Animal-Genome cDNA 20060611S-024606


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-024606
         (744 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: 817,033
Number of Sequences: 1040
Number of extensions: 23568
Number of successful extensions: 75
Number of sequences better than 1.0e-05: 0
Number of HSP's better than  0.0 without gapping: 70
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: 74
effective length of database: 357,660
effective search space used: 61875180
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-024606
         (744 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001035571.1| major histocompatibility complex, class II, ...   117   7e-27

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

 Score =  117 bits (294), Expect = 7e-27
 Identities = 63/122 (51%), Positives = 77/122 (63%)
 Frame = +2

Query: 317 ESTCLLDDEGTPQEFQYWVSFNKDLLTCWDAQETRMVPCVFGALDALATFFSVYLDPPEK 496
           ESTC+LDD+G P++F Y +SFNKDLLTCWD  +  M+P  FG L+ LA + S +L+    
Sbjct: 26  ESTCVLDDDGDPKDFSYCISFNKDLLTCWDPLQASMIPREFGVLNGLARYLSQFLNNNSY 85

Query: 497 LLQRLSNGLQNCATHTQTFRQIIDPQETARVPCQWAIPLPFNLKESVELGILYVGASNPA 676
           L+QRLSNGLQNCA HTQ F   +    T     Q A   PFN +ESV L   YV    PA
Sbjct: 86  LIQRLSNGLQNCAAHTQPFWSSL-THRTRPPTVQVAKTTPFNTRESVMLA-CYVWGFYPA 143

Query: 677 DV 682
           DV
Sbjct: 144 DV 145


  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: 30,672,282
Number of Sequences: 33508
Number of extensions: 900182
Number of successful extensions: 2888
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 2601
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): 2885
length of database: 16,112,626
effective HSP length: 99
effective length of database: 12,795,334
effective search space used: 1893709432
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-024606
         (744 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_002109.1| major histocompatibility complex, class II, DM ...   123   1e-28

>ref|NP_002109.1| major histocompatibility complex, class II, DM beta precursor [Homo
           sapiens]
          Length = 263

 Score =  123 bits (309), Expect = 1e-28
 Identities = 65/122 (53%), Positives = 79/122 (64%)
 Frame = +2

Query: 317 ESTCLLDDEGTPQEFQYWVSFNKDLLTCWDAQETRMVPCVFGALDALATFFSVYLDPPEK 496
           ESTCLLDD GTP++F Y +SFNKDLLTCWD +E +M PC FG L++LA   S +L+  + 
Sbjct: 26  ESTCLLDDAGTPKDFTYCISFNKDLLTCWDPEENKMAPCEFGVLNSLANVLSQHLNQKDT 85

Query: 497 LLQRLSNGLQNCATHTQTFRQIIDPQETARVPCQWAIPLPFNLKESVELGILYVGASNPA 676
           L+QRL NGLQNCATHTQ F   +    T     Q A   PFN +E V L   YV    PA
Sbjct: 86  LMQRLRNGLQNCATHTQPFWGSL-TNRTRPPSVQVAKTTPFNTREPVMLA-CYVWGFYPA 143

Query: 677 DV 682
           +V
Sbjct: 144 EV 145


  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: 34,932,348
Number of Sequences: 39411
Number of extensions: 1063537
Number of successful extensions: 3980
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 3351
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): 3973
length of database: 17,774,539
effective HSP length: 99
effective length of database: 13,872,850
effective search space used: 2053181800
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-024606
         (744 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|XP_849737.1| PREDICTED: similar to HLA class II histocompati...   127   1e-29

>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 =  127 bits (318), Expect = 1e-29
 Identities = 70/122 (57%), Positives = 81/122 (66%)
 Frame = +2

Query: 317 ESTCLLDDEGTPQEFQYWVSFNKDLLTCWDAQETRMVPCVFGALDALATFFSVYLDPPEK 496
           ES+CLLDD+GTP++F Y VSFNKDLLTCWD  E +MVP  FG L+ LA + S YL+  E 
Sbjct: 26  ESSCLLDDDGTPKDFTYCVSFNKDLLTCWDPDEAKMVPYEFGTLNVLANYLSDYLNQQEY 85

Query: 497 LLQRLSNGLQNCATHTQTFRQIIDPQETARVPCQWAIPLPFNLKESVELGILYVGASNPA 676
           L QRLSNGLQ+CATHTQ+F   +    T     Q A   PFN KESV L   YV    PA
Sbjct: 86  LHQRLSNGLQDCATHTQSFWGSL-THRTRPPTVQVAKSTPFNTKESVMLA-CYVWGFYPA 143

Query: 677 DV 682
           DV
Sbjct: 144 DV 145


  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: 35,958,191
Number of Sequences: 33732
Number of extensions: 1050642
Number of successful extensions: 3490
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 3105
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): 3487
length of database: 19,266,565
effective HSP length: 100
effective length of database: 15,893,365
effective search space used: 2336324655
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-024606
         (744 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ...   114   8e-26
Alignment   gi|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus ...   111   9e-25
Alignment   gi|XP_920798.1| PREDICTED: similar to Class II histocompatibili...   103   2e-22

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

 Score =  114 bits (286), Expect = 8e-26
 Identities = 62/122 (50%), Positives = 74/122 (60%)
 Frame = +2

Query: 317 ESTCLLDDEGTPQEFQYWVSFNKDLLTCWDAQETRMVPCVFGALDALATFFSVYLDPPEK 496
           ESTC+L+D GTPQ+F Y VSFNKDLL CWD    ++VPC FG L  LA   S  L+  E 
Sbjct: 26  ESTCVLNDAGTPQDFTYCVSFNKDLLACWDPDVGKIVPCEFGVLSRLAEIISNILNEQES 85

Query: 497 LLQRLSNGLQNCATHTQTFRQIIDPQETARVPCQWAIPLPFNLKESVELGILYVGASNPA 676
           L+ RL NGLQ+CATHTQ F  ++    T     + A   PFN +E V L   YV    PA
Sbjct: 86  LIHRLQNGLQDCATHTQPFWDVL-THRTRAPSVRVAQTTPFNTREPVMLA-CYVWGFYPA 143

Query: 677 DV 682
           DV
Sbjct: 144 DV 145


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

 Score =  111 bits (277), Expect = 9e-25
 Identities = 63/122 (51%), Positives = 73/122 (59%)
 Frame = +2

Query: 317 ESTCLLDDEGTPQEFQYWVSFNKDLLTCWDAQETRMVPCVFGALDALATFFSVYLDPPEK 496
           ESTC+LDD GTPQ+F Y VSFNKDLL CWD    ++VPC FG L   A  FS  L+  E 
Sbjct: 26  ESTCVLDDAGTPQDFTYCVSFNKDLLACWDPDVGKIVPCEFGVLYPWAENFSRILNKEES 85

Query: 497 LLQRLSNGLQNCATHTQTFRQIIDPQETARVPCQWAIPLPFNLKESVELGILYVGASNPA 676
           LLQRL NGL +CA+HTQ F   +    T     + A   PFN +E V L   YV    PA
Sbjct: 86  LLQRLQNGLLDCASHTQPFWNAL-THRTRAPSVRVAQTTPFNTREPVMLA-CYVWGFYPA 143

Query: 677 DV 682
           DV
Sbjct: 144 DV 145


>ref|XP_920798.1| PREDICTED: similar to Class II histocompatibility antigen, M beta 1
           chain precursor (H2-M beta 1 chain) [Mus musculus]
          Length = 167

 Score =  103 bits (257), Expect = 2e-22
 Identities = 50/79 (63%), Positives = 57/79 (72%)
 Frame = +2

Query: 317 ESTCLLDDEGTPQEFQYWVSFNKDLLTCWDAQETRMVPCVFGALDALATFFSVYLDPPEK 496
           ESTC+LDD GTPQ+F Y VSFNKDLL CWD    ++VPC FG L  LA  FS  L+  E 
Sbjct: 26  ESTCVLDDAGTPQDFTYCVSFNKDLLACWDPIVGKIVPCEFGVLYPLAENFSRILNKEES 85

Query: 497 LLQRLSNGLQNCATHTQTF 553
           LLQRL NGL +CA+HTQ F
Sbjct: 86  LLQRLQNGLPDCASHTQPF 104


  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: 41,009,691
Number of Sequences: 45328
Number of extensions: 1189706
Number of successful extensions: 4098
Number of sequences better than 1.0e-05: 3
Number of HSP's better than  0.0 without gapping: 3554
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): 4085
length of database: 21,768,885
effective HSP length: 101
effective length of database: 17,190,757
effective search space used: 2509850522
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)