Animal-Genome cDNA 20060611S-038855


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-038855
         (685 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: 634,612
Number of Sequences: 1040
Number of extensions: 15214
Number of successful extensions: 46
Number of sequences better than 1.0e-05: 0
Number of HSP's better than  0.0 without gapping: 44
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): 46
length of database: 434,620
effective HSP length: 74
effective length of database: 357,660
effective search space used: 54721980
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-038855
         (685 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]                 190   1e-48
Alignment   gi|NP_001012694.1| major histocompatibility complex, class II, ...   185   2e-47
Alignment   gi|NP_001012698.2| major histocompatibility complex, class II, ...   142   2e-34
Alignment   gi|NP_001012697.1| major histocompatibility complex, class II, ...   141   4e-34
Alignment   gi|NP_001013618.1| major histocompatibility complex, class II, ...   128   3e-30
Alignment   gi|XP_582099.2| PREDICTED: similar to major histocompatibility ...   124   5e-29
Alignment   gi|XP_876139.1| PREDICTED: similar to H-2 class II histocompati...    93   2e-19

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

 Score =  190 bits (482), Expect = 1e-48
 Identities = 96/156 (61%), Positives = 113/156 (72%)
 Frame = +3

Query: 51  MSGMVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVA 230
           MSGMVAL +PRGLWTA V V LV+L  P AEGRDSP+DFVVQFKG CYF NGT+RVR V 
Sbjct: 1   MSGMVALWIPRGLWTAVVMVTLVMLSTPGAEGRDSPKDFVVQFKGLCYFTNGTERVRYVT 60

Query: 231 RYIYNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEG 410
           RYIYNQEE++RFDSD   +RA+TPLGRP+A  WNSQ D  +  R   DT C+H++  +  
Sbjct: 61  RYIYNQEEYVRFDSDWDLYRALTPLGRPDAEYWNSQKDFLEQTRAEADTVCRHNYQAELI 120

Query: 411 TDPASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518
           T     RV+P+V ISPS  +AL H NLL C   DFY
Sbjct: 121 TS-LQRRVEPTVTISPSRTEALNHHNLLVCSVTDFY 155


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

 Score =  185 bits (470), Expect = 2e-47
 Identities = 95/156 (60%), Positives = 111/156 (71%)
 Frame = +3

Query: 51  MSGMVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVA 230
           MSGMVALR+PRGLWTAAV V L VL  P AEGRDSPQD VV F G+CYF NGT+RVR V 
Sbjct: 1   MSGMVALRIPRGLWTAAVMVTLAVLSTPGAEGRDSPQDTVVHFMGQCYFTNGTERVRYVT 60

Query: 231 RYIYNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEG 410
           RYIYNQEE   +DSDVGE+RAVT LGR  A  WNSQ D+ +  R  LDT C+H++ ++  
Sbjct: 61  RYIYNQEETAYYDSDVGEYRAVTQLGRTLAEYWNSQKDILEQTRAELDTVCRHNYQLEVI 120

Query: 411 TDPASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518
           T     +V+P+V IS S  +AL H NLL C   DFY
Sbjct: 121 TS-LQRQVEPTVTISLSRTEALNHHNLLVCSVTDFY 155


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

 Score =  142 bits (359), Expect = 2e-34
 Identities = 74/155 (47%), Positives = 99/155 (63%), Gaps = 2/155 (1%)
 Frame = +3

Query: 60  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239
           MV L    G W AA+ VML+VL  P+A  R+    F+  +KGEC+F+NGT+RVR + R+ 
Sbjct: 1   MVCLYFSGGSWMAALIVMLMVLCPPLAWAREIQPHFLEYYKGECHFFNGTERVRFLDRHF 60

Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419
           YN EE +RFDSD GEFRAVT LGRP A  WNSQ D  + KR  +D  C+H++    G + 
Sbjct: 61  YNGEEFVRFDSDWGEFRAVTELGRPAAEHWNSQKDFLEQKRAEVDRVCRHNY---GGVES 117

Query: 420 ASV--RVQPSVNISPSAADALRHRNLLCCRGDDFY 518
            +V  RV+P+V + P+    L+H NLL C  + FY
Sbjct: 118 FTVQRRVEPTVTVYPAKTQPLQHHNLLVCSVNGFY 152


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

 Score =  141 bits (356), Expect = 4e-34
 Identities = 79/152 (51%), Positives = 98/152 (64%), Gaps = 2/152 (1%)
 Frame = +3

Query: 75  LPRGLWTAAVTVMLV--VLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYIYNQ 248
           +PR   T A  VM V  VL  P A  RD+P++FV QFKG CYF NGT+ VRLVAR IYN+
Sbjct: 5   IPRNPGTVAGMVMAVFLVLRIPEAHCRDAPKNFVYQFKGMCYFTNGTEHVRLVARQIYNK 64

Query: 249 EEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDPASV 428
           EE L FDSD+GEF AVT LGR  A  WN+Q D+    R  +DT C+H++    G      
Sbjct: 65  EEILHFDSDLGEFVAVTELGRVCAEIWNTQKDLLAEFRAYVDTLCRHNYKETAGF-TVQR 123

Query: 429 RVQPSVNISPSAADALRHRNLLCCRGDDFYLR 524
           RV+P+V +SP++ +AL H NLL C   DFY R
Sbjct: 124 RVEPTVTVSPASTEALNHHNLLVCSVTDFYPR 155


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

 Score =  128 bits (322), Expect = 3e-30
 Identities = 64/145 (44%), Positives = 90/145 (62%), Gaps = 2/145 (1%)
 Frame = +3

Query: 90  WTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYIYNQEEHLRFD 269
           W        + L A V +GRDSP+DFV Q K +CYF NGT++VR V R+I+N E++ RFD
Sbjct: 8   WVVTFLSTALRLDASVTQGRDSPEDFVTQAKADCYFTNGTEKVRFVVRFIFNLEDYARFD 67

Query: 270 SDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDPASV--RVQPS 443
           SD+G F A+T LG+P+A  WN++ D+    R  +D  C+ ++++     P +V  RVQP 
Sbjct: 68  SDLGMFVALTELGKPDAERWNNRPDILARSRASVDMLCRRNYYLGA---PFTVGRRVQPE 124

Query: 444 VNISPSAADALRHRNLLCCRGDDFY 518
           V + P    AL+HRNLL C    FY
Sbjct: 125 VTVYPEKTPALQHRNLLLCLVTGFY 149


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

 Score =  124 bits (312), Expect = 5e-29
 Identities = 64/141 (45%), Positives = 89/141 (63%)
 Frame = +3

Query: 96  AAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYIYNQEEHLRFDSD 275
           AA+ V+L+VL  P +  R++   F+ QFKGEC F NG +R+R  ARYIYN +E + FDSD
Sbjct: 2   AALAVLLMVLSLPFSWARETQPHFIHQFKGECRFSNGLERMRFFARYIYNTQEDVHFDSD 61

Query: 276 VGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDPASVRVQPSVNIS 455
           VGEF A+T LGR +A  WN Q D  +  R  +DT C+ S++   G+     RV+P+V + 
Sbjct: 62  VGEFTALTELGRLDAEYWNQQKDFMEQMRAKVDTLCR-SNYQGIGSFLRQRRVEPTVTVY 120

Query: 456 PSAADALRHRNLLCCRGDDFY 518
           P+    L+H NLL C  + FY
Sbjct: 121 PAKTQPLQHHNLLVCSVNGFY 141


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

 Score = 93.2 bits (230), Expect = 2e-19
 Identities = 50/117 (42%), Positives = 67/117 (57%)
 Frame = +3

Query: 168 VVQFKGECYFYNGTQRVRLVARYIYNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDV 347
           +VQ K EC+F NGTQ+VR + RYIYN+EE ++FDS VGE+RA T +GRP A  WN     
Sbjct: 1   MVQGKSECHFSNGTQQVRFLDRYIYNREEQVQFDSLVGEYRARTEMGRPAAERWNRWPQA 60

Query: 348 PDHKRV*LDTPCKHSHHIKEGTDPASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518
               R  +   C  ++     +     RVQP+V + P  +  L H NLL C  + FY
Sbjct: 61  LQRARAAVHAYCASNYEF-FASRTVQRRVQPTVTVYPVKSRPLWHHNLLVCSVNGFY 116


  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: 23,671,325
Number of Sequences: 33508
Number of extensions: 579046
Number of successful extensions: 1809
Number of sequences better than 1.0e-05: 7
Number of HSP's better than  0.0 without gapping: 1667
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): 1798
length of database: 16,112,626
effective HSP length: 98
effective length of database: 12,828,842
effective search space used: 1654920618
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-038855
         (685 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 ...   180   8e-46
Alignment   gi|NP_872355.1| major histocompatibility complex, class II, DQ ...   171   7e-43
Alignment   gi|NP_002115.1| major histocompatibility complex, class II, DR ...   151   4e-37
Alignment   gi|XP_945926.1| PREDICTED: similar to HLA class II histocompati...   149   2e-36
Alignment   gi|XP_949921.1| PREDICTED: similar to HLA class II histocompati...   149   2e-36
Alignment   gi|NP_002116.2| major histocompatibility complex, class II, DR ...   149   2e-36
Alignment   gi|NP_002112.3| major histocompatibility complex, class II, DP ...   143   1e-34
Alignment   gi|NP_068818.4| major histocompatibility complex, class II, DR ...   142   2e-34
Alignment   gi|NP_072049.2| major histocompatibility complex, class II, DR ...   142   2e-34
Alignment   gi|NP_002111.1| major histocompatibility complex, class II, DO ...   126   1e-29

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

 Score =  180 bits (457), Expect = 8e-46
 Identities = 93/156 (59%), Positives = 112/156 (71%)
 Frame = +3

Query: 51  MSGMVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVA 230
           MS   ALR+P GL  A VT+ML +L  PVAEGRDSP+DFV QFKG CYF NGT+RVRLV+
Sbjct: 1   MSWKKALRIPGGLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVS 60

Query: 231 RYIYNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEG 410
           R IYN+EE +RFDSDVGEFRAVT LG P A  WNSQ D+ + KR  +D  C+H++ ++  
Sbjct: 61  RSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELR 120

Query: 411 TDPASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518
           T     RV+P+V ISPS  +AL H NLL C   DFY
Sbjct: 121 T-TLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFY 155


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

 Score =  171 bits (432), Expect = 7e-43
 Identities = 88/156 (56%), Positives = 110/156 (70%)
 Frame = +3

Query: 51  MSGMVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVA 230
           MS  +AL++P G W AAVTVMLV+L  PVAE RD P+DF+VQFKG CYF NGT+RVR VA
Sbjct: 1   MSWKMALQIPGGFWAAAVTVMLVMLSTPVAEARDFPKDFLVQFKGMCYFTNGTERVRGVA 60

Query: 231 RYIYNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEG 410
           RYIYN+EE+ RFDSDVGEF+AVT LGR     WN+  D  + +R  +D  C+H++  +  
Sbjct: 61  RYIYNREEYGRFDSDVGEFQAVTELGR-SIEDWNNYKDFLEQERAAVDKVCRHNYEAELR 119

Query: 411 TDPASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518
           T     +V+P+V ISPS  +AL H NLL C   DFY
Sbjct: 120 T-TLQRQVEPTVTISPSRTEALNHHNLLVCSVTDFY 154


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

 Score =  151 bits (382), Expect = 4e-37
 Identities = 77/153 (50%), Positives = 103/153 (67%)
 Frame = +3

Query: 60  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239
           MV L+LP G    A+TV L+VL +P+A   D+   F+ Q K EC+F+NGT+RVRL+ R I
Sbjct: 1   MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVRLLERCI 60

Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419
           YNQEE +RFDSDVGE+RAVT LGRP+A  WNSQ D+ + +R  +DT C+H++ + E +  
Sbjct: 61  YNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGE-SFT 119

Query: 420 ASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518
              RV+P V + PS    L+H NLL C    FY
Sbjct: 120 VQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFY 152


>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 =  149 bits (376), Expect = 2e-36
 Identities = 77/153 (50%), Positives = 102/153 (66%)
 Frame = +3

Query: 60  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239
           MV L+LP G   AA+TV L+VL +P+A   D+   F+ Q K EC+F+NGT+RVR + R I
Sbjct: 1   MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60

Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419
           YNQEE++RFDSDVGE+RAVT LGRP A SWNSQ D  + +R  +DT C+H++ + E +  
Sbjct: 61  YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGE-SFT 119

Query: 420 ASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518
              RV P V + P+    L+H NLL C    FY
Sbjct: 120 VQRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFY 152


>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 =  149 bits (376), Expect = 2e-36
 Identities = 77/153 (50%), Positives = 102/153 (66%)
 Frame = +3

Query: 60  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239
           MV L+LP G   AA+TV L+VL +P+A   D+   F+ Q K EC+F+NGT+RVR + R I
Sbjct: 1   MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60

Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419
           YNQEE++RFDSDVGE+RAVT LGRP A SWNSQ D  + +R  +DT C+H++ + E +  
Sbjct: 61  YNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAEVDTVCRHNYGVGE-SFT 119

Query: 420 ASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518
              RV P V + P+    L+H NLL C    FY
Sbjct: 120 VQRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFY 152


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

 Score =  149 bits (376), Expect = 2e-36
 Identities = 76/153 (49%), Positives = 103/153 (67%)
 Frame = +3

Query: 60  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239
           MV L+LP G + A +TV L+VL +P+A   D+   F+ Q K EC+F+NGT+RVR + R I
Sbjct: 1   MVCLKLPGGSYMAKLTVTLMVLSSPLALAGDTRPRFLQQDKYECHFFNGTERVRFLHRDI 60

Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419
           YNQEE LRFDSDVGE+RAVT LGRP+A  WNSQ D  + +R  +DT C+H++ + E +  
Sbjct: 61  YNQEEDLRFDSDVGEYRAVTELGRPDAEYWNSQKDFLEDRRAAVDTYCRHNYGVGE-SFT 119

Query: 420 ASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518
              RV+P V + P+    L+H NLL C  + FY
Sbjct: 120 VQRRVEPKVTVYPARTQTLQHHNLLVCSVNGFY 152


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

 Score =  143 bits (361), Expect = 1e-34
 Identities = 75/153 (49%), Positives = 99/153 (64%)
 Frame = +3

Query: 60  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239
           M+ L++     T A+T +L+VL   V +GR +P++++ Q + ECY +NGTQR   + RYI
Sbjct: 1   MMVLQVSAAPRTVALTALLMVLLTSVVQGRATPENYLFQGRQECYAFNGTQR--FLERYI 58

Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419
           YN+EE  RFDSDVGEFRAVT LGRP A  WNSQ D+ + KR   D  C+H++ +  G   
Sbjct: 59  YNREEFARFDSDVGEFRAVTELGRPAAEYWNSQKDILEEKRAVPDRMCRHNYEL-GGPMT 117

Query: 420 ASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518
              RVQP VN+SPS    L+H NLL C   DFY
Sbjct: 118 LQRRVQPRVNVSPSKKGPLQHHNLLVCHVTDFY 150


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

 Score =  142 bits (359), Expect = 2e-34
 Identities = 73/153 (47%), Positives = 102/153 (66%)
 Frame = +3

Query: 60  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239
           MV L+LP G   AA+TV L VL +P+A   D+   F+ Q K EC+F NGT+RV  + RYI
Sbjct: 1   MVCLKLPGGSCMAALTVTLTVLSSPLALAGDTQPRFLEQAKCECHFLNGTERVWNLIRYI 60

Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419
           YNQEE+ R++SD+GE++AVT LGRP+A  WNSQ D+ + +R  +DT C++++ + E +  
Sbjct: 61  YNQEEYARYNSDLGEYQAVTELGRPDAEYWNSQKDLLERRRAEVDTYCRYNYGVVE-SFT 119

Query: 420 ASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518
              RVQP V + PS    L+H NLL C  + FY
Sbjct: 120 VQRRVQPKVTVYPSKTQPLQHHNLLVCSVNGFY 152


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

 Score =  142 bits (359), Expect = 2e-34
 Identities = 75/153 (49%), Positives = 99/153 (64%)
 Frame = +3

Query: 60  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239
           MV L+LP G   AA+TV L+VL + +A   D+   F+   K EC+F+NGT+RVR + RY 
Sbjct: 1   MVCLKLPGGSSLAALTVTLMVLSSRLAFAGDTRPRFLELRKSECHFFNGTERVRYLDRYF 60

Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419
           +NQEE LRFDSDVGE+RAVT LGRP A SWNSQ D+ + KR  +D  C+H++ + E +  
Sbjct: 61  HNQEEFLRFDSDVGEYRAVTELGRPVAESWNSQKDLLEQKRGRVDNYCRHNYGVGE-SFT 119

Query: 420 ASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518
              RV P V + P+    L+H NLL C    FY
Sbjct: 120 VQRRVHPQVTVYPAKTQPLQHHNLLVCSVSGFY 152


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

 Score =  126 bits (317), Expect = 1e-29
 Identities = 63/145 (43%), Positives = 91/145 (62%), Gaps = 2/145 (1%)
 Frame = +3

Query: 90  WTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYIYNQEEHLRFD 269
           W  A+ V L  L + + +G DSP+DFV+Q K +CYF NGT++V+ V R+I+N EE++RFD
Sbjct: 8   WVVALLVNLTRLDSSMTQGTDSPEDFVIQAKADCYFTNGTEKVQFVVRFIFNLEEYVRFD 67

Query: 270 SDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDPASV--RVQPS 443
           SDVG F A+T LG+P+A  WNS+ D+ +  R  +D  C+H++ +     P +V  +VQP 
Sbjct: 68  SDVGMFVALTKLGQPDAEQWNSRLDLLERSRQAVDGVCRHNYRLGA---PFTVGRKVQPE 124

Query: 444 VNISPSAADALRHRNLLCCRGDDFY 518
           V + P     L   NLL C    FY
Sbjct: 125 VTVYPERTPLLHQHNLLHCSVTGFY 149


  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: 26,864,919
Number of Sequences: 39411
Number of extensions: 676289
Number of successful extensions: 2538
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 2288
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): 2519
length of database: 17,774,539
effective HSP length: 98
effective length of database: 13,912,261
effective search space used: 1794681669
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-038855
         (685 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 ...   153   1e-37
Alignment   gi|NP_034512.1| histocompatibility 2, class II antigen E beta [...   151   5e-37
Alignment   gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/...   119   3e-27
Alignment   gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ...   116   2e-26

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

 Score =  153 bits (387), Expect = 1e-37
 Identities = 81/152 (53%), Positives = 103/152 (67%)
 Frame = +3

Query: 63  VALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYIY 242
           +AL++P  L +AAV V+L+VL +P  EG DS + FV QF GECYF NGTQR+R V RYIY
Sbjct: 1   MALQIPSLLLSAAV-VVLMVLSSPGTEGGDSERHFVYQFMGECYFTNGTQRIRYVTRYIY 59

Query: 243 NQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDPA 422
           N+EE++R+DSDVGE RAVT LGRP+A  WNSQ ++ +  R  LDT C+H++   E     
Sbjct: 60  NREEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSL 119

Query: 423 SVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518
               QP+V IS S  +AL H N L C   DFY
Sbjct: 120 RRLEQPNVVISLSRTEALNHHNTLVCSVTDFY 151


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

 Score =  151 bits (382), Expect = 5e-37
 Identities = 79/148 (53%), Positives = 98/148 (66%)
 Frame = +3

Query: 75  LPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYIYNQEE 254
           LPR    AAV ++L VL  PVA  RDS   F+   K EC+FYNGTQRVR + RY YN EE
Sbjct: 4   LPRVPCVAAVILLLTVLSPPVALVRDSRPWFLEYCKSECHFYNGTQRVRFLKRYFYNLEE 63

Query: 255 HLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDPASVRV 434
           +LRFDSDVGEFRAVT LGRP+A +WNSQ ++ D KR  +DT C+H++ I +       RV
Sbjct: 64  NLRFDSDVGEFRAVTELGRPDAENWNSQPEILDEKRAAVDTYCRHNYEIFDNF-LVPRRV 122

Query: 435 QPSVNISPSAADALRHRNLLCCRGDDFY 518
           +P+V + P+    L H NLL C   DFY
Sbjct: 123 EPTVTVYPTKTQPLEHHNLLVCSVSDFY 150


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

 Score =  119 bits (298), Expect = 3e-27
 Identities = 66/153 (43%), Positives = 94/153 (61%)
 Frame = +3

Query: 60  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239
           MV+L LPRGL  AAV + L++L  PV   RD    F+ Q K EC+++NG +RV  V R+I
Sbjct: 1   MVSLWLPRGLCVAAVILSLMMLTPPVILVRDPRPRFLEQLKAECHYFNGKERVWSVTRFI 60

Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419
           YNQEE  RF+SD G+F AVT LGRP     N+Q D+ D+ R  +D  C++++ + +    
Sbjct: 61  YNQEEFARFNSDFGKFLAVTELGRPIVEYLNTQKDMLDNYRASVDR-CRNNYDLVD-IFM 118

Query: 420 ASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518
            +++ +P V + P+    L H NLL C   DFY
Sbjct: 119 LNLKAEPKVTVYPAKTQPLEHHNLLVCSVIDFY 151


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

 Score =  116 bits (290), Expect = 2e-26
 Identities = 60/148 (40%), Positives = 88/148 (59%), Gaps = 2/148 (1%)
 Frame = +3

Query: 81  RGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYIYNQEEHL 260
           R  W  A+ V L+ L + + EGRDSP++FV+Q K +CYF NGT++V L+ R+I+N EE+L
Sbjct: 5   RAPWVVALLVNLMRLDSFMIEGRDSPENFVIQAKADCYFTNGTEKVHLLVRFIFNLEEYL 64

Query: 261 RFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDPASV--RV 434
            FDSD+G F A+T LG P+A  WN + D+ +  R  ++  C+  + +     P +V   V
Sbjct: 65  HFDSDLGMFVALTELGEPDADQWNKRLDLLETSRAAVNMVCRQKYKLGA---PFTVERNV 121

Query: 435 QPSVNISPSAADALRHRNLLCCRGDDFY 518
            P V + P     L+  NLL C    FY
Sbjct: 122 PPEVTVYPERTPLLQQHNLLLCSVTGFY 149


  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: 31,860,424
Number of Sequences: 45328
Number of extensions: 776930
Number of successful extensions: 2794
Number of sequences better than 1.0e-05: 4
Number of HSP's better than  0.0 without gapping: 2318
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): 2779
length of database: 21,768,885
effective HSP length: 100
effective length of database: 17,236,085
effective search space used: 2188982795
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-038855
         (685 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...   190   9e-49
Alignment   gi|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis fami...   148   5e-36
Alignment   gi|XP_861384.1| PREDICTED: similar to HLA class II histocompati...   128   4e-30
Alignment   gi|XP_850395.1| PREDICTED: similar to HLA class II histocompati...   128   4e-30

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

 Score =  190 bits (483), Expect = 9e-49
 Identities = 95/156 (60%), Positives = 113/156 (72%)
 Frame = +3

Query: 51  MSGMVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVA 230
           MSG + L +PRG WTAAV ++LVVL  PVAEGRDSPQDFV Q+K ECYF NGT+RVRL+ 
Sbjct: 1   MSGKMTLCIPRGFWTAAVMMILVVLSIPVAEGRDSPQDFVFQYKAECYFTNGTERVRLLT 60

Query: 231 RYIYNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEG 410
           +YIYN+EE +RFDSDVGEFRAVT LGRP+A  WN Q D  D  R  LDT C+H++  +E 
Sbjct: 61  KYIYNREEFVRFDSDVGEFRAVTELGRPDAEYWNRQKDEMDRVRAELDTVCRHNYGREEL 120

Query: 411 TDPASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518
           T     RV+P+V I PS  + L H NLL C   DFY
Sbjct: 121 T-TLQRRVEPTVTIFPSKTEVLNHHNLLVCSVTDFY 155


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

 Score =  148 bits (373), Expect = 5e-36
 Identities = 74/153 (48%), Positives = 100/153 (65%)
 Frame = +3

Query: 60  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYI 239
           MV L    G W  A+ ++L+VL  P A  RD+P  F+   K ECYF NGT+RVR V RYI
Sbjct: 1   MVCLCFLGGSWMTALMLILMVLNPPFAWARDTPPHFLEVAKSECYFTNGTERVRFVERYI 60

Query: 240 YNQEEHLRFDSDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDP 419
           +N+EE +RFDSDVGEFRAVT LGRP A SWN Q ++ + +R  +DT C+H++ + E +  
Sbjct: 61  HNREEFVRFDSDVGEFRAVTELGRPVAESWNGQKEILEQERATVDTYCRHNYGVIE-SFT 119

Query: 420 ASVRVQPSVNISPSAADALRHRNLLCCRGDDFY 518
              RV+P+V + P+    L+H NLL C  + FY
Sbjct: 120 VQRRVEPTVTVYPTKTQTLQHHNLLVCSVNGFY 152


>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 =  128 bits (322), Expect = 4e-30
 Identities = 62/145 (42%), Positives = 92/145 (63%), Gaps = 2/145 (1%)
 Frame = +3

Query: 90  WTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYIYNQEEHLRFD 269
           W  A+ V +  L + + +GRDSP+DFV+Q K +CYF NGT++V+ V R+I+N EE+ RFD
Sbjct: 8   WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67

Query: 270 SDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDPASV--RVQPS 443
           S VG F A+T LG+P+A  WNSQ  + +  R  +D  C+H++ +     P +V  +VQP 
Sbjct: 68  SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGA---PFTVGRKVQPE 124

Query: 444 VNISPSAADALRHRNLLCCRGDDFY 518
           V + P    +++H NLL C    FY
Sbjct: 125 VTVYPERTPSMQHHNLLLCSVTGFY 149


>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 =  128 bits (322), Expect = 4e-30
 Identities = 62/145 (42%), Positives = 92/145 (63%), Gaps = 2/145 (1%)
 Frame = +3

Query: 90  WTAAVTVMLVVLGAPVAEGRDSPQDFVVQFKGECYFYNGTQRVRLVARYIYNQEEHLRFD 269
           W  A+ V +  L + + +GRDSP+DFV+Q K +CYF NGT++V+ V R+I+N EE+ RFD
Sbjct: 8   WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67

Query: 270 SDVGEFRAVTPLGRPEAYSWNSQNDVPDHKRV*LDTPCKHSHHIKEGTDPASV--RVQPS 443
           S VG F A+T LG+P+A  WNSQ  + +  R  +D  C+H++ +     P +V  +VQP 
Sbjct: 68  SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGA---PFTVGRKVQPE 124

Query: 444 VNISPSAADALRHRNLLCCRGDDFY 518
           V + P    +++H NLL C    FY
Sbjct: 125 VTVYPERTPSMQHHNLLLCSVTGFY 149


  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: 27,714,776
Number of Sequences: 33732
Number of extensions: 675472
Number of successful extensions: 2302
Number of sequences better than 1.0e-05: 4
Number of HSP's better than  0.0 without gapping: 2116
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): 2296
length of database: 19,266,565
effective HSP length: 99
effective length of database: 15,927,097
effective search space used: 2038668416
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)