Animal-Genome cDNA ITT01_0100_B02


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= ITT01_0100_B02
         (1398 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001012695.1| major histocompatibility complex, class II, ...   352   3e-97
Alignment   gi|XP_604082.2| PREDICTED: similar to HLA class II histocompati...   234   2e-61
Alignment   gi|XP_883292.1| PREDICTED: similar to HLA class II histocompati...   230   2e-60
Alignment   gi|NP_001013619.2| histocompatibility complex, class II, DQ alp...   220   2e-57
Alignment   gi|NP_001012693.1| major histocompatibility complex, class II, ...   206   3e-53
Alignment   gi|NP_001012696.1| major histocompatibility complex, class II, ...   206   5e-53
Alignment   gi|NP_001012699.1| major histocompatibility complex, class II, ...   199   3e-51
Alignment   gi|XP_608813.2| PREDICTED: similar to serine/threonine protein ...   104   1e-22
Alignment   gi|NP_001012692.2| major histocompatibility complex, class II, ...    68   2e-11
Alignment   gi|NP_001029840.2| MHC class II antigen [Bos taurus]                  59   7e-09

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

 Score =  352 bits (904), Expect = 3e-97
 Identities = 173/253 (68%), Positives = 192/253 (75%), Gaps = 1/253 (0%)
 Frame = +1

Query: 223 MTILGVPVLGFVITIL-NLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDM 399
           M I  VP+LG  IT+L  LQ+SWAI ENHVIIQAEFYL P++S EFMFDFDGDEIFHVDM
Sbjct: 1   MAITRVPILGLFITVLIGLQESWAIKENHVIIQAEFYLKPEESAEFMFDFDGDEIFHVDM 60

Query: 400 EKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKP 579
            K+ETVWRL EFGHFASFEAQGALAN+AV KANL+I+IKRS              L +KP
Sbjct: 61  GKKETVWRLPEFGHFASFEAQGALANMAVMKANLDIMIKRSNNTPNTNVPPEVTLLPNKP 120

Query: 580 VELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPS 759
           VELGEPN LICFIDKFSPPV++VTWLRNG PVT GV +TVFLPR DHLFRKFHYLPF+P+
Sbjct: 121 VELGEPNTLICFIDKFSPPVISVTWLRNGKPVTDGVSQTVFLPRNDHLFRKFHYLPFLPT 180

Query: 760 TEDVYDCQVEHWGLDKPLLKHWEFEARTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXX 939
           TEDVYDC+VEH GL++PLLKHWE+EA  PLPETTEN VCA                    
Sbjct: 181 TEDVYDCKVEHLGLNEPLLKHWEYEAPAPLPETTENAVCALGLIVALVGIIAGTIFIIKG 240

Query: 940 XRKGNATERRGPL 978
            RK N  ERRGPL
Sbjct: 241 VRKANTVERRGPL 253


>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 =  234 bits (596), Expect = 2e-61
 Identities = 114/222 (51%), Positives = 152/222 (68%), Gaps = 3/222 (1%)
 Frame = +1

Query: 223 MTILGVPVLGF--VITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHV 393
           M + G  VLG   ++T+L+LQ+  AI  +H+      FY S D +G+F +DFDG+++F V
Sbjct: 1   MVLRGRLVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSV 60

Query: 394 DMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSD 573
           D++KRE VWRL EFG+FA F+ Q  L +IA+ KA+LE L+KRS              L  
Sbjct: 61  DLKKREAVWRLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNVSPRVAVLPK 120

Query: 574 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFM 753
             V+LGEPN+LIC +DK  PPV+N+TWLRNG PVT+GV ++ F  + DHLFRKFHYL F+
Sbjct: 121 SHVQLGEPNVLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTFV 180

Query: 754 PSTEDVYDCQVEHWGLDKPLLKHWEFEARTPLPETTENTVCA 879
           P  +D YDC+VEHWGLD+PL +HWE +  T LP+TT   VCA
Sbjct: 181 PLVDDFYDCKVEHWGLDQPLFQHWEPQVPTALPDTTGTLVCA 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 =  230 bits (587), Expect = 2e-60
 Identities = 114/223 (51%), Positives = 153/223 (68%), Gaps = 4/223 (1%)
 Frame = +1

Query: 223 MTILGVPVLGF--VITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHV 393
           M + G  VLG   ++T+L+LQ+  AI  +H+      FY S D +G+F +DFDG+++F V
Sbjct: 1   MVLRGRLVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSV 60

Query: 394 DMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSD 573
           D++KRE VWRL EFG+FA F+ Q  L +IA+ KA+LE L+KRS              +  
Sbjct: 61  DLKKREAVWRLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNGSTPQVAVLP 120

Query: 574 KP-VELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPF 750
           K  V+LGEPN+LIC +DK  PPV+N+TWLRNG PVT+GV ++ F  + DHLFRKFHYL F
Sbjct: 121 KSHVQLGEPNVLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTF 180

Query: 751 MPSTEDVYDCQVEHWGLDKPLLKHWEFEARTPLPETTENTVCA 879
           +P  +D YDC+VEHWGLD+PL +HWE +  T LP+TT   VCA
Sbjct: 181 VPLVDDFYDCKVEHWGLDQPLFQHWEPQVPTALPDTTGTLVCA 223


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

 Score =  220 bits (561), Expect = 2e-57
 Identities = 112/240 (46%), Positives = 141/240 (58%), Gaps = 1/240 (0%)
 Frame = +1

Query: 262 TILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFG 438
           T+++   S  IV +H+       Y +   SG +  +FDGDE F+VD+EKRETVWRL  F 
Sbjct: 16  TMMSPSGSEDIVADHIGTYGISIYHTYGPSGYYTHEFDGDEEFYVDLEKRETVWRLPVFS 75

Query: 439 HFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFI 618
            FA+F+ QGAL NIA  K NLEI+I+RS               S  PV LG+PN LIC +
Sbjct: 76  KFATFDPQGALRNIATTKHNLEIVIQRSNSTAATNKVPEVTVFSKSPVMLGQPNTLICHV 135

Query: 619 DKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWG 798
           D   PPV+N+TWLRNG  VT GV ET FL + D+ F K +YL F+PS +DVYDC+VEHWG
Sbjct: 136 DNIFPPVINITWLRNGHSVTEGVSETSFLIKSDYSFLKINYLTFLPSDDDVYDCKVEHWG 195

Query: 799 LDKPLLKHWEFEARTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 978
           LD+PLLKHWE +   P+ E TE  VCA                     R G  +  +GPL
Sbjct: 196 LDEPLLKHWEPDIPAPMSELTETVVCALGLTVGLVGIMVGTILIIQGLRSGGPSRHQGPL 255


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

 Score =  206 bits (525), Expect = 3e-53
 Identities = 104/230 (45%), Positives = 131/230 (56%), Gaps = 1/230 (0%)
 Frame = +1

Query: 292 IVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 468
           IV +HV I     Y S   SG++  +FDGDE F+VD+EK+ET W+L  F    SF+ Q A
Sbjct: 26  IVADHVGIYGISIYQSYGPSGQYTHEFDGDEQFYVDLEKKETAWQLPLFSRMLSFDPQLA 85

Query: 469 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 648
           L NIA+ K +++ L K S               S  PV LG+PN LIC +D   PPV+N+
Sbjct: 86  LRNIAIMKLHVDFLTKFSNSTAATNKVPEVTVFSKSPVMLGQPNTLICHVDNIFPPVINI 145

Query: 649 TWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 828
           TWLRNG  VT GV ET FL R D+ F K  YL F+PS +D+YDC+VEHWGLD+PLLKHWE
Sbjct: 146 TWLRNGHSVTEGVSETSFLIRSDYSFLKIKYLAFLPSDDDIYDCKVEHWGLDEPLLKHWE 205

Query: 829 FEARTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 978
            E   P+ E TE  VC                      R G+ +  +GPL
Sbjct: 206 PEIPAPMSELTETVVCTLGLTMGLVGITVGTIFIIQGLRSGDPSRHQGPL 255


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

 Score =  206 bits (523), Expect = 5e-53
 Identities = 99/197 (50%), Positives = 121/197 (61%), Gaps = 1/197 (0%)
 Frame = +1

Query: 292 IVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 468
           IV +HV       Y +   SG+F F+FDGDE+F+VD+ K+ETVWRL EF +   FE Q A
Sbjct: 24  IVADHVGTYGTNVYQTYGASGQFTFEFDGDELFYVDLGKKETVWRLPEFSNITKFEVQSA 83

Query: 469 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 648
           L NI + K NL+ILIK S                   V LG PN LIC +D   PPV+N+
Sbjct: 84  LRNIVMSKRNLDILIKNSSFTPATSEIPEVAVFPKSSVVLGIPNTLICQVDNIFPPVINI 143

Query: 649 TWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 828
           TW  NG  V  G+ ET F P+ DH F KF YL F+P+ ED YDC+VEHWGL++PL+KHWE
Sbjct: 144 TWFYNGHFVAEGIAETTFYPKSDHSFLKFSYLTFLPTNEDFYDCRVEHWGLEEPLVKHWE 203

Query: 829 FEARTPLPETTENTVCA 879
            E  TP  E TE  VCA
Sbjct: 204 PEIPTPTSELTETVVCA 220


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

 Score =  199 bits (507), Expect = 3e-51
 Identities = 95/179 (53%), Positives = 118/179 (65%), Gaps = 1/179 (0%)
 Frame = +1

Query: 292 IVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 468
           IV +HV     E Y S   SG++  +FDGDE+F+VD+ K+ETVWRL  F  FA F+ Q A
Sbjct: 26  IVADHVGSYGTEIYQSHGPSGQYTQEFDGDEMFYVDLGKKETVWRLPMFSQFAGFDPQAA 85

Query: 469 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 648
           L+ IA  K NL++L KRS               S  PV LG+PN LIC +D   PPV+N+
Sbjct: 86  LSEIATAKHNLDVLTKRSNFTPVINEVPEVTVFSKSPVMLGQPNTLICHVDNIFPPVINI 145

Query: 649 TWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHW 825
           TWL+NG  VT GV ET FLP++DH F K  YL F+PS  D+YDC+VEHWGLD+PLLKHW
Sbjct: 146 TWLKNGHAVTEGVSETSFLPKDDHSFLKIGYLTFLPSDNDIYDCKVEHWGLDEPLLKHW 204


>ref|XP_608813.2| PREDICTED: similar to serine/threonine protein phosphatase with
           EF-hand motifs 2 isoform b [Bos taurus]
          Length = 886

 Score =  104 bits (260), Expect = 1e-22
 Identities = 46/53 (86%), Positives = 51/53 (96%)
 Frame = -2

Query: 167 QPGESANAVPHYHKLCSRVSHIWGNRRGQHIRSAMDKPRPGKTTSVIMVSPLP 9
           +PGESANAVPH+HKLCSRVSHIWGNRRGQHIRSAMD+P PG+TT +IMVSPLP
Sbjct: 569 KPGESANAVPHFHKLCSRVSHIWGNRRGQHIRSAMDEPHPGETTFMIMVSPLP 621


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

 Score = 67.8 bits (164), Expect = 2e-11
 Identities = 51/200 (25%), Positives = 80/200 (40%), Gaps = 6/200 (3%)
 Frame = +1

Query: 295 VENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGALA 474
           ++NH  +   +      +      +D D++F  D  +   V RL EF  +A     G  +
Sbjct: 39  LQNHTFLHTMYCQDWSPNVALSESYDEDQLFSFDFSQSIRVPRLPEFADWA--HQHGDTS 96

Query: 475 NIAVDKANLEILIKR-----SXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPV 639
           +I  DK     +I+                      + KP+E G+PN L+CFI    PP 
Sbjct: 97  DIMFDKGFCRAMIEEIGPELEGQIPVSRGFPIVQVFTLKPLEFGKPNTLVCFISNLFPPT 156

Query: 640 VNVTWLRNGSPVTRGVPETVFLPREDHL-FRKFHYLPFMPSTEDVYDCQVEHWGLDKPLL 816
           + V W    +PV    P   F+   D L F+ F YL   P+  D++ C V H       +
Sbjct: 157 LTVNWQHQSAPVEGAGP--TFVSAVDGLTFQAFSYLNVTPAPSDLFSCIVTHEIDGYTAI 214

Query: 817 KHWEFEARTPLPETTENTVC 876
             W  +   P  +  EN +C
Sbjct: 215 AFWVPQNALP-SDLLENVLC 233


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

 Score = 59.3 bits (142), Expect = 7e-09
 Identities = 28/86 (32%), Positives = 39/86 (45%)
 Frame = +1

Query: 586 LGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTE 765
           L   N+L+C +  F P  + V W RN    T GV  T  +   D  F+    L   P   
Sbjct: 141 LNHHNLLVCSVTDFYPSQIKVRWFRNDREETAGVVSTPLIRNGDWTFQILVMLEMTPQRG 200

Query: 766 DVYDCQVEHWGLDKPLLKHWEFEART 843
           DVY C VEH  L  P++  W  ++ +
Sbjct: 201 DVYTCHVEHPSLQSPIMVEWRAQSES 226


  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: 52,048,103
Number of Sequences: 33508
Number of extensions: 1447931
Number of successful extensions: 4946
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 4248
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): 4926
length of database: 16,112,626
effective HSP length: 105
effective length of database: 12,594,286
effective search space used: 4533942960
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= ITT01_0100_B02
         (1398 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris]    370   e-102
Alignment   gi|NP_001011726.1| MHC class II DLA DQalpha chain [Canis famili...   222   8e-58
Alignment   gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati...   207   2e-53
Alignment   gi|XP_851506.1| PREDICTED: similar to zinc finger protein 124 [...    88   2e-17
Alignment   gi|XP_538853.2| PREDICTED: similar to major histocompatibility ...    80   5e-15
Alignment   gi|XP_532104.2| PREDICTED: similar to HLA class II histocompati...    78   2e-14
Alignment   gi|XP_861572.1| PREDICTED: similar to major histocompatibility ...    64   5e-10
Alignment   gi|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis fami...    60   5e-09
Alignment   gi|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Ca...    59   1e-08
Alignment   gi|XP_535458.1| PREDICTED: similar to beta-2-microglobulin prec...    55   2e-07

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

 Score =  370 bits (949), Expect = e-102
 Identities = 182/254 (71%), Positives = 197/254 (77%), Gaps = 2/254 (0%)
 Frame = +1

Query: 223 MTILGVPVLGFVIT--ILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVD 396
           MTI GVPVLGF I   ++  Q+SWA+ E HVIIQAEFYL+PD SGEFMFDFDGDEIFHVD
Sbjct: 1   MTISGVPVLGFFIMAFLMGPQESWAVKEEHVIIQAEFYLTPDPSGEFMFDFDGDEIFHVD 60

Query: 397 MEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDK 576
           MEK+ETVWRLEEFG FASFEAQGALANIAVDKANL+ +IKRS              LS+ 
Sbjct: 61  MEKKETVWRLEEFGRFASFEAQGALANIAVDKANLDTMIKRSNHTPNTNVPPEVTVLSNT 120

Query: 577 PVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMP 756
           PVELGEPNILICFIDKFSPPV+NVTWLRNG+PVT GV ET+FLPREDHLFRKFHYLPF+P
Sbjct: 121 PVELGEPNILICFIDKFSPPVINVTWLRNGNPVTTGVSETIFLPREDHLFRKFHYLPFLP 180

Query: 757 STEDVYDCQVEHWGLDKPLLKHWEFEARTPLPETTENTVCAXXXXXXXXXXXXXXXXXXX 936
           S EDVYDC+VEHWGLD+PLLKHWEFE  TPLPETTEN VCA                   
Sbjct: 181 SAEDVYDCKVEHWGLDEPLLKHWEFEPPTPLPETTENVVCALGLIVGLVGIITGTIFIIK 240

Query: 937 XXRKGNATERRGPL 978
             RK  A ERRGPL
Sbjct: 241 GMRKVKAGERRGPL 254


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

 Score =  222 bits (565), Expect = 8e-58
 Identities = 116/255 (45%), Positives = 144/255 (56%), Gaps = 3/255 (1%)
 Frame = +1

Query: 223 MTILGVPVLGFVITILNLQKSWA--IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHV 393
           M +  V +LG +I  + +  S    IV +HV       Y S   SG++  +FDGDE F+V
Sbjct: 1   MILNRVLILGTLILTIMMSPSGGEEIVADHVANYGINVYQSYGPSGQYTHEFDGDEEFYV 60

Query: 394 DMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSD 573
           D+EK+ETVWRL  F  F SF+ QGAL N+A+ K NL I+ KRS               S 
Sbjct: 61  DLEKKETVWRLPVFSTFRSFDPQGALRNLAIIKQNLNIMTKRSNQTAATNEVPEVTVFSK 120

Query: 574 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFM 753
            PV LG+PN LIC +D   PPV+NVTWL+N   VT GV ET F  + DH F K  YL F+
Sbjct: 121 SPVMLGQPNTLICLVDNIFPPVINVTWLKNRHSVTEGVSETSFFAKGDHSFSKISYLTFL 180

Query: 754 PSTEDVYDCQVEHWGLDKPLLKHWEFEARTPLPETTENTVCAXXXXXXXXXXXXXXXXXX 933
           PS ED+YDC+VEHWGLD+PLLKHWE E  TP+ E TE  VCA                  
Sbjct: 181 PSAEDIYDCKVEHWGLDEPLLKHWEPEVPTPMSELTETVVCALGLAVGLVGIVMGTVFII 240

Query: 934 XXXRKGNATERRGPL 978
              R G  +  +GPL
Sbjct: 241 QGLRSGGTSRHQGPL 255


>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 =  207 bits (528), Expect = 2e-53
 Identities = 94/192 (48%), Positives = 131/192 (68%), Gaps = 7/192 (3%)
 Frame = +1

Query: 325 FYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLE 504
           FY S   SG+F  +FDG+++F V+++KR+ VWRL EFG+ A F+ Q  LA+IAV KA+L+
Sbjct: 8   FYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEFGNLAHFDPQNGLASIAVIKAHLD 67

Query: 505 ILIKRSXXXXXXXXXXXXXXLSDKP-------VELGEPNILICFIDKFSPPVVNVTWLRN 663
           +L++RS              L  +        VELG+PN+LIC +D   PPV+N+TWLRN
Sbjct: 68  VLVERSNRTRAINGTHLSSPLPPRVAVLPKFRVELGQPNVLICIVDNIFPPVINITWLRN 127

Query: 664 GSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWEFEART 843
           G  ++ GV +T F  + DHLFRKF YL F+PS ED+YDC+VEHWGL++PLL+HWE +   
Sbjct: 128 GQIISEGVAQTSFYSQPDHLFRKFCYLTFVPSAEDMYDCKVEHWGLEEPLLRHWEPQVPI 187

Query: 844 PLPETTENTVCA 879
           P+P+T E  +CA
Sbjct: 188 PVPDTIETLICA 199


>ref|XP_851506.1| PREDICTED: similar to zinc finger protein 124 [Canis familiaris]
          Length = 265

 Score = 87.8 bits (216), Expect = 2e-17
 Identities = 43/50 (86%), Positives = 43/50 (86%)
 Frame = -2

Query: 158 ESANAVPHYHKLCSRVSHIWGNRRGQHIRSAMDKPRPGKTTSVIMVSPLP 9
           ESANAVPHYH    RVSHIWGNRRGQHI SAMDKPRPG TT VIMVSPLP
Sbjct: 82  ESANAVPHYH----RVSHIWGNRRGQHIWSAMDKPRPGNTTFVIMVSPLP 127


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

 Score = 80.1 bits (196), Expect = 5e-15
 Identities = 53/199 (26%), Positives = 88/199 (44%), Gaps = 5/199 (2%)
 Frame = +1

Query: 295 VENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGALA 474
           ++NH  +   +  +   S   +  +DGD++F  +  +   V RL EF  +A  +  G + 
Sbjct: 45  LQNHTFLHTMYCQNWSPSIGLLEAYDGDQLFSFNFSQNTRVPRLPEFADWA--QKSGDMP 102

Query: 475 NIAVDKANLEILI-----KRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPV 639
            I+ DKA  + +I     K                 + KP+E G+PN+L+CFI    PP 
Sbjct: 103 TISFDKAFCQAMIEEIGPKLEGQIPVSRGFPMVDVFTLKPLEFGKPNMLVCFISNLFPPT 162

Query: 640 VNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLK 819
           + V W  +  PV  G+  T     +   F+ F YL F P+  D++ C V H   +   + 
Sbjct: 163 LTVNWWHHLDPV-EGIGPTFVSAVDGFSFQAFSYLNFTPAPSDLFSCVVTHEIDNYTAIA 221

Query: 820 HWEFEARTPLPETTENTVC 876
           +W      P  +  EN +C
Sbjct: 222 YWVPHDALP-SDLLENVLC 239


>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 = 78.2 bits (191), Expect = 2e-14
 Identities = 38/89 (42%), Positives = 63/89 (70%), Gaps = 1/89 (1%)
 Frame = +1

Query: 259 ITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEF 435
           +++L+  ++ AI  +H+      FY S   SG+F  +FDG+++F V+++KR+ VWRL EF
Sbjct: 1   MSLLSPHETGAIEADHMGSYGPAFYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEF 60

Query: 436 GHFASFEAQGALANIAVDKANLEILIKRS 522
           G+ A F+ Q  LA+IAV KA+L++L++RS
Sbjct: 61  GNLAHFDPQNGLASIAVIKAHLDVLVERS 89


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

 Score = 63.5 bits (153), Expect = 5e-10
 Identities = 33/101 (32%), Positives = 50/101 (49%)
 Frame = +1

Query: 574 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFM 753
           KP+E G+PN+L+CFI    PP + V W  +  PV  G+  T     +   F+ F YL F 
Sbjct: 46  KPLEFGKPNMLVCFISNLFPPTLTVNWWHHLDPV-EGIGPTFVSAVDGFSFQAFSYLNFT 104

Query: 754 PSTEDVYDCQVEHWGLDKPLLKHWEFEARTPLPETTENTVC 876
           P+  D++ C V H   +   + +W      P  +  EN +C
Sbjct: 105 PAPSDLFSCVVTHEIDNYTAIAYWVPHDALP-SDLLENVLC 144


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

 Score = 60.1 bits (144), Expect = 5e-09
 Identities = 30/88 (34%), Positives = 43/88 (48%)
 Frame = +1

Query: 574 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFM 753
           K   L   N+L+C ++ F P  + V WLRNG     GV  T  +   D  F+    L  +
Sbjct: 134 KTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNGDWTFQILVMLEIV 193

Query: 754 PSTEDVYDCQVEHWGLDKPLLKHWEFEA 837
           P + +VY CQVEH  L  P+   W  ++
Sbjct: 194 PQSGEVYTCQVEHPSLTSPVTVEWRAQS 221


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

 Score = 58.5 bits (140), Expect = 1e-08
 Identities = 28/86 (32%), Positives = 38/86 (44%)
 Frame = +1

Query: 586 LGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTE 765
           L   N+L+C +  F P  + V W RN    T GV  T  +   D  F+    L   P   
Sbjct: 141 LNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLIRNGDWTFQILVMLEMTPQRG 200

Query: 766 DVYDCQVEHWGLDKPLLKHWEFEART 843
           DVY C VEH  L  P+   W  ++ +
Sbjct: 201 DVYTCHVEHASLQSPITVQWRAQSES 226


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

 Score = 54.7 bits (130), Expect = 2e-07
 Identities = 26/87 (29%), Positives = 44/87 (50%)
 Frame = +1

Query: 568 SDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLP 747
           S  P E G+PN L C++  F PP + +  L+NG  +     +  F   +D  F    +  
Sbjct: 38  SRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSF--SKDWTFYLLVHTE 95

Query: 748 FMPSTEDVYDCQVEHWGLDKPLLKHWE 828
           F P+ +D + C+V+H  L +P +  W+
Sbjct: 96  FTPNEQDEFSCRVKHVTLSEPQIVKWD 122


  Database: RefSeqCP
    Posted date:  Aug 1, 2006  9:25 PM
  Number of letters in database: 19,266,565
  Number of sequences in database:  33,732
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 61,106,420
Number of Sequences: 33732
Number of extensions: 1696663
Number of successful extensions: 5583
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 4694
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): 5564
length of database: 19,266,565
effective HSP length: 107
effective length of database: 15,657,241
effective search space used: 5605292278
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= ITT01_0100_B02
         (1398 letters)

Database: RefSeqSP 
           1040 sequences; 434,620 total letters

Searching...done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001004039.1| SLA-DM alpha chain [Sus scrofa]                    72   3e-14
Alignment   gi|NP_999143.1| beta 2-microglobulin [Sus scrofa]                     59   4e-10
Alignment   gi|NP_998933.1| swine leukocyte antigen 7 [Sus scrofa]                50   1e-07
Alignment   gi|NP_999362.2| neonatal Fc receptor FcRn [Sus scrofa]                44   7e-06

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

 Score = 72.0 bits (175), Expect = 3e-14
 Identities = 49/175 (28%), Positives = 79/175 (45%), Gaps = 5/175 (2%)
 Frame = +1

Query: 367 FDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKR-----SXXX 531
           +DGD++F  +  +   V RL EF  +A  + +   A I  DK     +I++         
Sbjct: 63  YDGDQLFSFNFSQNIRVPRLPEFADWAH-QIEDTPA-IFFDKGFCREMIEKVGPLFEGKI 120

Query: 532 XXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPR 711
                       + KP+E G+PN L+CF+    PP + VTW  + +PV  G+  T     
Sbjct: 121 PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSAT 179

Query: 712 EDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWEFEARTPLPETTENTVC 876
           +D  F+ F YL F P+  D++ C V H       + +W  +   P  +  EN +C
Sbjct: 180 DDLSFQAFSYLNFTPTPSDLFSCVVTHELDGYVAISYWVPQNALP-SDLLENVLC 233


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

 Score = 58.5 bits (140), Expect = 4e-10
 Identities = 29/87 (33%), Positives = 44/87 (50%)
 Frame = +1

Query: 568 SDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLP 747
           S  P E G+PN L C++  F PP + +  L+NG  +     +  F   +D  F    +  
Sbjct: 31  SRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFYLLVHTE 88

Query: 748 FMPSTEDVYDCQVEHWGLDKPLLKHWE 828
           F P+  D Y C+V+H  LDKP +  W+
Sbjct: 89  FTPNAVDQYSCRVKHVTLDKPKIVKWD 115


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

 Score = 50.1 bits (118), Expect = 1e-07
 Identities = 27/83 (32%), Positives = 40/83 (48%)
 Frame = +1

Query: 604 LICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTEDVYDCQ 783
           L C+   F P  +++TW + G   ++ V      P  D  FRK+  L   P  E  Y C 
Sbjct: 222 LRCWALGFYPKEISLTWQQEGQDQSQDVEVVETRPSGDGTFRKWAALVVPPGEEQSYTCH 281

Query: 784 VEHWGLDKPLLKHWEFEARTPLP 852
           V+H GL +PL   W+   + P+P
Sbjct: 282 VQHEGLQEPLTLRWD-PPQPPVP 303


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

 Score = 44.3 bits (103), Expect = 7e-06
 Identities = 27/85 (31%), Positives = 40/85 (47%)
 Frame = +1

Query: 598 NILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTEDVYD 777
           ++L C    F PP + + +LRNG  +  G  E+   P  D  F  +  L      E  Y 
Sbjct: 218 SVLTCIAFSFYPPELQLRFLRNG--LAAGSGESDIGPNGDGSFHAWSSLTVKSGDEHHYC 275

Query: 778 CQVEHWGLDKPLLKHWEFEARTPLP 852
           C V+H GL +PL    E  A++ +P
Sbjct: 276 CVVQHAGLAQPLTVELESPAKSSMP 300


  Database: RefSeqSP
    Posted date:  Aug 1, 2006  7:14 PM
  Number of letters in database: 434,620
  Number of sequences in database:  1040
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,396,914
Number of Sequences: 1040
Number of extensions: 38037
Number of successful extensions: 137
Number of sequences better than 1.0e-05: 4
Number of HSP's better than  0.0 without gapping: 115
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): 134
length of database: 434,620
effective HSP length: 80
effective length of database: 351,420
effective search space used: 135296700
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= ITT01_0100_B02
         (1398 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_061984.2| major histocompatibility complex, class II, DR ...   370   e-102
Alignment   gi|NP_291032.2| major histocompatibility complex, class II, DP ...   240   2e-63
Alignment   gi|NP_002110.1| major histocompatibility complex, class II, DO ...   229   3e-60
Alignment   gi|NP_002113.2| major histocompatibility complex, class II, DQ ...   212   5e-55
Alignment   gi|XP_949974.1| PREDICTED: similar to HLA class II histocompati...   211   1e-54
Alignment   gi|XP_949973.1| PREDICTED: similar to HLA class II histocompati...   211   1e-54
Alignment   gi|XP_949971.1| PREDICTED: similar to HLA class II histocompati...   211   1e-54
Alignment   gi|XP_945969.1| PREDICTED: similar to HLA class II histocompati...   211   1e-54
Alignment   gi|NP_064440.1| major histocompatibility complex, class II, DQ ...   207   2e-53
Alignment   gi|XP_941306.1| PREDICTED: similar to HLA class II histocompati...   200   2e-51

>ref|NP_061984.2| major histocompatibility complex, class II, DR alpha precursor
           [Homo sapiens]
          Length = 254

 Score =  370 bits (949), Expect = e-102
 Identities = 181/254 (71%), Positives = 198/254 (77%), Gaps = 2/254 (0%)
 Frame = +1

Query: 223 MTILGVPVLGFVI--TILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVD 396
           M I GVPVLGF I   +++ Q+SWAI E HVIIQAEFYL+PD+SGEFMFDFDGDEIFHVD
Sbjct: 1   MAISGVPVLGFFIIAVLMSAQESWAIKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVD 60

Query: 397 MEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDK 576
           M K+ETVWRLEEFG FASFEAQGALANIAVDKANLEI+ KRS              L++ 
Sbjct: 61  MAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNS 120

Query: 577 PVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMP 756
           PVEL EPN+LICFIDKF+PPVVNVTWLRNG PVT GV ETVFLPREDHLFRKFHYLPF+P
Sbjct: 121 PVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLP 180

Query: 757 STEDVYDCQVEHWGLDKPLLKHWEFEARTPLPETTENTVCAXXXXXXXXXXXXXXXXXXX 936
           STEDVYDC+VEHWGLD+PLLKHWEF+A +PLPETTEN VCA                   
Sbjct: 181 STEDVYDCRVEHWGLDEPLLKHWEFDAPSPLPETTENVVCALGLTVGLVGIIIGTIFIIK 240

Query: 937 XXRKGNATERRGPL 978
             RK NA ERRGPL
Sbjct: 241 GLRKSNAAERRGPL 254


>ref|NP_291032.2| major histocompatibility complex, class II, DP alpha 1 precursor
           [Homo sapiens]
          Length = 260

 Score =  240 bits (612), Expect = 2e-63
 Identities = 116/205 (56%), Positives = 143/205 (69%)
 Frame = +1

Query: 265 ILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHF 444
           +L+L+ + AI  +HV   A F  +   +GEFMF+FD DE+F+VD++K+ETVW LEEFG  
Sbjct: 23  LLSLRGAGAIKADHVSTYAAFVQTHRPTGEFMFEFDEDEMFYVDLDKKETVWHLEEFGQA 82

Query: 445 ASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDK 624
            SFEAQG LANIA+   NL  LI+RS                 +PVELG+PN LIC IDK
Sbjct: 83  FSFEAQGGLANIAILNNNLNTLIQRSNHTQATNDPPEVTVFPKEPVELGQPNTLICHIDK 142

Query: 625 FSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLD 804
           F PPV+NVTWL NG  VT GV E++FLPR D+ F KFHYL F+PS ED YDC+VEHWGLD
Sbjct: 143 FFPPVLNVTWLCNGELVTEGVAESLFLPRTDYSFHKFHYLTFVPSAEDFYDCRVEHWGLD 202

Query: 805 KPLLKHWEFEARTPLPETTENTVCA 879
           +PLLKHWE +    +PETTE  +CA
Sbjct: 203 QPLLKHWEAQEPIQMPETTETVLCA 227


>ref|NP_002110.1| major histocompatibility complex, class II, DO alpha precursor
           [Homo sapiens]
          Length = 250

 Score =  229 bits (585), Expect = 3e-60
 Identities = 113/215 (52%), Positives = 143/215 (66%), Gaps = 3/215 (1%)
 Frame = +1

Query: 244 VLGF--VITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRET 414
           VLGF  ++T+L+ Q++ A   +H+      FY S   SG+F  +FD +++F VD++K E 
Sbjct: 8   VLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEA 67

Query: 415 VWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGE 594
           VWRL EFG FA F+ QG LA IA  KA+L+IL++RS              L    VELG+
Sbjct: 68  VWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQ 127

Query: 595 PNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTEDVY 774
           PNILIC +D   PPV+N+TWLRNG  VT GV +T F  + DHLFRKFHYLPF+PS EDVY
Sbjct: 128 PNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVY 187

Query: 775 DCQVEHWGLDKPLLKHWEFEARTPLPETTENTVCA 879
           DCQVEHWGLD PLL+HWE +   P P+  E  VCA
Sbjct: 188 DCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCA 222


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

 Score =  212 bits (540), Expect = 5e-55
 Identities = 106/230 (46%), Positives = 130/230 (56%), Gaps = 1/230 (0%)
 Frame = +1

Query: 292 IVENHVI-IQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 468
           IV +HV       Y     SG++  +FDGDE F+VD+E++ET WR  EF  F  F+ QGA
Sbjct: 26  IVADHVASCGVNLYQFYGPSGQYTHEFDGDEQFYVDLERKETAWRWPEFSKFGGFDPQGA 85

Query: 469 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 648
           L N+AV K NL I+IKR                S  PV LG+PN LIC +D   PPVVN+
Sbjct: 86  LRNMAVAKHNLNIMIKRYNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNI 145

Query: 649 TWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 828
           TWL NG  VT GV ET FL + DH F K  YL F+PS +++YDC+VEHWGLD+PLLKHWE
Sbjct: 146 TWLSNGQSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDQPLLKHWE 205

Query: 829 FEARTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 978
            E   P+ E TE  VCA                     R   A+  +GPL
Sbjct: 206 PEIPAPMSELTETVVCALGLSVGLMGIVVGTVFIIQGLRSVGASRHQGPL 255


>ref|XP_949974.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DQ(1) alpha chain precursor (DC-4 alpha chain) isoform
           10 [Homo sapiens]
          Length = 255

 Score =  211 bits (537), Expect = 1e-54
 Identities = 108/230 (46%), Positives = 132/230 (57%), Gaps = 1/230 (0%)
 Frame = +1

Query: 292 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 468
           IV +HV       Y S   SG++  +FDGDE F+VD+E++ETVW+L  F  F  F+ Q A
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFA 85

Query: 469 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 648
           L NIAV K NL I+IKRS               S  PV LG+PN LIC +D   PPVVN+
Sbjct: 86  LTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNI 145

Query: 649 TWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 828
           TWL NG  VT GV ET FL + DH F K  YL F+PS +++YDC+VEHWGLD+PLLKHWE
Sbjct: 146 TWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWE 205

Query: 829 FEARTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 978
            E   P+ E TE  VCA                     R   A+  +GPL
Sbjct: 206 PEIPAPMSELTETVVCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 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 =  211 bits (537), Expect = 1e-54
 Identities = 108/230 (46%), Positives = 132/230 (57%), Gaps = 1/230 (0%)
 Frame = +1

Query: 292 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 468
           IV +HV       Y S   SG++  +FDGDE F+VD+E++ETVW+L  F  F  F+ Q A
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFA 85

Query: 469 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 648
           L NIAV K NL I+IKRS               S  PV LG+PN LIC +D   PPVVN+
Sbjct: 86  LTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNI 145

Query: 649 TWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 828
           TWL NG  VT GV ET FL + DH F K  YL F+PS +++YDC+VEHWGLD+PLLKHWE
Sbjct: 146 TWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWE 205

Query: 829 FEARTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 978
            E   P+ E TE  VCA                     R   A+  +GPL
Sbjct: 206 PEIPAPMSELTETVVCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 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 =  211 bits (537), Expect = 1e-54
 Identities = 108/230 (46%), Positives = 132/230 (57%), Gaps = 1/230 (0%)
 Frame = +1

Query: 292 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 468
           IV +HV       Y S   SG++  +FDGDE F+VD+E++ETVW+L  F  F  F+ Q A
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFA 85

Query: 469 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 648
           L NIAV K NL I+IKRS               S  PV LG+PN LIC +D   PPVVN+
Sbjct: 86  LTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNI 145

Query: 649 TWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 828
           TWL NG  VT GV ET FL + DH F K  YL F+PS +++YDC+VEHWGLD+PLLKHWE
Sbjct: 146 TWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWE 205

Query: 829 FEARTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 978
            E   P+ E TE  VCA                     R   A+  +GPL
Sbjct: 206 PEIPAPMSELTETVVCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 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 =  211 bits (537), Expect = 1e-54
 Identities = 108/230 (46%), Positives = 132/230 (57%), Gaps = 1/230 (0%)
 Frame = +1

Query: 292 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 468
           IV +HV       Y S   SG++  +FDGDE F+VD+E++ETVW+L  F  F  F+ Q A
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFA 85

Query: 469 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 648
           L NIAV K NL I+IKRS               S  PV LG+PN LIC +D   PPVVN+
Sbjct: 86  LTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNI 145

Query: 649 TWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 828
           TWL NG  VT GV ET FL + DH F K  YL F+PS +++YDC+VEHWGLD+PLLKHWE
Sbjct: 146 TWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWE 205

Query: 829 FEARTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 978
            E   P+ E TE  VCA                     R   A+  +GPL
Sbjct: 206 PEIPAPMSELTETVVCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 255


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

 Score =  207 bits (527), Expect = 2e-53
 Identities = 100/197 (50%), Positives = 125/197 (63%), Gaps = 1/197 (0%)
 Frame = +1

Query: 292 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 468
           IV +HV      FY S   SG++  +FDGDE F+VD+E +ETVW+L  F  F SF+ Q A
Sbjct: 26  IVADHVASYGVNFYQSHGPSGQYTHEFDGDEEFYVDLETKETVWQLPMFSKFISFDPQSA 85

Query: 469 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 648
           L N+AV K  LE ++++S               S  PV LG+PN LIC +D   PPVVN+
Sbjct: 86  LRNMAVGKHTLEFMMRQSNSTAATNEVPEVTVFSKFPVTLGQPNTLICLVDNIFPPVVNI 145

Query: 649 TWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 828
           TWL NG  VT GV ET FL + DH F K  YL F+PS +++YDC+VEHWGLD+PLLKHWE
Sbjct: 146 TWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWE 205

Query: 829 FEARTPLPETTENTVCA 879
            E   P+ E TE  VCA
Sbjct: 206 PEIPAPMSELTETLVCA 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 =  200 bits (509), Expect = 2e-51
 Identities = 108/230 (46%), Positives = 127/230 (55%), Gaps = 1/230 (0%)
 Frame = +1

Query: 292 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 468
           IV +HV       Y S   SG++  +FDGDE F+VD+ ++ETVW L     F  F+ Q A
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFR-FDPQFA 84

Query: 469 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 648
           L NIAV K NL  LIKRS               S  PV LG+PNILIC +D   PPVVN+
Sbjct: 85  LTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVNI 144

Query: 649 TWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 828
           TWL NG  VT GV ET FL + DH F K  YL  +PS E+ YDC+VEHWGLDKPLLKHWE
Sbjct: 145 TWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHWE 204

Query: 829 FEARTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 978
            E   P+ E TE  VCA                     R   A+  +GPL
Sbjct: 205 PEIPAPMSELTETVVCALGLSVGLVGIVVGTVFIIRGLRSVGASRHQGPL 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: 58,871,251
Number of Sequences: 39411
Number of extensions: 1685115
Number of successful extensions: 5858
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 4865
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): 5826
length of database: 17,774,539
effective HSP length: 106
effective length of database: 13,596,973
effective search space used: 4881313307
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= ITT01_0100_B02
         (1398 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_034511.2| histocompatibility 2, class II antigen E alpha ...   328   8e-90
Alignment   gi|NP_032232.1| histocompatibility 2, O region alpha locus [Mus...   219   4e-57
Alignment   gi|NP_034508.2| histocompatibility 2, class II antigen A, alpha...   215   1e-55
Alignment   gi|NP_034516.2| histocompatibility 2, class II, locus DMa [Mus ...    79   2e-14
Alignment   gi|NP_996988.1| histocompatibility 2, class II antigen A, beta ...    58   3e-08
Alignment   gi|NP_034512.1| histocompatibility 2, class II antigen E beta [...    58   3e-08
Alignment   gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ...    57   4e-08
Alignment   gi|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus ...    57   4e-08
Alignment   gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/...    57   6e-08
Alignment   gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ...    56   8e-08

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

 Score =  328 bits (841), Expect = 8e-90
 Identities = 157/239 (65%), Positives = 176/239 (73%)
 Frame = +1

Query: 253 FVITILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEE 432
           F+  +++ QKSWAI E H IIQAEFYL PDK GEFMFDFDGDEIFHVD+EK ET+WRLEE
Sbjct: 13  FIAVLMSSQKSWAIKEEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEE 72

Query: 433 FGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILIC 612
           F  FASFEAQGALANIAVDKANL+++ +RS              LS  PV LGEPNILIC
Sbjct: 73  FAKFASFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPNILIC 132

Query: 613 FIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEH 792
           FIDKFSPPVVNVTW RNG PVT GV ETVFLPR+DHLFRKFHYL F+PST+D YDC+V+H
Sbjct: 133 FIDKFSPPVVNVTWFRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDH 192

Query: 793 WGLDKPLLKHWEFEARTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERR 969
           WGL++PL KHWEFE +T LPETTEN VCA                     +K N  ERR
Sbjct: 193 WGLEEPLRKHWEFEEKTLLPETTENVVCALGLFVGLVGIVVGIILIMKGIKKRNVVERR 251


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

 Score =  219 bits (559), Expect = 4e-57
 Identities = 107/214 (50%), Positives = 142/214 (66%), Gaps = 1/214 (0%)
 Frame = +1

Query: 238 VPVLGFVITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRET 414
           VPVL  V++ L+ +   AI  +H+      FY S D SG+F  +FDG++IF VD++  E 
Sbjct: 8   VPVLLTVMSFLSPRGVRAIKADHMGSYGPAFYQSYDASGQFTHEFDGEQIFSVDLKNEEV 67

Query: 415 VWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGE 594
           VWRL EFG FA  + Q  L +I++ KA+L+IL++RS              L    VELG+
Sbjct: 68  VWRLPEFGDFAHSDFQSGLMSISMIKAHLDILVERSNRTRAVSVPPRVTVLPKTRVELGK 127

Query: 595 PNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTEDVY 774
           PN+LIC +D   PPV+NVTWLRN  P+T+GV +T F  + +H FRKFHYL F+PS EDVY
Sbjct: 128 PNVLICIVDDIFPPVINVTWLRNSQPITKGVAQTSFYSQPNHRFRKFHYLTFVPSAEDVY 187

Query: 775 DCQVEHWGLDKPLLKHWEFEARTPLPETTENTVC 876
           DC+VEHWGLD PLL+HWE +  TP P+TTE  +C
Sbjct: 188 DCKVEHWGLDTPLLQHWEPQVLTPPPDTTETLIC 221


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

 Score =  215 bits (547), Expect = 1e-55
 Identities = 110/256 (42%), Positives = 142/256 (55%), Gaps = 1/256 (0%)
 Frame = +1

Query: 214 KEKMTILGVPVLGFVITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFH 390
           + +  ILGV  L  ++++   +    I  +HV       Y SP   G++ F+FDGDE+F+
Sbjct: 3   RSRALILGVLALTTMLSLCGGEDD--IEADHVGTYGISVYQSPGDIGQYTFEFDGDELFY 60

Query: 391 VDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLS 570
           VD++K+ETVW L EFG  ASF+ QG L NIAV K NL +L KRS                
Sbjct: 61  VDLDKKETVWMLPEFGQLASFDPQGGLQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFP 120

Query: 571 DKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPF 750
             PV LG+PN LICF+D   PPV+N+TWLRN   V  GV ET F    D+ F K  YL F
Sbjct: 121 KSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTF 180

Query: 751 MPSTEDVYDCQVEHWGLDKPLLKHWEFEARTPLPETTENTVCAXXXXXXXXXXXXXXXXX 930
           +PS +D+YDC+VEHWGL++P+LKHWE E   P+ E TE  VCA                 
Sbjct: 181 IPSDDDIYDCKVEHWGLEEPVLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTIFI 240

Query: 931 XXXXRKGNATERRGPL 978
               R G  +   GPL
Sbjct: 241 IQGLRSGGTSRHPGPL 256


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

 Score = 78.6 bits (192), Expect = 2e-14
 Identities = 62/230 (26%), Positives = 94/230 (40%), Gaps = 16/230 (6%)
 Frame = +1

Query: 235 GVPVLGFVITILNLQKSWAIVE-----------NHVIIQAEFYLSPDKSGEFMFDFDGDE 381
           G  +L  +  +  L  SWA++E           NH      F      +      +D DE
Sbjct: 8   GAVLLRLLRLLWLLPHSWAVLEASTPVLWDDPQNHTFRHTLFCQDGIPNIGLSETYDEDE 67

Query: 382 IFHVDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILI-----KRSXXXXXXXX 546
           +F  D  +   V +L +F  +A  + QG  + IA DK+  E+L+     K          
Sbjct: 68  LFSFDFSQNTRVPQLPDFAEWA--QGQGDASAIAFDKSFCEMLMREVSPKLEGQIPVSRG 125

Query: 547 XXXXXXLSDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLF 726
                  + KP+E G+PN L+CFI    PP + V W  + +PV  G   T     +   F
Sbjct: 126 LPVAEVFTLKPLEFGKPNTLVCFISNLFPPTLTVNWQLHSAPV-EGASPTSISAVDGLTF 184

Query: 727 RKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWEFEARTPLPETTENTVC 876
           + F YL F P   D+Y C V H       + +W  +   P  +  EN +C
Sbjct: 185 QAFSYLNFTPEPFDLYSCTVTHEIDRYTAIAYWVPQNALP-SDLLENALC 233


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

 Score = 57.8 bits (138), Expect = 3e-08
 Identities = 28/86 (32%), Positives = 38/86 (44%)
 Frame = +1

Query: 586 LGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTE 765
           L   N L+C +  F P  + V W RNG   T GV  T  +   D  F+    L   P   
Sbjct: 137 LNHHNTLVCSVTDFYPTQIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRG 196

Query: 766 DVYDCQVEHWGLDKPLLKHWEFEART 843
           +VY C VEH  L  P+   W  ++ +
Sbjct: 197 EVYTCHVEHPSLKSPITVEWRAQSES 222


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

 Score = 57.8 bits (138), Expect = 3e-08
 Identities = 28/88 (31%), Positives = 42/88 (47%)
 Frame = +1

Query: 574 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFM 753
           K   L   N+L+C +  F P  + V W RNG     G+  T  +   D  F+    L  +
Sbjct: 132 KTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETV 191

Query: 754 PSTEDVYDCQVEHWGLDKPLLKHWEFEA 837
           P + +VY CQVEH  L  P+   W+ ++
Sbjct: 192 PQSGEVYTCQVEHPSLTDPVTVEWKAQS 219


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

 Score = 57.4 bits (137), Expect = 4e-08
 Identities = 29/84 (34%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
 Frame = +1

Query: 577 PVELGEPNILICFIDKFSPPVVNVTWLRNGSPV-TRGVPETVFLPREDHLFRKFHYLPFM 753
           P    EP +L C++  F P  V +TW++NG  V +    E    P  D  ++   YL   
Sbjct: 124 PFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPNGDWTYQTVSYLALT 183

Query: 754 PSTEDVYDCQVEHWGLDKPLLKHW 825
           PS  DVY C V+H G  +P+   W
Sbjct: 184 PSYGDVYTCVVQHSGTSEPIRGDW 207


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

 Score = 57.4 bits (137), Expect = 4e-08
 Identities = 29/84 (34%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
 Frame = +1

Query: 577 PVELGEPNILICFIDKFSPPVVNVTWLRNGSPV-TRGVPETVFLPREDHLFRKFHYLPFM 753
           P    EP +L C++  F P  V +TW++NG  V +    E    P  D  ++   YL   
Sbjct: 124 PFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPNGDWTYQTVSYLALT 183

Query: 754 PSTEDVYDCQVEHWGLDKPLLKHW 825
           PS  DVY C V+H G  +P+   W
Sbjct: 184 PSYGDVYTCVVQHSGTSEPIRGDW 207


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

 Score = 56.6 bits (135), Expect = 6e-08
 Identities = 28/84 (33%), Positives = 38/84 (45%)
 Frame = +1

Query: 574 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFM 753
           K   L   N+L+C +  F P  + V W RNG     GV  T  +   D  ++    L  +
Sbjct: 133 KTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNRDWTYQTLVMLEMV 192

Query: 754 PSTEDVYDCQVEHWGLDKPLLKHW 825
           P   +VY CQVEH  L  P+   W
Sbjct: 193 PRGGEVYTCQVEHPSLTSPVTVEW 216


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

 Score = 56.2 bits (134), Expect = 8e-08
 Identities = 28/80 (35%), Positives = 40/80 (50%)
 Frame = +1

Query: 586 LGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVPETVFLPREDHLFRKFHYLPFMPSTE 765
           L + N+L+C +  F P  ++V W RNG     GV  T  +   D  F+    L  +P   
Sbjct: 135 LQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVRNGDWTFQTTVMLEMIPELG 194

Query: 766 DVYDCQVEHWGLDKPLLKHW 825
           D+Y C VEH GL +P+   W
Sbjct: 195 DIYSCLVEHPGLLRPVSVAW 214


  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: 69,976,705
Number of Sequences: 45328
Number of extensions: 1939466
Number of successful extensions: 6578
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 5411
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): 6567
length of database: 21,768,885
effective HSP length: 107
effective length of database: 16,918,789
effective search space used: 6056926462
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)