Animal-Genome cDNA 20060611C-005394


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-005394
         (1225 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]                70   1e-13
Alignment   gi|NP_999362.2| neonatal Fc receptor FcRn [Sus scrofa]                62   4e-11
Alignment   gi|NP_999143.1| beta 2-microglobulin [Sus scrofa]                     59   2e-10
Alignment   gi|NP_998996.1| CD1 antigen [Sus scrofa]                              56   2e-09

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

 Score = 69.7 bits (169), Expect = 1e-13
 Identities = 43/162 (26%), Positives = 73/162 (45%), Gaps = 5/162 (3%)
 Frame = +3

Query: 276 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYC---RHNYRISDT 446
           Y+G + +  + D+  + AV    +   + W   + + EQ RA ++  C    H Y  +  
Sbjct: 139 YDGADYIVLNEDLRSWTAVGMAAQITRRKWEE-ETVAEQSRAYLEVACVQSLHRYLANGK 197

Query: 447 FLVPRRAEPT--VTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTG 620
             + R   P   VT +P+    +     L C   GFYP  + + W + GQ+++  V    
Sbjct: 198 ETLQRSDPPKTHVTRHPSSDNKVT----LRCWALGFYPKEISLTWQQEGQDQSQDVEVVE 253

Query: 621 LIPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 746
             P+GD TF+    L   P   + Y+C V+H  L  P+T+ W
Sbjct: 254 TRPSGDGTFRKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRW 295


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

 Score = 61.6 bits (148), Expect = 4e-11
 Identities = 45/167 (26%), Positives = 71/167 (42%), Gaps = 4/167 (2%)
 Frame = +3

Query: 279 NGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVP 458
           NGEE ++FD+ +G +       R     W    D + + +  +   C H  R+       
Sbjct: 136 NGEEFMKFDTKLGTWDGEWPEARTIGSKWMQEPDAVNKEKTFLLYSCPH--RLLGHLERG 193

Query: 459 RR----AEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLI 626
           R      EP      A+       ++L C    FYP  +++R+ RNG   AAG   + + 
Sbjct: 194 RGNLEWKEPPSMRMKARPGTAPGFSVLTCIAFSFYPPELQLRFLRNGL--AAGSGESDIG 251

Query: 627 PNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESA 767
           PNGD +F     L         Y C V+H  L  P+TVE  + ++S+
Sbjct: 252 PNGDGSFHAWSSLTVKSGDEHHYCCVVQHAGLAQPLTVELESPAKSS 298


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

 Score = 59.3 bits (142), Expect = 2e-10
 Identities = 32/92 (34%), Positives = 48/92 (52%)
 Frame = +3

Query: 471 PTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQ 650
           P V VY          N L C V+GF+P  +E+   +NG++  A    + L  + DW+F 
Sbjct: 25  PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAE--QSDLSFSKDWSFY 82

Query: 651 TMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 746
            +V  E  P + + YSCRV+H +L  P  V+W
Sbjct: 83  LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKW 114


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

 Score = 56.2 bits (134), Expect = 2e-09
 Identities = 29/73 (39%), Positives = 39/73 (53%)
 Frame = +3

Query: 504 PLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLETVPQS 683
           P   H +LVC V+GFYP  + V W R+ QE+  G     ++PN D T+   V L+     
Sbjct: 215 PSPGHLMLVCHVSGFYPKPIWVMWMRDEQEQ-PGTQQGDILPNADGTWYLRVTLDVAAGE 273

Query: 684 GEVYSCRVEHPSL 722
               SCRV+H SL
Sbjct: 274 ASGLSCRVKHSSL 286


  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: 1,228,704
Number of Sequences: 1040
Number of extensions: 32888
Number of successful extensions: 138
Number of sequences better than 1.0e-05: 4
Number of HSP's better than  0.0 without gapping: 112
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): 133
length of database: 434,620
effective HSP length: 79
effective length of database: 352,460
effective search space used: 115606880
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqBP

BLASTX 2.2.10 [Oct-19-2004]


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

Query= 20060611C-005394
         (1225 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001012698.2| major histocompatibility complex, class II, ...   380   e-105
Alignment   gi|XP_582099.2| PREDICTED: similar to major histocompatibility ...   313   1e-85
Alignment   gi|NP_001012694.1| major histocompatibility complex, class II, ...   283   3e-76
Alignment   gi|NP_001029840.2| MHC class II antigen [Bos taurus]                 283   3e-76
Alignment   gi|XP_876139.1| PREDICTED: similar to H-2 class II histocompati...   267   1e-71
Alignment   gi|NP_001012697.1| major histocompatibility complex, class II, ...   254   1e-67
Alignment   gi|NP_001013618.1| major histocompatibility complex, class II, ...   239   2e-63
Alignment   gi|XP_874766.1| PREDICTED: similar to HLA class II histocompati...   209   5e-54
Alignment   gi|NP_001012399.1| hemochromatosis [Bos taurus]                       77   4e-14
Alignment   gi|NP_001029503.1| hypothetical protein LOC508800 [Bos taurus]        75   1e-13

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

 Score =  380 bits (975), Expect = e-105
 Identities = 186/266 (69%), Positives = 205/266 (77%)
 Frame = +3

Query: 96  MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHY 275
           M+ L FS G WMAAL VML+VL PPLA AR+  P             NGTERVR LDRH+
Sbjct: 1   MVCLYFSGGSWMAALIVMLMVLCPPLAWAREIQPHFLEYYKGECHFFNGTERVRFLDRHF 60

Query: 276 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLV 455
           YNGEE +RFDSD GE+RAVTELGRP A+ WNS+KD LEQ+RAEVD  CRHNY   ++F V
Sbjct: 61  YNGEEFVRFDSDWGEFRAVTELGRPAAEHWNSQKDFLEQKRAEVDRVCRHNYGGVESFTV 120

Query: 456 PRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 635
            RR EPTVTVYPAKTQPLQHHNLLVCSV GFYPGH+EVRWFRNG EE AGV+STGLI NG
Sbjct: 121 QRRVEPTVTVYPAKTQPLQHHNLLVCSVNGFYPGHIEVRWFRNGHEEEAGVISTGLIQNG 180

Query: 636 DWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSXXXXXXXXXX 815
           DWTFQTMVMLETVPQSGEVY+C+V+HP  TSP+TVEWRARS+SAQ KMMS          
Sbjct: 181 DWTFQTMVMLETVPQSGEVYTCQVDHPKRTSPITVEWRARSDSAQSKMMSGVGGFVLGLL 240

Query: 816 XXXXXXXIYFKNQKGRPALQPTGLLS 893
                  IYF+NQKGRP LQPTGLLS
Sbjct: 241 FLAVGLFIYFRNQKGRPTLQPTGLLS 266


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

 Score =  313 bits (803), Expect = 1e-85
 Identities = 155/252 (61%), Positives = 184/252 (73%)
 Frame = +3

Query: 129 MAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILRFDS 308
           MAAL V+L+VLS P + AR+T P             NG ER+R   R+ YN +E + FDS
Sbjct: 1   MAALAVLLMVLSLPFSWARETQPHFIHQFKGECRFSNGLERMRFFARYIYNTQEDVHFDS 60

Query: 309 DVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTVTVY 488
           DVGE+ A+TELGR +A+ WN +KD +EQ RA+VDT CR NY+   +FL  RR EPTVTVY
Sbjct: 61  DVGEFTALTELGRLDAEYWNQQKDFMEQMRAKVDTLCRSNYQGIGSFLRQRRVEPTVTVY 120

Query: 489 PAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLE 668
           PAKTQPLQHHNLLVCSV GFYPGH+EVRWF N  EE AGV+STGLI NGDWTFQTMVMLE
Sbjct: 121 PAKTQPLQHHNLLVCSVNGFYPGHIEVRWFWNSHEEEAGVISTGLIQNGDWTFQTMVMLE 180

Query: 669 TVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSXXXXXXXXXXXXXXXXXIYFK 848
           TVPQSGEVY+C+VEHPS TSP+TVEWRA+S+SAQ K+MS                 I+ +
Sbjct: 181 TVPQSGEVYTCQVEHPSRTSPLTVEWRAQSDSAQRKLMSGIGGFVLGLLFLGVGLFIHLR 240

Query: 849 NQKGRPALQPTG 884
           ++KG PALQP G
Sbjct: 241 SKKGHPALQPIG 252


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

 Score =  283 bits (723), Expect = 3e-76
 Identities = 138/232 (59%), Positives = 169/232 (72%)
 Frame = +3

Query: 90  SSMLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDR 269
           S M+ L   RG W AA+ V L VLS P A  RD+P              NGTERVR + R
Sbjct: 2   SGMVALRIPRGLWTAAVMVTLAVLSTPGAEGRDSPQDTVVHFMGQCYFTNGTERVRYVTR 61

Query: 270 HYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTF 449
           + YN EE   +DSDVGEYRAVT+LGR  A+ WNS+KDILEQ RAE+DT CRHNY++    
Sbjct: 62  YIYNQEETAYYDSDVGEYRAVTQLGRTLAEYWNSQKDILEQTRAELDTVCRHNYQLEVIT 121

Query: 450 LVPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIP 629
            + R+ EPTVT+  ++T+ L HHNLLVCSVT FYPG ++VRWF+NG+EE AG+VST LI 
Sbjct: 122 SLQRQVEPTVTISLSRTEALNHHNLLVCSVTDFYPGQIKVRWFQNGKEETAGIVSTPLIR 181

Query: 630 NGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMS 785
           NGDWTFQ +VMLE  P+ G+VY+C VEHPSL SP++VEWRA+SESAQ KM+S
Sbjct: 182 NGDWTFQILVMLEMTPKRGDVYTCHVEHPSLQSPISVEWRAQSESAQSKMLS 233


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

 Score =  283 bits (723), Expect = 3e-76
 Identities = 142/257 (55%), Positives = 171/257 (66%)
 Frame = +3

Query: 90  SSMLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDR 269
           S M+ L   RG W A + V LV+LS P A  RD+P              NGTERVR + R
Sbjct: 2   SGMVALWIPRGLWTAVVMVTLVMLSTPGAEGRDSPKDFVVQFKGLCYFTNGTERVRYVTR 61

Query: 270 HYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTF 449
           + YN EE +RFDSD   YRA+T LGRP+A+ WNS+KD LEQ RAE DT CRHNY+     
Sbjct: 62  YIYNQEEYVRFDSDWDLYRALTPLGRPDAEYWNSQKDFLEQTRAEADTVCRHNYQAELIT 121

Query: 450 LVPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIP 629
            + RR EPTVT+ P++T+ L HHNLLVCSVT FYP  ++VRWFRN +EE AGVVST LI 
Sbjct: 122 SLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPSQIKVRWFRNDREETAGVVSTPLIR 181

Query: 630 NGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSXXXXXXXX 809
           NGDWTFQ +VMLE  PQ G+VY+C VEHPSL SP+ VEWRA+SESAQ KM+S        
Sbjct: 182 NGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPIMVEWRAQSESAQSKMLSGVGGFVLG 241

Query: 810 XXXXXXXXXIYFKNQKG 860
                    I+ ++QKG
Sbjct: 242 LIFLGLGLIIHHRSQKG 258


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

 Score =  267 bits (683), Expect = 1e-71
 Identities = 127/183 (69%), Positives = 145/183 (79%)
 Frame = +3

Query: 237 NGTERVRLLDRHYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTY 416
           NGT++VR LDR+ YN EE ++FDS VGEYRA TE+GRP A+ WN     L++ RA V  Y
Sbjct: 12  NGTQQVRFLDRYIYNREEQVQFDSLVGEYRARTEMGRPAAERWNRWPQALQRARAAVHAY 71

Query: 417 CRHNYRISDTFLVPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEE 596
           C  NY    +  V RR +PTVTVYP K++PL HHNLLVCSV GFYPGH+EVRWFRNGQEE
Sbjct: 72  CASNYEFFASRTVQRRVQPTVTVYPVKSRPLWHHNLLVCSVNGFYPGHIEVRWFRNGQEE 131

Query: 597 AAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGK 776
            AGVVSTGLIPNGDWTFQ MVMLE VPQ GEVY+C VEHPS TSPVTVEWRA+ ES+Q K
Sbjct: 132 EAGVVSTGLIPNGDWTFQIMVMLEIVPQGGEVYACHVEHPSRTSPVTVEWRAQDESSQEK 191

Query: 777 MMS 785
           M+S
Sbjct: 192 MLS 194


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

 Score =  254 bits (649), Expect = 1e-67
 Identities = 129/213 (60%), Positives = 150/213 (70%)
 Frame = +3

Query: 147 MLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILRFDSDVGEYR 326
           + +VL  P A  RD P              NGTE VRL+ R  YN EEIL FDSD+GE+ 
Sbjct: 19  VFLVLRIPEAHCRDAPKNFVYQFKGMCYFTNGTEHVRLVARQIYNKEEILHFDSDLGEFV 78

Query: 327 AVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTVTVYPAKTQP 506
           AVTELGR  A+ WN++KD+L + RA VDT CRHNY+ +  F V RR EPTVTV PA T+ 
Sbjct: 79  AVTELGRVCAEIWNTQKDLLAEFRAYVDTLCRHNYKETAGFTVQRRVEPTVTVSPASTEA 138

Query: 507 LQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLETVPQSG 686
           L HHNLLVCSVT FYP  V+V+WFRN QE+ AGV  T L  NGDWT+Q  VMLETVPQ G
Sbjct: 139 LNHHNLLVCSVTDFYPRQVKVKWFRNQQEQTAGVGFTPLTQNGDWTYQIHVMLETVPQLG 198

Query: 687 EVYSCRVEHPSLTSPVTVEWRARSESAQGKMMS 785
           +VY C V+HPSL SP+TVEWRA+SESAQ KM S
Sbjct: 199 DVYVCHVDHPSLQSPITVEWRAQSESAQSKMQS 231


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

 Score =  239 bits (611), Expect = 2e-63
 Identities = 117/246 (47%), Positives = 152/246 (61%)
 Frame = +3

Query: 126 WMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILRFD 305
           W+       + L   +   RD+P              NGTE+VR + R  +N E+  RFD
Sbjct: 8   WVVTFLSTALRLDASVTQGRDSPEDFVTQAKADCYFTNGTEKVRFVVRFIFNLEDYARFD 67

Query: 306 SDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTVTV 485
           SD+G + A+TELG+P+A+ WN+R DIL + RA VD  CR NY +   F V RR +P VTV
Sbjct: 68  SDLGMFVALTELGKPDAERWNNRPDILARSRASVDMLCRRNYYLGAPFTVGRRVQPEVTV 127

Query: 486 YPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVML 665
           YP KT  LQH NLL+C VTGFYPG ++V WFRNGQE+  G++STGLI NGDWTFQ  VML
Sbjct: 128 YPEKTPALQHRNLLLCLVTGFYPGDIKVTWFRNGQEQREGIMSTGLIRNGDWTFQMTVML 187

Query: 666 ETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSXXXXXXXXXXXXXXXXXIYF 845
              P+ GEVY+C V+HPSL SPV+VEWRA+SE +  K++S                 ++ 
Sbjct: 188 AMTPELGEVYTCLVDHPSLLSPVSVEWRAQSEYSWRKILSGAAAFLVGLVFFLVEIVVHI 247

Query: 846 KNQKGR 863
           +  KGR
Sbjct: 248 RAWKGR 253


>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 =  209 bits (531), Expect = 5e-54
 Identities = 128/280 (45%), Positives = 159/280 (56%), Gaps = 2/280 (0%)
 Frame = +3

Query: 54  LPAPFTHCPLLFSSMLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXX 233
           L +PF   P LF+S + L FS+G WMAAL VM+  LSP L  AR+T              
Sbjct: 2   LSSPF---PFLFASTVCLYFSKGSWMAALLVMMG-LSPLLTWARETQ------------- 44

Query: 234 XNGTERVRLLDRHYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDT 413
                         Y     +  DS +    A++  G+P A +     D           
Sbjct: 45  --------------YKRTPWVVIDSQIS---AISH-GKPCALNGYRECD----------- 75

Query: 414 YCRH--NYRISDTFLVPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNG 587
            C H    + +    + ++ EPTVTVYPAKTQPLQH++LLVCSV GFY GHVEVRWF  G
Sbjct: 76  GCFHPIGLKANRDITLQKKVEPTVTVYPAKTQPLQHNHLLVCSVNGFYLGHVEVRWFWKG 135

Query: 588 QEEAAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESA 767
           QEE AGV+STGLI NGDWTF+T+VMLETV QSGEVY+C++EHPS  SP+  EWRA+S+SA
Sbjct: 136 QEEEAGVISTGLIQNGDWTFETIVMLETVLQSGEVYTCQLEHPSWRSPIAEEWRAQSDSA 195

Query: 768 QGKMMSXXXXXXXXXXXXXXXXXIYFKNQKGRPALQPTGL 887
           Q KMMS                  +F+NQKG   LQPTG+
Sbjct: 196 QSKMMSGTGGFALGLLFLVVGLFTHFRNQKGHSGLQPTGI 235


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

 Score = 76.6 bits (187), Expect = 4e-14
 Identities = 48/164 (29%), Positives = 78/164 (47%), Gaps = 4/164 (2%)
 Frame = +3

Query: 267 RHYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNY-RISD 443
           ++ Y+G++ L F  +  ++RA     +    +W   K   +Q RA +D  C      + +
Sbjct: 145 KYGYDGQDHLEFRPETLDWRAAEPRAQVTKLEWEVNKIRAKQNRAYLDRDCPEQLLHLLE 204

Query: 444 TFLVP--RRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQE-EAAGVVS 614
               P  ++  P V V    T  L     L C    FYP ++ +RW ++ Q  +A  +  
Sbjct: 205 LGRGPLEQQVPPLVKVTHHVTSSL---TTLRCRALNFYPQNITIRWLKDKQFLDAKEIKP 261

Query: 615 TGLIPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 746
             ++PNGD T+Q  V L  +P   + YSC+VEHP L  P+T  W
Sbjct: 262 EDVLPNGDGTYQAWVALAMLPGEEQRYSCQVEHPGLDQPLTATW 305


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

 Score = 74.7 bits (182), Expect = 1e-13
 Identities = 46/167 (27%), Positives = 82/167 (49%), Gaps = 4/167 (2%)
 Frame = +3

Query: 276 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYC----RHNYRISD 443
           Y+G++ ++FD ++  +  +    +   + W +    +++ +A ++  C    R     S 
Sbjct: 136 YDGQDFIKFDKEIPAWVPLDPAAQNTKRKWEAEAVYVQRAKAYLEEECPGMLRRYLPYSR 195

Query: 444 TFLVPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGL 623
           T L  R+  P+V+V      P  H   L C    FYP  + + W R G  + A      +
Sbjct: 196 THL-DRQESPSVSV-TGHAAP-GHKRTLKCLAYDFYPRSIGLHWTRAGDAQEAES-GGDV 251

Query: 624 IPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSES 764
           +P+G+ T+Q+ V++   P+    YSC VEH SLT P+TV W  R ++
Sbjct: 252 LPSGNGTYQSWVVVGVPPEDQAPYSCHVEHRSLTRPLTVPWDPRQQA 298


  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: 46,843,826
Number of Sequences: 33508
Number of extensions: 1345250
Number of successful extensions: 4939
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 4157
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 4895
length of database: 16,112,626
effective HSP length: 104
effective length of database: 12,627,794
effective search space used: 3826221582
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-005394
         (1225 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis fami...   366   e-101
Alignment   gi|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Ca...   305   5e-83
Alignment   gi|XP_850395.1| PREDICTED: similar to HLA class II histocompati...   256   4e-68
Alignment   gi|XP_861384.1| PREDICTED: similar to HLA class II histocompati...   244   1e-64
Alignment   gi|XP_849737.1| PREDICTED: similar to HLA class II histocompati...    73   5e-13
Alignment   gi|NP_001018646.1| MHC class Ib [Canis familiaris]                    69   7e-12
Alignment   gi|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris]     69   1e-11
Alignment   gi|XP_855624.1| PREDICTED: MHC class Ib [Canis familiaris]            67   4e-11
Alignment   gi|XP_536867.2| PREDICTED: similar to Zinc-alpha-2-glycoprotein...    67   4e-11
Alignment   gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati...    64   3e-10

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

 Score =  366 bits (940), Expect = e-101
 Identities = 177/266 (66%), Positives = 202/266 (75%)
 Frame = +3

Query: 96  MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHY 275
           M+ LCF  G WM AL ++L+VL+PP A ARDTPP             NGTERVR ++R+ 
Sbjct: 1   MVCLCFLGGSWMTALMLILMVLNPPFAWARDTPPHFLEVAKSECYFTNGTERVRFVERYI 60

Query: 276 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLV 455
           +N EE +RFDSDVGE+RAVTELGRP A+ WN +K+ILEQ RA VDTYCRHNY + ++F V
Sbjct: 61  HNREEFVRFDSDVGEFRAVTELGRPVAESWNGQKEILEQERATVDTYCRHNYGVIESFTV 120

Query: 456 PRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 635
            RR EPTVTVYP KTQ LQHHNLLVCSV GFYPGH+EVRW RNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVEPTVTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNG 180

Query: 636 DWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSXXXXXXXXXX 815
           DWTFQ +VMLE VPQSGEVY+C+VEHPSLTSPVTVEWRA+S+SAQ KM+S          
Sbjct: 181 DWTFQILVMLEIVPQSGEVYTCQVEHPSLTSPVTVEWRAQSDSAQSKMLSGIGGFVLGLL 240

Query: 816 XXXXXXXIYFKNQKGRPALQPTGLLS 893
                  IYF+NQKG   LQPTGLLS
Sbjct: 241 FLAVGLFIYFRNQKGHSGLQPTGLLS 266


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

 Score =  305 bits (782), Expect = 5e-83
 Identities = 150/267 (56%), Positives = 185/267 (69%)
 Frame = +3

Query: 90  SSMLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDR 269
           S  + LC  RGFW AA+ ++LVVLS P+A  RD+P              NGTERVRLL +
Sbjct: 2   SGKMTLCIPRGFWTAAVMMILVVLSIPVAEGRDSPQDFVFQYKAECYFTNGTERVRLLTK 61

Query: 270 HYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTF 449
           + YN EE +RFDSDVGE+RAVTELGRP+A+ WN +KD +++ RAE+DT CRHNY   +  
Sbjct: 62  YIYNREEFVRFDSDVGEFRAVTELGRPDAEYWNRQKDEMDRVRAELDTVCRHNYGREELT 121

Query: 450 LVPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIP 629
            + RR EPTVT++P+KT+ L HHNLLVCSVT FYPG ++VRWFRN QE+ AGVVST LI 
Sbjct: 122 TLQRRVEPTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLIR 181

Query: 630 NGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSXXXXXXXX 809
           NGDWTFQ +VMLE  PQ G+VY+C VEH SL SP+TV+WRA+SESAQ KM+S        
Sbjct: 182 NGDWTFQILVMLEMTPQRGDVYTCHVEHASLQSPITVQWRAQSESAQSKMLSGIGGFVLG 241

Query: 810 XXXXXXXXXIYFKNQKGRPALQPTGLL 890
                    I  ++QKG     P GLL
Sbjct: 242 LIFLGLGLIIRHRSQKGSRGSPPAGLL 268


>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 =  256 bits (653), Expect = 4e-68
 Identities = 127/253 (50%), Positives = 161/253 (63%)
 Frame = +3

Query: 126 WMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILRFD 305
           WM AL V +  L   +   RD+P              NGTE+V+ + R  +N EE  RFD
Sbjct: 8   WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67

Query: 306 SDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTVTV 485
           S VG + A+TELG+P+A+ WNS+  ILE+ RA VD  CRHNY +   F V R+ +P VTV
Sbjct: 68  SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTV 127

Query: 486 YPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVML 665
           YP +T  +QHHNLL+CSVTGFYPG ++++WFRNGQEE  GV+STGLI NGDWTFQTMVML
Sbjct: 128 YPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVML 187

Query: 666 ETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSXXXXXXXXXXXXXXXXXIYF 845
           E  P+ G+VY+C V HPSL SPV+VEWRA+S  +  KM+S                 I  
Sbjct: 188 EMTPELGDVYTCLVNHPSLLSPVSVEWRAQSTYSWRKMLSGIAAFLLGLIFLLVGTVICL 247

Query: 846 KNQKGRPALQPTG 884
           + QKG    Q +G
Sbjct: 248 RAQKGYVETQFSG 260


>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 =  244 bits (623), Expect = 1e-64
 Identities = 115/207 (55%), Positives = 144/207 (69%)
 Frame = +3

Query: 126 WMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILRFD 305
           WM AL V +  L   +   RD+P              NGTE+V+ + R  +N EE  RFD
Sbjct: 8   WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67

Query: 306 SDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTVTV 485
           S VG + A+TELG+P+A+ WNS+  ILE+ RA VD  CRHNY +   F V R+ +P VTV
Sbjct: 68  SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTV 127

Query: 486 YPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVML 665
           YP +T  +QHHNLL+CSVTGFYPG ++++WFRNGQEE  GV+STGLI NGDWTFQTMVML
Sbjct: 128 YPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVML 187

Query: 666 ETVPQSGEVYSCRVEHPSLTSPVTVEW 746
           E  P+ G+VY+C V HPSL SPV+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 = 73.2 bits (178), Expect = 5e-13
 Identities = 42/130 (32%), Positives = 63/130 (48%), Gaps = 1/130 (0%)
 Frame = +3

Query: 360 DWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTVTVYPAKTQPLQHHNLLVCSV 539
           D+ ++++ L QR +     C  + +     L  R   PTV V  +     +   +L C V
Sbjct: 78  DYLNQQEYLHQRLSNGLQDCATHTQSFWGSLTHRTRPPTVQVAKSTPFNTKESVMLACYV 137

Query: 540 TGFYPGHVEVRWFRNGQEEAAGVVSTGLI-PNGDWTFQTMVMLETVPQSGEVYSCRVEHP 716
            GFYP  V + W +NGQ   +   +  +  PNGDWT+QT+  L T P   + Y+C VEH 
Sbjct: 138 WGFYPADVTISWRKNGQPVPSHSSALNMAQPNGDWTYQTVSHLATTPSYEDTYTCVVEHI 197

Query: 717 SLTSPVTVEW 746
               PV  +W
Sbjct: 198 GAPEPVCEDW 207


>ref|NP_001018646.1| MHC class Ib [Canis familiaris]
          Length = 381

 Score = 69.3 bits (168), Expect = 7e-12
 Identities = 47/178 (26%), Positives = 78/178 (43%), Gaps = 7/178 (3%)
 Frame = +3

Query: 252 VRLLDRHYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNS------RKDILEQRRAEVDT 413
           +R   RH Y+G + +    D+  +     + +   + W++      RK+ LE R  E   
Sbjct: 140 LRGYQRHAYDGLDYITLSEDLRSWIVEDPVAQITRRKWDAATVAENRKNFLEGRCLE--W 197

Query: 414 YCRHNYRISDTFLVPRRAEPTVTVYPAKTQPLQHHNL-LVCSVTGFYPGHVEVRWFRNGQ 590
             RH     +T    +RA+P  T      +P+  H + L C   GFYP  + + W R+G+
Sbjct: 198 LRRHLENGRETL---QRADPPKT--SVTRRPISEHEVTLKCWALGFYPAEITLTWQRDGE 252

Query: 591 EEAAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSES 764
           ++          P GD TFQ    +       + Y+C + H SLT P+T+ W    +S
Sbjct: 253 DQTQDTELVETRPGGDGTFQKWAAVVVPSGEEQRYTCHILHKSLTKPITLRWEPPPQS 310


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

 Score = 68.6 bits (166), Expect = 1e-11
 Identities = 44/158 (27%), Positives = 68/158 (43%), Gaps = 1/158 (0%)
 Frame = +3

Query: 276 YNGEEILRFDSDVGE-YRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFL 452
           ++G+EI   D +  E    + E GR  + +       +   +A +DT  + +    +T  
Sbjct: 51  FDGDEIFHVDMEKKETVWRLEEFGRFASFEAQGALANIAVDKANLDTMIKRSNHTPNT-- 108

Query: 453 VPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPN 632
                 P VTV       L   N+L+C +  F P  + V W RNG     GV  T  +P 
Sbjct: 109 ---NVPPEVTVLSNTPVELGEPNILICFIDKFSPPVINVTWLRNGNPVTTGVSETIFLPR 165

Query: 633 GDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 746
            D  F+    L  +P + +VY C+VEH  L  P+   W
Sbjct: 166 EDHLFRKFHYLPFLPSAEDVYDCKVEHWGLDEPLLKHW 203


>ref|XP_855624.1| PREDICTED: MHC class Ib [Canis familiaris]
          Length = 381

 Score = 67.0 bits (162), Expect = 4e-11
 Identities = 46/178 (25%), Positives = 77/178 (43%), Gaps = 7/178 (3%)
 Frame = +3

Query: 252 VRLLDRHYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNS------RKDILEQRRAEVDT 413
           +R   RH Y+G + +    D+  +     + +   + W++      RK+ LE R  E   
Sbjct: 140 LRGYQRHAYDGLDYITLSEDLRSWIVEDPVAQITRRKWDAATVAENRKNFLEGRCLE--W 197

Query: 414 YCRHNYRISDTFLVPRRAEPTVTVYPAKTQPLQHHNL-LVCSVTGFYPGHVEVRWFRNGQ 590
             RH     +T    +RA+P  T      +P+  H + L C   GFYP  + + W R+G+
Sbjct: 198 LRRHLENGRETL---QRADPPKT--SVTRRPISEHEVTLKCWALGFYPAEITLTWQRDGE 252

Query: 591 EEAAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSES 764
           ++          P GD TFQ    +       + Y+C + H SL  P+T+ W    +S
Sbjct: 253 DQTQDTELVETRPGGDGTFQKWAAVVVPSGEEQRYTCHILHKSLPKPITLRWEPPPQS 310


>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 = 67.0 bits (162), Expect = 4e-11
 Identities = 45/178 (25%), Positives = 87/178 (48%), Gaps = 8/178 (4%)
 Frame = +3

Query: 267 RHYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYC----RHNYR 434
           R+ Y+G   + F+ ++  +           K W + +  +++ +A ++  C    +    
Sbjct: 136 RYAYDGRNFIEFNKEIPAWVPQDPAALNTKKKWEAEEVYVQRAKAYLEEECPVMLQRYLE 195

Query: 435 ISDTFLVPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFR--NGQEEAAGV 608
              T+L  R+  P+V++    T   +    L C V+GFYP  +++ W +  + QE  +G 
Sbjct: 196 YGKTYL-DRQEPPSVSITSHGTP--EGIQTLKCWVSGFYPQEIDLHWIQADDTQETKSG- 251

Query: 609 VSTGLIPNGDWTFQTMVMLETVPQ--SGEVYSCRVEHPSLTSPVTVEWRARSESAQGK 776
               L+P+G+ T+Q  V++   PQ  +   YSC V+H SL+ P+TV W  R  + + +
Sbjct: 252 --GALLPSGNNTYQAWVVMSASPQDLASFSYSCLVKHSSLSQPLTVLWDKRQGAVRAE 307


>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 = 63.9 bits (154), Expect = 3e-10
 Identities = 31/92 (33%), Positives = 43/92 (46%)
 Frame = +3

Query: 471 PTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQ 650
           P V V P     L   N+L+C V   +P  + + W RNGQ  + GV  T      D  F+
Sbjct: 90  PRVAVLPKFRVELGQPNVLICIVDNIFPPVINITWLRNGQIISEGVAQTSFYSQPDHLFR 149

Query: 651 TMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 746
               L  VP + ++Y C+VEH  L  P+   W
Sbjct: 150 KFCYLTFVPSAEDMYDCKVEHWGLEEPLLRHW 181


  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: 54,980,123
Number of Sequences: 33732
Number of extensions: 1573472
Number of successful extensions: 5982
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 4957
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): 5960
length of database: 19,266,565
effective HSP length: 105
effective length of database: 15,724,705
effective search space used: 4748860910
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-005394
         (1225 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_002115.1| major histocompatibility complex, class II, DR ...   363   e-100
Alignment   gi|XP_945926.1| PREDICTED: similar to HLA class II histocompati...   356   3e-98
Alignment   gi|NP_072049.2| major histocompatibility complex, class II, DR ...   353   1e-97
Alignment   gi|NP_002116.2| major histocompatibility complex, class II, DR ...   353   2e-97
Alignment   gi|NP_068818.4| major histocompatibility complex, class II, DR ...   345   3e-95
Alignment   gi|XP_949915.1| PREDICTED: similar to HLA class II histocompati...   330   2e-90
Alignment   gi|XP_949921.1| PREDICTED: similar to HLA class II histocompati...   313   2e-85
Alignment   gi|NP_002114.2| major histocompatibility complex, class II, DQ ...   285   6e-77
Alignment   gi|NP_872355.1| major histocompatibility complex, class II, DQ ...   266   2e-71
Alignment   gi|NP_002112.3| major histocompatibility complex, class II, DP ...   259   3e-69

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

 Score =  363 bits (932), Expect = e-100
 Identities = 182/266 (68%), Positives = 204/266 (76%)
 Frame = +3

Query: 96  MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHY 275
           M+ L    G  M ALTV L+VLS PLALA DT P             NGTERVRLL+R  
Sbjct: 1   MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVRLLERCI 60

Query: 276 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLV 455
           YN EE +RFDSDVGEYRAVTELGRP+A+ WNS+KD+LEQRRA VDTYCRHNY + ++F V
Sbjct: 61  YNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTV 120

Query: 456 PRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 635
            RR EP VTVYP+KTQPLQHHNLLVCSV+GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 636 DWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSXXXXXXXXXX 815
           DWTFQT+VMLETVP+SGEVY+C+VEHPS+TSP+TVEWRARSESAQ KM+S          
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSESAQSKMLSGVGGFVLGLL 240

Query: 816 XXXXXXXIYFKNQKGRPALQPTGLLS 893
                  IYF+NQKG   LQPTG LS
Sbjct: 241 FLGAGLFIYFRNQKGHSGLQPTGFLS 266


>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 =  356 bits (913), Expect = 3e-98
 Identities = 180/266 (67%), Positives = 199/266 (74%)
 Frame = +3

Query: 96  MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHY 275
           M+ L    G  MAALTV L+VLS PLALA DT P             NGTERVR L R  
Sbjct: 1   MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60

Query: 276 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLV 455
           YN EE +RFDSDVGEYRAVTELGRP A+ WNS+KD LE+RRAEVDT CRHNY + ++F V
Sbjct: 61  YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120

Query: 456 PRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 635
            RR  P VTVYPAKTQPLQHHNLLVCSV+GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 636 DWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSXXXXXXXXXX 815
           DWTFQT+VMLETVP+SGEVY+C+VEHPS+ SP+TVEWRARSESAQ KM+S          
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEWRARSESAQSKMLSGVGGFVLGLL 240

Query: 816 XXXXXXXIYFKNQKGRPALQPTGLLS 893
                  IYF+NQKG   LQPTG LS
Sbjct: 241 FLGAGLFIYFRNQKGHSGLQPTGFLS 266


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

 Score =  353 bits (907), Expect = 1e-97
 Identities = 176/266 (66%), Positives = 199/266 (74%)
 Frame = +3

Query: 96  MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHY 275
           M+ L    G  +AALTV L+VLS  LA A DT P             NGTERVR LDR++
Sbjct: 1   MVCLKLPGGSSLAALTVTLMVLSSRLAFAGDTRPRFLELRKSECHFFNGTERVRYLDRYF 60

Query: 276 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLV 455
           +N EE LRFDSDVGEYRAVTELGRP A+ WNS+KD+LEQ+R  VD YCRHNY + ++F V
Sbjct: 61  HNQEEFLRFDSDVGEYRAVTELGRPVAESWNSQKDLLEQKRGRVDNYCRHNYGVGESFTV 120

Query: 456 PRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 635
            RR  P VTVYPAKTQPLQHHNLLVCSV+GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVHPQVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 636 DWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSXXXXXXXXXX 815
           DWTFQT+VMLETVP+SGEVY+C+VEHPS+TS +TVEWRARSESAQ KM+S          
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSALTVEWRARSESAQSKMLSGVGGFVLGLL 240

Query: 816 XXXXXXXIYFKNQKGRPALQPTGLLS 893
                  IYF+NQKG   LQPTG LS
Sbjct: 241 FLGAGLFIYFRNQKGHSGLQPTGFLS 266


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

 Score =  353 bits (906), Expect = 2e-97
 Identities = 178/266 (66%), Positives = 198/266 (74%)
 Frame = +3

Query: 96  MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHY 275
           M+ L    G +MA LTV L+VLS PLALA DT P             NGTERVR L R  
Sbjct: 1   MVCLKLPGGSYMAKLTVTLMVLSSPLALAGDTRPRFLQQDKYECHFFNGTERVRFLHRDI 60

Query: 276 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLV 455
           YN EE LRFDSDVGEYRAVTELGRP+A+ WNS+KD LE RRA VDTYCRHNY + ++F V
Sbjct: 61  YNQEEDLRFDSDVGEYRAVTELGRPDAEYWNSQKDFLEDRRAAVDTYCRHNYGVGESFTV 120

Query: 456 PRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 635
            RR EP VTVYPA+TQ LQHHNLLVCSV GFYPG +EVRWFRN QEE AGVVSTGLI NG
Sbjct: 121 QRRVEPKVTVYPARTQTLQHHNLLVCSVNGFYPGSIEVRWFRNSQEEKAGVVSTGLIQNG 180

Query: 636 DWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSXXXXXXXXXX 815
           DWTFQT+VMLETVP+SGEVY+C+VEHPS+TSP+TVEWRA+SESAQ KM+S          
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRAQSESAQSKMLSGVGGFVLGLL 240

Query: 816 XXXXXXXIYFKNQKGRPALQPTGLLS 893
                  IYFKNQKG   L PTGL+S
Sbjct: 241 FLGAGLFIYFKNQKGHSGLHPTGLVS 266


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

 Score =  345 bits (886), Expect = 3e-95
 Identities = 173/266 (65%), Positives = 200/266 (75%)
 Frame = +3

Query: 96  MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHY 275
           M+ L    G  MAALTV L VLS PLALA DT P             NGTERV  L R+ 
Sbjct: 1   MVCLKLPGGSCMAALTVTLTVLSSPLALAGDTQPRFLEQAKCECHFLNGTERVWNLIRYI 60

Query: 276 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLV 455
           YN EE  R++SD+GEY+AVTELGRP+A+ WNS+KD+LE+RRAEVDTYCR+NY + ++F V
Sbjct: 61  YNQEEYARYNSDLGEYQAVTELGRPDAEYWNSQKDLLERRRAEVDTYCRYNYGVVESFTV 120

Query: 456 PRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 635
            RR +P VTVYP+KTQPLQHHNLLVCSV GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVQPKVTVYPSKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 636 DWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSXXXXXXXXXX 815
           DWTFQT+VMLETVP+SGEVY+C+VEHPS+ SP+TV+W ARSESAQ KM+S          
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSMMSPLTVQWSARSESAQSKMLSGVGGFVLGLL 240

Query: 816 XXXXXXXIYFKNQKGRPALQPTGLLS 893
                  IYF+NQKG   LQPTGLLS
Sbjct: 241 FLGTGLFIYFRNQKGHSGLQPTGLLS 266


>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 =  330 bits (845), Expect = 2e-90
 Identities = 159/219 (72%), Positives = 176/219 (80%)
 Frame = +3

Query: 237 NGTERVRLLDRHYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTY 416
           NGTERVR L R  YN EE +RFDSDVGEYRAVTELGRP A+ WNS+KD LE+RRAEVDT 
Sbjct: 66  NGTERVRYLHRGIYNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTV 125

Query: 417 CRHNYRISDTFLVPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEE 596
           CRHNY + ++F V RR  P VTVYPAKTQPLQHHNLLVCSV+GFYPG +EVRWFRNGQEE
Sbjct: 126 CRHNYGVGESFTVQRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEE 185

Query: 597 AAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGK 776
            AGVVSTGLI NGDWTFQT+VMLETVP+SGEVY+C+VEHPS+ SP+TVEWRARSESAQ K
Sbjct: 186 KAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEWRARSESAQSK 245

Query: 777 MMSXXXXXXXXXXXXXXXXXIYFKNQKGRPALQPTGLLS 893
           M+S                 IYF+NQKG   LQPTG LS
Sbjct: 246 MLSGVGGFVLGLLFLGAGLFIYFRNQKGHSGLQPTGFLS 284


>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 =  313 bits (802), Expect = 2e-85
 Identities = 155/217 (71%), Positives = 172/217 (79%)
 Frame = +3

Query: 96  MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHY 275
           M+ L    G  MAALTV L+VLS PLALA DT P             NGTERVR L R  
Sbjct: 1   MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60

Query: 276 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLV 455
           YN EE +RFDSDVGEYRAVTELGRP A+ WNS+KD LE+RRAEVDT CRHNY + ++F V
Sbjct: 61  YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120

Query: 456 PRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 635
            RR  P VTVYPAKTQPLQHHNLLVCSV+GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 636 DWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 746
           DWTFQT+VMLETVP+SGEVY+C+VEHPS+ SP+TVEW
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEW 217


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

 Score =  285 bits (729), Expect = 6e-77
 Identities = 142/247 (57%), Positives = 172/247 (69%)
 Frame = +3

Query: 120 GFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILR 299
           G   A +T+ML +LS P+A  RD+P              NGTERVRL+ R  YN EEI+R
Sbjct: 12  GLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVR 71

Query: 300 FDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTV 479
           FDSDVGE+RAVT LG P A+ WNS+KDILE++RA VD  CRHNY++     + RR EPTV
Sbjct: 72  FDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTV 131

Query: 480 TVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMV 659
           T+ P++T+ L HHNLLVCSVT FYP  ++VRWFRN QEE AGVVST LI NGDWTFQ +V
Sbjct: 132 TISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILV 191

Query: 660 MLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSXXXXXXXXXXXXXXXXXI 839
           MLE  PQ G+VY+C VEHPSL SP+TVEWRA+SESAQ KM+S                 I
Sbjct: 192 MLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVLGLIFLGLGLII 251

Query: 840 YFKNQKG 860
           + ++QKG
Sbjct: 252 HHRSQKG 258


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

 Score =  266 bits (681), Expect = 2e-71
 Identities = 131/218 (60%), Positives = 155/218 (71%)
 Frame = +3

Query: 120 GFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILR 299
           GFW AA+TVMLV+LS P+A ARD P              NGTERVR + R+ YN EE  R
Sbjct: 12  GFWAAAVTVMLVMLSTPVAEARDFPKDFLVQFKGMCYFTNGTERVRGVARYIYNREEYGR 71

Query: 300 FDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTV 479
           FDSDVGE++AVTELGR   +DWN+ KD LEQ RA VD  CRHNY       + R+ EPTV
Sbjct: 72  FDSDVGEFQAVTELGR-SIEDWNNYKDFLEQERAAVDKVCRHNYEAELRTTLQRQVEPTV 130

Query: 480 TVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMV 659
           T+ P++T+ L HHNLLVCSVT FYP  ++V+WFRN QEE AGVVST LI NGDWTFQ +V
Sbjct: 131 TISPSRTEALNHHNLLVCSVTDFYPAQIKVQWFRNDQEETAGVVSTSLIRNGDWTFQILV 190

Query: 660 MLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQG 773
           MLE  PQ G++Y+C+VEHPSL SP+TVEWR R     G
Sbjct: 191 MLEITPQRGDIYTCQVEHPSLQSPITVEWRPRGPPPAG 228


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

 Score =  259 bits (662), Expect = 3e-69
 Identities = 127/217 (58%), Positives = 154/217 (70%)
 Frame = +3

Query: 135 ALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILRFDSDV 314
           ALT +L+VL   +   R TP              NGT+R   L+R+ YN EE  RFDSDV
Sbjct: 14  ALTALLMVLLTSVVQGRATPENYLFQGRQECYAFNGTQR--FLERYIYNREEFARFDSDV 71

Query: 315 GEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTVTVYPA 494
           GE+RAVTELGRP A+ WNS+KDILE++RA  D  CRHNY +     + RR +P V V P+
Sbjct: 72  GEFRAVTELGRPAAEYWNSQKDILEEKRAVPDRMCRHNYELGGPMTLQRRVQPRVNVSPS 131

Query: 495 KTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLETV 674
           K  PLQHHNLLVC VT FYPG ++VRWF NGQEE AGVVST LI NGDWTFQ +VMLE  
Sbjct: 132 KKGPLQHHNLLVCHVTDFYPGSIQVRWFLNGQEETAGVVSTNLIRNGDWTFQILVMLEMT 191

Query: 675 PQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMS 785
           PQ G+VY+C+VEH SL SPVTVEW+A+S+SA+ K ++
Sbjct: 192 PQQGDVYTCQVEHTSLDSPVTVEWKAQSDSARSKTLT 228


  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: 53,426,807
Number of Sequences: 39411
Number of extensions: 1581641
Number of successful extensions: 6649
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 5197
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): 6568
length of database: 17,774,539
effective HSP length: 104
effective length of database: 13,675,795
effective search space used: 4143765885
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-005394
         (1225 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_034512.1| histocompatibility 2, class II antigen E beta [...   353   2e-97
Alignment   gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/...   273   4e-73
Alignment   gi|NP_996988.1| histocompatibility 2, class II antigen A, beta ...   258   9e-69
Alignment   gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ...   244   1e-64
Alignment   gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ...    75   1e-13
Alignment   gi|NP_032235.1| histocompatibility-2 complex class 1-like [Mus ...    72   2e-12
Alignment   gi|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus ...    71   2e-12
Alignment   gi|NP_034508.2| histocompatibility 2, class II antigen A, alpha...    70   5e-12
Alignment   gi|NP_032232.1| histocompatibility 2, O region alpha locus [Mus...    68   2e-11
Alignment   gi|NP_034511.2| histocompatibility 2, class II antigen E alpha ...    64   2e-10

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

 Score =  353 bits (906), Expect = 2e-97
 Identities = 168/255 (65%), Positives = 201/255 (78%)
 Frame = +3

Query: 129 MAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILRFDS 308
           +AA+ ++L VLSPP+AL RD+ P             NGT+RVR L R++YN EE LRFDS
Sbjct: 10  VAAVILLLTVLSPPVALVRDSRPWFLEYCKSECHFYNGTQRVRFLKRYFYNLEENLRFDS 69

Query: 309 DVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPTVTVY 488
           DVGE+RAVTELGRP+A++WNS+ +IL+++RA VDTYCRHNY I D FLVPRR EPTVTVY
Sbjct: 70  DVGEFRAVTELGRPDAENWNSQPEILDEKRAAVDTYCRHNYEIFDNFLVPRRVEPTVTVY 129

Query: 489 PAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLE 668
           P KTQPL+HHNLLVCSV+ FYPG++EVRWFRNG+EE  G+VSTGL+ NGDWTFQT+VMLE
Sbjct: 130 PTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLE 189

Query: 669 TVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSXXXXXXXXXXXXXXXXXIYFK 848
           TVPQSGEVY+C+VEHPSLT PVTVEW+A+S SAQ KM+S                 IYF+
Sbjct: 190 TVPQSGEVYTCQVEHPSLTDPVTVEWKAQSTSAQNKMLSGVGGFVLGLLFLRAGLFIYFR 249

Query: 849 NQKGRPALQPTGLLS 893
           NQKG+  LQPTGLLS
Sbjct: 250 NQKGQSGLQPTGLLS 264


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

 Score =  273 bits (697), Expect = 4e-73
 Identities = 136/230 (59%), Positives = 168/230 (73%)
 Frame = +3

Query: 96  MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHY 275
           M+ L   RG  +AA+ + L++L+PP+ L RD  P             NG ERV  + R  
Sbjct: 1   MVSLWLPRGLCVAAVILSLMMLTPPVILVRDPRPRFLEQLKAECHYFNGKERVWSVTRFI 60

Query: 276 YNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLV 455
           YN EE  RF+SD G++ AVTELGRP  +  N++KD+L+  RA VD  CR+NY + D F++
Sbjct: 61  YNQEEFARFNSDFGKFLAVTELGRPIVEYLNTQKDMLDNYRASVDR-CRNNYDLVDIFML 119

Query: 456 PRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 635
             +AEP VTVYPAKTQPL+HHNLLVCSV  FYPG +EVRWFRNG+EE  GVVSTGLI N 
Sbjct: 120 NLKAEPKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNR 179

Query: 636 DWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMS 785
           DWT+QT+VMLE VP+ GEVY+C+VEHPSLTSPVTVEWRARS SAQ K++S
Sbjct: 180 DWTYQTLVMLEMVPRGGEVYTCQVEHPSLTSPVTVEWRARSTSAQNKLLS 229


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

 Score =  258 bits (659), Expect = 9e-69
 Identities = 133/255 (52%), Positives = 166/255 (65%), Gaps = 1/255 (0%)
 Frame = +3

Query: 129 MAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEILRFDS 308
           ++A  V+L+VLS P     D+               NGT+R+R + R+ YN EE +R+DS
Sbjct: 10  LSAAVVVLMVLSSPGTEGGDSERHFVYQFMGECYFTNGTQRIRYVTRYIYNREEYVRYDS 69

Query: 309 DVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAE-PTVTV 485
           DVGE+RAVTELGRP+A+ WNS+ +ILE+ RAE+DT CRHNY   +T    RR E P V +
Sbjct: 70  DVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSLRRLEQPNVVI 129

Query: 486 YPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVML 665
             ++T+ L HHN LVCSVT FYP  ++VRWFRNGQEE  GV ST LI NGDWTFQ +VML
Sbjct: 130 SLSRTEALNHHNTLVCSVTDFYPTQIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVML 189

Query: 666 ETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSXXXXXXXXXXXXXXXXXIYF 845
           E  P+ GEVY+C VEHPSL SP+TVEWRA+SESA  KM+S                 I  
Sbjct: 190 EMTPRRGEVYTCHVEHPSLKSPITVEWRAQSESAWSKMLSGIGGCVLGVIFLGLGLFIRH 249

Query: 846 KNQKGRPALQPTGLL 890
           ++QKG     P GLL
Sbjct: 250 RSQKGPRGPPPAGLL 264


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

 Score =  244 bits (623), Expect = 1e-64
 Identities = 123/254 (48%), Positives = 154/254 (60%)
 Frame = +3

Query: 117 RGFWMAALTVMLVVLSPPLALARDTPPXXXXXXXXXXXXXNGTERVRLLDRHYYNGEEIL 296
           R  W+ AL V L+ L   +   RD+P              NGTE+V LL R  +N EE L
Sbjct: 5   RAPWVVALLVNLMRLDSFMIEGRDSPENFVIQAKADCYFTNGTEKVHLLVRFIFNLEEYL 64

Query: 297 RFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDTFLVPRRAEPT 476
            FDSD+G + A+TELG P+A  WN R D+LE  RA V+  CR  Y++   F V R   P 
Sbjct: 65  HFDSDLGMFVALTELGEPDADQWNKRLDLLETSRAAVNMVCRQKYKLGAPFTVERNVPPE 124

Query: 477 VTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTM 656
           VTVYP +T  LQ HNLL+CSVTGFYPG + V+WFRNGQEE +GV+STGL+ NGDWTFQT 
Sbjct: 125 VTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVRNGDWTFQTT 184

Query: 657 VMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSXXXXXXXXXXXXXXXXX 836
           VMLE +P+ G++YSC VEHP L  PV+V W A+SE +  K++S                 
Sbjct: 185 VMLEMIPELGDIYSCLVEHPGLLRPVSVAWMAQSEYSWKKILSGAAVFLLGLIVFLVGVV 244

Query: 837 IYFKNQKGRPALQP 878
           I+ K QK     QP
Sbjct: 245 IHLKAQKASVETQP 258


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

 Score = 75.5 bits (184), Expect = 1e-13
 Identities = 49/166 (29%), Positives = 78/166 (46%), Gaps = 9/166 (5%)
 Frame = +3

Query: 276 YNGEEILRFDSDVG-----EYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRIS 440
           +N + +  +D DVG     E+  ++ L    +   N ++ ++ + +  +     H     
Sbjct: 46  FNKDLLACWDPDVGKIVPCEFGVLSRLAEIISNILNEQESLIHRLQNGLQDCATHTQPFW 105

Query: 441 DTFLVPRRAEPTVTVYPAKTQPLQHHN--LLVCSVTGFYPGHVEVRWFRNGQ--EEAAGV 608
           D  L  R   P+V V  A+T P       +L C V GFYP  V + W +NGQ     +  
Sbjct: 106 DV-LTHRTRAPSVRV--AQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNK 162

Query: 609 VSTGLIPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 746
             T   PNGDWT+QT+  L   P  G+VY+C V+H   + P+  +W
Sbjct: 163 EKTAQ-PNGDWTYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDW 207


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

 Score = 71.6 bits (174), Expect = 2e-12
 Identities = 44/154 (28%), Positives = 74/154 (48%), Gaps = 5/154 (3%)
 Frame = +3

Query: 267 RHYYNGEEILRFDSDVGEYRAVTELGRPEAKDWNSRKDILEQRRAEVDTYC-----RHNY 431
           ++ Y+G++ + F+ D   + A+  +     + W +    L+ ++  ++  C     R   
Sbjct: 129 QYAYDGQDFIIFNKDTLSWLAMDYVAHITKQAWEANLHELQYQKNWLEEECIAWLKRFLE 188

Query: 432 RISDTFLVPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVV 611
              DT  + R   P V     +T P        C   GFYP  + + W +NG+E A  V 
Sbjct: 189 YGRDT--LERTEHPVVRTTRKETFP--GITTFFCRAHGFYPPEISMTWMKNGEEIAQEVD 244

Query: 612 STGLIPNGDWTFQTMVMLETVPQSGEVYSCRVEH 713
             G++P+GD T+QT + +   PQS +VYSC VEH
Sbjct: 245 YGGVLPSGDGTYQTWLSVNLDPQSNDVYSCHVEH 278


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

 Score = 71.2 bits (173), Expect = 2e-12
 Identities = 52/166 (31%), Positives = 81/166 (48%), Gaps = 9/166 (5%)
 Frame = +3

Query: 276 YNGEEILRFDSDVGEYRAVTELG--RPEAKDWN---SRKDILEQRRAEVDTYCRHNYRIS 440
           +N + +  +D DVG+     E G   P A++++   ++++ L QR       C  + +  
Sbjct: 46  FNKDLLACWDPDVGKI-VPCEFGVLYPWAENFSRILNKEESLLQRLQNGLLDCASHTQPF 104

Query: 441 DTFLVPRRAEPTVTVYPAKTQPLQHHN--LLVCSVTGFYPGHVEVRWFRNGQ--EEAAGV 608
              L  R   P+V V  A+T P       +L C V GFYP  V + W +NGQ     +  
Sbjct: 105 WNALTHRTRAPSVRV--AQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNK 162

Query: 609 VSTGLIPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 746
             T   PNGDWT+QT+  L   P  G+VY+C V+H   + P+  +W
Sbjct: 163 EKTAQ-PNGDWTYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDW 207


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

 Score = 70.1 bits (170), Expect = 5e-12
 Identities = 31/92 (33%), Positives = 44/92 (47%)
 Frame = +3

Query: 471 PTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQ 650
           P  TV+P     L   N L+C V   +P  + + W RN +  A GV  T    N D++F 
Sbjct: 114 PQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFH 173

Query: 651 TMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 746
            +  L  +P   ++Y C+VEH  L  PV   W
Sbjct: 174 KLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHW 205


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

 Score = 67.8 bits (164), Expect = 2e-11
 Identities = 46/160 (28%), Positives = 67/160 (41%), Gaps = 1/160 (0%)
 Frame = +3

Query: 270 HYYNGEEILRFDSDVGEYR-AVTELGRPEAKDWNSRKDILEQRRAEVDTYCRHNYRISDT 446
           H ++GE+I   D    E    + E G     D+ S    +   +A +D     + R    
Sbjct: 50  HEFDGEQIFSVDLKNEEVVWRLPEFGDFAHSDFQSGLMSISMIKAHLDILVERSNRTRAV 109

Query: 447 FLVPRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLI 626
            + PR     VTV P     L   N+L+C V   +P  + V W RN Q    GV  T   
Sbjct: 110 SVPPR-----VTVLPKTRVELGKPNVLICIVDDIFPPVINVTWLRNSQPITKGVAQTSFY 164

Query: 627 PNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 746
              +  F+    L  VP + +VY C+VEH  L +P+   W
Sbjct: 165 SQPNHRFRKFHYLTFVPSAEDVYDCKVEHWGLDTPLLQHW 204


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

 Score = 64.3 bits (155), Expect = 2e-10
 Identities = 32/92 (34%), Positives = 43/92 (46%)
 Frame = +3

Query: 471 PTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQ 650
           P VTV       L   N+L+C +  F P  V V WFRNG+    GV  T  +P  D  F+
Sbjct: 112 PEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWFRNGRPVTEGVSETVFLPRDDHLFR 171

Query: 651 TMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 746
               L  +P + + Y C V+H  L  P+   W
Sbjct: 172 KFHYLTFLPSTDDFYDCEVDHWGLEEPLRKHW 203


  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: 62,670,381
Number of Sequences: 45328
Number of extensions: 1776607
Number of successful extensions: 6948
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 5704
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): 6891
length of database: 21,768,885
effective HSP length: 106
effective length of database: 16,964,117
effective search space used: 5106199217
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)