Animal-Genome cDNA 20060611S-062545


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-062545
         (559 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: 560,622
Number of Sequences: 1040
Number of extensions: 14124
Number of successful extensions: 44
Number of sequences better than 1.0e-05: 0
Number of HSP's better than  0.0 without gapping: 43
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): 44
length of database: 434,620
effective HSP length: 71
effective length of database: 360,780
effective search space used: 41128920
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-062545
         (559 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001012695.1| major histocompatibility complex, class II, ...   129   2e-30
Alignment   gi|XP_604082.2| PREDICTED: similar to HLA class II histocompati...    70   1e-12
Alignment   gi|XP_883292.1| PREDICTED: similar to HLA class II histocompati...    70   1e-12
Alignment   gi|NP_001012696.1| major histocompatibility complex, class II, ...    55   4e-08
Alignment   gi|NP_001012699.1| major histocompatibility complex, class II, ...    52   2e-07
Alignment   gi|NP_001013619.2| histocompatibility complex, class II, DQ alp...    50   8e-07
Alignment   gi|NP_001012693.1| major histocompatibility complex, class II, ...    48   4e-06

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

 Score =  129 bits (323), Expect = 2e-30
 Identities = 80/157 (50%), Positives = 91/157 (57%), Gaps = 2/157 (1%)
 Frame = +3

Query: 93  MTILGVPVLGLVITIL-NLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDM 269
           M I  VP+LGL IT+L  LQ+SWAI ENHVIIQAEFYL P++S EFMFDFDGDEIFHVDM
Sbjct: 1   MAITRVPILGLFITVLIGLQESWAIKENHVIIQAEFYLKPEESAEFMFDFDGDEIFHVDM 60

Query: 270 EKRETVWRLEEFGHFGQXLRAQGCTFGAPQKTPNLKGPLGWTKAKP-LEIP*IKRLQPTP 446
            K+ETVWRL EFGHF     AQG          NL   +  +   P   +P    L P  
Sbjct: 61  GKKETVWRLPEFGHFA-SFEAQGALANMAVMKANLDIMIKRSNNTPNTNVPPEVTLLPNK 119

Query: 447 PERPXVTSRK*LCSQTSXVELGEPKHPHLFFIDKFLP 557
           P                 VELGEP +  + FIDKF P
Sbjct: 120 P-----------------VELGEP-NTLICFIDKFSP 138


>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 = 69.7 bits (169), Expect = 1e-12
 Identities = 37/77 (48%), Positives = 54/77 (70%), Gaps = 3/77 (3%)
 Frame = +3

Query: 93  MTILGVPVLGL--VITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHV 263
           M + G  VLGL  ++T+L+LQ+  AI  +H+      FY S D +G+F +DFDG+++F V
Sbjct: 1   MVLRGRLVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSV 60

Query: 264 DMEKRETVWRLEEFGHF 314
           D++KRE VWRL EFG+F
Sbjct: 61  DLKKREAVWRLPEFGNF 77


>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 = 69.7 bits (169), Expect = 1e-12
 Identities = 37/77 (48%), Positives = 54/77 (70%), Gaps = 3/77 (3%)
 Frame = +3

Query: 93  MTILGVPVLGL--VITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHV 263
           M + G  VLGL  ++T+L+LQ+  AI  +H+      FY S D +G+F +DFDG+++F V
Sbjct: 1   MVLRGRLVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSV 60

Query: 264 DMEKRETVWRLEEFGHF 314
           D++KRE VWRL EFG+F
Sbjct: 61  DLKKREAVWRLPEFGNF 77


>ref|NP_001012696.1| major histocompatibility complex, class II, DY alpha [Bos taurus]
          Length = 253

 Score = 54.7 bits (130), Expect = 4e-08
 Identities = 26/51 (50%), Positives = 35/51 (68%), Gaps = 1/51 (1%)
 Frame = +3

Query: 162 IVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGH 311
           IV +HV       Y +   SG+F F+FDGDE+F+VD+ K+ETVWRL EF +
Sbjct: 24  IVADHVGTYGTNVYQTYGASGQFTFEFDGDELFYVDLGKKETVWRLPEFSN 74


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

 Score = 52.4 bits (124), Expect = 2e-07
 Identities = 26/52 (50%), Positives = 34/52 (65%), Gaps = 1/52 (1%)
 Frame = +3

Query: 162 IVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHF 314
           IV +HV     E Y S   SG++  +FDGDE+F+VD+ K+ETVWRL  F  F
Sbjct: 26  IVADHVGSYGTEIYQSHGPSGQYTQEFDGDEMFYVDLGKKETVWRLPMFSQF 77


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

 Score = 50.4 bits (119), Expect = 8e-07
 Identities = 27/62 (43%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
 Frame = +3

Query: 132 TILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFG 308
           T+++   S  IV +H+       Y +   SG +  +FDGDE F+VD+EKRETVWRL  F 
Sbjct: 16  TMMSPSGSEDIVADHIGTYGISIYHTYGPSGYYTHEFDGDEEFYVDLEKRETVWRLPVFS 75

Query: 309 HF 314
            F
Sbjct: 76  KF 77


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

 Score = 48.1 bits (113), Expect = 4e-06
 Identities = 24/49 (48%), Positives = 32/49 (65%), Gaps = 1/49 (2%)
 Frame = +3

Query: 162 IVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEF 305
           IV +HV I     Y S   SG++  +FDGDE F+VD+EK+ET W+L  F
Sbjct: 26  IVADHVGIYGISIYQSYGPSGQYTHEFDGDEQFYVDLEKKETAWQLPLF 74


  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: 20,867,582
Number of Sequences: 33508
Number of extensions: 539550
Number of successful extensions: 1348
Number of sequences better than 1.0e-05: 7
Number of HSP's better than  0.0 without gapping: 1279
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): 1347
length of database: 16,112,626
effective HSP length: 95
effective length of database: 12,929,366
effective search space used: 1163642940
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-062545
         (559 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_061984.2| major histocompatibility complex, class II, DR ...   127   4e-30
Alignment   gi|NP_291032.2| major histocompatibility complex, class II, DP ...    65   3e-11
Alignment   gi|NP_002110.1| major histocompatibility complex, class II, DO ...    53   2e-07
Alignment   gi|NP_064440.1| major histocompatibility complex, class II, DQ ...    51   7e-07
Alignment   gi|NP_002113.2| major histocompatibility complex, class II, DQ ...    50   2e-06
Alignment   gi|XP_949974.1| PREDICTED: similar to HLA class II histocompati...    49   3e-06
Alignment   gi|XP_949973.1| PREDICTED: similar to HLA class II histocompati...    49   3e-06
Alignment   gi|XP_949971.1| PREDICTED: similar to HLA class II histocompati...    49   3e-06
Alignment   gi|XP_949969.1| PREDICTED: similar to HLA class II histocompati...    49   3e-06
Alignment   gi|XP_949965.1| PREDICTED: similar to HLA class II histocompati...    49   3e-06

>ref|NP_061984.2| major histocompatibility complex, class II, DR alpha precursor
           [Homo sapiens]
          Length = 254

 Score =  127 bits (320), Expect = 4e-30
 Identities = 78/157 (49%), Positives = 94/157 (59%), Gaps = 2/157 (1%)
 Frame = +3

Query: 93  MTILGVPVLG--LVITILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVD 266
           M I GVPVLG  ++  +++ Q+SWAI E HVIIQAEFYL+PD+SGEFMFDFDGDEIFHVD
Sbjct: 1   MAISGVPVLGFFIIAVLMSAQESWAIKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVD 60

Query: 267 MEKRETVWRLEEFGHFGQXLRAQGCTFGAPQKTPNLKGPLGWTKAKPLEIP*IKRLQPTP 446
           M K+ETVWRLEEFG F     AQG          NL+     +   P        +   P
Sbjct: 61  MAKKETVWRLEEFGRFA-SFEAQGALANIAVDKANLEIMTKRSNYTP--------ITNVP 111

Query: 447 PERPXVTSRK*LCSQTSXVELGEPKHPHLFFIDKFLP 557
           PE   +T+        S VEL EP +  + FIDKF P
Sbjct: 112 PEVTVLTN--------SPVELREP-NVLICFIDKFTP 139


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

 Score = 65.5 bits (158), Expect = 3e-11
 Identities = 30/58 (51%), Positives = 43/58 (74%)
 Frame = +3

Query: 135 ILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFG 308
           +L+L+ + AI  +HV   A F  +   +GEFMF+FD DE+F+VD++K+ETVW LEEFG
Sbjct: 23  LLSLRGAGAIKADHVSTYAAFVQTHRPTGEFMFEFDEDEMFYVDLDKKETVWHLEEFG 80


>ref|NP_002110.1| major histocompatibility complex, class II, DO alpha precursor
           [Homo sapiens]
          Length = 250

 Score = 52.8 bits (125), Expect = 2e-07
 Identities = 29/72 (40%), Positives = 45/72 (62%), Gaps = 3/72 (4%)
 Frame = +3

Query: 114 VLGL--VITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRET 284
           VLG   ++T+L+ Q++ A   +H+      FY S   SG+F  +FD +++F VD++K E 
Sbjct: 8   VLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEA 67

Query: 285 VWRLEEFGHFGQ 320
           VWRL EFG F +
Sbjct: 68  VWRLPEFGDFAR 79


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

 Score = 50.8 bits (120), Expect = 7e-07
 Identities = 25/52 (48%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
 Frame = +3

Query: 162 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHF 314
           IV +HV      FY S   SG++  +FDGDE F+VD+E +ETVW+L  F  F
Sbjct: 26  IVADHVASYGVNFYQSHGPSGQYTHEFDGDEEFYVDLETKETVWQLPMFSKF 77


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

 Score = 49.7 bits (117), Expect = 2e-06
 Identities = 24/53 (45%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
 Frame = +3

Query: 162 IVENHVI-IQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFG 317
           IV +HV       Y     SG++  +FDGDE F+VD+E++ET WR  EF  FG
Sbjct: 26  IVADHVASCGVNLYQFYGPSGQYTHEFDGDEQFYVDLERKETAWRWPEFSKFG 78


>ref|XP_949974.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DQ(1) alpha chain precursor (DC-4 alpha chain) isoform
           10 [Homo sapiens]
          Length = 255

 Score = 48.5 bits (114), Expect = 3e-06
 Identities = 24/52 (46%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
 Frame = +3

Query: 162 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHF 314
           IV +HV       Y S   SG++  +FDGDE F+VD+E++ETVW+L  F  F
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRF 77


>ref|XP_949973.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DQ(1) alpha chain precursor (DC-4 alpha chain) isoform 9
           [Homo sapiens]
          Length = 255

 Score = 48.5 bits (114), Expect = 3e-06
 Identities = 24/52 (46%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
 Frame = +3

Query: 162 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHF 314
           IV +HV       Y S   SG++  +FDGDE F+VD+E++ETVW+L  F  F
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRF 77


>ref|XP_949971.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DQ(1) alpha chain precursor (DC-4 alpha chain) isoform 8
           [Homo sapiens]
          Length = 255

 Score = 48.5 bits (114), Expect = 3e-06
 Identities = 24/52 (46%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
 Frame = +3

Query: 162 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHF 314
           IV +HV       Y S   SG++  +FDGDE F+VD+E++ETVW+L  F  F
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRF 77


>ref|XP_949969.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DQ(1) alpha chain precursor (DC-4 alpha chain) isoform 7
           [Homo sapiens]
          Length = 208

 Score = 48.5 bits (114), Expect = 3e-06
 Identities = 24/52 (46%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
 Frame = +3

Query: 162 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHF 314
           IV +HV       Y S   SG++  +FDGDE F+VD+E++ETVW+L  F  F
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRF 77


>ref|XP_949965.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DQ(1) alpha chain precursor (DC-4 alpha chain) isoform 6
           [Homo sapiens]
          Length = 161

 Score = 48.5 bits (114), Expect = 3e-06
 Identities = 24/52 (46%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
 Frame = +3

Query: 162 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHF 314
           IV +HV       Y S   SG++  +FDGDE F+VD+E++ETVW+L  F  F
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRF 77


  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: 23,572,141
Number of Sequences: 39411
Number of extensions: 628739
Number of successful extensions: 1862
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 1554
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): 1860
length of database: 17,774,539
effective HSP length: 96
effective length of database: 13,991,083
effective search space used: 1245206387
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-062545
         (559 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris]    129   2e-30
Alignment   gi|NP_001011726.1| MHC class II DLA DQalpha chain [Canis famili...    54   1e-07
Alignment   gi|XP_532104.2| PREDICTED: similar to HLA class II histocompati...    52   5e-07
Alignment   gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati...    51   8e-07

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

 Score =  129 bits (324), Expect = 2e-30
 Identities = 85/159 (53%), Positives = 94/159 (59%), Gaps = 4/159 (2%)
 Frame = +3

Query: 93  MTILGVPVLGLVIT--ILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVD 266
           MTI GVPVLG  I   ++  Q+SWA+ E HVIIQAEFYL+PD SGEFMFDFDGDEIFHVD
Sbjct: 1   MTISGVPVLGFFIMAFLMGPQESWAVKEEHVIIQAEFYLTPDPSGEFMFDFDGDEIFHVD 60

Query: 267 MEKRETVWRLEEFGHFGQXLRAQGCTFGAPQKTPNLKGPLGWTKAKPLEIP*IKRLQPTP 446
           MEK+ETVWRLEEFG F     AQG          NL                IKR   TP
Sbjct: 61  MEKKETVWRLEEFGRFA-SFEAQGALANIAVDKANLDTM-------------IKRSNHTP 106

Query: 447 PER--PXVTSRK*LCSQTSXVELGEPKHPHLFFIDKFLP 557
                P VT    + S T  VELGEP +  + FIDKF P
Sbjct: 107 NTNVPPEVT----VLSNTP-VELGEP-NILICFIDKFSP 139


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

 Score = 53.5 bits (127), Expect = 1e-07
 Identities = 32/77 (41%), Positives = 44/77 (57%), Gaps = 3/77 (3%)
 Frame = +3

Query: 93  MTILGVPVLGLVITILNLQKSWA--IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHV 263
           M +  V +LG +I  + +  S    IV +HV       Y S   SG++  +FDGDE F+V
Sbjct: 1   MILNRVLILGTLILTIMMSPSGGEEIVADHVANYGINVYQSYGPSGQYTHEFDGDEEFYV 60

Query: 264 DMEKRETVWRLEEFGHF 314
           D+EK+ETVWRL  F  F
Sbjct: 61  DLEKKETVWRLPVFSTF 77


>ref|XP_532104.2| PREDICTED: similar to HLA class II histocompatibility antigen, DO
           alpha chain precursor (MHC class II antigen DOA) (MHC DZ
           alpha) (MHC DN-alpha) isoform 10 [Canis familiaris]
          Length = 142

 Score = 51.6 bits (122), Expect = 5e-07
 Identities = 24/62 (38%), Positives = 42/62 (67%), Gaps = 1/62 (1%)
 Frame = +3

Query: 129 ITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEF 305
           +++L+  ++ AI  +H+      FY S   SG+F  +FDG+++F V+++KR+ VWRL EF
Sbjct: 1   MSLLSPHETGAIEADHMGSYGPAFYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEF 60

Query: 306 GH 311
           G+
Sbjct: 61  GN 62


>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 = 50.8 bits (120), Expect = 8e-07
 Identities = 20/39 (51%), Positives = 30/39 (76%)
 Frame = +3

Query: 195 FYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGH 311
           FY S   SG+F  +FDG+++F V+++KR+ VWRL EFG+
Sbjct: 8   FYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEFGN 46


  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: 24,551,494
Number of Sequences: 33732
Number of extensions: 637685
Number of successful extensions: 1492
Number of sequences better than 1.0e-05: 4
Number of HSP's better than  0.0 without gapping: 1393
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): 1491
length of database: 19,266,565
effective HSP length: 97
effective length of database: 15,994,561
effective search space used: 1407521368
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-062545
         (559 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_034511.2| histocompatibility 2, class II antigen E alpha ...   107   1e-23
Alignment   gi|NP_032232.1| histocompatibility 2, O region alpha locus [Mus...    59   3e-09
Alignment   gi|NP_034508.2| histocompatibility 2, class II antigen A, alpha...    57   9e-09

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

 Score =  107 bits (266), Expect = 1e-23
 Identities = 69/146 (47%), Positives = 78/146 (53%), Gaps = 2/146 (1%)
 Frame = +3

Query: 126 VITILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEF 305
           +  +++ QKSWAI E H IIQAEFYL PDK GEFMFDFDGDEIFHVD+EK ET+WRLEEF
Sbjct: 14  IAVLMSSQKSWAIKEEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEEF 73

Query: 306 GHFGQXLRAQGCTFGAPQKTPNLKGPLGWTKAKPLEIP*IKRLQPTPPER--PXVTSRK* 479
             F     AQG          NL                 +R   TP     P VT    
Sbjct: 74  AKFA-SFEAQGALANIAVDKANLDVMK-------------ERSNNTPDANVAPEVT---- 115

Query: 480 LCSQTSXVELGEPKHPHLFFIDKFLP 557
                S V LGEP +  + FIDKF P
Sbjct: 116 -VLSRSPVNLGEP-NILICFIDKFSP 139


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

 Score = 58.9 bits (141), Expect = 3e-09
 Identities = 32/70 (45%), Positives = 44/70 (62%), Gaps = 1/70 (1%)
 Frame = +3

Query: 108 VPVLGLVITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRET 284
           VPVL  V++ L+ +   AI  +H+      FY S D SG+F  +FDG++IF VD++  E 
Sbjct: 8   VPVLLTVMSFLSPRGVRAIKADHMGSYGPAFYQSYDASGQFTHEFDGEQIFSVDLKNEEV 67

Query: 285 VWRLEEFGHF 314
           VWRL EFG F
Sbjct: 68  VWRLPEFGDF 77


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

 Score = 57.4 bits (137), Expect = 9e-09
 Identities = 30/76 (39%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
 Frame = +3

Query: 84  KEKMTILGVPVLGLVITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFH 260
           + +  ILGV  L  ++++   +    I  +HV       Y SP   G++ F+FDGDE+F+
Sbjct: 3   RSRALILGVLALTTMLSLCGGEDD--IEADHVGTYGISVYQSPGDIGQYTFEFDGDELFY 60

Query: 261 VDMEKRETVWRLEEFG 308
           VD++K+ETVW L EFG
Sbjct: 61  VDLDKKETVWMLPEFG 76


  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: 27,868,970
Number of Sequences: 45328
Number of extensions: 715059
Number of successful extensions: 1793
Number of sequences better than 1.0e-05: 3
Number of HSP's better than  0.0 without gapping: 1695
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): 1791
length of database: 21,768,885
effective HSP length: 97
effective length of database: 17,372,069
effective search space used: 1528742072
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)