Animal-Genome cDNA 20060611S-055404


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= 20060611S-055404
         (783 letters)

Database: RefSeqSP 
           1040 sequences; 434,620 total letters

Searching...done

 ***** No hits found ******

  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: 779,409
Number of Sequences: 1040
Number of extensions: 20215
Number of successful extensions: 70
Number of sequences better than 1.0e-05: 0
Number of HSP's better than  0.0 without gapping: 61
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): 70
length of database: 434,620
effective HSP length: 75
effective length of database: 356,620
effective search space used: 65974700
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqBP

BLASTX 2.2.10 [Oct-19-2004]


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

Query= 20060611S-055404
         (783 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001029840.2| MHC class II antigen [Bos taurus]                 147   7e-36
Alignment   gi|NP_001012694.1| major histocompatibility complex, class II, ...   136   2e-32
Alignment   gi|NP_001012698.2| major histocompatibility complex, class II, ...   100   1e-21
Alignment   gi|NP_001013618.1| major histocompatibility complex, class II, ...    74   1e-16
Alignment   gi|NP_001012697.1| major histocompatibility complex, class II, ...    84   1e-16
Alignment   gi|XP_582099.2| PREDICTED: similar to major histocompatibility ...    79   5e-15
Alignment   gi|XP_876139.1| PREDICTED: similar to H-2 class II histocompati...    54   1e-10

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

 Score =  147 bits (372), Expect = 7e-36
 Identities = 105/255 (41%), Positives = 136/255 (53%), Gaps = 12/255 (4%)
 Frame = +1

Query: 55  LSGMEGLLLP*GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAV 234
           +SGM  L +P GLWTA + V LV L  P +EGR SP D   QF   C+F N  + VR  V
Sbjct: 1   MSGMVALWIPRGLWTAVVMVTLVMLSTPGAEGRDSPKDFVVQFKGLCYFTNGTERVRY-V 59

Query: 235 TDSSTCLDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEE 414
           T      +++VR       +RA+TPLGRPDA Y + Q DFLE T AE D VC+H YQ E 
Sbjct: 60  TRYIYNQEEYVRFDSDWDLYRALTPLGRPDAEYWNSQKDFLEQTRAEADTVCRHNYQAEL 119

Query: 415 RTTLPRAVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSR------IGLL*Y-- 570
            T+L R V P VT+S S  +AL HH+L VC+ TDF P+ + V+  R       G++    
Sbjct: 120 ITSLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPSQIKVRWFRNDREETAGVVSTPL 179

Query: 571 ----SWRCDLSSYSELRLYLGRARDA*HDSPPVRCLHVPRAALCLQIPILLYCRAQSDSA 738
                W   +    E+    G           V   HV   +  LQ PI++  RAQS+SA
Sbjct: 180 IRNGDWTFQILVMLEMTPQRG----------DVYTCHVEHPS--LQSPIMVEWRAQSESA 227

Query: 739 LSIILSAVWGFLLVL 783
            S +LS V GF+L L
Sbjct: 228 QSKMLSGVGGFVLGL 242


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

 Score =  136 bits (343), Expect = 2e-32
 Identities = 100/255 (39%), Positives = 129/255 (50%), Gaps = 12/255 (4%)
 Frame = +1

Query: 55  LSGMEGLLLP*GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAV 234
           +SGM  L +P GLWTAA+ V L  L  P +EGR SP D    F  +C+F N  + VR  V
Sbjct: 1   MSGMVALRIPRGLWTAAVMVTLAVLSTPGAEGRDSPQDTVVHFMGQCYFTNGTERVRY-V 59

Query: 235 TDSSTCLDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEE 414
           T      ++         E+RAVT LGR  A Y + Q D LE T AELD VC+H YQ+E 
Sbjct: 60  TRYIYNQEETAYYDSDVGEYRAVTQLGRTLAEYWNSQKDILEQTRAELDTVCRHNYQLEV 119

Query: 415 RTTLPRAVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG------------ 558
            T+L R V P VT+S S  +AL HH+L VC+ TDF P  + V+  + G            
Sbjct: 120 ITSLQRQVEPTVTISLSRTEALNHHNLLVCSVTDFYPGQIKVRWFQNGKEETAGIVSTPL 179

Query: 559 LL*YSWRCDLSSYSELRLYLGRARDA*HDSPPVRCLHVPRAALCLQIPILLYCRAQSDSA 738
           +    W   +    E+    G           V   HV   +  LQ PI +  RAQS+SA
Sbjct: 180 IRNGDWTFQILVMLEMTPKRG----------DVYTCHVEHPS--LQSPISVEWRAQSESA 227

Query: 739 LSIILSAVWGFLLVL 783
            S +LS V GF+L L
Sbjct: 228 QSKMLSGVGGFVLGL 242


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

 Score =  100 bits (250), Expect = 1e-21
 Identities = 90/252 (35%), Positives = 111/252 (44%), Gaps = 20/252 (7%)
 Frame = +1

Query: 88  GLWTAALCVMLVALGAPMSEGR-YSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTCLDDH 264
           G W AAL VML+ L  P++  R   P  + Y  G ECHFFN  + VR         LD H
Sbjct: 9   GSWMAALIVMLMVLCPPLAWAREIQPHFLEYYKG-ECHFFNGTERVRF--------LDRH 59

Query: 265 -------VRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTT 423
                  VR      EFRAVT LGRP A + + Q DFLE   AE+D VC+H Y   E  T
Sbjct: 60  FYNGEEFVRFDSDWGEFRAVTELGRPAAEHWNSQKDFLEQKRAEVDRVCRHNYGGVESFT 119

Query: 424 LPRAVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG------------LL* 567
           + R V P VTV  +  Q L HH+L VC+   F P  + V+  R G            +  
Sbjct: 120 VQRRVEPTVTVYPAKTQPLQHHNLLVCSVNGFYPGHIEVRWFRNGHEEEAGVISTGLIQN 179

Query: 568 YSWRCDLSSYSELRLYLGRARDA*HDSPPVRCLHVPRAALCLQIPILLYCRAQSDSALSI 747
             W        E     G       D P                PI +  RA+SDSA S 
Sbjct: 180 GDWTFQTMVMLETVPQSGEVYTCQVDHPK------------RTSPITVEWRARSDSAQSK 227

Query: 748 ILSAVWGFLLVL 783
           ++S V GF+L L
Sbjct: 228 MMSGVGGFVLGL 239


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

 Score = 74.3 bits (181), Expect(2) = 1e-16
 Identities = 50/155 (32%), Positives = 72/155 (46%)
 Frame = +1

Query: 94  WTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTCLDDHVRC 273
           W        + L A +++GR SP D   Q   +C+F N  + VR  V      L+D+ R 
Sbjct: 8   WVVTFLSTALRLDASVTQGRDSPEDFVTQAKADCYFTNGTEKVRFVVRFIFN-LEDYARF 66

Query: 274 SRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPRAVLPHVT 453
                 F A+T LG+PDA   + + D L  + A +D +C+  Y +    T+ R V P VT
Sbjct: 67  DSDLGMFVALTELGKPDAERWNNRPDILARSRASVDMLCRRNYYLGAPFTVGRRVQPEVT 126

Query: 454 VSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG 558
           V      AL H +L +C  T F P  + V   R G
Sbjct: 127 VYPEKTPALQHRNLLLCLVTGFYPGDIKVTWFRNG 161



 Score = 30.0 bits (66), Expect(2) = 1e-16
 Identities = 18/43 (41%), Positives = 24/43 (55%)
 Frame = +2

Query: 575 GGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRSP 703
           G +++ L  N D T  + VM  M   L +VYTCLV H +  SP
Sbjct: 167 GIMSTGLIRNGDWTFQMTVMLAMTPELGEVYTCLVDHPSLLSP 209


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

 Score = 84.0 bits (206), Expect = 1e-16
 Identities = 80/243 (32%), Positives = 109/243 (44%), Gaps = 14/243 (5%)
 Frame = +1

Query: 97  TAALCVMLV--ALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTCLDDHVR 270
           T A  VM V   L  P +  R +P +  YQF   C+F N  + VR          ++ + 
Sbjct: 11  TVAGMVMAVFLVLRIPEAHCRDAPKNFVYQFKGMCYFTNGTEHVRLVARQIYN-KEEILH 69

Query: 271 CSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPRAVLPHV 450
                 EF AVT LGR  A   + Q D L    A +D +C+H Y+     T+ R V P V
Sbjct: 70  FDSDLGEFVAVTELGRVCAEIWNTQKDLLAEFRAYVDTLCRHNYKETAGFTVQRRVEPTV 129

Query: 451 TVSRSNEQALYHHHLSVCAATDFCPTLVTV--------QCSRIGLL*YS----WRCDLSS 594
           TVS ++ +AL HH+L VC+ TDF P  V V        Q + +G    +    W   +  
Sbjct: 130 TVSPASTEALNHHNLLVCSVTDFYPRQVKVKWFRNQQEQTAGVGFTPLTQNGDWTYQIHV 189

Query: 595 YSELRLYLGRARDA*HDSPPVRCLHVPRAALCLQIPILLYCRAQSDSALSIILSAVWGFL 774
             E    LG           V   HV   +  LQ PI +  RAQS+SA S + S + GF+
Sbjct: 190 MLETVPQLG----------DVYVCHVDHPS--LQSPITVEWRAQSESAQSKMQSGIGGFV 237

Query: 775 LVL 783
           L L
Sbjct: 238 LGL 240


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

 Score = 78.6 bits (192), Expect = 5e-15
 Identities = 73/237 (30%), Positives = 105/237 (44%), Gaps = 9/237 (3%)
 Frame = +1

Query: 100 AALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTCLDDHVRCSR 279
           AAL V+L+ L  P S  R +     +QF  EC F N  + +R          +D V    
Sbjct: 2   AALAVLLMVLSLPFSWARETQPHFIHQFKGECRFSNGLERMRFFARYIYNTQED-VHFDS 60

Query: 280 YAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPRAVLPHVTVS 459
              EF A+T LGR DA Y + Q DF+E   A++D +C+  YQ        R V P VTV 
Sbjct: 61  DVGEFTALTELGRLDAEYWNQQKDFMEQMRAKVDTLCRSNYQGIGSFLRQRRVEPTVTVY 120

Query: 460 RSNEQALYHHHLSVCAATDFCPTLVTVQCSRIGLL*YSWRCDLSSYSELRLYLGRARDA* 639
            +  Q L HH+L VC+   F P  + V+        + W         +   L +  D  
Sbjct: 121 PAKTQPLQHHNLLVCSVNGFYPGHIEVR--------WFWNSHEEEAGVISTGLIQNGDWT 172

Query: 640 HDSPPVRCLHVPRA--ALCLQI-------PILLYCRAQSDSALSIILSAVWGFLLVL 783
             +  V    VP++      Q+       P+ +  RAQSDSA   ++S + GF+L L
Sbjct: 173 FQT-MVMLETVPQSGEVYTCQVEHPSRTSPLTVEWRAQSDSAQRKLMSGIGGFVLGL 228


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

 Score = 53.9 bits (128), Expect(2) = 1e-10
 Identities = 38/123 (30%), Positives = 55/123 (44%)
 Frame = +1

Query: 190 ECHFFNLNDIVRCAVTDSSTCLDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTL 369
           ECHF N    VR  +       ++ V+      E+RA T +GRP A   +     L+   
Sbjct: 7   ECHFSNGTQQVRF-LDRYIYNREEQVQFDSLVGEYRARTEMGRPAAERWNRWPQALQRAR 65

Query: 370 AELDPVCKHRYQIEERTTLPRAVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCS 549
           A +   C   Y+     T+ R V P VTV     + L+HH+L VC+   F P  + V+  
Sbjct: 66  AAVHAYCASNYEFFASRTVQRRVQPTVTVYPVKSRPLWHHNLLVCSVNGFYPGHIEVRWF 125

Query: 550 RIG 558
           R G
Sbjct: 126 RNG 128



 Score = 30.4 bits (67), Expect(2) = 1e-10
 Identities = 16/46 (34%), Positives = 27/46 (58%)
 Frame = +2

Query: 566 DTAGGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRSP 703
           + AG V++ L  N D T  ++VM +++    +VY C V+H +  SP
Sbjct: 131 EEAGVVSTGLIPNGDWTFQIMVMLEIVPQGGEVYACHVEHPSRTSP 176


  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: 29,583,703
Number of Sequences: 33508
Number of extensions: 800666
Number of successful extensions: 3783
Number of sequences better than 1.0e-05: 8
Number of HSP's better than  0.0 without gapping: 3156
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): 3766
length of database: 16,112,626
effective HSP length: 99
effective length of database: 12,795,334
effective search space used: 2060048774
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqCP

BLASTX 2.2.10 [Oct-19-2004]


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

Query= 20060611S-055404
         (783 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Ca...   142   4e-34
Alignment   gi|XP_850395.1| PREDICTED: similar to HLA class II histocompati...    88   6e-22
Alignment   gi|XP_861384.1| PREDICTED: similar to HLA class II histocompati...    88   6e-22
Alignment   gi|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis fami...    95   8e-20

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

 Score =  142 bits (358), Expect = 4e-34
 Identities = 100/255 (39%), Positives = 134/255 (52%), Gaps = 12/255 (4%)
 Frame = +1

Query: 55  LSGMEGLLLP*GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAV 234
           +SG   L +P G WTAA+ ++LV L  P++EGR SP D  +Q+  EC+F N  + VR  +
Sbjct: 1   MSGKMTLCIPRGFWTAAVMMILVVLSIPVAEGRDSPQDFVFQYKAECYFTNGTERVRL-L 59

Query: 235 TDSSTCLDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEE 414
           T      ++ VR      EFRAVT LGRPDA Y + Q D ++   AELD VC+H Y  EE
Sbjct: 60  TKYIYNREEFVRFDSDVGEFRAVTELGRPDAEYWNRQKDEMDRVRAELDTVCRHNYGREE 119

Query: 415 RTTLPRAVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSR------IGLL*Y-- 570
            TTL R V P VT+  S  + L HH+L VC+ TDF P  + V+  R       G++    
Sbjct: 120 LTTLQRRVEPTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPL 179

Query: 571 ----SWRCDLSSYSELRLYLGRARDA*HDSPPVRCLHVPRAALCLQIPILLYCRAQSDSA 738
                W   +    E+    G           V   HV  A+  LQ PI +  RAQS+SA
Sbjct: 180 IRNGDWTFQILVMLEMTPQRG----------DVYTCHVEHAS--LQSPITVQWRAQSESA 227

Query: 739 LSIILSAVWGFLLVL 783
            S +LS + GF+L L
Sbjct: 228 QSKMLSGIGGFVLGL 242


>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 = 87.8 bits (216), Expect(2) = 6e-22
 Identities = 51/155 (32%), Positives = 81/155 (52%)
 Frame = +1

Query: 94  WTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTCLDDHVRC 273
           W  AL V +  L + M++GR SP D   Q   +C+F N  + V+  V      L+++ R 
Sbjct: 8   WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFN-LEEYARF 66

Query: 274 SRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPRAVLPHVT 453
             +   F A+T LG+PDA   + Q   LE + A +D +C+H Y++    T+ R V P VT
Sbjct: 67  DSHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVT 126

Query: 454 VSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG 558
           V      ++ HH+L +C+ T F P  + ++  R G
Sbjct: 127 VYPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNG 161



 Score = 34.7 bits (78), Expect(2) = 6e-22
 Identities = 19/46 (41%), Positives = 26/46 (56%)
 Frame = +2

Query: 566 DTAGGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRSP 703
           +  G +++ L  N D T   +VM +M   L DVYTCLV H +  SP
Sbjct: 164 ERVGVMSTGLIRNGDWTFQTMVMLEMTPELGDVYTCLVNHPSLLSP 209


>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 = 87.8 bits (216), Expect(2) = 6e-22
 Identities = 51/155 (32%), Positives = 81/155 (52%)
 Frame = +1

Query: 94  WTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTCLDDHVRC 273
           W  AL V +  L + M++GR SP D   Q   +C+F N  + V+  V      L+++ R 
Sbjct: 8   WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFN-LEEYARF 66

Query: 274 SRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPRAVLPHVT 453
             +   F A+T LG+PDA   + Q   LE + A +D +C+H Y++    T+ R V P VT
Sbjct: 67  DSHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVT 126

Query: 454 VSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG 558
           V      ++ HH+L +C+ T F P  + ++  R G
Sbjct: 127 VYPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNG 161



 Score = 34.7 bits (78), Expect(2) = 6e-22
 Identities = 19/46 (41%), Positives = 26/46 (56%)
 Frame = +2

Query: 566 DTAGGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRSP 703
           +  G +++ L  N D T   +VM +M   L DVYTCLV H +  SP
Sbjct: 164 ERVGVMSTGLIRNGDWTFQTMVMLEMTPELGDVYTCLVNHPSLLSP 209


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

 Score = 94.7 bits (234), Expect = 8e-20
 Identities = 78/244 (31%), Positives = 107/244 (43%), Gaps = 12/244 (4%)
 Frame = +1

Query: 88  GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTCLDDHV 267
           G W  AL ++L+ L  P +  R +P         EC+F N  + VR  V       ++ V
Sbjct: 9   GSWMTALMLILMVLNPPFAWARDTPPHFLEVAKSECYFTNGTERVRF-VERYIHNREEFV 67

Query: 268 RCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPRAVLPH 447
           R      EFRAVT LGRP A   +GQ + LE   A +D  C+H Y + E  T+ R V P 
Sbjct: 68  RFDSDVGEFRAVTELGRPVAESWNGQKEILEQERATVDTYCRHNYGVIESFTVQRRVEPT 127

Query: 448 VTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG------------LL*YSWRCDLS 591
           VTV  +  Q L HH+L VC+   F P  + V+  R G            +    W   + 
Sbjct: 128 VTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNGDWTFQIL 187

Query: 592 SYSELRLYLGRARDA*HDSPPVRCLHVPRAALCLQIPILLYCRAQSDSALSIILSAVWGF 771
              E+    G       + P             L  P+ +  RAQSDSA S +LS + GF
Sbjct: 188 VMLEIVPQSGEVYTCQVEHP------------SLTSPVTVEWRAQSDSAQSKMLSGIGGF 235

Query: 772 LLVL 783
           +L L
Sbjct: 236 VLGL 239


  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: 34,728,271
Number of Sequences: 33732
Number of extensions: 940033
Number of successful extensions: 4504
Number of sequences better than 1.0e-05: 4
Number of HSP's better than  0.0 without gapping: 3704
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): 4469
length of database: 19,266,565
effective HSP length: 101
effective length of database: 15,859,633
effective search space used: 2521681647
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqHP

BLASTX 2.2.10 [Oct-19-2004]


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

Query= 20060611S-055404
         (783 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_002114.2| major histocompatibility complex, class II, DQ ...   133   2e-31
Alignment   gi|NP_872355.1| major histocompatibility complex, class II, DQ ...   112   6e-30
Alignment   gi|XP_949921.1| PREDICTED: similar to HLA class II histocompati...    97   1e-24
Alignment   gi|NP_068818.4| major histocompatibility complex, class II, DR ...    91   2e-22
Alignment   gi|NP_002115.1| major histocompatibility complex, class II, DR ...   100   1e-21
Alignment   gi|NP_002116.2| major histocompatibility complex, class II, DR ...   100   1e-21
Alignment   gi|XP_945926.1| PREDICTED: similar to HLA class II histocompati...    98   9e-21
Alignment   gi|NP_002111.1| major histocompatibility complex, class II, DO ...    82   1e-19
Alignment   gi|NP_072049.2| major histocompatibility complex, class II, DR ...    82   1e-18
Alignment   gi|XP_949915.1| PREDICTED: similar to HLA class II histocompati...    89   3e-18

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

 Score =  133 bits (334), Expect = 2e-31
 Identities = 99/255 (38%), Positives = 131/255 (51%), Gaps = 12/255 (4%)
 Frame = +1

Query: 55  LSGMEGLLLP*GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAV 234
           +S  + L +P GL  A + +ML  L  P++EGR SP D  YQF   C+F N  + VR  V
Sbjct: 1   MSWKKALRIPGGLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRL-V 59

Query: 235 TDSSTCLDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEE 414
           + S    ++ VR      EFRAVT LG P A Y + Q D LE   A +D VC+H YQ+E 
Sbjct: 60  SRSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLEL 119

Query: 415 RTTLPRAVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSR------IGLL*Y-- 570
           RTTL R V P VT+S S  +AL HH+L VC+ TDF P  + V+  R       G++    
Sbjct: 120 RTTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPL 179

Query: 571 ----SWRCDLSSYSELRLYLGRARDA*HDSPPVRCLHVPRAALCLQIPILLYCRAQSDSA 738
                W   +    E+    G           V   HV   +  LQ PI +  RAQS+SA
Sbjct: 180 IRNGDWTFQILVMLEMTPQRG----------DVYTCHVEHPS--LQSPITVEWRAQSESA 227

Query: 739 LSIILSAVWGFLLVL 783
            S +LS + GF+L L
Sbjct: 228 QSKMLSGIGGFVLGL 242


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

 Score =  112 bits (279), Expect(2) = 6e-30
 Identities = 70/166 (42%), Positives = 91/166 (54%)
 Frame = +1

Query: 55  LSGMEGLLLP*GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAV 234
           +S    L +P G W AA+ VMLV L  P++E R  P D   QF   C+F N  + VR  V
Sbjct: 1   MSWKMALQIPGGFWAAAVTVMLVMLSTPVAEARDFPKDFLVQFKGMCYFTNGTERVR-GV 59

Query: 235 TDSSTCLDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEE 414
                  +++ R      EF+AVT LGR    + +   DFLE   A +D VC+H Y+ E 
Sbjct: 60  ARYIYNREEYGRFDSDVGEFQAVTELGRSIEDW-NNYKDFLEQERAAVDKVCRHNYEAEL 118

Query: 415 RTTLPRAVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSR 552
           RTTL R V P VT+S S  +AL HH+L VC+ TDF P  + VQ  R
Sbjct: 119 RTTLQRQVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVQWFR 164



 Score = 37.4 bits (85), Expect(2) = 6e-30
 Identities = 19/46 (41%), Positives = 29/46 (63%)
 Frame = +2

Query: 566 DTAGGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRSP 703
           +TAG V++ L  N D T  +LVM ++     D+YTC V+H + +SP
Sbjct: 169 ETAGVVSTSLIRNGDWTFQILVMLEITPQRGDIYTCQVEHPSLQSP 214


>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 = 96.7 bits (239), Expect(2) = 1e-24
 Identities = 64/162 (39%), Positives = 85/162 (52%)
 Frame = +1

Query: 73  LLLP*GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTC 252
           L LP G   AAL V L+ L +P++    +      Q   ECHFFN  + VR         
Sbjct: 4   LKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGIYN- 62

Query: 253 LDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPR 432
            +++VR      E+RAVT LGRP A   + Q DFLE   AE+D VC+H Y + E  T+ R
Sbjct: 63  QEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTVQR 122

Query: 433 AVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG 558
            V P VTV  +  Q L HH+L VC+ + F P  + V+  R G
Sbjct: 123 RVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNG 164



 Score = 35.0 bits (79), Expect(2) = 1e-24
 Identities = 23/57 (40%), Positives = 32/57 (56%)
 Frame = +2

Query: 566 DTAGGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRSPSCCTVELSQTL 736
           + AG V++ L  N D T   LVM + +    +VYTC V+H +  SP   TVE S+ L
Sbjct: 167 EKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVMSP--LTVEWSEQL 221


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

 Score = 90.9 bits (224), Expect(2) = 2e-22
 Identities = 60/162 (37%), Positives = 82/162 (50%)
 Frame = +1

Query: 73  LLLP*GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTC 252
           L LP G   AAL V L  L +P++    +      Q   ECHF N  + V   +      
Sbjct: 4   LKLPGGSCMAALTVTLTVLSSPLALAGDTQPRFLEQAKCECHFLNGTERVWNLIRYIYN- 62

Query: 253 LDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPR 432
            +++ R +    E++AVT LGRPDA Y + Q D LE   AE+D  C++ Y + E  T+ R
Sbjct: 63  QEEYARYNSDLGEYQAVTELGRPDAEYWNSQKDLLERRRAEVDTYCRYNYGVVESFTVQR 122

Query: 433 AVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG 558
            V P VTV  S  Q L HH+L VC+   F P  + V+  R G
Sbjct: 123 RVQPKVTVYPSKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNG 164



 Score = 33.1 bits (74), Expect(2) = 2e-22
 Identities = 25/67 (37%), Positives = 34/67 (50%)
 Frame = +2

Query: 566 DTAGGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRSPSCCTVELSQTLP*A 745
           + AG V++ L  N D T   LVM + +    +VYTC V+H +  SP   TV+ S     A
Sbjct: 167 EKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSMMSP--LTVQWSARSESA 224

Query: 746 SY*ALSG 766
               LSG
Sbjct: 225 QSKMLSG 231


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

 Score =  100 bits (250), Expect = 1e-21
 Identities = 83/252 (32%), Positives = 112/252 (44%), Gaps = 15/252 (5%)
 Frame = +1

Query: 73  LLLP*GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTC 252
           L LP G    AL V L+ L +P++    +     +Q   ECHFFN  + VR        C
Sbjct: 4   LKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVRLL----ERC 59

Query: 253 L---DDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTT 423
           +   ++ VR      E+RAVT LGRPDA Y + Q D LE   A +D  C+H Y + E  T
Sbjct: 60  IYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFT 119

Query: 424 LPRAVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG------------LL* 567
           + R V P VTV  S  Q L HH+L VC+ + F P  + V+  R G            +  
Sbjct: 120 VQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQN 179

Query: 568 YSWRCDLSSYSELRLYLGRARDA*HDSPPVRCLHVPRAALCLQIPILLYCRAQSDSALSI 747
             W        E     G       + P V              P+ +  RA+S+SA S 
Sbjct: 180 GDWTFQTLVMLETVPRSGEVYTCQVEHPSVTS------------PLTVEWRARSESAQSK 227

Query: 748 ILSAVWGFLLVL 783
           +LS V GF+L L
Sbjct: 228 MLSGVGGFVLGL 239


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

 Score =  100 bits (250), Expect = 1e-21
 Identities = 85/249 (34%), Positives = 112/249 (44%), Gaps = 12/249 (4%)
 Frame = +1

Query: 73  LLLP*GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTC 252
           L LP G + A L V L+ L +P++    +      Q   ECHFFN  + VR    D    
Sbjct: 4   LKLPGGSYMAKLTVTLMVLSSPLALAGDTRPRFLQQDKYECHFFNGTERVRFLHRDIYNQ 63

Query: 253 LDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPR 432
            +D +R      E+RAVT LGRPDA Y + Q DFLE   A +D  C+H Y + E  T+ R
Sbjct: 64  EED-LRFDSDVGEYRAVTELGRPDAEYWNSQKDFLEDRRAAVDTYCRHNYGVGESFTVQR 122

Query: 433 AVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSR-----------IGLL*Y-SW 576
            V P VTV  +  Q L HH+L VC+   F P  + V+  R            GL+    W
Sbjct: 123 RVEPKVTVYPARTQTLQHHNLLVCSVNGFYPGSIEVRWFRNSQEEKAGVVSTGLIQNGDW 182

Query: 577 RCDLSSYSELRLYLGRARDA*HDSPPVRCLHVPRAALCLQIPILLYCRAQSDSALSIILS 756
                   E     G       + P V              P+ +  RAQS+SA S +LS
Sbjct: 183 TFQTLVMLETVPRSGEVYTCQVEHPSVTS------------PLTVEWRAQSESAQSKMLS 230

Query: 757 AVWGFLLVL 783
            V GF+L L
Sbjct: 231 GVGGFVLGL 239


>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 = 97.8 bits (242), Expect = 9e-21
 Identities = 83/249 (33%), Positives = 112/249 (44%), Gaps = 12/249 (4%)
 Frame = +1

Query: 73  LLLP*GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTC 252
           L LP G   AAL V L+ L +P++    +      Q   ECHFFN  + VR         
Sbjct: 4   LKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGIYN- 62

Query: 253 LDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPR 432
            +++VR      E+RAVT LGRP A   + Q DFLE   AE+D VC+H Y + E  T+ R
Sbjct: 63  QEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGESFTVQR 122

Query: 433 AVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG------------LL*YSW 576
            V P VTV  +  Q L HH+L VC+ + F P  + V+  R G            +    W
Sbjct: 123 RVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDW 182

Query: 577 RCDLSSYSELRLYLGRARDA*HDSPPVRCLHVPRAALCLQIPILLYCRAQSDSALSIILS 756
                   E     G       + P V              P+ +  RA+S+SA S +LS
Sbjct: 183 TFQTLVMLETVPRSGEVYTCQVEHPSV------------MSPLTVEWRARSESAQSKMLS 230

Query: 757 AVWGFLLVL 783
            V GF+L L
Sbjct: 231 GVGGFVLGL 239


>ref|NP_002111.1| major histocompatibility complex, class II, DO beta precursor [Homo
           sapiens]
          Length = 273

 Score = 82.0 bits (201), Expect(2) = 1e-19
 Identities = 50/144 (34%), Positives = 74/144 (51%)
 Frame = +1

Query: 94  WTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTCLDDHVRC 273
           W  AL V L  L + M++G  SP D   Q   +C+F N  + V+  V      L+++VR 
Sbjct: 8   WVVALLVNLTRLDSSMTQGTDSPEDFVIQAKADCYFTNGTEKVQFVVRFIFN-LEEYVRF 66

Query: 274 SRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPRAVLPHVT 453
                 F A+T LG+PDA   + ++D LE +   +D VC+H Y++    T+ R V P VT
Sbjct: 67  DSDVGMFVALTKLGQPDAEQWNSRLDLLERSRQAVDGVCRHNYRLGAPFTVGRKVQPEVT 126

Query: 454 VSRSNEQALYHHHLSVCAATDFCP 525
           V       L+ H+L  C+ T F P
Sbjct: 127 VYPERTPLLHQHNLLHCSVTGFYP 150



 Score = 32.3 bits (72), Expect(2) = 1e-19
 Identities = 19/46 (41%), Positives = 26/46 (56%)
 Frame = +2

Query: 566 DTAGGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRSP 703
           + AG +++    N D T   +VM +M   L  VYTCLV HS+  SP
Sbjct: 164 ERAGVMSTGPIRNGDWTFQTVVMLEMTPELGHVYTCLVDHSSLLSP 209


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

 Score = 81.6 bits (200), Expect(2) = 1e-18
 Identities = 59/163 (36%), Positives = 81/163 (49%), Gaps = 1/163 (0%)
 Frame = +1

Query: 73  LLLP*GLWTAALCVMLVALGAPMS-EGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSST 249
           L LP G   AAL V L+ L + ++  G   P  +  +   ECHFFN  + VR        
Sbjct: 4   LKLPGGSSLAALTVTLMVLSSRLAFAGDTRPRFLELR-KSECHFFNGTERVRYLDRYFHN 62

Query: 250 CLDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLP 429
             ++ +R      E+RAVT LGRP A   + Q D LE     +D  C+H Y + E  T+ 
Sbjct: 63  -QEEFLRFDSDVGEYRAVTELGRPVAESWNSQKDLLEQKRGRVDNYCRHNYGVGESFTVQ 121

Query: 430 RAVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG 558
           R V P VTV  +  Q L HH+L VC+ + F P  + V+  R G
Sbjct: 122 RRVHPQVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNG 164



 Score = 29.6 bits (65), Expect(2) = 1e-18
 Identities = 17/45 (37%), Positives = 25/45 (55%)
 Frame = +2

Query: 566 DTAGGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRS 700
           + AG V++ L  N D T   LVM + +    +VYTC V+H +  S
Sbjct: 167 EKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTS 211


>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 = 89.4 bits (220), Expect = 3e-18
 Identities = 71/210 (33%), Positives = 95/210 (45%), Gaps = 12/210 (5%)
 Frame = +1

Query: 190 ECHFFNLNDIVRCAVTDSSTCLDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTL 369
           ECHFFN  + VR          +++VR      E+RAVT LGRP A   + Q DFLE   
Sbjct: 61  ECHFFNGTERVRYLHRGIYN-QEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRR 119

Query: 370 AELDPVCKHRYQIEERTTLPRAVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCS 549
           AE+D VC+H Y + E  T+ R V P VTV  +  Q L HH+L VC+ + F P  + V+  
Sbjct: 120 AEVDTVCRHNYGVGESFTVQRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWF 179

Query: 550 RIG------------LL*YSWRCDLSSYSELRLYLGRARDA*HDSPPVRCLHVPRAALCL 693
           R G            +    W        E     G       + P V            
Sbjct: 180 RNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV------------ 227

Query: 694 QIPILLYCRAQSDSALSIILSAVWGFLLVL 783
             P+ +  RA+S+SA S +LS V GF+L L
Sbjct: 228 MSPLTVEWRARSESAQSKMLSGVGGFVLGL 257


  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: 33,659,514
Number of Sequences: 39411
Number of extensions: 942660
Number of successful extensions: 4521
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 3616
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): 4493
length of database: 17,774,539
effective HSP length: 100
effective length of database: 13,833,439
effective search space used: 2213350240
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqMP

BLASTX 2.2.10 [Oct-19-2004]


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

Query= 20060611S-055404
         (783 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_996988.1| histocompatibility 2, class II antigen A, beta ...   111   7e-25
Alignment   gi|NP_034512.1| histocompatibility 2, class II antigen E beta [...    87   4e-20
Alignment   gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ...    77   4e-18
Alignment   gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/...    71   3e-16

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

 Score =  111 bits (278), Expect = 7e-25
 Identities = 87/242 (35%), Positives = 119/242 (49%), Gaps = 13/242 (5%)
 Frame = +1

Query: 91  LWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTCLDDHVR 270
           L  +A  V+L+ L +P +EG  S     YQF  EC+F N    +R  VT      +++VR
Sbjct: 8   LLLSAAVVVLMVLSSPGTEGGDSERHFVYQFMGECYFTNGTQRIRY-VTRYIYNREEYVR 66

Query: 271 CSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQ-IEERTTLPRAVLPH 447
                 E RAVT LGRPDA Y + Q + LE T AELD VC+H Y+  E  T+L R   P+
Sbjct: 67  YDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSLRRLEQPN 126

Query: 448 VTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG------------LL*YSWRCDLS 591
           V +S S  +AL HH+  VC+ TDF PT + V+  R G            +    W   + 
Sbjct: 127 VVISLSRTEALNHHNTLVCSVTDFYPTQIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVL 186

Query: 592 SYSELRLYLGRARDA*HDSPPVRCLHVPRAALCLQIPILLYCRAQSDSALSIILSAVWGF 771
              E+    G           V   HV   +  L+ PI +  RAQS+SA S +LS + G 
Sbjct: 187 VMLEMTPRRGE----------VYTCHVEHPS--LKSPITVEWRAQSESAWSKMLSGIGGC 234

Query: 772 LL 777
           +L
Sbjct: 235 VL 236


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

 Score = 87.4 bits (215), Expect(2) = 4e-20
 Identities = 58/154 (37%), Positives = 83/154 (53%), Gaps = 1/154 (0%)
 Frame = +1

Query: 100 AALCVMLVALGAPMSEGRYS-PLDVPYQFGDECHFFNLNDIVRCAVTDSSTCLDDHVRCS 276
           AA+ ++L  L  P++  R S P  + Y    ECHF+N    VR         L++++R  
Sbjct: 11  AAVILLLTVLSPPVALVRDSRPWFLEY-CKSECHFYNGTQRVRFLKRYFYN-LEENLRFD 68

Query: 277 RYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPRAVLPHVTV 456
               EFRAVT LGRPDA   + Q + L+   A +D  C+H Y+I +   +PR V P VTV
Sbjct: 69  SDVGEFRAVTELGRPDAENWNSQPEILDEKRAAVDTYCRHNYEIFDNFLVPRRVEPTVTV 128

Query: 457 SRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG 558
             +  Q L HH+L VC+ +DF P  + V+  R G
Sbjct: 129 YPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNG 162



 Score = 29.3 bits (64), Expect(2) = 4e-20
 Identities = 16/46 (34%), Positives = 24/46 (52%)
 Frame = +2

Query: 566 DTAGGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRSP 703
           +  G V++ L  N D T   LVM + +    +VYTC V+H +   P
Sbjct: 165 EKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDP 210


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

 Score = 77.0 bits (188), Expect(2) = 4e-18
 Identities = 51/155 (32%), Positives = 79/155 (50%)
 Frame = +1

Query: 94  WTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDSSTCLDDHVRC 273
           W  AL V L+ L + M EGR SP +   Q   +C+F N  + V   V      L++++  
Sbjct: 8   WVVALLVNLMRLDSFMIEGRDSPENFVIQAKADCYFTNGTEKVHLLVRFIFN-LEEYLHF 66

Query: 274 SRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTTLPRAVLPHVT 453
                 F A+T LG PDA   + ++D LE + A ++ VC+ +Y++    T+ R V P VT
Sbjct: 67  DSDLGMFVALTELGEPDADQWNKRLDLLETSRAAVNMVCRQKYKLGAPFTVERNVPPEVT 126

Query: 454 VSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG 558
           V       L  H+L +C+ T F P  ++V+  R G
Sbjct: 127 VYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNG 161



 Score = 32.7 bits (73), Expect(2) = 4e-18
 Identities = 17/46 (36%), Positives = 26/46 (56%)
 Frame = +2

Query: 566 DTAGGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRSP 703
           + +G +++ L  N D T    VM +MI  L D+Y+CLV+H     P
Sbjct: 164 ERSGVMSTGLVRNGDWTFQTTVMLEMIPELGDIYSCLVEHPGLLRP 209


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

 Score = 71.2 bits (173), Expect(2) = 3e-16
 Identities = 56/165 (33%), Positives = 79/165 (47%)
 Frame = +1

Query: 64  MEGLLLP*GLWTAALCVMLVALGAPMSEGRYSPLDVPYQFGDECHFFNLNDIVRCAVTDS 243
           M  L LP GL  AA+ + L+ L  P+   R        Q   ECH+FN  + V  +VT  
Sbjct: 1   MVSLWLPRGLCVAAVILSLMMLTPPVILVRDPRPRFLEQLKAECHYFNGKERV-WSVTRF 59

Query: 244 STCLDDHVRCSRYAREFRAVTPLGRPDAYYCSGQMDFLELTLAELDPVCKHRYQIEERTT 423
               ++  R +    +F AVT LGRP   Y + Q D L+   A +D  C++ Y + +   
Sbjct: 60  IYNQEEFARFNSDFGKFLAVTELGRPIVEYLNTQKDMLDNYRASVDR-CRNNYDLVDIFM 118

Query: 424 LPRAVLPHVTVSRSNEQALYHHHLSVCAATDFCPTLVTVQCSRIG 558
           L     P VTV  +  Q L HH+L VC+  DF P  + V+  R G
Sbjct: 119 LNLKAEPKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNG 163



 Score = 32.3 bits (72), Expect(2) = 3e-16
 Identities = 18/46 (39%), Positives = 26/46 (56%)
 Frame = +2

Query: 566 DTAGGVTSPLTLN*DCT*DVLVMHDMILHL*DVYTCLVQHSASRSP 703
           +  G V++ L  N D T   LVM +M+    +VYTC V+H +  SP
Sbjct: 166 EKTGVVSTGLIQNRDWTYQTLVMLEMVPRGGEVYTCQVEHPSLTSP 211


  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: 39,721,620
Number of Sequences: 45328
Number of extensions: 1055993
Number of successful extensions: 4573
Number of sequences better than 1.0e-05: 4
Number of HSP's better than  0.0 without gapping: 3756
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): 4552
length of database: 21,768,885
effective HSP length: 101
effective length of database: 17,190,757
effective search space used: 2733330363
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)