Animal-Genome cDNA 20060611C-005392


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-005392
         (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]                70   9e-14
Alignment   gi|NP_999362.2| neonatal Fc receptor FcRn [Sus scrofa]                60   7e-11
Alignment   gi|NP_999143.1| beta 2-microglobulin [Sus scrofa]                     60   7e-11
Alignment   gi|NP_998996.1| CD1 antigen [Sus scrofa]                              56   1e-09

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

 Score = 70.1 bits (170), Expect = 9e-14
 Identities = 42/162 (25%), Positives = 76/162 (46%), Gaps = 5/162 (3%)
 Frame = +1

Query: 244 YNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYC---RHNYRTSDT 414
           Y+G +++  + D+  + AV    +   + +  ++ + EQ RA ++  C    H Y  +  
Sbjct: 139 YDGADYIVLNEDLRSWTAVGMAAQITRRKWE-EETVAEQSRAYLEVACVQSLHRYLANGK 197

Query: 415 FLVPRRAEPR--VTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTG 588
             + R   P+  VT +P+    +     L C   GFYP  + + W + GQ+++  V    
Sbjct: 198 ETLQRSDPPKTHVTRHPSSDNKVT----LRCWALGFYPKEISLTWQQEGQDQSQDVEVVE 253

Query: 589 LIPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 714
             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 = 60.5 bits (145), Expect = 7e-11
 Identities = 45/168 (26%), Positives = 72/168 (42%), Gaps = 5/168 (2%)
 Frame = +1

Query: 247 NGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLVP 426
           NGEEF++FD+ +G +       R     +  + D + + +  +   C H        L  
Sbjct: 136 NGEEFMKFDTKLGTWDGEWPEARTIGSKWMQEPDAVNKEKTFLLYSCPHRLLGH---LER 192

Query: 427 RRA-----EPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGL 591
            R      EP      A+       ++L C    FYP  +++R+ RNG   AAG   + +
Sbjct: 193 GRGNLEWKEPPSMRMKARPGTAPGFSVLTCIAFSFYPPELQLRFLRNGL--AAGSGESDI 250

Query: 592 IPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESA 735
            PNGD +F     L         Y C V+H  L  P+TVE  + ++S+
Sbjct: 251 GPNGDGSFHAWSSLTVKSGDEHHYCCVVQHAGLAQPLTVELESPAKSS 298


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

 Score = 60.5 bits (145), Expect = 7e-11
 Identities = 32/92 (34%), Positives = 49/92 (53%)
 Frame = +1

Query: 439 PRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQ 618
           P+V VY          N L C V+GF+P  +E+   +NG++  A    + L  + DW+F 
Sbjct: 25  PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAE--QSDLSFSKDWSFY 82

Query: 619 TMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 714
            +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 = 1e-09
 Identities = 29/73 (39%), Positives = 39/73 (53%)
 Frame = +1

Query: 472 PLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLETVPQS 651
           P   H +LVC V+GFYP  + V W R+ QE+  G     ++PN D T+   V L+     
Sbjct: 215 PSPGHLMLVCHVSGFYPKPIWVMWMRDEQEQ-PGTQQGDILPNADGTWYLRVTLDVAAGE 273

Query: 652 GEVYSCRVEHPSL 690
               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: 1,151,540
Number of Sequences: 1040
Number of extensions: 31573
Number of successful extensions: 123
Number of sequences better than 1.0e-05: 4
Number of HSP's better than  0.0 without gapping: 102
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): 117
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 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-005392
         (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_001012698.2| major histocompatibility complex, class II, ...   402   e-112
Alignment   gi|XP_582099.2| PREDICTED: similar to major histocompatibility ...   332   3e-91
Alignment   gi|NP_001029840.2| MHC class II antigen [Bos taurus]                 295   3e-80
Alignment   gi|NP_001012694.1| major histocompatibility complex, class II, ...   284   8e-77
Alignment   gi|XP_876139.1| PREDICTED: similar to H-2 class II histocompati...   279   3e-75
Alignment   gi|NP_001012697.1| major histocompatibility complex, class II, ...   268   4e-72
Alignment   gi|NP_001013618.1| major histocompatibility complex, class II, ...   251   7e-67
Alignment   gi|XP_874766.1| PREDICTED: similar to HLA class II histocompati...   213   2e-55
Alignment   gi|NP_001029503.1| hypothetical protein LOC508800 [Bos taurus]        78   1e-14
Alignment   gi|NP_001012399.1| hemochromatosis [Bos taurus]                       74   2e-13

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

 Score =  402 bits (1032), Expect = e-112
 Identities = 194/266 (72%), Positives = 216/266 (81%)
 Frame = +1

Query: 64  MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQY 243
           M+ L FS G WMAAL VML+VL PPLA AR+  PHFL   K ECHFFNGTE+VR L+R +
Sbjct: 1   MVCLYFSGGSWMAALIVMLMVLCPPLAWAREIQPHFLEYYKGECHFFNGTERVRFLDRHF 60

Query: 244 YNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLV 423
           YNGEEFVRFDSD GE+RAVTELGRP A+++NSQKD LEQ+RAEVD  CRHNY   ++F V
Sbjct: 61  YNGEEFVRFDSDWGEFRAVTELGRPAAEHWNSQKDFLEQKRAEVDRVCRHNYGGVESFTV 120

Query: 424 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 603
            RR EP VTVYPAKTQPLQHHNLLVCSV GFYPGH+EVRWFRNG EE AGV+STGLI NG
Sbjct: 121 QRRVEPTVTVYPAKTQPLQHHNLLVCSVNGFYPGHIEVRWFRNGHEEEAGVISTGLIQNG 180

Query: 604 DWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXX 783
           DWTFQTMVMLETVPQSGEVY+C+V+HP  TSP+TVEWRARS+SAQ KMMSG+        
Sbjct: 181 DWTFQTMVMLETVPQSGEVYTCQVDHPKRTSPITVEWRARSDSAQSKMMSGVGGFVLGLL 240

Query: 784 XXXXXXXIYFKNQKGRPALQPTGLLS 861
                  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 =  332 bits (851), Expect = 3e-91
 Identities = 163/252 (64%), Positives = 191/252 (75%)
 Frame = +1

Query: 97  MAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQYYNGEEFVRFDS 276
           MAAL V+L+VLS P + AR+T PHF+   K EC F NG E++R   R  YN +E V FDS
Sbjct: 1   MAALAVLLMVLSLPFSWARETQPHFIHQFKGECRFSNGLERMRFFARYIYNTQEDVHFDS 60

Query: 277 DVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLVPRRAEPRVTVY 456
           DVGE+ A+TELGR DA+ +N QKD +EQ RA+VDT CR NY+   +FL  RR EP VTVY
Sbjct: 61  DVGEFTALTELGRLDAEYWNQQKDFMEQMRAKVDTLCRSNYQGIGSFLRQRRVEPTVTVY 120

Query: 457 PAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLE 636
           PAKTQPLQHHNLLVCSV GFYPGH+EVRWF N  EE AGV+STGLI NGDWTFQTMVMLE
Sbjct: 121 PAKTQPLQHHNLLVCSVNGFYPGHIEVRWFWNSHEEEAGVISTGLIQNGDWTFQTMVMLE 180

Query: 637 TVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFK 816
           TVPQSGEVY+C+VEHPS TSP+TVEWRA+S+SAQ K+MSGI               I+ +
Sbjct: 181 TVPQSGEVYTCQVEHPSRTSPLTVEWRAQSDSAQRKLMSGIGGFVLGLLFLGVGLFIHLR 240

Query: 817 NQKGRPALQPTG 852
           ++KG PALQP G
Sbjct: 241 SKKGHPALQPIG 252


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

 Score =  295 bits (756), Expect = 3e-80
 Identities = 147/257 (57%), Positives = 178/257 (69%)
 Frame = +1

Query: 58  SSMLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLER 237
           S M+ L   RG W A + V LV+LS P A  RD+P  F+   K  C+F NGTE+VR + R
Sbjct: 2   SGMVALWIPRGLWTAVVMVTLVMLSTPGAEGRDSPKDFVVQFKGLCYFTNGTERVRYVTR 61

Query: 238 QYYNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTF 417
             YN EE+VRFDSD   YRA+T LGRPDA+ +NSQKD LEQ RAE DT CRHNY+     
Sbjct: 62  YIYNQEEYVRFDSDWDLYRALTPLGRPDAEYWNSQKDFLEQTRAEADTVCRHNYQAELIT 121

Query: 418 LVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIP 597
            + RR EP VT+ P++T+ L HHNLLVCSVT FYP  ++VRWFRN +EE AGVVST LI 
Sbjct: 122 SLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPSQIKVRWFRNDREETAGVVSTPLIR 181

Query: 598 NGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXX 777
           NGDWTFQ +VMLE  PQ G+VY+C VEHPSL SP+ VEWRA+SESAQ KM+SG+      
Sbjct: 182 NGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPIMVEWRAQSESAQSKMLSGVGGFVLG 241

Query: 778 XXXXXXXXXIYFKNQKG 828
                    I+ ++QKG
Sbjct: 242 LIFLGLGLIIHHRSQKG 258


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

 Score =  284 bits (727), Expect = 8e-77
 Identities = 141/257 (54%), Positives = 179/257 (69%)
 Frame = +1

Query: 58  SSMLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLER 237
           S M+ L   RG W AA+ V L VLS P A  RD+P   +     +C+F NGTE+VR + R
Sbjct: 2   SGMVALRIPRGLWTAAVMVTLAVLSTPGAEGRDSPQDTVVHFMGQCYFTNGTERVRYVTR 61

Query: 238 QYYNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTF 417
             YN EE   +DSDVGEYRAVT+LGR  A+ +NSQKD+LEQ RAE+DT CRHNY+     
Sbjct: 62  YIYNQEETAYYDSDVGEYRAVTQLGRTLAEYWNSQKDILEQTRAELDTVCRHNYQLEVIT 121

Query: 418 LVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIP 597
            + R+ EP VT+  ++T+ L HHNLLVCSVT FYPG ++VRWF+NG+EE AG+VST LI 
Sbjct: 122 SLQRQVEPTVTISLSRTEALNHHNLLVCSVTDFYPGQIKVRWFQNGKEETAGIVSTPLIR 181

Query: 598 NGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXX 777
           NGDWTFQ +VMLE  P+ G+VY+C VEHPSL SP++VEWRA+SESAQ KM+SG+      
Sbjct: 182 NGDWTFQILVMLEMTPKRGDVYTCHVEHPSLQSPISVEWRAQSESAQSKMLSGVGGFVLG 241

Query: 778 XXXXXXXXXIYFKNQKG 828
                    +  ++QKG
Sbjct: 242 LIFLGLGLIVRRRSQKG 258


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

 Score =  279 bits (713), Expect = 3e-75
 Identities = 134/193 (69%), Positives = 151/193 (78%)
 Frame = +1

Query: 181 GKFECHFFNGTEQVRLLERQYYNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQ 360
           GK ECHF NGT+QVR L+R  YN EE V+FDS VGEYRA TE+GRP A+ +N     L++
Sbjct: 4   GKSECHFSNGTQQVRFLDRYIYNREEQVQFDSLVGEYRARTEMGRPAAERWNRWPQALQR 63

Query: 361 RRAEVDTYCRHNYRTSDTFLVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVR 540
            RA V  YC  NY    +  V RR +P VTVYP K++PL HHNLLVCSV GFYPGH+EVR
Sbjct: 64  ARAAVHAYCASNYEFFASRTVQRRVQPTVTVYPVKSRPLWHHNLLVCSVNGFYPGHIEVR 123

Query: 541 WFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRA 720
           WFRNGQEE AGVVSTGLIPNGDWTFQ MVMLE VPQ GEVY+C VEHPS TSPVTVEWRA
Sbjct: 124 WFRNGQEEEAGVVSTGLIPNGDWTFQIMVMLEIVPQGGEVYACHVEHPSRTSPVTVEWRA 183

Query: 721 RSESAQGKMMSGI 759
           + ES+Q KM+SGI
Sbjct: 184 QDESSQEKMLSGI 196


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

 Score =  268 bits (686), Expect = 4e-72
 Identities = 134/215 (62%), Positives = 159/215 (73%)
 Frame = +1

Query: 115 MLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQYYNGEEFVRFDSDVGEYR 294
           + +VL  P A  RD P +F++  K  C+F NGTE VRL+ RQ YN EE + FDSD+GE+ 
Sbjct: 19  VFLVLRIPEAHCRDAPKNFVYQFKGMCYFTNGTEHVRLVARQIYNKEEILHFDSDLGEFV 78

Query: 295 AVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLVPRRAEPRVTVYPAKTQP 474
           AVTELGR  A+ +N+QKDLL + RA VDT CRHNY+ +  F V RR EP VTV PA T+ 
Sbjct: 79  AVTELGRVCAEIWNTQKDLLAEFRAYVDTLCRHNYKETAGFTVQRRVEPTVTVSPASTEA 138

Query: 475 LQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLETVPQSG 654
           L HHNLLVCSVT FYP  V+V+WFRN QE+ AGV  T L  NGDWT+Q  VMLETVPQ G
Sbjct: 139 LNHHNLLVCSVTDFYPRQVKVKWFRNQQEQTAGVGFTPLTQNGDWTYQIHVMLETVPQLG 198

Query: 655 EVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGI 759
           +VY C V+HPSL SP+TVEWRA+SESAQ KM SGI
Sbjct: 199 DVYVCHVDHPSLQSPITVEWRAQSESAQSKMQSGI 233


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

 Score =  251 bits (641), Expect = 7e-67
 Identities = 120/246 (48%), Positives = 160/246 (65%)
 Frame = +1

Query: 94  WMAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQYYNGEEFVRFD 273
           W+       + L   +   RD+P  F+   K +C+F NGTE+VR + R  +N E++ RFD
Sbjct: 8   WVVTFLSTALRLDASVTQGRDSPEDFVTQAKADCYFTNGTEKVRFVVRFIFNLEDYARFD 67

Query: 274 SDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLVPRRAEPRVTV 453
           SD+G + A+TELG+PDA+ +N++ D+L + RA VD  CR NY     F V RR +P VTV
Sbjct: 68  SDLGMFVALTELGKPDAERWNNRPDILARSRASVDMLCRRNYYLGAPFTVGRRVQPEVTV 127

Query: 454 YPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVML 633
           YP KT  LQH NLL+C VTGFYPG ++V WFRNGQE+  G++STGLI NGDWTFQ  VML
Sbjct: 128 YPEKTPALQHRNLLLCLVTGFYPGDIKVTWFRNGQEQREGIMSTGLIRNGDWTFQMTVML 187

Query: 634 ETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYF 813
              P+ GEVY+C V+HPSL SPV+VEWRA+SE +  K++SG                ++ 
Sbjct: 188 AMTPELGEVYTCLVDHPSLLSPVSVEWRAQSEYSWRKILSGAAAFLVGLVFFLVEIVVHI 247

Query: 814 KNQKGR 831
           +  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 =  213 bits (543), Expect = 2e-55
 Identities = 127/272 (46%), Positives = 157/272 (57%), Gaps = 2/272 (0%)
 Frame = +1

Query: 46  PLLFSSMLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVR 225
           P LF+S + L FS+G WMAAL VM+  LSP L  AR+T                      
Sbjct: 7   PFLFASTVCLYFSKGSWMAALLVMMG-LSPLLTWARETQ--------------------- 44

Query: 226 LLERQYYNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRH--NY 399
                 Y    +V  DS +    A++  G+P A N   + D            C H    
Sbjct: 45  ------YKRTPWVVIDSQIS---AISH-GKPCALNGYRECD-----------GCFHPIGL 83

Query: 400 RTSDTFLVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVV 579
           + +    + ++ EP VTVYPAKTQPLQH++LLVCSV GFY GHVEVRWF  GQEE AGV+
Sbjct: 84  KANRDITLQKKVEPTVTVYPAKTQPLQHNHLLVCSVNGFYLGHVEVRWFWKGQEEEAGVI 143

Query: 580 STGLIPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGI 759
           STGLI NGDWTF+T+VMLETV QSGEVY+C++EHPS  SP+  EWRA+S+SAQ KMMSG 
Sbjct: 144 STGLIQNGDWTFETIVMLETVLQSGEVYTCQLEHPSWRSPIAEEWRAQSDSAQSKMMSGT 203

Query: 760 XXXXXXXXXXXXXXXIYFKNQKGRPALQPTGL 855
                           +F+NQKG   LQPTG+
Sbjct: 204 GGFALGLLFLVVGLFTHFRNQKGHSGLQPTGI 235


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

 Score = 77.8 bits (190), Expect = 1e-14
 Identities = 52/210 (24%), Positives = 94/210 (44%), Gaps = 3/210 (1%)
 Frame = +1

Query: 112 VMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQYYNGEEFVRFDSDVGEY 291
           + +  LS  +   +D      F G F C   N  E         Y+G++F++FD ++  +
Sbjct: 93  IFMETLSDIMDYYKDREGSHTFQGAFGCELRNN-ESSGAFWGYAYDGQDFIKFDKEIPAW 151

Query: 292 RAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCR---HNYRTSDTFLVPRRAEPRVTVYPA 462
             +    +   + + ++   +++ +A ++  C      Y       + R+  P V+V   
Sbjct: 152 VPLDPAAQNTKRKWEAEAVYVQRAKAYLEEECPGMLRRYLPYSRTHLDRQESPSVSV-TG 210

Query: 463 KTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLETV 642
              P  H   L C    FYP  + + W R G  + A      ++P+G+ T+Q+ V++   
Sbjct: 211 HAAP-GHKRTLKCLAYDFYPRSIGLHWTRAGDAQEAES-GGDVLPSGNGTYQSWVVVGVP 268

Query: 643 PQSGEVYSCRVEHPSLTSPVTVEWRARSES 732
           P+    YSC VEH SLT P+TV W  R ++
Sbjct: 269 PEDQAPYSCHVEHRSLTRPLTVPWDPRQQA 298


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

 Score = 73.9 bits (180), Expect = 2e-13
 Identities = 49/176 (27%), Positives = 81/176 (46%), Gaps = 4/176 (2%)
 Frame = +1

Query: 244 YNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRH---NYRTSDT 414
           Y+G++ + F  +  ++RA     +     +   K   +Q RA +D  C     +      
Sbjct: 148 YDGQDHLEFRPETLDWRAAEPRAQVTKLEWEVNKIRAKQNRAYLDRDCPEQLLHLLELGR 207

Query: 415 FLVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQE-EAAGVVSTGL 591
             + ++  P V V    T  L     L C    FYP ++ +RW ++ Q  +A  +    +
Sbjct: 208 GPLEQQVPPLVKVTHHVTSSL---TTLRCRALNFYPQNITIRWLKDKQFLDAKEIKPEDV 264

Query: 592 IPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGI 759
           +PNGD T+Q  V L  +P   + YSC+VEHP L  P+T  W     S  G +++GI
Sbjct: 265 LPNGDGTYQAWVALAMLPGEEQRYSCQVEHPGLDQPLTATW---EPSLSGTLVTGI 317


  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: 43,989,244
Number of Sequences: 33508
Number of extensions: 1288079
Number of successful extensions: 5252
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 4436
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): 5211
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 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-005392
         (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_001014768.1| MHC class II DLA DRB1 beta chain [Canis fami...   386   e-107
Alignment   gi|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Ca...   325   4e-89
Alignment   gi|XP_850395.1| PREDICTED: similar to HLA class II histocompati...   275   7e-74
Alignment   gi|XP_861384.1| PREDICTED: similar to HLA class II histocompati...   258   6e-69
Alignment   gi|XP_849737.1| PREDICTED: similar to HLA class II histocompati...    74   3e-13
Alignment   gi|XP_536867.2| PREDICTED: similar to Zinc-alpha-2-glycoprotein...    71   2e-12
Alignment   gi|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris]     69   1e-11
Alignment   gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati...    66   5e-11
Alignment   gi|NP_001014767.1| MHC class I DLA-88 [Canis familiaris]              66   7e-11
Alignment   gi|NP_001014401.1| MHC class I DLA-12 [Canis familiaris]              66   7e-11

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

 Score =  386 bits (991), Expect = e-107
 Identities = 186/266 (69%), Positives = 212/266 (79%)
 Frame = +1

Query: 64  MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQY 243
           M+ LCF  G WM AL ++L+VL+PP A ARDTPPHFL + K EC+F NGTE+VR +ER  
Sbjct: 1   MVCLCFLGGSWMTALMLILMVLNPPFAWARDTPPHFLEVAKSECYFTNGTERVRFVERYI 60

Query: 244 YNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLV 423
           +N EEFVRFDSDVGE+RAVTELGRP A+++N QK++LEQ RA VDTYCRHNY   ++F V
Sbjct: 61  HNREEFVRFDSDVGEFRAVTELGRPVAESWNGQKEILEQERATVDTYCRHNYGVIESFTV 120

Query: 424 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 603
            RR EP VTVYP KTQ LQHHNLLVCSV GFYPGH+EVRW RNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVEPTVTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNG 180

Query: 604 DWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXX 783
           DWTFQ +VMLE VPQSGEVY+C+VEHPSLTSPVTVEWRA+S+SAQ KM+SGI        
Sbjct: 181 DWTFQILVMLEIVPQSGEVYTCQVEHPSLTSPVTVEWRAQSDSAQSKMLSGIGGFVLGLL 240

Query: 784 XXXXXXXIYFKNQKGRPALQPTGLLS 861
                  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 =  325 bits (834), Expect = 4e-89
 Identities = 159/267 (59%), Positives = 194/267 (72%)
 Frame = +1

Query: 58  SSMLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLER 237
           S  + LC  RGFW AA+ ++LVVLS P+A  RD+P  F+F  K EC+F NGTE+VRLL +
Sbjct: 2   SGKMTLCIPRGFWTAAVMMILVVLSIPVAEGRDSPQDFVFQYKAECYFTNGTERVRLLTK 61

Query: 238 QYYNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTF 417
             YN EEFVRFDSDVGE+RAVTELGRPDA+ +N QKD +++ RAE+DT CRHNY   +  
Sbjct: 62  YIYNREEFVRFDSDVGEFRAVTELGRPDAEYWNRQKDEMDRVRAELDTVCRHNYGREELT 121

Query: 418 LVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIP 597
            + RR EP VT++P+KT+ L HHNLLVCSVT FYPG ++VRWFRN QE+ AGVVST LI 
Sbjct: 122 TLQRRVEPTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLIR 181

Query: 598 NGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXX 777
           NGDWTFQ +VMLE  PQ G+VY+C VEH SL SP+TV+WRA+SESAQ KM+SGI      
Sbjct: 182 NGDWTFQILVMLEMTPQRGDVYTCHVEHASLQSPITVQWRAQSESAQSKMLSGIGGFVLG 241

Query: 778 XXXXXXXXXIYFKNQKGRPALQPTGLL 858
                    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 =  275 bits (702), Expect = 7e-74
 Identities = 133/253 (52%), Positives = 170/253 (67%)
 Frame = +1

Query: 94  WMAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQYYNGEEFVRFD 273
           WM AL V +  L   +   RD+P  F+   K +C+F NGTE+V+ + R  +N EE+ RFD
Sbjct: 8   WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67

Query: 274 SDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLVPRRAEPRVTV 453
           S VG + A+TELG+PDA+ +NSQ  +LE+ RA VD  CRHNY     F V R+ +P VTV
Sbjct: 68  SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTV 127

Query: 454 YPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVML 633
           YP +T  +QHHNLL+CSVTGFYPG ++++WFRNGQEE  GV+STGLI NGDWTFQTMVML
Sbjct: 128 YPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVML 187

Query: 634 ETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYF 813
           E  P+ G+VY+C V HPSL SPV+VEWRA+S  +  KM+SGI               I  
Sbjct: 188 EMTPELGDVYTCLVNHPSLLSPVSVEWRAQSTYSWRKMLSGIAAFLLGLIFLLVGTVICL 247

Query: 814 KNQKGRPALQPTG 852
           + 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 =  258 bits (660), Expect = 6e-69
 Identities = 119/207 (57%), Positives = 151/207 (72%)
 Frame = +1

Query: 94  WMAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQYYNGEEFVRFD 273
           WM AL V +  L   +   RD+P  F+   K +C+F NGTE+V+ + R  +N EE+ RFD
Sbjct: 8   WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67

Query: 274 SDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLVPRRAEPRVTV 453
           S VG + A+TELG+PDA+ +NSQ  +LE+ RA VD  CRHNY     F V R+ +P VTV
Sbjct: 68  SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTV 127

Query: 454 YPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVML 633
           YP +T  +QHHNLL+CSVTGFYPG ++++WFRNGQEE  GV+STGLI NGDWTFQTMVML
Sbjct: 128 YPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVML 187

Query: 634 ETVPQSGEVYSCRVEHPSLTSPVTVEW 714
           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 = 73.6 bits (179), Expect = 3e-13
 Identities = 42/130 (32%), Positives = 63/130 (48%), Gaps = 1/130 (0%)
 Frame = +1

Query: 328 NYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLVPRRAEPRVTVYPAKTQPLQHHNLLVCSV 507
           +Y +Q++ L QR +     C  + ++    L  R   P V V  +     +   +L C V
Sbjct: 78  DYLNQQEYLHQRLSNGLQDCATHTQSFWGSLTHRTRPPTVQVAKSTPFNTKESVMLACYV 137

Query: 508 TGFYPGHVEVRWFRNGQEEAAGVVSTGLI-PNGDWTFQTMVMLETVPQSGEVYSCRVEHP 684
            GFYP  V + W +NGQ   +   +  +  PNGDWT+QT+  L T P   + Y+C VEH 
Sbjct: 138 WGFYPADVTISWRKNGQPVPSHSSALNMAQPNGDWTYQTVSHLATTPSYEDTYTCVVEHI 197

Query: 685 SLTSPVTVEW 714
               PV  +W
Sbjct: 198 GAPEPVCEDW 207


>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 = 71.2 bits (173), Expect = 2e-12
 Identities = 52/218 (23%), Positives = 97/218 (44%), Gaps = 7/218 (3%)
 Frame = +1

Query: 112 VMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQYYNGEEFVRFDSDVGEY 291
           + +V L   +   +D      F G F C   N         R  Y+G  F+ F+ ++  +
Sbjct: 96  IFMVTLKDIMEYYKDKEGSHTFQGMFGCELQNNKNSGAFW-RYAYDGRNFIEFNKEIPAW 154

Query: 292 RAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCR---HNYRTSDTFLVPRRAEPRVTVYPA 462
                      K + +++  +++ +A ++  C      Y       + R+  P V++   
Sbjct: 155 VPQDPAALNTKKKWEAEEVYVQRAKAYLEEECPVMLQRYLEYGKTYLDRQEPPSVSITSH 214

Query: 463 KTQPLQHHNLLVCSVTGFYPGHVEVRWFR--NGQEEAAGVVSTGLIPNGDWTFQTMVMLE 636
            T   +    L C V+GFYP  +++ W +  + QE  +G     L+P+G+ T+Q  V++ 
Sbjct: 215 GTP--EGIQTLKCWVSGFYPQEIDLHWIQADDTQETKSG---GALLPSGNNTYQAWVVMS 269

Query: 637 TVPQ--SGEVYSCRVEHPSLTSPVTVEWRARSESAQGK 744
             PQ  +   YSC V+H SL+ P+TV W  R  + + +
Sbjct: 270 ASPQDLASFSYSCLVKHSSLSQPLTVLWDKRQGAVRAE 307


>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 = 67/158 (42%), Gaps = 1/158 (0%)
 Frame = +1

Query: 244 YNGEEFVRFDSDVGE-YRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFL 420
           ++G+E    D +  E    + E GR  +         +   +A +DT  + +  T +T  
Sbjct: 51  FDGDEIFHVDMEKKETVWRLEEFGRFASFEAQGALANIAVDKANLDTMIKRSNHTPNT-- 108

Query: 421 VPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPN 600
                 P VTV       L   N+L+C +  F P  + V W RNG     GV  T  +P 
Sbjct: 109 ---NVPPEVTVLSNTPVELGEPNILICFIDKFSPPVINVTWLRNGNPVTTGVSETIFLPR 165

Query: 601 GDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 714
            D  F+    L  +P + +VY C+VEH  L  P+   W
Sbjct: 166 EDHLFRKFHYLPFLPSAEDVYDCKVEHWGLDEPLLKHW 203


>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 = 66.2 bits (160), Expect = 5e-11
 Identities = 32/92 (34%), Positives = 44/92 (47%)
 Frame = +1

Query: 439 PRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQ 618
           PRV V P     L   N+L+C V   +P  + + W RNGQ  + GV  T      D  F+
Sbjct: 90  PRVAVLPKFRVELGQPNVLICIVDNIFPPVINITWLRNGQIISEGVAQTSFYSQPDHLFR 149

Query: 619 TMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 714
               L  VP + ++Y C+VEH  L  P+   W
Sbjct: 150 KFCYLTFVPSAEDMYDCKVEHWGLEEPLLRHW 181


>ref|NP_001014767.1| MHC class I DLA-88 [Canis familiaris]
          Length = 361

 Score = 65.9 bits (159), Expect = 7e-11
 Identities = 47/184 (25%), Positives = 76/184 (41%), Gaps = 8/184 (4%)
 Frame = +1

Query: 187 FECHFFNGTEQVRLLERQYYNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRR 366
           + C    G   +R   +  Y+G +++  + D+  + A     +   + + +     E  R
Sbjct: 123 YGCDLGPGGRLLRGYSQDAYDGADYIALNEDLRSWTAADTAAQITRRKWEAA-GTAEHDR 181

Query: 367 AEVDTYC-----RHNYRTSDTFLVPRRAEP---RVTVYPAKTQPLQHHNLLVCSVTGFYP 522
             ++T C     R+     +T L   RAEP   RVT +P       H   L C   GFYP
Sbjct: 182 NYLETTCVEWLRRYLEMGKETLL---RAEPPSTRVTRHPIS----DHEVTLRCWALGFYP 234

Query: 523 GHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPV 702
             + + W R+G+++          P GD TFQ    +       + Y+C V+H  L  PV
Sbjct: 235 AEITLTWQRDGEDQTQDTEVVDTRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLAEPV 294

Query: 703 TVEW 714
           T  W
Sbjct: 295 TRRW 298


>ref|NP_001014401.1| MHC class I DLA-12 [Canis familiaris]
          Length = 358

 Score = 65.9 bits (159), Expect = 7e-11
 Identities = 49/188 (26%), Positives = 76/188 (40%), Gaps = 8/188 (4%)
 Frame = +1

Query: 175 FLGKFECHFFNGTEQVRLLERQYYNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLL 354
           F   F C    G   +R   +  Y+G +++  + D+  + A     +   +   +  D  
Sbjct: 116 FQWMFGCDLGPGGRLLRGYSQDAYDGADYIALNEDLRSWTAADAAAQITRRKREAAGDAG 175

Query: 355 EQRRAEVDTYC-----RHNYRTSDTFLVPRRAEP---RVTVYPAKTQPLQHHNLLVCSVT 510
             R   ++T C     R+     +T L   RAEP   RVT +P       H   L C   
Sbjct: 176 HLRNY-LETTCVEWLRRYLEMGKETLL---RAEPPSTRVTRHPVS----DHEVTLRCWAL 227

Query: 511 GFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSL 690
           GFYP  + + W R+G+++          P GD TFQ    +       + Y+C V+H  L
Sbjct: 228 GFYPAEITLTWQRDGEDQTQDTEVVDTRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGL 287

Query: 691 TSPVTVEW 714
             PVT  W
Sbjct: 288 VEPVTRRW 295


  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: 51,629,847
Number of Sequences: 33732
Number of extensions: 1501026
Number of successful extensions: 6050
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 4980
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): 6027
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 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-005392
         (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_002115.1| major histocompatibility complex, class II, DR ...   394   e-110
Alignment   gi|XP_945926.1| PREDICTED: similar to HLA class II histocompati...   382   e-106
Alignment   gi|NP_002116.2| major histocompatibility complex, class II, DR ...   379   e-105
Alignment   gi|NP_072049.2| major histocompatibility complex, class II, DR ...   376   e-104
Alignment   gi|NP_068818.4| major histocompatibility complex, class II, DR ...   369   e-102
Alignment   gi|XP_949915.1| PREDICTED: similar to HLA class II histocompati...   350   1e-96
Alignment   gi|XP_949921.1| PREDICTED: similar to HLA class II histocompati...   335   5e-92
Alignment   gi|NP_002114.2| major histocompatibility complex, class II, DQ ...   294   8e-80
Alignment   gi|NP_002112.3| major histocompatibility complex, class II, DP ...   282   4e-76
Alignment   gi|NP_872355.1| major histocompatibility complex, class II, DQ ...   271   7e-73

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

 Score =  394 bits (1012), Expect = e-110
 Identities = 195/266 (73%), Positives = 216/266 (81%)
 Frame = +1

Query: 64  MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQY 243
           M+ L    G  M ALTV L+VLS PLALA DT P FL+  KFECHFFNGTE+VRLLER  
Sbjct: 1   MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVRLLERCI 60

Query: 244 YNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLV 423
           YN EE VRFDSDVGEYRAVTELGRPDA+ +NSQKDLLEQRRA VDTYCRHNY   ++F V
Sbjct: 61  YNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTV 120

Query: 424 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 603
            RR EP+VTVYP+KTQPLQHHNLLVCSV+GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 604 DWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXX 783
           DWTFQT+VMLETVP+SGEVY+C+VEHPS+TSP+TVEWRARSESAQ KM+SG+        
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSESAQSKMLSGVGGFVLGLL 240

Query: 784 XXXXXXXIYFKNQKGRPALQPTGLLS 861
                  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 =  382 bits (980), Expect = e-106
 Identities = 190/266 (71%), Positives = 210/266 (78%)
 Frame = +1

Query: 64  MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQY 243
           M+ L    G  MAALTV L+VLS PLALA DT P FL   KFECHFFNGTE+VR L R  
Sbjct: 1   MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60

Query: 244 YNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLV 423
           YN EE VRFDSDVGEYRAVTELGRP A+++NSQKD LE+RRAEVDT CRHNY   ++F V
Sbjct: 61  YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120

Query: 424 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 603
            RR  P VTVYPAKTQPLQHHNLLVCSV+GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 604 DWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXX 783
           DWTFQT+VMLETVP+SGEVY+C+VEHPS+ SP+TVEWRARSESAQ KM+SG+        
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEWRARSESAQSKMLSGVGGFVLGLL 240

Query: 784 XXXXXXXIYFKNQKGRPALQPTGLLS 861
                  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 =  379 bits (972), Expect = e-105
 Identities = 186/266 (69%), Positives = 209/266 (78%)
 Frame = +1

Query: 64  MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQY 243
           M+ L    G +MA LTV L+VLS PLALA DT P FL   K+ECHFFNGTE+VR L R  
Sbjct: 1   MVCLKLPGGSYMAKLTVTLMVLSSPLALAGDTRPRFLQQDKYECHFFNGTERVRFLHRDI 60

Query: 244 YNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLV 423
           YN EE +RFDSDVGEYRAVTELGRPDA+ +NSQKD LE RRA VDTYCRHNY   ++F V
Sbjct: 61  YNQEEDLRFDSDVGEYRAVTELGRPDAEYWNSQKDFLEDRRAAVDTYCRHNYGVGESFTV 120

Query: 424 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 603
            RR EP+VTVYPA+TQ LQHHNLLVCSV GFYPG +EVRWFRN QEE AGVVSTGLI NG
Sbjct: 121 QRRVEPKVTVYPARTQTLQHHNLLVCSVNGFYPGSIEVRWFRNSQEEKAGVVSTGLIQNG 180

Query: 604 DWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXX 783
           DWTFQT+VMLETVP+SGEVY+C+VEHPS+TSP+TVEWRA+SESAQ KM+SG+        
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRAQSESAQSKMLSGVGGFVLGLL 240

Query: 784 XXXXXXXIYFKNQKGRPALQPTGLLS 861
                  IYFKNQKG   L PTGL+S
Sbjct: 241 FLGAGLFIYFKNQKGHSGLHPTGLVS 266


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

 Score =  376 bits (965), Expect = e-104
 Identities = 185/266 (69%), Positives = 211/266 (79%)
 Frame = +1

Query: 64  MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQY 243
           M+ L    G  +AALTV L+VLS  LA A DT P FL L K ECHFFNGTE+VR L+R +
Sbjct: 1   MVCLKLPGGSSLAALTVTLMVLSSRLAFAGDTRPRFLELRKSECHFFNGTERVRYLDRYF 60

Query: 244 YNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLV 423
           +N EEF+RFDSDVGEYRAVTELGRP A+++NSQKDLLEQ+R  VD YCRHNY   ++F V
Sbjct: 61  HNQEEFLRFDSDVGEYRAVTELGRPVAESWNSQKDLLEQKRGRVDNYCRHNYGVGESFTV 120

Query: 424 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 603
            RR  P+VTVYPAKTQPLQHHNLLVCSV+GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVHPQVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 604 DWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXX 783
           DWTFQT+VMLETVP+SGEVY+C+VEHPS+TS +TVEWRARSESAQ KM+SG+        
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSALTVEWRARSESAQSKMLSGVGGFVLGLL 240

Query: 784 XXXXXXXIYFKNQKGRPALQPTGLLS 861
                  IYF+NQKG   LQPTG LS
Sbjct: 241 FLGAGLFIYFRNQKGHSGLQPTGFLS 266


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

 Score =  369 bits (947), Expect = e-102
 Identities = 182/266 (68%), Positives = 209/266 (78%)
 Frame = +1

Query: 64  MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQY 243
           M+ L    G  MAALTV L VLS PLALA DT P FL   K ECHF NGTE+V  L R  
Sbjct: 1   MVCLKLPGGSCMAALTVTLTVLSSPLALAGDTQPRFLEQAKCECHFLNGTERVWNLIRYI 60

Query: 244 YNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLV 423
           YN EE+ R++SD+GEY+AVTELGRPDA+ +NSQKDLLE+RRAEVDTYCR+NY   ++F V
Sbjct: 61  YNQEEYARYNSDLGEYQAVTELGRPDAEYWNSQKDLLERRRAEVDTYCRYNYGVVESFTV 120

Query: 424 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 603
            RR +P+VTVYP+KTQPLQHHNLLVCSV GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVQPKVTVYPSKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 604 DWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXX 783
           DWTFQT+VMLETVP+SGEVY+C+VEHPS+ SP+TV+W ARSESAQ KM+SG+        
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSMMSPLTVQWSARSESAQSKMLSGVGGFVLGLL 240

Query: 784 XXXXXXXIYFKNQKGRPALQPTGLLS 861
                  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 =  350 bits (898), Expect = 1e-96
 Identities = 169/231 (73%), Positives = 187/231 (80%)
 Frame = +1

Query: 169 FLFLGKFECHFFNGTEQVRLLERQYYNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKD 348
           FL   KFECHFFNGTE+VR L R  YN EE VRFDSDVGEYRAVTELGRP A+++NSQKD
Sbjct: 54  FLKQDKFECHFFNGTERVRYLHRGIYNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKD 113

Query: 349 LLEQRRAEVDTYCRHNYRTSDTFLVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGH 528
            LE+RRAEVDT CRHNY   ++F V RR  P VTVYPAKTQPLQHHNLLVCSV+GFYPG 
Sbjct: 114 FLERRRAEVDTVCRHNYGVGESFTVQRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGS 173

Query: 529 VEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTV 708
           +EVRWFRNGQEE AGVVSTGLI NGDWTFQT+VMLETVP+SGEVY+C+VEHPS+ SP+TV
Sbjct: 174 IEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTV 233

Query: 709 EWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFKNQKGRPALQPTGLLS 861
           EWRARSESAQ KM+SG+               IYF+NQKG   LQPTG LS
Sbjct: 234 EWRARSESAQSKMLSGVGGFVLGLLFLGAGLFIYFRNQKGHSGLQPTGFLS 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 =  335 bits (858), Expect = 5e-92
 Identities = 164/217 (75%), Positives = 181/217 (83%)
 Frame = +1

Query: 64  MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQY 243
           M+ L    G  MAALTV L+VLS PLALA DT P FL   KFECHFFNGTE+VR L R  
Sbjct: 1   MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60

Query: 244 YNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLV 423
           YN EE VRFDSDVGEYRAVTELGRP A+++NSQKD LE+RRAEVDT CRHNY   ++F V
Sbjct: 61  YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTV 120

Query: 424 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 603
            RR  P VTVYPAKTQPLQHHNLLVCSV+GFYPG +EVRWFRNGQEE AGVVSTGLI NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 604 DWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 714
           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 =  294 bits (753), Expect = 8e-80
 Identities = 145/247 (58%), Positives = 178/247 (72%)
 Frame = +1

Query: 88  GFWMAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQYYNGEEFVR 267
           G   A +T+ML +LS P+A  RD+P  F++  K  C+F NGTE+VRL+ R  YN EE VR
Sbjct: 12  GLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVR 71

Query: 268 FDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLVPRRAEPRV 447
           FDSDVGE+RAVT LG P A+ +NSQKD+LE++RA VD  CRHNY+      + RR EP V
Sbjct: 72  FDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTV 131

Query: 448 TVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMV 627
           T+ P++T+ L HHNLLVCSVT FYP  ++VRWFRN QEE AGVVST LI NGDWTFQ +V
Sbjct: 132 TISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILV 191

Query: 628 MLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXI 807
           MLE  PQ G+VY+C VEHPSL SP+TVEWRA+SESAQ KM+SGI               I
Sbjct: 192 MLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVLGLIFLGLGLII 251

Query: 808 YFKNQKG 828
           + ++QKG
Sbjct: 252 HHRSQKG 258


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

 Score =  282 bits (721), Expect = 4e-76
 Identities = 136/218 (62%), Positives = 165/218 (75%)
 Frame = +1

Query: 103 ALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQYYNGEEFVRFDSDV 282
           ALT +L+VL   +   R TP ++LF G+ EC+ FNGT+  R LER  YN EEF RFDSDV
Sbjct: 14  ALTALLMVLLTSVVQGRATPENYLFQGRQECYAFNGTQ--RFLERYIYNREEFARFDSDV 71

Query: 283 GEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLVPRRAEPRVTVYPA 462
           GE+RAVTELGRP A+ +NSQKD+LE++RA  D  CRHNY       + RR +PRV V P+
Sbjct: 72  GEFRAVTELGRPAAEYWNSQKDILEEKRAVPDRMCRHNYELGGPMTLQRRVQPRVNVSPS 131

Query: 463 KTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLETV 642
           K  PLQHHNLLVC VT FYPG ++VRWF NGQEE AGVVST LI NGDWTFQ +VMLE  
Sbjct: 132 KKGPLQHHNLLVCHVTDFYPGSIQVRWFLNGQEETAGVVSTNLIRNGDWTFQILVMLEMT 191

Query: 643 PQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSG 756
           PQ G+VY+C+VEH SL SPVTVEW+A+S+SA+ K ++G
Sbjct: 192 PQQGDVYTCQVEHTSLDSPVTVEWKAQSDSARSKTLTG 229


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

 Score =  271 bits (693), Expect = 7e-73
 Identities = 132/218 (60%), Positives = 160/218 (73%)
 Frame = +1

Query: 88  GFWMAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQYYNGEEFVR 267
           GFW AA+TVMLV+LS P+A ARD P  FL   K  C+F NGTE+VR + R  YN EE+ R
Sbjct: 12  GFWAAAVTVMLVMLSTPVAEARDFPKDFLVQFKGMCYFTNGTERVRGVARYIYNREEYGR 71

Query: 268 FDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLVPRRAEPRV 447
           FDSDVGE++AVTELGR   +++N+ KD LEQ RA VD  CRHNY       + R+ EP V
Sbjct: 72  FDSDVGEFQAVTELGR-SIEDWNNYKDFLEQERAAVDKVCRHNYEAELRTTLQRQVEPTV 130

Query: 448 TVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMV 627
           T+ P++T+ L HHNLLVCSVT FYP  ++V+WFRN QEE AGVVST LI NGDWTFQ +V
Sbjct: 131 TISPSRTEALNHHNLLVCSVTDFYPAQIKVQWFRNDQEETAGVVSTSLIRNGDWTFQILV 190

Query: 628 MLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQG 741
           MLE  PQ G++Y+C+VEHPSL SP+TVEWR R     G
Sbjct: 191 MLEITPQRGDIYTCQVEHPSLQSPITVEWRPRGPPPAG 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: 50,170,276
Number of Sequences: 39411
Number of extensions: 1515545
Number of successful extensions: 6678
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 5212
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): 6586
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 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-005392
         (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_034512.1| histocompatibility 2, class II antigen E beta [...   370   e-102
Alignment   gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/...   298   5e-81
Alignment   gi|NP_996988.1| histocompatibility 2, class II antigen A, beta ...   279   4e-75
Alignment   gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ...   257   2e-68
Alignment   gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ...    77   4e-14
Alignment   gi|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus ...    73   6e-13
Alignment   gi|NP_034508.2| histocompatibility 2, class II antigen A, alpha...    71   2e-12
Alignment   gi|NP_032235.1| histocompatibility-2 complex class 1-like [Mus ...    70   4e-12
Alignment   gi|NP_038506.1| alpha-2-glycoprotein 1, zinc [Mus musculus]           67   4e-11
Alignment   gi|NP_032232.1| histocompatibility 2, O region alpha locus [Mus...    66   7e-11

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

 Score =  370 bits (950), Expect = e-102
 Identities = 173/255 (67%), Positives = 209/255 (81%)
 Frame = +1

Query: 97  MAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQYYNGEEFVRFDS 276
           +AA+ ++L VLSPP+AL RD+ P FL   K ECHF+NGT++VR L+R +YN EE +RFDS
Sbjct: 10  VAAVILLLTVLSPPVALVRDSRPWFLEYCKSECHFYNGTQRVRFLKRYFYNLEENLRFDS 69

Query: 277 DVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLVPRRAEPRVTVY 456
           DVGE+RAVTELGRPDA+N+NSQ ++L+++RA VDTYCRHNY   D FLVPRR EP VTVY
Sbjct: 70  DVGEFRAVTELGRPDAENWNSQPEILDEKRAAVDTYCRHNYEIFDNFLVPRRVEPTVTVY 129

Query: 457 PAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLE 636
           P KTQPL+HHNLLVCSV+ FYPG++EVRWFRNG+EE  G+VSTGL+ NGDWTFQT+VMLE
Sbjct: 130 PTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLE 189

Query: 637 TVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYFK 816
           TVPQSGEVY+C+VEHPSLT PVTVEW+A+S SAQ KM+SG+               IYF+
Sbjct: 190 TVPQSGEVYTCQVEHPSLTDPVTVEWKAQSTSAQNKMLSGVGGFVLGLLFLRAGLFIYFR 249

Query: 817 NQKGRPALQPTGLLS 861
           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 =  298 bits (764), Expect = 5e-81
 Identities = 147/252 (58%), Positives = 182/252 (72%)
 Frame = +1

Query: 64  MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQY 243
           M+ L   RG  +AA+ + L++L+PP+ L RD  P FL   K ECH+FNG E+V  + R  
Sbjct: 1   MVSLWLPRGLCVAAVILSLMMLTPPVILVRDPRPRFLEQLKAECHYFNGKERVWSVTRFI 60

Query: 244 YNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLV 423
           YN EEF RF+SD G++ AVTELGRP  +  N+QKD+L+  RA VD  CR+NY   D F++
Sbjct: 61  YNQEEFARFNSDFGKFLAVTELGRPIVEYLNTQKDMLDNYRASVDR-CRNNYDLVDIFML 119

Query: 424 PRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 603
             +AEP+VTVYPAKTQPL+HHNLLVCSV  FYPG +EVRWFRNG+EE  GVVSTGLI N 
Sbjct: 120 NLKAEPKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNR 179

Query: 604 DWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXX 783
           DWT+QT+VMLE VP+ GEVY+C+VEHPSLTSPVTVEWRARS SAQ K++SG+        
Sbjct: 180 DWTYQTLVMLEMVPRGGEVYTCQVEHPSLTSPVTVEWRARSTSAQNKLLSGVMGMALGLF 239

Query: 784 XXXXXXXIYFKN 819
                   Y +N
Sbjct: 240 ILAVGLFFYLRN 251


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

 Score =  279 bits (713), Expect = 4e-75
 Identities = 140/255 (54%), Positives = 176/255 (69%), Gaps = 1/255 (0%)
 Frame = +1

Query: 97  MAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQYYNGEEFVRFDS 276
           ++A  V+L+VLS P     D+  HF++    EC+F NGT+++R + R  YN EE+VR+DS
Sbjct: 10  LSAAVVVLMVLSSPGTEGGDSERHFVYQFMGECYFTNGTQRIRYVTRYIYNREEYVRYDS 69

Query: 277 DVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLVPRRAE-PRVTV 453
           DVGE+RAVTELGRPDA+ +NSQ ++LE+ RAE+DT CRHNY   +T    RR E P V +
Sbjct: 70  DVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSLRRLEQPNVVI 129

Query: 454 YPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVML 633
             ++T+ L HHN LVCSVT FYP  ++VRWFRNGQEE  GV ST LI NGDWTFQ +VML
Sbjct: 130 SLSRTEALNHHNTLVCSVTDFYPTQIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVML 189

Query: 634 ETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXXIYF 813
           E  P+ GEVY+C VEHPSL SP+TVEWRA+SESA  KM+SGI               I  
Sbjct: 190 EMTPRRGEVYTCHVEHPSLKSPITVEWRAQSESAWSKMLSGIGGCVLGVIFLGLGLFIRH 249

Query: 814 KNQKGRPALQPTGLL 858
           ++QKG     P GLL
Sbjct: 250 RSQKGPRGPPPAGLL 264


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

 Score =  257 bits (656), Expect = 2e-68
 Identities = 127/254 (50%), Positives = 163/254 (64%)
 Frame = +1

Query: 85  RGFWMAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQYYNGEEFV 264
           R  W+ AL V L+ L   +   RD+P +F+   K +C+F NGTE+V LL R  +N EE++
Sbjct: 5   RAPWVVALLVNLMRLDSFMIEGRDSPENFVIQAKADCYFTNGTEKVHLLVRFIFNLEEYL 64

Query: 265 RFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSDTFLVPRRAEPR 444
            FDSD+G + A+TELG PDA  +N + DLLE  RA V+  CR  Y+    F V R   P 
Sbjct: 65  HFDSDLGMFVALTELGEPDADQWNKRLDLLETSRAAVNMVCRQKYKLGAPFTVERNVPPE 124

Query: 445 VTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTM 624
           VTVYP +T  LQ HNLL+CSVTGFYPG + V+WFRNGQEE +GV+STGL+ NGDWTFQT 
Sbjct: 125 VTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVRNGDWTFQTT 184

Query: 625 VMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMSGIXXXXXXXXXXXXXXX 804
           VMLE +P+ G++YSC VEHP L  PV+V W A+SE +  K++SG                
Sbjct: 185 VMLEMIPELGDIYSCLVEHPGLLRPVSVAWMAQSEYSWKKILSGAAVFLLGLIVFLVGVV 244

Query: 805 IYFKNQKGRPALQP 846
           I+ K QK     QP
Sbjct: 245 IHLKAQKASVETQP 258


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

 Score = 76.6 bits (187), Expect = 4e-14
 Identities = 67/225 (29%), Positives = 98/225 (43%), Gaps = 19/225 (8%)
 Frame = +1

Query: 97  MAALTVMLVVLSPPLALARDTPPHFLFLGKFECHFFN-------GTEQVRLLERQY---Y 246
           MAAL ++L+VLS           H +  G F  H  +       GT Q    +  Y   +
Sbjct: 1   MAALWLLLLVLSL----------HCMGAGGFVAHVESTCVLNDAGTPQ----DFTYCVSF 46

Query: 247 NGEEFVRFDSDVG-----EYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRHNYRTSD 411
           N +    +D DVG     E+  ++ L    +   N Q+ L+ + +  +     H     D
Sbjct: 47  NKDLLACWDPDVGKIVPCEFGVLSRLAEIISNILNEQESLIHRLQNGLQDCATHTQPFWD 106

Query: 412 TFLVPRRAEPRVTVYPAKTQPLQHHN--LLVCSVTGFYPGHVEVRWFRNGQ--EEAAGVV 579
             L  R   P V V  A+T P       +L C V GFYP  V + W +NGQ     +   
Sbjct: 107 V-LTHRTRAPSVRV--AQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKE 163

Query: 580 STGLIPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 714
            T   PNGDWT+QT+  L   P  G+VY+C V+H   + P+  +W
Sbjct: 164 KTAQ-PNGDWTYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDW 207


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

 Score = 72.8 bits (177), Expect = 6e-13
 Identities = 53/166 (31%), Positives = 79/166 (47%), Gaps = 9/166 (5%)
 Frame = +1

Query: 244 YNGEEFVRFDSDVGEYRAVTELG--RPDAKNYN---SQKDLLEQRRAEVDTYCRHNYRTS 408
           +N +    +D DVG+     E G   P A+N++   ++++ L QR       C  + +  
Sbjct: 46  FNKDLLACWDPDVGKI-VPCEFGVLYPWAENFSRILNKEESLLQRLQNGLLDCASHTQPF 104

Query: 409 DTFLVPRRAEPRVTVYPAKTQPLQHHN--LLVCSVTGFYPGHVEVRWFRNGQ--EEAAGV 576
              L  R   P V V  A+T P       +L C V GFYP  V + W +NGQ     +  
Sbjct: 105 WNALTHRTRAPSVRV--AQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNK 162

Query: 577 VSTGLIPNGDWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 714
             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 = 70.9 bits (172), Expect = 2e-12
 Identities = 31/92 (33%), Positives = 45/92 (48%)
 Frame = +1

Query: 439 PRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQ 618
           P+ TV+P     L   N L+C V   +P  + + W RN +  A GV  T    N D++F 
Sbjct: 114 PQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFH 173

Query: 619 TMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 714
            +  L  +P   ++Y C+VEH  L  PV   W
Sbjct: 174 KLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHW 205


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

 Score = 70.1 bits (170), Expect = 4e-12
 Identities = 44/151 (29%), Positives = 73/151 (48%), Gaps = 5/151 (3%)
 Frame = +1

Query: 244 YNGEEFVRFDSDVGEYRAVTELGRPDAKNYNSQKDLLEQRRAEVDTYC-----RHNYRTS 408
           Y+G++F+ F+ D   + A+  +     + + +    L+ ++  ++  C     R      
Sbjct: 132 YDGQDFIIFNKDTLSWLAMDYVAHITKQAWEANLHELQYQKNWLEEECIAWLKRFLEYGR 191

Query: 409 DTFLVPRRAEPRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTG 588
           DT  + R   P V     +T P        C   GFYP  + + W +NG+E A  V   G
Sbjct: 192 DT--LERTEHPVVRTTRKETFP--GITTFFCRAHGFYPPEISMTWMKNGEEIAQEVDYGG 247

Query: 589 LIPNGDWTFQTMVMLETVPQSGEVYSCRVEH 681
           ++P+GD T+QT + +   PQS +VYSC VEH
Sbjct: 248 VLPSGDGTYQTWLSVNLDPQSNDVYSCHVEH 278


>ref|NP_038506.1| alpha-2-glycoprotein 1, zinc [Mus musculus]
          Length = 307

 Score = 66.6 bits (161), Expect = 4e-11
 Identities = 44/207 (21%), Positives = 87/207 (42%), Gaps = 6/207 (2%)
 Frame = +1

Query: 112 VMLVVLSPPLALARDTPPHFLFLGKFECHFFNGTEQVRLLERQYYNGEEFVRFDSDVGEY 291
           + LV L   +   +DT     F G F C   N      +  R  Y+GE+F+ F+ ++  +
Sbjct: 91  IFLVTLKDIMDYYKDTTGSHTFQGMFGCEITNNRSSGAVW-RYAYDGEDFIEFNKEIPAW 149

Query: 292 RAVTELGRPDAKNYNSQKDLLEQRRAEVDTYCRH------NYRTSDTFLVPRRAEPRVTV 453
             +          + ++K  +++ +A ++  C        NY  S       R +P    
Sbjct: 150 IPLDPAAANTKLKWEAEKVYVQRAKAYLEEECPEMLKRYLNYSRSHL----DRIDPPTVT 205

Query: 454 YPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVML 633
             ++  P   + +  C   GFYP  + + W     ++ A     G+ PNG+ T+ +   +
Sbjct: 206 ITSRVIP-GGNRIFKCLAYGFYPQRISLHW-NKANKKLAFEPERGVFPNGNGTYLSWAEV 263

Query: 634 ETVPQSGEVYSCRVEHPSLTSPVTVEW 714
           E  PQ  + + C ++H   +  ++V+W
Sbjct: 264 EVSPQDIDPFFCLIDHRGFSQSLSVQW 290


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

 Score = 65.9 bits (159), Expect = 7e-11
 Identities = 33/92 (35%), Positives = 44/92 (47%)
 Frame = +1

Query: 439 PRVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQ 618
           PRVTV P     L   N+L+C V   +P  + V W RN Q    GV  T      +  F+
Sbjct: 113 PRVTVLPKTRVELGKPNVLICIVDDIFPPVINVTWLRNSQPITKGVAQTSFYSQPNHRFR 172

Query: 619 TMVMLETVPQSGEVYSCRVEHPSLTSPVTVEW 714
               L  VP + +VY C+VEH  L +P+   W
Sbjct: 173 KFHYLTFVPSAEDVYDCKVEHWGLDTPLLQHW 204


  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: 58,936,844
Number of Sequences: 45328
Number of extensions: 1708497
Number of successful extensions: 7270
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 5787
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): 7216
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)