Animal-Genome cDNA AMP01_0001_H11


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= AMP01_0001_H11
         (1332 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...   374   e-104
Alignment   gi|NP_001012693.1| major histocompatibility complex, class II, ...   372   e-103
Alignment   gi|NP_001012699.1| major histocompatibility complex, class II, ...   328   6e-90
Alignment   gi|NP_001012696.1| major histocompatibility complex, class II, ...   310   2e-84
Alignment   gi|XP_604082.2| PREDICTED: similar to HLA class II histocompati...   245   5e-65
Alignment   gi|XP_883292.1| PREDICTED: similar to HLA class II histocompati...   243   2e-64
Alignment   gi|NP_001012695.1| major histocompatibility complex, class II, ...   226   2e-59
Alignment   gi|NP_776318.1| beta-2-microglobulin [Bos taurus]                     73   6e-13
Alignment   gi|NP_001012692.2| major histocompatibility complex, class II, ...    69   1e-11
Alignment   gi|NP_001012694.1| major histocompatibility complex, class II, ...    62   1e-09

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

 Score =  374 bits (961), Expect = e-104
 Identities = 174/222 (78%), Positives = 199/222 (89%)
 Frame = +3

Query: 51  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYV 230
           MV  R L+ GALALT +MS  G EDI ADH+ +YG+++Y +YG SGYYTHEFDGDE+FYV
Sbjct: 1   MVLNRALILGALALTTMMSPSGSEDIVADHIGTYGISIYHTYGPSGYYTHEFDGDEEFYV 60

Query: 231 DLEKKETVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNNTAAVNKVPEVTVFSK 410
           DLEK+ETVW+LP+FSKF +FDPQGALRNIA  K  L I+ +RSN+TAA NKVPEVTVFSK
Sbjct: 61  DLEKRETVWRLPVFSKFATFDPQGALRNIATTKHNLEIVIQRSNSTAATNKVPEVTVFSK 120

Query: 411 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 590
           SPV+LGQPNTLICHVD+IFPPVINITWL+NGHSVTEG SETSFL ++D+SFLKI+YLTFL
Sbjct: 121 SPVMLGQPNTLICHVDNIFPPVINITWLRNGHSVTEGVSETSFLIKSDYSFLKINYLTFL 180

Query: 591 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 716
           PSDDD YDCKVEHWGLD+PLLKHWEP+IPAPMSELTETVVCA
Sbjct: 181 PSDDDVYDCKVEHWGLDEPLLKHWEPDIPAPMSELTETVVCA 222


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

 Score =  372 bits (956), Expect = e-103
 Identities = 178/221 (80%), Positives = 194/221 (87%)
 Frame = +3

Query: 51  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYV 230
           MV  R L+ G LALT +MS  GGEDI ADHV  YG+++YQSYG SG YTHEFDGDEQFYV
Sbjct: 1   MVLNRALILGTLALTTMMSPSGGEDIVADHVGIYGISIYQSYGPSGQYTHEFDGDEQFYV 60

Query: 231 DLEKKETVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNNTAAVNKVPEVTVFSK 410
           DLEKKET WQLPLFS+  SFDPQ ALRNIA+ KL ++ LTK SN+TAA NKVPEVTVFSK
Sbjct: 61  DLEKKETAWQLPLFSRMLSFDPQLALRNIAIMKLHVDFLTKFSNSTAATNKVPEVTVFSK 120

Query: 411 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 590
           SPV+LGQPNTLICHVD+IFPPVINITWL+NGHSVTEG SETSFL R+D+SFLKI YL FL
Sbjct: 121 SPVMLGQPNTLICHVDNIFPPVINITWLRNGHSVTEGVSETSFLIRSDYSFLKIKYLAFL 180

Query: 591 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVC 713
           PSDDD YDCKVEHWGLD+PLLKHWEPEIPAPMSELTETVVC
Sbjct: 181 PSDDDIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETVVC 221


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

 Score =  328 bits (841), Expect = 6e-90
 Identities = 154/204 (75%), Positives = 173/204 (84%)
 Frame = +3

Query: 51  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYV 230
           MV  R L+ GALALT +MS+ GGEDI ADHV SYG  +YQS+G SG YT EFDGDE FYV
Sbjct: 1   MVLNRALILGALALTTMMSSSGGEDIVADHVGSYGTEIYQSHGPSGQYTQEFDGDEMFYV 60

Query: 231 DLEKKETVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNNTAAVNKVPEVTVFSK 410
           DL KKETVW+LP+FS+F  FDPQ AL  IA  K  L++LTKRSN T  +N+VPEVTVFSK
Sbjct: 61  DLGKKETVWRLPMFSQFAGFDPQAALSEIATAKHNLDVLTKRSNFTPVINEVPEVTVFSK 120

Query: 411 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 590
           SPV+LGQPNTLICHVD+IFPPVINITWLKNGH+VTEG SETSFL ++DHSFLKI YLTFL
Sbjct: 121 SPVMLGQPNTLICHVDNIFPPVINITWLKNGHAVTEGVSETSFLPKDDHSFLKIGYLTFL 180

Query: 591 PSDDDFYDCKVEHWGLDKPLLKHW 662
           PSD+D YDCKVEHWGLD+PLLKHW
Sbjct: 181 PSDNDIYDCKVEHWGLDEPLLKHW 204


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

 Score =  310 bits (794), Expect = 2e-84
 Identities = 145/218 (66%), Positives = 173/218 (79%)
 Frame = +3

Query: 63  RVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYVDLEK 242
           + L+  AL L  +MS  GGEDI ADHV +YG NVYQ+YG+SG +T EFDGDE FYVDL K
Sbjct: 3   KALILRALTLATMMSPYGGEDIVADHVGTYGTNVYQTYGASGQFTFEFDGDELFYVDLGK 62

Query: 243 KETVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNNTAAVNKVPEVTVFSKSPVI 422
           KETVW+LP FS  T F+ Q ALRNI + K  L+IL K S+ T A +++PEV VF KS V+
Sbjct: 63  KETVWRLPEFSNITKFEVQSALRNIVMSKRNLDILIKNSSFTPATSEIPEVAVFPKSSVV 122

Query: 423 LGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFLPSDD 602
           LG PNTLIC VD+IFPPVINITW  NGH V EG +ET+F  ++DHSFLK SYLTFLP+++
Sbjct: 123 LGIPNTLICQVDNIFPPVINITWFYNGHFVAEGIAETTFYPKSDHSFLKFSYLTFLPTNE 182

Query: 603 DFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 716
           DFYDC+VEHWGL++PL+KHWEPEIP P SELTETVVCA
Sbjct: 183 DFYDCRVEHWGLEEPLVKHWEPEIPTPTSELTETVVCA 220


>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 =  245 bits (626), Expect = 5e-65
 Identities = 118/216 (54%), Positives = 149/216 (68%)
 Frame = +3

Query: 69  LMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYVDLEKKE 248
           L+ G   L  ++S      I ADH+ SYG   YQSY  +G +T++FDG++ F VDL+K+E
Sbjct: 7   LVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSVDLKKRE 66

Query: 249 TVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNNTAAVNKVPEVTVFSKSPVILG 428
            VW+LP F  F  FDPQ  L +IA+ K  L  L KRSN T A N  P V V  KS V LG
Sbjct: 67  AVWRLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNVSPRVAVLPKSHVQLG 126

Query: 429 QPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFLPSDDDF 608
           +PN LIC VD IFPPVINITWL+NGH VT+G +++SF ++ DH F K  YLTF+P  DDF
Sbjct: 127 EPNVLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTFVPLVDDF 186

Query: 609 YDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 716
           YDCKVEHWGLD+PL +HWEP++P  + + T T+VCA
Sbjct: 187 YDCKVEHWGLDQPLFQHWEPQVPTALPDTTGTLVCA 222


>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 =  243 bits (620), Expect = 2e-64
 Identities = 118/217 (54%), Positives = 150/217 (69%), Gaps = 1/217 (0%)
 Frame = +3

Query: 69  LMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYVDLEKKE 248
           L+ G   L  ++S      I ADH+ SYG   YQSY  +G +T++FDG++ F VDL+K+E
Sbjct: 7   LVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSVDLKKRE 66

Query: 249 TVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNNTAAVN-KVPEVTVFSKSPVIL 425
            VW+LP F  F  FDPQ  L +IA+ K  L  L KRSN T A N   P+V V  KS V L
Sbjct: 67  AVWRLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNGSTPQVAVLPKSHVQL 126

Query: 426 GQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFLPSDDD 605
           G+PN LIC VD IFPPVINITWL+NGH VT+G +++SF ++ DH F K  YLTF+P  DD
Sbjct: 127 GEPNVLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTFVPLVDD 186

Query: 606 FYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 716
           FYDCKVEHWGLD+PL +HWEP++P  + + T T+VCA
Sbjct: 187 FYDCKVEHWGLDQPLFQHWEPQVPTALPDTTGTLVCA 223


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

 Score =  226 bits (577), Expect = 2e-59
 Identities = 107/178 (60%), Positives = 129/178 (72%)
 Frame = +3

Query: 183 SGYYTHEFDGDEQFYVDLEKKETVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSN 362
           S  +  +FDGDE F+VD+ KKETVW+LP F  F SF+ QGAL N+AV K  L+I+ KRSN
Sbjct: 43  SAEFMFDFDGDEIFHVDMGKKETVWRLPEFGHFASFEAQGALANMAVMKANLDIMIKRSN 102

Query: 363 NTAAVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFL 542
           NT   N  PEVT+    PV LG+PNTLIC +D   PPVI++TWL+NG  VT+G S+T FL
Sbjct: 103 NTPNTNVPPEVTLLPNKPVELGEPNTLICFIDKFSPPVISVTWLRNGKPVTDGVSQTVFL 162

Query: 543 SRNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 716
            RNDH F K  YL FLP+ +D YDCKVEH GL++PLLKHWE E PAP+ E TE  VCA
Sbjct: 163 PRNDHLFRKFHYLPFLPTTEDVYDCKVEHLGLNEPLLKHWEYEAPAPLPETTENAVCA 220


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

 Score = 72.8 bits (177), Expect = 6e-13
 Identities = 36/101 (35%), Positives = 57/101 (56%)
 Frame = +3

Query: 372 AVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRN 551
           A+ + P++ V+S+ P   G+PN L C+V    PP I I  LKNG  +    S+ SF    
Sbjct: 20  AIQRPPKIQVYSRHPPEDGKPNYLNCYVYGFHPPQIEIDLLKNGEKIKSEQSDLSF--SK 77

Query: 552 DHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEI 674
           D SF  +S+  F P+  D Y C+V+H  L++P +  W+ ++
Sbjct: 78  DWSFYLLSHAEFTPNSKDQYSCRVKHVTLEQPRIVKWDRDL 118


>ref|NP_001012692.2| major histocompatibility complex, class II, DM alpha-chain,
           expressed [Bos taurus]
          Length = 260

 Score = 68.6 bits (166), Expect = 1e-11
 Identities = 48/187 (25%), Positives = 81/187 (43%), Gaps = 5/187 (2%)
 Frame = +3

Query: 168 QSYGSSGYYTHEFDGDEQFYVDLEKKETVWQLPLFSKFTSFDPQGALRNIAVGK-----L 332
           Q +  +   +  +D D+ F  D  +   V +LP F+ +      G   +I   K     +
Sbjct: 51  QDWSPNVALSESYDEDQLFSFDFSQSIRVPRLPEFADWAH--QHGDTSDIMFDKGFCRAM 108

Query: 333 TLNILTKRSNNTAAVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSV 512
              I  +           P V VF+  P+  G+PNTL+C + ++FPP + + W ++  + 
Sbjct: 109 IEEIGPELEGQIPVSRGFPIVQVFTLKPLEFGKPNTLVCFISNLFPPTLTVNW-QHQSAP 167

Query: 513 TEGFSETSFLSRNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSE 692
            EG   T   + +  +F   SYL   P+  D + C V H       +  W P+   P S+
Sbjct: 168 VEGAGPTFVSAVDGLTFQAFSYLNVTPAPSDLFSCIVTHEIDGYTAIAFWVPQNALP-SD 226

Query: 693 LTETVVC 713
           L E V+C
Sbjct: 227 LLENVLC 233


>ref|NP_001012694.1| major histocompatibility complex, class II, DQ beta [Bos taurus]
          Length = 261

 Score = 62.0 bits (149), Expect = 1e-09
 Identities = 31/107 (28%), Positives = 44/107 (41%)
 Frame = +3

Query: 387 PEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFL 566
           P VT+       L   N L+C V   +P  I + W +NG   T G   T  +   D +F 
Sbjct: 129 PTVTISLSRTEALNHHNLLVCSVTDFYPGQIKVRWFQNGKEETAGIVSTPLIRNGDWTFQ 188

Query: 567 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETV 707
            +  L   P   D Y C VEH  L  P+   W  +  +  S++   V
Sbjct: 189 ILVMLEMTPKRGDVYTCHVEHPSLQSPISVEWRAQSESAQSKMLSGV 235


  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: 41,503,538
Number of Sequences: 33508
Number of extensions: 996883
Number of successful extensions: 3048
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 2748
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): 3040
length of database: 16,112,626
effective HSP length: 105
effective length of database: 12,594,286
effective search space used: 4256868668
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= AMP01_0001_H11
         (1332 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...   370   e-102
Alignment   gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati...   237   2e-62
Alignment   gi|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris]    236   4e-62
Alignment   gi|XP_532104.2| PREDICTED: similar to HLA class II histocompati...   101   1e-21
Alignment   gi|XP_538853.2| PREDICTED: similar to major histocompatibility ...    77   3e-14
Alignment   gi|XP_861572.1| PREDICTED: similar to major histocompatibility ...    72   2e-12
Alignment   gi|XP_535458.1| PREDICTED: similar to beta-2-microglobulin prec...    67   3e-11
Alignment   gi|XP_850148.1| PREDICTED: similar to beta-2-microglobulin prec...    67   3e-11
Alignment   gi|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Ca...    65   1e-10
Alignment   gi|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis fami...    64   3e-10

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

 Score =  370 bits (949), Expect = e-102
 Identities = 174/222 (78%), Positives = 195/222 (87%)
 Frame = +3

Query: 51  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYV 230
           M+  RVL+ G L LT +MS  GGE+I ADHVA+YG+NVYQSYG SG YTHEFDGDE+FYV
Sbjct: 1   MILNRVLILGTLILTIMMSPSGGEEIVADHVANYGINVYQSYGPSGQYTHEFDGDEEFYV 60

Query: 231 DLEKKETVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNNTAAVNKVPEVTVFSK 410
           DLEKKETVW+LP+FS F SFDPQGALRN+A+ K  LNI+TKRSN TAA N+VPEVTVFSK
Sbjct: 61  DLEKKETVWRLPVFSTFRSFDPQGALRNLAIIKQNLNIMTKRSNQTAATNEVPEVTVFSK 120

Query: 411 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 590
           SPV+LGQPNTLIC VD+IFPPVIN+TWLKN HSVTEG SETSF ++ DHSF KISYLTFL
Sbjct: 121 SPVMLGQPNTLICLVDNIFPPVINVTWLKNRHSVTEGVSETSFFAKGDHSFSKISYLTFL 180

Query: 591 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 716
           PS +D YDCKVEHWGLD+PLLKHWEPE+P PMSELTETVVCA
Sbjct: 181 PSAEDIYDCKVEHWGLDEPLLKHWEPEVPTPMSELTETVVCA 222


>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 =  237 bits (604), Expect = 2e-62
 Identities = 110/199 (55%), Positives = 142/199 (71%), Gaps = 7/199 (3%)
 Frame = +3

Query: 141 VASYGLNVYQSYGSSGYYTHEFDGDEQFYVDLEKKETVWQLPLFSKFTSFDPQGALRNIA 320
           + SYG   YQSYGSSG + HEFDG++ F V+L+K++ VW+LP F     FDPQ  L +IA
Sbjct: 1   MGSYGPAFYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEFGNLAHFDPQNGLASIA 60

Query: 321 VGKLTLNILTKRSNNTAAVNKV-------PEVTVFSKSPVILGQPNTLICHVDSIFPPVI 479
           V K  L++L +RSN T A+N         P V V  K  V LGQPN LIC VD+IFPPVI
Sbjct: 61  VIKAHLDVLVERSNRTRAINGTHLSSPLPPRVAVLPKFRVELGQPNVLICIVDNIFPPVI 120

Query: 480 NITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKH 659
           NITWL+NG  ++EG ++TSF S+ DH F K  YLTF+PS +D YDCKVEHWGL++PLL+H
Sbjct: 121 NITWLRNGQIISEGVAQTSFYSQPDHLFRKFCYLTFVPSAEDMYDCKVEHWGLEEPLLRH 180

Query: 660 WEPEIPAPMSELTETVVCA 716
           WEP++P P+ +  ET++CA
Sbjct: 181 WEPQVPIPVPDTIETLICA 199


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

 Score =  236 bits (602), Expect = 4e-62
 Identities = 113/184 (61%), Positives = 133/184 (72%)
 Frame = +3

Query: 165 YQSYGSSGYYTHEFDGDEQFYVDLEKKETVWQLPLFSKFTSFDPQGALRNIAVGKLTLNI 344
           Y +   SG +  +FDGDE F+VD+EKKETVW+L  F +F SF+ QGAL NIAV K  L+ 
Sbjct: 38  YLTPDPSGEFMFDFDGDEIFHVDMEKKETVWRLEEFGRFASFEAQGALANIAVDKANLDT 97

Query: 345 LTKRSNNTAAVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGF 524
           + KRSN+T   N  PEVTV S +PV LG+PN LIC +D   PPVIN+TWL+NG+ VT G 
Sbjct: 98  MIKRSNHTPNTNVPPEVTVLSNTPVELGEPNILICFIDKFSPPVINVTWLRNGNPVTTGV 157

Query: 525 SETSFLSRNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 704
           SET FL R DH F K  YL FLPS +D YDCKVEHWGLD+PLLKHWE E P P+ E TE 
Sbjct: 158 SETIFLPREDHLFRKFHYLPFLPSAEDVYDCKVEHWGLDEPLLKHWEFEPPTPLPETTEN 217

Query: 705 VVCA 716
           VVCA
Sbjct: 218 VVCA 221


>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 =  101 bits (252), Expect = 1e-21
 Identities = 52/108 (48%), Positives = 70/108 (64%)
 Frame = +3

Query: 126 IAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYVDLEKKETVWQLPLFSKFTSFDPQGA 305
           I ADH+ SYG   YQSYGSSG + HEFDG++ F V+L+K++ VW+LP F     FDPQ  
Sbjct: 12  IEADHMGSYGPAFYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEFGNLAHFDPQNG 71

Query: 306 LRNIAVGKLTLNILTKRSNNTAAVNKVPEVTVFSKSPVILGQPNTLIC 449
           L +IAV K  L++L +RSN T A+N+ P+V +     +      TLIC
Sbjct: 72  LASIAVIKAHLDVLVERSNRTRAINE-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 = 77.4 bits (189), Expect = 3e-14
 Identities = 52/187 (27%), Positives = 83/187 (44%), Gaps = 5/187 (2%)
 Frame = +3

Query: 168 QSYGSSGYYTHEFDGDEQFYVDLEKKETVWQLPLFSKFTSFDPQGALRNIAVGK-----L 332
           Q++  S      +DGD+ F  +  +   V +LP F+ +      G +  I+  K     +
Sbjct: 57  QNWSPSIGLLEAYDGDQLFSFNFSQNTRVPRLPEFADWAQ--KSGDMPTISFDKAFCQAM 114

Query: 333 TLNILTKRSNNTAAVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSV 512
              I  K           P V VF+  P+  G+PN L+C + ++FPP + + W  +   V
Sbjct: 115 IEEIGPKLEGQIPVSRGFPMVDVFTLKPLEFGKPNMLVCFISNLFPPTLTVNWWHHLDPV 174

Query: 513 TEGFSETSFLSRNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSE 692
            EG   T   + +  SF   SYL F P+  D + C V H   +   + +W P    P S+
Sbjct: 175 -EGIGPTFVSAVDGFSFQAFSYLNFTPAPSDLFSCVVTHEIDNYTAIAYWVPHDALP-SD 232

Query: 693 LTETVVC 713
           L E V+C
Sbjct: 233 LLENVLC 239


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

 Score = 71.6 bits (174), Expect = 2e-12
 Identities = 40/126 (31%), Positives = 62/126 (49%)
 Frame = +3

Query: 336 LNILTKRSNNTAAVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVT 515
           L++L     +  A    P V VF+  P+  G+PN L+C + ++FPP + + W  +   V 
Sbjct: 21  LHLLWLLPYSRTAPEGFPMVDVFTLKPLEFGKPNMLVCFISNLFPPTLTVNWWHHLDPV- 79

Query: 516 EGFSETSFLSRNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 695
           EG   T   + +  SF   SYL F P+  D + C V H   +   + +W P    P S+L
Sbjct: 80  EGIGPTFVSAVDGFSFQAFSYLNFTPAPSDLFSCVVTHEIDNYTAIAYWVPHDALP-SDL 138

Query: 696 TETVVC 713
            E V+C
Sbjct: 139 LENVLC 144


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

 Score = 67.4 bits (163), Expect = 3e-11
 Identities = 36/114 (31%), Positives = 59/114 (51%)
 Frame = +3

Query: 324 GKLTLNILTKRSNNTAAVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNG 503
           G L L ++   +    AV   P++ V+S+ P   G+PN L C+V    PP I I  LKNG
Sbjct: 11  GFLALLLILLAACRLDAVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNG 70

Query: 504 HSVTEGFSETSFLSRNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 665
             +    ++ SF    D +F  + +  F P++ D + C+V+H  L +P +  W+
Sbjct: 71  KEMKAEQTDLSF--SKDWTFYLLVHTEFTPNEQDEFSCRVKHVTLSEPQIVKWD 122


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

 Score = 67.4 bits (163), Expect = 3e-11
 Identities = 36/114 (31%), Positives = 59/114 (51%)
 Frame = +3

Query: 324 GKLTLNILTKRSNNTAAVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNG 503
           G L L ++   +    AV   P++ V+S+ P   G+PN L C+V    PP I I  LKNG
Sbjct: 11  GFLALLLILLAACRLDAVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNG 70

Query: 504 HSVTEGFSETSFLSRNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 665
             +    ++ SF    D +F  + +  F P++ D + C+V+H  L +P +  W+
Sbjct: 71  KEMKAEQTDLSF--SKDWTFYLLVHTEFTPNEQDEFSCRVKHVTLSEPQIVKWD 122


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

 Score = 65.5 bits (158), Expect = 1e-10
 Identities = 30/103 (29%), Positives = 44/103 (42%)
 Frame = +3

Query: 387 PEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFL 566
           P VT+F     +L   N L+C V   +P  I + W +N    T G   T  +   D +F 
Sbjct: 129 PTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLIRNGDWTFQ 188

Query: 567 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 695
            +  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 = 64.3 bits (155), Expect = 3e-10
 Identities = 30/103 (29%), Positives = 47/103 (45%)
 Frame = +3

Query: 387 PEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFL 566
           P VTV+      L   N L+C V+  +P  I + WL+NG     G   T  +   D +F 
Sbjct: 126 PTVTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNGDWTFQ 185

Query: 567 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 695
            +  L  +P   + Y C+VEH  L  P+   W  +  +  S++
Sbjct: 186 ILVMLEIVPQSGEVYTCQVEHPSLTSPVTVEWRAQSDSAQSKM 228


  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: 48,734,091
Number of Sequences: 33732
Number of extensions: 1173761
Number of successful extensions: 3531
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 3072
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): 3516
length of database: 19,266,565
effective HSP length: 106
effective length of database: 15,690,973
effective search space used: 5287857901
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 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= AMP01_0001_H11
         (1332 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]                    80   1e-16
Alignment   gi|NP_999143.1| beta 2-microglobulin [Sus scrofa]                     73   2e-14
Alignment   gi|NP_998933.1| swine leukocyte antigen 7 [Sus scrofa]                51   5e-08
Alignment   gi|NP_999362.2| neonatal Fc receptor FcRn [Sus scrofa]                45   5e-06

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

 Score = 79.7 bits (195), Expect = 1e-16
 Identities = 59/212 (27%), Positives = 92/212 (43%), Gaps = 10/212 (4%)
 Frame = +3

Query: 108 ACGGEDIAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYVDLEKKETVWQLPLFSKFTS 287
           A G  D   +H   Y +         G  +  +DGD+ F  +  +   V +LP F+ +  
Sbjct: 32  APGWRDELQNHTFQYTMYCQDGNPEVGL-SEVYDGDQLFSFNFSQNIRVPRLPEFADWAH 90

Query: 288 --------FDPQGALRNIA--VGKLTLNILTKRSNNTAAVNKVPEVTVFSKSPVILGQPN 437
                   F  +G  R +   VG L                 +P   VF+  P+  G+PN
Sbjct: 91  QIEDTPAIFFDKGFCREMIEKVGPLF-------EGKIPVSRGLPIAEVFTLKPLEFGKPN 143

Query: 438 TLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFLPSDDDFYDC 617
           TL+C V ++FPP + +TW ++  +  EG   T   + +D SF   SYL F P+  D + C
Sbjct: 144 TLVCFVSNLFPPALTVTW-EHHSAPVEGIGPTFVSATDDLSFQAFSYLNFTPTPSDLFSC 202

Query: 618 KVEHWGLDKPLLKHWEPEIPAPMSELTETVVC 713
            V H       + +W P+   P S+L E V+C
Sbjct: 203 VVTHELDGYVAISYWVPQNALP-SDLLENVLC 233


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

 Score = 72.8 bits (177), Expect = 2e-14
 Identities = 39/98 (39%), Positives = 54/98 (55%)
 Frame = +3

Query: 372 AVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRN 551
           AV + P+V V+S+ P   G+PN L C+V    PP I I  LKNG  +    S+ SF    
Sbjct: 20  AVARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SK 77

Query: 552 DHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 665
           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 = 51.2 bits (121), Expect = 5e-08
 Identities = 24/80 (30%), Positives = 37/80 (46%)
 Frame = +3

Query: 438 TLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFLPSDDDFYDC 617
           TL C     +P  I++TW + G   ++           D +F K + L   P ++  Y C
Sbjct: 221 TLRCWALGFYPKEISLTWQQEGQDQSQDVEVVETRPSGDGTFRKWAALVVPPGEEQSYTC 280

Query: 618 KVEHWGLDKPLLKHWEPEIP 677
            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 = 5e-06
 Identities = 30/85 (35%), Positives = 41/85 (48%)
 Frame = +3

Query: 435 NTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFLPSDDDFYD 614
           + L C   S +PP + + +L+NG  +  G  E+      D SF   S LT    D+  Y 
Sbjct: 218 SVLTCIAFSFYPPELQLRFLRNG--LAAGSGESDIGPNGDGSFHAWSSLTVKSGDEHHYC 275

Query: 615 CKVEHWGLDKPLLKHWEPEIPAPMS 689
           C V+H GL +PL    E E PA  S
Sbjct: 276 CVVQHAGLAQPLTV--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: 1,119,257
Number of Sequences: 1040
Number of extensions: 26255
Number of successful extensions: 65
Number of sequences better than 1.0e-05: 4
Number of HSP's better than  0.0 without gapping: 60
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): 62
length of database: 434,620
effective HSP length: 80
effective length of database: 351,420
effective search space used: 127565460
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= AMP01_0001_H11
         (1332 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...   378   e-105
Alignment   gi|XP_949973.1| PREDICTED: similar to HLA class II histocompati...   378   e-105
Alignment   gi|XP_949971.1| PREDICTED: similar to HLA class II histocompati...   378   e-105
Alignment   gi|XP_945969.1| PREDICTED: similar to HLA class II histocompati...   378   e-105
Alignment   gi|NP_064440.1| major histocompatibility complex, class II, DQ ...   375   e-104
Alignment   gi|NP_002113.2| major histocompatibility complex, class II, DQ ...   367   e-101
Alignment   gi|XP_941306.1| PREDICTED: similar to HLA class II histocompati...   357   1e-98
Alignment   gi|XP_941305.1| PREDICTED: similar to HLA class II histocompati...   357   1e-98
Alignment   gi|XP_941304.1| PREDICTED: similar to HLA class II histocompati...   357   1e-98
Alignment   gi|XP_941255.1| PREDICTED: similar to HLA class II histocompati...   357   1e-98

>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 =  378 bits (970), Expect = e-105
 Identities = 180/222 (81%), Positives = 197/222 (88%)
 Frame = +3

Query: 51  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYV 230
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYG SG Y+HEFDGDE+FYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYV 60

Query: 231 DLEKKETVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNNTAAVNKVPEVTVFSK 410
           DLE+KETVWQLPLF +F  FDPQ AL NIAV K  LNI+ KRSN+TAA N+VPEVTVFSK
Sbjct: 61  DLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSK 120

Query: 411 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 590
           SPV LGQPNTLIC VD+IFPPV+NITWL NGHSVTEG SETSFLS++DHSF KISYLTFL
Sbjct: 121 SPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFL 180

Query: 591 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 716
           PSDD+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTETVVCA
Sbjct: 181 PSDDEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETVVCA 222


>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 =  378 bits (970), Expect = e-105
 Identities = 180/222 (81%), Positives = 197/222 (88%)
 Frame = +3

Query: 51  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYV 230
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYG SG Y+HEFDGDE+FYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYV 60

Query: 231 DLEKKETVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNNTAAVNKVPEVTVFSK 410
           DLE+KETVWQLPLF +F  FDPQ AL NIAV K  LNI+ KRSN+TAA N+VPEVTVFSK
Sbjct: 61  DLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSK 120

Query: 411 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 590
           SPV LGQPNTLIC VD+IFPPV+NITWL NGHSVTEG SETSFLS++DHSF KISYLTFL
Sbjct: 121 SPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFL 180

Query: 591 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 716
           PSDD+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTETVVCA
Sbjct: 181 PSDDEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETVVCA 222


>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 =  378 bits (970), Expect = e-105
 Identities = 180/222 (81%), Positives = 197/222 (88%)
 Frame = +3

Query: 51  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYV 230
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYG SG Y+HEFDGDE+FYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYV 60

Query: 231 DLEKKETVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNNTAAVNKVPEVTVFSK 410
           DLE+KETVWQLPLF +F  FDPQ AL NIAV K  LNI+ KRSN+TAA N+VPEVTVFSK
Sbjct: 61  DLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSK 120

Query: 411 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 590
           SPV LGQPNTLIC VD+IFPPV+NITWL NGHSVTEG SETSFLS++DHSF KISYLTFL
Sbjct: 121 SPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFL 180

Query: 591 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 716
           PSDD+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTETVVCA
Sbjct: 181 PSDDEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETVVCA 222


>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 =  378 bits (970), Expect = e-105
 Identities = 180/222 (81%), Positives = 197/222 (88%)
 Frame = +3

Query: 51  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYV 230
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYG SG Y+HEFDGDE+FYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYV 60

Query: 231 DLEKKETVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNNTAAVNKVPEVTVFSK 410
           DLE+KETVWQLPLF +F  FDPQ AL NIAV K  LNI+ KRSN+TAA N+VPEVTVFSK
Sbjct: 61  DLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSK 120

Query: 411 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 590
           SPV LGQPNTLIC VD+IFPPV+NITWL NGHSVTEG SETSFLS++DHSF KISYLTFL
Sbjct: 121 SPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFL 180

Query: 591 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 716
           PSDD+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTETVVCA
Sbjct: 181 PSDDEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETVVCA 222


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

 Score =  375 bits (964), Expect = e-104
 Identities = 177/222 (79%), Positives = 197/222 (88%)
 Frame = +3

Query: 51  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYV 230
           M+  + L+ GALALTAVMS CGGEDI ADHVASYG+N YQS+G SG YTHEFDGDE+FYV
Sbjct: 1   MILNKALLLGALALTAVMSPCGGEDIVADHVASYGVNFYQSHGPSGQYTHEFDGDEEFYV 60

Query: 231 DLEKKETVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNNTAAVNKVPEVTVFSK 410
           DLE KETVWQLP+FSKF SFDPQ ALRN+AVGK TL  + ++SN+TAA N+VPEVTVFSK
Sbjct: 61  DLETKETVWQLPMFSKFISFDPQSALRNMAVGKHTLEFMMRQSNSTAATNEVPEVTVFSK 120

Query: 411 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 590
            PV LGQPNTLIC VD+IFPPV+NITWL NGHSVTEG SETSFLS++DHSF KISYLTFL
Sbjct: 121 FPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFL 180

Query: 591 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 716
           PS D+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET+VCA
Sbjct: 181 PSADEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETLVCA 222


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

 Score =  367 bits (941), Expect = e-101
 Identities = 175/222 (78%), Positives = 192/222 (86%)
 Frame = +3

Query: 51  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYV 230
           M+  + L+ GALALT VMS CGGEDI ADHVAS G+N+YQ YG SG YTHEFDGDEQFYV
Sbjct: 1   MILNKALLLGALALTTVMSPCGGEDIVADHVASCGVNLYQFYGPSGQYTHEFDGDEQFYV 60

Query: 231 DLEKKETVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNNTAAVNKVPEVTVFSK 410
           DLE+KET W+ P FSKF  FDPQGALRN+AV K  LNI+ KR N+TAA N+VPEVTVFSK
Sbjct: 61  DLERKETAWRWPEFSKFGGFDPQGALRNMAVAKHNLNIMIKRYNSTAATNEVPEVTVFSK 120

Query: 411 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 590
           SPV LGQPNTLIC VD+IFPPV+NITWL NG SVTEG SETSFLS++DHSF KISYLTFL
Sbjct: 121 SPVTLGQPNTLICLVDNIFPPVVNITWLSNGQSVTEGVSETSFLSKSDHSFFKISYLTFL 180

Query: 591 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 716
           PS D+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTETVVCA
Sbjct: 181 PSADEIYDCKVEHWGLDQPLLKHWEPEIPAPMSELTETVVCA 222


>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 =  357 bits (916), Expect = 1e-98
 Identities = 175/222 (78%), Positives = 190/222 (85%)
 Frame = +3

Query: 51  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYV 230
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYG SG YTHEFDGDEQFYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYV 60

Query: 231 DLEKKETVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNNTAAVNKVPEVTVFSK 410
           DL +KETVW LP+  +F  FDPQ AL NIAV K  LN L KRSN+TAA N+VPEVTVFSK
Sbjct: 61  DLGRKETVWCLPVLRQFR-FDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSK 119

Query: 411 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 590
           SPV LGQPN LIC VD+IFPPV+NITWL NGHSVTEG SETSFLS++DHSF KISYLT L
Sbjct: 120 SPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLL 179

Query: 591 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 716
           PS ++ YDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA
Sbjct: 180 PSAEESYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 221


>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 =  357 bits (916), Expect = 1e-98
 Identities = 175/222 (78%), Positives = 190/222 (85%)
 Frame = +3

Query: 51  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYV 230
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYG SG YTHEFDGDEQFYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYV 60

Query: 231 DLEKKETVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNNTAAVNKVPEVTVFSK 410
           DL +KETVW LP+  +F  FDPQ AL NIAV K  LN L KRSN+TAA N+VPEVTVFSK
Sbjct: 61  DLGRKETVWCLPVLRQFR-FDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSK 119

Query: 411 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 590
           SPV LGQPN LIC VD+IFPPV+NITWL NGHSVTEG SETSFLS++DHSF KISYLT L
Sbjct: 120 SPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLL 179

Query: 591 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 716
           PS ++ YDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA
Sbjct: 180 PSAEESYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 221


>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 =  357 bits (916), Expect = 1e-98
 Identities = 175/222 (78%), Positives = 190/222 (85%)
 Frame = +3

Query: 51  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYV 230
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYG SG YTHEFDGDEQFYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYV 60

Query: 231 DLEKKETVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNNTAAVNKVPEVTVFSK 410
           DL +KETVW LP+  +F  FDPQ AL NIAV K  LN L KRSN+TAA N+VPEVTVFSK
Sbjct: 61  DLGRKETVWCLPVLRQFR-FDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSK 119

Query: 411 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 590
           SPV LGQPN LIC VD+IFPPV+NITWL NGHSVTEG SETSFLS++DHSF KISYLT L
Sbjct: 120 SPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLL 179

Query: 591 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 716
           PS ++ YDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA
Sbjct: 180 PSAEESYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 221


>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 =  357 bits (916), Expect = 1e-98
 Identities = 175/222 (78%), Positives = 190/222 (85%)
 Frame = +3

Query: 51  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYV 230
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYG SG YTHEFDGDEQFYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYV 60

Query: 231 DLEKKETVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNNTAAVNKVPEVTVFSK 410
           DL +KETVW LP+  +F  FDPQ AL NIAV K  LN L KRSN+TAA N+VPEVTVFSK
Sbjct: 61  DLGRKETVWCLPVLRQFR-FDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSK 119

Query: 411 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 590
           SPV LGQPN LIC VD+IFPPV+NITWL NGHSVTEG SETSFLS++DHSF KISYLT L
Sbjct: 120 SPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLL 179

Query: 591 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 716
           PS ++ YDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA
Sbjct: 180 PSAEESYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 221


  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: 46,847,053
Number of Sequences: 39411
Number of extensions: 1155087
Number of successful extensions: 3524
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 3021
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): 3499
length of database: 17,774,539
effective HSP length: 105
effective length of database: 13,636,384
effective search space used: 4609097792
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= AMP01_0001_H11
         (1332 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...   327   2e-89
Alignment   gi|NP_032232.1| histocompatibility 2, O region alpha locus [Mus...   236   3e-62
Alignment   gi|NP_034511.2| histocompatibility 2, class II antigen E alpha ...   232   8e-61
Alignment   gi|NP_034516.2| histocompatibility 2, class II, locus DMa [Mus ...    84   3e-16
Alignment   gi|NP_033865.2| beta-2-microglobulin [Mus musculus]                   70   5e-12
Alignment   gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ...    68   2e-11
Alignment   gi|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus ...    65   2e-10
Alignment   gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ...    64   3e-10
Alignment   gi|NP_996988.1| histocompatibility 2, class II antigen A, beta ...    64   5e-10
Alignment   gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/...    60   4e-09

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

 Score =  327 bits (837), Expect = 2e-89
 Identities = 156/223 (69%), Positives = 179/223 (80%), Gaps = 1/223 (0%)
 Frame = +3

Query: 51  MVPGRVLMWGALALTAVMSACGGED-IAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFY 227
           M   R L+ G LALT ++S CGGED I ADHV +YG++VYQS G  G YT EFDGDE FY
Sbjct: 1   MPRSRALILGVLALTTMLSLCGGEDDIEADHVGTYGISVYQSPGDIGQYTFEFDGDELFY 60

Query: 228 VDLEKKETVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNNTAAVNKVPEVTVFS 407
           VDL+KKETVW LP F +  SFDPQG L+NIAV K  L +LTKRSN+T A N+ P+ TVF 
Sbjct: 61  VDLDKKETVWMLPEFGQLASFDPQGGLQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFP 120

Query: 408 KSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTF 587
           KSPV+LGQPNTLIC VD+IFPPVINITWL+N  SV +G  ETSF    D+SF K+SYLTF
Sbjct: 121 KSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTF 180

Query: 588 LPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 716
           +PSDDD YDCKVEHWGL++P+LKHWEPEIPAPMSELTETVVCA
Sbjct: 181 IPSDDDIYDCKVEHWGLEEPVLKHWEPEIPAPMSELTETVVCA 223


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

 Score =  236 bits (603), Expect = 3e-62
 Identities = 112/210 (53%), Positives = 147/210 (70%)
 Frame = +3

Query: 84  LALTAVMSACGGEDIAADHVASYGLNVYQSYGSSGYYTHEFDGDEQFYVDLEKKETVWQL 263
           L + + +S  G   I ADH+ SYG   YQSY +SG +THEFDG++ F VDL+ +E VW+L
Sbjct: 12  LTVMSFLSPRGVRAIKADHMGSYGPAFYQSYDASGQFTHEFDGEQIFSVDLKNEEVVWRL 71

Query: 264 PLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNNTAAVNKVPEVTVFSKSPVILGQPNTL 443
           P F  F   D Q  L +I++ K  L+IL +RSN T AV+  P VTV  K+ V LG+PN L
Sbjct: 72  PEFGDFAHSDFQSGLMSISMIKAHLDILVERSNRTRAVSVPPRVTVLPKTRVELGKPNVL 131

Query: 444 ICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFLPSDDDFYDCKV 623
           IC VD IFPPVIN+TWL+N   +T+G ++TSF S+ +H F K  YLTF+PS +D YDCKV
Sbjct: 132 ICIVDDIFPPVINVTWLRNSQPITKGVAQTSFYSQPNHRFRKFHYLTFVPSAEDVYDCKV 191

Query: 624 EHWGLDKPLLKHWEPEIPAPMSELTETVVC 713
           EHWGLD PLL+HWEP++  P  + TET++C
Sbjct: 192 EHWGLDTPLLQHWEPQVLTPPPDTTETLIC 221


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

 Score =  232 bits (591), Expect = 8e-61
 Identities = 107/177 (60%), Positives = 131/177 (74%)
 Frame = +3

Query: 186 GYYTHEFDGDEQFYVDLEKKETVWQLPLFSKFTSFDPQGALRNIAVGKLTLNILTKRSNN 365
           G +  +FDGDE F+VD+EK ET+W+L  F+KF SF+ QGAL NIAV K  L+++ +RSNN
Sbjct: 45  GEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLDVMKERSNN 104

Query: 366 TAAVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLS 545
           T   N  PEVTV S+SPV LG+PN LIC +D   PPV+N+TW +NG  VTEG SET FL 
Sbjct: 105 TPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWFRNGRPVTEGVSETVFLP 164

Query: 546 RNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 716
           R+DH F K  YLTFLPS DDFYDC+V+HWGL++PL KHWE E    + E TE VVCA
Sbjct: 165 RDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEEPLRKHWEFEEKTLLPETTENVVCA 221


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

 Score = 84.0 bits (206), Expect = 3e-16
 Identities = 55/175 (31%), Positives = 80/175 (45%), Gaps = 5/175 (2%)
 Frame = +3

Query: 204 FDGDEQFYVDLEKKETVWQLPLFSKFTSFDPQGALRNIAVGK-----LTLNILTKRSNNT 368
           +D DE F  D  +   V QLP F+++     QG    IA  K     L   +  K     
Sbjct: 63  YDEDELFSFDFSQNTRVPQLPDFAEWAQ--GQGDASAIAFDKSFCEMLMREVSPKLEGQI 120

Query: 369 AAVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSR 548
                +P   VF+  P+  G+PNTL+C + ++FPP + + W  +   V EG S TS  + 
Sbjct: 121 PVSRGLPVAEVFTLKPLEFGKPNTLVCFISNLFPPTLTVNWQLHSAPV-EGASPTSISAV 179

Query: 549 NDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVC 713
           +  +F   SYL F P   D Y C V H       + +W P+   P S+L E  +C
Sbjct: 180 DGLTFQAFSYLNFTPEPFDLYSCTVTHEIDRYTAIAYWVPQNALP-SDLLENALC 233


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

 Score = 70.1 bits (170), Expect = 5e-12
 Identities = 35/102 (34%), Positives = 58/102 (56%), Gaps = 1/102 (0%)
 Frame = +3

Query: 372 AVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTE-GFSETSFLSR 548
           A+ K P++ V+S+ P   G+PN L C+V    PP I I  LKNG  + +   S+ SF   
Sbjct: 20  AIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSF--S 77

Query: 549 NDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEI 674
            D SF  +++  F P++ D Y C+V+H  + +P   +W+ ++
Sbjct: 78  KDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM 119


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

 Score = 67.8 bits (164), Expect = 2e-11
 Identities = 34/99 (34%), Positives = 47/99 (47%)
 Frame = +3

Query: 366 TAAVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLS 545
           T   N  PEVTV+ +   +L Q N L+C V   +P  I++ W +NG     G   T  + 
Sbjct: 116 TVERNVPPEVTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVR 175

Query: 546 RNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHW 662
             D +F     L  +P   D Y C VEH GL +P+   W
Sbjct: 176 NGDWTFQTTVMLEMIPELGDIYSCLVEHPGLLRPVSVAW 214


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

 Score = 64.7 bits (156), Expect = 2e-10
 Identities = 39/127 (30%), Positives = 60/127 (47%), Gaps = 1/127 (0%)
 Frame = +3

Query: 339 NILTKRSNNTAAVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSV-T 515
           N LT R+       + P V V   +P    +P  L C+V   +P  + ITW+KNG  V +
Sbjct: 106 NALTHRT-------RAPSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPS 158

Query: 516 EGFSETSFLSRNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 695
               E +     D ++  +SYL   PS  D Y C V+H G  +P+   W P + +P+  +
Sbjct: 159 HSNKEKTAQPNGDWTYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDWTPGL-SPIQTV 217

Query: 696 TETVVCA 716
             +V  A
Sbjct: 218 KVSVSAA 224


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

 Score = 64.3 bits (155), Expect = 3e-10
 Identities = 35/113 (30%), Positives = 55/113 (48%), Gaps = 1/113 (0%)
 Frame = +3

Query: 381 KVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSV-TEGFSETSFLSRNDH 557
           + P V V   +P    +P  L C+V   +P  + ITW+KNG  V +    E +     D 
Sbjct: 113 RAPSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPNGDW 172

Query: 558 SFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCA 716
           ++  +SYL   PS  D Y C V+H G  +P+   W P + +P+  +  +V  A
Sbjct: 173 TYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDWTPGL-SPIQTVKVSVSAA 224


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

 Score = 63.5 bits (153), Expect = 5e-10
 Identities = 30/103 (29%), Positives = 44/103 (42%)
 Frame = +3

Query: 387 PEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFL 566
           P V +       L   NTL+C V   +P  I + W +NG   T G S T  +   D +F 
Sbjct: 125 PNVVISLSRTEALNHHNTLVCSVTDFYPTQIKVRWFRNGQEETVGVSSTQLIRNGDWTFQ 184

Query: 567 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 695
            +  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 = 60.5 bits (145), Expect = 4e-09
 Identities = 29/108 (26%), Positives = 47/108 (43%)
 Frame = +3

Query: 387 PEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFL 566
           P+VTV+      L   N L+C V   +P  I + W +NG     G   T  +   D ++ 
Sbjct: 125 PKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNRDWTYQ 184

Query: 567 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVV 710
            +  L  +P   + Y C+VEH  L  P+   W     +  ++L   V+
Sbjct: 185 TLVMLEMVPRGGEVYTCQVEHPSLTSPVTVEWRARSTSAQNKLLSGVM 232


  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: 56,079,230
Number of Sequences: 45328
Number of extensions: 1347076
Number of successful extensions: 4073
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 3663
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): 4060
length of database: 21,768,885
effective HSP length: 107
effective length of database: 16,918,789
effective search space used: 5684713104
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)