Animal-Genome cDNA 20060611S-015082


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-015082
         (1138 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]                    74   6e-15
Alignment   gi|NP_999143.1| beta 2-microglobulin [Sus scrofa]                     71   4e-14
Alignment   gi|NP_998933.1| swine leukocyte antigen 7 [Sus scrofa]                52   3e-08
Alignment   gi|NP_999362.2| neonatal Fc receptor FcRn [Sus scrofa]                45   4e-06

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

 Score = 73.9 bits (180), Expect = 6e-15
 Identities = 38/106 (35%), Positives = 56/106 (52%)
 Frame = +2

Query: 344 VPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSF 523
           +P   VF   P+  G+PNTL+C V N+FPP + +TW ++  +  EG   T   + +D SF
Sbjct: 126 LPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTW-EHHSAPVEGIGPTFVSATDDLSF 184

Query: 524 LKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 661
              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 = 71.2 bits (173), Expect = 4e-14
 Identities = 38/98 (38%), Positives = 53/98 (54%)
 Frame = +2

Query: 332 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN 511
           AV + P+V V+ + P   G+PN L C+V    PP I I  LKNG  +    S+ SF    
Sbjct: 20  AVARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SK 77

Query: 512 DHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 625
           D SF  + +  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 = 51.6 bits (122), Expect = 3e-08
 Identities = 24/80 (30%), Positives = 37/80 (46%)
 Frame = +2

Query: 398 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 577
           TL C     +P  I++TW + G   ++           D +F K + L   P ++  Y C
Sbjct: 221 TLRCWALGFYPKEISLTWQQEGQDQSQDVEVVETRPSGDGTFRKWAALVVPPGEEQSYTC 280

Query: 578 KVEHWGLDKPLLKHWEPEIP 637
            V+H GL +PL   W+P  P
Sbjct: 281 HVQHEGLQEPLTLRWDPPQP 300


>ref|NP_999362.2| neonatal Fc receptor FcRn [Sus scrofa]
          Length = 356

 Score = 44.7 bits (104), Expect = 4e-06
 Identities = 34/101 (33%), Positives = 46/101 (45%), Gaps = 6/101 (5%)
 Frame = +2

Query: 365 PKSPVMLGQPNT------LICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 526
           P S  M  +P T      L C   + +PP + + +L+NG  +  G  E+      D SF 
Sbjct: 202 PPSMRMKARPGTAPGFSVLTCIAFSFYPPELQLRFLRNG--LAAGSGESDIGPNGDGSFH 259

Query: 527 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMS 649
             S LT    D+  Y C V+H GL +PL    E E PA  S
Sbjct: 260 AWSSLTVKSGDEHHYCCVVQHAGLAQPLTV--ELESPAKSS 298


  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: 992,528
Number of Sequences: 1040
Number of extensions: 23387
Number of successful extensions: 61
Number of sequences better than 1.0e-05: 4
Number of HSP's better than  0.0 without gapping: 53
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): 58
length of database: 434,620
effective HSP length: 78
effective length of database: 353,500
effective search space used: 106050000
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-015082
         (1138 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...   291   1e-96
Alignment   gi|NP_001012693.1| major histocompatibility complex, class II, ...   269   4e-90
Alignment   gi|NP_001012699.1| major histocompatibility complex, class II, ...   239   1e-80
Alignment   gi|NP_001012696.1| major histocompatibility complex, class II, ...   222   3e-71
Alignment   gi|XP_604082.2| PREDICTED: similar to HLA class II histocompati...   190   6e-54
Alignment   gi|XP_883292.1| PREDICTED: similar to HLA class II histocompati...   188   3e-53
Alignment   gi|NP_001012695.1| major histocompatibility complex, class II, ...   192   3e-49
Alignment   gi|NP_776318.1| beta-2-microglobulin [Bos taurus]                     71   1e-12
Alignment   gi|NP_001013618.1| major histocompatibility complex, class II, ...    65   8e-11
Alignment   gi|NP_001029840.2| MHC class II antigen [Bos taurus]                  65   1e-10

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

 Score =  291 bits (744), Expect(2) = 1e-96
 Identities = 140/186 (75%), Positives = 153/186 (82%)
 Frame = +2

Query: 218 QLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 397
           +LP+FSKF +FDPQGALRNIAT KHNL I+I+RSN+TAA N+VPEVTVF KSPVMLGQPN
Sbjct: 70  RLPVFSKFATFDPQGALRNIATTKHNLEIVIQRSNSTAATNKVPEVTVFSKSPVMLGQPN 129

Query: 398 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 577
           TLICHVDNIFPPVINITWL+NGHSVTEG SETSFL K+D+SFLKI+YLTFLPSDDD YDC
Sbjct: 130 TLICHVDNIFPPVINITWLRNGHSVTEGVSETSFLIKSDYSFLKINYLTFLPSDDDVYDC 189

Query: 578 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXXXLRSGGPS 757
           KVEHWGLD+PLLKHWEP+IPAPMSELTET                        LRSGGPS
Sbjct: 190 KVEHWGLDEPLLKHWEPDIPAPMSELTETVVCALGLTVGLVGIMVGTILIIQGLRSGGPS 249

Query: 758 RHQGSL 775
           RHQG L
Sbjct: 250 RHQGPL 255



 Score = 81.6 bits (200), Expect(2) = 1e-96
 Identities = 35/55 (63%), Positives = 44/55 (80%)
 Frame = +3

Query: 54  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGN 218
           MV  R L+ GALALT +MS  G EDI ADH+ +YG+++Y +YGPSGYYTHEFDG+
Sbjct: 1   MVLNRALILGALALTTMMSPSGSEDIVADHIGTYGISIYHTYGPSGYYTHEFDGD 55


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

 Score =  269 bits (688), Expect(2) = 4e-90
 Identities = 133/186 (71%), Positives = 144/186 (77%)
 Frame = +2

Query: 218 QLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 397
           QLPLFS+  SFDPQ ALRNIA  K +++ L K SN+TAA N+VPEVTVF KSPVMLGQPN
Sbjct: 70  QLPLFSRMLSFDPQLALRNIAIMKLHVDFLTKFSNSTAATNKVPEVTVFSKSPVMLGQPN 129

Query: 398 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 577
           TLICHVDNIFPPVINITWL+NGHSVTEG SETSFL ++D+SFLKI YL FLPSDDD YDC
Sbjct: 130 TLICHVDNIFPPVINITWLRNGHSVTEGVSETSFLIRSDYSFLKIKYLAFLPSDDDIYDC 189

Query: 578 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXXXLRSGGPS 757
           KVEHWGLD+PLLKHWEPEIPAPMSELTET                        LRSG PS
Sbjct: 190 KVEHWGLDEPLLKHWEPEIPAPMSELTETVVCTLGLTMGLVGITVGTIFIIQGLRSGDPS 249

Query: 758 RHQGSL 775
           RHQG L
Sbjct: 250 RHQGPL 255



 Score = 81.6 bits (200), Expect(2) = 4e-90
 Identities = 37/55 (67%), Positives = 43/55 (78%)
 Frame = +3

Query: 54  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGN 218
           MV  R L+ G LALT +MS  GGEDI ADHV  YG+++YQSYGPSG YTHEFDG+
Sbjct: 1   MVLNRALILGTLALTTMMSPSGGEDIVADHVGIYGISIYQSYGPSGQYTHEFDGD 55


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

 Score =  239 bits (611), Expect(2) = 1e-80
 Identities = 110/135 (81%), Positives = 121/135 (89%)
 Frame = +2

Query: 218 QLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 397
           +LP+FS+F  FDPQ AL  IATAKHNL++L KRSN T  +N+VPEVTVF KSPVMLGQPN
Sbjct: 70  RLPMFSQFAGFDPQAALSEIATAKHNLDVLTKRSNFTPVINEVPEVTVFSKSPVMLGQPN 129

Query: 398 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 577
           TLICHVDNIFPPVINITWLKNGH+VTEG SETSFL K+DHSFLKI YLTFLPSD+D YDC
Sbjct: 130 TLICHVDNIFPPVINITWLKNGHAVTEGVSETSFLPKDDHSFLKIGYLTFLPSDNDIYDC 189

Query: 578 KVEHWGLDKPLLKHW 622
           KVEHWGLD+PLLKHW
Sbjct: 190 KVEHWGLDEPLLKHW 204



 Score = 79.7 bits (195), Expect(2) = 1e-80
 Identities = 37/55 (67%), Positives = 43/55 (78%)
 Frame = +3

Query: 54  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGN 218
           MV  R L+ GALALT +MS+ GGEDI ADHV SYG  +YQS+GPSG YT EFDG+
Sbjct: 1   MVLNRALILGALALTTMMSSSGGEDIVADHVGSYGTEIYQSHGPSGQYTQEFDGD 55


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

 Score =  222 bits (565), Expect(2) = 3e-71
 Identities = 102/149 (68%), Positives = 121/149 (81%)
 Frame = +2

Query: 218 QLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 397
           +LP FS    F+ Q ALRNI  +K NL+ILIK S+ T A +++PEV VFPKS V+LG PN
Sbjct: 68  RLPEFSNITKFEVQSALRNIVMSKRNLDILIKNSSFTPATSEIPEVAVFPKSSVVLGIPN 127

Query: 398 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 577
           TLIC VDNIFPPVINITW  NGH V EG +ET+F  K+DHSFLK SYLTFLP+++DFYDC
Sbjct: 128 TLICQVDNIFPPVINITWFYNGHFVAEGIAETTFYPKSDHSFLKFSYLTFLPTNEDFYDC 187

Query: 578 KVEHWGLDKPLLKHWEPEIPAPMSELTET 664
           +VEHWGL++PL+KHWEPEIP P SELTET
Sbjct: 188 RVEHWGLEEPLVKHWEPEIPTPTSELTET 216



 Score = 65.9 bits (159), Expect(2) = 3e-71
 Identities = 30/51 (58%), Positives = 37/51 (72%)
 Frame = +3

Query: 66  RVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGN 218
           + L+  AL L  +MS  GGEDI ADHV +YG NVYQ+YG SG +T EFDG+
Sbjct: 3   KALILRALTLATMMSPYGGEDIVADHVGTYGTNVYQTYGASGQFTFEFDGD 53


>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 =  190 bits (483), Expect(2) = 6e-54
 Identities = 88/149 (59%), Positives = 107/149 (71%)
 Frame = +2

Query: 218 QLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 397
           +LP F  F  FDPQ  L +IA  K +L  L+KRSN T A N  P V V PKS V LG+PN
Sbjct: 70  RLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNVSPRVAVLPKSHVQLGEPN 129

Query: 398 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 577
            LIC VD IFPPVINITWL+NGH VT+G +++SF ++ DH F K  YLTF+P  DDFYDC
Sbjct: 130 VLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTFVPLVDDFYDC 189

Query: 578 KVEHWGLDKPLLKHWEPEIPAPMSELTET 664
           KVEHWGLD+PL +HWEP++P  + + T T
Sbjct: 190 KVEHWGLDQPLFQHWEPQVPTALPDTTGT 218



 Score = 39.7 bits (91), Expect(2) = 6e-54
 Identities = 20/48 (41%), Positives = 28/48 (58%)
 Frame = +3

Query: 72  LMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDG 215
           L+ G   L  ++S      I ADH+ SYG   YQSY  +G +T++FDG
Sbjct: 7   LVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDG 54


>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 =  188 bits (477), Expect(2) = 3e-53
 Identities = 88/150 (58%), Positives = 108/150 (72%), Gaps = 1/150 (0%)
 Frame = +2

Query: 218 QLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVN-QVPEVTVFPKSPVMLGQP 394
           +LP F  F  FDPQ  L +IA  K +L  L+KRSN T A N   P+V V PKS V LG+P
Sbjct: 70  RLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNGSTPQVAVLPKSHVQLGEP 129

Query: 395 NTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYD 574
           N LIC VD IFPPVINITWL+NGH VT+G +++SF ++ DH F K  YLTF+P  DDFYD
Sbjct: 130 NVLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTFVPLVDDFYD 189

Query: 575 CKVEHWGLDKPLLKHWEPEIPAPMSELTET 664
           CKVEHWGLD+PL +HWEP++P  + + T T
Sbjct: 190 CKVEHWGLDQPLFQHWEPQVPTALPDTTGT 219



 Score = 39.7 bits (91), Expect(2) = 3e-53
 Identities = 20/48 (41%), Positives = 28/48 (58%)
 Frame = +3

Query: 72  LMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDG 215
           L+ G   L  ++S      I ADH+ SYG   YQSY  +G +T++FDG
Sbjct: 7   LVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDG 54


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

 Score =  192 bits (489), Expect = 3e-49
 Identities = 90/148 (60%), Positives = 109/148 (73%)
 Frame = +2

Query: 218 QLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 397
           +LP F  F SF+ QGAL N+A  K NL+I+IKRSNNT   N  PEVT+ P  PV LG+PN
Sbjct: 68  RLPEFGHFASFEAQGALANMAVMKANLDIMIKRSNNTPNTNVPPEVTLLPNKPVELGEPN 127

Query: 398 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 577
           TLIC +D   PPVI++TWL+NG  VT+G S+T FL +NDH F K  YL FLP+ +D YDC
Sbjct: 128 TLICFIDKFSPPVISVTWLRNGKPVTDGVSQTVFLPRNDHLFRKFHYLPFLPTTEDVYDC 187

Query: 578 KVEHWGLDKPLLKHWEPEIPAPMSELTE 661
           KVEH GL++PLLKHWE E PAP+ E TE
Sbjct: 188 KVEHLGLNEPLLKHWEYEAPAPLPETTE 215


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

 Score = 71.2 bits (173), Expect = 1e-12
 Identities = 35/101 (34%), Positives = 56/101 (55%)
 Frame = +2

Query: 332 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN 511
           A+ + P++ V+ + P   G+PN L C+V    PP I I  LKNG  +    S+ SF    
Sbjct: 20  AIQRPPKIQVYSRHPPEDGKPNYLNCYVYGFHPPQIEIDLLKNGEKIKSEQSDLSF--SK 77

Query: 512 DHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEI 634
           D SF  +S+  F P+  D Y C+V+H  L++P +  W+ ++
Sbjct: 78  DWSFYLLSHAEFTPNSKDQYSCRVKHVTLEQPRIVKWDRDL 118


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

 Score = 65.5 bits (158), Expect = 8e-11
 Identities = 36/124 (29%), Positives = 57/124 (45%), Gaps = 5/124 (4%)
 Frame = +2

Query: 275 IATAKHNLNILIKRSNNTAAVNQV-----PEVTVFPKSPVMLGQPNTLICHVDNIFPPVI 439
           +A ++ ++++L +R+    A   V     PEVTV+P+    L   N L+C V   +P  I
Sbjct: 94  LARSRASVDMLCRRNYYLGAPFTVGRRVQPEVTVYPEKTPALQHRNLLLCLVTGFYPGDI 153

Query: 440 NITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKH 619
            +TW +NG    EG   T  +   D +F     L   P   + Y C V+H  L  P+   
Sbjct: 154 KVTWFRNGQEQREGIMSTGLIRNGDWTFQMTVMLAMTPELGEVYTCLVDHPSLLSPVSVE 213

Query: 620 WEPE 631
           W  +
Sbjct: 214 WRAQ 217


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

 Score = 65.1 bits (157), Expect = 1e-10
 Identities = 30/103 (29%), Positives = 45/103 (43%)
 Frame = +2

Query: 347 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 526
           P VT+ P     L   N L+C V + +P  I + W +N    T G   T  +   D +F 
Sbjct: 129 PTVTISPSRTEALNHHNLLVCSVTDFYPSQIKVRWFRNDREETAGVVSTPLIRNGDWTFQ 188

Query: 527 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 655
            +  L   P   D Y C VEH  L  P++  W  +  +  S++
Sbjct: 189 ILVMLEMTPQRGDVYTCHVEHPSLQSPIMVEWRAQSESAQSKM 231


  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: 37,084,034
Number of Sequences: 33508
Number of extensions: 899144
Number of successful extensions: 2542
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 2347
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): 2530
length of database: 16,112,626
effective HSP length: 103
effective length of database: 12,661,302
effective search space used: 3481858050
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-015082
         (1138 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...   278   1e-95
Alignment   gi|XP_949973.1| PREDICTED: similar to HLA class II histocompati...   278   1e-95
Alignment   gi|XP_949971.1| PREDICTED: similar to HLA class II histocompati...   278   1e-95
Alignment   gi|XP_945969.1| PREDICTED: similar to HLA class II histocompati...   278   1e-95
Alignment   gi|NP_002113.2| major histocompatibility complex, class II, DQ ...   271   6e-92
Alignment   gi|NP_064440.1| major histocompatibility complex, class II, DQ ...   266   6e-92
Alignment   gi|XP_941306.1| PREDICTED: similar to HLA class II histocompati...   258   3e-90
Alignment   gi|XP_941305.1| PREDICTED: similar to HLA class II histocompati...   258   3e-90
Alignment   gi|XP_941304.1| PREDICTED: similar to HLA class II histocompati...   258   3e-90
Alignment   gi|XP_941255.1| PREDICTED: similar to HLA class II histocompati...   258   3e-90

>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 =  278 bits (711), Expect(2) = 1e-95
 Identities = 137/186 (73%), Positives = 145/186 (77%)
 Frame = +2

Query: 218 QLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 397
           QLPLF +FR FDPQ AL NIA  KHNLNI+IKRSN+TAA N+VPEVTVF KSPV LGQPN
Sbjct: 70  QLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPN 129

Query: 398 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 577
           TLIC VDNIFPPV+NITWL NGHSVTEG SETSFLSK+DHSF KISYLTFLPSDD+ YDC
Sbjct: 130 TLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDC 189

Query: 578 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXXXLRSGGPS 757
           KVEHWGLD+PLLKHWEPEIPAPMSELTET                        LRS G S
Sbjct: 190 KVEHWGLDEPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVLIIRGLRSVGAS 249

Query: 758 RHQGSL 775
           RHQG L
Sbjct: 250 RHQGPL 255



 Score = 91.3 bits (225), Expect(2) = 1e-95
 Identities = 41/55 (74%), Positives = 47/55 (85%)
 Frame = +3

Query: 54  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGN 218
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG Y+HEFDG+
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGD 55


>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 =  278 bits (711), Expect(2) = 1e-95
 Identities = 137/186 (73%), Positives = 145/186 (77%)
 Frame = +2

Query: 218 QLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 397
           QLPLF +FR FDPQ AL NIA  KHNLNI+IKRSN+TAA N+VPEVTVF KSPV LGQPN
Sbjct: 70  QLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPN 129

Query: 398 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 577
           TLIC VDNIFPPV+NITWL NGHSVTEG SETSFLSK+DHSF KISYLTFLPSDD+ YDC
Sbjct: 130 TLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDC 189

Query: 578 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXXXLRSGGPS 757
           KVEHWGLD+PLLKHWEPEIPAPMSELTET                        LRS G S
Sbjct: 190 KVEHWGLDEPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVLIIRGLRSVGAS 249

Query: 758 RHQGSL 775
           RHQG L
Sbjct: 250 RHQGPL 255



 Score = 91.3 bits (225), Expect(2) = 1e-95
 Identities = 41/55 (74%), Positives = 47/55 (85%)
 Frame = +3

Query: 54  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGN 218
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG Y+HEFDG+
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGD 55


>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 =  278 bits (711), Expect(2) = 1e-95
 Identities = 137/186 (73%), Positives = 145/186 (77%)
 Frame = +2

Query: 218 QLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 397
           QLPLF +FR FDPQ AL NIA  KHNLNI+IKRSN+TAA N+VPEVTVF KSPV LGQPN
Sbjct: 70  QLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPN 129

Query: 398 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 577
           TLIC VDNIFPPV+NITWL NGHSVTEG SETSFLSK+DHSF KISYLTFLPSDD+ YDC
Sbjct: 130 TLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDC 189

Query: 578 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXXXLRSGGPS 757
           KVEHWGLD+PLLKHWEPEIPAPMSELTET                        LRS G S
Sbjct: 190 KVEHWGLDEPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVLIIRGLRSVGAS 249

Query: 758 RHQGSL 775
           RHQG L
Sbjct: 250 RHQGPL 255



 Score = 91.3 bits (225), Expect(2) = 1e-95
 Identities = 41/55 (74%), Positives = 47/55 (85%)
 Frame = +3

Query: 54  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGN 218
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG Y+HEFDG+
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGD 55


>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 =  278 bits (711), Expect(2) = 1e-95
 Identities = 137/186 (73%), Positives = 145/186 (77%)
 Frame = +2

Query: 218 QLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 397
           QLPLF +FR FDPQ AL NIA  KHNLNI+IKRSN+TAA N+VPEVTVF KSPV LGQPN
Sbjct: 70  QLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPN 129

Query: 398 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 577
           TLIC VDNIFPPV+NITWL NGHSVTEG SETSFLSK+DHSF KISYLTFLPSDD+ YDC
Sbjct: 130 TLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDC 189

Query: 578 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXXXLRSGGPS 757
           KVEHWGLD+PLLKHWEPEIPAPMSELTET                        LRS G S
Sbjct: 190 KVEHWGLDEPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVLIIRGLRSVGAS 249

Query: 758 RHQGSL 775
           RHQG L
Sbjct: 250 RHQGPL 255



 Score = 91.3 bits (225), Expect(2) = 1e-95
 Identities = 41/55 (74%), Positives = 47/55 (85%)
 Frame = +3

Query: 54  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGN 218
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG Y+HEFDG+
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGD 55


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

 Score =  271 bits (693), Expect(2) = 6e-92
 Identities = 134/184 (72%), Positives = 142/184 (77%)
 Frame = +2

Query: 224 PLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTL 403
           P FSKF  FDPQGALRN+A AKHNLNI+IKR N+TAA N+VPEVTVF KSPV LGQPNTL
Sbjct: 72  PEFSKFGGFDPQGALRNMAVAKHNLNIMIKRYNSTAATNEVPEVTVFSKSPVTLGQPNTL 131

Query: 404 ICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDCKV 583
           IC VDNIFPPV+NITWL NG SVTEG SETSFLSK+DHSF KISYLTFLPS D+ YDCKV
Sbjct: 132 ICLVDNIFPPVVNITWLSNGQSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKV 191

Query: 584 EHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXXXLRSGGPSRH 763
           EHWGLD+PLLKHWEPEIPAPMSELTET                        LRS G SRH
Sbjct: 192 EHWGLDQPLLKHWEPEIPAPMSELTETVVCALGLSVGLMGIVVGTVFIIQGLRSVGASRH 251

Query: 764 QGSL 775
           QG L
Sbjct: 252 QGPL 255



 Score = 85.9 bits (211), Expect(2) = 6e-92
 Identities = 39/55 (70%), Positives = 45/55 (81%)
 Frame = +3

Query: 54  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGN 218
           M+  + L+ GALALT VMS CGGEDI ADHVAS G+N+YQ YGPSG YTHEFDG+
Sbjct: 1   MILNKALLLGALALTTVMSPCGGEDIVADHVASCGVNLYQFYGPSGQYTHEFDGD 55


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

 Score =  266 bits (681), Expect(2) = 6e-92
 Identities = 130/186 (69%), Positives = 142/186 (76%)
 Frame = +2

Query: 218 QLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 397
           QLP+FSKF SFDPQ ALRN+A  KH L  ++++SN+TAA N+VPEVTVF K PV LGQPN
Sbjct: 70  QLPMFSKFISFDPQSALRNMAVGKHTLEFMMRQSNSTAATNEVPEVTVFSKFPVTLGQPN 129

Query: 398 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 577
           TLIC VDNIFPPV+NITWL NGHSVTEG SETSFLSK+DHSF KISYLTFLPS D+ YDC
Sbjct: 130 TLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDC 189

Query: 578 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXXXLRSGGPS 757
           KVEHWGLD+PLLKHWEPEIPAPMSELTET                        LRS G S
Sbjct: 190 KVEHWGLDEPLLKHWEPEIPAPMSELTETLVCALGLSVGLMGIVVGTVFIIQGLRSVGAS 249

Query: 758 RHQGSL 775
           RHQG L
Sbjct: 250 RHQGLL 255



 Score = 90.5 bits (223), Expect(2) = 6e-92
 Identities = 41/55 (74%), Positives = 47/55 (85%)
 Frame = +3

Query: 54  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGN 218
           M+  + L+ GALALTAVMS CGGEDI ADHVASYG+N YQS+GPSG YTHEFDG+
Sbjct: 1   MILNKALLLGALALTAVMSPCGGEDIVADHVASYGVNFYQSHGPSGQYTHEFDGD 55


>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 =  258 bits (660), Expect(2) = 3e-90
 Identities = 131/185 (70%), Positives = 139/185 (75%)
 Frame = +2

Query: 221 LPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNT 400
           LP+  +FR FDPQ AL NIA  KHNLN LIKRSN+TAA N+VPEVTVF KSPV LGQPN 
Sbjct: 71  LPVLRQFR-FDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNI 129

Query: 401 LICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDCK 580
           LIC VDNIFPPV+NITWL NGHSVTEG SETSFLSK+DHSF KISYLT LPS ++ YDCK
Sbjct: 130 LICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCK 189

Query: 581 VEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXXXLRSGGPSR 760
           VEHWGLDKPLLKHWEPEIPAPMSELTET                        LRS G SR
Sbjct: 190 VEHWGLDKPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVFIIRGLRSVGASR 249

Query: 761 HQGSL 775
           HQG L
Sbjct: 250 HQGPL 254



 Score = 92.8 bits (229), Expect(2) = 3e-90
 Identities = 42/55 (76%), Positives = 47/55 (85%)
 Frame = +3

Query: 54  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGN 218
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG YTHEFDG+
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGD 55


>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 =  258 bits (660), Expect(2) = 3e-90
 Identities = 131/185 (70%), Positives = 139/185 (75%)
 Frame = +2

Query: 221 LPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNT 400
           LP+  +FR FDPQ AL NIA  KHNLN LIKRSN+TAA N+VPEVTVF KSPV LGQPN 
Sbjct: 71  LPVLRQFR-FDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNI 129

Query: 401 LICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDCK 580
           LIC VDNIFPPV+NITWL NGHSVTEG SETSFLSK+DHSF KISYLT LPS ++ YDCK
Sbjct: 130 LICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCK 189

Query: 581 VEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXXXLRSGGPSR 760
           VEHWGLDKPLLKHWEPEIPAPMSELTET                        LRS G SR
Sbjct: 190 VEHWGLDKPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVFIIRGLRSVGASR 249

Query: 761 HQGSL 775
           HQG L
Sbjct: 250 HQGPL 254



 Score = 92.8 bits (229), Expect(2) = 3e-90
 Identities = 42/55 (76%), Positives = 47/55 (85%)
 Frame = +3

Query: 54  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGN 218
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG YTHEFDG+
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGD 55


>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 =  258 bits (660), Expect(2) = 3e-90
 Identities = 131/185 (70%), Positives = 139/185 (75%)
 Frame = +2

Query: 221 LPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNT 400
           LP+  +FR FDPQ AL NIA  KHNLN LIKRSN+TAA N+VPEVTVF KSPV LGQPN 
Sbjct: 71  LPVLRQFR-FDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNI 129

Query: 401 LICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDCK 580
           LIC VDNIFPPV+NITWL NGHSVTEG SETSFLSK+DHSF KISYLT LPS ++ YDCK
Sbjct: 130 LICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCK 189

Query: 581 VEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXXXLRSGGPSR 760
           VEHWGLDKPLLKHWEPEIPAPMSELTET                        LRS G SR
Sbjct: 190 VEHWGLDKPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVFIIRGLRSVGASR 249

Query: 761 HQGSL 775
           HQG L
Sbjct: 250 HQGPL 254



 Score = 92.8 bits (229), Expect(2) = 3e-90
 Identities = 42/55 (76%), Positives = 47/55 (85%)
 Frame = +3

Query: 54  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGN 218
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG YTHEFDG+
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGD 55


>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 =  258 bits (660), Expect(2) = 3e-90
 Identities = 131/185 (70%), Positives = 139/185 (75%)
 Frame = +2

Query: 221 LPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNT 400
           LP+  +FR FDPQ AL NIA  KHNLN LIKRSN+TAA N+VPEVTVF KSPV LGQPN 
Sbjct: 71  LPVLRQFR-FDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNI 129

Query: 401 LICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDCK 580
           LIC VDNIFPPV+NITWL NGHSVTEG SETSFLSK+DHSF KISYLT LPS ++ YDCK
Sbjct: 130 LICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCK 189

Query: 581 VEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXXXLRSGGPSR 760
           VEHWGLDKPLLKHWEPEIPAPMSELTET                        LRS G SR
Sbjct: 190 VEHWGLDKPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVFIIRGLRSVGASR 249

Query: 761 HQGSL 775
           HQG L
Sbjct: 250 HQGPL 254



 Score = 92.8 bits (229), Expect(2) = 3e-90
 Identities = 42/55 (76%), Positives = 47/55 (85%)
 Frame = +3

Query: 54  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGN 218
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG YTHEFDG+
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGD 55


  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: 42,033,409
Number of Sequences: 39411
Number of extensions: 1049826
Number of successful extensions: 3039
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 2678
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): 3004
length of database: 17,774,539
effective HSP length: 104
effective length of database: 13,675,795
effective search space used: 3747167830
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-015082
         (1138 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...   248   5e-79
Alignment   gi|NP_034511.2| histocompatibility 2, class II antigen E alpha ...   186   3e-47
Alignment   gi|NP_032232.1| histocompatibility 2, O region alpha locus [Mus...   179   6e-45
Alignment   gi|NP_034516.2| histocompatibility 2, class II, locus DMa [Mus ...    72   1e-12
Alignment   gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ...    71   2e-12
Alignment   gi|NP_033865.2| beta-2-microglobulin [Mus musculus]                   67   3e-11
Alignment   gi|NP_034512.1| histocompatibility 2, class II antigen E beta [...    64   3e-10
Alignment   gi|NP_996988.1| histocompatibility 2, class II antigen A, beta ...    64   4e-10
Alignment   gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/...    64   4e-10
Alignment   gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ...    64   4e-10

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

 Score =  248 bits (633), Expect(2) = 5e-79
 Identities = 118/185 (63%), Positives = 133/185 (71%)
 Frame = +2

Query: 221 LPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNT 400
           LP F +  SFDPQG L+NIA  KHNL +L KRSN+T A N+ P+ TVFPKSPV+LGQPNT
Sbjct: 72  LPEFGQLASFDPQGGLQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNT 131

Query: 401 LICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDCK 580
           LIC VDNIFPPVINITWL+N  SV +G  ETSF    D+SF K+SYLTF+PSDDD YDCK
Sbjct: 132 LICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCK 191

Query: 581 VEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXXXLRSGGPSR 760
           VEHWGL++P+LKHWEPEIPAPMSELTET                        LRSGG SR
Sbjct: 192 VEHWGLEEPVLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTIFIIQGLRSGGTSR 251

Query: 761 HQGSL 775
           H G L
Sbjct: 252 HPGPL 256



 Score = 66.2 bits (160), Expect(2) = 5e-79
 Identities = 33/56 (58%), Positives = 40/56 (71%), Gaps = 1/56 (1%)
 Frame = +3

Query: 54  MVPGRVLMWGALALTAVMSACGGED-IAADHVASYGLNVYQSYGPSGYYTHEFDGN 218
           M   R L+ G LALT ++S CGGED I ADHV +YG++VYQS G  G YT EFDG+
Sbjct: 1   MPRSRALILGVLALTTMLSLCGGEDDIEADHVGTYGISVYQSPGDIGQYTFEFDGD 56


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

 Score =  186 bits (473), Expect = 3e-47
 Identities = 87/148 (58%), Positives = 107/148 (72%)
 Frame = +2

Query: 218 QLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 397
           +L  F+KF SF+ QGAL NIA  K NL+++ +RSNNT   N  PEVTV  +SPV LG+PN
Sbjct: 69  RLEEFAKFASFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPN 128

Query: 398 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 577
            LIC +D   PPV+N+TW +NG  VTEG SET FL ++DH F K  YLTFLPS DDFYDC
Sbjct: 129 ILICFIDKFSPPVVNVTWFRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDC 188

Query: 578 KVEHWGLDKPLLKHWEPEIPAPMSELTE 661
           +V+HWGL++PL KHWE E    + E TE
Sbjct: 189 EVDHWGLEEPLRKHWEFEEKTLLPETTE 216


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

 Score =  179 bits (453), Expect = 6e-45
 Identities = 83/149 (55%), Positives = 108/149 (72%)
 Frame = +2

Query: 218 QLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 397
           +LP F  F   D Q  L +I+  K +L+IL++RSN T AV+  P VTV PK+ V LG+PN
Sbjct: 70  RLPEFGDFAHSDFQSGLMSISMIKAHLDILVERSNRTRAVSVPPRVTVLPKTRVELGKPN 129

Query: 398 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 577
            LIC VD+IFPPVIN+TWL+N   +T+G ++TSF S+ +H F K  YLTF+PS +D YDC
Sbjct: 130 VLICIVDDIFPPVINVTWLRNSQPITKGVAQTSFYSQPNHRFRKFHYLTFVPSAEDVYDC 189

Query: 578 KVEHWGLDKPLLKHWEPEIPAPMSELTET 664
           KVEHWGLD PLL+HWEP++  P  + TET
Sbjct: 190 KVEHWGLDTPLLQHWEPQVLTPPPDTTET 218


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

 Score = 71.6 bits (174), Expect = 1e-12
 Identities = 49/153 (32%), Positives = 70/153 (45%), Gaps = 5/153 (3%)
 Frame = +2

Query: 218 QLPLFSKFRSFDPQGALRNIATAKHNLNILI-----KRSNNTAAVNQVPEVTVFPKSPVM 382
           QLP F+++     QG    IA  K    +L+     K          +P   VF   P+ 
Sbjct: 81  QLPDFAEWAQ--GQGDASAIAFDKSFCEMLMREVSPKLEGQIPVSRGLPVAEVFTLKPLE 138

Query: 383 LGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDD 562
            G+PNTL+C + N+FPP + + W  +   V EG S TS  + +  +F   SYL F P   
Sbjct: 139 FGKPNTLVCFISNLFPPTLTVNWQLHSAPV-EGASPTSISAVDGLTFQAFSYLNFTPEPF 197

Query: 563 DFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 661
           D Y C V H       + +W P+   P S+L E
Sbjct: 198 DLYSCTVTHEIDRYTAIAYWVPQNALP-SDLLE 229


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

 Score = 70.9 bits (172), Expect = 2e-12
 Identities = 35/99 (35%), Positives = 48/99 (48%)
 Frame = +2

Query: 326 TAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLS 505
           T   N  PEVTV+P+   +L Q N L+C V   +P  I++ W +NG     G   T  + 
Sbjct: 116 TVERNVPPEVTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVR 175

Query: 506 KNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHW 622
             D +F     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 = 67.4 bits (163), Expect = 3e-11
 Identities = 33/102 (32%), Positives = 57/102 (55%), Gaps = 1/102 (0%)
 Frame = +2

Query: 332 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTE-GFSETSFLSK 508
           A+ + P++ V+ + P   G+PN L C+V    PP I I  LKNG  + +   S+ SF   
Sbjct: 20  AIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSF--S 77

Query: 509 NDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEI 634
            D SF  +++  F P++ D Y C+V+H  + +P   +W+ ++
Sbjct: 78  KDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM 119


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

 Score = 63.9 bits (154), Expect = 3e-10
 Identities = 29/103 (28%), Positives = 48/103 (46%)
 Frame = +2

Query: 347 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 526
           P VTV+P     L   N L+C V + +P  I + W +NG     G   T  +   D +F 
Sbjct: 124 PTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQ 183

Query: 527 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 655
            +  L  +P   + Y C+VEH  L  P+   W+ +  +  +++
Sbjct: 184 TLVMLETVPQSGEVYTCQVEHPSLTDPVTVEWKAQSTSAQNKM 226


>ref|NP_996988.1| histocompatibility 2, class II antigen A, beta 1 [Mus musculus]
          Length = 265

 Score = 63.5 bits (153), Expect = 4e-10
 Identities = 30/103 (29%), Positives = 45/103 (43%)
 Frame = +2

Query: 347 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 526
           P V +       L   NTL+C V + +P  I + W +NG   T G S T  +   D +F 
Sbjct: 125 PNVVISLSRTEALNHHNTLVCSVTDFYPTQIKVRWFRNGQEETVGVSSTQLIRNGDWTFQ 184

Query: 527 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 655
            +  L   P   + Y C VEH  L  P+   W  +  +  S++
Sbjct: 185 VLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRAQSESAWSKM 227


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

 Score = 63.5 bits (153), Expect = 4e-10
 Identities = 29/103 (28%), Positives = 47/103 (45%)
 Frame = +2

Query: 347 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 526
           P+VTV+P     L   N L+C V + +P  I + W +NG     G   T  +   D ++ 
Sbjct: 125 PKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNRDWTYQ 184

Query: 527 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 655
            +  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 = 63.5 bits (153), Expect = 4e-10
 Identities = 32/97 (32%), Positives = 47/97 (48%), Gaps = 1/97 (1%)
 Frame = +2

Query: 341 QVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN-DH 517
           + P V V   +P    +P  L C+V   +P  + ITW+KNG  V    ++      N D 
Sbjct: 113 RAPSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPNGDW 172

Query: 518 SFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEP 628
           ++  +SYL   PS  D Y C V+H G  +P+   W P
Sbjct: 173 TYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDWTP 209


  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: 49,919,467
Number of Sequences: 45328
Number of extensions: 1212248
Number of successful extensions: 3348
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 3038
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): 3337
length of database: 21,768,885
effective HSP length: 105
effective length of database: 17,009,445
effective search space used: 4643578485
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-015082
         (1138 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...   273   5e-92
Alignment   gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati...   187   5e-52
Alignment   gi|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris]    189   4e-48
Alignment   gi|XP_532104.2| PREDICTED: similar to HLA class II histocompati...    45   4e-12
Alignment   gi|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Ca...    68   1e-11
Alignment   gi|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis fami...    68   2e-11
Alignment   gi|XP_861572.1| PREDICTED: similar to major histocompatibility ...    68   2e-11
Alignment   gi|XP_538853.2| PREDICTED: similar to major histocompatibility ...    68   2e-11
Alignment   gi|XP_535458.1| PREDICTED: similar to beta-2-microglobulin prec...    65   9e-11
Alignment   gi|XP_850148.1| PREDICTED: similar to beta-2-microglobulin prec...    65   9e-11

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

 Score =  273 bits (699), Expect(2) = 5e-92
 Identities = 133/186 (71%), Positives = 143/186 (76%)
 Frame = +2

Query: 218 QLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 397
           +LP+FS FRSFDPQGALRN+A  K NLNI+ KRSN TAA N+VPEVTVF KSPVMLGQPN
Sbjct: 70  RLPVFSTFRSFDPQGALRNLAIIKQNLNIMTKRSNQTAATNEVPEVTVFSKSPVMLGQPN 129

Query: 398 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 577
           TLIC VDNIFPPVIN+TWLKN HSVTEG SETSF +K DHSF KISYLTFLPS +D YDC
Sbjct: 130 TLICLVDNIFPPVINVTWLKNRHSVTEGVSETSFFAKGDHSFSKISYLTFLPSAEDIYDC 189

Query: 578 KVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXXXXLRSGGPS 757
           KVEHWGLD+PLLKHWEPE+P PMSELTET                        LRSGG S
Sbjct: 190 KVEHWGLDEPLLKHWEPEVPTPMSELTETVVCALGLAVGLVGIVMGTVFIIQGLRSGGTS 249

Query: 758 RHQGSL 775
           RHQG L
Sbjct: 250 RHQGPL 255



 Score = 84.0 bits (206), Expect(2) = 5e-92
 Identities = 38/55 (69%), Positives = 45/55 (81%)
 Frame = +3

Query: 54  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGN 218
           M+  RVL+ G L LT +MS  GGE+I ADHVA+YG+NVYQSYGPSG YTHEFDG+
Sbjct: 1   MILNRVLILGTLILTIMMSPSGGEEIVADHVANYGINVYQSYGPSGQYTHEFDGD 55


>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 =  187 bits (475), Expect(2) = 5e-52
 Identities = 87/156 (55%), Positives = 110/156 (70%), Gaps = 7/156 (4%)
 Frame = +2

Query: 218 QLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQV-------PEVTVFPKSP 376
           +LP F     FDPQ  L +IA  K +L++L++RSN T A+N         P V V PK  
Sbjct: 40  RLPEFGNLAHFDPQNGLASIAVIKAHLDVLVERSNRTRAINGTHLSSPLPPRVAVLPKFR 99

Query: 377 VMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPS 556
           V LGQPN LIC VDNIFPPVINITWL+NG  ++EG ++TSF S+ DH F K  YLTF+PS
Sbjct: 100 VELGQPNVLICIVDNIFPPVINITWLRNGQIISEGVAQTSFYSQPDHLFRKFCYLTFVPS 159

Query: 557 DDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 664
            +D YDCKVEHWGL++PLL+HWEP++P P+ +  ET
Sbjct: 160 AEDMYDCKVEHWGLEEPLLRHWEPQVPIPVPDTIET 195



 Score = 36.6 bits (83), Expect(2) = 5e-52
 Identities = 15/24 (62%), Positives = 17/24 (70%)
 Frame = +3

Query: 144 VASYGLNVYQSYGPSGYYTHEFDG 215
           + SYG   YQSYG SG + HEFDG
Sbjct: 1   MGSYGPAFYQSYGSSGQFAHEFDG 24


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

 Score =  189 bits (480), Expect = 4e-48
 Identities = 90/148 (60%), Positives = 106/148 (71%)
 Frame = +2

Query: 218 QLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 397
           +L  F +F SF+ QGAL NIA  K NL+ +IKRSN+T   N  PEVTV   +PV LG+PN
Sbjct: 69  RLEEFGRFASFEAQGALANIAVDKANLDTMIKRSNHTPNTNVPPEVTVLSNTPVELGEPN 128

Query: 398 TLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDC 577
            LIC +D   PPVIN+TWL+NG+ VT G SET FL + DH F K  YL FLPS +D YDC
Sbjct: 129 ILICFIDKFSPPVINVTWLRNGNPVTTGVSETIFLPREDHLFRKFHYLPFLPSAEDVYDC 188

Query: 578 KVEHWGLDKPLLKHWEPEIPAPMSELTE 661
           KVEHWGLD+PLLKHWE E P P+ E TE
Sbjct: 189 KVEHWGLDEPLLKHWEFEPPTPLPETTE 216


>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 = 45.4 bits (106), Expect(2) = 4e-12
 Identities = 25/64 (39%), Positives = 37/64 (57%)
 Frame = +2

Query: 218 QLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPN 397
           +LP F     FDPQ  L +IA  K +L++L++RSN T A+N+ P+V +     +      
Sbjct: 56  RLPEFGNLAHFDPQNGLASIAVIKAHLDVLVERSNRTRAINE-PQVPIPVPDTI-----E 109

Query: 398 TLIC 409
           TLIC
Sbjct: 110 TLIC 113



 Score = 44.7 bits (104), Expect(2) = 4e-12
 Identities = 19/29 (65%), Positives = 21/29 (72%)
 Frame = +3

Query: 129 IAADHVASYGLNVYQSYGPSGYYTHEFDG 215
           I ADH+ SYG   YQSYG SG + HEFDG
Sbjct: 12  IEADHMGSYGPAFYQSYGSSGQFAHEFDG 40


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

 Score = 68.2 bits (165), Expect = 1e-11
 Identities = 31/103 (30%), Positives = 46/103 (44%)
 Frame = +2

Query: 347 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 526
           P VT+FP    +L   N L+C V + +P  I + W +N    T G   T  +   D +F 
Sbjct: 129 PTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLIRNGDWTFQ 188

Query: 527 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 655
            +  L   P   D Y C VEH  L  P+   W  +  +  S++
Sbjct: 189 ILVMLEMTPQRGDVYTCHVEHASLQSPITVQWRAQSESAQSKM 231


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

 Score = 67.8 bits (164), Expect = 2e-11
 Identities = 34/123 (27%), Positives = 55/123 (44%)
 Frame = +2

Query: 287 KHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGH 466
           +HN  ++    + T      P VTV+P     L   N L+C V+  +P  I + WL+NG 
Sbjct: 109 RHNYGVI---ESFTVQRRVEPTVTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQ 165

Query: 467 SVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPM 646
               G   T  +   D +F  +  L  +P   + Y C+VEH  L  P+   W  +  +  
Sbjct: 166 EEEAGVVSTGLIRNGDWTFQILVMLEIVPQSGEVYTCQVEHPSLTSPVTVEWRAQSDSAQ 225

Query: 647 SEL 655
           S++
Sbjct: 226 SKM 228


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

 Score = 67.8 bits (164), Expect = 2e-11
 Identities = 36/105 (34%), Positives = 52/105 (49%)
 Frame = +2

Query: 347 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 526
           P V VF   P+  G+PN L+C + N+FPP + + W  +   V EG   T   + +  SF 
Sbjct: 38  PMVDVFTLKPLEFGKPNMLVCFISNLFPPTLTVNWWHHLDPV-EGIGPTFVSAVDGFSFQ 96

Query: 527 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 661
             SYL F P+  D + C V H   +   + +W P    P S+L E
Sbjct: 97  AFSYLNFTPAPSDLFSCVVTHEIDNYTAIAYWVPHDALP-SDLLE 140


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

 Score = 67.8 bits (164), Expect = 2e-11
 Identities = 36/105 (34%), Positives = 52/105 (49%)
 Frame = +2

Query: 347 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 526
           P V VF   P+  G+PN L+C + N+FPP + + W  +   V EG   T   + +  SF 
Sbjct: 133 PMVDVFTLKPLEFGKPNMLVCFISNLFPPTLTVNWWHHLDPV-EGIGPTFVSAVDGFSFQ 191

Query: 527 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 661
             SYL F P+  D + C V H   +   + +W P    P S+L E
Sbjct: 192 AFSYLNFTPAPSDLFSCVVTHEIDNYTAIAYWVPHDALP-SDLLE 235


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

 Score = 65.5 bits (158), Expect = 9e-11
 Identities = 32/98 (32%), Positives = 52/98 (53%)
 Frame = +2

Query: 332 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN 511
           AV   P++ V+ + P   G+PN L C+V    PP I I  LKNG  +    ++ SF    
Sbjct: 27  AVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSF--SK 84

Query: 512 DHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 625
           D +F  + +  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 = 65.5 bits (158), Expect = 9e-11
 Identities = 32/98 (32%), Positives = 52/98 (53%)
 Frame = +2

Query: 332 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN 511
           AV   P++ V+ + P   G+PN L C+V    PP I I  LKNG  +    ++ SF    
Sbjct: 27  AVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSF--SK 84

Query: 512 DHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 625
           D +F  + +  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: 43,560,075
Number of Sequences: 33732
Number of extensions: 1052211
Number of successful extensions: 2882
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 2570
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): 2865
length of database: 19,266,565
effective HSP length: 105
effective length of database: 15,724,705
effective search space used: 4292844465
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)