Animal-Genome cDNA 20060611S-027234


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-027234
         (1213 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]                    72   3e-14
Alignment   gi|NP_999143.1| beta 2-microglobulin [Sus scrofa]                     69   2e-13
Alignment   gi|NP_998933.1| swine leukocyte antigen 7 [Sus scrofa]                49   2e-07

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

 Score = 71.6 bits (174), Expect = 3e-14
 Identities = 37/106 (34%), Positives = 55/106 (51%)
 Frame = +1

Query: 385 VPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSL 564
           +P   VF   P+  G+PNTL+C V N+FPP + +TW ++  +  EG   T   + +D S 
Sbjct: 126 LPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTW-EHHSAPVEGIGPTFVSATDDLSF 184

Query: 565 LKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 702
              SYL F P+  D + C V H       + +W P+   P S+L E
Sbjct: 185 QAFSYLNFTPTPSDLFSCVVTHELDGYVAISYWVPQNALP-SDLLE 229


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

 Score = 68.9 bits (167), Expect = 2e-13
 Identities = 37/98 (37%), Positives = 52/98 (53%)
 Frame = +1

Query: 373 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN 552
           AV + P+V V+ + P   G+PN L C+V    PP I I  LKNG  +    S+ SF    
Sbjct: 20  AVARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SK 77

Query: 553 DHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 666
           D S   + +  F P+  D Y C+V+H  LDKP +  W+
Sbjct: 78  DWSFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 115


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

 Score = 49.3 bits (116), Expect = 2e-07
 Identities = 23/80 (28%), Positives = 36/80 (45%)
 Frame = +1

Query: 439 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSLLKISYLTFLPSDDDFYDC 618
           TL C     +P  I++TW + G   ++           D +  K + L   P ++  Y C
Sbjct: 221 TLRCWALGFYPKEISLTWQQEGQDQSQDVEVVETRPSGDGTFRKWAALVVPPGEEQSYTC 280

Query: 619 KVEHWGLDKPLLKHWEPEIP 678
            V+H GL +PL   W+P  P
Sbjct: 281 HVQHEGLQEPLTLRWDPPQP 300


  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: 1,081,334
Number of Sequences: 1040
Number of extensions: 26073
Number of successful extensions: 70
Number of sequences better than 1.0e-05: 3
Number of HSP's better than  0.0 without gapping: 62
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): 67
length of database: 434,620
effective HSP length: 79
effective length of database: 352,460
effective search space used: 114197040
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-027234
         (1213 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...   246   e-105
Alignment   gi|NP_001012693.1| major histocompatibility complex, class II, ...   239   9e-99
Alignment   gi|NP_001012699.1| major histocompatibility complex, class II, ...   197   2e-88
Alignment   gi|XP_604082.2| PREDICTED: similar to HLA class II histocompati...   167   8e-59
Alignment   gi|XP_883292.1| PREDICTED: similar to HLA class II histocompati...   165   4e-58
Alignment   gi|NP_001012695.1| major histocompatibility complex, class II, ...   162   9e-54
Alignment   gi|NP_001012696.1| major histocompatibility complex, class II, ...   192   6e-49
Alignment   gi|NP_776318.1| beta-2-microglobulin [Bos taurus]                     69   7e-12
Alignment   gi|NP_001029840.2| MHC class II antigen [Bos taurus]                  63   5e-10
Alignment   gi|NP_001013618.1| major histocompatibility complex, class II, ...    62   7e-10

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

 Score =  246 bits (628), Expect(2) = e-105
 Identities = 118/157 (75%), Positives = 128/157 (81%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 525
           +I+RSN+TAA N+VPEVTVF KSPVMLGQPNTLICHVDNIFPPVINITWL+NGHSVTEG 
Sbjct: 99  VIQRSNSTAATNKVPEVTVFSKSPVMLGQPNTLICHVDNIFPPVINITWLRNGHSVTEGV 158

Query: 526 SETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 705
           SETSFL K+D+S LKI+YLTFLPSDDD YDCKVEHWGLD+PLLKHWEP+IPAPMSELTET
Sbjct: 159 SETSFLIKSDYSFLKINYLTFLPSDDDVYDCKVEHWGLDEPLLKHWEPDIPAPMSELTET 218

Query: 706 XXXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 816
                                 QGLRSGGPSRHQG L
Sbjct: 219 VVCALGLTVGLVGIMVGTILIIQGLRSGGPSRHQGPL 255



 Score =  155 bits (391), Expect(2) = e-105
 Identities = 70/96 (72%), Positives = 82/96 (85%)
 Frame = +2

Query: 56  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 235
           MV  R L+ GALALT +MS  G EDI ADH+ +YG+++Y +YGPSGYYTHEFDGDEEFYV
Sbjct: 1   MVLNRALILGALALTTMMSPSGSEDIVADHIGTYGISIYHTYGPSGYYTHEFDGDEEFYV 60

Query: 236 DLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNL 343
           DL K+ETVW+LP+FSKF +FDPQGALRNIAT KHNL
Sbjct: 61  DLEKRETVWRLPVFSKFATFDPQGALRNIATTKHNL 96


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

 Score =  239 bits (611), Expect(2) = 9e-99
 Identities = 116/157 (73%), Positives = 123/157 (78%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 525
           L K SN+TAA N+VPEVTVF KSPVMLGQPNTLICHVDNIFPPVINITWL+NGHSVTEG 
Sbjct: 99  LTKFSNSTAATNKVPEVTVFSKSPVMLGQPNTLICHVDNIFPPVINITWLRNGHSVTEGV 158

Query: 526 SETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 705
           SETSFL ++D+S LKI YL FLPSDDD YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET
Sbjct: 159 SETSFLIRSDYSFLKIKYLAFLPSDDDIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTET 218

Query: 706 XXXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 816
                                 QGLRSG PSRHQG L
Sbjct: 219 VVCTLGLTMGLVGITVGTIFIIQGLRSGDPSRHQGPL 255



 Score =  140 bits (352), Expect(2) = 9e-99
 Identities = 67/93 (72%), Positives = 74/93 (79%)
 Frame = +2

Query: 56  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 235
           MV  R L+ G LALT +MS  GGEDI ADHV  YG+++YQSYGPSG YTHEFDGDE+FYV
Sbjct: 1   MVLNRALILGTLALTTMMSPSGGEDIVADHVGIYGISIYQSYGPSGQYTHEFDGDEQFYV 60

Query: 236 DLGKKETVWQLPLFSKFRSFDPQGALRNIATAK 334
           DL KKET WQLPLFS+  SFDPQ ALRNIA  K
Sbjct: 61  DLEKKETAWQLPLFSRMLSFDPQLALRNIAIMK 93


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

 Score =  197 bits (500), Expect(2) = 2e-88
 Identities = 90/106 (84%), Positives = 96/106 (90%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 525
           L KRSN T  +N+VPEVTVF KSPVMLGQPNTLICHVDNIFPPVINITWLKNGH+VTEG 
Sbjct: 99  LTKRSNFTPVINEVPEVTVFSKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHAVTEGV 158

Query: 526 SETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHW 663
           SETSFL K+DHS LKI YLTFLPSD+D YDCKVEHWGLD+PLLKHW
Sbjct: 159 SETSFLPKDDHSFLKIGYLTFLPSDNDIYDCKVEHWGLDEPLLKHW 204



 Score =  148 bits (373), Expect(2) = 2e-88
 Identities = 70/97 (72%), Positives = 79/97 (81%)
 Frame = +2

Query: 56  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 235
           MV  R L+ GALALT +MS+ GGEDI ADHV SYG  +YQS+GPSG YT EFDGDE FYV
Sbjct: 1   MVLNRALILGALALTTMMSSSGGEDIVADHVGSYGTEIYQSHGPSGQYTQEFDGDEMFYV 60

Query: 236 DLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLN 346
           DLGKKETVW+LP+FS+F  FDPQ AL  IATAKHNL+
Sbjct: 61  DLGKKETVWRLPMFSQFAGFDPQAALSEIATAKHNLD 97


>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 =  167 bits (424), Expect(2) = 8e-59
 Identities = 74/121 (61%), Positives = 91/121 (75%)
 Frame = +1

Query: 343 ELIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEG 522
           +L+KRSN T A N  P V V PKS V LG+PN LIC VD IFPPVINITWL+NGH VT+G
Sbjct: 98  DLVKRSNGTRAPNVSPRVAVLPKSHVQLGEPNVLICIVDKIFPPVINITWLRNGHPVTQG 157

Query: 523 FSETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 702
            +++SF ++ DH   K  YLTF+P  DDFYDCKVEHWGLD+PL +HWEP++P  + + T 
Sbjct: 158 VTQSSFYAQPDHLFRKFHYLTFVPLVDDFYDCKVEHWGLDQPLFQHWEPQVPTALPDTTG 217

Query: 703 T 705
           T
Sbjct: 218 T 218



 Score = 79.0 bits (193), Expect(2) = 8e-59
 Identities = 41/90 (45%), Positives = 55/90 (61%)
 Frame = +2

Query: 74  LMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYVDLGKKE 253
           L+ G   L  ++S      I ADH+ SYG   YQSY  +G +T++FDG++ F VDL K+E
Sbjct: 7   LVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSVDLKKRE 66

Query: 254 TVWQLPLFSKFRSFDPQGALRNIATAKHNL 343
            VW+LP F  F  FDPQ  L +IA  K +L
Sbjct: 67  AVWRLPEFGNFAYFDPQSGLVSIAMIKAHL 96


>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 =  165 bits (418), Expect(2) = 4e-58
 Identities = 74/122 (60%), Positives = 92/122 (75%), Gaps = 1/122 (0%)
 Frame = +1

Query: 343 ELIKRSNNTAAVN-QVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTE 519
           +L+KRSN T A N   P+V V PKS V LG+PN LIC VD IFPPVINITWL+NGH VT+
Sbjct: 98  DLVKRSNGTRAPNGSTPQVAVLPKSHVQLGEPNVLICIVDKIFPPVINITWLRNGHPVTQ 157

Query: 520 GFSETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELT 699
           G +++SF ++ DH   K  YLTF+P  DDFYDCKVEHWGLD+PL +HWEP++P  + + T
Sbjct: 158 GVTQSSFYAQPDHLFRKFHYLTFVPLVDDFYDCKVEHWGLDQPLFQHWEPQVPTALPDTT 217

Query: 700 ET 705
            T
Sbjct: 218 GT 219



 Score = 79.0 bits (193), Expect(2) = 4e-58
 Identities = 41/90 (45%), Positives = 55/90 (61%)
 Frame = +2

Query: 74  LMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYVDLGKKE 253
           L+ G   L  ++S      I ADH+ SYG   YQSY  +G +T++FDG++ F VDL K+E
Sbjct: 7   LVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSVDLKKRE 66

Query: 254 TVWQLPLFSKFRSFDPQGALRNIATAKHNL 343
            VW+LP F  F  FDPQ  L +IA  K +L
Sbjct: 67  AVWRLPEFGNFAYFDPQSGLVSIAMIKAHL 96


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

 Score =  162 bits (409), Expect(2) = 9e-54
 Identities = 77/157 (49%), Positives = 95/157 (60%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 525
           +IKRSNNT   N  PEVT+ P  PV LG+PNTLIC +D   PPVI++TWL+NG  VT+G 
Sbjct: 97  MIKRSNNTPNTNVPPEVTLLPNKPVELGEPNTLICFIDKFSPPVISVTWLRNGKPVTDGV 156

Query: 526 SETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 705
           S+T FL +NDH   K  YL FLP+ +D YDCKVEH GL++PLLKHWE E PAP+ E TE 
Sbjct: 157 SQTVFLPRNDHLFRKFHYLPFLPTTEDVYDCKVEHLGLNEPLLKHWEYEAPAPLPETTEN 216

Query: 706 XXXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 816
                                 +G+R       +G L
Sbjct: 217 AVCALGLIVALVGIIAGTIFIIKGVRKANTVERRGPL 253



 Score = 67.8 bits (164), Expect(2) = 9e-54
 Identities = 31/53 (58%), Positives = 39/53 (73%)
 Frame = +2

Query: 188 SGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLN 346
           S  +  +FDGDE F+VD+GKKETVW+LP F  F SF+ QGAL N+A  K NL+
Sbjct: 43  SAEFMFDFDGDEIFHVDMGKKETVWRLPEFGHFASFEAQGALANMAVMKANLD 95


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

 Score =  192 bits (487), Expect = 6e-49
 Identities = 86/120 (71%), Positives = 101/120 (84%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 525
           LIK S+ T A +++PEV VFPKS V+LG PNTLIC VDNIFPPVINITW  NGH V EG 
Sbjct: 97  LIKNSSFTPATSEIPEVAVFPKSSVVLGIPNTLICQVDNIFPPVINITWFYNGHFVAEGI 156

Query: 526 SETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 705
           +ET+F  K+DHS LK SYLTFLP+++DFYDC+VEHWGL++PL+KHWEPEIP P SELTET
Sbjct: 157 AETTFYPKSDHSFLKFSYLTFLPTNEDFYDCRVEHWGLEEPLVKHWEPEIPTPTSELTET 216



 Score =  121 bits (304), Expect = 1e-27
 Identities = 63/106 (59%), Positives = 73/106 (68%), Gaps = 2/106 (1%)
 Frame = +2

Query: 68  RVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYVDLGK 247
           + L+  AL L  +MS  GGEDI ADHV +YG NVYQ+YG SG +T EFDGDE FYVDLGK
Sbjct: 3   KALILRALTLATMMSPYGGEDIVADHVGTYGTNVYQTYGASGQFTFEFDGDELFYVDLGK 62

Query: 248 KETVWQLPLFSKFRSFDPQGALRNIATAKHNLN*L--NVPTTPRLS 379
           KETVW+LP FS    F+ Q ALRNI  +K NL+ L  N   TP  S
Sbjct: 63  KETVWRLPEFSNITKFEVQSALRNIVMSKRNLDILIKNSSFTPATS 108


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

 Score = 68.9 bits (167), Expect = 7e-12
 Identities = 34/101 (33%), Positives = 55/101 (54%)
 Frame = +1

Query: 373 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN 552
           A+ + P++ V+ + P   G+PN L C+V    PP I I  LKNG  +    S+ SF    
Sbjct: 20  AIQRPPKIQVYSRHPPEDGKPNYLNCYVYGFHPPQIEIDLLKNGEKIKSEQSDLSF--SK 77

Query: 553 DHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEI 675
           D S   +S+  F P+  D Y C+V+H  L++P +  W+ ++
Sbjct: 78  DWSFYLLSHAEFTPNSKDQYSCRVKHVTLEQPRIVKWDRDL 118


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

 Score = 62.8 bits (151), Expect = 5e-10
 Identities = 29/103 (28%), Positives = 44/103 (42%)
 Frame = +1

Query: 388 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSLL 567
           P VT+ P     L   N L+C V + +P  I + W +N    T G   T  +   D +  
Sbjct: 129 PTVTISPSRTEALNHHNLLVCSVTDFYPSQIKVRWFRNDREETAGVVSTPLIRNGDWTFQ 188

Query: 568 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 696
            +  L   P   D Y C VEH  L  P++  W  +  +  S++
Sbjct: 189 ILVMLEMTPQRGDVYTCHVEHPSLQSPIMVEWRAQSESAQSKM 231


>ref|NP_001013618.1| major histocompatibility complex, class II, DO beta [Bos taurus]
          Length = 271

 Score = 62.4 bits (150), Expect = 7e-10
 Identities = 30/95 (31%), Positives = 42/95 (44%)
 Frame = +1

Query: 388 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSLL 567
           PEVTV+P+    L   N L+C V   +P  I +TW +NG    EG   T  +   D +  
Sbjct: 123 PEVTVYPEKTPALQHRNLLLCLVTGFYPGDIKVTWFRNGQEQREGIMSTGLIRNGDWTFQ 182

Query: 568 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPE 672
               L   P   + Y C V+H  L  P+   W  +
Sbjct: 183 MTVMLAMTPELGEVYTCLVDHPSLLSPVSVEWRAQ 217


  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: 40,468,899
Number of Sequences: 33508
Number of extensions: 1007576
Number of successful extensions: 2857
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 2591
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): 2843
length of database: 16,112,626
effective HSP length: 104
effective length of database: 12,627,794
effective search space used: 3775710406
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-027234
         (1213 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...   236   e-104
Alignment   gi|XP_949973.1| PREDICTED: similar to HLA class II histocompati...   236   e-104
Alignment   gi|XP_949971.1| PREDICTED: similar to HLA class II histocompati...   236   e-104
Alignment   gi|XP_945969.1| PREDICTED: similar to HLA class II histocompati...   236   e-104
Alignment   gi|NP_002113.2| major histocompatibility complex, class II, DQ ...   230   1e-99
Alignment   gi|XP_941306.1| PREDICTED: similar to HLA class II histocompati...   229   3e-99
Alignment   gi|XP_941305.1| PREDICTED: similar to HLA class II histocompati...   229   3e-99
Alignment   gi|XP_941304.1| PREDICTED: similar to HLA class II histocompati...   229   3e-99
Alignment   gi|XP_941255.1| PREDICTED: similar to HLA class II histocompati...   229   3e-99
Alignment   gi|XP_941221.1| PREDICTED: similar to HLA class II histocompati...   229   3e-99

>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 =  236 bits (603), Expect(2) = e-104
 Identities = 115/157 (73%), Positives = 123/157 (78%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 525
           +IKRSN+TAA N+VPEVTVF KSPV LGQPNTLIC VDNIFPPV+NITWL NGHSVTEG 
Sbjct: 99  VIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGV 158

Query: 526 SETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 705
           SETSFLSK+DHS  KISYLTFLPSDD+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET
Sbjct: 159 SETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTET 218

Query: 706 XXXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 816
                                 +GLRS G SRHQG L
Sbjct: 219 VVCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 255



 Score =  160 bits (404), Expect(2) = e-104
 Identities = 75/97 (77%), Positives = 82/97 (84%)
 Frame = +2

Query: 56  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 235
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG Y+HEFDGDEEFYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYV 60

Query: 236 DLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLN 346
           DL +KETVWQLPLF +FR FDPQ AL NIA  KHNLN
Sbjct: 61  DLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLN 97


>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 =  236 bits (603), Expect(2) = e-104
 Identities = 115/157 (73%), Positives = 123/157 (78%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 525
           +IKRSN+TAA N+VPEVTVF KSPV LGQPNTLIC VDNIFPPV+NITWL NGHSVTEG 
Sbjct: 99  VIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGV 158

Query: 526 SETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 705
           SETSFLSK+DHS  KISYLTFLPSDD+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET
Sbjct: 159 SETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTET 218

Query: 706 XXXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 816
                                 +GLRS G SRHQG L
Sbjct: 219 VVCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 255



 Score =  160 bits (404), Expect(2) = e-104
 Identities = 75/97 (77%), Positives = 82/97 (84%)
 Frame = +2

Query: 56  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 235
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG Y+HEFDGDEEFYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYV 60

Query: 236 DLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLN 346
           DL +KETVWQLPLF +FR FDPQ AL NIA  KHNLN
Sbjct: 61  DLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLN 97


>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 =  236 bits (603), Expect(2) = e-104
 Identities = 115/157 (73%), Positives = 123/157 (78%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 525
           +IKRSN+TAA N+VPEVTVF KSPV LGQPNTLIC VDNIFPPV+NITWL NGHSVTEG 
Sbjct: 99  VIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGV 158

Query: 526 SETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 705
           SETSFLSK+DHS  KISYLTFLPSDD+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET
Sbjct: 159 SETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTET 218

Query: 706 XXXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 816
                                 +GLRS G SRHQG L
Sbjct: 219 VVCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 255



 Score =  160 bits (404), Expect(2) = e-104
 Identities = 75/97 (77%), Positives = 82/97 (84%)
 Frame = +2

Query: 56  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 235
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG Y+HEFDGDEEFYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYV 60

Query: 236 DLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLN 346
           DL +KETVWQLPLF +FR FDPQ AL NIA  KHNLN
Sbjct: 61  DLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLN 97


>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 =  236 bits (603), Expect(2) = e-104
 Identities = 115/157 (73%), Positives = 123/157 (78%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 525
           +IKRSN+TAA N+VPEVTVF KSPV LGQPNTLIC VDNIFPPV+NITWL NGHSVTEG 
Sbjct: 99  VIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGV 158

Query: 526 SETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 705
           SETSFLSK+DHS  KISYLTFLPSDD+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET
Sbjct: 159 SETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTET 218

Query: 706 XXXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 816
                                 +GLRS G SRHQG L
Sbjct: 219 VVCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 255



 Score =  160 bits (404), Expect(2) = e-104
 Identities = 75/97 (77%), Positives = 82/97 (84%)
 Frame = +2

Query: 56  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 235
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG Y+HEFDGDEEFYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYV 60

Query: 236 DLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLN 346
           DL +KETVWQLPLF +FR FDPQ AL NIA  KHNLN
Sbjct: 61  DLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLN 97


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

 Score =  230 bits (586), Expect(2) = 1e-99
 Identities = 113/157 (71%), Positives = 120/157 (76%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 525
           +IKR N+TAA N+VPEVTVF KSPV LGQPNTLIC VDNIFPPV+NITWL NG SVTEG 
Sbjct: 99  MIKRYNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGQSVTEGV 158

Query: 526 SETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 705
           SETSFLSK+DHS  KISYLTFLPS D+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET
Sbjct: 159 SETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDQPLLKHWEPEIPAPMSELTET 218

Query: 706 XXXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 816
                                 QGLRS G SRHQG L
Sbjct: 219 VVCALGLSVGLMGIVVGTVFIIQGLRSVGASRHQGPL 255



 Score =  152 bits (385), Expect(2) = 1e-99
 Identities = 71/97 (73%), Positives = 80/97 (82%)
 Frame = +2

Query: 56  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 235
           M+  + L+ GALALT VMS CGGEDI ADHVAS G+N+YQ YGPSG YTHEFDGDE+FYV
Sbjct: 1   MILNKALLLGALALTTVMSPCGGEDIVADHVASCGVNLYQFYGPSGQYTHEFDGDEQFYV 60

Query: 236 DLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLN 346
           DL +KET W+ P FSKF  FDPQGALRN+A AKHNLN
Sbjct: 61  DLERKETAWRWPEFSKFGGFDPQGALRNMAVAKHNLN 97


>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 =  229 bits (584), Expect(2) = 3e-99
 Identities = 113/157 (71%), Positives = 120/157 (76%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 525
           LIKRSN+TAA N+VPEVTVF KSPV LGQPN LIC VDNIFPPV+NITWL NGHSVTEG 
Sbjct: 98  LIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGV 157

Query: 526 SETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 705
           SETSFLSK+DHS  KISYLT LPS ++ YDCKVEHWGLDKPLLKHWEPEIPAPMSELTET
Sbjct: 158 SETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 217

Query: 706 XXXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 816
                                 +GLRS G SRHQG L
Sbjct: 218 VVCALGLSVGLVGIVVGTVFIIRGLRSVGASRHQGPL 254



 Score =  152 bits (384), Expect(2) = 3e-99
 Identities = 73/97 (75%), Positives = 81/97 (83%)
 Frame = +2

Query: 56  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 235
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG YTHEFDGDE+FYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYV 60

Query: 236 DLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLN 346
           DLG+KETVW LP+  +FR FDPQ AL NIA  KHNLN
Sbjct: 61  DLGRKETVWCLPVLRQFR-FDPQFALTNIAVLKHNLN 96


>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 =  229 bits (584), Expect(2) = 3e-99
 Identities = 113/157 (71%), Positives = 120/157 (76%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 525
           LIKRSN+TAA N+VPEVTVF KSPV LGQPN LIC VDNIFPPV+NITWL NGHSVTEG 
Sbjct: 98  LIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGV 157

Query: 526 SETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 705
           SETSFLSK+DHS  KISYLT LPS ++ YDCKVEHWGLDKPLLKHWEPEIPAPMSELTET
Sbjct: 158 SETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 217

Query: 706 XXXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 816
                                 +GLRS G SRHQG L
Sbjct: 218 VVCALGLSVGLVGIVVGTVFIIRGLRSVGASRHQGPL 254



 Score =  152 bits (384), Expect(2) = 3e-99
 Identities = 73/97 (75%), Positives = 81/97 (83%)
 Frame = +2

Query: 56  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 235
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG YTHEFDGDE+FYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYV 60

Query: 236 DLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLN 346
           DLG+KETVW LP+  +FR FDPQ AL NIA  KHNLN
Sbjct: 61  DLGRKETVWCLPVLRQFR-FDPQFALTNIAVLKHNLN 96


>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 =  229 bits (584), Expect(2) = 3e-99
 Identities = 113/157 (71%), Positives = 120/157 (76%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 525
           LIKRSN+TAA N+VPEVTVF KSPV LGQPN LIC VDNIFPPV+NITWL NGHSVTEG 
Sbjct: 98  LIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGV 157

Query: 526 SETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 705
           SETSFLSK+DHS  KISYLT LPS ++ YDCKVEHWGLDKPLLKHWEPEIPAPMSELTET
Sbjct: 158 SETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 217

Query: 706 XXXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 816
                                 +GLRS G SRHQG L
Sbjct: 218 VVCALGLSVGLVGIVVGTVFIIRGLRSVGASRHQGPL 254



 Score =  152 bits (384), Expect(2) = 3e-99
 Identities = 73/97 (75%), Positives = 81/97 (83%)
 Frame = +2

Query: 56  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 235
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG YTHEFDGDE+FYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYV 60

Query: 236 DLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLN 346
           DLG+KETVW LP+  +FR FDPQ AL NIA  KHNLN
Sbjct: 61  DLGRKETVWCLPVLRQFR-FDPQFALTNIAVLKHNLN 96


>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 =  229 bits (584), Expect(2) = 3e-99
 Identities = 113/157 (71%), Positives = 120/157 (76%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 525
           LIKRSN+TAA N+VPEVTVF KSPV LGQPN LIC VDNIFPPV+NITWL NGHSVTEG 
Sbjct: 98  LIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGV 157

Query: 526 SETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 705
           SETSFLSK+DHS  KISYLT LPS ++ YDCKVEHWGLDKPLLKHWEPEIPAPMSELTET
Sbjct: 158 SETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 217

Query: 706 XXXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 816
                                 +GLRS G SRHQG L
Sbjct: 218 VVCALGLSVGLVGIVVGTVFIIRGLRSVGASRHQGPL 254



 Score =  152 bits (384), Expect(2) = 3e-99
 Identities = 73/97 (75%), Positives = 81/97 (83%)
 Frame = +2

Query: 56  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 235
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG YTHEFDGDE+FYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYV 60

Query: 236 DLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLN 346
           DLG+KETVW LP+  +FR FDPQ AL NIA  KHNLN
Sbjct: 61  DLGRKETVWCLPVLRQFR-FDPQFALTNIAVLKHNLN 96


>ref|XP_941221.1| 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 =  229 bits (584), Expect(2) = 3e-99
 Identities = 113/157 (71%), Positives = 120/157 (76%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 525
           LIKRSN+TAA N+VPEVTVF KSPV LGQPN LIC VDNIFPPV+NITWL NGHSVTEG 
Sbjct: 98  LIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGV 157

Query: 526 SETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 705
           SETSFLSK+DHS  KISYLT LPS ++ YDCKVEHWGLDKPLLKHWEPEIPAPMSELTET
Sbjct: 158 SETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 217

Query: 706 XXXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 816
                                 +GLRS G SRHQG L
Sbjct: 218 VVCALGLSVGLVGIVVGTVFIIRGLRSVGASRHQGPL 254



 Score =  152 bits (384), Expect(2) = 3e-99
 Identities = 73/97 (75%), Positives = 81/97 (83%)
 Frame = +2

Query: 56  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 235
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG YTHEFDGDE+FYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYV 60

Query: 236 DLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLN 346
           DLG+KETVW LP+  +FR FDPQ AL NIA  KHNLN
Sbjct: 61  DLGRKETVWCLPVLRQFR-FDPQFALTNIAVLKHNLN 96


  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: 45,953,781
Number of Sequences: 39411
Number of extensions: 1177427
Number of successful extensions: 3468
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 2987
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): 3421
length of database: 17,774,539
effective HSP length: 104
effective length of database: 13,675,795
effective search space used: 4089062705
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-027234
         (1213 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...   215   3e-87
Alignment   gi|NP_032232.1| histocompatibility 2, O region alpha locus [Mus...   160   1e-55
Alignment   gi|NP_034511.2| histocompatibility 2, class II antigen E alpha ...   155   2e-50
Alignment   gi|NP_034516.2| histocompatibility 2, class II, locus DMa [Mus ...    69   1e-11
Alignment   gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ...    69   1e-11
Alignment   gi|NP_033865.2| beta-2-microglobulin [Mus musculus]                   65   1e-10
Alignment   gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/...    62   1e-09
Alignment   gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ...    62   1e-09
Alignment   gi|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus ...    62   1e-09
Alignment   gi|NP_034512.1| histocompatibility 2, class II antigen E beta [...    62   2e-09

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

 Score =  215 bits (547), Expect(2) = 3e-87
 Identities = 102/157 (64%), Positives = 114/157 (72%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 525
           L KRSN+T A N+ P+ TVFPKSPV+LGQPNTLIC VDNIFPPVINITWL+N  SV +G 
Sbjct: 100 LTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGV 159

Query: 526 SETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 705
            ETSF    D+S  K+SYLTF+PSDDD YDCKVEHWGL++P+LKHWEPEIPAPMSELTET
Sbjct: 160 YETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEPEIPAPMSELTET 219

Query: 706 XXXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 816
                                 QGLRSGG SRH G L
Sbjct: 220 VVCALGLSVGLVGIVVGTIFIIQGLRSGGTSRHPGPL 256



 Score =  127 bits (318), Expect(2) = 3e-87
 Identities = 63/97 (64%), Positives = 71/97 (73%), Gaps = 1/97 (1%)
 Frame = +2

Query: 56  MVPGRVLMWGALALTAVMSACGGED-IAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFY 232
           M   R L+ G LALT ++S CGGED I ADHV +YG++VYQS G  G YT EFDGDE FY
Sbjct: 1   MPRSRALILGVLALTTMLSLCGGEDDIEADHVGTYGISVYQSPGDIGQYTFEFDGDELFY 60

Query: 233 VDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNL 343
           VDL KKETVW LP F +  SFDPQG L+NIA  KHNL
Sbjct: 61  VDLDKKETVWMLPEFGQLASFDPQGGLQNIAVVKHNL 97


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

 Score =  160 bits (404), Expect(2) = 1e-55
 Identities = 71/120 (59%), Positives = 91/120 (75%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 525
           L++RSN T AV+  P VTV PK+ V LG+PN LIC VD+IFPPVIN+TWL+N   +T+G 
Sbjct: 99  LVERSNRTRAVSVPPRVTVLPKTRVELGKPNVLICIVDDIFPPVINVTWLRNSQPITKGV 158

Query: 526 SETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 705
           ++TSF S+ +H   K  YLTF+PS +D YDCKVEHWGLD PLL+HWEP++  P  + TET
Sbjct: 159 AQTSFYSQPNHRFRKFHYLTFVPSAEDVYDCKVEHWGLDTPLLQHWEPQVLTPPPDTTET 218



 Score = 76.3 bits (186), Expect(2) = 1e-55
 Identities = 39/86 (45%), Positives = 52/86 (60%)
 Frame = +2

Query: 89  LALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYVDLGKKETVWQL 268
           L + + +S  G   I ADH+ SYG   YQSY  SG +THEFDG++ F VDL  +E VW+L
Sbjct: 12  LTVMSFLSPRGVRAIKADHMGSYGPAFYQSYDASGQFTHEFDGEQIFSVDLKNEEVVWRL 71

Query: 269 PLFSKFRSFDPQGALRNIATAKHNLN 346
           P F  F   D Q  L +I+  K +L+
Sbjct: 72  PEFGDFAHSDFQSGLMSISMIKAHLD 97


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

 Score =  155 bits (392), Expect(2) = 2e-50
 Identities = 70/117 (59%), Positives = 84/117 (71%)
 Frame = +1

Query: 352 KRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSE 531
           +RSNNT   N  PEVTV  +SPV LG+PN LIC +D   PPV+N+TW +NG  VTEG SE
Sbjct: 100 ERSNNTPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWFRNGRPVTEGVSE 159

Query: 532 TSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 702
           T FL ++DH   K  YLTFLPS DDFYDC+V+HWGL++PL KHWE E    + E TE
Sbjct: 160 TVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEEPLRKHWEFEEKTLLPETTE 216



 Score = 63.5 bits (153), Expect(2) = 2e-50
 Identities = 29/52 (55%), Positives = 38/52 (73%)
 Frame = +2

Query: 191 GYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLN 346
           G +  +FDGDE F+VD+ K ET+W+L  F+KF SF+ QGAL NIA  K NL+
Sbjct: 45  GEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLD 96


>ref|NP_034516.2| histocompatibility 2, class II, locus DMa [Mus musculus]
          Length = 261

 Score = 68.9 bits (167), Expect = 1e-11
 Identities = 37/106 (34%), Positives = 53/106 (50%)
 Frame = +1

Query: 385 VPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSL 564
           +P   VF   P+  G+PNTL+C + N+FPP + + W  +   V EG S TS  + +  + 
Sbjct: 126 LPVAEVFTLKPLEFGKPNTLVCFISNLFPPTLTVNWQLHSAPV-EGASPTSISAVDGLTF 184

Query: 565 LKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 702
              SYL F P   D Y C V H       + +W P+   P S+L E
Sbjct: 185 QAFSYLNFTPEPFDLYSCTVTHEIDRYTAIAYWVPQNALP-SDLLE 229


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

 Score = 68.6 bits (166), Expect = 1e-11
 Identities = 34/99 (34%), Positives = 47/99 (47%)
 Frame = +1

Query: 367 TAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLS 546
           T   N  PEVTV+P+   +L Q N L+C V   +P  I++ W +NG     G   T  + 
Sbjct: 116 TVERNVPPEVTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVR 175

Query: 547 KNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHW 663
             D +      L  +P   D Y C VEH GL +P+   W
Sbjct: 176 NGDWTFQTTVMLEMIPELGDIYSCLVEHPGLLRPVSVAW 214


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

 Score = 65.1 bits (157), Expect = 1e-10
 Identities = 32/102 (31%), Positives = 56/102 (54%), Gaps = 1/102 (0%)
 Frame = +1

Query: 373 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTE-GFSETSFLSK 549
           A+ + P++ V+ + P   G+PN L C+V    PP I I  LKNG  + +   S+ SF   
Sbjct: 20  AIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSF--S 77

Query: 550 NDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEI 675
            D S   +++  F P++ D Y C+V+H  + +P   +W+ ++
Sbjct: 78  KDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM 119


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

 Score = 62.0 bits (149), Expect = 1e-09
 Identities = 29/103 (28%), Positives = 46/103 (44%)
 Frame = +1

Query: 388 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSLL 567
           P+VTV+P     L   N L+C V + +P  I + W +NG     G   T  +   D +  
Sbjct: 125 PKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNRDWTYQ 184

Query: 568 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 696
            +  L  +P   + Y C+VEH  L  P+   W     +  ++L
Sbjct: 185 TLVMLEMVPRGGEVYTCQVEHPSLTSPVTVEWRARSTSAQNKL 227


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

 Score = 62.0 bits (149), Expect = 1e-09
 Identities = 32/97 (32%), Positives = 46/97 (47%), Gaps = 1/97 (1%)
 Frame = +1

Query: 382 QVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSV-TEGFSETSFLSKNDH 558
           + P V V   +P    +P  L C+V   +P  + ITW+KNG  V +    E +     D 
Sbjct: 113 RAPSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPNGDW 172

Query: 559 SLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEP 669
           +   +SYL   PS  D Y C V+H G  +P+   W P
Sbjct: 173 TYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDWTP 209


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

 Score = 62.0 bits (149), Expect = 1e-09
 Identities = 32/97 (32%), Positives = 46/97 (47%), Gaps = 1/97 (1%)
 Frame = +1

Query: 382 QVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSV-TEGFSETSFLSKNDH 558
           + P V V   +P    +P  L C+V   +P  + ITW+KNG  V +    E +     D 
Sbjct: 113 RAPSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPNGDW 172

Query: 559 SLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEP 669
           +   +SYL   PS  D Y C V+H G  +P+   W P
Sbjct: 173 TYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDWTP 209


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

 Score = 61.6 bits (148), Expect = 2e-09
 Identities = 28/103 (27%), Positives = 47/103 (45%)
 Frame = +1

Query: 388 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSLL 567
           P VTV+P     L   N L+C V + +P  I + W +NG     G   T  +   D +  
Sbjct: 124 PTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQ 183

Query: 568 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 696
            +  L  +P   + Y C+VEH  L  P+   W+ +  +  +++
Sbjct: 184 TLVMLETVPQSGEVYTCQVEHPSLTDPVTVEWKAQSTSAQNKM 226


  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: 54,318,895
Number of Sequences: 45328
Number of extensions: 1347679
Number of successful extensions: 3858
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 3424
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): 3831
length of database: 21,768,885
effective HSP length: 106
effective length of database: 16,964,117
effective search space used: 5038342749
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-027234
         (1213 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...   232   e-101
Alignment   gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati...   162   4e-55
Alignment   gi|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris]    160   9e-54
Alignment   gi|XP_532104.2| PREDICTED: similar to HLA class II histocompati...    81   6e-16
Alignment   gi|XP_538853.2| PREDICTED: similar to major histocompatibility ...    65   1e-11
Alignment   gi|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Ca...    67   4e-11
Alignment   gi|XP_861572.1| PREDICTED: similar to major histocompatibility ...    65   1e-10
Alignment   gi|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis fami...    65   1e-10
Alignment   gi|XP_535458.1| PREDICTED: similar to beta-2-microglobulin prec...    63   5e-10
Alignment   gi|XP_850148.1| PREDICTED: similar to beta-2-microglobulin prec...    63   5e-10

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

 Score =  232 bits (591), Expect(2) = e-101
 Identities = 112/157 (71%), Positives = 119/157 (75%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 525
           + KRSN TAA N+VPEVTVF KSPVMLGQPNTLIC VDNIFPPVIN+TWLKN HSVTEG 
Sbjct: 99  MTKRSNQTAATNEVPEVTVFSKSPVMLGQPNTLICLVDNIFPPVINVTWLKNRHSVTEGV 158

Query: 526 SETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 705
           SETSF +K DHS  KISYLTFLPS +D YDCKVEHWGLD+PLLKHWEPE+P PMSELTET
Sbjct: 159 SETSFFAKGDHSFSKISYLTFLPSAEDIYDCKVEHWGLDEPLLKHWEPEVPTPMSELTET 218

Query: 706 XXXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 816
                                 QGLRSGG SRHQG L
Sbjct: 219 VVCALGLAVGLVGIVMGTVFIIQGLRSGGTSRHQGPL 255



 Score =  155 bits (392), Expect(2) = e-101
 Identities = 73/97 (75%), Positives = 82/97 (84%)
 Frame = +2

Query: 56  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 235
           M+  RVL+ G L LT +MS  GGE+I ADHVA+YG+NVYQSYGPSG YTHEFDGDEEFYV
Sbjct: 1   MILNRVLILGTLILTIMMSPSGGEEIVADHVANYGINVYQSYGPSGQYTHEFDGDEEFYV 60

Query: 236 DLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLN 346
           DL KKETVW+LP+FS FRSFDPQGALRN+A  K NLN
Sbjct: 61  DLEKKETVWRLPVFSTFRSFDPQGALRNLAIIKQNLN 97


>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 =  162 bits (409), Expect(2) = 4e-55
 Identities = 74/127 (58%), Positives = 92/127 (72%), Gaps = 7/127 (5%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQV-------PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNG 504
           L++RSN T A+N         P V V PK  V LGQPN LIC VDNIFPPVINITWL+NG
Sbjct: 69  LVERSNRTRAINGTHLSSPLPPRVAVLPKFRVELGQPNVLICIVDNIFPPVINITWLRNG 128

Query: 505 HSVTEGFSETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAP 684
             ++EG ++TSF S+ DH   K  YLTF+PS +D YDCKVEHWGL++PLL+HWEP++P P
Sbjct: 129 QIISEGVAQTSFYSQPDHLFRKFCYLTFVPSAEDMYDCKVEHWGLEEPLLRHWEPQVPIP 188

Query: 685 MSELTET 705
           + +  ET
Sbjct: 189 VPDTIET 195



 Score = 72.8 bits (177), Expect(2) = 4e-55
 Identities = 33/67 (49%), Positives = 44/67 (65%)
 Frame = +2

Query: 146 VASYGLNVYQSYGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIA 325
           + SYG   YQSYG SG + HEFDG++ F V+L K++ VW+LP F     FDPQ  L +IA
Sbjct: 1   MGSYGPAFYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEFGNLAHFDPQNGLASIA 60

Query: 326 TAKHNLN 346
             K +L+
Sbjct: 61  VIKAHLD 67


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

 Score =  160 bits (406), Expect(2) = 9e-54
 Identities = 74/119 (62%), Positives = 86/119 (72%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 525
           +IKRSN+T   N  PEVTV   +PV LG+PN LIC +D   PPVIN+TWL+NG+ VT G 
Sbjct: 98  MIKRSNHTPNTNVPPEVTVLSNTPVELGEPNILICFIDKFSPPVINVTWLRNGNPVTTGV 157

Query: 526 SETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 702
           SET FL + DH   K  YL FLPS +D YDCKVEHWGLD+PLLKHWE E P P+ E TE
Sbjct: 158 SETIFLPREDHLFRKFHYLPFLPSAEDVYDCKVEHWGLDEPLLKHWEFEPPTPLPETTE 216



 Score = 69.3 bits (168), Expect(2) = 9e-54
 Identities = 33/59 (55%), Positives = 42/59 (71%)
 Frame = +2

Query: 170 YQSYGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLN 346
           Y +  PSG +  +FDGDE F+VD+ KKETVW+L  F +F SF+ QGAL NIA  K NL+
Sbjct: 38  YLTPDPSGEFMFDFDGDEIFHVDMEKKETVWRLEEFGRFASFEAQGALANIAVDKANLD 96


>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 = 80.9 bits (198), Expect(2) = 6e-16
 Identities = 37/72 (51%), Positives = 48/72 (66%)
 Frame = +2

Query: 131 IAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGA 310
           I ADH+ SYG   YQSYG SG + HEFDG++ F V+L K++ VW+LP F     FDPQ  
Sbjct: 12  IEADHMGSYGPAFYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEFGNLAHFDPQNG 71

Query: 311 LRNIATAKHNLN 346
           L +IA  K +L+
Sbjct: 72  LASIAVIKAHLD 83



 Score = 22.3 bits (46), Expect(2) = 6e-16
 Identities = 13/35 (37%), Positives = 20/35 (57%)
 Frame = +1

Query: 346 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLIC 450
           L++RSN T A+N+ P+V +     +      TLIC
Sbjct: 85  LVERSNRTRAINE-PQVPIPVPDTI-----ETLIC 113


>ref|XP_538853.2| PREDICTED: similar to major histocompatibility complex, class II,
           DM alpha precursor isoform 1 [Canis familiaris]
          Length = 265

 Score = 65.5 bits (158), Expect(2) = 1e-11
 Identities = 35/105 (33%), Positives = 51/105 (48%)
 Frame = +1

Query: 388 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSLL 567
           P V VF   P+  G+PN L+C + N+FPP + + W  +   V EG   T   + +  S  
Sbjct: 133 PMVDVFTLKPLEFGKPNMLVCFISNLFPPTLTVNWWHHLDPV-EGIGPTFVSAVDGFSFQ 191

Query: 568 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 702
             SYL F P+  D + C V H   +   + +W P    P S+L E
Sbjct: 192 AFSYLNFTPAPSDLFSCVVTHEIDNYTAIAYWVPHDALP-SDLLE 235



 Score = 23.1 bits (48), Expect(2) = 1e-11
 Identities = 11/36 (30%), Positives = 19/36 (52%)
 Frame = +2

Query: 173 QSYGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFS 280
           Q++ PS      +DGD+ F  +  +   V +LP F+
Sbjct: 57  QNWSPSIGLLEAYDGDQLFSFNFSQNTRVPRLPEFA 92


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

 Score = 67.0 bits (162), Expect = 4e-11
 Identities = 34/126 (26%), Positives = 53/126 (42%)
 Frame = +1

Query: 319 HSYGKT*FELIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLK 498
           H+YG+     ++R          P VT+FP    +L   N L+C V + +P  I + W +
Sbjct: 113 HNYGREELTTLQRRVE-------PTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKVRWFR 165

Query: 499 NGHSVTEGFSETSFLSKNDHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIP 678
           N    T G   T  +   D +   +  L   P   D Y C VEH  L  P+   W  +  
Sbjct: 166 NDQEQTAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHASLQSPITVQWRAQSE 225

Query: 679 APMSEL 696
           +  S++
Sbjct: 226 SAQSKM 231


>ref|XP_861572.1| PREDICTED: similar to major histocompatibility complex, class II,
           DM alpha precursor isoform 2 [Canis familiaris]
          Length = 170

 Score = 65.5 bits (158), Expect = 1e-10
 Identities = 35/105 (33%), Positives = 51/105 (48%)
 Frame = +1

Query: 388 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSLL 567
           P V VF   P+  G+PN L+C + N+FPP + + W  +   V EG   T   + +  S  
Sbjct: 38  PMVDVFTLKPLEFGKPNMLVCFISNLFPPTLTVNWWHHLDPV-EGIGPTFVSAVDGFSFQ 96

Query: 568 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 702
             SYL F P+  D + C V H   +   + +W P    P S+L E
Sbjct: 97  AFSYLNFTPAPSDLFSCVVTHEIDNYTAIAYWVPHDALP-SDLLE 140


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

 Score = 65.1 bits (157), Expect = 1e-10
 Identities = 30/103 (29%), Positives = 47/103 (45%)
 Frame = +1

Query: 388 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSLL 567
           P VTV+P     L   N L+C V+  +P  I + WL+NG     G   T  +   D +  
Sbjct: 126 PTVTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNGDWTFQ 185

Query: 568 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 696
            +  L  +P   + Y C+VEH  L  P+   W  +  +  S++
Sbjct: 186 ILVMLEIVPQSGEVYTCQVEHPSLTSPVTVEWRAQSDSAQSKM 228


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

 Score = 63.2 bits (152), Expect = 5e-10
 Identities = 31/98 (31%), Positives = 51/98 (52%)
 Frame = +1

Query: 373 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN 552
           AV   P++ V+ + P   G+PN L C+V    PP I I  LKNG  +    ++ SF    
Sbjct: 27  AVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSF--SK 84

Query: 553 DHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 666
           D +   + +  F P++ D + C+V+H  L +P +  W+
Sbjct: 85  DWTFYLLVHTEFTPNEQDEFSCRVKHVTLSEPQIVKWD 122


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

 Score = 63.2 bits (152), Expect = 5e-10
 Identities = 31/98 (31%), Positives = 51/98 (52%)
 Frame = +1

Query: 373 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN 552
           AV   P++ V+ + P   G+PN L C+V    PP I I  LKNG  +    ++ SF    
Sbjct: 27  AVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSF--SK 84

Query: 553 DHSLLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 666
           D +   + +  F P++ D + C+V+H  L +P +  W+
Sbjct: 85  DWTFYLLVHTEFTPNEQDEFSCRVKHVTLSEPQIVKWD 122


  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: 47,576,030
Number of Sequences: 33732
Number of extensions: 1185439
Number of successful extensions: 3367
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 2947
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): 3353
length of database: 19,266,565
effective HSP length: 105
effective length of database: 15,724,705
effective search space used: 4685962090
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)