Animal-Genome cDNA 20060611S-029724


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-029724
         (1203 letters)

Database: RefSeqSP 
           1040 sequences; 434,620 total letters

Searching...done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001004039.1| SLA-DM alpha chain [Sus scrofa]                    51   5e-08

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

 Score = 51.2 bits (121), Expect = 5e-08
 Identities = 45/170 (26%), Positives = 66/170 (38%), Gaps = 11/170 (6%)
 Frame = +2

Query: 116 GGEDIAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYGDLEKIETVWRVPLFTEFTS-- 289
           G  D   +H   Y +Y  Q   P    +  +DGD+ F  +  +   V R+P F ++    
Sbjct: 34  GWRDELQNHTFQYTMYC-QDGNPEVGLSEVYDGDQLFSFNFSQNIRVPRLPEFADWAHQI 92

Query: 290 ------FDPQGALRNIATLKHNL---TIVTNRSNDTAAVYQXXXXXXXXXXXXILGHPLP 442
                 F  +G  R +      L    I  +R    A V+               G P  
Sbjct: 93  EDTPAIFFDKGFCREMIEKVGPLFEGKIPVSRGLPIAEVFTLKPLE--------FGKPNT 144

Query: 443 LICPVDSIFPPVINIAWFEIGLSVEGFSDTIFLSYNDLSFLNISYLTFLP 592
           L+C V ++FPP + + W      VEG   T   + +DLSF   SYL F P
Sbjct: 145 LVCFVSNLFPPALTVTWEHHSAPVEGIGPTFVSATDDLSFQAFSYLNFTP 194


  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: 833,831
Number of Sequences: 1040
Number of extensions: 20363
Number of successful extensions: 91
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 72
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): 91
length of database: 434,620
effective HSP length: 79
effective length of database: 352,460
effective search space used: 113139660
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-029724
         (1203 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001013619.2| histocompatibility complex, class II, DQ alp...   218   1e-67
Alignment   gi|NP_001012693.1| major histocompatibility complex, class II, ...   194   7e-61
Alignment   gi|NP_001012699.1| major histocompatibility complex, class II, ...   199   1e-57
Alignment   gi|NP_001012696.1| major histocompatibility complex, class II, ...   171   1e-52
Alignment   gi|XP_604082.2| PREDICTED: similar to HLA class II histocompati...   124   9e-37
Alignment   gi|XP_883292.1| PREDICTED: similar to HLA class II histocompati...   122   3e-36
Alignment   gi|NP_001012695.1| major histocompatibility complex, class II, ...   110   3e-30

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

 Score =  218 bits (555), Expect(3) = 1e-67
 Identities = 111/181 (61%), Positives = 130/181 (71%), Gaps = 1/181 (0%)
 Frame = +2

Query: 53  MVPGRVLMWGALALSTVMSA*GGEDIAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYG 232
           MV  R L+ GALAL+T+MS  G EDI ADH+ +YG+ +Y  Y PSGY+THEFDGDEEFY 
Sbjct: 1   MVLNRALILGALALTTMMSPSGSEDIVADHIGTYGISIYHTYGPSGYYTHEFDGDEEFYV 60

Query: 233 DLEKIETVWRVPLFTEFTSFDPQGALRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXX 412
           DLEK ETVWR+P+F++F +FDPQGALRNIAT KHNL IV  RSN TAA  +         
Sbjct: 61  DLEKRETVWRLPVFSKFATFDPQGALRNIATTKHNLEIVIQRSNSTAATNKVPEVTVFSK 120

Query: 413 XXXILGHPLPLICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFL 589
              +LG P  LIC VD+IFPPVINI W   G SV EG S+T FL  +D SFL I+YLTFL
Sbjct: 121 SPVMLGQPNTLICHVDNIFPPVINITWLRNGHSVTEGVSETSFLIKSDYSFLKINYLTFL 180

Query: 590 P 592
           P
Sbjct: 181 P 181



 Score = 47.8 bits (112), Expect(3) = 1e-67
 Identities = 17/20 (85%), Positives = 18/20 (90%)
 Frame = +3

Query: 609 YDCQVEHWGLDNPLLTHWEP 668
           YDC+VEHWGLD PLL HWEP
Sbjct: 187 YDCKVEHWGLDEPLLKHWEP 206



 Score = 31.6 bits (70), Expect(3) = 1e-67
 Identities = 14/19 (73%), Positives = 15/19 (78%)
 Frame = +1

Query: 667 PEIPAPMS*LTETAVCPPG 723
           P+IPAPMS LTET VC  G
Sbjct: 206 PDIPAPMSELTETVVCALG 224


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

 Score =  194 bits (492), Expect(3) = 7e-61
 Identities = 102/181 (56%), Positives = 121/181 (66%), Gaps = 1/181 (0%)
 Frame = +2

Query: 53  MVPGRVLMWGALALSTVMSA*GGEDIAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYG 232
           MV  R L+ G LAL+T+MS  GGEDI ADHV  YG+ +YQ Y PSG +THEFDGDE+FY 
Sbjct: 1   MVLNRALILGTLALTTMMSPSGGEDIVADHVGIYGISIYQSYGPSGQYTHEFDGDEQFYV 60

Query: 233 DLEKIETVWRVPLFTEFTSFDPQGALRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXX 412
           DLEK ET W++PLF+   SFDPQ ALRNIA +K ++  +T  SN TAA  +         
Sbjct: 61  DLEKKETAWQLPLFSRMLSFDPQLALRNIAIMKLHVDFLTKFSNSTAATNKVPEVTVFSK 120

Query: 413 XXXILGHPLPLICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFL 589
              +LG P  LIC VD+IFPPVINI W   G SV EG S+T FL  +D SFL I YL FL
Sbjct: 121 SPVMLGQPNTLICHVDNIFPPVINITWLRNGHSVTEGVSETSFLIRSDYSFLKIKYLAFL 180

Query: 590 P 592
           P
Sbjct: 181 P 181



 Score = 47.8 bits (112), Expect(3) = 7e-61
 Identities = 17/20 (85%), Positives = 18/20 (90%)
 Frame = +3

Query: 609 YDCQVEHWGLDNPLLTHWEP 668
           YDC+VEHWGLD PLL HWEP
Sbjct: 187 YDCKVEHWGLDEPLLKHWEP 206



 Score = 32.7 bits (73), Expect(3) = 7e-61
 Identities = 15/19 (78%), Positives = 15/19 (78%)
 Frame = +1

Query: 667 PEIPAPMS*LTETAVCPPG 723
           PEIPAPMS LTET VC  G
Sbjct: 206 PEIPAPMSELTETVVCTLG 224


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

 Score =  199 bits (507), Expect(2) = 1e-57
 Identities = 103/181 (56%), Positives = 124/181 (68%), Gaps = 1/181 (0%)
 Frame = +2

Query: 53  MVPGRVLMWGALALSTVMSA*GGEDIAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYG 232
           MV  R L+ GALAL+T+MS+ GGEDI ADHV SYG  +YQ + PSG +T EFDGDE FY 
Sbjct: 1   MVLNRALILGALALTTMMSSSGGEDIVADHVGSYGTEIYQSHGPSGQYTQEFDGDEMFYV 60

Query: 233 DLEKIETVWRVPLFTEFTSFDPQGALRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXX 412
           DL K ETVWR+P+F++F  FDPQ AL  IAT KHNL ++T RSN T  + +         
Sbjct: 61  DLGKKETVWRLPMFSQFAGFDPQAALSEIATAKHNLDVLTKRSNFTPVINEVPEVTVFSK 120

Query: 413 XXXILGHPLPLICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFL 589
              +LG P  LIC VD+IFPPVINI W + G +V EG S+T FL  +D SFL I YLTFL
Sbjct: 121 SPVMLGQPNTLICHVDNIFPPVINITWLKNGHAVTEGVSETSFLPKDDHSFLKIGYLTFL 180

Query: 590 P 592
           P
Sbjct: 181 P 181



 Score = 43.1 bits (100), Expect(2) = 1e-57
 Identities = 15/18 (83%), Positives = 16/18 (88%)
 Frame = +3

Query: 609 YDCQVEHWGLDNPLLTHW 662
           YDC+VEHWGLD PLL HW
Sbjct: 187 YDCKVEHWGLDEPLLKHW 204


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

 Score =  171 bits (432), Expect(3) = 1e-52
 Identities = 94/177 (53%), Positives = 110/177 (62%), Gaps = 1/177 (0%)
 Frame = +2

Query: 65  RVLMWGALALSTVMSA*GGEDIAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYGDLEK 244
           + L+  AL L+T+MS  GGEDI ADHV +YG  VYQ Y  SG FT EFDGDE FY DL K
Sbjct: 3   KALILRALTLATMMSPYGGEDIVADHVGTYGTNVYQTYGASGQFTFEFDGDELFYVDLGK 62

Query: 245 IETVWRVPLFTEFTSFDPQGALRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXXXXXI 424
            ETVWR+P F+  T F+ Q ALRNI   K NL I+   S+ T A  +            +
Sbjct: 63  KETVWRLPEFSNITKFEVQSALRNIVMSKRNLDILIKNSSFTPATSEIPEVAVFPKSSVV 122

Query: 425 LGHPLPLICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFLP 592
           LG P  LIC VD+IFPPVINI WF  G  V EG ++T F   +D SFL  SYLTFLP
Sbjct: 123 LGIPNTLICQVDNIFPPVINITWFYNGHFVAEGIAETTFYPKSDHSFLKFSYLTFLP 179



 Score = 47.4 bits (111), Expect(3) = 1e-52
 Identities = 16/21 (76%), Positives = 19/21 (90%)
 Frame = +3

Query: 606 FYDCQVEHWGLDNPLLTHWEP 668
           FYDC+VEHWGL+ PL+ HWEP
Sbjct: 184 FYDCRVEHWGLEEPLVKHWEP 204



 Score = 28.9 bits (63), Expect(3) = 1e-52
 Identities = 13/19 (68%), Positives = 13/19 (68%)
 Frame = +1

Query: 667 PEIPAPMS*LTETAVCPPG 723
           PEIP P S LTET VC  G
Sbjct: 204 PEIPTPTSELTETVVCALG 222


>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 =  124 bits (311), Expect(2) = 9e-37
 Identities = 74/175 (42%), Positives = 94/175 (53%), Gaps = 1/175 (0%)
 Frame = +2

Query: 71  LMWGALALSTVMSA*GGEDIAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYGDLEKIE 250
           L+ G   L T++S      I ADH+ SYG   YQ Y  +G FT++FDG++ F  DL+K E
Sbjct: 7   LVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSVDLKKRE 66

Query: 251 TVWRVPLFTEFTSFDPQGALRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXXXXXILG 430
            VWR+P F  F  FDPQ  L +IA +K +L  +  RSN T A                LG
Sbjct: 67  AVWRLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNVSPRVAVLPKSHVQLG 126

Query: 431 HPLPLICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFLP 592
            P  LIC VD IFPPVINI W   G  V +G + + F +  D  F    YLTF+P
Sbjct: 127 EPNVLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTFVP 181



 Score = 48.5 bits (114), Expect(2) = 9e-37
 Identities = 17/21 (80%), Positives = 18/21 (85%)
 Frame = +3

Query: 606 FYDCQVEHWGLDNPLLTHWEP 668
           FYDC+VEHWGLD PL  HWEP
Sbjct: 186 FYDCKVEHWGLDQPLFQHWEP 206


>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 =  122 bits (306), Expect(2) = 3e-36
 Identities = 74/176 (42%), Positives = 95/176 (53%), Gaps = 2/176 (1%)
 Frame = +2

Query: 71  LMWGALALSTVMSA*GGEDIAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYGDLEKIE 250
           L+ G   L T++S      I ADH+ SYG   YQ Y  +G FT++FDG++ F  DL+K E
Sbjct: 7   LVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSVDLKKRE 66

Query: 251 TVWRVPLFTEFTSFDPQGALRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXXXXXI-L 427
            VWR+P F  F  FDPQ  L +IA +K +L  +  RSN T A               + L
Sbjct: 67  AVWRLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNGSTPQVAVLPKSHVQL 126

Query: 428 GHPLPLICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFLP 592
           G P  LIC VD IFPPVINI W   G  V +G + + F +  D  F    YLTF+P
Sbjct: 127 GEPNVLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTFVP 182



 Score = 48.5 bits (114), Expect(2) = 3e-36
 Identities = 17/21 (80%), Positives = 18/21 (85%)
 Frame = +3

Query: 606 FYDCQVEHWGLDNPLLTHWEP 668
           FYDC+VEHWGLD PL  HWEP
Sbjct: 187 FYDCKVEHWGLDQPLFQHWEP 207


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

 Score =  110 bits (275), Expect(3) = 3e-30
 Identities = 65/156 (41%), Positives = 82/156 (52%), Gaps = 1/156 (0%)
 Frame = +2

Query: 128 IAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYGDLEKIETVWRVPLFTEFTSFDPQGA 307
           I  +HV     +  +P   S  F  +FDGDE F+ D+ K ETVWR+P F  F SF+ QGA
Sbjct: 25  IKENHVIIQAEFYLKP-EESAEFMFDFDGDEIFHVDMGKKETVWRLPEFGHFASFEAQGA 83

Query: 308 LRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXXXXXILGHPLPLICPVDSIFPPVINI 487
           L N+A +K NL I+  RSN+T                  LG P  LIC +D   PPVI++
Sbjct: 84  LANMAVMKANLDIMIKRSNNTPNTNVPPEVTLLPNKPVELGEPNTLICFIDKFSPPVISV 143

Query: 488 AWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFLP 592
            W   G  V +G S T+FL  ND  F    YL FLP
Sbjct: 144 TWLRNGKPVTDGVSQTVFLPRNDHLFRKFHYLPFLP 179



 Score = 38.1 bits (87), Expect(3) = 3e-30
 Identities = 14/19 (73%), Positives = 16/19 (84%)
 Frame = +3

Query: 609 YDCQVEHWGLDNPLLTHWE 665
           YDC+VEH GL+ PLL HWE
Sbjct: 185 YDCKVEHLGLNEPLLKHWE 203



 Score = 22.7 bits (47), Expect(3) = 3e-30
 Identities = 10/18 (55%), Positives = 11/18 (61%)
 Frame = +1

Query: 670 EIPAPMS*LTETAVCPPG 723
           E PAP+   TE AVC  G
Sbjct: 205 EAPAPLPETTENAVCALG 222


  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: 32,072,378
Number of Sequences: 33508
Number of extensions: 828537
Number of successful extensions: 3847
Number of sequences better than 1.0e-05: 7
Number of HSP's better than  0.0 without gapping: 3015
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): 3775
length of database: 16,112,626
effective HSP length: 104
effective length of database: 12,627,794
effective search space used: 3737827024
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-029724
         (1203 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|XP_949974.1| PREDICTED: similar to HLA class II histocompati...   211   4e-66
Alignment   gi|XP_949973.1| PREDICTED: similar to HLA class II histocompati...   211   4e-66
Alignment   gi|XP_949971.1| PREDICTED: similar to HLA class II histocompati...   211   4e-66
Alignment   gi|XP_945969.1| PREDICTED: similar to HLA class II histocompati...   211   4e-66
Alignment   gi|NP_002113.2| major histocompatibility complex, class II, DQ ...   202   2e-63
Alignment   gi|NP_064440.1| major histocompatibility complex, class II, DQ ...   200   1e-62
Alignment   gi|XP_949969.1| PREDICTED: similar to HLA class II histocompati...   211   3e-61
Alignment   gi|XP_941306.1| PREDICTED: similar to HLA class II histocompati...   194   6e-61
Alignment   gi|XP_941305.1| PREDICTED: similar to HLA class II histocompati...   194   6e-61
Alignment   gi|XP_941304.1| PREDICTED: similar to HLA class II histocompati...   194   6e-61

>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 =  211 bits (538), Expect(3) = 4e-66
 Identities = 111/181 (61%), Positives = 126/181 (69%), Gaps = 1/181 (0%)
 Frame = +2

Query: 53  MVPGRVLMWGALALSTVMSA*GGEDIAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYG 232
           M+  + LM GALAL+TVMS  GGEDI ADHVASYG+ +YQ Y PSG ++HEFDGDEEFY 
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYV 60

Query: 233 DLEKIETVWRVPLFTEFTSFDPQGALRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXX 412
           DLE+ ETVW++PLF  F  FDPQ AL NIA LKHNL IV  RSN TAA  +         
Sbjct: 61  DLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSK 120

Query: 413 XXXILGHPLPLICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFL 589
               LG P  LIC VD+IFPPV+NI W   G SV EG S+T FLS +D SF  ISYLTFL
Sbjct: 121 SPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFL 180

Query: 590 P 592
           P
Sbjct: 181 P 181



 Score = 47.8 bits (112), Expect(3) = 4e-66
 Identities = 17/20 (85%), Positives = 18/20 (90%)
 Frame = +3

Query: 609 YDCQVEHWGLDNPLLTHWEP 668
           YDC+VEHWGLD PLL HWEP
Sbjct: 187 YDCKVEHWGLDEPLLKHWEP 206



 Score = 32.7 bits (73), Expect(3) = 4e-66
 Identities = 15/19 (78%), Positives = 15/19 (78%)
 Frame = +1

Query: 667 PEIPAPMS*LTETAVCPPG 723
           PEIPAPMS LTET VC  G
Sbjct: 206 PEIPAPMSELTETVVCALG 224


>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 =  211 bits (538), Expect(3) = 4e-66
 Identities = 111/181 (61%), Positives = 126/181 (69%), Gaps = 1/181 (0%)
 Frame = +2

Query: 53  MVPGRVLMWGALALSTVMSA*GGEDIAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYG 232
           M+  + LM GALAL+TVMS  GGEDI ADHVASYG+ +YQ Y PSG ++HEFDGDEEFY 
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYV 60

Query: 233 DLEKIETVWRVPLFTEFTSFDPQGALRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXX 412
           DLE+ ETVW++PLF  F  FDPQ AL NIA LKHNL IV  RSN TAA  +         
Sbjct: 61  DLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSK 120

Query: 413 XXXILGHPLPLICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFL 589
               LG P  LIC VD+IFPPV+NI W   G SV EG S+T FLS +D SF  ISYLTFL
Sbjct: 121 SPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFL 180

Query: 590 P 592
           P
Sbjct: 181 P 181



 Score = 47.8 bits (112), Expect(3) = 4e-66
 Identities = 17/20 (85%), Positives = 18/20 (90%)
 Frame = +3

Query: 609 YDCQVEHWGLDNPLLTHWEP 668
           YDC+VEHWGLD PLL HWEP
Sbjct: 187 YDCKVEHWGLDEPLLKHWEP 206



 Score = 32.7 bits (73), Expect(3) = 4e-66
 Identities = 15/19 (78%), Positives = 15/19 (78%)
 Frame = +1

Query: 667 PEIPAPMS*LTETAVCPPG 723
           PEIPAPMS LTET VC  G
Sbjct: 206 PEIPAPMSELTETVVCALG 224


>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 =  211 bits (538), Expect(3) = 4e-66
 Identities = 111/181 (61%), Positives = 126/181 (69%), Gaps = 1/181 (0%)
 Frame = +2

Query: 53  MVPGRVLMWGALALSTVMSA*GGEDIAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYG 232
           M+  + LM GALAL+TVMS  GGEDI ADHVASYG+ +YQ Y PSG ++HEFDGDEEFY 
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYV 60

Query: 233 DLEKIETVWRVPLFTEFTSFDPQGALRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXX 412
           DLE+ ETVW++PLF  F  FDPQ AL NIA LKHNL IV  RSN TAA  +         
Sbjct: 61  DLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSK 120

Query: 413 XXXILGHPLPLICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFL 589
               LG P  LIC VD+IFPPV+NI W   G SV EG S+T FLS +D SF  ISYLTFL
Sbjct: 121 SPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFL 180

Query: 590 P 592
           P
Sbjct: 181 P 181



 Score = 47.8 bits (112), Expect(3) = 4e-66
 Identities = 17/20 (85%), Positives = 18/20 (90%)
 Frame = +3

Query: 609 YDCQVEHWGLDNPLLTHWEP 668
           YDC+VEHWGLD PLL HWEP
Sbjct: 187 YDCKVEHWGLDEPLLKHWEP 206



 Score = 32.7 bits (73), Expect(3) = 4e-66
 Identities = 15/19 (78%), Positives = 15/19 (78%)
 Frame = +1

Query: 667 PEIPAPMS*LTETAVCPPG 723
           PEIPAPMS LTET VC  G
Sbjct: 206 PEIPAPMSELTETVVCALG 224


>ref|XP_945969.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DQ(1) alpha chain precursor (DC-4 alpha chain) isoform 1
           [Homo sapiens]
          Length = 255

 Score =  211 bits (538), Expect(3) = 4e-66
 Identities = 111/181 (61%), Positives = 126/181 (69%), Gaps = 1/181 (0%)
 Frame = +2

Query: 53  MVPGRVLMWGALALSTVMSA*GGEDIAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYG 232
           M+  + LM GALAL+TVMS  GGEDI ADHVASYG+ +YQ Y PSG ++HEFDGDEEFY 
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYV 60

Query: 233 DLEKIETVWRVPLFTEFTSFDPQGALRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXX 412
           DLE+ ETVW++PLF  F  FDPQ AL NIA LKHNL IV  RSN TAA  +         
Sbjct: 61  DLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSK 120

Query: 413 XXXILGHPLPLICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFL 589
               LG P  LIC VD+IFPPV+NI W   G SV EG S+T FLS +D SF  ISYLTFL
Sbjct: 121 SPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFL 180

Query: 590 P 592
           P
Sbjct: 181 P 181



 Score = 47.8 bits (112), Expect(3) = 4e-66
 Identities = 17/20 (85%), Positives = 18/20 (90%)
 Frame = +3

Query: 609 YDCQVEHWGLDNPLLTHWEP 668
           YDC+VEHWGLD PLL HWEP
Sbjct: 187 YDCKVEHWGLDEPLLKHWEP 206



 Score = 32.7 bits (73), Expect(3) = 4e-66
 Identities = 15/19 (78%), Positives = 15/19 (78%)
 Frame = +1

Query: 667 PEIPAPMS*LTETAVCPPG 723
           PEIPAPMS LTET VC  G
Sbjct: 206 PEIPAPMSELTETVVCALG 224


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

 Score =  202 bits (515), Expect(3) = 2e-63
 Identities = 106/181 (58%), Positives = 124/181 (68%), Gaps = 1/181 (0%)
 Frame = +2

Query: 53  MVPGRVLMWGALALSTVMSA*GGEDIAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYG 232
           M+  + L+ GALAL+TVMS  GGEDI ADHVAS G+ +YQ Y PSG +THEFDGDE+FY 
Sbjct: 1   MILNKALLLGALALTTVMSPCGGEDIVADHVASCGVNLYQFYGPSGQYTHEFDGDEQFYV 60

Query: 233 DLEKIETVWRVPLFTEFTSFDPQGALRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXX 412
           DLE+ ET WR P F++F  FDPQGALRN+A  KHNL I+  R N TAA  +         
Sbjct: 61  DLERKETAWRWPEFSKFGGFDPQGALRNMAVAKHNLNIMIKRYNSTAATNEVPEVTVFSK 120

Query: 413 XXXILGHPLPLICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFL 589
               LG P  LIC VD+IFPPV+NI W   G SV EG S+T FLS +D SF  ISYLTFL
Sbjct: 121 SPVTLGQPNTLICLVDNIFPPVVNITWLSNGQSVTEGVSETSFLSKSDHSFFKISYLTFL 180

Query: 590 P 592
           P
Sbjct: 181 P 181



 Score = 47.8 bits (112), Expect(3) = 2e-63
 Identities = 17/20 (85%), Positives = 18/20 (90%)
 Frame = +3

Query: 609 YDCQVEHWGLDNPLLTHWEP 668
           YDC+VEHWGLD PLL HWEP
Sbjct: 187 YDCKVEHWGLDQPLLKHWEP 206



 Score = 32.7 bits (73), Expect(3) = 2e-63
 Identities = 15/19 (78%), Positives = 15/19 (78%)
 Frame = +1

Query: 667 PEIPAPMS*LTETAVCPPG 723
           PEIPAPMS LTET VC  G
Sbjct: 206 PEIPAPMSELTETVVCALG 224


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

 Score =  200 bits (509), Expect(3) = 1e-62
 Identities = 104/181 (57%), Positives = 124/181 (68%), Gaps = 1/181 (0%)
 Frame = +2

Query: 53  MVPGRVLMWGALALSTVMSA*GGEDIAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYG 232
           M+  + L+ GALAL+ VMS  GGEDI ADHVASYG+  YQ + PSG +THEFDGDEEFY 
Sbjct: 1   MILNKALLLGALALTAVMSPCGGEDIVADHVASYGVNFYQSHGPSGQYTHEFDGDEEFYV 60

Query: 233 DLEKIETVWRVPLFTEFTSFDPQGALRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXX 412
           DLE  ETVW++P+F++F SFDPQ ALRN+A  KH L  +  +SN TAA  +         
Sbjct: 61  DLETKETVWQLPMFSKFISFDPQSALRNMAVGKHTLEFMMRQSNSTAATNEVPEVTVFSK 120

Query: 413 XXXILGHPLPLICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFL 589
               LG P  LIC VD+IFPPV+NI W   G SV EG S+T FLS +D SF  ISYLTFL
Sbjct: 121 FPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFL 180

Query: 590 P 592
           P
Sbjct: 181 P 181



 Score = 47.8 bits (112), Expect(3) = 1e-62
 Identities = 17/20 (85%), Positives = 18/20 (90%)
 Frame = +3

Query: 609 YDCQVEHWGLDNPLLTHWEP 668
           YDC+VEHWGLD PLL HWEP
Sbjct: 187 YDCKVEHWGLDEPLLKHWEP 206



 Score = 32.3 bits (72), Expect(3) = 1e-62
 Identities = 15/19 (78%), Positives = 15/19 (78%)
 Frame = +1

Query: 667 PEIPAPMS*LTETAVCPPG 723
           PEIPAPMS LTET VC  G
Sbjct: 206 PEIPAPMSELTETLVCALG 224


>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 =  211 bits (538), Expect(2) = 3e-61
 Identities = 111/181 (61%), Positives = 126/181 (69%), Gaps = 1/181 (0%)
 Frame = +2

Query: 53  MVPGRVLMWGALALSTVMSA*GGEDIAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYG 232
           M+  + LM GALAL+TVMS  GGEDI ADHVASYG+ +YQ Y PSG ++HEFDGDEEFY 
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYV 60

Query: 233 DLEKIETVWRVPLFTEFTSFDPQGALRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXX 412
           DLE+ ETVW++PLF  F  FDPQ AL NIA LKHNL IV  RSN TAA  +         
Sbjct: 61  DLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSK 120

Query: 413 XXXILGHPLPLICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFL 589
               LG P  LIC VD+IFPPV+NI W   G SV EG S+T FLS +D SF  ISYLTFL
Sbjct: 121 SPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFL 180

Query: 590 P 592
           P
Sbjct: 181 P 181



 Score = 43.1 bits (100), Expect(2) = 3e-61
 Identities = 15/18 (83%), Positives = 16/18 (88%)
 Frame = +3

Query: 609 YDCQVEHWGLDNPLLTHW 662
           YDC+VEHWGLD PLL HW
Sbjct: 187 YDCKVEHWGLDEPLLKHW 204


>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 =  194 bits (493), Expect(3) = 6e-61
 Identities = 105/181 (58%), Positives = 122/181 (67%), Gaps = 1/181 (0%)
 Frame = +2

Query: 53  MVPGRVLMWGALALSTVMSA*GGEDIAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYG 232
           M+  + LM GALAL+TVMS  GGEDI ADHVASYG+ +YQ Y PSG +THEFDGDE+FY 
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYV 60

Query: 233 DLEKIETVWRVPLFTEFTSFDPQGALRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXX 412
           DL + ETVW +P+  +F  FDPQ AL NIA LKHNL  +  RSN TAA  +         
Sbjct: 61  DLGRKETVWCLPVLRQF-RFDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSK 119

Query: 413 XXXILGHPLPLICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFL 589
               LG P  LIC VD+IFPPV+NI W   G SV EG S+T FLS +D SF  ISYLT L
Sbjct: 120 SPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLL 179

Query: 590 P 592
           P
Sbjct: 180 P 180



 Score = 47.8 bits (112), Expect(3) = 6e-61
 Identities = 17/20 (85%), Positives = 18/20 (90%)
 Frame = +3

Query: 609 YDCQVEHWGLDNPLLTHWEP 668
           YDC+VEHWGLD PLL HWEP
Sbjct: 186 YDCKVEHWGLDKPLLKHWEP 205



 Score = 32.7 bits (73), Expect(3) = 6e-61
 Identities = 15/19 (78%), Positives = 15/19 (78%)
 Frame = +1

Query: 667 PEIPAPMS*LTETAVCPPG 723
           PEIPAPMS LTET VC  G
Sbjct: 205 PEIPAPMSELTETVVCALG 223


>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 =  194 bits (493), Expect(3) = 6e-61
 Identities = 105/181 (58%), Positives = 122/181 (67%), Gaps = 1/181 (0%)
 Frame = +2

Query: 53  MVPGRVLMWGALALSTVMSA*GGEDIAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYG 232
           M+  + LM GALAL+TVMS  GGEDI ADHVASYG+ +YQ Y PSG +THEFDGDE+FY 
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYV 60

Query: 233 DLEKIETVWRVPLFTEFTSFDPQGALRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXX 412
           DL + ETVW +P+  +F  FDPQ AL NIA LKHNL  +  RSN TAA  +         
Sbjct: 61  DLGRKETVWCLPVLRQF-RFDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSK 119

Query: 413 XXXILGHPLPLICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFL 589
               LG P  LIC VD+IFPPV+NI W   G SV EG S+T FLS +D SF  ISYLT L
Sbjct: 120 SPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLL 179

Query: 590 P 592
           P
Sbjct: 180 P 180



 Score = 47.8 bits (112), Expect(3) = 6e-61
 Identities = 17/20 (85%), Positives = 18/20 (90%)
 Frame = +3

Query: 609 YDCQVEHWGLDNPLLTHWEP 668
           YDC+VEHWGLD PLL HWEP
Sbjct: 186 YDCKVEHWGLDKPLLKHWEP 205



 Score = 32.7 bits (73), Expect(3) = 6e-61
 Identities = 15/19 (78%), Positives = 15/19 (78%)
 Frame = +1

Query: 667 PEIPAPMS*LTETAVCPPG 723
           PEIPAPMS LTET VC  G
Sbjct: 205 PEIPAPMSELTETVVCALG 223


>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 =  194 bits (493), Expect(3) = 6e-61
 Identities = 105/181 (58%), Positives = 122/181 (67%), Gaps = 1/181 (0%)
 Frame = +2

Query: 53  MVPGRVLMWGALALSTVMSA*GGEDIAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYG 232
           M+  + LM GALAL+TVMS  GGEDI ADHVASYG+ +YQ Y PSG +THEFDGDE+FY 
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYV 60

Query: 233 DLEKIETVWRVPLFTEFTSFDPQGALRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXX 412
           DL + ETVW +P+  +F  FDPQ AL NIA LKHNL  +  RSN TAA  +         
Sbjct: 61  DLGRKETVWCLPVLRQF-RFDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSK 119

Query: 413 XXXILGHPLPLICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFL 589
               LG P  LIC VD+IFPPV+NI W   G SV EG S+T FLS +D SF  ISYLT L
Sbjct: 120 SPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLL 179

Query: 590 P 592
           P
Sbjct: 180 P 180



 Score = 47.8 bits (112), Expect(3) = 6e-61
 Identities = 17/20 (85%), Positives = 18/20 (90%)
 Frame = +3

Query: 609 YDCQVEHWGLDNPLLTHWEP 668
           YDC+VEHWGLD PLL HWEP
Sbjct: 186 YDCKVEHWGLDKPLLKHWEP 205



 Score = 32.7 bits (73), Expect(3) = 6e-61
 Identities = 15/19 (78%), Positives = 15/19 (78%)
 Frame = +1

Query: 667 PEIPAPMS*LTETAVCPPG 723
           PEIPAPMS LTET VC  G
Sbjct: 205 PEIPAPMSELTETVVCALG 223


  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: 36,579,175
Number of Sequences: 39411
Number of extensions: 984329
Number of successful extensions: 5181
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 3627
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): 4990
length of database: 17,774,539
effective HSP length: 104
effective length of database: 13,675,795
effective search space used: 4048035320
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-029724
         (1203 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_034508.2| histocompatibility 2, class II antigen A, alpha...   171   3e-53
Alignment   gi|NP_032232.1| histocompatibility 2, O region alpha locus [Mus...   122   8e-36
Alignment   gi|NP_034511.2| histocompatibility 2, class II antigen E alpha ...   116   2e-32

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

 Score =  171 bits (434), Expect(3) = 3e-53
 Identities = 93/182 (51%), Positives = 114/182 (62%), Gaps = 2/182 (1%)
 Frame = +2

Query: 53  MVPGRVLMWGALALSTVMSA*GGED-IAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFY 229
           M   R L+ G LAL+T++S  GGED I ADHV +YG+ VYQ     G +T EFDGDE FY
Sbjct: 1   MPRSRALILGVLALTTMLSLCGGEDDIEADHVGTYGISVYQSPGDIGQYTFEFDGDELFY 60

Query: 230 GDLEKIETVWRVPLFTEFTSFDPQGALRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXX 409
            DL+K ETVW +P F +  SFDPQG L+NIA +KHNL ++T RSN T A  +        
Sbjct: 61  VDLDKKETVWMLPEFGQLASFDPQGGLQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFP 120

Query: 410 XXXXILGHPLPLICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTF 586
               +LG P  LIC VD+IFPPVINI W     SV +G  +T F    D SF  +SYLTF
Sbjct: 121 KSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTF 180

Query: 587 LP 592
           +P
Sbjct: 181 IP 182



 Score = 45.1 bits (105), Expect(3) = 3e-53
 Identities = 15/20 (75%), Positives = 18/20 (90%)
 Frame = +3

Query: 609 YDCQVEHWGLDNPLLTHWEP 668
           YDC+VEHWGL+ P+L HWEP
Sbjct: 188 YDCKVEHWGLEEPVLKHWEP 207



 Score = 32.7 bits (73), Expect(3) = 3e-53
 Identities = 15/19 (78%), Positives = 15/19 (78%)
 Frame = +1

Query: 667 PEIPAPMS*LTETAVCPPG 723
           PEIPAPMS LTET VC  G
Sbjct: 207 PEIPAPMSELTETVVCALG 225


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

 Score =  122 bits (306), Expect(2) = 8e-36
 Identities = 71/170 (41%), Positives = 91/170 (53%), Gaps = 1/170 (0%)
 Frame = +2

Query: 86  LALSTVMSA*GGEDIAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYGDLEKIETVWRV 265
           L + + +S  G   I ADH+ SYG   YQ Y  SG FTHEFDG++ F  DL+  E VWR+
Sbjct: 12  LTVMSFLSPRGVRAIKADHMGSYGPAFYQSYDASGQFTHEFDGEQIFSVDLKNEEVVWRL 71

Query: 266 PLFTEFTSFDPQGALRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXXXXXILGHPLPL 445
           P F +F   D Q  L +I+ +K +L I+  RSN T AV               LG P  L
Sbjct: 72  PEFGDFAHSDFQSGLMSISMIKAHLDILVERSNRTRAVSVPPRVTVLPKTRVELGKPNVL 131

Query: 446 ICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFLP 592
           IC VD IFPPVIN+ W      + +G + T F S  +  F    YLTF+P
Sbjct: 132 ICIVDDIFPPVINVTWLRNSQPITKGVAQTSFYSQPNHRFRKFHYLTFVP 181



 Score = 47.8 bits (112), Expect(2) = 8e-36
 Identities = 17/20 (85%), Positives = 18/20 (90%)
 Frame = +3

Query: 609 YDCQVEHWGLDNPLLTHWEP 668
           YDC+VEHWGLD PLL HWEP
Sbjct: 187 YDCKVEHWGLDTPLLQHWEP 206


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

 Score =  116 bits (290), Expect(2) = 2e-32
 Identities = 62/136 (45%), Positives = 78/136 (57%), Gaps = 1/136 (0%)
 Frame = +2

Query: 188 GYFTHEFDGDEEFYGDLEKIETVWRVPLFTEFTSFDPQGALRNIATLKHNLTIVTNRSND 367
           G F  +FDGDE F+ D+EK ET+WR+  F +F SF+ QGAL NIA  K NL ++  RSN+
Sbjct: 45  GEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLDVMKERSNN 104

Query: 368 TAAVYQXXXXXXXXXXXXILGHPLPLICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLS 544
           T                  LG P  LIC +D   PPV+N+ WF  G  V EG S+T+FL 
Sbjct: 105 TPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWFRNGRPVTEGVSETVFLP 164

Query: 545 YNDLSFLNISYLTFLP 592
            +D  F    YLTFLP
Sbjct: 165 RDDHLFRKFHYLTFLP 180



 Score = 42.7 bits (99), Expect(2) = 2e-32
 Identities = 14/20 (70%), Positives = 17/20 (85%)
 Frame = +3

Query: 606 FYDCQVEHWGLDNPLLTHWE 665
           FYDC+V+HWGL+ PL  HWE
Sbjct: 185 FYDCEVDHWGLEEPLRKHWE 204


  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: 42,706,509
Number of Sequences: 45328
Number of extensions: 1085293
Number of successful extensions: 4925
Number of sequences better than 1.0e-05: 3
Number of HSP's better than  0.0 without gapping: 3900
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): 4822
length of database: 21,768,885
effective HSP length: 106
effective length of database: 16,964,117
effective search space used: 4987450398
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-029724
         (1203 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001011726.1| MHC class II DLA DQalpha chain [Canis famili...   206   8e-64
Alignment   gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati...   116   8e-34
Alignment   gi|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris]    109   3e-31
Alignment   gi|XP_532104.2| PREDICTED: similar to HLA class II histocompati...    85   2e-16

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

 Score =  206 bits (524), Expect(3) = 8e-64
 Identities = 106/181 (58%), Positives = 127/181 (70%), Gaps = 1/181 (0%)
 Frame = +2

Query: 53  MVPGRVLMWGALALSTVMSA*GGEDIAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYG 232
           M+  RVL+ G L L+ +MS  GGE+I ADHVA+YG+ VYQ Y PSG +THEFDGDEEFY 
Sbjct: 1   MILNRVLILGTLILTIMMSPSGGEEIVADHVANYGINVYQSYGPSGQYTHEFDGDEEFYV 60

Query: 233 DLEKIETVWRVPLFTEFTSFDPQGALRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXX 412
           DLEK ETVWR+P+F+ F SFDPQGALRN+A +K NL I+T RSN TAA  +         
Sbjct: 61  DLEKKETVWRLPVFSTFRSFDPQGALRNLAIIKQNLNIMTKRSNQTAATNEVPEVTVFSK 120

Query: 413 XXXILGHPLPLICPVDSIFPPVINIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFL 589
              +LG P  LIC VD+IFPPVIN+ W +   SV EG S+T F +  D SF  ISYLTFL
Sbjct: 121 SPVMLGQPNTLICLVDNIFPPVINVTWLKNRHSVTEGVSETSFFAKGDHSFSKISYLTFL 180

Query: 590 P 592
           P
Sbjct: 181 P 181



 Score = 47.8 bits (112), Expect(3) = 8e-64
 Identities = 17/20 (85%), Positives = 18/20 (90%)
 Frame = +3

Query: 609 YDCQVEHWGLDNPLLTHWEP 668
           YDC+VEHWGLD PLL HWEP
Sbjct: 187 YDCKVEHWGLDEPLLKHWEP 206



 Score = 30.8 bits (68), Expect(3) = 8e-64
 Identities = 13/19 (68%), Positives = 14/19 (73%)
 Frame = +1

Query: 667 PEIPAPMS*LTETAVCPPG 723
           PE+P PMS LTET VC  G
Sbjct: 206 PEVPTPMSELTETVVCALG 224


>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 =  116 bits (291), Expect(3) = 8e-34
 Identities = 66/158 (41%), Positives = 84/158 (53%), Gaps = 8/158 (5%)
 Frame = +2

Query: 143 VASYGLYVYQPYRPSGYFTHEFDGDEEFYGDLEKIETVWRVPLFTEFTSFDPQGALRNIA 322
           + SYG   YQ Y  SG F HEFDG++ F  +L+K + VWR+P F     FDPQ  L +IA
Sbjct: 1   MGSYGPAFYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEFGNLAHFDPQNGLASIA 60

Query: 323 TLKHNLTIVTNRSNDTAAVYQXXXXXXXXXXXXI-------LGHPLPLICPVDSIFPPVI 481
            +K +L ++  RSN T A+              +       LG P  LIC VD+IFPPVI
Sbjct: 61  VIKAHLDVLVERSNRTRAINGTHLSSPLPPRVAVLPKFRVELGQPNVLICIVDNIFPPVI 120

Query: 482 NIAWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFLP 592
           NI W   G  + EG + T F S  D  F    YLTF+P
Sbjct: 121 NITWLRNGQIISEGVAQTSFYSQPDHLFRKFCYLTFVP 158



 Score = 46.2 bits (108), Expect(3) = 8e-34
 Identities = 16/20 (80%), Positives = 18/20 (90%)
 Frame = +3

Query: 609 YDCQVEHWGLDNPLLTHWEP 668
           YDC+VEHWGL+ PLL HWEP
Sbjct: 164 YDCKVEHWGLEEPLLRHWEP 183



 Score = 20.8 bits (42), Expect(3) = 8e-34
 Identities = 7/19 (36%), Positives = 11/19 (57%)
 Frame = +1

Query: 667 PEIPAPMS*LTETAVCPPG 723
           P++P P+    ET +C  G
Sbjct: 183 PQVPIPVPDTIETLICALG 201


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

 Score =  109 bits (273), Expect(2) = 3e-31
 Identities = 67/156 (42%), Positives = 79/156 (50%), Gaps = 1/156 (0%)
 Frame = +2

Query: 128 IAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYGDLEKIETVWRVPLFTEFTSFDPQGA 307
           +  +HV     +   P  PSG F  +FDGDE F+ D+EK ETVWR+  F  F SF+ QGA
Sbjct: 26  VKEEHVIIQAEFYLTP-DPSGEFMFDFDGDEIFHVDMEKKETVWRLEEFGRFASFEAQGA 84

Query: 308 LRNIATLKHNLTIVTNRSNDTAAVYQXXXXXXXXXXXXILGHPLPLICPVDSIFPPVINI 487
           L NIA  K NL  +  RSN T                  LG P  LIC +D   PPVIN+
Sbjct: 85  LANIAVDKANLDTMIKRSNHTPNTNVPPEVTVLSNTPVELGEPNILICFIDKFSPPVINV 144

Query: 488 AWFEIGLSV-EGFSDTIFLSYNDLSFLNISYLTFLP 592
            W   G  V  G S+TIFL   D  F    YL FLP
Sbjct: 145 TWLRNGNPVTTGVSETIFLPREDHLFRKFHYLPFLP 180



 Score = 45.1 bits (105), Expect(2) = 3e-31
 Identities = 16/19 (84%), Positives = 17/19 (89%)
 Frame = +3

Query: 609 YDCQVEHWGLDNPLLTHWE 665
           YDC+VEHWGLD PLL HWE
Sbjct: 186 YDCKVEHWGLDEPLLKHWE 204


>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 = 84.7 bits (208), Expect = 2e-16
 Identities = 40/84 (47%), Positives = 53/84 (63%)
 Frame = +2

Query: 128 IAADHVASYGLYVYQPYRPSGYFTHEFDGDEEFYGDLEKIETVWRVPLFTEFTSFDPQGA 307
           I ADH+ SYG   YQ Y  SG F HEFDG++ F  +L+K + VWR+P F     FDPQ  
Sbjct: 12  IEADHMGSYGPAFYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEFGNLAHFDPQNG 71

Query: 308 LRNIATLKHNLTIVTNRSNDTAAV 379
           L +IA +K +L ++  RSN T A+
Sbjct: 72  LASIAVIKAHLDVLVERSNRTRAI 95


  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: 37,740,455
Number of Sequences: 33732
Number of extensions: 983987
Number of successful extensions: 5003
Number of sequences better than 1.0e-05: 4
Number of HSP's better than  0.0 without gapping: 3775
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): 4921
length of database: 19,266,565
effective HSP length: 105
effective length of database: 15,724,705
effective search space used: 4638787975
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)