Animal-Genome cDNA 20060611S-062998


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-062998
         (1156 letters)

Database: RefSeqSP 
           1040 sequences; 434,620 total letters

Searching...done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_999143.1| beta 2-microglobulin [Sus scrofa]                    209   8e-56
Alignment   gi|NP_998933.1| swine leukocyte antigen 7 [Sus scrofa]                49   3e-07
Alignment   gi|NP_001004039.1| SLA-DM alpha chain [Sus scrofa]                    47   7e-07

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

 Score =  209 bits (533), Expect = 8e-56
 Identities = 96/96 (100%), Positives = 96/96 (100%)
 Frame = +2

Query: 95  RPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWSFY 274
           RPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWSFY
Sbjct: 23  RPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWSFY 82

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH 382
           LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH
Sbjct: 83  LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH 118


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

 Score = 48.5 bits (114), Expect = 3e-07
 Identities = 28/94 (29%), Positives = 45/94 (47%), Gaps = 2/94 (2%)
 Frame = +2

Query: 98  PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGE--KMNAEQSDLSFSKDWSF 271
           PPK  V +RHP+ + K   L C+  GF+P +I +   + G+    + E  +   S D +F
Sbjct: 205 PPKTHV-TRHPSSDNKVT-LRCWALGFYPKEISLTWQQEGQDQSQDVEVVETRPSGDGTF 262

Query: 272 YLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
                    P     Y+C V+H  L +P  ++WD
Sbjct: 263 RKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRWD 296


>ref|NP_001004039.1| SLA-DM alpha chain [Sus scrofa]
          Length = 260

 Score = 47.4 bits (111), Expect = 7e-07
 Identities = 26/80 (32%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNA-EQSDLSFSKDWSFYL 277
           P  +V++  P E GKPN L C+VS   PP + +    +   +     + +S + D SF  
Sbjct: 127 PIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPVEGIGPTFVSATDDLSFQA 186

Query: 278 LVHTEFTPNAVDQYSCRVKH 337
             +  FTP   D +SC V H
Sbjct: 187 FSYLNFTPTPSDLFSCVVTH 206


  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: 962,196
Number of Sequences: 1040
Number of extensions: 22096
Number of successful extensions: 66
Number of sequences better than 1.0e-05: 3
Number of HSP's better than  0.0 without gapping: 56
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): 63
length of database: 434,620
effective HSP length: 78
effective length of database: 353,500
effective search space used: 108171000
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-062998
         (1156 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_776318.1| beta-2-microglobulin [Bos taurus]                    183   3e-46
Alignment   gi|NP_001013619.2| histocompatibility complex, class II, DQ alp...    72   8e-13
Alignment   gi|NP_001012693.1| major histocompatibility complex, class II, ...    70   3e-12
Alignment   gi|NP_001012699.1| major histocompatibility complex, class II, ...    68   1e-11
Alignment   gi|NP_001012695.1| major histocompatibility complex, class II, ...    63   4e-10
Alignment   gi|NP_001012694.1| major histocompatibility complex, class II, ...    57   2e-08
Alignment   gi|NP_001029840.2| MHC class II antigen [Bos taurus]                  56   5e-08
Alignment   gi|XP_876139.1| PREDICTED: similar to H-2 class II histocompati...    56   6e-08
Alignment   gi|XP_604082.2| PREDICTED: similar to HLA class II histocompati...    54   2e-07
Alignment   gi|XP_883292.1| PREDICTED: similar to HLA class II histocompati...    54   2e-07

>ref|NP_776318.1| beta-2-microglobulin [Bos taurus]
          Length = 118

 Score =  183 bits (464), Expect = 3e-46
 Identities = 81/95 (85%), Positives = 89/95 (93%)
 Frame = +2

Query: 95  RPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWSFY 274
           RPPK+QVYSRHP E+GKPNYLNCYV GFHPPQIEIDLLKNGEK+ +EQSDLSFSKDWSFY
Sbjct: 23  RPPKIQVYSRHPPEDGKPNYLNCYVYGFHPPQIEIDLLKNGEKIKSEQSDLSFSKDWSFY 82

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRD 379
           LL H EFTPN+ DQYSCRVKHVTL++P+IVKWDRD
Sbjct: 83  LLSHAEFTPNSKDQYSCRVKHVTLEQPRIVKWDRD 117


>ref|NP_001013619.2| histocompatibility complex, class II, DQ alpha, type 1 [Bos taurus]
          Length = 255

 Score = 72.0 bits (175), Expect = 8e-13
 Identities = 36/95 (37%), Positives = 53/95 (55%), Gaps = 2/95 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 274
           P+V V+S+ P   G+PN L C+V    PP I I  L+NG  +    S+ SF    D+SF 
Sbjct: 113 PEVTVFSKSPVMLGQPNTLICHVDNIFPPVINITWLRNGHSVTEGVSETSFLIKSDYSFL 172

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRD 379
            + +  F P+  D Y C+V+H  LD+P +  W+ D
Sbjct: 173 KINYLTFLPSDDDVYDCKVEHWGLDEPLLKHWEPD 207


>ref|NP_001012693.1| major histocompatibility complex, class II, DQ alpha [Bos taurus]
          Length = 255

 Score = 70.1 bits (170), Expect = 3e-12
 Identities = 35/93 (37%), Positives = 52/93 (55%), Gaps = 2/93 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 274
           P+V V+S+ P   G+PN L C+V    PP I I  L+NG  +    S+ SF    D+SF 
Sbjct: 113 PEVTVFSKSPVMLGQPNTLICHVDNIFPPVINITWLRNGHSVTEGVSETSFLIRSDYSFL 172

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
            + +  F P+  D Y C+V+H  LD+P +  W+
Sbjct: 173 KIKYLAFLPSDDDIYDCKVEHWGLDEPLLKHWE 205


>ref|NP_001012699.1| major histocompatibility complex, class II, DQ alpha 1 [Bos taurus]
          Length = 268

 Score = 68.2 bits (165), Expect = 1e-11
 Identities = 36/92 (39%), Positives = 50/92 (54%), Gaps = 2/92 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 274
           P+V V+S+ P   G+PN L C+V    PP I I  LKNG  +    S+ SF    D SF 
Sbjct: 113 PEVTVFSKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHAVTEGVSETSFLPKDDHSFL 172

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKW 370
            + +  F P+  D Y C+V+H  LD+P +  W
Sbjct: 173 KIGYLTFLPSDNDIYDCKVEHWGLDEPLLKHW 204


>ref|NP_001012695.1| major histocompatibility complex, class II, DR alpha [Bos taurus]
          Length = 253

 Score = 63.2 bits (152), Expect = 4e-10
 Identities = 31/94 (32%), Positives = 48/94 (51%), Gaps = 2/94 (2%)
 Frame = +2

Query: 98  PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSF 271
           PP+V +    P E G+PN L C++  F PP I +  L+NG+ +    S   F    D  F
Sbjct: 110 PPEVTLLPNKPVELGEPNTLICFIDKFSPPVISVTWLRNGKPVTDGVSQTVFLPRNDHLF 169

Query: 272 YLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
               +  F P   D Y C+V+H+ L++P +  W+
Sbjct: 170 RKFHYLPFLPTTEDVYDCKVEHLGLNEPLLKHWE 203


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

 Score = 57.4 bits (137), Expect = 2e-08
 Identities = 29/76 (38%), Positives = 44/76 (57%), Gaps = 2/76 (2%)
 Frame = +2

Query: 149 NYLNCYVSGFHPPQIEIDLLKNGEKMNAE--QSDLSFSKDWSFYLLVHTEFTPNAVDQYS 322
           N L C V+ F+P QI++   +NG++  A    + L  + DW+F +LV  E TP   D Y+
Sbjct: 145 NLLVCSVTDFYPGQIKVRWFQNGKEETAGIVSTPLIRNGDWTFQILVMLEMTPKRGDVYT 204

Query: 323 CRVKHVTLDKPKIVKW 370
           C V+H +L  P  V+W
Sbjct: 205 CHVEHPSLQSPISVEW 220


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

 Score = 56.2 bits (134), Expect = 5e-08
 Identities = 28/76 (36%), Positives = 43/76 (56%), Gaps = 2/76 (2%)
 Frame = +2

Query: 149 NYLNCYVSGFHPPQIEIDLLKNGEKMNAE--QSDLSFSKDWSFYLLVHTEFTPNAVDQYS 322
           N L C V+ F+P QI++   +N  +  A    + L  + DW+F +LV  E TP   D Y+
Sbjct: 145 NLLVCSVTDFYPSQIKVRWFRNDREETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYT 204

Query: 323 CRVKHVTLDKPKIVKW 370
           C V+H +L  P +V+W
Sbjct: 205 CHVEHPSLQSPIMVEW 220


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

 Score = 55.8 bits (133), Expect = 6e-08
 Identities = 30/92 (32%), Positives = 46/92 (50%), Gaps = 2/92 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAE--QSDLSFSKDWSFY 274
           P V VY          N L C V+GF+P  IE+   +NG++  A    + L  + DW+F 
Sbjct: 90  PTVTVYPVKSRPLWHHNLLVCSVNGFYPGHIEVRWFRNGQEEEAGVVSTGLIPNGDWTFQ 149

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKW 370
           ++V  E  P   + Y+C V+H +   P  V+W
Sbjct: 150 IMVMLEIVPQGGEVYACHVEHPSRTSPVTVEW 181


>ref|XP_604082.2| PREDICTED: similar to HLA class II histocompatibility antigen, DO
           alpha chain precursor (MHC class II antigen DOA) (MHC DZ
           alpha) (MHC DN-alpha) isoform 1 [Bos taurus]
          Length = 250

 Score = 54.3 bits (129), Expect = 2e-07
 Identities = 31/93 (33%), Positives = 42/93 (45%), Gaps = 2/93 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKM--NAEQSDLSFSKDWSFY 274
           P+V V  +   + G+PN L C V    PP I I  L+NG  +     QS      D  F 
Sbjct: 113 PRVAVLPKSHVQLGEPNVLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFR 172

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
              +  F P   D Y C+V+H  LD+P    W+
Sbjct: 173 KFHYLTFVPLVDDFYDCKVEHWGLDQPLFQHWE 205


>ref|XP_883292.1| PREDICTED: similar to HLA class II histocompatibility antigen, DO
           alpha chain precursor (MHC class II antigen DOA) (MHC DZ
           alpha) (MHC DN-alpha) isoform 2 [Bos taurus]
          Length = 251

 Score = 53.9 bits (128), Expect = 2e-07
 Identities = 31/93 (33%), Positives = 42/93 (45%), Gaps = 2/93 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKM--NAEQSDLSFSKDWSFY 274
           P+V V  +   + G+PN L C V    PP I I  L+NG  +     QS      D  F 
Sbjct: 114 PQVAVLPKSHVQLGEPNVLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFR 173

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
              +  F P   D Y C+V+H  LD+P    W+
Sbjct: 174 KFHYLTFVPLVDDFYDCKVEHWGLDQPLFQHWE 206


  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: 35,270,173
Number of Sequences: 33508
Number of extensions: 818560
Number of successful extensions: 2204
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 2033
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): 2160
length of database: 16,112,626
effective HSP length: 103
effective length of database: 12,661,302
effective search space used: 3557825862
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-062998
         (1156 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_004039.1| beta-2-microglobulin precursor [Homo sapiens]        161   1e-39
Alignment   gi|NP_291032.2| major histocompatibility complex, class II, DP ...    73   4e-13
Alignment   gi|XP_941306.1| PREDICTED: similar to HLA class II histocompati...    70   3e-12
Alignment   gi|XP_941305.1| PREDICTED: similar to HLA class II histocompati...    70   3e-12
Alignment   gi|XP_941304.1| PREDICTED: similar to HLA class II histocompati...    70   3e-12
Alignment   gi|XP_941255.1| PREDICTED: similar to HLA class II histocompati...    70   3e-12
Alignment   gi|XP_941303.1| PREDICTED: similar to HLA class II histocompati...    70   3e-12
Alignment   gi|XP_941302.1| PREDICTED: similar to HLA class II histocompati...    70   3e-12
Alignment   gi|XP_941300.1| PREDICTED: similar to HLA class II histocompati...    70   3e-12
Alignment   gi|XP_941299.1| PREDICTED: similar to HLA class II histocompati...    70   3e-12

>ref|NP_004039.1| beta-2-microglobulin precursor [Homo sapiens]
          Length = 119

 Score =  161 bits (407), Expect = 1e-39
 Identities = 73/96 (76%), Positives = 82/96 (85%), Gaps = 1/96 (1%)
 Frame = +2

Query: 95  RPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMN-AEQSDLSFSKDWSF 271
           R PK+QVYSRHPAENGK N+LNCYVSGFHP  IE+DLLKNGE++   E SDLSFSKDWSF
Sbjct: 23  RTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSF 82

Query: 272 YLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRD 379
           YLL +TEFTP   D+Y+CRV HVTL +PKIVKWDRD
Sbjct: 83  YLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRD 118


>ref|NP_291032.2| major histocompatibility complex, class II, DP alpha 1 precursor
           [Homo sapiens]
          Length = 260

 Score = 73.2 bits (178), Expect = 4e-13
 Identities = 35/94 (37%), Positives = 54/94 (57%), Gaps = 2/94 (2%)
 Frame = +2

Query: 98  PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSF 271
           PP+V V+ + P E G+PN L C++  F PP + +  L NGE +    ++  F    D+SF
Sbjct: 117 PPEVTVFPKEPVELGQPNTLICHIDKFFPPVLNVTWLCNGELVTEGVAESLFLPRTDYSF 176

Query: 272 YLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
           +   +  F P+A D Y CRV+H  LD+P +  W+
Sbjct: 177 HKFHYLTFVPSAEDFYDCRVEHWGLDQPLLKHWE 210


>ref|XP_941306.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DQ(3) alpha chain precursor (DC-alpha) (HLA-DCA)
           (HLA-DQA1*05011) (HLA-DQA1*0502) isoform 10 [Homo
           sapiens]
          Length = 254

 Score = 70.5 bits (171), Expect = 3e-12
 Identities = 34/93 (36%), Positives = 50/93 (53%), Gaps = 2/93 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 274
           P+V V+S+ P   G+PN L C V    PP + I  L NG  +    S+ SF    D SF+
Sbjct: 112 PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 171

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
            + +    P+A + Y C+V+H  LDKP +  W+
Sbjct: 172 KISYLTLLPSAEESYDCKVEHWGLDKPLLKHWE 204


>ref|XP_941305.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DQ(3) alpha chain precursor (DC-alpha) (HLA-DCA)
           (HLA-DQA1*05011) (HLA-DQA1*0502) isoform 9 [Homo
           sapiens]
          Length = 254

 Score = 70.5 bits (171), Expect = 3e-12
 Identities = 34/93 (36%), Positives = 50/93 (53%), Gaps = 2/93 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 274
           P+V V+S+ P   G+PN L C V    PP + I  L NG  +    S+ SF    D SF+
Sbjct: 112 PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 171

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
            + +    P+A + Y C+V+H  LDKP +  W+
Sbjct: 172 KISYLTLLPSAEESYDCKVEHWGLDKPLLKHWE 204


>ref|XP_941304.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DQ(3) alpha chain precursor (DC-alpha) (HLA-DCA)
           (HLA-DQA1*05011) (HLA-DQA1*0502) isoform 8 [Homo
           sapiens]
          Length = 254

 Score = 70.5 bits (171), Expect = 3e-12
 Identities = 34/93 (36%), Positives = 50/93 (53%), Gaps = 2/93 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 274
           P+V V+S+ P   G+PN L C V    PP + I  L NG  +    S+ SF    D SF+
Sbjct: 112 PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 171

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
            + +    P+A + Y C+V+H  LDKP +  W+
Sbjct: 172 KISYLTLLPSAEESYDCKVEHWGLDKPLLKHWE 204


>ref|XP_941255.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DQ(3) alpha chain precursor (DC-alpha) (HLA-DCA)
           (HLA-DQA1*05011) (HLA-DQA1*0502) isoform 1 [Homo
           sapiens]
          Length = 254

 Score = 70.5 bits (171), Expect = 3e-12
 Identities = 34/93 (36%), Positives = 50/93 (53%), Gaps = 2/93 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 274
           P+V V+S+ P   G+PN L C V    PP + I  L NG  +    S+ SF    D SF+
Sbjct: 112 PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 171

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
            + +    P+A + Y C+V+H  LDKP +  W+
Sbjct: 172 KISYLTLLPSAEESYDCKVEHWGLDKPLLKHWE 204


>ref|XP_941303.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DQ(3) alpha chain precursor (DC-alpha) (HLA-DCA)
           (HLA-DQA1*05011) (HLA-DQA1*0502) isoform 7 [Homo
           sapiens]
          Length = 172

 Score = 70.5 bits (171), Expect = 3e-12
 Identities = 34/93 (36%), Positives = 50/93 (53%), Gaps = 2/93 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 274
           P+V V+S+ P   G+PN L C V    PP + I  L NG  +    S+ SF    D SF+
Sbjct: 30  PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 89

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
            + +    P+A + Y C+V+H  LDKP +  W+
Sbjct: 90  KISYLTLLPSAEESYDCKVEHWGLDKPLLKHWE 122


>ref|XP_941302.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DQ(3) alpha chain precursor (DC-alpha) (HLA-DCA)
           (HLA-DQA1*05011) (HLA-DQA1*0502) isoform 6 [Homo
           sapiens]
          Length = 172

 Score = 70.5 bits (171), Expect = 3e-12
 Identities = 34/93 (36%), Positives = 50/93 (53%), Gaps = 2/93 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 274
           P+V V+S+ P   G+PN L C V    PP + I  L NG  +    S+ SF    D SF+
Sbjct: 30  PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 89

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
            + +    P+A + Y C+V+H  LDKP +  W+
Sbjct: 90  KISYLTLLPSAEESYDCKVEHWGLDKPLLKHWE 122


>ref|XP_941300.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DQ(3) alpha chain precursor (DC-alpha) (HLA-DCA)
           (HLA-DQA1*05011) (HLA-DQA1*0502) isoform 4 [Homo
           sapiens]
          Length = 172

 Score = 70.5 bits (171), Expect = 3e-12
 Identities = 34/93 (36%), Positives = 50/93 (53%), Gaps = 2/93 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 274
           P+V V+S+ P   G+PN L C V    PP + I  L NG  +    S+ SF    D SF+
Sbjct: 30  PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 89

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
            + +    P+A + Y C+V+H  LDKP +  W+
Sbjct: 90  KISYLTLLPSAEESYDCKVEHWGLDKPLLKHWE 122


>ref|XP_941299.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DQ(3) alpha chain precursor (DC-alpha) (HLA-DCA)
           (HLA-DQA1*05011) (HLA-DQA1*0502) isoform 3 [Homo
           sapiens]
          Length = 172

 Score = 70.5 bits (171), Expect = 3e-12
 Identities = 34/93 (36%), Positives = 50/93 (53%), Gaps = 2/93 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 274
           P+V V+S+ P   G+PN L C V    PP + I  L NG  +    S+ SF    D SF+
Sbjct: 30  PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 89

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
            + +    P+A + Y C+V+H  LDKP +  W+
Sbjct: 90  KISYLTLLPSAEESYDCKVEHWGLDKPLLKHWE 122


  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: 39,522,381
Number of Sequences: 39411
Number of extensions: 931181
Number of successful extensions: 2823
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 2412
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): 2699
length of database: 17,774,539
effective HSP length: 104
effective length of database: 13,675,795
effective search space used: 3829222600
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-062998
         (1156 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|XP_535458.1| PREDICTED: similar to beta-2-microglobulin prec...   182   7e-46
Alignment   gi|XP_850148.1| PREDICTED: similar to beta-2-microglobulin prec...   182   7e-46
Alignment   gi|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris]     70   4e-12
Alignment   gi|NP_001011726.1| MHC class II DLA DQalpha chain [Canis famili...    67   3e-11
Alignment   gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati...    64   3e-10
Alignment   gi|XP_849737.1| PREDICTED: similar to HLA class II histocompati...    64   3e-10
Alignment   gi|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis fami...    62   8e-10
Alignment   gi|XP_861384.1| PREDICTED: similar to HLA class II histocompati...    62   1e-09
Alignment   gi|XP_850395.1| PREDICTED: similar to HLA class II histocompati...    61   2e-09
Alignment   gi|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Ca...    60   4e-09

>ref|XP_535458.1| PREDICTED: similar to beta-2-microglobulin precursor isoform 2
           [Canis familiaris]
          Length = 125

 Score =  182 bits (461), Expect = 7e-46
 Identities = 79/95 (83%), Positives = 91/95 (95%)
 Frame = +2

Query: 98  PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWSFYL 277
           PPK+QVYSRHPAENGKPN+LNCYVSGFHPP+IEIDLLKNG++M AEQ+DLSFSKDW+FYL
Sbjct: 31  PPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSFSKDWTFYL 90

Query: 278 LVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH 382
           LVHTEFTPN  D++SCRVKHVTL +P+IVKWDRD+
Sbjct: 91  LVHTEFTPNEQDEFSCRVKHVTLSEPQIVKWDRDN 125


>ref|XP_850148.1| PREDICTED: similar to beta-2-microglobulin precursor isoform 3
           [Canis familiaris]
          Length = 125

 Score =  182 bits (461), Expect = 7e-46
 Identities = 79/95 (83%), Positives = 91/95 (95%)
 Frame = +2

Query: 98  PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWSFYL 277
           PPK+QVYSRHPAENGKPN+LNCYVSGFHPP+IEIDLLKNG++M AEQ+DLSFSKDW+FYL
Sbjct: 31  PPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSFSKDWTFYL 90

Query: 278 LVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH 382
           LVHTEFTPN  D++SCRVKHVTL +P+IVKWDRD+
Sbjct: 91  LVHTEFTPNEQDEFSCRVKHVTLSEPQIVKWDRDN 125


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

 Score = 70.1 bits (170), Expect = 4e-12
 Identities = 35/94 (37%), Positives = 51/94 (54%), Gaps = 2/94 (2%)
 Frame = +2

Query: 98  PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSF 271
           PP+V V S  P E G+PN L C++  F PP I +  L+NG  +    S+  F   +D  F
Sbjct: 111 PPEVTVLSNTPVELGEPNILICFIDKFSPPVINVTWLRNGNPVTTGVSETIFLPREDHLF 170

Query: 272 YLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
               +  F P+A D Y C+V+H  LD+P +  W+
Sbjct: 171 RKFHYLPFLPSAEDVYDCKVEHWGLDEPLLKHWE 204


>ref|NP_001011726.1| MHC class II DLA DQalpha chain [Canis familiaris]
          Length = 255

 Score = 67.0 bits (162), Expect = 3e-11
 Identities = 35/93 (37%), Positives = 50/93 (53%), Gaps = 2/93 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 274
           P+V V+S+ P   G+PN L C V    PP I +  LKN   +    S+ SF    D SF 
Sbjct: 113 PEVTVFSKSPVMLGQPNTLICLVDNIFPPVINVTWLKNRHSVTEGVSETSFFAKGDHSFS 172

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
            + +  F P+A D Y C+V+H  LD+P +  W+
Sbjct: 173 KISYLTFLPSAEDIYDCKVEHWGLDEPLLKHWE 205


>ref|XP_850803.1| PREDICTED: similar to HLA class II histocompatibility antigen, DO
           alpha chain precursor (MHC class II antigen DOA) (MHC DZ
           alpha) (MHC DN-alpha) isoform 11 [Canis familiaris]
          Length = 227

 Score = 63.9 bits (154), Expect = 3e-10
 Identities = 33/94 (35%), Positives = 49/94 (52%), Gaps = 2/94 (2%)
 Frame = +2

Query: 98  PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSF 271
           PP+V V  +   E G+PN L C V    PP I I  L+NG+ ++   +  SF    D  F
Sbjct: 89  PPRVAVLPKFRVELGQPNVLICIVDNIFPPVINITWLRNGQIISEGVAQTSFYSQPDHLF 148

Query: 272 YLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
               +  F P+A D Y C+V+H  L++P +  W+
Sbjct: 149 RKFCYLTFVPSAEDMYDCKVEHWGLEEPLLRHWE 182


>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 = 63.9 bits (154), Expect = 3e-10
 Identities = 32/95 (33%), Positives = 49/95 (51%), Gaps = 3/95 (3%)
 Frame = +2

Query: 95  RPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSK---DW 265
           RPP VQV    P    +   L CYV GF+P  + I   KNG+ + +  S L+ ++   DW
Sbjct: 113 RPPTVQVAKSTPFNTKESVMLACYVWGFYPADVTISWRKNGQPVPSHSSALNMAQPNGDW 172

Query: 266 SFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKW 370
           ++  + H   TP+  D Y+C V+H+   +P    W
Sbjct: 173 TYQTVSHLATTPSYEDTYTCVVEHIGAPEPVCEDW 207


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

 Score = 62.4 bits (150), Expect = 8e-10
 Identities = 33/92 (35%), Positives = 50/92 (54%), Gaps = 2/92 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAE--QSDLSFSKDWSFY 274
           P V VY          N L C V+GF+P  IE+  L+NG++  A    + L  + DW+F 
Sbjct: 126 PTVTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNGDWTFQ 185

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKW 370
           +LV  E  P + + Y+C+V+H +L  P  V+W
Sbjct: 186 ILVMLEIVPQSGEVYTCQVEHPSLTSPVTVEW 217


>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 = 61.6 bits (148), Expect = 1e-09
 Identities = 33/95 (34%), Positives = 48/95 (50%), Gaps = 2/95 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNG--EKMNAEQSDLSFSKDWSFY 274
           P+V VY          N L C V+GF+P  I+I   +NG  E++    + L  + DW+F 
Sbjct: 123 PEVTVYPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQ 182

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRD 379
            +V  E TP   D Y+C V H +L  P  V+W  +
Sbjct: 183 TMVMLEMTPELGDVYTCLVNHPSLLSPVSVEWSEN 217


>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 = 61.2 bits (147), Expect = 2e-09
 Identities = 33/92 (35%), Positives = 47/92 (51%), Gaps = 2/92 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNG--EKMNAEQSDLSFSKDWSFY 274
           P+V VY          N L C V+GF+P  I+I   +NG  E++    + L  + DW+F 
Sbjct: 123 PEVTVYPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQ 182

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKW 370
            +V  E TP   D Y+C V H +L  P  V+W
Sbjct: 183 TMVMLEMTPELGDVYTCLVNHPSLLSPVSVEW 214


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

 Score = 60.1 bits (144), Expect = 4e-09
 Identities = 32/93 (34%), Positives = 49/93 (52%), Gaps = 2/93 (2%)
 Frame = +2

Query: 98  PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAE--QSDLSFSKDWSF 271
           P K +V + H       N L C V+ F+P QI++   +N ++  A    + L  + DW+F
Sbjct: 135 PSKTEVLNHH-------NLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLIRNGDWTF 187

Query: 272 YLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKW 370
            +LV  E TP   D Y+C V+H +L  P  V+W
Sbjct: 188 QILVMLEMTPQRGDVYTCHVEHASLQSPITVQW 220


  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: 41,527,286
Number of Sequences: 33732
Number of extensions: 957704
Number of successful extensions: 2715
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 2496
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): 2687
length of database: 19,266,565
effective HSP length: 105
effective length of database: 15,724,705
effective search space used: 4387192695
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-062998
         (1156 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_033865.2| beta-2-microglobulin [Mus musculus]                  147   2e-35
Alignment   gi|NP_034508.2| histocompatibility 2, class II antigen A, alpha...    63   5e-10
Alignment   gi|NP_032232.1| histocompatibility 2, O region alpha locus [Mus...    60   3e-09
Alignment   gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/...    60   6e-09
Alignment   gi|NP_034512.1| histocompatibility 2, class II antigen E beta [...    58   2e-08
Alignment   gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ...    58   2e-08
Alignment   gi|NP_996988.1| histocompatibility 2, class II antigen A, beta ...    57   3e-08
Alignment   gi|NP_034511.2| histocompatibility 2, class II antigen E alpha ...    57   3e-08
Alignment   gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ...    54   4e-07
Alignment   gi|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus ...    54   4e-07

>ref|NP_033865.2| beta-2-microglobulin [Mus musculus]
          Length = 119

 Score =  147 bits (371), Expect = 2e-35
 Identities = 64/96 (66%), Positives = 77/96 (80%), Gaps = 1/96 (1%)
 Frame = +2

Query: 95  RPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKM-NAEQSDLSFSKDWSF 271
           + P++QVYSRHP ENGKPN LNCYV+ FHPP IEI +LKNG+K+   E SD+SFSKDWSF
Sbjct: 23  KTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSF 82

Query: 272 YLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRD 379
           Y+L HTEFTP   D Y+CRVKH ++ +PK V WDRD
Sbjct: 83  YILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRD 118


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

 Score = 63.2 bits (152), Expect = 5e-10
 Identities = 31/93 (33%), Positives = 52/93 (55%), Gaps = 2/93 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 274
           P+  V+ + P   G+PN L C+V    PP I I  L+N + +     + SF  ++D+SF+
Sbjct: 114 PQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFH 173

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
            L +  F P+  D Y C+V+H  L++P +  W+
Sbjct: 174 KLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWE 206


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

 Score = 60.5 bits (145), Expect = 3e-09
 Identities = 32/94 (34%), Positives = 46/94 (48%), Gaps = 2/94 (2%)
 Frame = +2

Query: 98  PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSF 271
           PP+V V  +   E GKPN L C V    PP I +  L+N + +    +  SF    +  F
Sbjct: 112 PPRVTVLPKTRVELGKPNVLICIVDDIFPPVINVTWLRNSQPITKGVAQTSFYSQPNHRF 171

Query: 272 YLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
               +  F P+A D Y C+V+H  LD P +  W+
Sbjct: 172 RKFHYLTFVPSAEDVYDCKVEHWGLDTPLLQHWE 205


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

 Score = 59.7 bits (143), Expect = 6e-09
 Identities = 32/92 (34%), Positives = 46/92 (50%), Gaps = 2/92 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGE--KMNAEQSDLSFSKDWSFY 274
           PKV VY          N L C V  F+P  IE+   +NGE  K     + L  ++DW++ 
Sbjct: 125 PKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNRDWTYQ 184

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKW 370
            LV  E  P   + Y+C+V+H +L  P  V+W
Sbjct: 185 TLVMLEMVPRGGEVYTCQVEHPSLTSPVTVEW 216


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

 Score = 58.2 bits (139), Expect = 2e-08
 Identities = 33/92 (35%), Positives = 46/92 (50%), Gaps = 2/92 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNG--EKMNAEQSDLSFSKDWSFY 274
           P V VY          N L C VS F+P  IE+   +NG  EK     + L  + DW+F 
Sbjct: 124 PTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQ 183

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKW 370
            LV  E  P + + Y+C+V+H +L  P  V+W
Sbjct: 184 TLVMLETVPQSGEVYTCQVEHPSLTDPVTVEW 215


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

 Score = 58.2 bits (139), Expect = 2e-08
 Identities = 33/93 (35%), Positives = 45/93 (48%), Gaps = 2/93 (2%)
 Frame = +2

Query: 98  PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNG--EKMNAEQSDLSFSKDWSF 271
           PP+V VY        + N L C V+GF+P  I +   +NG  E+     + L  + DW+F
Sbjct: 122 PPEVTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVRNGDWTF 181

Query: 272 YLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKW 370
              V  E  P   D YSC V+H  L +P  V W
Sbjct: 182 QTTVMLEMIPELGDIYSCLVEHPGLLRPVSVAW 214


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

 Score = 57.4 bits (137), Expect = 3e-08
 Identities = 28/76 (36%), Positives = 43/76 (56%), Gaps = 2/76 (2%)
 Frame = +2

Query: 149 NYLNCYVSGFHPPQIEIDLLKNG--EKMNAEQSDLSFSKDWSFYLLVHTEFTPNAVDQYS 322
           N L C V+ F+P QI++   +NG  E +    + L  + DW+F +LV  E TP   + Y+
Sbjct: 141 NTLVCSVTDFYPTQIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYT 200

Query: 323 CRVKHVTLDKPKIVKW 370
           C V+H +L  P  V+W
Sbjct: 201 CHVEHPSLKSPITVEW 216


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

 Score = 57.4 bits (137), Expect = 3e-08
 Identities = 30/93 (32%), Positives = 44/93 (47%), Gaps = 2/93 (2%)
 Frame = +2

Query: 101 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 274
           P+V V SR P   G+PN L C++  F PP + +   +NG  +    S+  F    D  F 
Sbjct: 112 PEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWFRNGRPVTEGVSETVFLPRDDHLFR 171

Query: 275 LLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 373
              +  F P+  D Y C V H  L++P    W+
Sbjct: 172 KFHYLTFLPSTDDFYDCEVDHWGLEEPLRKHWE 204


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

 Score = 53.5 bits (127), Expect = 4e-07
 Identities = 28/95 (29%), Positives = 47/95 (49%), Gaps = 3/95 (3%)
 Frame = +2

Query: 95  RPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSK---DW 265
           R P V+V    P    +P  L CYV GF+P  + I  +KNG+ + +  +    ++   DW
Sbjct: 113 RAPSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPNGDW 172

Query: 266 SFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKW 370
           ++  + +   TP+  D Y+C V+H    +P    W
Sbjct: 173 TYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDW 207


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

 Score = 53.5 bits (127), Expect = 4e-07
 Identities = 28/95 (29%), Positives = 47/95 (49%), Gaps = 3/95 (3%)
 Frame = +2

Query: 95  RPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSK---DW 265
           R P V+V    P    +P  L CYV GF+P  + I  +KNG+ + +  +    ++   DW
Sbjct: 113 RAPSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPNGDW 172

Query: 266 SFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKW 370
           ++  + +   TP+  D Y+C V+H    +P    W
Sbjct: 173 TYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDW 207


  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: 47,546,797
Number of Sequences: 45328
Number of extensions: 1095923
Number of successful extensions: 3101
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 2813
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): 3008
length of database: 21,768,885
effective HSP length: 105
effective length of database: 17,009,445
effective search space used: 4745635155
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)