Animal-Genome cDNA 20060611S-029585


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-029585
         (1010 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: 867,712
Number of Sequences: 1040
Number of extensions: 21770
Number of successful extensions: 62
Number of sequences better than 1.0e-05: 0
Number of HSP's better than  0.0 without gapping: 52
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 62
length of database: 434,620
effective HSP length: 77
effective length of database: 354,540
effective search space used: 91825860
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-029585
         (1010 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, ...   160   1e-39
Alignment   gi|XP_604082.2| PREDICTED: similar to HLA class II histocompati...    95   1e-19
Alignment   gi|XP_883292.1| PREDICTED: similar to HLA class II histocompati...    95   1e-19
Alignment   gi|NP_001013619.2| histocompatibility complex, class II, DQ alp...    84   2e-16
Alignment   gi|NP_001012696.1| major histocompatibility complex, class II, ...    84   2e-16
Alignment   gi|NP_001012699.1| major histocompatibility complex, class II, ...    81   1e-15
Alignment   gi|NP_001012693.1| major histocompatibility complex, class II, ...    70   3e-12

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

 Score =  160 bits (405), Expect = 1e-39
 Identities = 80/105 (76%), Positives = 89/105 (84%), Gaps = 1/105 (0%)
 Frame = +2

Query: 77  MTILGVPVLGFVITIL-NLQKSWAIVENHVIIQAEFYPSPDKSGEFMFDFDGDEIFHVDM 253
           M I  VP+LG  IT+L  LQ+SWAI ENHVIIQAEFY  P++S EFMFDFDGDEIFHVDM
Sbjct: 1   MAITRVPILGLFITVLIGLQESWAIKENHVIIQAEFYLKPEESAEFMFDFDGDEIFHVDM 60

Query: 254 EKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSNPPP 388
            K+ETVWRL EFGHFASFEAQGALAN+AV KANL+I+IKRSN  P
Sbjct: 61  GKKETVWRLPEFGHFASFEAQGALANMAVMKANLDIMIKRSNNTP 105


>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 = 94.7 bits (234), Expect = 1e-19
 Identities = 51/104 (49%), Positives = 73/104 (70%), Gaps = 3/104 (2%)
 Frame = +2

Query: 77  MTILGVPVLGF--VITILNLQKSWAIVENHV-IIQAEFYPSPDKSGEFMFDFDGDEIFHV 247
           M + G  VLG   ++T+L+LQ+  AI  +H+      FY S D +G+F +DFDG+++F V
Sbjct: 1   MVLRGRLVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSV 60

Query: 248 DMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSN 379
           D++KRE VWRL EFG+FA F+ Q  L +IA+ KA+LE L+KRSN
Sbjct: 61  DLKKREAVWRLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSN 104


>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 = 94.7 bits (234), Expect = 1e-19
 Identities = 51/104 (49%), Positives = 73/104 (70%), Gaps = 3/104 (2%)
 Frame = +2

Query: 77  MTILGVPVLGF--VITILNLQKSWAIVENHV-IIQAEFYPSPDKSGEFMFDFDGDEIFHV 247
           M + G  VLG   ++T+L+LQ+  AI  +H+      FY S D +G+F +DFDG+++F V
Sbjct: 1   MVLRGRLVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSV 60

Query: 248 DMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSN 379
           D++KRE VWRL EFG+FA F+ Q  L +IA+ KA+LE L+KRSN
Sbjct: 61  DLKKREAVWRLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSN 104


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

 Score = 84.0 bits (206), Expect = 2e-16
 Identities = 45/89 (50%), Positives = 59/89 (66%), Gaps = 1/89 (1%)
 Frame = +2

Query: 116 TILNLQKSWAIVENHV-IIQAEFYPSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFG 292
           T+++   S  IV +H+       Y +   SG +  +FDGDE F+VD+EKRETVWRL  F 
Sbjct: 16  TMMSPSGSEDIVADHIGTYGISIYHTYGPSGYYTHEFDGDEEFYVDLEKRETVWRLPVFS 75

Query: 293 HFASFEAQGALANIAVDKANLEILIKRSN 379
            FA+F+ QGAL NIA  K NLEI+I+RSN
Sbjct: 76  KFATFDPQGALRNIATTKHNLEIVIQRSN 104


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

 Score = 83.6 bits (205), Expect = 2e-16
 Identities = 42/82 (51%), Positives = 54/82 (65%), Gaps = 1/82 (1%)
 Frame = +2

Query: 146 IVENHV-IIQAEFYPSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 322
           IV +HV       Y +   SG+F F+FDGDE+F+VD+ K+ETVWRL EF +   FE Q A
Sbjct: 24  IVADHVGTYGTNVYQTYGASGQFTFEFDGDELFYVDLGKKETVWRLPEFSNITKFEVQSA 83

Query: 323 LANIAVDKANLEILIKRSNPPP 388
           L NI + K NL+ILIK S+  P
Sbjct: 84  LRNIVMSKRNLDILIKNSSFTP 105


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

 Score = 81.3 bits (199), Expect = 1e-15
 Identities = 42/82 (51%), Positives = 54/82 (65%), Gaps = 1/82 (1%)
 Frame = +2

Query: 146 IVENHV-IIQAEFYPSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 322
           IV +HV     E Y S   SG++  +FDGDE+F+VD+ K+ETVWRL  F  FA F+ Q A
Sbjct: 26  IVADHVGSYGTEIYQSHGPSGQYTQEFDGDEMFYVDLGKKETVWRLPMFSQFAGFDPQAA 85

Query: 323 LANIAVDKANLEILIKRSNPPP 388
           L+ IA  K NL++L KRSN  P
Sbjct: 86  LSEIATAKHNLDVLTKRSNFTP 107


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

 Score = 69.7 bits (169), Expect = 3e-12
 Identities = 37/79 (46%), Positives = 50/79 (63%), Gaps = 1/79 (1%)
 Frame = +2

Query: 146 IVENHV-IIQAEFYPSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 322
           IV +HV I     Y S   SG++  +FDGDE F+VD+EK+ET W+L  F    SF+ Q A
Sbjct: 26  IVADHVGIYGISIYQSYGPSGQYTHEFDGDEQFYVDLEKKETAWQLPLFSRMLSFDPQLA 85

Query: 323 LANIAVDKANLEILIKRSN 379
           L NIA+ K +++ L K SN
Sbjct: 86  LRNIAIMKLHVDFLTKFSN 104


  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: 32,088,987
Number of Sequences: 33508
Number of extensions: 818930
Number of successful extensions: 2406
Number of sequences better than 1.0e-05: 7
Number of HSP's better than  0.0 without gapping: 2216
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): 2403
length of database: 16,112,626
effective HSP length: 102
effective length of database: 12,694,810
effective search space used: 2970585540
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-029585
         (1010 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 ...   166   4e-41
Alignment   gi|NP_291032.2| major histocompatibility complex, class II, DP ...    96   5e-20
Alignment   gi|NP_002110.1| major histocompatibility complex, class II, DO ...    85   1e-16
Alignment   gi|NP_002113.2| major histocompatibility complex, class II, DQ ...    77   3e-14
Alignment   gi|XP_949974.1| PREDICTED: similar to HLA class II histocompati...    76   4e-14
Alignment   gi|XP_949973.1| PREDICTED: similar to HLA class II histocompati...    76   4e-14
Alignment   gi|XP_949971.1| PREDICTED: similar to HLA class II histocompati...    76   4e-14
Alignment   gi|XP_949969.1| PREDICTED: similar to HLA class II histocompati...    76   4e-14
Alignment   gi|XP_949965.1| PREDICTED: similar to HLA class II histocompati...    76   4e-14
Alignment   gi|XP_945969.1| PREDICTED: similar to HLA class II histocompati...    76   4e-14

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

 Score =  166 bits (419), Expect = 4e-41
 Identities = 83/106 (78%), Positives = 91/106 (85%), Gaps = 2/106 (1%)
 Frame = +2

Query: 77  MTILGVPVLGFVI--TILNLQKSWAIVENHVIIQAEFYPSPDKSGEFMFDFDGDEIFHVD 250
           M I GVPVLGF I   +++ Q+SWAI E HVIIQAEFY +PD+SGEFMFDFDGDEIFHVD
Sbjct: 1   MAISGVPVLGFFIIAVLMSAQESWAIKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVD 60

Query: 251 MEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSNPPP 388
           M K+ETVWRLEEFG FASFEAQGALANIAVDKANLEI+ KRSN  P
Sbjct: 61  MAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTP 106


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

 Score = 95.9 bits (237), Expect = 5e-20
 Identities = 48/87 (55%), Positives = 63/87 (72%)
 Frame = +2

Query: 119 ILNLQKSWAIVENHVIIQAEFYPSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHF 298
           +L+L+ + AI  +HV   A F  +   +GEFMF+FD DE+F+VD++K+ETVW LEEFG  
Sbjct: 23  LLSLRGAGAIKADHVSTYAAFVQTHRPTGEFMFEFDEDEMFYVDLDKKETVWHLEEFGQA 82

Query: 299 ASFEAQGALANIAVDKANLEILIKRSN 379
            SFEAQG LANIA+   NL  LI+RSN
Sbjct: 83  FSFEAQGGLANIAILNNNLNTLIQRSN 109


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

 Score = 84.7 bits (208), Expect = 1e-16
 Identities = 46/97 (47%), Positives = 66/97 (68%), Gaps = 3/97 (3%)
 Frame = +2

Query: 98  VLGF--VITILNLQKSWAIVENHV-IIQAEFYPSPDKSGEFMFDFDGDEIFHVDMEKRET 268
           VLGF  ++T+L+ Q++ A   +H+      FY S   SG+F  +FD +++F VD++K E 
Sbjct: 8   VLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEA 67

Query: 269 VWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSN 379
           VWRL EFG FA F+ QG LA IA  KA+L+IL++RSN
Sbjct: 68  VWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSN 104


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

 Score = 76.6 bits (187), Expect = 3e-14
 Identities = 39/79 (49%), Positives = 50/79 (63%), Gaps = 1/79 (1%)
 Frame = +2

Query: 146 IVENHVI-IQAEFYPSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 322
           IV +HV       Y     SG++  +FDGDE F+VD+E++ET WR  EF  F  F+ QGA
Sbjct: 26  IVADHVASCGVNLYQFYGPSGQYTHEFDGDEQFYVDLERKETAWRWPEFSKFGGFDPQGA 85

Query: 323 LANIAVDKANLEILIKRSN 379
           L N+AV K NL I+IKR N
Sbjct: 86  LRNMAVAKHNLNIMIKRYN 104


>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 = 76.3 bits (186), Expect = 4e-14
 Identities = 41/79 (51%), Positives = 52/79 (65%), Gaps = 1/79 (1%)
 Frame = +2

Query: 146 IVENHVIIQA-EFYPSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 322
           IV +HV       Y S   SG++  +FDGDE F+VD+E++ETVW+L  F  F  F+ Q A
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFA 85

Query: 323 LANIAVDKANLEILIKRSN 379
           L NIAV K NL I+IKRSN
Sbjct: 86  LTNIAVLKHNLNIVIKRSN 104


>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 = 76.3 bits (186), Expect = 4e-14
 Identities = 41/79 (51%), Positives = 52/79 (65%), Gaps = 1/79 (1%)
 Frame = +2

Query: 146 IVENHVIIQA-EFYPSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 322
           IV +HV       Y S   SG++  +FDGDE F+VD+E++ETVW+L  F  F  F+ Q A
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFA 85

Query: 323 LANIAVDKANLEILIKRSN 379
           L NIAV K NL I+IKRSN
Sbjct: 86  LTNIAVLKHNLNIVIKRSN 104


>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 = 76.3 bits (186), Expect = 4e-14
 Identities = 41/79 (51%), Positives = 52/79 (65%), Gaps = 1/79 (1%)
 Frame = +2

Query: 146 IVENHVIIQA-EFYPSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 322
           IV +HV       Y S   SG++  +FDGDE F+VD+E++ETVW+L  F  F  F+ Q A
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFA 85

Query: 323 LANIAVDKANLEILIKRSN 379
           L NIAV K NL I+IKRSN
Sbjct: 86  LTNIAVLKHNLNIVIKRSN 104


>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 = 76.3 bits (186), Expect = 4e-14
 Identities = 41/79 (51%), Positives = 52/79 (65%), Gaps = 1/79 (1%)
 Frame = +2

Query: 146 IVENHVIIQA-EFYPSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 322
           IV +HV       Y S   SG++  +FDGDE F+VD+E++ETVW+L  F  F  F+ Q A
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFA 85

Query: 323 LANIAVDKANLEILIKRSN 379
           L NIAV K NL I+IKRSN
Sbjct: 86  LTNIAVLKHNLNIVIKRSN 104


>ref|XP_949965.1| PREDICTED: similar to HLA class II histocompatibility antigen,
           DQ(1) alpha chain precursor (DC-4 alpha chain) isoform 6
           [Homo sapiens]
          Length = 161

 Score = 76.3 bits (186), Expect = 4e-14
 Identities = 41/79 (51%), Positives = 52/79 (65%), Gaps = 1/79 (1%)
 Frame = +2

Query: 146 IVENHVIIQA-EFYPSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 322
           IV +HV       Y S   SG++  +FDGDE F+VD+E++ETVW+L  F  F  F+ Q A
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFA 85

Query: 323 LANIAVDKANLEILIKRSN 379
           L NIAV K NL I+IKRSN
Sbjct: 86  LTNIAVLKHNLNIVIKRSN 104


>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 = 76.3 bits (186), Expect = 4e-14
 Identities = 41/79 (51%), Positives = 52/79 (65%), Gaps = 1/79 (1%)
 Frame = +2

Query: 146 IVENHVIIQA-EFYPSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 322
           IV +HV       Y S   SG++  +FDGDE F+VD+E++ETVW+L  F  F  F+ Q A
Sbjct: 26  IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFA 85

Query: 323 LANIAVDKANLEILIKRSN 379
           L NIAV K NL I+IKRSN
Sbjct: 86  LTNIAVLKHNLNIVIKRSN 104


  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: 36,139,592
Number of Sequences: 39411
Number of extensions: 939048
Number of successful extensions: 2825
Number of sequences better than 1.0e-05: 10
Number of HSP's better than  0.0 without gapping: 2557
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): 2807
length of database: 17,774,539
effective HSP length: 103
effective length of database: 13,715,206
effective search space used: 3195642998
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-029585
         (1010 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 ...   147   2e-35
Alignment   gi|NP_034508.2| histocompatibility 2, class II antigen A, alpha...    91   2e-18
Alignment   gi|NP_032232.1| histocompatibility 2, O region alpha locus [Mus...    80   3e-15

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

 Score =  147 bits (370), Expect = 2e-35
 Identities = 69/94 (73%), Positives = 79/94 (84%)
 Frame = +2

Query: 107 FVITILNLQKSWAIVENHVIIQAEFYPSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEE 286
           F+  +++ QKSWAI E H IIQAEFY  PDK GEFMFDFDGDEIFHVD+EK ET+WRLEE
Sbjct: 13  FIAVLMSSQKSWAIKEEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEE 72

Query: 287 FGHFASFEAQGALANIAVDKANLEILIKRSNPPP 388
           F  FASFEAQGALANIAVDKANL+++ +RSN  P
Sbjct: 73  FAKFASFEAQGALANIAVDKANLDVMKERSNNTP 106


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

 Score = 90.5 bits (223), Expect = 2e-18
 Identities = 49/108 (45%), Positives = 67/108 (62%), Gaps = 1/108 (0%)
 Frame = +2

Query: 68  KEKMTILGVPVLGFVITILNLQKSWAIVENHV-IIQAEFYPSPDKSGEFMFDFDGDEIFH 244
           + +  ILGV  L  ++++   +    I  +HV       Y SP   G++ F+FDGDE+F+
Sbjct: 3   RSRALILGVLALTTMLSLCGGEDD--IEADHVGTYGISVYQSPGDIGQYTFEFDGDELFY 60

Query: 245 VDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSNPPP 388
           VD++K+ETVW L EFG  ASF+ QG L NIAV K NL +L KRSN  P
Sbjct: 61  VDLDKKETVWMLPEFGQLASFDPQGGLQNIAVVKHNLGVLTKRSNSTP 108


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

 Score = 80.5 bits (197), Expect = 3e-15
 Identities = 44/97 (45%), Positives = 64/97 (65%), Gaps = 1/97 (1%)
 Frame = +2

Query: 92  VPVLGFVITILNLQKSWAIVENHV-IIQAEFYPSPDKSGEFMFDFDGDEIFHVDMEKRET 268
           VPVL  V++ L+ +   AI  +H+      FY S D SG+F  +FDG++IF VD++  E 
Sbjct: 8   VPVLLTVMSFLSPRGVRAIKADHMGSYGPAFYQSYDASGQFTHEFDGEQIFSVDLKNEEV 67

Query: 269 VWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSN 379
           VWRL EFG FA  + Q  L +I++ KA+L+IL++RSN
Sbjct: 68  VWRLPEFGDFAHSDFQSGLMSISMIKAHLDILVERSN 104


  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: 43,294,546
Number of Sequences: 45328
Number of extensions: 1100772
Number of successful extensions: 3193
Number of sequences better than 1.0e-05: 3
Number of HSP's better than  0.0 without gapping: 2857
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): 3193
length of database: 21,768,885
effective HSP length: 104
effective length of database: 17,054,773
effective search space used: 3956707336
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-029585
         (1010 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]    166   3e-41
Alignment   gi|NP_001011726.1| MHC class II DLA DQalpha chain [Canis famili...    84   2e-16
Alignment   gi|XP_532104.2| PREDICTED: similar to HLA class II histocompati...    81   2e-15
Alignment   gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati...    80   3e-15

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

 Score =  166 bits (421), Expect = 3e-41
 Identities = 83/106 (78%), Positives = 91/106 (85%), Gaps = 2/106 (1%)
 Frame = +2

Query: 77  MTILGVPVLGFVIT--ILNLQKSWAIVENHVIIQAEFYPSPDKSGEFMFDFDGDEIFHVD 250
           MTI GVPVLGF I   ++  Q+SWA+ E HVIIQAEFY +PD SGEFMFDFDGDEIFHVD
Sbjct: 1   MTISGVPVLGFFIMAFLMGPQESWAVKEEHVIIQAEFYLTPDPSGEFMFDFDGDEIFHVD 60

Query: 251 MEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSNPPP 388
           MEK+ETVWRLEEFG FASFEAQGALANIAVDKANL+ +IKRSN  P
Sbjct: 61  MEKKETVWRLEEFGRFASFEAQGALANIAVDKANLDTMIKRSNHTP 106


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

 Score = 84.0 bits (206), Expect = 2e-16
 Identities = 48/104 (46%), Positives = 64/104 (61%), Gaps = 3/104 (2%)
 Frame = +2

Query: 77  MTILGVPVLGFVITILNLQKSWA--IVENHVIIQA-EFYPSPDKSGEFMFDFDGDEIFHV 247
           M +  V +LG +I  + +  S    IV +HV       Y S   SG++  +FDGDE F+V
Sbjct: 1   MILNRVLILGTLILTIMMSPSGGEEIVADHVANYGINVYQSYGPSGQYTHEFDGDEEFYV 60

Query: 248 DMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSN 379
           D+EK+ETVWRL  F  F SF+ QGAL N+A+ K NL I+ KRSN
Sbjct: 61  DLEKKETVWRLPVFSTFRSFDPQGALRNLAIIKQNLNIMTKRSN 104


>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 = 80.9 bits (198), Expect(2) = 2e-15
 Identities = 39/90 (43%), Positives = 64/90 (71%), Gaps = 1/90 (1%)
 Frame = +2

Query: 113 ITILNLQKSWAIVENHV-IIQAEFYPSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEF 289
           +++L+  ++ AI  +H+      FY S   SG+F  +FDG+++F V+++KR+ VWRL EF
Sbjct: 1   MSLLSPHETGAIEADHMGSYGPAFYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEF 60

Query: 290 GHFASFEAQGALANIAVDKANLEILIKRSN 379
           G+ A F+ Q  LA+IAV KA+L++L++RSN
Sbjct: 61  GNLAHFDPQNGLASIAVIKAHLDVLVERSN 90



 Score = 20.4 bits (41), Expect(2) = 2e-15
 Identities = 6/12 (50%), Positives = 9/12 (75%)
 Frame = +3

Query: 381 PLPETTENTVCA 416
           P+P+T E  +CA
Sbjct: 103 PVPDTIETLICA 114


>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 = 80.1 bits (196), Expect = 3e-15
 Identities = 35/67 (52%), Positives = 52/67 (77%)
 Frame = +2

Query: 179 FYPSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLE 358
           FY S   SG+F  +FDG+++F V+++KR+ VWRL EFG+ A F+ Q  LA+IAV KA+L+
Sbjct: 8   FYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEFGNLAHFDPQNGLASIAVIKAHLD 67

Query: 359 ILIKRSN 379
           +L++RSN
Sbjct: 68  VLVERSN 74


  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: 37,746,534
Number of Sequences: 33732
Number of extensions: 963618
Number of successful extensions: 2948
Number of sequences better than 1.0e-05: 4
Number of HSP's better than  0.0 without gapping: 2613
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): 2940
length of database: 19,266,565
effective HSP length: 103
effective length of database: 15,792,169
effective search space used: 3679575377
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)