Animal-Genome cDNA 20060611S-005603


Search to RefSeqSP

BLASTX 2.2.10 [Oct-19-2004]


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

Query= 20060611S-005603
         (835 letters)

Database: RefSeqSP 
           1040 sequences; 434,620 total letters

Searching...done

 ***** No hits found ******

  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: 825,998
Number of Sequences: 1040
Number of extensions: 20788
Number of successful extensions: 57
Number of sequences better than 1.0e-05: 0
Number of HSP's better than  0.0 without gapping: 51
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): 56
length of database: 434,620
effective HSP length: 75
effective length of database: 356,620
effective search space used: 72037240
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqBP

BLASTX 2.2.10 [Oct-19-2004]


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

Query= 20060611S-005603
         (835 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, ...   164   8e-41
Alignment   gi|XP_604082.2| PREDICTED: similar to HLA class II histocompati...   121   6e-28
Alignment   gi|XP_883292.1| PREDICTED: similar to HLA class II histocompati...   115   5e-26
Alignment   gi|NP_001013619.2| histocompatibility complex, class II, DQ alp...   109   5e-25
Alignment   gi|NP_001012693.1| major histocompatibility complex, class II, ...   105   3e-23
Alignment   gi|NP_001012699.1| major histocompatibility complex, class II, ...   103   1e-22
Alignment   gi|NP_001012696.1| major histocompatibility complex, class II, ...   100   1e-21

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

 Score =  164 bits (415), Expect = 8e-41
 Identities = 89/193 (46%), Positives = 121/193 (62%), Gaps = 1/193 (0%)
 Frame = +3

Query: 159 HVIILPEFYLTPD*SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLA 338
           HVII  EFYL P+ S +F FDFD ++ FHV M  +ET W LP      +++A GAL+++A
Sbjct: 29  HVIIQAEFYLKPEESAEFMFDFDGDEIFHVDMGKKETVWRLPEFGHFASFEAQGALANMA 88

Query: 339 VDKSHLEILIIRSNNPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQN 518
           V K++L+I+I RSNN P T VPP++T+L  K V L  PN L+C + ++ P ++SV  L+N
Sbjct: 89  VMKANLDIMIKRSNNTPNTNVPPEVTLLPNKPVELGEPNTLICFIDKFSPPVISVTWLRN 148

Query: 519 VSPGPVVVSDPLVLVREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCEF-ASH 695
             P    VS  + L R DHLFR FH L F+P+TE  YDC VEH  L+ PL +  E+ A  
Sbjct: 149 GKPVTDGVSQTVFLPRNDHLFRKFHYLPFLPTTEDVYDCKVEHLGLNEPLLKHWEYEAPA 208

Query: 696 PLLHRLHTSSCVL 734
           PL      + C L
Sbjct: 209 PLPETTENAVCAL 221


>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 =  121 bits (304), Expect = 6e-28
 Identities = 67/170 (39%), Positives = 90/170 (52%)
 Frame = +3

Query: 174 PEFYLTPD*SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLAVDKSH 353
           P FY + D +GQF +DFD E  F V +  RE  W LP       +D    L  +A+ K+H
Sbjct: 36  PAFYQSYDGAGQFTYDFDGEQLFSVDLKKREAVWRLPEFGNFAYFDPQSGLVSIAMIKAH 95

Query: 354 LEILIIRSNNPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQNVSPGP 533
           LE L+ RSN      V P++ VL    V L  PN L+C + +  P ++++  L+N  P  
Sbjct: 96  LEDLVKRSNGTRAPNVSPRVAVLPKSHVQLGEPNVLICIVDKIFPPVINITWLRNGHPVT 155

Query: 534 VVVSDPLVLVREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCE 683
             V+      + DHLFR FH L FVP  +  YDC VEHW LD PL +  E
Sbjct: 156 QGVTQSSFYAQPDHLFRKFHYLTFVPLVDDFYDCKVEHWGLDQPLFQHWE 205


>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 =  115 bits (287), Expect = 5e-26
 Identities = 68/174 (39%), Positives = 91/174 (52%), Gaps = 4/174 (2%)
 Frame = +3

Query: 174 PEFYLTPD*SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLAVDKSH 353
           P FY + D +GQF +DFD E  F V +  RE  W LP       +D    L  +A+ K+H
Sbjct: 36  PAFYQSYDGAGQFTYDFDGEQLFSVDLKKREAVWRLPEFGNFAYFDPQSGLVSIAMIKAH 95

Query: 354 LEILIIRSNNPPQTTVP----PKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQNV 521
           LE L+ RSN    T  P    P++ VL    V L  PN L+C + +  P ++++  L+N 
Sbjct: 96  LEDLVKRSNG---TRAPNGSTPQVAVLPKSHVQLGEPNVLICIVDKIFPPVINITWLRNG 152

Query: 522 SPGPVVVSDPLVLVREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCE 683
            P    V+      + DHLFR FH L FVP  +  YDC VEHW LD PL +  E
Sbjct: 153 HPVTQGVTQSSFYAQPDHLFRKFHYLTFVPLVDDFYDCKVEHWGLDQPLFQHWE 206


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

 Score =  109 bits (273), Expect(2) = 5e-25
 Identities = 61/167 (36%), Positives = 93/167 (55%)
 Frame = +3

Query: 183 YLTPD*SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLAVDKSHLEI 362
           Y T   SG +  +FD ++ F+V ++ RET W LP   +   +D  GAL ++A  K +LEI
Sbjct: 39  YHTYGPSGYYTHEFDGDEEFYVDLEKRETVWRLPVFSKFATFDPQGALRNIATTKHNLEI 98

Query: 363 LIIRSNNPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQNVSPGPVVV 542
           +I RSN+   T   P++TV +   V L  PN L+C +    P ++++  L+N       V
Sbjct: 99  VIQRSNSTAATNKVPEVTVFSKSPVMLGQPNTLICHVDNIFPPVINITWLRNGHSVTEGV 158

Query: 543 SDPLVLVREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCE 683
           S+   L++ D+ F   + L F+PS +  YDC VEHW LD PL +  E
Sbjct: 159 SETSFLIKSDYSFLKINYLTFLPSDDDVYDCKVEHWGLDEPLLKHWE 205



 Score = 23.1 bits (48), Expect(2) = 5e-25
 Identities = 11/21 (52%), Positives = 13/21 (61%)
 Frame = +2

Query: 713 TYIIVCPLDLIVALVRIMIRT 775
           T  +VC L L V LV IM+ T
Sbjct: 216 TETVVCALGLTVGLVGIMVGT 236


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

 Score =  105 bits (263), Expect = 3e-23
 Identities = 58/161 (36%), Positives = 90/161 (55%)
 Frame = +3

Query: 201 SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLAVDKSHLEILIIRSN 380
           SGQ+  +FD ++ F+V ++ +ETAW LP   R  ++D   AL ++A+ K H++ L   SN
Sbjct: 45  SGQYTHEFDGDEQFYVDLEKKETAWQLPLFSRMLSFDPQLALRNIAIMKLHVDFLTKFSN 104

Query: 381 NPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQNVSPGPVVVSDPLVL 560
           +   T   P++TV +   V L  PN L+C +    P ++++  L+N       VS+   L
Sbjct: 105 STAATNKVPEVTVFSKSPVMLGQPNTLICHVDNIFPPVINITWLRNGHSVTEGVSETSFL 164

Query: 561 VREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCE 683
           +R D+ F     L F+PS +  YDC VEHW LD PL +  E
Sbjct: 165 IRSDYSFLKIKYLAFLPSDDDIYDCKVEHWGLDEPLLKHWE 205


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

 Score =  103 bits (258), Expect = 1e-22
 Identities = 62/180 (34%), Positives = 93/180 (51%), Gaps = 1/180 (0%)
 Frame = +3

Query: 177 EFYLTPD*SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLAVDKSHL 356
           E Y +   SGQ+  +FD ++ F+V +  +ET W LP   +   +D   ALS +A  K +L
Sbjct: 37  EIYQSHGPSGQYTQEFDGDEMFYVDLGKKETVWRLPMFSQFAGFDPQAALSEIATAKHNL 96

Query: 357 EILIIRSNNPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQNVSPGPV 536
           ++L  RSN  P     P++TV +   V L  PN L+C +    P ++++  L+N      
Sbjct: 97  DVLTKRSNFTPVINEVPEVTVFSKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHAVTE 156

Query: 537 VVSDPLVLVREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNP-LREQCEFASHPLLHRL 713
            VS+   L ++DH F     L F+PS    YDC VEHW LD P L+    +  HP  + L
Sbjct: 157 GVSETSFLPKDDHSFLKIGYLTFLPSDNDIYDCKVEHWGLDEPLLKHWGMYEFHPFRYSL 216


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

 Score =  100 bits (249), Expect = 1e-21
 Identities = 56/167 (33%), Positives = 87/167 (52%)
 Frame = +3

Query: 183 YLTPD*SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLAVDKSHLEI 362
           Y T   SGQF F+FD ++ F+V +  +ET W LP     T ++   AL ++ + K +L+I
Sbjct: 37  YQTYGASGQFTFEFDGDELFYVDLGKKETVWRLPEFSNITKFEVQSALRNIVMSKRNLDI 96

Query: 363 LIIRSNNPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQNVSPGPVVV 542
           LI  S+  P T+  P++ V     V L  PN L+C +    P ++++    N       +
Sbjct: 97  LIKNSSFTPATSEIPEVAVFPKSSVVLGIPNTLICQVDNIFPPVINITWFYNGHFVAEGI 156

Query: 543 SDPLVLVREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCE 683
           ++     + DH F  F  L F+P+ E  YDC VEHW L+ PL +  E
Sbjct: 157 AETTFYPKSDHSFLKFSYLTFLPTNEDFYDCRVEHWGLEEPLVKHWE 203


  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: 30,717,455
Number of Sequences: 33508
Number of extensions: 794701
Number of successful extensions: 2088
Number of sequences better than 1.0e-05: 7
Number of HSP's better than  0.0 without gapping: 1924
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): 2078
length of database: 16,112,626
effective HSP length: 100
effective length of database: 12,761,826
effective search space used: 2258843202
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqCP

BLASTX 2.2.10 [Oct-19-2004]


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

Query= 20060611S-005603
         (835 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]    180   2e-46
Alignment   gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati...   108   6e-24
Alignment   gi|NP_001011726.1| MHC class II DLA DQalpha chain [Canis famili...   108   8e-24
Alignment   gi|XP_532104.2| PREDICTED: similar to HLA class II histocompati...    61   1e-09

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

 Score =  180 bits (457), Expect(2) = 2e-46
 Identities = 90/177 (50%), Positives = 122/177 (68%)
 Frame = +3

Query: 156 EHVIILPEFYLTPD*SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHL 335
           EHVII  EFYLTPD SG+F FDFD ++ FHV M+ +ET W L    R  +++A GAL+++
Sbjct: 29  EHVIIQAEFYLTPDPSGEFMFDFDGDEIFHVDMEKKETVWRLEEFGRFASFEAQGALANI 88

Query: 336 AVDKSHLEILIIRSNNPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQ 515
           AVDK++L+ +I RSN+ P T VPP++TVL+   V L  PN L+C + ++ P +++V  L+
Sbjct: 89  AVDKANLDTMIKRSNHTPNTNVPPEVTVLSNTPVELGEPNILICFIDKFSPPVINVTWLR 148

Query: 516 NVSPGPVVVSDPLVLVREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCEF 686
           N +P    VS+ + L REDHLFR FH L F+PS E  YDC VEHW LD PL +  EF
Sbjct: 149 NGNPVTTGVSETIFLPREDHLFRKFHYLPFLPSAEDVYDCKVEHWGLDEPLLKHWEF 205



 Score = 24.3 bits (51), Expect(2) = 2e-46
 Identities = 13/24 (54%), Positives = 15/24 (62%)
 Frame = +2

Query: 704 P*TTYIIVCPLDLIVALVRIMIRT 775
           P TT  +VC L LIV LV I+  T
Sbjct: 212 PETTENVVCALGLIVGLVGIITGT 235


>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 =  108 bits (270), Expect = 6e-24
 Identities = 64/177 (36%), Positives = 90/177 (50%), Gaps = 7/177 (3%)
 Frame = +3

Query: 174 PEFYLTPD*SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLAVDKSH 353
           P FY +   SGQF  +FD E  F V +  R+  W LP      ++D    L+ +AV K+H
Sbjct: 6   PAFYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEFGNLAHFDPQNGLASIAVIKAH 65

Query: 354 LEILIIRSNNPP-------QTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRL 512
           L++L+ RSN           + +PP++ VL    V L  PN L+C +    P ++++  L
Sbjct: 66  LDVLVERSNRTRAINGTHLSSPLPPRVAVLPKFRVELGQPNVLICIVDNIFPPVINITWL 125

Query: 513 QNVSPGPVVVSDPLVLVREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCE 683
           +N       V+      + DHLFR F  L FVPS E  YDC VEHW L+ PL    E
Sbjct: 126 RNGQIISEGVAQTSFYSQPDHLFRKFCYLTFVPSAEDMYDCKVEHWGLEEPLLRHWE 182


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

 Score =  108 bits (269), Expect = 8e-24
 Identities = 60/161 (37%), Positives = 87/161 (54%)
 Frame = +3

Query: 201 SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLAVDKSHLEILIIRSN 380
           SGQ+  +FD ++ F+V ++ +ET W LP      ++D  GAL +LA+ K +L I+  RSN
Sbjct: 45  SGQYTHEFDGDEEFYVDLEKKETVWRLPVFSTFRSFDPQGALRNLAIIKQNLNIMTKRSN 104

Query: 381 NPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQNVSPGPVVVSDPLVL 560
               T   P++TV +   V L  PN L+C +    P +++V  L+N       VS+    
Sbjct: 105 QTAATNEVPEVTVFSKSPVMLGQPNTLICLVDNIFPPVINVTWLKNRHSVTEGVSETSFF 164

Query: 561 VREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCE 683
            + DH F     L F+PS E  YDC VEHW LD PL +  E
Sbjct: 165 AKGDHSFSKISYLTFLPSAEDIYDCKVEHWGLDEPLLKHWE 205


>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 = 60.8 bits (146), Expect = 1e-09
 Identities = 33/89 (37%), Positives = 47/89 (52%), Gaps = 5/89 (5%)
 Frame = +3

Query: 174 PEFYLTPD*SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLAVDKSH 353
           P FY +   SGQF  +FD E  F V +  R+  W LP      ++D    L+ +AV K+H
Sbjct: 22  PAFYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEFGNLAHFDPQNGLASIAVIKAH 81

Query: 354 LEILIIRSN-----NPPQTTVPPKMTVLT 425
           L++L+ RSN     N PQ  +P   T+ T
Sbjct: 82  LDVLVERSNRTRAINEPQVPIPVPDTIET 110


  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: 36,132,591
Number of Sequences: 33732
Number of extensions: 933220
Number of successful extensions: 2473
Number of sequences better than 1.0e-05: 4
Number of HSP's better than  0.0 without gapping: 2268
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): 2468
length of database: 19,266,565
effective HSP length: 101
effective length of database: 15,859,633
effective search space used: 2791295408
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqHP

BLASTX 2.2.10 [Oct-19-2004]


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

Query= 20060611S-005603
         (835 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 ...   182   3e-46
Alignment   gi|NP_002110.1| major histocompatibility complex, class II, DO ...   122   1e-28
Alignment   gi|NP_291032.2| major histocompatibility complex, class II, DP ...   120   1e-27
Alignment   gi|XP_949974.1| PREDICTED: similar to HLA class II histocompati...   107   1e-23
Alignment   gi|XP_949973.1| PREDICTED: similar to HLA class II histocompati...   107   1e-23
Alignment   gi|XP_949971.1| PREDICTED: similar to HLA class II histocompati...   107   1e-23
Alignment   gi|XP_945969.1| PREDICTED: similar to HLA class II histocompati...   107   1e-23
Alignment   gi|NP_002113.2| major histocompatibility complex, class II, DQ ...   107   2e-23
Alignment   gi|NP_064440.1| major histocompatibility complex, class II, DQ ...   106   2e-23
Alignment   gi|XP_949969.1| PREDICTED: similar to HLA class II histocompati...   106   2e-23

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

 Score =  182 bits (462), Expect = 3e-46
 Identities = 98/194 (50%), Positives = 125/194 (64%), Gaps = 1/194 (0%)
 Frame = +3

Query: 156 EHVIILPEFYLTPD*SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHL 335
           EHVII  EFYL PD SG+F FDFD ++ FHV M  +ET W L    R  +++A GAL+++
Sbjct: 29  EHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANI 88

Query: 336 AVDKSHLEILIIRSNNPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQ 515
           AVDK++LEI+  RSN  P T VPP++TVLT   V L+ PN L+C + ++ P +V+V  L+
Sbjct: 89  AVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLR 148

Query: 516 NVSPGPVVVSDPLVLVREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCEF-AS 692
           N  P    VS+ + L REDHLFR FH L F+PSTE  YDC VEHW LD PL +  EF A 
Sbjct: 149 NGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFDAP 208

Query: 693 HPLLHRLHTSSCVL 734
            PL        C L
Sbjct: 209 SPLPETTENVVCAL 222


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

 Score =  122 bits (306), Expect(2) = 1e-28
 Identities = 69/170 (40%), Positives = 89/170 (52%)
 Frame = +3

Query: 174 PEFYLTPD*SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLAVDKSH 353
           P FY +   SGQF  +FD E  F V +   E  W LP       +D  G L+ +A  K+H
Sbjct: 36  PAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAH 95

Query: 354 LEILIIRSNNPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQNVSPGP 533
           L+IL+ RSN      VPP++TVL    V L  PN L+C +    P ++++  L+N     
Sbjct: 96  LDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVT 155

Query: 534 VVVSDPLVLVREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCE 683
             V+      + DHLFR FH L FVPS E  YDC VEHW LD PL    E
Sbjct: 156 EGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWE 205



 Score = 22.3 bits (46), Expect(2) = 1e-28
 Identities = 11/38 (28%), Positives = 17/38 (44%)
 Frame = +2

Query: 662 PSSRAMRICISSTPP*TTYIIVCPLDLIVALVRIMIRT 775
           P  R   + +   PP     +VC L L + LV  ++ T
Sbjct: 199 PLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGT 236


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

 Score =  120 bits (302), Expect = 1e-27
 Identities = 69/182 (37%), Positives = 104/182 (57%)
 Frame = +3

Query: 156 EHVIILPEFYLTPD*SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHL 335
           +HV     F  T   +G+F F+FD ++ F+V +D +ET W L    +  +++A G L+++
Sbjct: 35  DHVSTYAAFVQTHRPTGEFMFEFDEDEMFYVDLDKKETVWHLEEFGQAFSFEAQGGLANI 94

Query: 336 AVDKSHLEILIIRSNNPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQ 515
           A+  ++L  LI RSN+   T  PP++TV   + V L  PN L+C + ++ P +++V  L 
Sbjct: 95  AILNNNLNTLIQRSNHTQATNDPPEVTVFPKEPVELGQPNTLICHIDKFFPPVLNVTWLC 154

Query: 516 NVSPGPVVVSDPLVLVREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCEFASH 695
           N       V++ L L R D+ F  FH L FVPS E  YDC VEHW LD PL +  E A  
Sbjct: 155 NGELVTEGVAESLFLPRTDYSFHKFHYLTFVPSAEDFYDCRVEHWGLDQPLLKHWE-AQE 213

Query: 696 PL 701
           P+
Sbjct: 214 PI 215


>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 =  107 bits (267), Expect = 1e-23
 Identities = 61/161 (37%), Positives = 89/161 (55%)
 Frame = +3

Query: 201 SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLAVDKSHLEILIIRSN 380
           SGQ+  +FD ++ F+V ++ +ET W LP   R   +D   AL+++AV K +L I+I RSN
Sbjct: 45  SGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSN 104

Query: 381 NPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQNVSPGPVVVSDPLVL 560
           +   T   P++TV +   V L  PN L+C +    P +V++  L N       VS+   L
Sbjct: 105 STAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFL 164

Query: 561 VREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCE 683
            + DH F     L F+PS +  YDC VEHW LD PL +  E
Sbjct: 165 SKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWE 205


>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 =  107 bits (267), Expect = 1e-23
 Identities = 61/161 (37%), Positives = 89/161 (55%)
 Frame = +3

Query: 201 SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLAVDKSHLEILIIRSN 380
           SGQ+  +FD ++ F+V ++ +ET W LP   R   +D   AL+++AV K +L I+I RSN
Sbjct: 45  SGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSN 104

Query: 381 NPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQNVSPGPVVVSDPLVL 560
           +   T   P++TV +   V L  PN L+C +    P +V++  L N       VS+   L
Sbjct: 105 STAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFL 164

Query: 561 VREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCE 683
            + DH F     L F+PS +  YDC VEHW LD PL +  E
Sbjct: 165 SKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWE 205


>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 =  107 bits (267), Expect = 1e-23
 Identities = 61/161 (37%), Positives = 89/161 (55%)
 Frame = +3

Query: 201 SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLAVDKSHLEILIIRSN 380
           SGQ+  +FD ++ F+V ++ +ET W LP   R   +D   AL+++AV K +L I+I RSN
Sbjct: 45  SGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSN 104

Query: 381 NPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQNVSPGPVVVSDPLVL 560
           +   T   P++TV +   V L  PN L+C +    P +V++  L N       VS+   L
Sbjct: 105 STAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFL 164

Query: 561 VREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCE 683
            + DH F     L F+PS +  YDC VEHW LD PL +  E
Sbjct: 165 SKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWE 205


>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 =  107 bits (267), Expect = 1e-23
 Identities = 61/161 (37%), Positives = 89/161 (55%)
 Frame = +3

Query: 201 SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLAVDKSHLEILIIRSN 380
           SGQ+  +FD ++ F+V ++ +ET W LP   R   +D   AL+++AV K +L I+I RSN
Sbjct: 45  SGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSN 104

Query: 381 NPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQNVSPGPVVVSDPLVL 560
           +   T   P++TV +   V L  PN L+C +    P +V++  L N       VS+   L
Sbjct: 105 STAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFL 164

Query: 561 VREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCE 683
            + DH F     L F+PS +  YDC VEHW LD PL +  E
Sbjct: 165 SKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWE 205


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

 Score =  107 bits (266), Expect = 2e-23
 Identities = 60/161 (37%), Positives = 88/161 (54%)
 Frame = +3

Query: 201 SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLAVDKSHLEILIIRSN 380
           SGQ+  +FD ++ F+V ++ +ETAW  P   +   +D  GAL ++AV K +L I+I R N
Sbjct: 45  SGQYTHEFDGDEQFYVDLERKETAWRWPEFSKFGGFDPQGALRNMAVAKHNLNIMIKRYN 104

Query: 381 NPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQNVSPGPVVVSDPLVL 560
           +   T   P++TV +   V L  PN L+C +    P +V++  L N       VS+   L
Sbjct: 105 STAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGQSVTEGVSETSFL 164

Query: 561 VREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCE 683
            + DH F     L F+PS +  YDC VEHW LD PL +  E
Sbjct: 165 SKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDQPLLKHWE 205


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

 Score =  106 bits (265), Expect = 2e-23
 Identities = 60/168 (35%), Positives = 91/168 (54%)
 Frame = +3

Query: 180 FYLTPD*SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLAVDKSHLE 359
           FY +   SGQ+  +FD ++ F+V ++ +ET W LP   +  ++D   AL ++AV K  LE
Sbjct: 38  FYQSHGPSGQYTHEFDGDEEFYVDLETKETVWQLPMFSKFISFDPQSALRNMAVGKHTLE 97

Query: 360 ILIIRSNNPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQNVSPGPVV 539
            ++ +SN+   T   P++TV +   V L  PN L+C +    P +V++  L N       
Sbjct: 98  FMMRQSNSTAATNEVPEVTVFSKFPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEG 157

Query: 540 VSDPLVLVREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCE 683
           VS+   L + DH F     L F+PS +  YDC VEHW LD PL +  E
Sbjct: 158 VSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWE 205


>ref|XP_949969.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DQ(1) alpha chain precursor (DC-4 alpha chain) isoform 7
           [Homo sapiens]
          Length = 208

 Score =  106 bits (265), Expect = 2e-23
 Identities = 60/156 (38%), Positives = 87/156 (55%)
 Frame = +3

Query: 201 SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLAVDKSHLEILIIRSN 380
           SGQ+  +FD ++ F+V ++ +ET W LP   R   +D   AL+++AV K +L I+I RSN
Sbjct: 45  SGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSN 104

Query: 381 NPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQNVSPGPVVVSDPLVL 560
           +   T   P++TV +   V L  PN L+C +    P +V++  L N       VS+   L
Sbjct: 105 STAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFL 164

Query: 561 VREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPL 668
            + DH F     L F+PS +  YDC VEHW LD PL
Sbjct: 165 SKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPL 200


  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: 34,769,469
Number of Sequences: 39411
Number of extensions: 922065
Number of successful extensions: 2538
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 2271
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): 2525
length of database: 17,774,539
effective HSP length: 101
effective length of database: 13,794,028
effective search space used: 2427748928
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqMP

BLASTX 2.2.10 [Oct-19-2004]


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

Query= 20060611S-005603
         (835 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 ...   168   5e-42
Alignment   gi|NP_032232.1| histocompatibility 2, O region alpha locus [Mus...   121   1e-28
Alignment   gi|NP_034508.2| histocompatibility 2, class II antigen A, alpha...   107   1e-23

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

 Score =  168 bits (426), Expect = 5e-42
 Identities = 84/194 (43%), Positives = 121/194 (62%)
 Frame = +3

Query: 123 LEDSKIMTYHREHVIILPEFYLTPD*SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCT 302
           +   K      EH II  EFYL PD  G+F FDFD ++ FHV ++  ET W L    +  
Sbjct: 18  MSSQKSWAIKEEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFA 77

Query: 303 NYDAHGALSHLAVDKSHLEILIIRSNNPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQY 482
           +++A GAL+++AVDK++L+++  RSNN P   V P++TVL+   V+L  PN L+C + ++
Sbjct: 78  SFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPNILICFIDKF 137

Query: 483 PPQMVSVGRLQNVSPGPVVVSDPLVLVREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDN 662
            P +V+V   +N  P    VS+ + L R+DHLFR FH L F+PST+  YDC V+HW L+ 
Sbjct: 138 SPPVVNVTWFRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEE 197

Query: 663 PLREQCEFASHPLL 704
           PLR+  EF    LL
Sbjct: 198 PLRKHWEFEEKTLL 211


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

 Score =  121 bits (303), Expect(2) = 1e-28
 Identities = 68/170 (40%), Positives = 91/170 (53%)
 Frame = +3

Query: 174 PEFYLTPD*SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLAVDKSH 353
           P FY + D SGQF  +FD E  F V +   E  W LP      + D    L  +++ K+H
Sbjct: 36  PAFYQSYDASGQFTHEFDGEQIFSVDLKNEEVVWRLPEFGDFAHSDFQSGLMSISMIKAH 95

Query: 354 LEILIIRSNNPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQNVSPGP 533
           L+IL+ RSN     +VPP++TVL    V L  PN L+C +    P +++V  L+N  P  
Sbjct: 96  LDILVERSNRTRAVSVPPRVTVLPKTRVELGKPNVLICIVDDIFPPVINVTWLRNSQPIT 155

Query: 534 VVVSDPLVLVREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCE 683
             V+      + +H FR FH L FVPS E  YDC VEHW LD PL +  E
Sbjct: 156 KGVAQTSFYSQPNHRFRKFHYLTFVPSAEDVYDCKVEHWGLDTPLLQHWE 205



 Score = 23.9 bits (50), Expect(2) = 1e-28
 Identities = 9/29 (31%), Positives = 18/29 (62%)
 Frame = +2

Query: 689 ISSTPP*TTYIIVCPLDLIVALVRIMIRT 775
           + + PP TT  ++C L L++ L+  ++ T
Sbjct: 208 VLTPPPDTTETLICGLGLVLGLMGCLLGT 236


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

 Score =  107 bits (267), Expect = 1e-23
 Identities = 58/167 (34%), Positives = 89/167 (53%)
 Frame = +3

Query: 183 YLTPD*SGQFKFDFDCEDTFHVYMDPRETAWPLP*LVRCTNYDAHGALSHLAVDKSHLEI 362
           Y +P   GQ+ F+FD ++ F+V +D +ET W LP   +  ++D  G L ++AV K +L +
Sbjct: 40  YQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFGQLASFDPQGGLQNIAVVKHNLGV 99

Query: 363 LIIRSNNPPQTTVPPKMTVLTYKLVHLQ*PNFLLCCMAQYPPQMVSVGRLQNVSPGPVVV 542
           L  RSN+ P T   P+ TV     V L  PN L+C +    P ++++  L+N       V
Sbjct: 100 LTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGV 159

Query: 543 SDPLVLVREDHLFRDFHSLCFVPSTEHDYDCHVEHW*LDNPLREQCE 683
            +    V  D+ F     L F+PS +  YDC VEHW L+ P+ +  E
Sbjct: 160 YETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWE 206


  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: 41,468,326
Number of Sequences: 45328
Number of extensions: 1077323
Number of successful extensions: 2747
Number of sequences better than 1.0e-05: 3
Number of HSP's better than  0.0 without gapping: 2536
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): 2743
length of database: 21,768,885
effective HSP length: 102
effective length of database: 17,145,429
effective search space used: 3000450075
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)