Animal-Genome cDNA 20060611C-005425


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= 20060611C-005425
         (1263 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]                    73   1e-14
Alignment   gi|NP_999143.1| beta 2-microglobulin [Sus scrofa]                     60   8e-11
Alignment   gi|NP_998933.1| swine leukocyte antigen 7 [Sus scrofa]                52   3e-08
Alignment   gi|NP_999362.2| neonatal Fc receptor FcRn [Sus scrofa]                45   5e-06

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

 Score = 73.2 bits (178), Expect = 1e-14
 Identities = 51/176 (28%), Positives = 80/176 (45%), Gaps = 6/176 (3%)
 Frame = +2

Query: 236 FDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKR-----SXXX 400
           +DGD++F  +  +   V RL EF  +A  + +   A I  DK     +I++         
Sbjct: 63  YDGDQLFSFNFSQNIRVPRLPEFADWAH-QIEDTPA-IFFDKGFCREMIEKVGPLFEGKI 120

Query: 401 XXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPR 580
                       + KP+E G+PN L+CF+    PP + VTW  + +PV  G+  T     
Sbjct: 121 PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSAT 179

Query: 581 EDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLP-ETTENTVC 745
           +D  F+ F YL F P+  D++ C V H       + +W    Q  LP +  EN +C
Sbjct: 180 DDLSFQAFSYLNFTPTPSDLFSCVVTHELDGYVAISYW--VPQNALPSDLLENVLC 233


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

 Score = 60.5 bits (145), Expect = 8e-11
 Identities = 30/87 (34%), Positives = 45/87 (51%)
 Frame = +2

Query: 437 SDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLP 616
           S  P E G+PN L C++  F PP + +  L+NG  +    S+  F   +D  F    +  
Sbjct: 31  SRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFYLLVHTE 88

Query: 617 FMPSTEDVYDCQVEHWGLDKPLLKHWE 697
           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 = 52.0 bits (123), Expect = 3e-08
 Identities = 28/83 (33%), Positives = 40/83 (48%)
 Frame = +2

Query: 473 LICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQ 652
           L C+   F P  +++TW + G   ++ V      P  D  FRK+  L   P  E  Y C 
Sbjct: 222 LRCWALGFYPKEISLTWQQEGQDQSQDVEVVETRPSGDGTFRKWAALVVPPGEEQSYTCH 281

Query: 653 VEHWGLDKPLLKHWEFEAQTPLP 721
           V+H GL +PL   W+   Q P+P
Sbjct: 282 VQHEGLQEPLTLRWD-PPQPPVP 303


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

 Score = 44.7 bits (104), Expect = 5e-06
 Identities = 27/85 (31%), Positives = 40/85 (47%)
 Frame = +2

Query: 467 NILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYD 646
           ++L C    F PP + + +LRNG  +  G  E+   P  D  F  +  L      E  Y 
Sbjct: 218 SVLTCIAFSFYPPELQLRFLRNG--LAAGSGESDIGPNGDGSFHAWSSLTVKSGDEHHYC 275

Query: 647 CQVEHWGLDKPLLKHWEFEAQTPLP 721
           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: 1,207,194
Number of Sequences: 1040
Number of extensions: 31855
Number of successful extensions: 118
Number of sequences better than 1.0e-05: 4
Number of HSP's better than  0.0 without gapping: 96
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): 115
length of database: 434,620
effective HSP length: 79
effective length of database: 352,460
effective search space used: 120188860
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqBP

BLASTX 2.2.10 [Oct-19-2004]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= 20060611C-005425
         (1263 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, ...   355   5e-98
Alignment   gi|XP_604082.2| PREDICTED: similar to HLA class II histocompati...   235   6e-62
Alignment   gi|XP_883292.1| PREDICTED: similar to HLA class II histocompati...   231   7e-61
Alignment   gi|NP_001013619.2| histocompatibility complex, class II, DQ alp...   223   3e-58
Alignment   gi|NP_001012693.1| major histocompatibility complex, class II, ...   209   5e-54
Alignment   gi|NP_001012696.1| major histocompatibility complex, class II, ...   207   2e-53
Alignment   gi|NP_001012699.1| major histocompatibility complex, class II, ...   201   8e-52
Alignment   gi|NP_001012692.2| major histocompatibility complex, class II, ...    68   1e-11
Alignment   gi|NP_001029840.2| MHC class II antigen [Bos taurus]                  60   4e-09
Alignment   gi|NP_001012694.1| major histocompatibility complex, class II, ...    59   6e-09

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

 Score =  355 bits (910), Expect = 5e-98
 Identities = 174/253 (68%), Positives = 193/253 (76%), Gaps = 1/253 (0%)
 Frame = +2

Query: 92  MTILGVPVLGFVITIL-NLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDM 268
           M I  VP+LG  IT+L  LQ+SWAI ENHVIIQAEFYL P++S EFMFDFDGDEIFHVDM
Sbjct: 1   MAITRVPILGLFITVLIGLQESWAIKENHVIIQAEFYLKPEESAEFMFDFDGDEIFHVDM 60

Query: 269 EKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKP 448
            K+ETVWRL EFGHFASFEAQGALAN+AV KANL+I+IKRS              L +KP
Sbjct: 61  GKKETVWRLPEFGHFASFEAQGALANMAVMKANLDIMIKRSNNTPNTNVPPEVTLLPNKP 120

Query: 449 VELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPS 628
           VELGEPN LICFIDKFSPPV++VTWLRNG PVT GVS+TVFLPR DHLFRKFHYLPF+P+
Sbjct: 121 VELGEPNTLICFIDKFSPPVISVTWLRNGKPVTDGVSQTVFLPRNDHLFRKFHYLPFLPT 180

Query: 629 TEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXX 808
           TEDVYDC+VEH GL++PLLKHWE+EA  PLPETTEN VCA                    
Sbjct: 181 TEDVYDCKVEHLGLNEPLLKHWEYEAPAPLPETTENAVCALGLIVALVGIIAGTIFIIKG 240

Query: 809 XRKGNATERRGPL 847
            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 =  235 bits (599), Expect = 6e-62
 Identities = 114/222 (51%), Positives = 153/222 (68%), Gaps = 3/222 (1%)
 Frame = +2

Query: 92  MTILGVPVLGF--VITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHV 262
           M + G  VLG   ++T+L+LQ+  AI  +H+      FY S D +G+F +DFDG+++F V
Sbjct: 1   MVLRGRLVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSV 60

Query: 263 DMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSD 442
           D++KRE VWRL EFG+FA F+ Q  L +IA+ KA+LE L+KRS              L  
Sbjct: 61  DLKKREAVWRLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNVSPRVAVLPK 120

Query: 443 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFM 622
             V+LGEPN+LIC +DK  PPV+N+TWLRNG PVT+GV+++ F  + DHLFRKFHYL F+
Sbjct: 121 SHVQLGEPNVLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTFV 180

Query: 623 PSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCA 748
           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 =  231 bits (590), Expect = 7e-61
 Identities = 114/223 (51%), Positives = 154/223 (69%), Gaps = 4/223 (1%)
 Frame = +2

Query: 92  MTILGVPVLGF--VITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHV 262
           M + G  VLG   ++T+L+LQ+  AI  +H+      FY S D +G+F +DFDG+++F V
Sbjct: 1   MVLRGRLVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSV 60

Query: 263 DMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSD 442
           D++KRE VWRL EFG+FA F+ Q  L +IA+ KA+LE L+KRS              +  
Sbjct: 61  DLKKREAVWRLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNGSTPQVAVLP 120

Query: 443 KP-VELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPF 619
           K  V+LGEPN+LIC +DK  PPV+N+TWLRNG PVT+GV+++ F  + DHLFRKFHYL F
Sbjct: 121 KSHVQLGEPNVLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTF 180

Query: 620 MPSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCA 748
           +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 =  223 bits (567), Expect = 3e-58
 Identities = 113/240 (47%), Positives = 142/240 (59%), Gaps = 1/240 (0%)
 Frame = +2

Query: 131 TILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFG 307
           T+++   S  IV +H+       Y +   SG +  +FDGDE F+VD+EKRETVWRL  F 
Sbjct: 16  TMMSPSGSEDIVADHIGTYGISIYHTYGPSGYYTHEFDGDEEFYVDLEKRETVWRLPVFS 75

Query: 308 HFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFI 487
            FA+F+ QGAL NIA  K NLEI+I+RS               S  PV LG+PN LIC +
Sbjct: 76  KFATFDPQGALRNIATTKHNLEIVIQRSNSTAATNKVPEVTVFSKSPVMLGQPNTLICHV 135

Query: 488 DKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWG 667
           D   PPV+N+TWLRNG  VT GVSET FL + D+ F K +YL F+PS +DVYDC+VEHWG
Sbjct: 136 DNIFPPVINITWLRNGHSVTEGVSETSFLIKSDYSFLKINYLTFLPSDDDVYDCKVEHWG 195

Query: 668 LDKPLLKHWEFEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 847
           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 =  209 bits (531), Expect = 5e-54
 Identities = 105/230 (45%), Positives = 132/230 (57%), Gaps = 1/230 (0%)
 Frame = +2

Query: 161 IVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 337
           IV +HV I     Y S   SG++  +FDGDE F+VD+EK+ET W+L  F    SF+ Q A
Sbjct: 26  IVADHVGIYGISIYQSYGPSGQYTHEFDGDEQFYVDLEKKETAWQLPLFSRMLSFDPQLA 85

Query: 338 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 517
           L NIA+ K +++ L K S               S  PV LG+PN LIC +D   PPV+N+
Sbjct: 86  LRNIAIMKLHVDFLTKFSNSTAATNKVPEVTVFSKSPVMLGQPNTLICHVDNIFPPVINI 145

Query: 518 TWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 697
           TWLRNG  VT GVSET FL R D+ F K  YL F+PS +D+YDC+VEHWGLD+PLLKHWE
Sbjct: 146 TWLRNGHSVTEGVSETSFLIRSDYSFLKIKYLAFLPSDDDIYDCKVEHWGLDEPLLKHWE 205

Query: 698 FEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 847
            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 =  207 bits (526), Expect = 2e-53
 Identities = 99/197 (50%), Positives = 122/197 (61%), Gaps = 1/197 (0%)
 Frame = +2

Query: 161 IVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 337
           IV +HV       Y +   SG+F F+FDGDE+F+VD+ K+ETVWRL EF +   FE Q A
Sbjct: 24  IVADHVGTYGTNVYQTYGASGQFTFEFDGDELFYVDLGKKETVWRLPEFSNITKFEVQSA 83

Query: 338 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 517
           L NI + K NL+ILIK S                   V LG PN LIC +D   PPV+N+
Sbjct: 84  LRNIVMSKRNLDILIKNSSFTPATSEIPEVAVFPKSSVVLGIPNTLICQVDNIFPPVINI 143

Query: 518 TWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 697
           TW  NG  V  G++ET F P+ DH F KF YL F+P+ ED YDC+VEHWGL++PL+KHWE
Sbjct: 144 TWFYNGHFVAEGIAETTFYPKSDHSFLKFSYLTFLPTNEDFYDCRVEHWGLEEPLVKHWE 203

Query: 698 FEAQTPLPETTENTVCA 748
            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 =  201 bits (512), Expect = 8e-52
 Identities = 96/179 (53%), Positives = 119/179 (66%), Gaps = 1/179 (0%)
 Frame = +2

Query: 161 IVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 337
           IV +HV     E Y S   SG++  +FDGDE+F+VD+ K+ETVWRL  F  FA F+ Q A
Sbjct: 26  IVADHVGSYGTEIYQSHGPSGQYTQEFDGDEMFYVDLGKKETVWRLPMFSQFAGFDPQAA 85

Query: 338 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 517
           L+ IA  K NL++L KRS               S  PV LG+PN LIC +D   PPV+N+
Sbjct: 86  LSEIATAKHNLDVLTKRSNFTPVINEVPEVTVFSKSPVMLGQPNTLICHVDNIFPPVINI 145

Query: 518 TWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHW 694
           TWL+NG  VT GVSET FLP++DH F K  YL F+PS  D+YDC+VEHWGLD+PLLKHW
Sbjct: 146 TWLKNGHAVTEGVSETSFLPKDDHSFLKIGYLTFLPSDNDIYDCKVEHWGLDEPLLKHW 204


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

 Score = 68.2 bits (165), Expect = 1e-11
 Identities = 51/200 (25%), Positives = 79/200 (39%), Gaps = 6/200 (3%)
 Frame = +2

Query: 164 VENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGALA 343
           ++NH  +   +      +      +D D++F  D  +   V RL EF  +A     G  +
Sbjct: 39  LQNHTFLHTMYCQDWSPNVALSESYDEDQLFSFDFSQSIRVPRLPEFADWA--HQHGDTS 96

Query: 344 NIAVDKANLEILIKR-----SXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPV 508
           +I  DK     +I+                      + KP+E G+PN L+CFI    PP 
Sbjct: 97  DIMFDKGFCRAMIEEIGPELEGQIPVSRGFPIVQVFTLKPLEFGKPNTLVCFISNLFPPT 156

Query: 509 VNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLK 688
           + V W    +PV  G   T     +   F+ F YL   P+  D++ C V H       + 
Sbjct: 157 LTVNWQHQSAPV-EGAGPTFVSAVDGLTFQAFSYLNVTPAPSDLFSCIVTHEIDGYTAIA 215

Query: 689 HWEFEAQTPLP-ETTENTVC 745
            W    Q  LP +  EN +C
Sbjct: 216 FW--VPQNALPSDLLENVLC 233


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

 Score = 60.1 bits (144), Expect = 4e-09
 Identities = 28/86 (32%), Positives = 40/86 (46%)
 Frame = +2

Query: 455 LGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTE 634
           L   N+L+C +  F P  + V W RN    T GV  T  +   D  F+    L   P   
Sbjct: 141 LNHHNLLVCSVTDFYPSQIKVRWFRNDREETAGVVSTPLIRNGDWTFQILVMLEMTPQRG 200

Query: 635 DVYDCQVEHWGLDKPLLKHWEFEAQT 712
           DVY C VEH  L  P++  W  ++++
Sbjct: 201 DVYTCHVEHPSLQSPIMVEWRAQSES 226


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

 Score = 59.3 bits (142), Expect = 6e-09
 Identities = 27/86 (31%), Positives = 40/86 (46%)
 Frame = +2

Query: 455 LGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTE 634
           L   N+L+C +  F P  + V W +NG   T G+  T  +   D  F+    L   P   
Sbjct: 141 LNHHNLLVCSVTDFYPGQIKVRWFQNGKEETAGIVSTPLIRNGDWTFQILVMLEMTPKRG 200

Query: 635 DVYDCQVEHWGLDKPLLKHWEFEAQT 712
           DVY C VEH  L  P+   W  ++++
Sbjct: 201 DVYTCHVEHPSLQSPISVEWRAQSES 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: 44,857,245
Number of Sequences: 33508
Number of extensions: 1208680
Number of successful extensions: 4111
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 3548
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): 4091
length of database: 16,112,626
effective HSP length: 104
effective length of database: 12,627,794
effective search space used: 3990382904
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= 20060611C-005425
         (1263 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]    372   e-103
Alignment   gi|NP_001011726.1| MHC class II DLA DQalpha chain [Canis famili...   224   1e-58
Alignment   gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati...   209   6e-54
Alignment   gi|XP_538853.2| PREDICTED: similar to major histocompatibility ...    81   2e-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   2e-10
Alignment   gi|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis fami...    60   3e-09
Alignment   gi|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Ca...    59   8e-09
Alignment   gi|XP_535458.1| PREDICTED: similar to beta-2-microglobulin prec...    55   1e-07
Alignment   gi|XP_850148.1| PREDICTED: similar to beta-2-microglobulin prec...    55   1e-07

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

 Score =  372 bits (955), Expect = e-103
 Identities = 183/254 (72%), Positives = 198/254 (77%), Gaps = 2/254 (0%)
 Frame = +2

Query: 92  MTILGVPVLGFVIT--ILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVD 265
           MTI GVPVLGF I   ++  Q+SWA+ E HVIIQAEFYL+PD SGEFMFDFDGDEIFHVD
Sbjct: 1   MTISGVPVLGFFIMAFLMGPQESWAVKEEHVIIQAEFYLTPDPSGEFMFDFDGDEIFHVD 60

Query: 266 MEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDK 445
           MEK+ETVWRLEEFG FASFEAQGALANIAVDKANL+ +IKRS              LS+ 
Sbjct: 61  MEKKETVWRLEEFGRFASFEAQGALANIAVDKANLDTMIKRSNHTPNTNVPPEVTVLSNT 120

Query: 446 PVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMP 625
           PVELGEPNILICFIDKFSPPV+NVTWLRNG+PVT GVSET+FLPREDHLFRKFHYLPF+P
Sbjct: 121 PVELGEPNILICFIDKFSPPVINVTWLRNGNPVTTGVSETIFLPREDHLFRKFHYLPFLP 180

Query: 626 STEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXX 805
           S EDVYDC+VEHWGLD+PLLKHWEFE  TPLPETTEN VCA                   
Sbjct: 181 SAEDVYDCKVEHWGLDEPLLKHWEFEPPTPLPETTENVVCALGLIVGLVGIITGTIFIIK 240

Query: 806 XXRKGNATERRGPL 847
             RK  A ERRGPL
Sbjct: 241 GMRKVKAGERRGPL 254


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

 Score =  224 bits (571), Expect = 1e-58
 Identities = 117/255 (45%), Positives = 145/255 (56%), Gaps = 3/255 (1%)
 Frame = +2

Query: 92  MTILGVPVLGFVITILNLQKSWA--IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHV 262
           M +  V +LG +I  + +  S    IV +HV       Y S   SG++  +FDGDE F+V
Sbjct: 1   MILNRVLILGTLILTIMMSPSGGEEIVADHVANYGINVYQSYGPSGQYTHEFDGDEEFYV 60

Query: 263 DMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSD 442
           D+EK+ETVWRL  F  F SF+ QGAL N+A+ K NL I+ KRS               S 
Sbjct: 61  DLEKKETVWRLPVFSTFRSFDPQGALRNLAIIKQNLNIMTKRSNQTAATNEVPEVTVFSK 120

Query: 443 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFM 622
            PV LG+PN LIC +D   PPV+NVTWL+N   VT GVSET F  + DH F K  YL F+
Sbjct: 121 SPVMLGQPNTLICLVDNIFPPVINVTWLKNRHSVTEGVSETSFFAKGDHSFSKISYLTFL 180

Query: 623 PSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXX 802
           PS ED+YDC+VEHWGLD+PLLKHWE E  TP+ E TE  VCA                  
Sbjct: 181 PSAEDIYDCKVEHWGLDEPLLKHWEPEVPTPMSELTETVVCALGLAVGLVGIVMGTVFII 240

Query: 803 XXXRKGNATERRGPL 847
              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 =  209 bits (531), Expect = 6e-54
 Identities = 94/192 (48%), Positives = 132/192 (68%), Gaps = 7/192 (3%)
 Frame = +2

Query: 194 FYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLE 373
           FY S   SG+F  +FDG+++F V+++KR+ VWRL EFG+ A F+ Q  LA+IAV KA+L+
Sbjct: 8   FYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEFGNLAHFDPQNGLASIAVIKAHLD 67

Query: 374 ILIKRSXXXXXXXXXXXXXXLSDKP-------VELGEPNILICFIDKFSPPVVNVTWLRN 532
           +L++RS              L  +        VELG+PN+LIC +D   PPV+N+TWLRN
Sbjct: 68  VLVERSNRTRAINGTHLSSPLPPRVAVLPKFRVELGQPNVLICIVDNIFPPVINITWLRN 127

Query: 533 GSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWEFEAQT 712
           G  ++ GV++T F  + DHLFRKF YL F+PS ED+YDC+VEHWGL++PLL+HWE +   
Sbjct: 128 GQIISEGVAQTSFYSQPDHLFRKFCYLTFVPSAEDMYDCKVEHWGLEEPLLRHWEPQVPI 187

Query: 713 PLPETTENTVCA 748
           P+P+T E  +CA
Sbjct: 188 PVPDTIETLICA 199


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

 Score = 80.9 bits (198), Expect = 2e-15
 Identities = 53/199 (26%), Positives = 88/199 (44%), Gaps = 5/199 (2%)
 Frame = +2

Query: 164 VENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGALA 343
           ++NH  +   +  +   S   +  +DGD++F  +  +   V RL EF  +A  +  G + 
Sbjct: 45  LQNHTFLHTMYCQNWSPSIGLLEAYDGDQLFSFNFSQNTRVPRLPEFADWA--QKSGDMP 102

Query: 344 NIAVDKANLEILI-----KRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPV 508
            I+ DKA  + +I     K                 + KP+E G+PN+L+CFI    PP 
Sbjct: 103 TISFDKAFCQAMIEEIGPKLEGQIPVSRGFPMVDVFTLKPLEFGKPNMLVCFISNLFPPT 162

Query: 509 VNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLK 688
           + V W  +  PV  G+  T     +   F+ F YL F P+  D++ C V H   +   + 
Sbjct: 163 LTVNWWHHLDPV-EGIGPTFVSAVDGFSFQAFSYLNFTPAPSDLFSCVVTHEIDNYTAIA 221

Query: 689 HWEFEAQTPLPETTENTVC 745
           +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 = +2

Query: 128 ITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEF 304
           +++L+  ++ AI  +H+      FY S   SG+F  +FDG+++F V+++KR+ VWRL EF
Sbjct: 1   MSLLSPHETGAIEADHMGSYGPAFYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEF 60

Query: 305 GHFASFEAQGALANIAVDKANLEILIKRS 391
           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 = 64.3 bits (155), Expect = 2e-10
 Identities = 33/101 (32%), Positives = 50/101 (49%)
 Frame = +2

Query: 443 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFM 622
           KP+E G+PN+L+CFI    PP + V W  +  PV  G+  T     +   F+ F YL F 
Sbjct: 46  KPLEFGKPNMLVCFISNLFPPTLTVNWWHHLDPV-EGIGPTFVSAVDGFSFQAFSYLNFT 104

Query: 623 PSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVC 745
           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 = 60.5 bits (145), Expect = 3e-09
 Identities = 30/90 (33%), Positives = 44/90 (48%)
 Frame = +2

Query: 443 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFM 622
           K   L   N+L+C ++ F P  + V WLRNG     GV  T  +   D  F+    L  +
Sbjct: 134 KTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNGDWTFQILVMLEIV 193

Query: 623 PSTEDVYDCQVEHWGLDKPLLKHWEFEAQT 712
           P + +VY CQVEH  L  P+   W  ++ +
Sbjct: 194 PQSGEVYTCQVEHPSLTSPVTVEWRAQSDS 223


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

 Score = 59.3 bits (142), Expect = 8e-09
 Identities = 28/86 (32%), Positives = 39/86 (45%)
 Frame = +2

Query: 455 LGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTE 634
           L   N+L+C +  F P  + V W RN    T GV  T  +   D  F+    L   P   
Sbjct: 141 LNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLIRNGDWTFQILVMLEMTPQRG 200

Query: 635 DVYDCQVEHWGLDKPLLKHWEFEAQT 712
           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 = 55.5 bits (132), Expect = 1e-07
 Identities = 26/87 (29%), Positives = 45/87 (51%)
 Frame = +2

Query: 437 SDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLP 616
           S  P E G+PN L C++  F PP + +  L+NG  +    ++  F   +D  F    +  
Sbjct: 38  SRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSF--SKDWTFYLLVHTE 95

Query: 617 FMPSTEDVYDCQVEHWGLDKPLLKHWE 697
           F P+ +D + C+V+H  L +P +  W+
Sbjct: 96  FTPNEQDEFSCRVKHVTLSEPQIVKWD 122


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

 Score = 55.5 bits (132), Expect = 1e-07
 Identities = 26/87 (29%), Positives = 45/87 (51%)
 Frame = +2

Query: 437 SDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLP 616
           S  P E G+PN L C++  F PP + +  L+NG  +    ++  F   +D  F    +  
Sbjct: 38  SRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSF--SKDWTFYLLVHTE 95

Query: 617 FMPSTEDVYDCQVEHWGLDKPLLKHWE 697
           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: 52,668,588
Number of Sequences: 33732
Number of extensions: 1417105
Number of successful extensions: 4756
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 4024
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): 4739
length of database: 19,266,565
effective HSP length: 106
effective length of database: 15,690,973
effective search space used: 4926965522
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= 20060611C-005425
         (1263 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 ...   372   e-103
Alignment   gi|NP_291032.2| major histocompatibility complex, class II, DP ...   241   1e-63
Alignment   gi|NP_002110.1| major histocompatibility complex, class II, DO ...   231   1e-60
Alignment   gi|NP_002113.2| major histocompatibility complex, class II, DQ ...   214   1e-55
Alignment   gi|XP_949974.1| PREDICTED: similar to HLA class II histocompati...   213   2e-55
Alignment   gi|XP_949973.1| PREDICTED: similar to HLA class II histocompati...   213   2e-55
Alignment   gi|XP_949971.1| PREDICTED: similar to HLA class II histocompati...   213   2e-55
Alignment   gi|XP_945969.1| PREDICTED: similar to HLA class II histocompati...   213   2e-55
Alignment   gi|NP_064440.1| major histocompatibility complex, class II, DQ ...   209   3e-54
Alignment   gi|XP_941306.1| PREDICTED: similar to HLA class II histocompati...   202   4e-52

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

 Score =  372 bits (955), Expect = e-103
 Identities = 182/254 (71%), Positives = 199/254 (78%), Gaps = 2/254 (0%)
 Frame = +2

Query: 92  MTILGVPVLGFVI--TILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVD 265
           M I GVPVLGF I   +++ Q+SWAI E HVIIQAEFYL+PD+SGEFMFDFDGDEIFHVD
Sbjct: 1   MAISGVPVLGFFIIAVLMSAQESWAIKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVD 60

Query: 266 MEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDK 445
           M K+ETVWRLEEFG FASFEAQGALANIAVDKANLEI+ KRS              L++ 
Sbjct: 61  MAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNS 120

Query: 446 PVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMP 625
           PVEL EPN+LICFIDKF+PPVVNVTWLRNG PVT GVSETVFLPREDHLFRKFHYLPF+P
Sbjct: 121 PVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLP 180

Query: 626 STEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXX 805
           STEDVYDC+VEHWGLD+PLLKHWEF+A +PLPETTEN VCA                   
Sbjct: 181 STEDVYDCRVEHWGLDEPLLKHWEFDAPSPLPETTENVVCALGLTVGLVGIIIGTIFIIK 240

Query: 806 XXRKGNATERRGPL 847
             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 =  241 bits (615), Expect = 1e-63
 Identities = 116/205 (56%), Positives = 144/205 (70%)
 Frame = +2

Query: 134 ILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHF 313
           +L+L+ + AI  +HV   A F  +   +GEFMF+FD DE+F+VD++K+ETVW LEEFG  
Sbjct: 23  LLSLRGAGAIKADHVSTYAAFVQTHRPTGEFMFEFDEDEMFYVDLDKKETVWHLEEFGQA 82

Query: 314 ASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDK 493
            SFEAQG LANIA+   NL  LI+RS                 +PVELG+PN LIC IDK
Sbjct: 83  FSFEAQGGLANIAILNNNLNTLIQRSNHTQATNDPPEVTVFPKEPVELGQPNTLICHIDK 142

Query: 494 FSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLD 673
           F PPV+NVTWL NG  VT GV+E++FLPR D+ F KFHYL F+PS ED YDC+VEHWGLD
Sbjct: 143 FFPPVLNVTWLCNGELVTEGVAESLFLPRTDYSFHKFHYLTFVPSAEDFYDCRVEHWGLD 202

Query: 674 KPLLKHWEFEAQTPLPETTENTVCA 748
           +PLLKHWE +    +PETTE  +CA
Sbjct: 203 QPLLKHWEAQEPIQMPETTETVLCA 227


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

 Score =  231 bits (588), Expect = 1e-60
 Identities = 113/215 (52%), Positives = 144/215 (66%), Gaps = 3/215 (1%)
 Frame = +2

Query: 113 VLGF--VITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRET 283
           VLGF  ++T+L+ Q++ A   +H+      FY S   SG+F  +FD +++F VD++K E 
Sbjct: 8   VLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEA 67

Query: 284 VWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGE 463
           VWRL EFG FA F+ QG LA IA  KA+L+IL++RS              L    VELG+
Sbjct: 68  VWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQ 127

Query: 464 PNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVY 643
           PNILIC +D   PPV+N+TWLRNG  VT GV++T F  + DHLFRKFHYLPF+PS EDVY
Sbjct: 128 PNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVY 187

Query: 644 DCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCA 748
           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 =  214 bits (546), Expect = 1e-55
 Identities = 107/230 (46%), Positives = 131/230 (56%), Gaps = 1/230 (0%)
 Frame = +2

Query: 161 IVENHVI-IQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 337
           IV +HV       Y     SG++  +FDGDE F+VD+E++ET WR  EF  F  F+ QGA
Sbjct: 26  IVADHVASCGVNLYQFYGPSGQYTHEFDGDEQFYVDLERKETAWRWPEFSKFGGFDPQGA 85

Query: 338 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 517
           L N+AV K NL I+IKR                S  PV LG+PN LIC +D   PPVVN+
Sbjct: 86  LRNMAVAKHNLNIMIKRYNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNI 145

Query: 518 TWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 697
           TWL NG  VT GVSET FL + DH F K  YL F+PS +++YDC+VEHWGLD+PLLKHWE
Sbjct: 146 TWLSNGQSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDQPLLKHWE 205

Query: 698 FEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 847
            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 =  213 bits (543), Expect = 2e-55
 Identities = 109/230 (47%), Positives = 133/230 (57%), Gaps = 1/230 (0%)
 Frame = +2

Query: 161 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 337
           IV +HV       Y S   SG++  +FDGDE F+VD+E++ETVW+L  F  F  F+ Q A
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFA 85

Query: 338 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 517
           L NIAV K NL I+IKRS               S  PV LG+PN LIC +D   PPVVN+
Sbjct: 86  LTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNI 145

Query: 518 TWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 697
           TWL NG  VT GVSET FL + DH F K  YL F+PS +++YDC+VEHWGLD+PLLKHWE
Sbjct: 146 TWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWE 205

Query: 698 FEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 847
            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 =  213 bits (543), Expect = 2e-55
 Identities = 109/230 (47%), Positives = 133/230 (57%), Gaps = 1/230 (0%)
 Frame = +2

Query: 161 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 337
           IV +HV       Y S   SG++  +FDGDE F+VD+E++ETVW+L  F  F  F+ Q A
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFA 85

Query: 338 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 517
           L NIAV K NL I+IKRS               S  PV LG+PN LIC +D   PPVVN+
Sbjct: 86  LTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNI 145

Query: 518 TWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 697
           TWL NG  VT GVSET FL + DH F K  YL F+PS +++YDC+VEHWGLD+PLLKHWE
Sbjct: 146 TWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWE 205

Query: 698 FEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 847
            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 =  213 bits (543), Expect = 2e-55
 Identities = 109/230 (47%), Positives = 133/230 (57%), Gaps = 1/230 (0%)
 Frame = +2

Query: 161 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 337
           IV +HV       Y S   SG++  +FDGDE F+VD+E++ETVW+L  F  F  F+ Q A
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFA 85

Query: 338 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 517
           L NIAV K NL I+IKRS               S  PV LG+PN LIC +D   PPVVN+
Sbjct: 86  LTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNI 145

Query: 518 TWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 697
           TWL NG  VT GVSET FL + DH F K  YL F+PS +++YDC+VEHWGLD+PLLKHWE
Sbjct: 146 TWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWE 205

Query: 698 FEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 847
            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 =  213 bits (543), Expect = 2e-55
 Identities = 109/230 (47%), Positives = 133/230 (57%), Gaps = 1/230 (0%)
 Frame = +2

Query: 161 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 337
           IV +HV       Y S   SG++  +FDGDE F+VD+E++ETVW+L  F  F  F+ Q A
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFA 85

Query: 338 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 517
           L NIAV K NL I+IKRS               S  PV LG+PN LIC +D   PPVVN+
Sbjct: 86  LTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNI 145

Query: 518 TWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 697
           TWL NG  VT GVSET FL + DH F K  YL F+PS +++YDC+VEHWGLD+PLLKHWE
Sbjct: 146 TWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWE 205

Query: 698 FEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 847
            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 =  209 bits (533), Expect = 3e-54
 Identities = 101/197 (51%), Positives = 126/197 (63%), Gaps = 1/197 (0%)
 Frame = +2

Query: 161 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 337
           IV +HV      FY S   SG++  +FDGDE F+VD+E +ETVW+L  F  F SF+ Q A
Sbjct: 26  IVADHVASYGVNFYQSHGPSGQYTHEFDGDEEFYVDLETKETVWQLPMFSKFISFDPQSA 85

Query: 338 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 517
           L N+AV K  LE ++++S               S  PV LG+PN LIC +D   PPVVN+
Sbjct: 86  LRNMAVGKHTLEFMMRQSNSTAATNEVPEVTVFSKFPVTLGQPNTLICLVDNIFPPVVNI 145

Query: 518 TWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 697
           TWL NG  VT GVSET FL + DH F K  YL F+PS +++YDC+VEHWGLD+PLLKHWE
Sbjct: 146 TWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWE 205

Query: 698 FEAQTPLPETTENTVCA 748
            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 =  202 bits (515), Expect = 4e-52
 Identities = 109/230 (47%), Positives = 128/230 (55%), Gaps = 1/230 (0%)
 Frame = +2

Query: 161 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 337
           IV +HV       Y S   SG++  +FDGDE F+VD+ ++ETVW L     F  F+ Q A
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFR-FDPQFA 84

Query: 338 LANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 517
           L NIAV K NL  LIKRS               S  PV LG+PNILIC +D   PPVVN+
Sbjct: 85  LTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVNI 144

Query: 518 TWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 697
           TWL NG  VT GVSET FL + DH F K  YL  +PS E+ YDC+VEHWGLDKPLLKHWE
Sbjct: 145 TWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHWE 204

Query: 698 FEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 847
            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: 50,703,795
Number of Sequences: 39411
Number of extensions: 1404342
Number of successful extensions: 4741
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 4054
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): 4713
length of database: 17,774,539
effective HSP length: 105
effective length of database: 13,636,384
effective search space used: 4295460960
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= 20060611C-005425
         (1263 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 ...   330   3e-90
Alignment   gi|NP_032232.1| histocompatibility 2, O region alpha locus [Mus...   220   2e-57
Alignment   gi|NP_034508.2| histocompatibility 2, class II antigen A, alpha...   216   5e-56
Alignment   gi|NP_034516.2| histocompatibility 2, class II, locus DMa [Mus ...    81   3e-15
Alignment   gi|NP_996988.1| histocompatibility 2, class II antigen A, beta ...    60   4e-09
Alignment   gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ...    58   2e-08
Alignment   gi|NP_034512.1| histocompatibility 2, class II antigen E beta [...    58   2e-08
Alignment   gi|NP_034517.2| histocompatibility 2, class II, locus Mb1 [Mus ...    58   2e-08
Alignment   gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ...    57   4e-08
Alignment   gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/...    57   5e-08

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

 Score =  330 bits (845), Expect = 3e-90
 Identities = 158/239 (66%), Positives = 177/239 (74%)
 Frame = +2

Query: 122 FVITILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEE 301
           F+  +++ QKSWAI E H IIQAEFYL PDK GEFMFDFDGDEIFHVD+EK ET+WRLEE
Sbjct: 13  FIAVLMSSQKSWAIKEEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEE 72

Query: 302 FGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILIC 481
           F  FASFEAQGALANIAVDKANL+++ +RS              LS  PV LGEPNILIC
Sbjct: 73  FAKFASFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPNILIC 132

Query: 482 FIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEH 661
           FIDKFSPPVVNVTW RNG PVT GVSETVFLPR+DHLFRKFHYL F+PST+D YDC+V+H
Sbjct: 133 FIDKFSPPVVNVTWFRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDH 192

Query: 662 WGLDKPLLKHWEFEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERR 838
           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 =  220 bits (561), Expect = 2e-57
 Identities = 107/214 (50%), Positives = 143/214 (66%), Gaps = 1/214 (0%)
 Frame = +2

Query: 107 VPVLGFVITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRET 283
           VPVL  V++ L+ +   AI  +H+      FY S D SG+F  +FDG++IF VD++  E 
Sbjct: 8   VPVLLTVMSFLSPRGVRAIKADHMGSYGPAFYQSYDASGQFTHEFDGEQIFSVDLKNEEV 67

Query: 284 VWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLSDKPVELGE 463
           VWRL EFG FA  + Q  L +I++ KA+L+IL++RS              L    VELG+
Sbjct: 68  VWRLPEFGDFAHSDFQSGLMSISMIKAHLDILVERSNRTRAVSVPPRVTVLPKTRVELGK 127

Query: 464 PNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVY 643
           PN+LIC +D   PPV+NVTWLRN  P+T+GV++T F  + +H FRKFHYL F+PS EDVY
Sbjct: 128 PNVLICIVDDIFPPVINVTWLRNSQPITKGVAQTSFYSQPNHRFRKFHYLTFVPSAEDVY 187

Query: 644 DCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVC 745
           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 =  216 bits (549), Expect = 5e-56
 Identities = 110/256 (42%), Positives = 142/256 (55%), Gaps = 1/256 (0%)
 Frame = +2

Query: 83  KEKMTILGVPVLGFVITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFH 259
           + +  ILGV  L  ++++   +    I  +HV       Y SP   G++ F+FDGDE+F+
Sbjct: 3   RSRALILGVLALTTMLSLCGGEDD--IEADHVGTYGISVYQSPGDIGQYTFEFDGDELFY 60

Query: 260 VDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSXXXXXXXXXXXXXXLS 439
           VD++K+ETVW L EFG  ASF+ QG L NIAV K NL +L KRS                
Sbjct: 61  VDLDKKETVWMLPEFGQLASFDPQGGLQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFP 120

Query: 440 DKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPF 619
             PV LG+PN LICF+D   PPV+N+TWLRN   V  GV ET F    D+ F K  YL F
Sbjct: 121 KSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTF 180

Query: 620 MPSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXX 799
           +PS +D+YDC+VEHWGL++P+LKHWE E   P+ E TE  VCA                 
Sbjct: 181 IPSDDDIYDCKVEHWGLEEPVLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTIFI 240

Query: 800 XXXXRKGNATERRGPL 847
               R G  +   GPL
Sbjct: 241 IQGLRSGGTSRHPGPL 256


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

 Score = 80.9 bits (198), Expect = 3e-15
 Identities = 65/231 (28%), Positives = 96/231 (41%), Gaps = 17/231 (7%)
 Frame = +2

Query: 104 GVPVLGFVITILNLQKSWAIVE-----------NHVIIQAEFYLSPDKSGEFMFDFDGDE 250
           G  +L  +  +  L  SWA++E           NH      F      +      +D DE
Sbjct: 8   GAVLLRLLRLLWLLPHSWAVLEASTPVLWDDPQNHTFRHTLFCQDGIPNIGLSETYDEDE 67

Query: 251 IFHVDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILI-----KRSXXXXXXXX 415
           +F  D  +   V +L +F  +A  + QG  + IA DK+  E+L+     K          
Sbjct: 68  LFSFDFSQNTRVPQLPDFAEWA--QGQGDASAIAFDKSFCEMLMREVSPKLEGQIPVSRG 125

Query: 416 XXXXXXLSDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLF 595
                  + KP+E G+PN L+CFI    PP + V W  + +PV  G S T     +   F
Sbjct: 126 LPVAEVFTLKPLEFGKPNTLVCFISNLFPPTLTVNWQLHSAPV-EGASPTSISAVDGLTF 184

Query: 596 RKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLP-ETTENTVC 745
           + F YL F P   D+Y C V H       + +W    Q  LP +  EN +C
Sbjct: 185 QAFSYLNFTPEPFDLYSCTVTHEIDRYTAIAYW--VPQNALPSDLLENALC 233


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

 Score = 60.5 bits (145), Expect = 4e-09
 Identities = 29/86 (33%), Positives = 40/86 (46%)
 Frame = +2

Query: 455 LGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTE 634
           L   N L+C +  F P  + V W RNG   T GVS T  +   D  F+    L   P   
Sbjct: 137 LNHHNTLVCSVTDFYPTQIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRG 196

Query: 635 DVYDCQVEHWGLDKPLLKHWEFEAQT 712
           +VY C VEH  L  P+   W  ++++
Sbjct: 197 EVYTCHVEHPSLKSPITVEWRAQSES 222


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

 Score = 57.8 bits (138), Expect = 2e-08
 Identities = 29/84 (34%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
 Frame = +2

Query: 446 PVELGEPNILICFIDKFSPPVVNVTWLRNGSPV-TRGVSETVFLPREDHLFRKFHYLPFM 622
           P    EP +L C++  F P  V +TW++NG  V +    E    P  D  ++   YL   
Sbjct: 124 PFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPNGDWTYQTVSYLALT 183

Query: 623 PSTEDVYDCQVEHWGLDKPLLKHW 694
           PS  DVY C V+H G  +P+   W
Sbjct: 184 PSYGDVYTCVVQHSGTSEPIRGDW 207


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

 Score = 57.8 bits (138), Expect = 2e-08
 Identities = 28/88 (31%), Positives = 42/88 (47%)
 Frame = +2

Query: 443 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFM 622
           K   L   N+L+C +  F P  + V W RNG     G+  T  +   D  F+    L  +
Sbjct: 132 KTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETV 191

Query: 623 PSTEDVYDCQVEHWGLDKPLLKHWEFEA 706
           P + +VY CQVEH  L  P+   W+ ++
Sbjct: 192 PQSGEVYTCQVEHPSLTDPVTVEWKAQS 219


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

 Score = 57.8 bits (138), Expect = 2e-08
 Identities = 29/84 (34%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
 Frame = +2

Query: 446 PVELGEPNILICFIDKFSPPVVNVTWLRNGSPV-TRGVSETVFLPREDHLFRKFHYLPFM 622
           P    EP +L C++  F P  V +TW++NG  V +    E    P  D  ++   YL   
Sbjct: 124 PFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPNGDWTYQTVSYLALT 183

Query: 623 PSTEDVYDCQVEHWGLDKPLLKHW 694
           PS  DVY C V+H G  +P+   W
Sbjct: 184 PSYGDVYTCVVQHSGTSEPIRGDW 207


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

 Score = 57.0 bits (136), Expect = 4e-08
 Identities = 28/85 (32%), Positives = 43/85 (50%)
 Frame = +2

Query: 455 LGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTE 634
           L + N+L+C +  F P  ++V W RNG     GV  T  +   D  F+    L  +P   
Sbjct: 135 LQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVRNGDWTFQTTVMLEMIPELG 194

Query: 635 DVYDCQVEHWGLDKPLLKHWEFEAQ 709
           D+Y C VEH GL +P+   W  +++
Sbjct: 195 DIYSCLVEHPGLLRPVSVAWMAQSE 219


>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 = 5e-08
 Identities = 28/84 (33%), Positives = 38/84 (45%)
 Frame = +2

Query: 443 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFM 622
           K   L   N+L+C +  F P  + V W RNG     GV  T  +   D  ++    L  +
Sbjct: 133 KTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNRDWTYQTLVMLEMV 192

Query: 623 PSTEDVYDCQVEHWGLDKPLLKHW 694
           P   +VY CQVEH  L  P+   W
Sbjct: 193 PRGGEVYTCQVEHPSLTSPVTVEW 216


  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: 60,315,915
Number of Sequences: 45328
Number of extensions: 1622428
Number of successful extensions: 5368
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 4496
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): 5356
length of database: 21,768,885
effective HSP length: 106
effective length of database: 16,964,117
effective search space used: 5326732738
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)