Animal-Genome cDNA 20060611S-059361


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-059361
         (1063 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: 1,038,508
Number of Sequences: 1040
Number of extensions: 26992
Number of successful extensions: 104
Number of sequences better than 1.0e-05: 0
Number of HSP's better than  0.0 without gapping: 94
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): 103
length of database: 434,620
effective HSP length: 78
effective length of database: 353,500
effective search space used: 97212500
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-059361
         (1063 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, ...   240   1e-63
Alignment   gi|XP_582099.2| PREDICTED: similar to major histocompatibility ...   204   1e-52
Alignment   gi|XP_876139.1| PREDICTED: similar to H-2 class II histocompati...   188   5e-48
Alignment   gi|NP_001029840.2| MHC class II antigen [Bos taurus]                 185   5e-47
Alignment   gi|NP_001012694.1| major histocompatibility complex, class II, ...   183   2e-46
Alignment   gi|NP_001012697.1| major histocompatibility complex, class II, ...   179   4e-45
Alignment   gi|NP_001013618.1| major histocompatibility complex, class II, ...   164   8e-41
Alignment   gi|XP_874766.1| PREDICTED: similar to HLA class II histocompati...   110   2e-24
Alignment   gi|NP_001035571.1| major histocompatibility complex, class II, ...    52   6e-07

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

 Score =  240 bits (613), Expect = 1e-63
 Identities = 120/193 (62%), Positives = 138/193 (71%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           CHFF GTERVR L+R +YNGEEF+RF SD G +RAVTELGRP A  WNS KD LEQ+RAE
Sbjct: 44  CHFFNGTERVRFLDRHFYNGEEFVRFDSDWGEFRAVTELGRPAAEHWNSQKDFLEQKRAE 103

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           VD  CRHN+  +++F V RR EPTVTVYPAKTQPLQ HNLLVCSV  FYPGH+EV W +N
Sbjct: 104 VDRVCRHNYGGVESFTVQRRVEPTVTVYPAKTQPLQHHNLLVCSVNGFYPGHIEVRWFRN 163

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPES 704
           GH+E A V+STGLI NG WTFQT+VMLETVP         +  P    P T E +A  +S
Sbjct: 164 GHEEEAGVISTGLIQNGDWTFQTMVMLETVPQSGEVYTCQVDHPKRTSPITVEWRARSDS 223

Query: 705 SPG*NYDWGSGGF 743
           +       G GGF
Sbjct: 224 AQS-KMMSGVGGF 235


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

 Score =  204 bits (519), Expect = 1e-52
 Identities = 102/181 (56%), Positives = 121/181 (66%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           C F  G ER+R   R  YN +E + F SDVG + A+TELGR DA  WN  KD +EQ RA+
Sbjct: 33  CRFSNGLERMRFFARYIYNTQEDVHFDSDVGEFTALTELGRLDAEYWNQQKDFMEQMRAK 92

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           VDT CR N++ + +FL  RR EPTVTVYPAKTQPLQ HNLLVCSV  FYPGH+EV W  N
Sbjct: 93  VDTLCRSNYQGIGSFLRQRRVEPTVTVYPAKTQPLQHHNLLVCSVNGFYPGHIEVRWFWN 152

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPES 704
            H+E A V+STGLI NG WTFQT+VMLETVP         +  P    P T E +A  +S
Sbjct: 153 SHEEEAGVISTGLIQNGDWTFQTMVMLETVPQSGEVYTCQVEHPSRTSPLTVEWRAQSDS 212

Query: 705 S 707
           +
Sbjct: 213 A 213


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

 Score =  188 bits (478), Expect = 5e-48
 Identities = 96/181 (53%), Positives = 115/181 (63%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           CHF  GT++VR L+R  YN EE ++F S VG YRA TE+GRP A  WN     L++ RA 
Sbjct: 8   CHFSNGTQQVRFLDRYIYNREEQVQFDSLVGEYRARTEMGRPAAERWNRWPQALQRARAA 67

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           V  YC  N+    +  V RR +PTVTVYP K++PL  HNLLVCSV  FYPGH+EV W +N
Sbjct: 68  VHAYCASNYEFFASRTVQRRVQPTVTVYPVKSRPLWHHNLLVCSVNGFYPGHIEVRWFRN 127

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPES 704
           G +E A VVSTGLIPNG WTFQ +VMLE VP         +  P    P T E +A  ES
Sbjct: 128 GQEEEAGVVSTGLIPNGDWTFQIMVMLEIVPQGGEVYACHVEHPSRTSPVTVEWRAQDES 187

Query: 705 S 707
           S
Sbjct: 188 S 188


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

 Score =  185 bits (470), Expect = 5e-47
 Identities = 100/193 (51%), Positives = 119/193 (61%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           C+F  GTERVR + R  YN EE++RF SD   YRA+T LGRPDA  WNS KD LEQ RAE
Sbjct: 47  CYFTNGTERVRYVTRYIYNQEEYVRFDSDWDLYRALTPLGRPDAEYWNSQKDFLEQTRAE 106

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
            DT CRHN++      + RR EPTVT+ P++T+ L  HNLLVCSVT FYP  ++V W +N
Sbjct: 107 ADTVCRHNYQAELITSLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPSQIKVRWFRN 166

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPES 704
             +E A VVST LI NG WTFQ LVMLE  P         +  P L  P   E +A  ES
Sbjct: 167 DREETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPIMVEWRAQSES 226

Query: 705 SPG*NYDWGSGGF 743
           +       G GGF
Sbjct: 227 AQSKMLS-GVGGF 238


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

 Score =  183 bits (465), Expect = 2e-46
 Identities = 99/193 (51%), Positives = 122/193 (63%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           C+F  GTERVR + R  YN EE   + SDVG YRAVT+LGR  A  WNS KD+LEQ RAE
Sbjct: 47  CYFTNGTERVRYVTRYIYNQEETAYYDSDVGEYRAVTQLGRTLAEYWNSQKDILEQTRAE 106

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           +DT CRHN+++     + R+ EPTVT+  ++T+ L  HNLLVCSVT FYPG ++V W QN
Sbjct: 107 LDTVCRHNYQLEVITSLQRQVEPTVTISLSRTEALNHHNLLVCSVTDFYPGQIKVRWFQN 166

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPES 704
           G +E A +VST LI NG WTFQ LVMLE  P         +  P L  P + E +A  ES
Sbjct: 167 GKEETAGIVSTPLIRNGDWTFQILVMLEMTPKRGDVYTCHVEHPSLQSPISVEWRAQSES 226

Query: 705 SPG*NYDWGSGGF 743
           +       G GGF
Sbjct: 227 AQSKMLS-GVGGF 238


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

 Score =  179 bits (453), Expect = 4e-45
 Identities = 100/193 (51%), Positives = 118/193 (61%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           C+F  GTE VRL+ RQ YN EE L F SD+G + AVTELGR  A  WN+ KDLL + RA 
Sbjct: 45  CYFTNGTEHVRLVARQIYNKEEILHFDSDLGEFVAVTELGRVCAEIWNTQKDLLAEFRAY 104

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           VDT CRHN++    F V RR EPTVTV PA T+ L  HNLLVCSVT FYP  V+V W +N
Sbjct: 105 VDTLCRHNYKETAGFTVQRRVEPTVTVSPASTEALNHHNLLVCSVTDFYPRQVKVKWFRN 164

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPES 704
             ++ A V  T L  NG WT+Q  VMLETVP      +  +  P L  P T E +A  ES
Sbjct: 165 QQEQTAGVGFTPLTQNGDWTYQIHVMLETVPQLGDVYVCHVDHPSLQSPITVEWRAQSES 224

Query: 705 SPG*NYDWGSGGF 743
           +       G GGF
Sbjct: 225 AQS-KMQSGIGGF 236


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

 Score =  164 bits (416), Expect = 8e-41
 Identities = 84/181 (46%), Positives = 111/181 (61%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           C+F  GTE+VR + R  +N E++ RF SD+G + A+TELG+PDA  WN+  D+L + RA 
Sbjct: 41  CYFTNGTEKVRFVVRFIFNLEDYARFDSDLGMFVALTELGKPDAERWNNRPDILARSRAS 100

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           VD  CR N+ +   F V RR +P VTVYP KT  LQ  NLL+C VT FYPG ++V W +N
Sbjct: 101 VDMLCRRNYYLGAPFTVGRRVQPEVTVYPEKTPALQHRNLLLCLVTGFYPGDIKVTWFRN 160

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPES 704
           G ++   ++STGLI NG WTFQ  VML   P         +  P L  P + E +A  E 
Sbjct: 161 GQEQREGIMSTGLIRNGDWTFQMTVMLAMTPELGEVYTCLVDHPSLLSPVSVEWRAQSEY 220

Query: 705 S 707
           S
Sbjct: 221 S 221


>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 =  110 bits (275), Expect = 2e-24
 Identities = 59/115 (51%), Positives = 72/115 (62%)
 Frame = +3

Query: 399 RRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQNGHQEAASVVSTGLIPNGY 578
           ++ EPTVTVYPAKTQPLQ ++LLVCSV  FY GHVEV W   G +E A V+STGLI NG 
Sbjct: 93  KKVEPTVTVYPAKTQPLQHNHLLVCSVNGFYLGHVEVRWFWKGQEEEAGVISTGLIQNGD 152

Query: 579 WTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPESSPG*NYDWGSGGF 743
           WTF+T+VMLETV          +  P    P   E +A  +S+       G+GGF
Sbjct: 153 WTFETIVMLETVLQSGEVYTCQLEHPSWRSPIAEEWRAQSDSAQS-KMMSGTGGF 206


>ref|NP_001035571.1| major histocompatibility complex, class II, DM beta-chain,
           expressed [Bos taurus]
          Length = 262

 Score = 52.4 bits (124), Expect = 6e-07
 Identities = 36/97 (37%), Positives = 46/97 (47%), Gaps = 3/97 (3%)
 Frame = +3

Query: 390 LVPRRAEPTVTVYPAKTQPLQLHN--LLVCSVTWFYPGHVEVMWLQNGHQEAASVVSTGL 563
           L  R   PTV V  AKT P       +L C V  FYP  V + W +NG +      +  +
Sbjct: 108 LTHRTRPPTVQV--AKTTPFNTRESVMLACYVWGFYPADVAITWRRNGQEVLPHGRAWRI 165

Query: 564 I-PNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYP 671
           I PNG WT+QT+  L T PS+  G     V  H+  P
Sbjct: 166 IQPNGDWTYQTVSHLATTPSF--GDTYTCVVEHIGAP 200


  Database: RefSeqBP
    Posted date:  Aug 1, 2006  7:14 PM
  Number of letters in database: 16,112,626
  Number of sequences in database:  33,508
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 38,825,998
Number of Sequences: 33508
Number of extensions: 1053064
Number of successful extensions: 3353
Number of sequences better than 1.0e-05: 9
Number of HSP's better than  0.0 without gapping: 3018
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): 3329
length of database: 16,112,626
effective HSP length: 102
effective length of database: 12,694,810
effective search space used: 3186397310
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-059361
         (1063 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...   227   2e-59
Alignment   gi|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Ca...   191   8e-49
Alignment   gi|XP_861384.1| PREDICTED: similar to HLA class II histocompati...   172   1e-44
Alignment   gi|XP_850395.1| PREDICTED: similar to HLA class II histocompati...   174   1e-43
Alignment   gi|XP_849737.1| PREDICTED: similar to HLA class II histocompati...    53   6e-07

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

 Score =  227 bits (578), Expect = 2e-59
 Identities = 120/211 (56%), Positives = 143/211 (67%)
 Frame = +3

Query: 111 FGQETPHTHYLAPD*NS*CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRP 290
           + ++TP  H+L     S C+F  GTERVR +ER  +N EEF+RF SDVG +RAVTELGRP
Sbjct: 28  WARDTP-PHFLEVA-KSECYFTNGTERVRFVERYIHNREEFVRFDSDVGEFRAVTELGRP 85

Query: 291 DANDWNSLKDLLEQRRAEVDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLV 470
            A  WN  K++LEQ RA VDTYCRHN+ ++++F V RR EPTVTVYP KTQ LQ HNLLV
Sbjct: 86  VAESWNGQKEILEQERATVDTYCRHNYGVIESFTVQRRVEPTVTVYPTKTQTLQHHNLLV 145

Query: 471 CSVTWFYPGHVEVMWLQNGHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIV 650
           CSV  FYPGH+EV WL+NG +E A VVSTGLI NG WTFQ LVMLE VP         + 
Sbjct: 146 CSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNGDWTFQILVMLEIVPQSGEVYTCQVE 205

Query: 651 TPHLNYPFTFECKAPPESSPG*NYDWGSGGF 743
            P L  P T E +A  +S+       G GGF
Sbjct: 206 HPSLTSPVTVEWRAQSDSAQSKMLS-GIGGF 235


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

 Score =  191 bits (486), Expect = 8e-49
 Identities = 101/193 (52%), Positives = 125/193 (64%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           C+F  GTERVRLL +  YN EEF+RF SDVG +RAVTELGRPDA  WN  KD +++ RAE
Sbjct: 47  CYFTNGTERVRLLTKYIYNREEFVRFDSDVGEFRAVTELGRPDAEYWNRQKDEMDRVRAE 106

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           +DT CRHN+   +   + RR EPTVT++P+KT+ L  HNLLVCSVT FYPG ++V W +N
Sbjct: 107 LDTVCRHNYGREELTTLQRRVEPTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKVRWFRN 166

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPES 704
             ++ A VVST LI NG WTFQ LVMLE  P         +    L  P T + +A  ES
Sbjct: 167 DQEQTAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHASLQSPITVQWRAQSES 226

Query: 705 SPG*NYDWGSGGF 743
           +       G GGF
Sbjct: 227 AQSKMLS-GIGGF 238


>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 =  172 bits (437), Expect(2) = 1e-44
 Identities = 81/151 (53%), Positives = 106/151 (70%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           C+F  GTE+V+ + R  +N EE+ RF S VG + A+TELG+PDA  WNS   +LE+ RA 
Sbjct: 41  CYFINGTEKVQFVVRFIFNLEEYARFDSHVGMFVALTELGKPDAELWNSQPGILERSRAS 100

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           VD  CRHN+ +   F V R+ +P VTVYP +T  +Q HNLL+CSVT FYPG +++ W +N
Sbjct: 101 VDLLCRHNYELGAPFTVGRKVQPEVTVYPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRN 160

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVP 617
           G +E   V+STGLI NG WTFQT+VMLE  P
Sbjct: 161 GQEERVGVMSTGLIRNGDWTFQTMVMLEMTP 191



 Score = 26.6 bits (57), Expect(2) = 1e-44
 Identities = 9/23 (39%), Positives = 17/23 (73%)
 Frame = +1

Query: 604 LKQFPRIGEVFSCLL*HPT*TTP 672
           L+  P +G+V++CL+ HP+  +P
Sbjct: 187 LEMTPELGDVYTCLVNHPSLLSP 209


>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 =  174 bits (441), Expect = 1e-43
 Identities = 86/176 (48%), Positives = 114/176 (64%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           C+F  GTE+V+ + R  +N EE+ RF S VG + A+TELG+PDA  WNS   +LE+ RA 
Sbjct: 41  CYFINGTEKVQFVVRFIFNLEEYARFDSHVGMFVALTELGKPDAELWNSQPGILERSRAS 100

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           VD  CRHN+ +   F V R+ +P VTVYP +T  +Q HNLL+CSVT FYPG +++ W +N
Sbjct: 101 VDLLCRHNYELGAPFTVGRKVQPEVTVYPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRN 160

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKA 692
           G +E   V+STGLI NG WTFQT+VMLE  P         +  P L  P + E +A
Sbjct: 161 GQEERVGVMSTGLIRNGDWTFQTMVMLEMTPELGDVYTCLVNHPSLLSPVSVEWRA 216


>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 = 52.8 bits (125), Expect = 6e-07
 Identities = 38/116 (32%), Positives = 54/116 (46%), Gaps = 7/116 (6%)
 Frame = +3

Query: 297 NDWNSLKDLLEQRRAEVDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHN--LLV 470
           +D+ + ++ L QR +     C  + +     L  R   PTV V  AK+ P       +L 
Sbjct: 77  SDYLNQQEYLHQRLSNGLQDCATHTQSFWGSLTHRTRPPTVQV--AKSTPFNTKESVMLA 134

Query: 471 CSVTWFYPGHVEVMWLQNG-----HQEAASVVSTGLIPNGYWTFQTLVMLETVPSY 623
           C V  FYP  V + W +NG     H  A ++      PNG WT+QT+  L T PSY
Sbjct: 135 CYVWGFYPADVTISWRKNGQPVPSHSSALNMAQ----PNGDWTYQTVSHLATTPSY 186


  Database: RefSeqCP
    Posted date:  Aug 1, 2006  9:25 PM
  Number of letters in database: 19,266,565
  Number of sequences in database:  33,732
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 45,717,982
Number of Sequences: 33732
Number of extensions: 1241622
Number of successful extensions: 4064
Number of sequences better than 1.0e-05: 5
Number of HSP's better than  0.0 without gapping: 3550
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): 4040
length of database: 19,266,565
effective HSP length: 104
effective length of database: 15,758,437
effective search space used: 3923850813
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-059361
         (1063 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 ...   241   8e-64
Alignment   gi|NP_072049.2| major histocompatibility complex, class II, DR ...   232   4e-61
Alignment   gi|NP_002116.2| major histocompatibility complex, class II, DR ...   231   1e-60
Alignment   gi|XP_945926.1| PREDICTED: similar to HLA class II histocompati...   229   2e-60
Alignment   gi|XP_949915.1| PREDICTED: similar to HLA class II histocompati...   229   2e-60
Alignment   gi|NP_068818.4| major histocompatibility complex, class II, DR ...   225   6e-59
Alignment   gi|XP_949921.1| PREDICTED: similar to HLA class II histocompati...   224   7e-59
Alignment   gi|NP_002114.2| major histocompatibility complex, class II, DQ ...   186   2e-47
Alignment   gi|NP_002112.3| major histocompatibility complex, class II, DP ...   183   2e-46
Alignment   gi|NP_872355.1| major histocompatibility complex, class II, DQ ...   173   2e-43

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

 Score =  241 bits (615), Expect = 8e-64
 Identities = 125/193 (64%), Positives = 139/193 (72%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           CHFF GTERVRLLER  YN EE +RF SDVG YRAVTELGRPDA  WNS KDLLEQRRA 
Sbjct: 44  CHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAA 103

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           VDTYCRHN+ + ++F V RR EP VTVYP+KTQPLQ HNLLVCSV+ FYPG +EV W +N
Sbjct: 104 VDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRN 163

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPES 704
           G +E A VVSTGLI NG WTFQTLVMLETVP         +  P +  P T E +A  ES
Sbjct: 164 GQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSES 223

Query: 705 SPG*NYDWGSGGF 743
           +       G GGF
Sbjct: 224 AQSKMLS-GVGGF 235


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

 Score =  232 bits (592), Expect = 4e-61
 Identities = 119/193 (61%), Positives = 135/193 (69%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           CHFF GTERVR L+R ++N EEFLRF SDVG YRAVTELGRP A  WNS KDLLEQ+R  
Sbjct: 44  CHFFNGTERVRYLDRYFHNQEEFLRFDSDVGEYRAVTELGRPVAESWNSQKDLLEQKRGR 103

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           VD YCRHN+ + ++F V RR  P VTVYPAKTQPLQ HNLLVCSV+ FYPG +EV W +N
Sbjct: 104 VDNYCRHNYGVGESFTVQRRVHPQVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRN 163

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPES 704
           G +E A VVSTGLI NG WTFQTLVMLETVP         +  P +    T E +A  ES
Sbjct: 164 GQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSALTVEWRARSES 223

Query: 705 SPG*NYDWGSGGF 743
           +       G GGF
Sbjct: 224 AQSKMLS-GVGGF 235


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

 Score =  231 bits (588), Expect = 1e-60
 Identities = 120/193 (62%), Positives = 132/193 (68%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           CHFF GTERVR L R  YN EE LRF SDVG YRAVTELGRPDA  WNS KD LE RRA 
Sbjct: 44  CHFFNGTERVRFLHRDIYNQEEDLRFDSDVGEYRAVTELGRPDAEYWNSQKDFLEDRRAA 103

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           VDTYCRHN+ + ++F V RR EP VTVYPA+TQ LQ HNLLVCSV  FYPG +EV W +N
Sbjct: 104 VDTYCRHNYGVGESFTVQRRVEPKVTVYPARTQTLQHHNLLVCSVNGFYPGSIEVRWFRN 163

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPES 704
             +E A VVSTGLI NG WTFQTLVMLETVP         +  P +  P T E +A  ES
Sbjct: 164 SQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRAQSES 223

Query: 705 SPG*NYDWGSGGF 743
           +       G GGF
Sbjct: 224 AQSKMLS-GVGGF 235


>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 =  229 bits (585), Expect = 2e-60
 Identities = 120/193 (62%), Positives = 134/193 (69%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           CHFF GTERVR L R  YN EE +RF SDVG YRAVTELGRP A  WNS KD LE+RRAE
Sbjct: 44  CHFFNGTERVRYLHRGIYNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAE 103

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           VDT CRHN+ + ++F V RR  P VTVYPAKTQPLQ HNLLVCSV+ FYPG +EV W +N
Sbjct: 104 VDTVCRHNYGVGESFTVQRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRN 163

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPES 704
           G +E A VVSTGLI NG WTFQTLVMLETVP         +  P +  P T E +A  ES
Sbjct: 164 GQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEWRARSES 223

Query: 705 SPG*NYDWGSGGF 743
           +       G GGF
Sbjct: 224 AQSKMLS-GVGGF 235


>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 =  229 bits (585), Expect = 2e-60
 Identities = 120/193 (62%), Positives = 134/193 (69%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           CHFF GTERVR L R  YN EE +RF SDVG YRAVTELGRP A  WNS KD LE+RRAE
Sbjct: 62  CHFFNGTERVRYLHRGIYNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAE 121

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           VDT CRHN+ + ++F V RR  P VTVYPAKTQPLQ HNLLVCSV+ FYPG +EV W +N
Sbjct: 122 VDTVCRHNYGVGESFTVQRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRN 181

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPES 704
           G +E A VVSTGLI NG WTFQTLVMLETVP         +  P +  P T E +A  ES
Sbjct: 182 GQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEWRARSES 241

Query: 705 SPG*NYDWGSGGF 743
           +       G GGF
Sbjct: 242 AQSKMLS-GVGGF 253


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

 Score =  225 bits (573), Expect = 6e-59
 Identities = 115/193 (59%), Positives = 135/193 (69%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           CHF  GTERV  L R  YN EE+ R+ SD+G Y+AVTELGRPDA  WNS KDLLE+RRAE
Sbjct: 44  CHFLNGTERVWNLIRYIYNQEEYARYNSDLGEYQAVTELGRPDAEYWNSQKDLLERRRAE 103

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           VDTYCR+N+ ++++F V RR +P VTVYP+KTQPLQ HNLLVCSV  FYPG +EV W +N
Sbjct: 104 VDTYCRYNYGVVESFTVQRRVQPKVTVYPSKTQPLQHHNLLVCSVNGFYPGSIEVRWFRN 163

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPES 704
           G +E A VVSTGLI NG WTFQTLVMLETVP         +  P +  P T +  A  ES
Sbjct: 164 GQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSMMSPLTVQWSARSES 223

Query: 705 SPG*NYDWGSGGF 743
           +       G GGF
Sbjct: 224 AQSKMLS-GVGGF 235


>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 =  224 bits (572), Expect = 7e-59
 Identities = 113/173 (65%), Positives = 125/173 (72%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           CHFF GTERVR L R  YN EE +RF SDVG YRAVTELGRP A  WNS KD LE+RRAE
Sbjct: 44  CHFFNGTERVRYLHRGIYNQEENVRFDSDVGEYRAVTELGRPVAESWNSQKDFLERRRAE 103

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           VDT CRHN+ + ++F V RR  P VTVYPAKTQPLQ HNLLVCSV+ FYPG +EV W +N
Sbjct: 104 VDTVCRHNYGVGESFTVQRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRN 163

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFE 683
           G +E A VVSTGLI NG WTFQTLVMLETVP         +  P +  P T E
Sbjct: 164 GQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVE 216


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

 Score =  186 bits (473), Expect = 2e-47
 Identities = 100/193 (51%), Positives = 122/193 (63%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           C+F  GTERVRL+ R  YN EE +RF SDVG +RAVT LG P A  WNS KD+LE++RA 
Sbjct: 47  CYFTNGTERVRLVSRSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAA 106

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           VD  CRHN+++     + RR EPTVT+ P++T+ L  HNLLVCSVT FYP  ++V W +N
Sbjct: 107 VDRVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRN 166

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPES 704
             +E A VVST LI NG WTFQ LVMLE  P         +  P L  P T E +A  ES
Sbjct: 167 DQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSES 226

Query: 705 SPG*NYDWGSGGF 743
           +       G GGF
Sbjct: 227 AQSKMLS-GIGGF 238


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

 Score =  183 bits (464), Expect = 2e-46
 Identities = 100/193 (51%), Positives = 119/193 (61%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           C+ F GT+R   LER  YN EEF RF SDVG +RAVTELGRP A  WNS KD+LE++RA 
Sbjct: 44  CYAFNGTQR--FLERYIYNREEFARFDSDVGEFRAVTELGRPAAEYWNSQKDILEEKRAV 101

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
            D  CRHN+ +     + RR +P V V P+K  PLQ HNLLVC VT FYPG ++V W  N
Sbjct: 102 PDRMCRHNYELGGPMTLQRRVQPRVNVSPSKKGPLQHHNLLVCHVTDFYPGSIQVRWFLN 161

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPES 704
           G +E A VVST LI NG WTFQ LVMLE  P         +    L+ P T E KA  +S
Sbjct: 162 GQEETAGVVSTNLIRNGDWTFQILVMLEMTPQQGDVYTCQVEHTSLDSPVTVEWKAQSDS 221

Query: 705 SPG*NYDWGSGGF 743
           +       G+GGF
Sbjct: 222 ARSKTLT-GAGGF 233


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

 Score =  173 bits (439), Expect = 2e-43
 Identities = 93/180 (51%), Positives = 112/180 (62%), Gaps = 2/180 (1%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           C+F  GTERVR + R  YN EE+ RF SDVG ++AVTELGR    DWN+ KD LEQ RA 
Sbjct: 47  CYFTNGTERVRGVARYIYNREEYGRFDSDVGEFQAVTELGR-SIEDWNNYKDFLEQERAA 105

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           VD  CRHN+       + R+ EPTVT+ P++T+ L  HNLLVCSVT FYP  ++V W +N
Sbjct: 106 VDKVCRHNYEAELRTTLQRQVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVQWFRN 165

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFEC--KAPP 698
             +E A VVST LI NG WTFQ LVMLE  P         +  P L  P T E   + PP
Sbjct: 166 DQEETAGVVSTSLIRNGDWTFQILVMLEITPQRGDIYTCQVEHPSLQSPITVEWRPRGPP 225


  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: 43,959,796
Number of Sequences: 39411
Number of extensions: 1221145
Number of successful extensions: 4356
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 3694
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): 4298
length of database: 17,774,539
effective HSP length: 103
effective length of database: 13,715,206
effective search space used: 3428801500
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-059361
         (1063 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 [...   236   2e-62
Alignment   gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/...   183   3e-46
Alignment   gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ...   169   1e-43
Alignment   gi|NP_996988.1| histocompatibility 2, class II antigen A, beta ...   173   3e-43

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

 Score =  236 bits (603), Expect = 2e-62
 Identities = 117/193 (60%), Positives = 139/193 (72%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           CHF+ GT+RVR L+R +YN EE LRF SDVG +RAVTELGRPDA +WNS  ++L+++RA 
Sbjct: 42  CHFYNGTQRVRFLKRYFYNLEENLRFDSDVGEFRAVTELGRPDAENWNSQPEILDEKRAA 101

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           VDTYCRHN+ I D FLVPRR EPTVTVYP KTQPL+ HNLLVCSV+ FYPG++EV W +N
Sbjct: 102 VDTYCRHNYEIFDNFLVPRRVEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRN 161

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPES 704
           G +E   +VSTGL+ NG WTFQTLVMLETVP         +  P L  P T E KA   S
Sbjct: 162 GKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEWKAQSTS 221

Query: 705 SPG*NYDWGSGGF 743
           +       G GGF
Sbjct: 222 AQNKMLS-GVGGF 233


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

 Score =  183 bits (464), Expect = 3e-46
 Identities = 97/181 (53%), Positives = 118/181 (65%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           CH+F G ERV  + R  YN EEF RF SD G + AVTELGRP     N+ KD+L+  RA 
Sbjct: 44  CHYFNGKERVWSVTRFIYNQEEFARFNSDFGKFLAVTELGRPIVEYLNTQKDMLDNYRAS 103

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           VD  CR+N+ ++D F++  +AEP VTVYPAKTQPL+ HNLLVCSV  FYPG +EV W +N
Sbjct: 104 VDR-CRNNYDLVDIFMLNLKAEPKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRN 162

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPES 704
           G +E   VVSTGLI N  WT+QTLVMLE VP         +  P L  P T E +A   S
Sbjct: 163 GEEEKTGVVSTGLIQNRDWTYQTLVMLEMVPRGGEVYTCQVEHPSLTSPVTVEWRARSTS 222

Query: 705 S 707
           +
Sbjct: 223 A 223


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

 Score =  169 bits (429), Expect(2) = 1e-43
 Identities = 82/151 (54%), Positives = 103/151 (68%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           C+F  GTE+V LL R  +N EE+L F SD+G + A+TELG PDA+ WN   DLLE  RA 
Sbjct: 41  CYFTNGTEKVHLLVRFIFNLEEYLHFDSDLGMFVALTELGEPDADQWNKRLDLLETSRAA 100

Query: 345 VDTYCRHNFRILDTFLVPRRAEPTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQN 524
           V+  CR  +++   F V R   P VTVYP +T  LQ HNLL+CSVT FYPG + V W +N
Sbjct: 101 VNMVCRQKYKLGAPFTVERNVPPEVTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRN 160

Query: 525 GHQEAASVVSTGLIPNGYWTFQTLVMLETVP 617
           G +E + V+STGL+ NG WTFQT VMLE +P
Sbjct: 161 GQEERSGVMSTGLVRNGDWTFQTTVMLEMIP 191



 Score = 26.6 bits (57), Expect(2) = 1e-43
 Identities = 8/18 (44%), Positives = 14/18 (77%)
 Frame = +1

Query: 604 LKQFPRIGEVFSCLL*HP 657
           L+  P +G+++SCL+ HP
Sbjct: 187 LEMIPELGDIYSCLVEHP 204


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

 Score =  173 bits (438), Expect = 3e-43
 Identities = 90/182 (49%), Positives = 115/182 (63%), Gaps = 1/182 (0%)
 Frame = +3

Query: 165 CHFFYGTERVRLLERQYYNGEEFLRFYSDVG*YRAVTELGRPDANDWNSLKDLLEQRRAE 344
           C+F  GT+R+R + R  YN EE++R+ SDVG +RAVTELGRPDA  WNS  ++LE+ RAE
Sbjct: 42  CYFTNGTQRIRYVTRYIYNREEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAE 101

Query: 345 VDTYCRHNFRILDTFLVPRRAE-PTVTVYPAKTQPLQLHNLLVCSVTWFYPGHVEVMWLQ 521
           +DT CRHN+   +T    RR E P V +  ++T+ L  HN LVCSVT FYP  ++V W +
Sbjct: 102 LDTVCRHNYEGPETHTSLRRLEQPNVVISLSRTEALNHHNTLVCSVTDFYPTQIKVRWFR 161

Query: 522 NGHQEAASVVSTGLIPNGYWTFQTLVMLETVPSYWRGLLLPIVTPHLNYPFTFECKAPPE 701
           NG +E   V ST LI NG WTFQ LVMLE  P         +  P L  P T E +A  E
Sbjct: 162 NGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRAQSE 221

Query: 702 SS 707
           S+
Sbjct: 222 SA 223


  Database: RefSeqMP
    Posted date:  Aug 2, 2006 12:58 AM
  Number of letters in database: 21,768,885
  Number of sequences in database:  45,328
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 52,015,009
Number of Sequences: 45328
Number of extensions: 1402213
Number of successful extensions: 4367
Number of sequences better than 1.0e-05: 4
Number of HSP's better than  0.0 without gapping: 3827
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): 4354
length of database: 21,768,885
effective HSP length: 104
effective length of database: 17,054,773
effective search space used: 4246638477
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)