Animal-Genome cDNA UTR01_0038_H10


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= UTR01_0038_H10
         (1178 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...   401   e-112
Alignment   gi|NP_001012693.1| major histocompatibility complex, class II, ...   384   e-107
Alignment   gi|NP_001012699.1| major histocompatibility complex, class II, ...   337   8e-93
Alignment   gi|NP_001012696.1| major histocompatibility complex, class II, ...   301   7e-82
Alignment   gi|XP_604082.2| PREDICTED: similar to HLA class II histocompati...   238   5e-63
Alignment   gi|XP_883292.1| PREDICTED: similar to HLA class II histocompati...   236   3e-62
Alignment   gi|NP_001012695.1| major histocompatibility complex, class II, ...   223   3e-58
Alignment   gi|NP_776318.1| beta-2-microglobulin [Bos taurus]                     73   5e-13
Alignment   gi|NP_001012692.2| major histocompatibility complex, class II, ...    65   8e-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 =  401 bits (1031), Expect = e-112
 Identities = 190/255 (74%), Positives = 213/255 (83%)
 Frame = +1

Query: 55  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 234
           MV  R L+ GALALT +MS  G EDI ADH+ +YG+++Y +YGPSGYYTHEFDGDEEFYV
Sbjct: 1   MVLNRALILGALALTTMMSPSGSEDIVADHIGTYGISIYHTYGPSGYYTHEFDGDEEFYV 60

Query: 235 DLEKKETVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFSK 414
           DLEK+ETVW+LP+FSKF +FDPQGALRNIAT KHNL IV +RSN+TAA NKVPEVTVFSK
Sbjct: 61  DLEKRETVWRLPVFSKFATFDPQGALRNIATTKHNLEIVIQRSNSTAATNKVPEVTVFSK 120

Query: 415 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 594
           SPV+LGQPNTLICHVD+IFPPVINITWL+NGHSVTEG SETSFL ++D+SFLKI+YLTFL
Sbjct: 121 SPVMLGQPNTLICHVDNIFPPVINITWLRNGHSVTEGVSETSFLIKSDYSFLKINYLTFL 180

Query: 595 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXX 774
           PSDDD YDCKVEHWGLD+PLLKHWEP+IPAPMSELTET                      
Sbjct: 181 PSDDDVYDCKVEHWGLDEPLLKHWEPDIPAPMSELTETVVCALGLTVGLVGIMVGTILII 240

Query: 775 QGLRSGGPSRHQGSL 819
           QGLRSGGPSRHQG L
Sbjct: 241 QGLRSGGPSRHQGPL 255


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

 Score =  384 bits (986), Expect = e-107
 Identities = 186/255 (72%), Positives = 205/255 (80%)
 Frame = +1

Query: 55  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 234
           MV  R L+ G LALT +MS  GGEDI ADHV  YG+++YQSYGPSG YTHEFDGDE+FYV
Sbjct: 1   MVLNRALILGTLALTTMMSPSGGEDIVADHVGIYGISIYQSYGPSGQYTHEFDGDEQFYV 60

Query: 235 DLEKKETVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFSK 414
           DLEKKET WQLPLFS+  SFDPQ ALRNIA +K +++ +TK SN+TAA NKVPEVTVFSK
Sbjct: 61  DLEKKETAWQLPLFSRMLSFDPQLALRNIAIMKLHVDFLTKFSNSTAATNKVPEVTVFSK 120

Query: 415 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 594
           SPV+LGQPNTLICHVD+IFPPVINITWL+NGHSVTEG SETSFL R+D+SFLKI YL FL
Sbjct: 121 SPVMLGQPNTLICHVDNIFPPVINITWLRNGHSVTEGVSETSFLIRSDYSFLKIKYLAFL 180

Query: 595 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXX 774
           PSDDD YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET                      
Sbjct: 181 PSDDDIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETVVCTLGLTMGLVGITVGTIFII 240

Query: 775 QGLRSGGPSRHQGSL 819
           QGLRSG PSRHQG L
Sbjct: 241 QGLRSGDPSRHQGPL 255


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

 Score =  337 bits (865), Expect = 8e-93
 Identities = 157/204 (76%), Positives = 177/204 (86%)
 Frame = +1

Query: 55  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 234
           MV  R L+ GALALT +MS+ GGEDI ADHV SYG  +YQS+GPSG YT EFDGDE FYV
Sbjct: 1   MVLNRALILGALALTTMMSSSGGEDIVADHVGSYGTEIYQSHGPSGQYTQEFDGDEMFYV 60

Query: 235 DLEKKETVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFSK 414
           DL KKETVW+LP+FS+F  FDPQ AL  IAT KHNL+++TKRSN T  +N+VPEVTVFSK
Sbjct: 61  DLGKKETVWRLPMFSQFAGFDPQAALSEIATAKHNLDVLTKRSNFTPVINEVPEVTVFSK 120

Query: 415 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 594
           SPV+LGQPNTLICHVD+IFPPVINITWLKNGH+VTEG SETSFL ++DHSFLKI YLTFL
Sbjct: 121 SPVMLGQPNTLICHVDNIFPPVINITWLKNGHAVTEGVSETSFLPKDDHSFLKIGYLTFL 180

Query: 595 PSDDDFYDCKVEHWGLDKPLLKHW 666
           PSD+D YDCKVEHWGLD+PLLKHW
Sbjct: 181 PSDNDIYDCKVEHWGLDEPLLKHW 204


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

 Score =  301 bits (771), Expect = 7e-82
 Identities = 141/214 (65%), Positives = 168/214 (78%)
 Frame = +1

Query: 67  RVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYVDLEK 246
           + L+  AL L  +MS  GGEDI ADHV +YG NVYQ+YG SG +T EFDGDE FYVDL K
Sbjct: 3   KALILRALTLATMMSPYGGEDIVADHVGTYGTNVYQTYGASGQFTFEFDGDELFYVDLGK 62

Query: 247 KETVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFSKSPVI 426
           KETVW+LP FS  T F+ Q ALRNI   K NL+I+ K S+ T A +++PEV VF KS V+
Sbjct: 63  KETVWRLPEFSNITKFEVQSALRNIVMSKRNLDILIKNSSFTPATSEIPEVAVFPKSSVV 122

Query: 427 LGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFLPSDD 606
           LG PNTLIC VD+IFPPVINITW  NGH V EG +ET+F  ++DHSFLK SYLTFLP+++
Sbjct: 123 LGIPNTLICQVDNIFPPVINITWFYNGHFVAEGIAETTFYPKSDHSFLKFSYLTFLPTNE 182

Query: 607 DFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 708
           DFYDC+VEHWGL++PL+KHWEPEIP P SELTET
Sbjct: 183 DFYDCRVEHWGLEEPLVKHWEPEIPTPTSELTET 216


>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 =  238 bits (608), Expect = 5e-63
 Identities = 114/212 (53%), Positives = 146/212 (68%)
 Frame = +1

Query: 73  LMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYVDLEKKE 252
           L+ G   L  ++S      I ADH+ SYG   YQSY  +G +T++FDG++ F VDL+K+E
Sbjct: 7   LVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSVDLKKRE 66

Query: 253 TVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFSKSPVILG 432
            VW+LP F  F  FDPQ  L +IA +K +L  + KRSN T A N  P V V  KS V LG
Sbjct: 67  AVWRLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNVSPRVAVLPKSHVQLG 126

Query: 433 QPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFLPSDDDF 612
           +PN LIC VD IFPPVINITWL+NGH VT+G +++SF ++ DH F K  YLTF+P  DDF
Sbjct: 127 EPNVLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTFVPLVDDF 186

Query: 613 YDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 708
           YDCKVEHWGLD+PL +HWEP++P  + + T T
Sbjct: 187 YDCKVEHWGLDQPLFQHWEPQVPTALPDTTGT 218


>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 =  236 bits (602), Expect = 3e-62
 Identities = 114/213 (53%), Positives = 147/213 (69%), Gaps = 1/213 (0%)
 Frame = +1

Query: 73  LMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYVDLEKKE 252
           L+ G   L  ++S      I ADH+ SYG   YQSY  +G +T++FDG++ F VDL+K+E
Sbjct: 7   LVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSVDLKKRE 66

Query: 253 TVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVN-KVPEVTVFSKSPVIL 429
            VW+LP F  F  FDPQ  L +IA +K +L  + KRSN T A N   P+V V  KS V L
Sbjct: 67  AVWRLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNGSTPQVAVLPKSHVQL 126

Query: 430 GQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFLPSDDD 609
           G+PN LIC VD IFPPVINITWL+NGH VT+G +++SF ++ DH F K  YLTF+P  DD
Sbjct: 127 GEPNVLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTFVPLVDD 186

Query: 610 FYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 708
           FYDCKVEHWGLD+PL +HWEP++P  + + T T
Sbjct: 187 FYDCKVEHWGLDQPLFQHWEPQVPTALPDTTGT 219


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

 Score =  223 bits (567), Expect = 3e-58
 Identities = 108/211 (51%), Positives = 134/211 (63%)
 Frame = +1

Query: 187 SGYYTHEFDGDEEFYVDLEKKETVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSN 366
           S  +  +FDGDE F+VD+ KKETVW+LP F  F SF+ QGAL N+A +K NL+I+ KRSN
Sbjct: 43  SAEFMFDFDGDEIFHVDMGKKETVWRLPEFGHFASFEAQGALANMAVMKANLDIMIKRSN 102

Query: 367 NTAAVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFL 546
           NT   N  PEVT+    PV LG+PNTLIC +D   PPVI++TWL+NG  VT+G S+T FL
Sbjct: 103 NTPNTNVPPEVTLLPNKPVELGEPNTLICFIDKFSPPVISVTWLRNGKPVTDGVSQTVFL 162

Query: 547 SRNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXX 726
            RNDH F K  YL FLP+ +D YDCKVEH GL++PLLKHWE E PAP+ E TE       
Sbjct: 163 PRNDHLFRKFHYLPFLPTTEDVYDCKVEHLGLNEPLLKHWEYEAPAPLPETTENAVCALG 222

Query: 727 XXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 819
                           +G+R       +G L
Sbjct: 223 LIVALVGIIAGTIFIIKGVRKANTVERRGPL 253


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

 Score = 72.8 bits (177), Expect = 5e-13
 Identities = 36/101 (35%), Positives = 57/101 (56%)
 Frame = +1

Query: 376 AVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRN 555
           A+ + P++ V+S+ P   G+PN L C+V    PP I I  LKNG  +    S+ SF    
Sbjct: 20  AIQRPPKIQVYSRHPPEDGKPNYLNCYVYGFHPPQIEIDLLKNGEKIKSEQSDLSF--SK 77

Query: 556 DHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEI 678
           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 = 65.5 bits (158), Expect = 8e-11
 Identities = 45/181 (24%), Positives = 81/181 (44%), Gaps = 3/181 (1%)
 Frame = +1

Query: 172 QSYGPSGYYTHEFDGDEEFYVDLEKKETVWQLPLFSKFTSF--DPQGALRNIATLKHNLN 345
           Q + P+   +  +D D+ F  D  +   V +LP F+ +     D    + +    +  + 
Sbjct: 51  QDWSPNVALSESYDEDQLFSFDFSQSIRVPRLPEFADWAHQHGDTSDIMFDKGFCRAMIE 110

Query: 346 IVTKRSNNTAAVNK-VPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTE 522
            +         V++  P V VF+  P+  G+PNTL+C + ++FPP + + W ++  +  E
Sbjct: 111 EIGPELEGQIPVSRGFPIVQVFTLKPLEFGKPNTLVCFISNLFPPTLTVNW-QHQSAPVE 169

Query: 523 GFSETSFLSRNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELT 702
           G   T   + +  +F   SYL   P+  D + C V H       +  W P+   P S+L 
Sbjct: 170 GAGPTFVSAVDGLTFQAFSYLNVTPAPSDLFSCIVTHEIDGYTAIAFWVPQNALP-SDLL 228

Query: 703 E 705
           E
Sbjct: 229 E 229


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

 Score = 61.6 bits (148), Expect = 1e-09
 Identities = 30/103 (29%), Positives = 43/103 (41%)
 Frame = +1

Query: 391 PEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFL 570
           P VT+       L   N L+C V   +P  I + W +NG   T G   T  +   D +F 
Sbjct: 129 PTVTISLSRTEALNHHNLLVCSVTDFYPGQIKVRWFQNGKEETAGIVSTPLIRNGDWTFQ 188

Query: 571 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 699
            +  L   P   D Y C VEH  L  P+   W  +  +  S++
Sbjct: 189 ILVMLEMTPKRGDVYTCHVEHPSLQSPISVEWRAQSESAQSKM 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: 38,338,998
Number of Sequences: 33508
Number of extensions: 952053
Number of successful extensions: 2904
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 2622
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): 2891
length of database: 16,112,626
effective HSP length: 103
effective length of database: 12,661,302
effective search space used: 3659116278
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= UTR01_0038_H10
         (1178 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...   387   e-107
Alignment   gi|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris]    230   2e-60
Alignment   gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati...   228   7e-60
Alignment   gi|XP_532104.2| PREDICTED: similar to HLA class II histocompati...   100   5e-21
Alignment   gi|XP_538853.2| PREDICTED: similar to major histocompatibility ...    72   8e-13
Alignment   gi|XP_861572.1| PREDICTED: similar to major histocompatibility ...    67   4e-11
Alignment   gi|XP_535458.1| PREDICTED: similar to beta-2-microglobulin prec...    66   6e-11
Alignment   gi|XP_850148.1| PREDICTED: similar to beta-2-microglobulin prec...    66   6e-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...    65   1e-10

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

 Score =  387 bits (994), Expect = e-107
 Identities = 186/255 (72%), Positives = 206/255 (80%)
 Frame = +1

Query: 55  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 234
           M+  RVL+ G L LT +MS  GGE+I ADHVA+YG+NVYQSYGPSG YTHEFDGDEEFYV
Sbjct: 1   MILNRVLILGTLILTIMMSPSGGEEIVADHVANYGINVYQSYGPSGQYTHEFDGDEEFYV 60

Query: 235 DLEKKETVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFSK 414
           DLEKKETVW+LP+FS F SFDPQGALRN+A +K NLNI+TKRSN TAA N+VPEVTVFSK
Sbjct: 61  DLEKKETVWRLPVFSTFRSFDPQGALRNLAIIKQNLNIMTKRSNQTAATNEVPEVTVFSK 120

Query: 415 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 594
           SPV+LGQPNTLIC VD+IFPPVIN+TWLKN HSVTEG SETSF ++ DHSF KISYLTFL
Sbjct: 121 SPVMLGQPNTLICLVDNIFPPVINVTWLKNRHSVTEGVSETSFFAKGDHSFSKISYLTFL 180

Query: 595 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXX 774
           PS +D YDCKVEHWGLD+PLLKHWEPE+P PMSELTET                      
Sbjct: 181 PSAEDIYDCKVEHWGLDEPLLKHWEPEVPTPMSELTETVVCALGLAVGLVGIVMGTVFII 240

Query: 775 QGLRSGGPSRHQGSL 819
           QGLRSGG SRHQG L
Sbjct: 241 QGLRSGGTSRHQGPL 255


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

 Score =  230 bits (586), Expect = 2e-60
 Identities = 110/179 (61%), Positives = 130/179 (72%)
 Frame = +1

Query: 169 YQSYGPSGYYTHEFDGDEEFYVDLEKKETVWQLPLFSKFTSFDPQGALRNIATLKHNLNI 348
           Y +  PSG +  +FDGDE F+VD+EKKETVW+L  F +F SF+ QGAL NIA  K NL+ 
Sbjct: 38  YLTPDPSGEFMFDFDGDEIFHVDMEKKETVWRLEEFGRFASFEAQGALANIAVDKANLDT 97

Query: 349 VTKRSNNTAAVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGF 528
           + KRSN+T   N  PEVTV S +PV LG+PN LIC +D   PPVIN+TWL+NG+ VT G 
Sbjct: 98  MIKRSNHTPNTNVPPEVTVLSNTPVELGEPNILICFIDKFSPPVINVTWLRNGNPVTTGV 157

Query: 529 SETSFLSRNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 705
           SET FL R DH F K  YL FLPS +D YDCKVEHWGLD+PLLKHWE E P P+ E TE
Sbjct: 158 SETIFLPREDHLFRKFHYLPFLPSAEDVYDCKVEHWGLDEPLLKHWEFEPPTPLPETTE 216


>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 =  228 bits (582), Expect = 7e-60
 Identities = 105/195 (53%), Positives = 138/195 (70%), Gaps = 7/195 (3%)
 Frame = +1

Query: 145 VASYGLNVYQSYGPSGYYTHEFDGDEEFYVDLEKKETVWQLPLFSKFTSFDPQGALRNIA 324
           + SYG   YQSYG SG + HEFDG++ F V+L+K++ VW+LP F     FDPQ  L +IA
Sbjct: 1   MGSYGPAFYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEFGNLAHFDPQNGLASIA 60

Query: 325 TLKHNLNIVTKRSNNTAAVNKV-------PEVTVFSKSPVILGQPNTLICHVDSIFPPVI 483
            +K +L+++ +RSN T A+N         P V V  K  V LGQPN LIC VD+IFPPVI
Sbjct: 61  VIKAHLDVLVERSNRTRAINGTHLSSPLPPRVAVLPKFRVELGQPNVLICIVDNIFPPVI 120

Query: 484 NITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKH 663
           NITWL+NG  ++EG ++TSF S+ DH F K  YLTF+PS +D YDCKVEHWGL++PLL+H
Sbjct: 121 NITWLRNGQIISEGVAQTSFYSQPDHLFRKFCYLTFVPSAEDMYDCKVEHWGLEEPLLRH 180

Query: 664 WEPEIPAPMSELTET 708
           WEP++P P+ +  ET
Sbjct: 181 WEPQVPIPVPDTIET 195


>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 = 99.8 bits (247), Expect = 5e-21
 Identities = 49/108 (45%), Positives = 70/108 (64%)
 Frame = +1

Query: 130 IAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYVDLEKKETVWQLPLFSKFTSFDPQGA 309
           I ADH+ SYG   YQSYG SG + HEFDG++ F V+L+K++ VW+LP F     FDPQ  
Sbjct: 12  IEADHMGSYGPAFYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEFGNLAHFDPQNG 71

Query: 310 LRNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFSKSPVILGQPNTLIC 453
           L +IA +K +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 = 72.4 bits (176), Expect = 8e-13
 Identities = 50/181 (27%), Positives = 84/181 (46%), Gaps = 3/181 (1%)
 Frame = +1

Query: 172 QSYGPSGYYTHEFDGDEEFYVDLEKKETVWQLPLFSKFT--SFDPQGALRNIATLKHNLN 345
           Q++ PS      +DGD+ F  +  +   V +LP F+ +   S D      + A  +  + 
Sbjct: 57  QNWSPSIGLLEAYDGDQLFSFNFSQNTRVPRLPEFADWAQKSGDMPTISFDKAFCQAMIE 116

Query: 346 IVTKRSNNTAAVNK-VPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTE 522
            +  +      V++  P V VF+  P+  G+PN L+C + ++FPP + + W  +   V E
Sbjct: 117 EIGPKLEGQIPVSRGFPMVDVFTLKPLEFGKPNMLVCFISNLFPPTLTVNWWHHLDPV-E 175

Query: 523 GFSETSFLSRNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELT 702
           G   T   + +  SF   SYL F P+  D + C V H   +   + +W P    P S+L 
Sbjct: 176 GIGPTFVSAVDGFSFQAFSYLNFTPAPSDLFSCVVTHEIDNYTAIAYWVPHDALP-SDLL 234

Query: 703 E 705
           E
Sbjct: 235 E 235


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

 Score = 66.6 bits (161), Expect = 4e-11
 Identities = 40/131 (30%), Positives = 62/131 (47%)
 Frame = +1

Query: 313 RNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINIT 492
           R  A L   L+++     +  A    P V VF+  P+  G+PN L+C + ++FPP + + 
Sbjct: 12  RQGAALLRLLHLLWLLPYSRTAPEGFPMVDVFTLKPLEFGKPNMLVCFISNLFPPTLTVN 71

Query: 493 WLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEP 672
           W  +   V EG   T   + +  SF   SYL F P+  D + C V H   +   + +W P
Sbjct: 72  WWHHLDPV-EGIGPTFVSAVDGFSFQAFSYLNFTPAPSDLFSCVVTHEIDNYTAIAYWVP 130

Query: 673 EIPAPMSELTE 705
               P S+L E
Sbjct: 131 HDALP-SDLLE 140


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

 Score = 66.2 bits (160), Expect = 6e-11
 Identities = 33/98 (33%), Positives = 53/98 (54%)
 Frame = +1

Query: 376 AVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRN 555
           AV   P++ V+S+ P   G+PN L C+V    PP I I  LKNG  +    ++ SF    
Sbjct: 27  AVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSF--SK 84

Query: 556 DHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 669
           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 = 66.2 bits (160), Expect = 6e-11
 Identities = 33/98 (33%), Positives = 53/98 (54%)
 Frame = +1

Query: 376 AVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRN 555
           AV   P++ V+S+ P   G+PN L C+V    PP I I  LKNG  +    ++ SF    
Sbjct: 27  AVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSF--SK 84

Query: 556 DHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 669
           D +F  + +  F P++ D + C+V+H  L +P +  W+
Sbjct: 85  DWTFYLLVHTEFTPNEQDEFSCRVKHVTLSEPQIVKWD 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 = +1

Query: 391 PEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFL 570
           P VT+F     +L   N L+C V   +P  I + W +N    T G   T  +   D +F 
Sbjct: 129 PTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLIRNGDWTFQ 188

Query: 571 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 699
            +  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 = 65.1 bits (157), Expect = 1e-10
 Identities = 33/123 (26%), Positives = 54/123 (43%)
 Frame = +1

Query: 331 KHNLNIVTKRSNNTAAVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGH 510
           +HN  ++    + T      P VTV+      L   N L+C V+  +P  I + WL+NG 
Sbjct: 109 RHNYGVI---ESFTVQRRVEPTVTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQ 165

Query: 511 SVTEGFSETSFLSRNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPM 690
               G   T  +   D +F  +  L  +P   + Y C+VEH  L  P+   W  +  +  
Sbjct: 166 EEEAGVVSTGLIRNGDWTFQILVMLEIVPQSGEVYTCQVEHPSLTSPVTVEWRAQSDSAQ 225

Query: 691 SEL 699
           S++
Sbjct: 226 SKM 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: 45,018,437
Number of Sequences: 33732
Number of extensions: 1117324
Number of successful extensions: 3443
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 2957
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): 3427
length of database: 19,266,565
effective HSP length: 105
effective length of database: 15,724,705
effective search space used: 4512990335
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= UTR01_0038_H10
         (1178 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...   396   e-110
Alignment   gi|XP_949973.1| PREDICTED: similar to HLA class II histocompati...   396   e-110
Alignment   gi|XP_949971.1| PREDICTED: similar to HLA class II histocompati...   396   e-110
Alignment   gi|XP_945969.1| PREDICTED: similar to HLA class II histocompati...   396   e-110
Alignment   gi|NP_064440.1| major histocompatibility complex, class II, DQ ...   383   e-106
Alignment   gi|NP_002113.2| major histocompatibility complex, class II, DQ ...   379   e-105
Alignment   gi|XP_941306.1| PREDICTED: similar to HLA class II histocompati...   370   e-102
Alignment   gi|XP_941305.1| PREDICTED: similar to HLA class II histocompati...   370   e-102
Alignment   gi|XP_941304.1| PREDICTED: similar to HLA class II histocompati...   370   e-102
Alignment   gi|XP_941255.1| PREDICTED: similar to HLA class II histocompati...   370   e-102

>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 =  396 bits (1017), Expect = e-110
 Identities = 192/255 (75%), Positives = 208/255 (81%)
 Frame = +1

Query: 55  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 234
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG Y+HEFDGDEEFYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYV 60

Query: 235 DLEKKETVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFSK 414
           DLE+KETVWQLPLF +F  FDPQ AL NIA LKHNLNIV KRSN+TAA N+VPEVTVFSK
Sbjct: 61  DLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSK 120

Query: 415 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 594
           SPV LGQPNTLIC VD+IFPPV+NITWL NGHSVTEG SETSFLS++DHSF KISYLTFL
Sbjct: 121 SPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFL 180

Query: 595 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXX 774
           PSDD+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET                      
Sbjct: 181 PSDDEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVLII 240

Query: 775 QGLRSGGPSRHQGSL 819
           +GLRS G SRHQG L
Sbjct: 241 RGLRSVGASRHQGPL 255


>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 =  396 bits (1017), Expect = e-110
 Identities = 192/255 (75%), Positives = 208/255 (81%)
 Frame = +1

Query: 55  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 234
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG Y+HEFDGDEEFYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYV 60

Query: 235 DLEKKETVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFSK 414
           DLE+KETVWQLPLF +F  FDPQ AL NIA LKHNLNIV KRSN+TAA N+VPEVTVFSK
Sbjct: 61  DLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSK 120

Query: 415 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 594
           SPV LGQPNTLIC VD+IFPPV+NITWL NGHSVTEG SETSFLS++DHSF KISYLTFL
Sbjct: 121 SPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFL 180

Query: 595 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXX 774
           PSDD+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET                      
Sbjct: 181 PSDDEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVLII 240

Query: 775 QGLRSGGPSRHQGSL 819
           +GLRS G SRHQG L
Sbjct: 241 RGLRSVGASRHQGPL 255


>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 =  396 bits (1017), Expect = e-110
 Identities = 192/255 (75%), Positives = 208/255 (81%)
 Frame = +1

Query: 55  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 234
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG Y+HEFDGDEEFYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYV 60

Query: 235 DLEKKETVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFSK 414
           DLE+KETVWQLPLF +F  FDPQ AL NIA LKHNLNIV KRSN+TAA N+VPEVTVFSK
Sbjct: 61  DLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSK 120

Query: 415 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 594
           SPV LGQPNTLIC VD+IFPPV+NITWL NGHSVTEG SETSFLS++DHSF KISYLTFL
Sbjct: 121 SPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFL 180

Query: 595 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXX 774
           PSDD+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET                      
Sbjct: 181 PSDDEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVLII 240

Query: 775 QGLRSGGPSRHQGSL 819
           +GLRS G SRHQG L
Sbjct: 241 RGLRSVGASRHQGPL 255


>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 =  396 bits (1017), Expect = e-110
 Identities = 192/255 (75%), Positives = 208/255 (81%)
 Frame = +1

Query: 55  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 234
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG Y+HEFDGDEEFYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYV 60

Query: 235 DLEKKETVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFSK 414
           DLE+KETVWQLPLF +F  FDPQ AL NIA LKHNLNIV KRSN+TAA N+VPEVTVFSK
Sbjct: 61  DLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSK 120

Query: 415 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 594
           SPV LGQPNTLIC VD+IFPPV+NITWL NGHSVTEG SETSFLS++DHSF KISYLTFL
Sbjct: 121 SPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFL 180

Query: 595 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXX 774
           PSDD+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET                      
Sbjct: 181 PSDDEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVLII 240

Query: 775 QGLRSGGPSRHQGSL 819
           +GLRS G SRHQG L
Sbjct: 241 RGLRSVGASRHQGPL 255


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

 Score =  383 bits (984), Expect = e-106
 Identities = 186/255 (72%), Positives = 204/255 (80%)
 Frame = +1

Query: 55  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 234
           M+  + L+ GALALTAVMS CGGEDI ADHVASYG+N YQS+GPSG YTHEFDGDEEFYV
Sbjct: 1   MILNKALLLGALALTAVMSPCGGEDIVADHVASYGVNFYQSHGPSGQYTHEFDGDEEFYV 60

Query: 235 DLEKKETVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFSK 414
           DLE KETVWQLP+FSKF SFDPQ ALRN+A  KH L  + ++SN+TAA N+VPEVTVFSK
Sbjct: 61  DLETKETVWQLPMFSKFISFDPQSALRNMAVGKHTLEFMMRQSNSTAATNEVPEVTVFSK 120

Query: 415 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 594
            PV LGQPNTLIC VD+IFPPV+NITWL NGHSVTEG SETSFLS++DHSF KISYLTFL
Sbjct: 121 FPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFL 180

Query: 595 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXX 774
           PS D+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET                      
Sbjct: 181 PSADEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETLVCALGLSVGLMGIVVGTVFII 240

Query: 775 QGLRSGGPSRHQGSL 819
           QGLRS G SRHQG L
Sbjct: 241 QGLRSVGASRHQGLL 255


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

 Score =  379 bits (973), Expect = e-105
 Identities = 184/255 (72%), Positives = 202/255 (79%)
 Frame = +1

Query: 55  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 234
           M+  + L+ GALALT VMS CGGEDI ADHVAS G+N+YQ YGPSG YTHEFDGDE+FYV
Sbjct: 1   MILNKALLLGALALTTVMSPCGGEDIVADHVASCGVNLYQFYGPSGQYTHEFDGDEQFYV 60

Query: 235 DLEKKETVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFSK 414
           DLE+KET W+ P FSKF  FDPQGALRN+A  KHNLNI+ KR N+TAA N+VPEVTVFSK
Sbjct: 61  DLERKETAWRWPEFSKFGGFDPQGALRNMAVAKHNLNIMIKRYNSTAATNEVPEVTVFSK 120

Query: 415 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 594
           SPV LGQPNTLIC VD+IFPPV+NITWL NG SVTEG SETSFLS++DHSF KISYLTFL
Sbjct: 121 SPVTLGQPNTLICLVDNIFPPVVNITWLSNGQSVTEGVSETSFLSKSDHSFFKISYLTFL 180

Query: 595 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXX 774
           PS D+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET                      
Sbjct: 181 PSADEIYDCKVEHWGLDQPLLKHWEPEIPAPMSELTETVVCALGLSVGLMGIVVGTVFII 240

Query: 775 QGLRSGGPSRHQGSL 819
           QGLRS G SRHQG L
Sbjct: 241 QGLRSVGASRHQGPL 255


>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 =  370 bits (951), Expect = e-102
 Identities = 183/255 (71%), Positives = 201/255 (78%)
 Frame = +1

Query: 55  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 234
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG YTHEFDGDE+FYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYV 60

Query: 235 DLEKKETVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFSK 414
           DL +KETVW LP+  +F  FDPQ AL NIA LKHNLN + KRSN+TAA N+VPEVTVFSK
Sbjct: 61  DLGRKETVWCLPVLRQFR-FDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSK 119

Query: 415 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 594
           SPV LGQPN LIC VD+IFPPV+NITWL NGHSVTEG SETSFLS++DHSF KISYLT L
Sbjct: 120 SPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLL 179

Query: 595 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXX 774
           PS ++ YDCKVEHWGLDKPLLKHWEPEIPAPMSELTET                      
Sbjct: 180 PSAEESYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVFII 239

Query: 775 QGLRSGGPSRHQGSL 819
           +GLRS G SRHQG L
Sbjct: 240 RGLRSVGASRHQGPL 254


>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 =  370 bits (951), Expect = e-102
 Identities = 183/255 (71%), Positives = 201/255 (78%)
 Frame = +1

Query: 55  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 234
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG YTHEFDGDE+FYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYV 60

Query: 235 DLEKKETVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFSK 414
           DL +KETVW LP+  +F  FDPQ AL NIA LKHNLN + KRSN+TAA N+VPEVTVFSK
Sbjct: 61  DLGRKETVWCLPVLRQFR-FDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSK 119

Query: 415 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 594
           SPV LGQPN LIC VD+IFPPV+NITWL NGHSVTEG SETSFLS++DHSF KISYLT L
Sbjct: 120 SPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLL 179

Query: 595 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXX 774
           PS ++ YDCKVEHWGLDKPLLKHWEPEIPAPMSELTET                      
Sbjct: 180 PSAEESYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVFII 239

Query: 775 QGLRSGGPSRHQGSL 819
           +GLRS G SRHQG L
Sbjct: 240 RGLRSVGASRHQGPL 254


>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 =  370 bits (951), Expect = e-102
 Identities = 183/255 (71%), Positives = 201/255 (78%)
 Frame = +1

Query: 55  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 234
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG YTHEFDGDE+FYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYV 60

Query: 235 DLEKKETVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFSK 414
           DL +KETVW LP+  +F  FDPQ AL NIA LKHNLN + KRSN+TAA N+VPEVTVFSK
Sbjct: 61  DLGRKETVWCLPVLRQFR-FDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSK 119

Query: 415 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 594
           SPV LGQPN LIC VD+IFPPV+NITWL NGHSVTEG SETSFLS++DHSF KISYLT L
Sbjct: 120 SPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLL 179

Query: 595 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXX 774
           PS ++ YDCKVEHWGLDKPLLKHWEPEIPAPMSELTET                      
Sbjct: 180 PSAEESYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVFII 239

Query: 775 QGLRSGGPSRHQGSL 819
           +GLRS G SRHQG L
Sbjct: 240 RGLRSVGASRHQGPL 254


>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 =  370 bits (951), Expect = e-102
 Identities = 183/255 (71%), Positives = 201/255 (78%)
 Frame = +1

Query: 55  MVPGRVLMWGALALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYV 234
           M+  + LM GALALT VMS CGGEDI ADHVASYG+N+YQSYGPSG YTHEFDGDE+FYV
Sbjct: 1   MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYV 60

Query: 235 DLEKKETVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFSK 414
           DL +KETVW LP+  +F  FDPQ AL NIA LKHNLN + KRSN+TAA N+VPEVTVFSK
Sbjct: 61  DLGRKETVWCLPVLRQFR-FDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSK 119

Query: 415 SPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFL 594
           SPV LGQPN LIC VD+IFPPV+NITWL NGHSVTEG SETSFLS++DHSF KISYLT L
Sbjct: 120 SPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLL 179

Query: 595 PSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXXX 774
           PS ++ YDCKVEHWGLDKPLLKHWEPEIPAPMSELTET                      
Sbjct: 180 PSAEESYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVFII 239

Query: 775 QGLRSGGPSRHQGSL 819
           +GLRS G SRHQG L
Sbjct: 240 RGLRSVGASRHQGPL 254


  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: 43,410,643
Number of Sequences: 39411
Number of extensions: 1112287
Number of successful extensions: 3552
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 3093
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): 3503
length of database: 17,774,539
effective HSP length: 104
effective length of database: 13,675,795
effective search space used: 3938628960
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= UTR01_0038_H10
         (1178 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]                    76   2e-15
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   4e-06

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

 Score = 75.9 bits (185), Expect = 2e-15
 Identities = 55/201 (27%), Positives = 90/201 (44%), Gaps = 3/201 (1%)
 Frame = +1

Query: 112 ACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYVDLEKKETVWQLPLFSKFTS 291
           A G  D   +H   Y +   Q   P    +  +DGD+ F  +  +   V +LP F+ +  
Sbjct: 32  APGWRDELQNHTFQYTMYC-QDGNPEVGLSEVYDGDQLFSFNFSQNIRVPRLPEFADWAH 90

Query: 292 F--DPQGALRNIATLKHNLNIVTKRSNNTAAVNK-VPEVTVFSKSPVILGQPNTLICHVD 462
              D      +    +  +  V         V++ +P   VF+  P+  G+PNTL+C V 
Sbjct: 91  QIEDTPAIFFDKGFCREMIEKVGPLFEGKIPVSRGLPIAEVFTLKPLEFGKPNTLVCFVS 150

Query: 463 SIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFLPSDDDFYDCKVEHWGL 642
           ++FPP + +TW ++  +  EG   T   + +D SF   SYL F P+  D + C V H   
Sbjct: 151 NLFPPALTVTW-EHHSAPVEGIGPTFVSATDDLSFQAFSYLNFTPTPSDLFSCVVTHELD 209

Query: 643 DKPLLKHWEPEIPAPMSELTE 705
               + +W P+   P S+L E
Sbjct: 210 GYVAISYWVPQNALP-SDLLE 229


>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 = +1

Query: 376 AVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRN 555
           AV + P+V V+S+ P   G+PN L C+V    PP I I  LKNG  +    S+ SF    
Sbjct: 20  AVARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SK 77

Query: 556 DHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 669
           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 = +1

Query: 442 TLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFLPSDDDFYDC 621
           TL C     +P  I++TW + G   ++           D +F K + L   P ++  Y C
Sbjct: 221 TLRCWALGFYPKEISLTWQQEGQDQSQDVEVVETRPSGDGTFRKWAALVVPPGEEQSYTC 280

Query: 622 KVEHWGLDKPLLKHWEPEIP 681
            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 = 30/85 (35%), Positives = 41/85 (48%)
 Frame = +1

Query: 439 NTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFLPSDDDFYD 618
           + L C   S +PP + + +L+NG  +  G  E+      D SF   S LT    D+  Y 
Sbjct: 218 SVLTCIAFSFYPPELQLRFLRNG--LAAGSGESDIGPNGDGSFHAWSSLTVKSGDEHHYC 275

Query: 619 CKVEHWGLDKPLLKHWEPEIPAPMS 693
           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: 1,027,399
Number of Sequences: 1040
Number of extensions: 24499
Number of successful extensions: 58
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): 55
length of database: 434,620
effective HSP length: 79
effective length of database: 352,460
effective search space used: 110319980
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= UTR01_0038_H10
         (1178 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...   338   5e-93
Alignment   gi|NP_032232.1| histocompatibility 2, O region alpha locus [Mus...   232   7e-61
Alignment   gi|NP_034511.2| histocompatibility 2, class II antigen E alpha ...   223   4e-58
Alignment   gi|NP_034516.2| histocompatibility 2, class II, locus DMa [Mus ...    76   6e-14
Alignment   gi|NP_033865.2| beta-2-microglobulin [Mus musculus]                   70   4e-12
Alignment   gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ...    68   2e-11
Alignment   gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ...    64   3e-10
Alignment   gi|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus ...    64   3e-10
Alignment   gi|NP_996988.1| histocompatibility 2, class II antigen A, beta ...    64   4e-10
Alignment   gi|NP_034512.1| histocompatibility 2, class II antigen E beta [...    60   4e-09

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

 Score =  338 bits (868), Expect = 5e-93
 Identities = 164/256 (64%), Positives = 189/256 (73%), Gaps = 1/256 (0%)
 Frame = +1

Query: 55  MVPGRVLMWGALALTAVMSACGGED-IAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFY 231
           M   R L+ G LALT ++S CGGED I ADHV +YG++VYQS G  G YT EFDGDE FY
Sbjct: 1   MPRSRALILGVLALTTMLSLCGGEDDIEADHVGTYGISVYQSPGDIGQYTFEFDGDELFY 60

Query: 232 VDLEKKETVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFS 411
           VDL+KKETVW LP F +  SFDPQG L+NIA +KHNL ++TKRSN+T A N+ P+ TVF 
Sbjct: 61  VDLDKKETVWMLPEFGQLASFDPQGGLQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFP 120

Query: 412 KSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTF 591
           KSPV+LGQPNTLIC VD+IFPPVINITWL+N  SV +G  ETSF    D+SF K+SYLTF
Sbjct: 121 KSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTF 180

Query: 592 LPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXXXXXXXXXXXXXXXXX 771
           +PSDDD YDCKVEHWGL++P+LKHWEPEIPAPMSELTET                     
Sbjct: 181 IPSDDDIYDCKVEHWGLEEPVLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTIFI 240

Query: 772 XQGLRSGGPSRHQGSL 819
            QGLRSGG SRH G L
Sbjct: 241 IQGLRSGGTSRHPGPL 256


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

 Score =  232 bits (591), Expect = 7e-61
 Identities = 110/207 (53%), Positives = 144/207 (69%)
 Frame = +1

Query: 88  LALTAVMSACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYVDLEKKETVWQL 267
           L + + +S  G   I ADH+ SYG   YQSY  SG +THEFDG++ F VDL+ +E VW+L
Sbjct: 12  LTVMSFLSPRGVRAIKADHMGSYGPAFYQSYDASGQFTHEFDGEQIFSVDLKNEEVVWRL 71

Query: 268 PLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNNTAAVNKVPEVTVFSKSPVILGQPNTL 447
           P F  F   D Q  L +I+ +K +L+I+ +RSN T AV+  P VTV  K+ V LG+PN L
Sbjct: 72  PEFGDFAHSDFQSGLMSISMIKAHLDILVERSNRTRAVSVPPRVTVLPKTRVELGKPNVL 131

Query: 448 ICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFLKISYLTFLPSDDDFYDCKV 627
           IC VD IFPPVIN+TWL+N   +T+G ++TSF S+ +H F K  YLTF+PS +D YDCKV
Sbjct: 132 ICIVDDIFPPVINVTWLRNSQPITKGVAQTSFYSQPNHRFRKFHYLTFVPSAEDVYDCKV 191

Query: 628 EHWGLDKPLLKHWEPEIPAPMSELTET 708
           EHWGLD PLL+HWEP++  P  + TET
Sbjct: 192 EHWGLDTPLLQHWEPQVLTPPPDTTET 218


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

 Score =  223 bits (567), Expect = 4e-58
 Identities = 103/172 (59%), Positives = 127/172 (73%)
 Frame = +1

Query: 190 GYYTHEFDGDEEFYVDLEKKETVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVTKRSNN 369
           G +  +FDGDE F+VD+EK ET+W+L  F+KF SF+ QGAL NIA  K NL+++ +RSNN
Sbjct: 45  GEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLDVMKERSNN 104

Query: 370 TAAVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLS 549
           T   N  PEVTV S+SPV LG+PN LIC +D   PPV+N+TW +NG  VTEG SET FL 
Sbjct: 105 TPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWFRNGRPVTEGVSETVFLP 164

Query: 550 RNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 705
           R+DH F K  YLTFLPS DDFYDC+V+HWGL++PL KHWE E    + E TE
Sbjct: 165 RDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEEPLRKHWEFEEKTLLPETTE 216


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

 Score = 76.3 bits (186), Expect = 6e-14
 Identities = 53/171 (30%), Positives = 78/171 (45%), Gaps = 5/171 (2%)
 Frame = +1

Query: 208 FDGDEEFYVDLEKKETVWQLPLFSKFTSFDPQGALRNIATLKHNLNIVT-----KRSNNT 372
           +D DE F  D  +   V QLP F+++     QG    IA  K    ++      K     
Sbjct: 63  YDEDELFSFDFSQNTRVPQLPDFAEWAQ--GQGDASAIAFDKSFCEMLMREVSPKLEGQI 120

Query: 373 AAVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSR 552
                +P   VF+  P+  G+PNTL+C + ++FPP + + W  +   V EG S TS  + 
Sbjct: 121 PVSRGLPVAEVFTLKPLEFGKPNTLVCFISNLFPPTLTVNWQLHSAPV-EGASPTSISAV 179

Query: 553 NDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 705
           +  +F   SYL F P   D Y C V H       + +W P+   P S+L E
Sbjct: 180 DGLTFQAFSYLNFTPEPFDLYSCTVTHEIDRYTAIAYWVPQNALP-SDLLE 229


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

 Score = 70.1 bits (170), Expect = 4e-12
 Identities = 35/102 (34%), Positives = 58/102 (56%), Gaps = 1/102 (0%)
 Frame = +1

Query: 376 AVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTE-GFSETSFLSR 552
           A+ K P++ V+S+ P   G+PN L C+V    PP I I  LKNG  + +   S+ SF   
Sbjct: 20  AIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSF--S 77

Query: 553 NDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEI 678
            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 = +1

Query: 370 TAAVNKVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLS 549
           T   N  PEVTV+ +   +L Q N L+C V   +P  I++ W +NG     G   T  + 
Sbjct: 116 TVERNVPPEVTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVR 175

Query: 550 RNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHW 666
             D +F     L  +P   D Y C VEH GL +P+   W
Sbjct: 176 NGDWTFQTTVMLEMIPELGDIYSCLVEHPGLLRPVSVAW 214


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

 Score = 63.9 bits (154), Expect = 3e-10
 Identities = 32/97 (32%), Positives = 47/97 (48%), Gaps = 1/97 (1%)
 Frame = +1

Query: 385 KVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSV-TEGFSETSFLSRNDH 561
           + P V V   +P    +P  L C+V   +P  + ITW+KNG  V +    E +     D 
Sbjct: 113 RAPSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPNGDW 172

Query: 562 SFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEP 672
           ++  +SYL   PS  D Y C V+H G  +P+   W P
Sbjct: 173 TYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDWTP 209


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

 Score = 63.9 bits (154), Expect = 3e-10
 Identities = 32/97 (32%), Positives = 47/97 (48%), Gaps = 1/97 (1%)
 Frame = +1

Query: 385 KVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSV-TEGFSETSFLSRNDH 561
           + P V V   +P    +P  L C+V   +P  + ITW+KNG  V +    E +     D 
Sbjct: 113 RAPSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPNGDW 172

Query: 562 SFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEP 672
           ++  +SYL   PS  D Y C V+H G  +P+   W P
Sbjct: 173 TYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDWTP 209


>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 = 44/103 (42%)
 Frame = +1

Query: 391 PEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFL 570
           P V +       L   NTL+C V   +P  I + W +NG   T G S T  +   D +F 
Sbjct: 125 PNVVISLSRTEALNHHNTLVCSVTDFYPTQIKVRWFRNGQEETVGVSSTQLIRNGDWTFQ 184

Query: 571 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 699
            +  L   P   + Y C VEH  L  P+   W  +  +  S++
Sbjct: 185 VLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRAQSESAWSKM 227


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

 Score = 60.1 bits (144), Expect = 4e-09
 Identities = 28/103 (27%), Positives = 46/103 (44%)
 Frame = +1

Query: 391 PEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSVTEGFSETSFLSRNDHSFL 570
           P VTV+      L   N L+C V   +P  I + W +NG     G   T  +   D +F 
Sbjct: 124 PTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQ 183

Query: 571 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 699
            +  L  +P   + Y C+VEH  L  P+   W+ +  +  +++
Sbjct: 184 TLVMLETVPQSGEVYTCQVEHPSLTDPVTVEWKAQSTSAQNKM 226


  Database: RefSeqMP
    Posted date:  Aug 2, 2006 12:58 AM
  Number of letters in database: 21,768,885
  Number of sequences in database:  45,328
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 51,725,210
Number of Sequences: 45328
Number of extensions: 1282957
Number of successful extensions: 4138
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 3706
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): 4126
length of database: 21,768,885
effective HSP length: 105
effective length of database: 17,009,445
effective search space used: 4881710715
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)