Animal-Genome cDNA 20060611S-000638


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-000638
         (1339 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]                    157   2e-46

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

 Score =  157 bits (398), Expect(2) = 2e-46
 Identities = 73/78 (93%), Positives = 74/78 (94%)
 Frame = +1

Query: 94  RPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWSFY 273
           RPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWSFY
Sbjct: 23  RPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWSFY 82

Query: 274 LLVHTEFTPNAVEARDSR 327
           LLVHTEFTPNAV+    R
Sbjct: 83  LLVHTEFTPNAVDQYSCR 100



 Score = 42.4 bits (98), Expect(2) = 2e-46
 Identities = 17/17 (100%), Positives = 17/17 (100%)
 Frame = +2

Query: 311 KHVTLDKPKIVKWDRDH 361
           KHVTLDKPKIVKWDRDH
Sbjct: 102 KHVTLDKPKIVKWDRDH 118


  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: 1,116,085
Number of Sequences: 1040
Number of extensions: 25573
Number of successful extensions: 75
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 68
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): 75
length of database: 434,620
effective HSP length: 80
effective length of database: 351,420
effective search space used: 128268300
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-000638
         (1339 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]                    138   6e-37
Alignment   gi|NP_001013619.2| histocompatibility complex, class II, DQ alp...    51   2e-06
Alignment   gi|NP_001012693.1| major histocompatibility complex, class II, ...    50   3e-06
Alignment   gi|NP_001012699.1| major histocompatibility complex, class II, ...    49   7e-06

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

 Score =  138 bits (348), Expect(2) = 6e-37
 Identities = 62/78 (79%), Positives = 68/78 (87%)
 Frame = +1

Query: 94  RPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWSFY 273
           RPPK+QVYSRHP E+GKPNYLNCYV GFHPPQIEIDLLKNGEK+ +EQSDLSFSKDWSFY
Sbjct: 23  RPPKIQVYSRHPPEDGKPNYLNCYVYGFHPPQIEIDLLKNGEKIKSEQSDLSFSKDWSFY 82

Query: 274 LLVHTEFTPNAVEARDSR 327
           LL H EFTPN+ +    R
Sbjct: 83  LLSHAEFTPNSKDQYSCR 100



 Score = 35.0 bits (79), Expect(2) = 6e-37
 Identities = 13/16 (81%), Positives = 16/16 (100%)
 Frame = +2

Query: 311 KHVTLDKPKIVKWDRD 358
           KHVTL++P+IVKWDRD
Sbjct: 102 KHVTLEQPRIVKWDRD 117


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

 Score = 50.8 bits (120), Expect = 2e-06
 Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
 Frame = +1

Query: 100 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 273
           P+V V+S+ P   G+PN L C+V    PP I I  L+NG  +    S+ SF    D+SF 
Sbjct: 113 PEVTVFSKSPVMLGQPNTLICHVDNIFPPVINITWLRNGHSVTEGVSETSFLIKSDYSFL 172

Query: 274 LLVHTEFTPNAVEARDSR 327
            + +  F P+  +  D +
Sbjct: 173 KINYLTFLPSDDDVYDCK 190


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

 Score = 50.4 bits (119), Expect = 3e-06
 Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
 Frame = +1

Query: 100 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 273
           P+V V+S+ P   G+PN L C+V    PP I I  L+NG  +    S+ SF    D+SF 
Sbjct: 113 PEVTVFSKSPVMLGQPNTLICHVDNIFPPVINITWLRNGHSVTEGVSETSFLIRSDYSFL 172

Query: 274 LLVHTEFTPNAVEARDSR 327
            + +  F P+  +  D +
Sbjct: 173 KIKYLAFLPSDDDIYDCK 190


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

 Score = 49.3 bits (116), Expect = 7e-06
 Identities = 28/78 (35%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
 Frame = +1

Query: 100 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 273
           P+V V+S+ P   G+PN L C+V    PP I I  LKNG  +    S+ SF    D SF 
Sbjct: 113 PEVTVFSKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHAVTEGVSETSFLPKDDHSFL 172

Query: 274 LLVHTEFTPNAVEARDSR 327
            + +  F P+  +  D +
Sbjct: 173 KIGYLTFLPSDNDIYDCK 190


  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: 40,450,189
Number of Sequences: 33508
Number of extensions: 912647
Number of successful extensions: 2482
Number of sequences better than 1.0e-05: 4
Number of HSP's better than  0.0 without gapping: 2332
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): 2478
length of database: 16,112,626
effective HSP length: 105
effective length of database: 12,594,286
effective search space used: 4282057240
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-000638
         (1339 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]        120   5e-31
Alignment   gi|NP_291032.2| major histocompatibility complex, class II, DP ...    53   5e-07
Alignment   gi|NP_002113.2| major histocompatibility complex, class II, DQ ...    53   5e-07
Alignment   gi|NP_064440.1| major histocompatibility complex, class II, DQ ...    52   9e-07
Alignment   gi|XP_941306.1| PREDICTED: similar to HLA class II histocompati...    52   2e-06
Alignment   gi|XP_941305.1| PREDICTED: similar to HLA class II histocompati...    52   2e-06
Alignment   gi|XP_941304.1| PREDICTED: similar to HLA class II histocompati...    52   2e-06
Alignment   gi|XP_941255.1| PREDICTED: similar to HLA class II histocompati...    52   2e-06
Alignment   gi|XP_941303.1| PREDICTED: similar to HLA class II histocompati...    52   2e-06
Alignment   gi|XP_941302.1| PREDICTED: similar to HLA class II histocompati...    52   2e-06

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

 Score =  120 bits (301), Expect(2) = 5e-31
 Identities = 55/70 (78%), Positives = 61/70 (87%), Gaps = 1/70 (1%)
 Frame = +1

Query: 94  RPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKM-NAEQSDLSFSKDWSF 270
           R PK+QVYSRHPAENGK N+LNCYVSGFHP  IE+DLLKNGE++   E SDLSFSKDWSF
Sbjct: 23  RTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSF 82

Query: 271 YLLVHTEFTP 300
           YLL +TEFTP
Sbjct: 83  YLLYYTEFTP 92



 Score = 33.5 bits (75), Expect(2) = 5e-31
 Identities = 13/15 (86%), Positives = 14/15 (93%)
 Frame = +2

Query: 314 HVTLDKPKIVKWDRD 358
           HVTL +PKIVKWDRD
Sbjct: 104 HVTLSQPKIVKWDRD 118


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

 Score = 53.1 bits (126), Expect = 5e-07
 Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
 Frame = +1

Query: 97  PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSF 270
           PP+V V+ + P E G+PN L C++  F PP + +  L NGE +    ++  F    D+SF
Sbjct: 117 PPEVTVFPKEPVELGQPNTLICHIDKFFPPVLNVTWLCNGELVTEGVAESLFLPRTDYSF 176

Query: 271 YLLVHTEFTPNAVEARDSR 327
           +   +  F P+A +  D R
Sbjct: 177 HKFHYLTFVPSAEDFYDCR 195


>ref|NP_002113.2| major histocompatibility complex, class II, DQ alpha 1 precursor
           [Homo sapiens]
          Length = 255

 Score = 53.1 bits (126), Expect = 5e-07
 Identities = 28/78 (35%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
 Frame = +1

Query: 100 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 273
           P+V V+S+ P   G+PN L C V    PP + I  L NG+ +    S+ SF    D SF+
Sbjct: 113 PEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGQSVTEGVSETSFLSKSDHSFF 172

Query: 274 LLVHTEFTPNAVEARDSR 327
            + +  F P+A E  D +
Sbjct: 173 KISYLTFLPSADEIYDCK 190


>ref|NP_064440.1| major histocompatibility complex, class II, DQ alpha 2 [Homo
           sapiens]
          Length = 255

 Score = 52.4 bits (124), Expect = 9e-07
 Identities = 28/78 (35%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
 Frame = +1

Query: 100 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 273
           P+V V+S+ P   G+PN L C V    PP + I  L NG  +    S+ SF    D SF+
Sbjct: 113 PEVTVFSKFPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 172

Query: 274 LLVHTEFTPNAVEARDSR 327
            + +  F P+A E  D +
Sbjct: 173 KISYLTFLPSADEIYDCK 190


>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 = 51.6 bits (122), Expect = 2e-06
 Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
 Frame = +1

Query: 100 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 273
           P+V V+S+ P   G+PN L C V    PP + I  L NG  +    S+ SF    D SF+
Sbjct: 112 PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 171

Query: 274 LLVHTEFTPNAVEARDSR 327
            + +    P+A E+ D +
Sbjct: 172 KISYLTLLPSAEESYDCK 189


>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 = 51.6 bits (122), Expect = 2e-06
 Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
 Frame = +1

Query: 100 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 273
           P+V V+S+ P   G+PN L C V    PP + I  L NG  +    S+ SF    D SF+
Sbjct: 112 PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 171

Query: 274 LLVHTEFTPNAVEARDSR 327
            + +    P+A E+ D +
Sbjct: 172 KISYLTLLPSAEESYDCK 189


>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 = 51.6 bits (122), Expect = 2e-06
 Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
 Frame = +1

Query: 100 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 273
           P+V V+S+ P   G+PN L C V    PP + I  L NG  +    S+ SF    D SF+
Sbjct: 112 PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 171

Query: 274 LLVHTEFTPNAVEARDSR 327
            + +    P+A E+ D +
Sbjct: 172 KISYLTLLPSAEESYDCK 189


>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 = 51.6 bits (122), Expect = 2e-06
 Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
 Frame = +1

Query: 100 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 273
           P+V V+S+ P   G+PN L C V    PP + I  L NG  +    S+ SF    D SF+
Sbjct: 112 PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 171

Query: 274 LLVHTEFTPNAVEARDSR 327
            + +    P+A E+ D +
Sbjct: 172 KISYLTLLPSAEESYDCK 189


>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 = 51.6 bits (122), Expect = 2e-06
 Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
 Frame = +1

Query: 100 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 273
           P+V V+S+ P   G+PN L C V    PP + I  L NG  +    S+ SF    D SF+
Sbjct: 30  PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 89

Query: 274 LLVHTEFTPNAVEARDSR 327
            + +    P+A E+ D +
Sbjct: 90  KISYLTLLPSAEESYDCK 107


>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 = 51.6 bits (122), Expect = 2e-06
 Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
 Frame = +1

Query: 100 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 273
           P+V V+S+ P   G+PN L C V    PP + I  L NG  +    S+ SF    D SF+
Sbjct: 30  PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 89

Query: 274 LLVHTEFTPNAVEARDSR 327
            + +    P+A E+ D +
Sbjct: 90  KISYLTLLPSAEESYDCK 107


  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: 45,100,245
Number of Sequences: 39411
Number of extensions: 1030950
Number of successful extensions: 3004
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 2783
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): 2999
length of database: 17,774,539
effective HSP length: 105
effective length of database: 13,636,384
effective search space used: 4636370560
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-000638
         (1339 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...   140   3e-37
Alignment   gi|XP_850148.1| PREDICTED: similar to beta-2-microglobulin prec...   140   3e-37
Alignment   gi|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris]     50   4e-06

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

 Score =  140 bits (354), Expect(2) = 3e-37
 Identities = 61/69 (88%), Positives = 68/69 (98%)
 Frame = +1

Query: 97  PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWSFYL 276
           PPK+QVYSRHPAENGKPN+LNCYVSGFHPP+IEIDLLKNG++M AEQ+DLSFSKDW+FYL
Sbjct: 31  PPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSFSKDWTFYL 90

Query: 277 LVHTEFTPN 303
           LVHTEFTPN
Sbjct: 91  LVHTEFTPN 99



 Score = 34.3 bits (77), Expect(2) = 3e-37
 Identities = 13/17 (76%), Positives = 16/17 (94%)
 Frame = +2

Query: 311 KHVTLDKPKIVKWDRDH 361
           KHVTL +P+IVKWDRD+
Sbjct: 109 KHVTLSEPQIVKWDRDN 125


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

 Score =  140 bits (354), Expect(2) = 3e-37
 Identities = 61/69 (88%), Positives = 68/69 (98%)
 Frame = +1

Query: 97  PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWSFYL 276
           PPK+QVYSRHPAENGKPN+LNCYVSGFHPP+IEIDLLKNG++M AEQ+DLSFSKDW+FYL
Sbjct: 31  PPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSFSKDWTFYL 90

Query: 277 LVHTEFTPN 303
           LVHTEFTPN
Sbjct: 91  LVHTEFTPN 99



 Score = 34.3 bits (77), Expect(2) = 3e-37
 Identities = 13/17 (76%), Positives = 16/17 (94%)
 Frame = +2

Query: 311 KHVTLDKPKIVKWDRDH 361
           KHVTL +P+IVKWDRD+
Sbjct: 109 KHVTLSEPQIVKWDRDN 125


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

 Score = 50.4 bits (119), Expect = 4e-06
 Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 2/79 (2%)
 Frame = +1

Query: 97  PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSF 270
           PP+V V S  P E G+PN L C++  F PP I +  L+NG  +    S+  F   +D  F
Sbjct: 111 PPEVTVLSNTPVELGEPNILICFIDKFSPPVINVTWLRNGNPVTTGVSETIFLPREDHLF 170

Query: 271 YLLVHTEFTPNAVEARDSR 327
               +  F P+A +  D +
Sbjct: 171 RKFHYLPFLPSAEDVYDCK 189


  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: 47,710,806
Number of Sequences: 33732
Number of extensions: 1077181
Number of successful extensions: 3016
Number of sequences better than 1.0e-05: 3
Number of HSP's better than  0.0 without gapping: 2832
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): 3007
length of database: 19,266,565
effective HSP length: 106
effective length of database: 15,690,973
effective search space used: 5319239847
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-000638
         (1339 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]                  114   5e-27

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

 Score =  114 bits (286), Expect(2) = 5e-27
 Identities = 50/74 (67%), Positives = 60/74 (81%), Gaps = 1/74 (1%)
 Frame = +1

Query: 94  RPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKM-NAEQSDLSFSKDWSF 270
           + P++QVYSRHP ENGKPN LNCYV+ FHPP IEI +LKNG+K+   E SD+SFSKDWSF
Sbjct: 23  KTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSF 82

Query: 271 YLLVHTEFTPNAVE 312
           Y+L HTEFTP   +
Sbjct: 83  YILAHTEFTPTETD 96



 Score = 26.2 bits (56), Expect(2) = 5e-27
 Identities = 9/16 (56%), Positives = 12/16 (75%)
 Frame = +2

Query: 311 KHVTLDKPKIVKWDRD 358
           KH ++ +PK V WDRD
Sbjct: 103 KHASMAEPKTVYWDRD 118


  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: 54,560,045
Number of Sequences: 45328
Number of extensions: 1229451
Number of successful extensions: 3288
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 3060
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): 3285
length of database: 21,768,885
effective HSP length: 107
effective length of database: 16,918,789
effective search space used: 5718550682
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)