T+
Sbjct: 61  YNQEEDLRFDSDVGEYRAVTELGRPDAEYWNSQKDFLEDRRAAVDTYCRHNYGVGESFTV 120

Query: 455 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 634
           QRRV+P VT+ P++ + L HHNLLVC+V  FYP  ++V+WFRN QEE AGVVST LI+NG
Sbjct: 121 QRRVEPKVTVYPARTQTLQHHNLLVCSVNGFYPGSIEVRWFRNSQEEKAGVVSTGLIQNG 180

Query: 635 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 784
           DWT+Q LVMLE   + G+VYTC+VEH S+ SP+ VEWRAQSESAQSKMLS
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRAQSESAQSKMLS 230


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

 Score =  301 bits (772), Expect = 5e-82
 Identities = 148/255 (58%), Positives = 185/255 (72%)
 Frame = +2

Query: 95  MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRYI 274
           MV L+LP G   AALTV L VL +P+A   D+   F+ Q K EC+F NGT+RV  L RYI
Sbjct: 1   MVCLKLPGGSCMAALTVTLTVLSSPLALAGDTQPRFLEQAKCECHFLNGTERVWNLIRYI 60

Query: 275 YNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 454
           YNQEE+ R++S++GEY+AVT LGRPDA+YWN QKD+LE+ RAE+DT C++NY + E  T+
Sbjct: 61  YNQEEYARYNSDLGEYQAVTELGRPDAEYWNSQKDLLERRRAEVDTYCRYNYGVVESFTV 120

Query: 455 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 634
           QRRVQP VT+ PSK + L HHNLLVC+V  FYP  ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVQPKVTVYPSKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 635 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 814
           DWT+Q LVMLE   + G+VYTC+VEH S+ SP+ V+W A+SESAQSKMLS          
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSMMSPLTVQWSARSESAQSKMLSGVGGFVLGLL 240

Query: 815 XXXXXXXXRHRSQKG 859
                     R+QKG
Sbjct: 241 FLGTGLFIYFRNQKG 255


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

 Score =  300 bits (769), Expect = 1e-81
 Identities = 144/230 (62%), Positives = 181/230 (78%)
 Frame = +2

Query: 95  MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRYI 274
           M+ L++     T ALT +L+VL   V +GR +P+++++Q + ECY FNGTQR   L RYI
Sbjct: 1   MMVLQVSAAPRTVALTALLMVLLTSVVQGRATPENYLFQGRQECYAFNGTQR--FLERYI 58

Query: 275 YNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 454
           YN+EE  RFDS+VGE+RAVT LGRP A+YWN QKD+LE+ RA  D +C+HNY++    TL
Sbjct: 59  YNREEFARFDSDVGEFRAVTELGRPAAEYWNSQKDILEEKRAVPDRMCRHNYELGGPMTL 118

Query: 455 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 634
           QRRVQP V +SPSK   L HHNLLVC VTDFYP  ++V+WF NGQEETAGVVST LIRNG
Sbjct: 119 QRRVQPRVNVSPSKKGPLQHHNLLVCHVTDFYPGSIQVRWFLNGQEETAGVVSTNLIRNG 178

Query: 635 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 784
           DWT+Q+LVMLEM  Q+GDVYTC+VEH+SL SP+ VEW+AQS+SA+SK L+
Sbjct: 179 DWTFQILVMLEMTPQQGDVYTCQVEHTSLDSPVTVEWKAQSDSARSKTLT 228


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

 Score =  291 bits (744), Expect = 9e-79
 Identities = 146/255 (57%), Positives = 180/255 (70%)
 Frame = +2

Query: 95  MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRYI 274
           MV L+LP G   AALTV L+VL + +A   D+   F+   K EC+FFNGT+RVR L RY 
Sbjct: 1   MVCLKLPGGSSLAALTVTLMVLSSRLAFAGDTRPRFLELRKSECHFFNGTERVRYLDRYF 60

Query: 275 YNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 454
           +NQEE +RFDS+VGEYRAVT LGRP A+ WN QKD+LEQ R  +D  C+HNY + E  T+
Sbjct: 61  HNQEEFLRFDSDVGEYRAVTELGRPVAESWNSQKDLLEQKRGRVDNYCRHNYGVGESFTV 120

Query: 455 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 634
           QRRV P VT+ P+K + L HHNLLVC+V+ FYP  ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVHPQVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 635 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 814
           DWT+Q LVMLE   + G+VYTC+VEH S+ S + VEWRA+SESAQSKMLS          
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSALTVEWRARSESAQSKMLSGVGGFVLGLL 240

Query: 815 XXXXXXXXRHRSQKG 859
                     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 =  290 bits (742), Expect = 1e-78
 Identities = 140/220 (63%), Positives = 171/220 (77%)
 Frame = +2

Query: 95  MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRYI 274
           MV L+LP G   AALTV L+VL +P+A   D+   F+ Q KFEC+FFNGT+RVR L R I
Sbjct: 1   MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60

Query: 275 YNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 454
           YNQEE+VRFDS+VGEYRAVT LGRP A+ WN QKD LE+ RAE+DTVC+HNY + E  T+
Sbjct: 61  YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120

Query: 455 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 634
           QRRV P VT+ P+K + L HHNLLVC+V+ FYP  ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 635 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQ 754
           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 (726), Expect = 1e-76
 Identities = 138/220 (62%), Positives = 166/220 (75%)
 Frame = +2

Query: 200 FVYQFKFECYFFNGTQRVRLLTRYIYNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKD 379
           F+ Q KFEC+FFNGT+RVR L R IYNQEE+VRFDS+VGEYRAVT LGRP A+ WN QKD
Sbjct: 54  FLKQDKFECHFFNGTERVRYLHRGIYNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKD 113

Query: 380 VLEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQ 559
            LE+ RAE+DTVC+HNY + E  T+QRRV P VT+ P+K + L HHNLLVC+V+ FYP  
Sbjct: 114 FLERRRAEVDTVCRHNYGVGESFTVQRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGS 173

Query: 560 VKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILV 739
           ++V+WFRNGQEE AGVVST LI+NGDWT+Q LVMLE   + G+VYTC+VEH S+ SP+ V
Sbjct: 174 IEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTV 233

Query: 740 EWRAQSESAQSKMLSXXXXXXXXXXXXXXXXXXRHRSQKG 859
           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: 44,356,564
Number of Sequences: 39411
Number of extensions: 1279233
Number of successful extensions: 5872
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 4739
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): 5805
length of database: 17,774,539
effective HSP length: 103
effective length of database: 13,715,206
effective search space used: 3607099178
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= 20060611C-000186
         (1101 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...   390   e-108
Alignment   gi|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis fami...   306   2e-83
Alignment   gi|XP_850395.1| PREDICTED: similar to HLA class II histocompati...   271   8e-73
Alignment   gi|XP_861384.1| PREDICTED: similar to HLA class II histocompati...   258   9e-69
Alignment   gi|XP_849737.1| PREDICTED: similar to HLA class II histocompati...    73   6e-13
Alignment   gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati...    69   8e-12
Alignment   gi|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris]     67   2e-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...    63   4e-10
Alignment   gi|XP_853335.1| PREDICTED: similar to T-cell surface glycoprote...    59   6e-09

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

 Score =  390 bits (1002), Expect = e-108
 Identities = 188/258 (72%), Positives = 214/258 (82%)
 Frame = +2

Query: 86  MSGMVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLT 265
           MSG + L +PRG WTAA+ ++LVVL  PVAEGRDSPQDFV+Q+K ECYF NGT+RVRLLT
Sbjct: 1   MSGKMTLCIPRGFWTAAVMMILVVLSIPVAEGRDSPQDFVFQYKAECYFTNGTERVRLLT 60

Query: 266 RYIYNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEG 445
           +YIYN+EE VRFDS+VGE+RAVT LGRPDA+YWN QKD +++ RAELDTVC+HNY  EE 
Sbjct: 61  KYIYNREEFVRFDSDVGEFRAVTELGRPDAEYWNRQKDEMDRVRAELDTVCRHNYGREEL 120

Query: 446 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 625
           TTLQRRV+PTVTI PSK E LNHHNLLVC+VTDFYP Q+KV+WFRN QE+TAGVVSTPLI
Sbjct: 121 TTLQRRVEPTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLI 180

Query: 626 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 805
           RNGDWT+Q+LVMLEM  QRGDVYTC VEH+SLQSPI V+WRAQSESAQSKMLS       
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHASLQSPITVQWRAQSESAQSKMLSGIGGFVL 240

Query: 806 XXXXXXXXXXXRHRSQKG 859
                      RHRSQKG
Sbjct: 241 GLIFLGLGLIIRHRSQKG 258


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

 Score =  306 bits (784), Expect = 2e-83
 Identities = 150/255 (58%), Positives = 184/255 (72%)
 Frame = +2

Query: 95  MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRYI 274
           MV L    G W  AL ++L+VL  P A  RD+P  F+   K ECYF NGT+RVR + RYI
Sbjct: 1   MVCLCFLGGSWMTALMLILMVLNPPFAWARDTPPHFLEVAKSECYFTNGTERVRFVERYI 60

Query: 275 YNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 454
           +N+EE VRFDS+VGE+RAVT LGRP A+ WNGQK++LEQ RA +DT C+HNY + E  T+
Sbjct: 61  HNREEFVRFDSDVGEFRAVTELGRPVAESWNGQKEILEQERATVDTYCRHNYGVIESFTV 120

Query: 455 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 634
           QRRV+PTVT+ P+K + L HHNLLVC+V  FYP  ++V+W RNGQEE AGVVST LIRNG
Sbjct: 121 QRRVEPTVTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNG 180

Query: 635 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 814
           DWT+Q+LVMLE+  Q G+VYTC+VEH SL SP+ VEWRAQS+SAQSKMLS          
Sbjct: 181 DWTFQILVMLEIVPQSGEVYTCQVEHPSLTSPVTVEWRAQSDSAQSKMLSGIGGFVLGLL 240

Query: 815 XXXXXXXXRHRSQKG 859
                     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 =  271 bits (693), Expect = 8e-73
 Identities = 126/247 (51%), Positives = 170/247 (68%)
 Frame = +2

Query: 125 WTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRYIYNQEEHVRFD 304
           W  AL V +  L + + +GRDSP+DFV Q K +CYF NGT++V+ + R+I+N EE+ RFD
Sbjct: 8   WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67

Query: 305 SNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTI 484
           S+VG + A+T LG+PDA+ WN Q  +LE++RA +D +C+HNY++    T+ R+VQP VT+
Sbjct: 68  SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTV 127

Query: 485 SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVML 664
            P +  ++ HHNLL+C+VT FYP  +K++WFRNGQEE  GV+ST LIRNGDWT+Q +VML
Sbjct: 128 YPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVML 187

Query: 665 EMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXXXXXXXXXXRH 844
           EM  + GDVYTC V H SL SP+ VEWRAQS  +  KMLS                    
Sbjct: 188 EMTPELGDVYTCLVNHPSLLSPVSVEWRAQSTYSWRKMLSGIAAFLLGLIFLLVGTVICL 247

Query: 845 RSQKGLV 865
           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 =  258 bits (658), Expect = 9e-69
 Identities = 113/207 (54%), Positives = 155/207 (74%)
 Frame = +2

Query: 125 WTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRYIYNQEEHVRFD 304
           W  AL V +  L + + +GRDSP+DFV Q K +CYF NGT++V+ + R+I+N EE+ RFD
Sbjct: 8   WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67

Query: 305 SNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTI 484
           S+VG + A+T LG+PDA+ WN Q  +LE++RA +D +C+HNY++    T+ R+VQP VT+
Sbjct: 68  SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTV 127

Query: 485 SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVML 664
            P +  ++ HHNLL+C+VT FYP  +K++WFRNGQEE  GV+ST LIRNGDWT+Q +VML
Sbjct: 128 YPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVML 187

Query: 665 EMNLQRGDVYTCRVEHSSLQSPILVEW 745
           EM  + GDVYTC V H SL SP+ VEW
Sbjct: 188 EMTPELGDVYTCLVNHPSLLSPVSVEW 214


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

 Score = 72.8 bits (177), Expect = 6e-13
 Identities = 55/187 (29%), Positives = 83/187 (44%), Gaps = 1/187 (0%)
 Frame = +2

Query: 188 SPQDFVYQFKFECYFFNGTQRVRLLTRYIYNQEEHVRFDSNVGEYRAVTPLGRPDADYWN 367
           +P+DF Y     C  FN      LLT +  ++ + V +     E+  +  L    +DY N
Sbjct: 36  TPKDFTY-----CVSFNKD----LLTCWDPDEAKMVPY-----EFGTLNVLANYLSDYLN 81

Query: 368 GQKDVLEQTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDF 547
            Q++ L Q  +     C  + Q   G+   R   PTV ++ S         +L C V  F
Sbjct: 82  -QQEYLHQRLSNGLQDCATHTQSFWGSLTHRTRPPTVQVAKSTPFNTKESVMLACYVWGF 140

Query: 548 YPSQVKVQWFRNGQEETAGVVSTPLIR-NGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQ 724
           YP+ V + W +NGQ   +   +  + + NGDWTYQ +  L       D YTC VEH    
Sbjct: 141 YPADVTISWRKNGQPVPSHSSALNMAQPNGDWTYQTVSHLATTPSYEDTYTCVVEHIGAP 200

Query: 725 SPILVEW 745
            P+  +W
Sbjct: 201 EPVCEDW 207


>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 = 8e-12
 Identities = 36/122 (29%), Positives = 56/122 (45%), Gaps = 2/122 (1%)
 Frame = +2

Query: 395 RAELDTVCKHNYQIE--EGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKV 568
           +A LD + + + +     GT L   + P V + P     L   N+L+C V + +P  + +
Sbjct: 63  KAHLDVLVERSNRTRAINGTHLSSPLPPRVAVLPKFRVELGQPNVLICIVDNIFPPVINI 122

Query: 569 QWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWR 748
            W RNGQ  + GV  T      D  ++    L       D+Y C+VEH  L+ P+L  W 
Sbjct: 123 TWLRNGQIISEGVAQTSFYSQPDHLFRKFCYLTFVPSAEDMYDCKVEHWGLEEPLLRHWE 182

Query: 749 AQ 754
            Q
Sbjct: 183 PQ 184


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

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

Query: 395 RAELDTVCKHNYQIEEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQW 574
           +A LDT+ K +       T    V P VT+  +    L   N+L+C +  F P  + V W
Sbjct: 92  KANLDTMIKRSNH-----TPNTNVPPEVTVLSNTPVELGEPNILICFIDKFSPPVINVTW 146

Query: 575 FRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 745
            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: 470 PTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQ 649
           P VT+       L   N L+C V + +P  + V W +N    T GV  T     GD ++ 
Sbjct: 113 PEVTVFSKSPVMLGQPNTLICLVDNIFPPVINVTWLKNRHSVTEGVSETSFFAKGDHSFS 172

Query: 650 VLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKM 778
            +  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 = 63.2 bits (152), Expect = 4e-10
 Identities = 59/230 (25%), Positives = 98/230 (42%), Gaps = 8/230 (3%)
 Frame = +2

Query: 80  SIMSGMVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRL 259
           S M G+        L  A   + +V L   +   +D      +Q  F C   N  +    
Sbjct: 75  SQMEGIEDWEKESKLQKAREDIFMVTLKDIMEYYKDKEGSHTFQGMFGCELQNN-KNSGA 133

Query: 260 LTRYIYNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQ-- 433
             RY Y+    + F+  +  +    P        W  ++  +++ +A L+  C    Q  
Sbjct: 134 FWRYAYDGRNFIEFNKEIPAWVPQDPAALNTKKKWEAEEVYVQRAKAYLEEECPVMLQRY 193

Query: 434 IEEGTT-LQRRVQPTVTI-SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFR--NGQEETA 601
           +E G T L R+  P+V+I S    E +     L C V+ FYP ++ + W +  + QE  +
Sbjct: 194 LEYGKTYLDRQEPPSVSITSHGTPEGIQ---TLKCWVSGFYPQEIDLHWIQADDTQETKS 250

Query: 602 GVVSTPLIRNGDWTYQVLVMLEMNLQ--RGDVYTCRVEHSSLQSPILVEW 745
           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 = 6e-09
 Identities = 33/90 (36%), Positives = 50/90 (55%)
 Frame = +2

Query: 452 LQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRN 631
           LQR+V+P   +S   +    H  L VC V+ FYP  V V W R G++E  G + + ++ N
Sbjct: 199 LQRKVRPEAWLSAGSSPGPGHLRL-VCHVSGFYPKPVWVSWMR-GEQEQQGTLYSDILPN 256

Query: 632 GDWTYQVLVMLEMNLQRGDVYTCRVEHSSL 721
            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: 45,642,161
Number of Sequences: 33732
Number of extensions: 1266202
Number of successful extensions: 5763
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 4741
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: 104
effective length of database: 15,758,437
effective search space used: 4128710494
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= 20060611C-000186
         (1101 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 ...   332   4e-91
Alignment   gi|NP_034512.1| histocompatibility 2, class II antigen E beta [...   288   7e-78
Alignment   gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/...   257   2e-68
Alignment   gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ...   246   3e-65
Alignment   gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ...    74   3e-13
Alignment   gi|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus ...    74   4e-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   1e-11
Alignment   gi|NP_034511.2| histocompatibility 2, class II antigen E alpha ...    62   8e-10
Alignment   gi|XP_908790.2| PREDICTED: similar to histocompatibility 2, Q r...    62   1e-09

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

 Score =  332 bits (851), Expect = 4e-91
 Identities = 167/255 (65%), Positives = 200/255 (78%), Gaps = 1/255 (0%)
 Frame = +2

Query: 98  VALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRYIY 277
           +AL++P  L +AA+ V+L+VL +P  EG DS + FVYQF  ECYF NGTQR+R +TRYIY
Sbjct: 1   MALQIPSLLLSAAV-VVLMVLSSPGTEGGDSERHFVYQFMGECYFTNGTQRIRYVTRYIY 59

Query: 278 NQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQ-IEEGTTL 454
           N+EE+VR+DS+VGE+RAVT LGRPDA+YWN Q ++LE+TRAELDTVC+HNY+  E  T+L
Sbjct: 60  NREEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSL 119

Query: 455 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 634
           +R  QP V IS S+ EALNHHN LVC+VTDFYP+Q+KV+WFRNGQEET GV ST LIRNG
Sbjct: 120 RRLEQPNVVISLSRTEALNHHNTLVCSVTDFYPTQIKVRWFRNGQEETVGVSSTQLIRNG 179

Query: 635 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 814
           DWT+QVLVMLEM  +RG+VYTC VEH SL+SPI VEWRAQSESA SKMLS          
Sbjct: 180 DWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRAQSESAWSKMLSGIGGCVLGVI 239

Query: 815 XXXXXXXXRHRSQKG 859
                   RHRSQKG
Sbjct: 240 FLGLGLFIRHRSQKG 254


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

 Score =  288 bits (737), Expect = 7e-78
 Identities = 139/250 (55%), Positives = 178/250 (71%)
 Frame = +2

Query: 110 LPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRYIYNQEE 289
           LPR    AA+ ++L VL  PVA  RDS   F+   K EC+F+NGTQRVR L RY YN EE
Sbjct: 4   LPRVPCVAAVILLLTVLSPPVALVRDSRPWFLEYCKSECHFYNGTQRVRFLKRYFYNLEE 63

Query: 290 HVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRRVQ 469
           ++RFDS+VGE+RAVT LGRPDA+ WN Q ++L++ RA +DT C+HNY+I +   + RRV+
Sbjct: 64  NLRFDSDVGEFRAVTELGRPDAENWNSQPEILDEKRAAVDTYCRHNYEIFDNFLVPRRVE 123

Query: 470 PTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQ 649
           PTVT+ P+K + L HHNLLVC+V+DFYP  ++V+WFRNG+EE  G+VST L+RNGDWT+Q
Sbjct: 124 PTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQ 183

Query: 650 VLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXXXXXXX 829
            LVMLE   Q G+VYTC+VEH SL  P+ VEW+AQS SAQ+KMLS               
Sbjct: 184 TLVMLETVPQSGEVYTCQVEHPSLTDPVTVEWKAQSTSAQNKMLSGVGGFVLGLLFLRAG 243

Query: 830 XXXRHRSQKG 859
                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 =  257 bits (656), Expect = 2e-68
 Identities = 127/230 (55%), Positives = 168/230 (73%)
 Frame = +2

Query: 95  MVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRYI 274
           MV+L LPRGL  AA+ + L++L  PV   RD    F+ Q K EC++FNG +RV  +TR+I
Sbjct: 1   MVSLWLPRGLCVAAVILSLMMLTPPVILVRDPRPRFLEQLKAECHYFNGKERVWSVTRFI 60

Query: 275 YNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEGTTL 454
           YNQEE  RF+S+ G++ AVT LGRP  +Y N QKD+L+  RA +D  C++NY + +   L
Sbjct: 61  YNQEEFARFNSDFGKFLAVTELGRPIVEYLNTQKDMLDNYRASVDR-CRNNYDLVDIFML 119

Query: 455 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 634
             + +P VT+ P+K + L HHNLLVC+V DFYP  ++V+WFRNG+EE  GVVST LI+N 
Sbjct: 120 NLKAEPKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNR 179

Query: 635 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 784
           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 =  246 bits (628), Expect = 3e-65
 Identities = 115/223 (51%), Positives = 157/223 (70%)
 Frame = +2

Query: 116 RGLWTAALTVMLVVLGAPVAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRYIYNQEEHV 295
           R  W  AL V L+ L + + EGRDSP++FV Q K +CYF NGT++V LL R+I+N EE++
Sbjct: 5   RAPWVVALLVNLMRLDSFMIEGRDSPENFVIQAKADCYFTNGTEKVHLLVRFIFNLEEYL 64

Query: 296 RFDSNVGEYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQIEEGTTLQRRVQPT 475
            FDS++G + A+T LG PDAD WN + D+LE +RA ++ VC+  Y++    T++R V P 
Sbjct: 65  HFDSDLGMFVALTELGEPDADQWNKRLDLLETSRAAVNMVCRQKYKLGAPFTVERNVPPE 124

Query: 476 VTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVL 655
           VT+ P +   L  HNLL+C+VT FYP  + V+WFRNGQEE +GV+ST L+RNGDWT+Q  
Sbjct: 125 VTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVRNGDWTFQTT 184

Query: 656 VMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 784
           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 = 73.9 bits (180), Expect = 3e-13
 Identities = 61/231 (26%), Positives = 93/231 (40%), Gaps = 23/231 (9%)
 Frame = +2

Query: 122 LWTAALTVMLVVLGAP----------VAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRY 271
           LW   L + L  +GA           V     +PQDF Y   F                 
Sbjct: 4   LWLLLLVLSLHCMGAGGFVAHVESTCVLNDAGTPQDFTYCVSF----------------- 46

Query: 272 IYNQEEHVRFDSNVG-----EYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQI 436
             N++    +D +VG     E+  ++ L    ++  N Q+ ++ + +  L     H    
Sbjct: 47  --NKDLLACWDPDVGKIVPCEFGVLSRLAEIISNILNEQESLIHRLQNGLQDCATHTQPF 104

Query: 437 EEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQ--------E 592
            +  T + R  P+V ++ +         +L C V  FYP+ V + W +NGQ        E
Sbjct: 105 WDVLTHRTRA-PSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKE 163

Query: 593 ETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 745
           +TA         NGDWTYQ +  L +    GDVYTC V+HS    PI  +W
Sbjct: 164 KTAQP-------NGDWTYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDW 207


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

 Score = 73.6 bits (179), Expect = 4e-13
 Identities = 61/231 (26%), Positives = 92/231 (39%), Gaps = 23/231 (9%)
 Frame = +2

Query: 122 LWTAALTVMLVVLGAP----------VAEGRDSPQDFVYQFKFECYFFNGTQRVRLLTRY 271
           LW   L + L  +GA           V +   +PQDF Y   F                 
Sbjct: 4   LWLLLLVLSLDCMGAGGFVAHVESTCVLDDAGTPQDFTYCVSF----------------- 46

Query: 272 IYNQEEHVRFDSNVG-----EYRAVTPLGRPDADYWNGQKDVLEQTRAELDTVCKHNYQI 436
             N++    +D +VG     E+  + P     +   N ++ +L++ +  L     H    
Sbjct: 47  --NKDLLACWDPDVGKIVPCEFGVLYPWAENFSRILNKEESLLQRLQNGLLDCASHTQPF 104

Query: 437 EEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQ--------E 592
               T + R  P+V ++ +         +L C V  FYP+ V + W +NGQ        E
Sbjct: 105 WNALTHRTRA-PSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKE 163

Query: 593 ETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 745
           +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: 413 VCKHNYQI---EEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRN 583
           V KHN  +      +T      P  T+ P     L   N L+C V + +P  + + W RN
Sbjct: 92  VVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRN 151

Query: 584 GQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSES 763
            +    GV  T    N D+++  L  L       D+Y C+VEH  L+ P+L  W  +  +
Sbjct: 152 SKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEPEIPA 211

Query: 764 AQSKM 778
             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 = 1e-11
 Identities = 34/97 (35%), Positives = 45/97 (46%)
 Frame = +2

Query: 464 VQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWT 643
           V P VT+ P     L   N+L+C V D +P  + V W RN Q  T GV  T      +  
Sbjct: 111 VPPRVTVLPKTRVELGKPNVLICIVDDIFPPVINVTWLRNSQPITKGVAQTSFYSQPNHR 170

Query: 644 YQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQ 754
           ++    L       DVY C+VEH  L +P+L  W  Q
Sbjct: 171 FRKFHYLTFVPSAEDVYDCKVEHWGLDTPLLQHWEPQ 207


>ref|NP_034511.2| histocompatibility 2, class II antigen E alpha [Mus musculus]
          Length = 255

 Score = 62.4 bits (150), Expect = 8e-10
 Identities = 32/105 (30%), Positives = 46/105 (43%)
 Frame = +2

Query: 449 TLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIR 628
           T    V P VT+       L   N+L+C +  F P  V V WFRNG+  T GV  T  + 
Sbjct: 105 TPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWFRNGRPVTEGVSETVFLP 164

Query: 629 NGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSES 763
             D  ++    L       D Y C V+H  L+ P+   W  + ++
Sbjct: 165 RDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEEPLRKHWEFEEKT 209


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

 Score = 62.0 bits (149), Expect = 1e-09
 Identities = 42/184 (22%), Positives = 76/184 (41%), Gaps = 5/184 (2%)
 Frame = +2

Query: 209 QFKFECYFFNGTQRVRLLTRYIYNQEEHVRFDSNVGEYRAVTPLGRPDADYWNGQKDVLE 388
           Q+ + C   +  + +R   ++ Y   +++  + ++  + A     +     W  Q  + E
Sbjct: 233 QWMYGCDVGSDERLLRGYLQFAYEGRDYIALNEDLKTWTAADMAAQITLHKWE-QAGIAE 291

Query: 389 QTRAELDTVCKHNYQIEEGTTLQRRVQPTVTISPSKAEALNHHN-----LLVCAVTDFYP 553
           + RA L+  C  + +      LQ R +  +   P KA   +H        L C    FYP
Sbjct: 292 RDRAYLEGACVQSLR----RYLQLRKETLLCTDPPKAHVTHHPRSYGAVTLRCWALGFYP 347

Query: 554 SQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPI 733
           + + + W  NG+E T  +        GD T+Q    + + L +   YTC V H  L  P+
Sbjct: 348 ADITLTWQLNGEELTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCHVNHEGLPEPL 407

Query: 734 LVEW 745
            + 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: 52,175,478
Number of Sequences: 45328
Number of extensions: 1442728
Number of successful extensions: 6438
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 5195
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): 6361
length of database: 21,768,885
effective HSP length: 105
effective length of database: 17,009,445
effective search space used: 4439465145
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)