Search to RefSeqBP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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= 20110601C-012854
(1115 letters)
Database: RefSeq49_BP.fasta
33,088 sequences; 17,681,374 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001012692.2| major histocompatibility complex, class II, ... 393 e-109
Alignment gi|XP_002702914.1| PREDICTED: BOLA-DQA2 protein-like [Bos tauru... 97 3e-20
Alignment gi|NP_001013619.3| major histocompatibility complex, class II, ... 89 5e-18
Alignment gi|NP_001012699.1| major histocompatibility complex, class II, ... 89 7e-18
Alignment gi|NP_001012696.1| major histocompatibility complex, class II, ... 86 5e-17
Alignment gi|NP_001012695.1| major histocompatibility complex, class II, ... 83 4e-16
Alignment gi|NP_001012693.1| major histocompatibility complex, class II, ... 83 5e-16
Alignment gi|NP_001073045.1| major histocompatibility complex, class II, ... 82 7e-16
Alignment gi|NP_001192849.1| HLA class II histocompatibility antigen, DO ... 81 1e-15
Alignment gi|XP_002697222.1| PREDICTED: MHC class II antigen-like [Bos ta... 81 1e-15
>ref|NP_001012692.2| major histocompatibility complex, class II, DM alpha-chain,
expressed [Bos taurus].
Length = 260
Score = 393 bits (1009), Expect = e-109
Identities = 189/258 (73%), Positives = 204/258 (79%)
Frame = +3
Query: 93 MDHELSQGAAXXXXXXXXXXXPHSWTAPEAPAPGWRDELQNHTFQYTMYCQDGNPEVGLS 272
MDHELSQ AA P SWTAPEAPAPGWRDELQNHTF +TMYCQD +P V LS
Sbjct: 1 MDHELSQEAALLRLLSFLWLLPLSWTAPEAPAPGWRDELQNHTFLHTMYCQDWSPNVALS 60
Query: 273 EVYDGDQLFSFNFSQNIRVPRLPEFADWAHQIEDTPAIFFDKGFCREMIEKVGPLFEGKI 452
E YD DQLFSF+FSQ+IRVPRLPEFADWAHQ DT I FDKGFCR MIE++GP EG+I
Sbjct: 61 ESYDEDQLFSFDFSQSIRVPRLPEFADWAHQHGDTSDIMFDKGFCRAMIEEIGPELEGQI 120
Query: 453 PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPVEGIGPTFVSATD 632
PVSRG PI +VFTLKPLEFGKPNTLVCF+SNLFPP LTV W+H SAPVEG GPTFVSA D
Sbjct: 121 PVSRGFPIVQVFTLKPLEFGKPNTLVCFISNLFPPTLTVNWQHQSAPVEGAGPTFVSAVD 180
Query: 633 DLSFQAFSYLNFTPTPSDLFSCVVTHELDGYIAISYWVPQNALPSDLLENVLCGVAFXXX 812
L+FQAFSYLN TP PSDLFSC+VTHE+DGY AI++WVPQNALPSDLLENVLCGVAF
Sbjct: 181 GLTFQAFSYLNVTPAPSDLFSCIVTHEIDGYTAIAFWVPQNALPSDLLENVLCGVAF-GL 239
Query: 813 XXXXXXXXXXXXYSRKPC 866
Y RKPC
Sbjct: 240 GVLGIIVGLVLFYCRKPC 257
>ref|XP_002702914.1| PREDICTED: BOLA-DQA2 protein-like [Bos taurus].
Length = 254
Score = 96.7 bits (239), Expect = 3e-20
Identities = 63/205 (30%), Positives = 99/205 (48%), Gaps = 3/205 (1%)
Frame = +3
Query: 192 GWRDELQNHTFQY-TMYCQDGNPEVGLSEVYDGDQLFSFNFSQNIRVPRLPEFADWAHQI 368
G D + +H Y T+ Q P ++ +DGD+LF + + V RLP F+ +A
Sbjct: 22 GGEDIVADHVGSYGTVISQSHGPSDQYTQEFDGDKLFYVDLEKKETVWRLPMFSQFASF- 80
Query: 369 EDTPAIFFDKGFCREMIEKVGPLFEGKIPVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNL 548
D AI + + + + + IP +P VF+ P+ G+PNTL+C + N
Sbjct: 81 -DPQAILRNIAISKHNLN-IMIKYSNFIPAINEVPEVTVFSKSPMVLGQPNTLICHMDN- 137
Query: 549 FPPALTVTW-EHHSAPVEGIGPTFVSATDDLSFQAFSYLNFTPTPSDLFSCVVTHELDGY 725
FPP + +TW ++ A EG+ T DD SF YL F P+ D++ C V H
Sbjct: 138 FPPVINITWLKNGHAVTEGVSETSFLPKDDHSFLKIGYLTFLPSDDDVYDCKVEHWSLDE 197
Query: 726 IAISYWVPQNALP-SDLLENVLCGV 797
+ +W P+ P S+L E V+C +
Sbjct: 198 PLLKHWEPEVPAPMSELTETVVCAL 222
>ref|NP_001013619.3| major histocompatibility complex, class II, DQ alpha, type 1 [Bos
taurus].
Length = 255
Score = 89.4 bits (220), Expect = 5e-18
Identities = 59/206 (28%), Positives = 93/206 (45%), Gaps = 4/206 (1%)
Frame = +3
Query: 192 GWRDELQNHTFQYTM-YCQDGNPEVGLSEVYDGDQLFSFNFSQNIRVPRLPEFADW-AHQ 365
G D + +H Y + Q P +DGD+LF + + V +LP F + + +
Sbjct: 22 GGEDIVADHIGTYGADFYQSHGPSGQYIHEFDGDELFYVDLGKKETVWQLPMFGELTSFE 81
Query: 366 IEDTPAIFFDKGFCREMIEKVGPLFEGKIPVSRGLPIAEVFTLKPLEFGKPNTLVCFVSN 545
+D +++ K PV +P VF+ P+ G+PNTL+C V N
Sbjct: 82 AQDALNEIAKAKHTLDVLTKRSNF----TPVINEVPEVTVFSKSPMMLGQPNTLICHVDN 137
Query: 546 LFPPALTVTW-EHHSAPVEGIGPTFVSATDDLSFQAFSYLNFTPTPSDLFSCVVTHELDG 722
+FPP + +TW + A EG+ T D SF YL F P+ D++ C V H
Sbjct: 138 IFPPVINITWLRNGHAVTEGVSETSFLPKSDYSFLKIGYLTFLPSDDDVYDCKVEHWGLD 197
Query: 723 YIAISYWVPQNALP-SDLLENVLCGV 797
+ +W P+ P S+L E V+C +
Sbjct: 198 EPLLKHWEPEIPAPMSELTETVVCAL 223
>ref|NP_001012699.1| major histocompatibility complex, class II, DQ alpha 2 [Bos
taurus].
Length = 268
Score = 89.0 bits (219), Expect = 7e-18
Identities = 54/175 (30%), Positives = 85/175 (48%), Gaps = 2/175 (1%)
Frame = +3
Query: 192 GWRDELQNHTFQY-TMYCQDGNPEVGLSEVYDGDQLFSFNFSQNIRVPRLPEFADWAHQI 368
G D + +H Y T Q P ++ +DGD++F + + V RLP F+ +A
Sbjct: 22 GGEDIVADHVGSYGTEIYQSHGPSGQYTQEFDGDEMFYVDLGKKETVWRLPMFSQFAGF- 80
Query: 369 EDTPAIFFDKGFCREMIEKVGPLFEGKIPVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNL 548
D A + + ++ + PV +P VF+ P+ G+PNTL+C V N+
Sbjct: 81 -DPQAALSEIATAKHNLDVLTKR-SNFTPVINEVPEVTVFSKSPVMLGQPNTLICHVDNI 138
Query: 549 FPPALTVTW-EHHSAPVEGIGPTFVSATDDLSFQAFSYLNFTPTPSDLFSCVVTH 710
FPP + +TW ++ A EG+ T DD SF YL F P+ +D++ C V H
Sbjct: 139 FPPVINITWLKNGHAVTEGVSETSFLPKDDHSFLKIGYLTFLPSDNDIYDCKVEH 193
>ref|NP_001012696.1| major histocompatibility complex, class II, DY alpha [Bos taurus].
Length = 253
Score = 86.3 bits (212), Expect = 5e-17
Identities = 60/178 (33%), Positives = 85/178 (47%), Gaps = 5/178 (2%)
Frame = +3
Query: 279 YDGDQLFSFNFSQNIRVPRLPEFADWAHQIEDTPA---IFFDKGFCREMIEKVGPLFEGK 449
+DGD+LF + + V RLPEF++ + E A I K +I+
Sbjct: 50 FDGDELFYVDLGKKETVWRLPEFSNIT-KFEVQSALRNIVMSKRNLDILIKN-----SSF 103
Query: 450 IPVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSA 626
P + +P VF + G PNTL+C V N+FPP + +TW ++ V EGI T
Sbjct: 104 TPATSEIPEVAVFPKSSVVLGIPNTLICQVDNIFPPVINITWFYNGHFVAEGIAETTFYP 163
Query: 627 TDDLSFQAFSYLNFTPTPSDLFSCVVTHELDGYIAISYWVPQNALP-SDLLENVLCGV 797
D SF FSYL F PT D + C V H + +W P+ P S+L E V+C +
Sbjct: 164 KSDHSFLKFSYLTFLPTNEDFYDCRVEHWGLEEPLVKHWEPEIPTPTSELTETVVCAL 221
>ref|NP_001012695.1| major histocompatibility complex, class II, DR alpha [Bos taurus].
Length = 253
Score = 83.2 bits (204), Expect = 4e-16
Identities = 54/178 (30%), Positives = 84/178 (47%), Gaps = 5/178 (2%)
Frame = +3
Query: 279 YDGDQLFSFNFSQNIRVPRLPEFADWAHQIEDTPAIF---FDKGFCREMIEKVGPLFEGK 449
+DGD++F + + V RLPEF +A E A+ K MI++
Sbjct: 50 FDGDEIFHVDMGKKETVWRLPEFGHFA-SFEAQGALANMAVMKANLDIMIKRSNNTPNTN 108
Query: 450 IPVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSA 626
+P P + KP+E G+PNTL+CF+ PP ++VTW + PV +G+ T
Sbjct: 109 VP-----PEVTLLPNKPVELGEPNTLICFIDKFSPPVISVTWLRNGKPVTDGVSQTVFLP 163
Query: 627 TDDLSFQAFSYLNFTPTPSDLFSCVVTHELDGYIAISYWVPQNALP-SDLLENVLCGV 797
+D F+ F YL F PT D++ C V H + +W + P + EN +C +
Sbjct: 164 RNDHLFRKFHYLPFLPTTEDVYDCKVEHLGLNEPLLKHWEYEAPAPLPETTENAVCAL 221
>ref|NP_001012693.1| major histocompatibility complex, class II, DQ alpha 5 [Bos
taurus].
Length = 255
Score = 82.8 bits (203), Expect = 5e-16
Identities = 55/203 (27%), Positives = 88/203 (43%), Gaps = 3/203 (1%)
Frame = +3
Query: 192 GWRDELQNHTFQYTMYC-QDGNPEVGLSEVYDGDQLFSFNFSQNIRVPRLPEFADWAHQI 368
G D + +H Y + Q P + +DGD+ F + + +LP F+ +
Sbjct: 22 GGEDIVADHVGIYGISIYQSYGPSGQYTHEFDGDEQFYVDLEKKETAWQLPLFS---RML 78
Query: 369 EDTPAIFFDKGFCREMIEKVGPLFEGKIPVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNL 548
P + ++ F + +P VF+ P+ G+PNTL+C V N+
Sbjct: 79 SFDPQLALRNIAIMKLHVDFLTKFSNSTAATNKVPEVTVFSKSPVMLGQPNTLICHVDNI 138
Query: 549 FPPALTVTWEHHSAPV-EGIGPTFVSATDDLSFQAFSYLNFTPTPSDLFSCVVTHELDGY 725
FPP + +TW + V EG+ T D SF YL F P+ D++ C V H
Sbjct: 139 FPPVINITWLRNGHSVTEGVSETSFLIRSDYSFLKIKYLAFLPSDDDIYDCKVEHWGLDE 198
Query: 726 IAISYWVPQNALP-SDLLENVLC 791
+ +W P+ P S+L E V+C
Sbjct: 199 PLLKHWEPEIPAPMSELTETVVC 221
>ref|NP_001073045.1| major histocompatibility complex, class II, DQ alpha, type 3 [Bos
taurus].
Length = 254
Score = 82.4 bits (202), Expect = 7e-16
Identities = 57/205 (27%), Positives = 91/205 (44%), Gaps = 3/205 (1%)
Frame = +3
Query: 192 GWRDELQNHTFQY-TMYCQDGNPEVGLSEVYDGDQLFSFNFSQNIRVPRLPEFADWAHQI 368
G D + +H Y T + Q P +DGD+ F + + V RLP F
Sbjct: 22 GGEDIVADHVGTYGTDFYQSHGPSGQYIHQFDGDEEFYVDLEKEEAVWRLPMFDKLRFHP 81
Query: 369 EDTPAIFFDKGFCREMIEKVGPLFEGKIPVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNL 548
+ + + ++ + L+ PV +P VF+ P+ +PNTL+C V N+
Sbjct: 82 QGA---LRNIAIAKHNLDVLTKLYNFT-PVINEVPEVTVFSKSPVMLSQPNTLICHVDNI 137
Query: 549 FPPALTVTWEHHSAPV-EGIGPTFVSATDDLSFQAFSYLNFTPTPSDLFSCVVTHELDGY 725
FPP + +TW + V E + T D S+ SYL F P+ D++ C V H
Sbjct: 138 FPPVINITWLRNGHSVTEHVSETSFLLRSDYSYLKISYLPFRPSDDDVYDCKVEHWGLDE 197
Query: 726 IAISYWVPQNALP-SDLLENVLCGV 797
+ +W P+ P S+L E V+C +
Sbjct: 198 PLLKHWEPEIPAPMSELTETVVCAL 222
>ref|NP_001192849.1| HLA class II histocompatibility antigen, DO alpha chain [Bos
taurus].
Length = 250
Score = 81.3 bits (199), Expect = 1e-15
Identities = 55/182 (30%), Positives = 81/182 (44%), Gaps = 9/182 (4%)
Frame = +3
Query: 279 YDGDQLFSFNFSQNIRVPRLPEFADWAHQIEDTPAIFFDKGFCREMIEKVGPLFEGKIPV 458
+DG+QLFS + + V RLPEF ++A +FD I + E +
Sbjct: 52 FDGEQLFSVDLKKREAVWRLPEFGNFA---------YFDPQSGLVSIAMIKAHLEDLVKR 102
Query: 459 SRGL------PIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTF 617
S G P V ++ G+PN L+C V +FPP + +TW + PV +G+ +
Sbjct: 103 SNGTRAPNVSPRVAVLPKSHVQLGEPNVLICIVDKIFPPVINITWLRNGHPVTQGVTQSS 162
Query: 618 VSATDDLSFQAFSYLNFTPTPSDLFSCVVTHELDGYIAISYWVPQ--NALPSDLLENVLC 791
A D F+ F YL F P D + C V H +W PQ ALP D ++C
Sbjct: 163 FYAQPDHLFRKFHYLTFVPLVDDFYDCKVEHWGLDQPLFQHWEPQVPTALP-DTTGTLVC 221
Query: 792 GV 797
+
Sbjct: 222 AL 223
>ref|XP_002697222.1| PREDICTED: MHC class II antigen-like [Bos taurus].
Length = 250
Score = 81.3 bits (199), Expect = 1e-15
Identities = 55/182 (30%), Positives = 81/182 (44%), Gaps = 9/182 (4%)
Frame = +3
Query: 279 YDGDQLFSFNFSQNIRVPRLPEFADWAHQIEDTPAIFFDKGFCREMIEKVGPLFEGKIPV 458
+DG+QLFS + + V RLPEF ++A +FD I + E +
Sbjct: 52 FDGEQLFSVDLKKREAVWRLPEFGNFA---------YFDPQSGLVSIAMIKAHLEDLVKR 102
Query: 459 SRGL------PIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTF 617
S G P V ++ G+PN L+C V +FPP + +TW + PV +G+ +
Sbjct: 103 SNGTRAPNVSPRVAVLPKSHVQLGEPNVLICIVDKIFPPVINITWLRNGHPVTQGVTQSS 162
Query: 618 VSATDDLSFQAFSYLNFTPTPSDLFSCVVTHELDGYIAISYWVPQ--NALPSDLLENVLC 791
A D F+ F YL F P D + C V H +W PQ ALP D ++C
Sbjct: 163 FYAQPDHLFRKFHYLTFVPLVDDFYDCKVEHWGLDQPLFQHWEPQVPTALP-DTTGTLVC 221
Query: 792 GV 797
+
Sbjct: 222 AL 223
Database: RefSeq49_BP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 17,681,374
Number of sequences in database: 33,088
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 Sequences: 33088
Number of Hits to DB: 44,484,464
Number of extensions: 1247104
Number of successful extensions: 4887
Number of sequences better than 1.0e-05: 11
Number of HSP's gapped: 4850
Number of HSP's successfully gapped: 12
Length of query: 371
Length of database: 17,681,374
Length adjustment: 104
Effective length of query: 267
Effective length of database: 14,240,222
Effective search space: 3802139274
Effective search space used: 3802139274
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 35 (18.1 bits)
Animal-Genome cDNA 20110601C-012854
Search to RefSeqCP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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= 20110601C-012854
(1115 letters)
Database: RefSeq49_CP.fasta
33,336 sequences; 18,874,504 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001041564.1| major histocompatibility complex, class II, ... 209 5e-54
Alignment gi|NP_001011726.1| major histocompatibility complex, class II, ... 89 1e-17
Alignment gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati... 86 5e-17
Alignment gi|NP_001011723.1| MHC class II DR alpha chain [Canis lupus fam... 81 2e-15
Alignment gi|XP_858541.1| PREDICTED: similar to immunoglobulin iota chain... 54 4e-07
Alignment gi|XP_855821.1| PREDICTED: similar to Immunoglobulin lambda-lik... 52 1e-06
Alignment gi|XP_850308.1| PREDICTED: similar to Immunoglobulin lambda-lik... 51 2e-06
Alignment gi|XP_850294.1| PREDICTED: similar to Immunoglobulin lambda-lik... 51 2e-06
Alignment gi|XP_859660.1| PREDICTED: similar to immunoglobulin iota chain... 51 2e-06
Alignment gi|XP_859630.1| PREDICTED: similar to immunoglobulin iota chain... 51 2e-06
>ref|NP_001041564.1| major histocompatibility complex, class II, DM alpha [Canis lupus
familiaris].
Length = 170
Score = 209 bits (531), Expect = 5e-54
Identities = 101/144 (70%), Positives = 108/144 (75%), Gaps = 4/144 (2%)
Frame = +3
Query: 450 IPVSR----GLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPVEGIGPTF 617
+P SR G P+ +VFTLKPLEFGKPN LVCF+SNLFPP LTV W HH PVEGIGPTF
Sbjct: 27 LPYSRTAPEGFPMVDVFTLKPLEFGKPNMLVCFISNLFPPTLTVNWWHHLDPVEGIGPTF 86
Query: 618 VSATDDLSFQAFSYLNFTPTPSDLFSCVVTHELDGYIAISYWVPQNALPSDLLENVLCGV 797
VSA D SFQAFSYLNFTP PSDLFSCVVTHE+D Y AI+YWVP +ALPSDLLENVLCGV
Sbjct: 87 VSAVDGFSFQAFSYLNFTPAPSDLFSCVVTHEIDNYTAIAYWVPHDALPSDLLENVLCGV 146
Query: 798 AFXXXXXXXXXXXXXXXYSRKPCS 869
AF Y RKPCS
Sbjct: 147 AFGLGMLGIIVGLVLIVYFRKPCS 170
>ref|NP_001011726.1| major histocompatibility complex, class II, DQ alpha [Canis lupus
familiaris].
Length = 255
Score = 88.6 bits (218), Expect = 1e-17
Identities = 57/205 (27%), Positives = 96/205 (46%), Gaps = 3/205 (1%)
Frame = +3
Query: 192 GWRDELQNHTFQYTMYC-QDGNPEVGLSEVYDGDQLFSFNFSQNIRVPRLPEFADWAHQI 368
G + + +H Y + Q P + +DGD+ F + + V RLP F+ + +
Sbjct: 22 GGEEIVADHVANYGINVYQSYGPSGQYTHEFDGDEEFYVDLEKKETVWRLPVFSTF--RS 79
Query: 369 EDTPAIFFDKGFCREMIEKVGPLFEGKIPVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNL 548
D + ++ + + + + +P VF+ P+ G+PNTL+C V N+
Sbjct: 80 FDPQGALRNLAIIKQNLN-IMTKRSNQTAATNEVPEVTVFSKSPVMLGQPNTLICLVDNI 138
Query: 549 FPPALTVTW-EHHSAPVEGIGPTFVSATDDLSFQAFSYLNFTPTPSDLFSCVVTHELDGY 725
FPP + VTW ++ + EG+ T A D SF SYL F P+ D++ C V H
Sbjct: 139 FPPVINVTWLKNRHSVTEGVSETSFFAKGDHSFSKISYLTFLPSAEDIYDCKVEHWGLDE 198
Query: 726 IAISYWVPQNALP-SDLLENVLCGV 797
+ +W P+ P S+L E V+C +
Sbjct: 199 PLLKHWEPEVPTPMSELTETVVCAL 223
>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 = 86.3 bits (212), Expect = 5e-17
Identities = 55/179 (30%), Positives = 84/179 (46%), Gaps = 6/179 (3%)
Frame = +3
Query: 279 YDGDQLFSFNFSQNIRVPRLPEFADWAH--QIEDTPAIFFDKGFCREMIEKVGPL--FEG 446
+DG+QLFS + V RLPEF + AH +I K ++E+ G
Sbjct: 22 FDGEQLFSVELKKRQAVWRLPEFGNLAHFDPQNGLASIAVIKAHLDVLVERSNRTRAING 81
Query: 447 KIPVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVS 623
S P V +E G+PN L+C V N+FPP + +TW + + EG+ T
Sbjct: 82 THLSSPLPPRVAVLPKFRVELGQPNVLICIVDNIFPPVINITWLRNGQIISEGVAQTSFY 141
Query: 624 ATDDLSFQAFSYLNFTPTPSDLFSCVVTHELDGYIAISYWVPQNALP-SDLLENVLCGV 797
+ D F+ F YL F P+ D++ C V H + +W PQ +P D +E ++C +
Sbjct: 142 SQPDHLFRKFCYLTFVPSAEDMYDCKVEHWGLEEPLLRHWEPQVPIPVPDTIETLICAL 200
>ref|NP_001011723.1| MHC class II DR alpha chain [Canis lupus familiaris].
Length = 254
Score = 81.3 bits (199), Expect = 2e-15
Identities = 55/178 (30%), Positives = 84/178 (47%), Gaps = 5/178 (2%)
Frame = +3
Query: 279 YDGDQLFSFNFSQNIRVPRLPEFADWAH-QIEDTPA-IFFDKGFCREMIEKVGPLFEGKI 452
+DGD++F + + V RL EF +A + + A I DK MI++ +
Sbjct: 51 FDGDEIFHVDMEKKETVWRLEEFGRFASFEAQGALANIAVDKANLDTMIKRSNHTPNTNV 110
Query: 453 PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSAT 629
P P V + P+E G+PN L+CF+ PP + VTW + PV G+ T
Sbjct: 111 P-----PEVTVLSNTPVELGEPNILICFIDKFSPPVINVTWLRNGNPVTTGVSETIFLPR 165
Query: 630 DDLSFQAFSYLNFTPTPSDLFSCVVTHELDGYIAISYW--VPQNALPSDLLENVLCGV 797
+D F+ F YL F P+ D++ C V H + +W P LP + ENV+C +
Sbjct: 166 EDHLFRKFHYLPFLPSAEDVYDCKVEHWGLDEPLLKHWEFEPPTPLP-ETTENVVCAL 222
>ref|XP_858541.1| PREDICTED: similar to immunoglobulin iota chain preproprotein
isoform 29 [Canis familiaris].
Length = 243
Score = 53.5 bits (127), Expect = 4e-07
Identities = 42/116 (36%), Positives = 56/116 (48%), Gaps = 12/116 (10%)
Frame = +3
Query: 402 FCREMIEKVGPLF---EGKIPVSRGLPIAE--VFTLKPL--EFGKPN-TLVCFVSNLFPP 557
FC + +V P F EG G P A V PL E G TLVC +S+ +P
Sbjct: 114 FCTTYMNQVSPWFVFSEGIELTVLGQPKASPSVTLFLPLSGELGADKATLVCLISDFYPS 173
Query: 558 ALTVTWEHHSAPV-EGIGPTFVSATDDLSFQAFSYLNFTP---TPSDLFSCVVTHE 713
+TV W+ +PV +G+ T S + + A SYL+ TP FSC+VTHE
Sbjct: 174 GVTVAWKADGSPVTQGVETTKPSRQSNNKYAASSYLSLTPDKWKSHSSFSCLVTHE 229
>ref|XP_855821.1| PREDICTED: similar to Immunoglobulin lambda-like polypeptide 1
precursor (Immunoglobulin-related 14.1 protein)
(Immunoglobulin omega polypeptide) (Lambda 5) (CD179b
antigen) isoform 3 [Canis familiaris].
Length = 231
Score = 52.0 bits (123), Expect = 1e-06
Identities = 38/127 (29%), Positives = 59/127 (46%), Gaps = 5/127 (3%)
Frame = +3
Query: 348 ADWAHQIEDTPAIFFDKGFCREMIEKVGPLFEGKIPVSRGLPIAEVFTLKPLEFGKPN-T 524
AD+ Q+ D+ A+ F G ++ + + P +F E G T
Sbjct: 102 ADYYCQVWDSSALVFGGGTHLTVLGQ-----------PKASPSVTLFPPSSEELGANKAT 150
Query: 525 LVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSATDDLSFQAFSYLNFTP---TPSDLF 692
LVC +S+ +P +TV W+ +PV +G+ T S + + A SYL+ TP F
Sbjct: 151 LVCLISDFYPSGVTVAWKADGSPVTQGVETTKPSKQSNNKYAASSYLSLTPDKWKSHSSF 210
Query: 693 SCVVTHE 713
SC+VTHE
Sbjct: 211 SCLVTHE 217
>ref|XP_850308.1| PREDICTED: similar to Immunoglobulin lambda-like polypeptide 1
precursor (Immunoglobulin-related 14.1 protein)
(Immunoglobulin omega polypeptide) (Lambda 5) (CD179b
antigen) [Canis familiaris].
Length = 126
Score = 51.2 bits (121), Expect = 2e-06
Identities = 27/68 (39%), Positives = 39/68 (57%), Gaps = 4/68 (5%)
Frame = +3
Query: 522 TLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSATDDLSFQAFSYLNFTP---TPSDL 689
TLVC +S+ +P +TV W+ +PV +G+ T S + + A SYL+ TP
Sbjct: 45 TLVCLISDFYPSGVTVAWKADGSPVTQGVETTKPSKQSNNKYAASSYLSLTPDKWKSHSS 104
Query: 690 FSCVVTHE 713
FSC+VTHE
Sbjct: 105 FSCLVTHE 112
>ref|XP_850294.1| PREDICTED: similar to Immunoglobulin lambda-like polypeptide 1
precursor (Immunoglobulin-related 14.1 protein)
(Immunoglobulin omega polypeptide) (Lambda 5) (CD179b
antigen) [Canis familiaris].
Length = 126
Score = 51.2 bits (121), Expect = 2e-06
Identities = 27/68 (39%), Positives = 39/68 (57%), Gaps = 4/68 (5%)
Frame = +3
Query: 522 TLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSATDDLSFQAFSYLNFTP---TPSDL 689
TLVC +S+ +P +TV W+ +PV +G+ T S + + A SYL+ TP
Sbjct: 45 TLVCLISDFYPSGVTVAWKADGSPVTQGVETTKPSKQSNNKYAASSYLSLTPDKWKSHSS 104
Query: 690 FSCVVTHE 713
FSC+VTHE
Sbjct: 105 FSCLVTHE 112
>ref|XP_859660.1| PREDICTED: similar to immunoglobulin iota chain preproprotein
isoform 59 [Canis familiaris].
Length = 241
Score = 51.2 bits (121), Expect = 2e-06
Identities = 27/68 (39%), Positives = 39/68 (57%), Gaps = 4/68 (5%)
Frame = +3
Query: 522 TLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSATDDLSFQAFSYLNFTP---TPSDL 689
TLVC +S+ +P +TV W+ +PV +G+ T S + + A SYL+ TP
Sbjct: 160 TLVCLISDFYPSGVTVAWKADGSPVTQGVETTKPSRQSNNKYAASSYLSLTPDKWKSHSS 219
Query: 690 FSCVVTHE 713
FSC+VTHE
Sbjct: 220 FSCLVTHE 227
>ref|XP_859630.1| PREDICTED: similar to immunoglobulin iota chain preproprotein
isoform 58 [Canis familiaris].
Length = 242
Score = 51.2 bits (121), Expect = 2e-06
Identities = 27/68 (39%), Positives = 39/68 (57%), Gaps = 4/68 (5%)
Frame = +3
Query: 522 TLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSATDDLSFQAFSYLNFTP---TPSDL 689
TLVC +S+ +P +TV W+ +PV +G+ T S + + A SYL+ TP
Sbjct: 161 TLVCLISDFYPSGVTVAWKADGSPVTQGVETTKPSRQSNNKYAASSYLSLTPDKWKSHSS 220
Query: 690 FSCVVTHE 713
FSC+VTHE
Sbjct: 221 FSCLVTHE 228
Database: RefSeq49_CP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 18,874,504
Number of sequences in database: 33,336
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 Sequences: 33336
Number of Hits to DB: 46,329,861
Number of extensions: 1268454
Number of successful extensions: 5099
Number of sequences better than 1.0e-05: 74
Number of HSP's gapped: 4935
Number of HSP's successfully gapped: 74
Length of query: 371
Length of database: 18,874,504
Length adjustment: 104
Effective length of query: 267
Effective length of database: 15,407,560
Effective search space: 4113818520
Effective search space used: 4113818520
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 35 (18.1 bits)
Search to RefSeqSP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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= 20110601C-012854
(1115 letters)
Database: RefSeq49_SP.fasta
24,897 sequences; 11,343,932 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001004039.1| SLA-DM alpha chain [Sus scrofa]. 486 e-138
Alignment gi|NP_001107177.1| major histocompatibility complex, class II, ... 486 e-138
Alignment gi|NP_001172072.1| src-like-adapter [Sus scrofa]. 94 1e-19
Alignment gi|NP_001107534.2| SLA class II histocompatibility antigen, DQ ... 87 2e-17
Alignment gi|NP_001123696.1| SLA class II histocompatibility antigen, DQ ... 82 7e-16
Alignment gi|NP_001107178.1| MHC class II DR-alpha [Sus scrofa]. 81 1e-15
>ref|NP_001004039.1| SLA-DM alpha chain [Sus scrofa].
Length = 260
Score = 486 bits (1252), Expect = e-138
Identities = 233/260 (89%), Positives = 234/260 (90%)
Frame = +3
Query: 93 MDHELSQGAAXXXXXXXXXXXPHSWTAPEAPAPGWRDELQNHTFQYTMYCQDGNPEVGLS 272
MDHELSQGAA PHSWTAPEAPAPGWRDELQNHTFQYTMYCQDGNPEVGLS
Sbjct: 1 MDHELSQGAALLRLLHLLWLLPHSWTAPEAPAPGWRDELQNHTFQYTMYCQDGNPEVGLS 60
Query: 273 EVYDGDQLFSFNFSQNIRVPRLPEFADWAHQIEDTPAIFFDKGFCREMIEKVGPLFEGKI 452
EVYDGDQLFSFNFSQNIRVPRLPEFADWAHQIEDTPAIFFDKGFCREMIEKVGPLFEGKI
Sbjct: 61 EVYDGDQLFSFNFSQNIRVPRLPEFADWAHQIEDTPAIFFDKGFCREMIEKVGPLFEGKI 120
Query: 453 PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPVEGIGPTFVSATD 632
PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPVEGIGPTFVSATD
Sbjct: 121 PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPVEGIGPTFVSATD 180
Query: 633 DLSFQAFSYLNFTPTPSDLFSCVVTHELDGYIAISYWVPQNALPSDLLENVLCGVAFXXX 812
DLSFQAFSYLNFTPTPSDLFSCVVTHELDGY+AISYWVPQNALPSDLLENVLCGVAF
Sbjct: 181 DLSFQAFSYLNFTPTPSDLFSCVVTHELDGYVAISYWVPQNALPSDLLENVLCGVAFGLG 240
Query: 813 XXXXXXXXXXXXYSRKPCSA 872
YSRKPCSA
Sbjct: 241 VLGIIVGLVLIIYSRKPCSA 260
>ref|NP_001107177.1| major histocompatibility complex, class II, DO alpha [Sus scrofa].
Length = 260
Score = 486 bits (1252), Expect = e-138
Identities = 233/260 (89%), Positives = 234/260 (90%)
Frame = +3
Query: 93 MDHELSQGAAXXXXXXXXXXXPHSWTAPEAPAPGWRDELQNHTFQYTMYCQDGNPEVGLS 272
MDHELSQGAA PHSWTAPEAPAPGWRDELQNHTFQYTMYCQDGNPEVGLS
Sbjct: 1 MDHELSQGAALLRLLHLLWLLPHSWTAPEAPAPGWRDELQNHTFQYTMYCQDGNPEVGLS 60
Query: 273 EVYDGDQLFSFNFSQNIRVPRLPEFADWAHQIEDTPAIFFDKGFCREMIEKVGPLFEGKI 452
EVYDGDQLFSFNFSQNIRVPRLPEFADWAHQIEDTPAIFFDKGFCREMIEKVGPLFEGKI
Sbjct: 61 EVYDGDQLFSFNFSQNIRVPRLPEFADWAHQIEDTPAIFFDKGFCREMIEKVGPLFEGKI 120
Query: 453 PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPVEGIGPTFVSATD 632
PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPVEGIGPTFVSATD
Sbjct: 121 PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPVEGIGPTFVSATD 180
Query: 633 DLSFQAFSYLNFTPTPSDLFSCVVTHELDGYIAISYWVPQNALPSDLLENVLCGVAFXXX 812
DLSFQAFSYLNFTPTPSDLFSCVVTHELDGY+AISYWVPQNALPSDLLENVLCGVAF
Sbjct: 181 DLSFQAFSYLNFTPTPSDLFSCVVTHELDGYVAISYWVPQNALPSDLLENVLCGVAFGLG 240
Query: 813 XXXXXXXXXXXXYSRKPCSA 872
YSRKPCSA
Sbjct: 241 VLGIIVGLVLIIYSRKPCSA 260
>ref|NP_001172072.1| src-like-adapter [Sus scrofa].
Length = 250
Score = 94.4 bits (233), Expect = 1e-19
Identities = 56/177 (31%), Positives = 85/177 (48%), Gaps = 4/177 (2%)
Frame = +3
Query: 279 YDGDQLFSFNFSQNIRVPRLPEFADWAH--QIEDTPAIFFDKGFCREMIEKVGPLFEGKI 452
+DG+QLFS + + V RLPEF+++A I + ++E+ +
Sbjct: 52 FDGEQLFSVDLKKREAVWRLPEFSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNV 111
Query: 453 PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSAT 629
P P V P+ G+PN L+C V N+FPP + +TW H+ V EG+ T A
Sbjct: 112 P-----PRVTVLPKSPVALGQPNVLICIVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQ 166
Query: 630 DDLSFQAFSYLNFTPTPSDLFSCVVTHELDGYIAISYWVPQNALP-SDLLENVLCGV 797
D SF+ F YL F P+ D + C V H ++W PQ +P D E ++C +
Sbjct: 167 PDHSFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWEPQVTMPLPDTTETLVCAL 223
>ref|NP_001107534.2| SLA class II histocompatibility antigen, DQ haplotype C alpha chain
precursor [Sus scrofa].
Length = 254
Score = 87.0 bits (214), Expect = 2e-17
Identities = 58/206 (28%), Positives = 94/206 (45%), Gaps = 2/206 (0%)
Frame = +3
Query: 186 APGWRDELQNHTFQYTMYC-QDGNPEVGLSEVYDGDQLFSFNFSQNIRVPRLPEFADWAH 362
A G D +H Y + Q P + +DGD+ F + + V RLP F+++
Sbjct: 20 ACGGEDIAADHVASYGLNVYQSYGPSGYFTHEFDGDEEFYVDLEKKETVWRLPLFSEFTS 79
Query: 363 QIEDTPAIFFDKGFCREMIEKVGPLFEGKIPVSRGLPIAEVFTLKPLEFGKPNTLVCFVS 542
D + + + V V++ +P VF+ P+ G+PNTL+C V
Sbjct: 80 F--DPQGALRNIATLKHNLNIVTKRSNNTAAVNQ-VPEVTVFSKSPVILGQPNTLICHVD 136
Query: 543 NLFPPALTVTWEHHSAPVEGIGPTFVSATDDLSFQAFSYLNFTPTPSDLFSCVVTHELDG 722
++FPP + +TW + V+G T + +D SF SYL F P+ D + C V H
Sbjct: 137 SIFPPVINITWLKNGHSVKGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLD 196
Query: 723 YIAISYWVPQNALP-SDLLENVLCGV 797
+ +W P+ P S+L E V+C +
Sbjct: 197 KPLLKHWEPEIPAPMSELTETVVCAL 222
>ref|NP_001123696.1| SLA class II histocompatibility antigen, DQ haplotype D alpha chain
precursor [Sus scrofa].
Length = 255
Score = 81.6 bits (200), Expect = 7e-16
Identities = 61/215 (28%), Positives = 94/215 (43%), Gaps = 11/215 (5%)
Frame = +3
Query: 186 APGWRDELQNHTFQYTMYC-QDGNPEVGLSEVYDGDQLFSFNFSQNIRVPRLPEFADWAH 362
A G D +H Y + Q P + +DGD+ F + + V +LP F+ +
Sbjct: 20 ACGGEDIAADHVASYGLNVYQSYGPSGYYTHEFDGDEEFYVDLEKKETVWQLPLFSKFTS 79
Query: 363 QIEDTPAIFFDKGFCREMIEKVGPLFEGKIPVSRG--------LPIAEVFTLKPLEFGKP 518
F +G R + L I + R +P VF P+ G+P
Sbjct: 80 --------FDPQGALRNIATAKHNL---NILIKRSNNTAAVNQVPEVTVFPKSPVMLGQP 128
Query: 519 NTLVCFVSNLFPPALTVTW-EHHSAPVEGIGPTFVSATDDLSFQAFSYLNFTPTPSDLFS 695
NTL+C V N+FPP + +TW ++ + EG T + +D SF SYL F P+ D +
Sbjct: 129 NTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYD 188
Query: 696 CVVTHELDGYIAISYWVPQNALP-SDLLENVLCGV 797
C V H + +W P+ P S+L E V+C +
Sbjct: 189 CKVEHWGLDKPLLKHWEPEIPAPMSELTETVVCAL 223
>ref|NP_001107178.1| MHC class II DR-alpha [Sus scrofa].
Length = 252
Score = 80.9 bits (198), Expect = 1e-15
Identities = 54/178 (30%), Positives = 85/178 (47%), Gaps = 5/178 (2%)
Frame = +3
Query: 279 YDGDQLFSFNFSQNIRVPRLPEFADWAH-QIEDTPA-IFFDKGFCREMIEKVGPLFEGKI 452
+DGD++F + + V RL EF +A + + A I DK +I++ +
Sbjct: 49 FDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSNNTPNTNV 108
Query: 453 PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSAT 629
P P V + KP+E G+PN L+CF+ PP + VTW + +PV G+ T
Sbjct: 109 P-----PEVTVLSDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPR 163
Query: 630 DDLSFQAFSYLNFTPTPSDLFSCVVTHELDGYIAISYW--VPQNALPSDLLENVLCGV 797
+D F+ F YL F P+ D++ C V H + +W Q LP + EN +C +
Sbjct: 164 EDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLP-ETTENTVCAL 220
Database: RefSeq49_SP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 11,343,932
Number of sequences in database: 24,897
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 Sequences: 24897
Number of Hits to DB: 28,865,527
Number of extensions: 827223
Number of successful extensions: 3133
Number of sequences better than 1.0e-05: 6
Number of HSP's gapped: 3118
Number of HSP's successfully gapped: 6
Length of query: 371
Length of database: 11,343,932
Length adjustment: 100
Effective length of query: 271
Effective length of database: 8,854,232
Effective search space: 2399496872
Effective search space used: 2399496872
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Search to RefSeqMP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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= 20110601C-012854
(1115 letters)
Database: RefSeq49_MP.fasta
30,036 sequences; 15,617,559 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_034516.3| class II histocompatibility antigen, M alpha ch... 340 9e-94
Alignment gi|NP_032232.2| histocompatibility 2, O region alpha locus [Mus... 96 7e-20
Alignment gi|NP_034508.2| histocompatibility 2, class II antigen A, alpha... 94 2e-19
Alignment gi|NP_034511.2| histocompatibility 2, class II antigen E alpha ... 84 3e-16
Alignment gi|NP_033865.2| beta-2-microglobulin precursor [Mus musculus]. 55 1e-07
>ref|NP_034516.3| class II histocompatibility antigen, M alpha chain precursor [Mus
musculus].
Length = 261
Score = 340 bits (873), Expect = 9e-94
Identities = 161/259 (62%), Positives = 187/259 (72%)
Frame = +3
Query: 93 MDHELSQGAAXXXXXXXXXXXPHSWTAPEAPAPGWRDELQNHTFQYTMYCQDGNPEVGLS 272
M+HE GA PHSW EA P + D+ QNHTF++T++CQDG P +GLS
Sbjct: 1 MEHEQKSGAVLLRLLRLLWLLPHSWAVLEASTPVFWDDPQNHTFRHTLFCQDGIPNIGLS 60
Query: 273 EVYDGDQLFSFNFSQNIRVPRLPEFADWAHQIEDTPAIFFDKGFCREMIEKVGPLFEGKI 452
E YD D+LFSF+FSQN RVPRLP+FA+WA D AI FDK FC ++ +V P EG+I
Sbjct: 61 ETYDEDELFSFDFSQNTRVPRLPDFAEWAQGQGDASAIAFDKSFCEMLMREVSPKLEGQI 120
Query: 453 PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPVEGIGPTFVSATD 632
PVSRGLP+AEVFTLKPLEFGKPNTLVCF+SNLFPP LTV W+ HSAPVEG PT +SA D
Sbjct: 121 PVSRGLPVAEVFTLKPLEFGKPNTLVCFISNLFPPTLTVNWQLHSAPVEGASPTSISAVD 180
Query: 633 DLSFQAFSYLNFTPTPSDLFSCVVTHELDGYIAISYWVPQNALPSDLLENVLCGVAFXXX 812
L+FQAFSYLNFTP P DL+SC VTHE+D Y AI+YWVPQNALPSDLLEN LCGVAF
Sbjct: 181 GLTFQAFSYLNFTPEPFDLYSCTVTHEIDRYTAIAYWVPQNALPSDLLENALCGVAFGLG 240
Query: 813 XXXXXXXXXXXXYSRKPCS 869
S++PCS
Sbjct: 241 VLGTIMGIVFFLCSQRPCS 259
>ref|NP_032232.2| histocompatibility 2, O region alpha locus [Mus musculus].
Length = 250
Score = 95.5 bits (236), Expect = 7e-20
Identities = 56/177 (31%), Positives = 88/177 (49%), Gaps = 4/177 (2%)
Frame = +3
Query: 279 YDGDQLFSFNFSQNIRVPRLPEFADWAHQIEDTP--AIFFDKGFCREMIEKVGPLFEGKI 452
+DG+Q+FS + V RLPEF D+AH + +I K ++E+ +
Sbjct: 52 FDGEQIFSVDLKNEEVVWRLPEFGDFAHSDFQSGLMSISMIKAHLDILVERSNRTRAVSV 111
Query: 453 PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSAT 629
P P V +E GKPN L+C V ++FPP + VTW +S P+ +G+ T +
Sbjct: 112 P-----PRVTVLPKTRVELGKPNVLICIVDDIFPPVINVTWLRNSQPITKGVAQTSFYSQ 166
Query: 630 DDLSFQAFSYLNFTPTPSDLFSCVVTHELDGYIAISYWVPQNAL-PSDLLENVLCGV 797
+ F+ F YL F P+ D++ C V H + +W PQ P D +E ++CG+
Sbjct: 167 PNHRFRKFHYLTFVPSAEDVYDCKVEHWGLDTPLLQHWEPQVLTPPPDTIETLICGL 223
>ref|NP_034508.2| histocompatibility 2, class II antigen A, alpha precursor [Mus
musculus].
Length = 256
Score = 94.0 bits (232), Expect = 2e-19
Identities = 64/211 (30%), Positives = 100/211 (47%), Gaps = 9/211 (4%)
Frame = +3
Query: 192 GWRDELQ-NHTFQYTMYCQDGNPEVG-LSEVYDGDQLFSFNFSQNIRVPRLPEFADWAHQ 365
G D+++ +H Y + ++G + +DGD+LF + + V LPEF A
Sbjct: 22 GGEDDIEADHVGTYGISVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFGQLAS- 80
Query: 366 IEDTPAIFFDKGFCREMI---EKVGPLFE--GKIPVSRGLPIAEVFTLKPLEFGKPNTLV 530
F +G + + +G L + P + P A VF P+ G+PNTL+
Sbjct: 81 -------FDPQGGLQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLI 133
Query: 531 CFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSATDDLSFQAFSYLNFTPTPSDLFSCVVT 707
CFV N+FPP + +TW +S V +G+ T D SF SYL F P+ D++ C V
Sbjct: 134 CFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVE 193
Query: 708 HELDGYIAISYWVPQNALP-SDLLENVLCGV 797
H + +W P+ P S+L E V+C +
Sbjct: 194 HWGLEEPVLKHWEPEIPAPMSELTETVVCAL 224
>ref|NP_034511.2| histocompatibility 2, class II antigen E alpha precursor [Mus
musculus].
Length = 255
Score = 83.6 bits (205), Expect = 3e-16
Identities = 54/177 (30%), Positives = 84/177 (47%), Gaps = 4/177 (2%)
Frame = +3
Query: 279 YDGDQLFSFNFSQNIRVPRLPEFADWAH-QIEDTPA-IFFDKGFCREMIEKVGPLFEGKI 452
+DGD++F + ++ + RL EFA +A + + A I DK M E+
Sbjct: 51 FDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLDVMKER-----SNNT 105
Query: 453 PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSAT 629
P + P V + P+ G+PN L+CF+ PP + VTW + PV EG+ T
Sbjct: 106 PDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWFRNGRPVTEGVSETVFLPR 165
Query: 630 DDLSFQAFSYLNFTPTPSDLFSCVVTH-ELDGYIAISYWVPQNALPSDLLENVLCGV 797
DD F+ F YL F P+ D + C V H L+ + + + L + ENV+C +
Sbjct: 166 DDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEEPLRKHWEFEEKTLLPETTENVVCAL 222
>ref|NP_033865.2| beta-2-microglobulin precursor [Mus musculus].
Length = 119
Score = 55.1 bits (131), Expect = 1e-07
Identities = 27/91 (29%), Positives = 45/91 (49%)
Frame = +3
Query: 471 PIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPVEGIGPTFVSATDDLSFQA 650
P +V++ P E GKPN L C+V+ PP + + + + + + +S + D SF
Sbjct: 25 PQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYI 84
Query: 651 FSYLNFTPTPSDLFSCVVTHELDGYIAISYW 743
++ FTPT +D ++C V H YW
Sbjct: 85 LAHTEFTPTETDTYACRVKHASMAEPKTVYW 115
Database: RefSeq49_MP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 15,617,559
Number of sequences in database: 30,036
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 Sequences: 30036
Number of Hits to DB: 38,353,526
Number of extensions: 1036034
Number of successful extensions: 3872
Number of sequences better than 1.0e-05: 5
Number of HSP's gapped: 3846
Number of HSP's successfully gapped: 5
Length of query: 371
Length of database: 15,617,559
Length adjustment: 103
Effective length of query: 268
Effective length of database: 12,523,851
Effective search space: 3356392068
Effective search space used: 3356392068
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 35 (18.1 bits)
Search to RefSeqHP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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= 20110601C-012854
(1115 letters)
Database: RefSeq49_HP.fasta
32,964 sequences; 18,297,164 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_006111.2| HLA class II histocompatibility antigen, DM alp... 387 e-107
Alignment gi|XP_003120319.1| PREDICTED: HLA class II histocompatibility a... 85 1e-16
Alignment gi|XP_003120317.1| PREDICTED: HLA class II histocompatibility a... 85 1e-16
Alignment gi|XP_003119375.1| PREDICTED: HLA class II histocompatibility a... 84 3e-16
Alignment gi|XP_003119374.1| PREDICTED: HLA class II histocompatibility a... 84 3e-16
Alignment gi|XP_003120318.1| PREDICTED: HLA class II histocompatibility a... 83 5e-16
Alignment gi|NP_002113.2| HLA class II histocompatibility antigen, DQ alp... 83 5e-16
Alignment gi|NP_064440.1| HLA class II histocompatibility antigen, DQ alp... 82 7e-16
Alignment gi|XP_003119376.1| PREDICTED: HLA class II histocompatibility a... 82 1e-15
Alignment gi|NP_002110.1| HLA class II histocompatibility antigen, DO alp... 82 1e-15
>ref|NP_006111.2| HLA class II histocompatibility antigen, DM alpha chain precursor
[Homo sapiens].
Length = 261
Score = 387 bits (993), Expect = e-107
Identities = 182/259 (70%), Positives = 199/259 (76%)
Frame = +3
Query: 93 MDHELSQGAAXXXXXXXXXXXPHSWTAPEAPAPGWRDELQNHTFQYTMYCQDGNPEVGLS 272
M HE +QGAA PHSW PEAP P W D+LQNHTF +T+YCQDG+P VGLS
Sbjct: 1 MGHEQNQGAALLQMLPLLWLLPHSWAVPEAPTPMWPDDLQNHTFLHTVYCQDGSPSVGLS 60
Query: 273 EVYDGDQLFSFNFSQNIRVPRLPEFADWAHQIEDTPAIFFDKGFCREMIEKVGPLFEGKI 452
E YD DQLF F+FSQN RVPRLPEFADWA + D PAI FDK FC MI+++GP +GKI
Sbjct: 61 EAYDEDQLFFFDFSQNTRVPRLPEFADWAQEQGDAPAILFDKEFCEWMIQQIGPKLDGKI 120
Query: 453 PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPVEGIGPTFVSATD 632
PVSRG PIAEVFTLKPLEFGKPNTLVCFVSNLFPP LTV W+HHS PVEG GPTFVSA D
Sbjct: 121 PVSRGFPIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPVEGFGPTFVSAVD 180
Query: 633 DLSFQAFSYLNFTPTPSDLFSCVVTHELDGYIAISYWVPQNALPSDLLENVLCGVAFXXX 812
LSFQAFSYLNFTP PSD+FSC+VTHE+D Y AI+YWVP+NALPSDLLENVLCGVAF
Sbjct: 181 GLSFQAFSYLNFTPEPSDIFSCIVTHEIDRYTAIAYWVPRNALPSDLLENVLCGVAFGLG 240
Query: 813 XXXXXXXXXXXXYSRKPCS 869
Y RKPCS
Sbjct: 241 VLGIIVGIVLIIYFRKPCS 259
>ref|XP_003120319.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 3 [Homo sapiens].
Length = 254
Score = 84.7 bits (208), Expect = 1e-16
Identities = 56/205 (27%), Positives = 91/205 (44%), Gaps = 3/205 (1%)
Frame = +3
Query: 192 GWRDELQNHTFQYTMYC-QDGNPEVGLSEVYDGDQLFSFNFSQNIRVPRLPEFADWAHQI 368
G D + +H Y + Q P + +DGD+ F + + V +LP F H++
Sbjct: 22 GGEDIVADHVASYGVNLYQSYGPSGQFTHEFDGDEEFYVDLERKETVWKLPLF----HRL 77
Query: 369 EDTPAIFFDKGFCREMIEKVGPLFEGKIPVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNL 548
P + + + +P VF+ P+ G+PNTL+C V N+
Sbjct: 78 RFDPQFALTNIAVLKHNLNILIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNI 137
Query: 549 FPPALTVTWEHHSAPV-EGIGPTFVSATDDLSFQAFSYLNFTPTPSDLFSCVVTHELDGY 725
FPP + +TW + V EG+ T + D SF SYL F P+ +++ C V H
Sbjct: 138 FPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDE 197
Query: 726 IAISYWVPQNALP-SDLLENVLCGV 797
+ +W P+ P S+L E V+C +
Sbjct: 198 PLLKHWEPEIPAPMSELTETVVCAL 222
>ref|XP_003120317.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 1 [Homo sapiens].
Length = 254
Score = 84.7 bits (208), Expect = 1e-16
Identities = 56/205 (27%), Positives = 91/205 (44%), Gaps = 3/205 (1%)
Frame = +3
Query: 192 GWRDELQNHTFQYTMYC-QDGNPEVGLSEVYDGDQLFSFNFSQNIRVPRLPEFADWAHQI 368
G D + +H Y + Q P + +DGD+ F + + V +LP F H++
Sbjct: 22 GGEDIVADHVASYGVNLYQSYGPSGQFTHEFDGDEEFYVDLERKETVWKLPLF----HRL 77
Query: 369 EDTPAIFFDKGFCREMIEKVGPLFEGKIPVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNL 548
P + + + +P VF+ P+ G+PNTL+C V N+
Sbjct: 78 RFDPQFALTNIAVLKHNLNILIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNI 137
Query: 549 FPPALTVTWEHHSAPV-EGIGPTFVSATDDLSFQAFSYLNFTPTPSDLFSCVVTHELDGY 725
FPP + +TW + V EG+ T + D SF SYL F P+ +++ C V H
Sbjct: 138 FPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDE 197
Query: 726 IAISYWVPQNALP-SDLLENVLCGV 797
+ +W P+ P S+L E V+C +
Sbjct: 198 PLLKHWEPEIPAPMSELTETVVCAL 222
>ref|XP_003119375.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 2 [Homo sapiens].
Length = 255
Score = 83.6 bits (205), Expect = 3e-16
Identities = 61/211 (28%), Positives = 92/211 (43%), Gaps = 9/211 (4%)
Frame = +3
Query: 192 GWRDELQNHTFQYTMYC-QDGNPEVGLSEVYDGDQLFSFNFSQNIRVPRLPEFADWAHQI 368
G D + +H Y + Q P S +DGD+ F + + V +LP F +
Sbjct: 22 GGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRR-- 79
Query: 369 EDTPAIFFDKGFCREMIEKVGPLFEGKIPVSRG------LPIAEVFTLKPLEFGKPNTLV 530
FD F I + I S +P VF+ P+ G+PNTL+
Sbjct: 80 -------FDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLI 132
Query: 531 CFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSATDDLSFQAFSYLNFTPTPSDLFSCVVT 707
C V N+FPP + +TW + V EG+ T + D SF SYL F P+ +++ C V
Sbjct: 133 CLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVE 192
Query: 708 HELDGYIAISYWVPQNALP-SDLLENVLCGV 797
H + +W P+ P S+L E V+C +
Sbjct: 193 HWGLDEPLLKHWEPEIPTPMSELTETVVCAL 223
>ref|XP_003119374.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 1 [Homo sapiens].
Length = 255
Score = 83.6 bits (205), Expect = 3e-16
Identities = 61/211 (28%), Positives = 92/211 (43%), Gaps = 9/211 (4%)
Frame = +3
Query: 192 GWRDELQNHTFQYTMYC-QDGNPEVGLSEVYDGDQLFSFNFSQNIRVPRLPEFADWAHQI 368
G D + +H Y + Q P S +DGD+ F + + V +LP F +
Sbjct: 22 GGEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRR-- 79
Query: 369 EDTPAIFFDKGFCREMIEKVGPLFEGKIPVSRG------LPIAEVFTLKPLEFGKPNTLV 530
FD F I + I S +P VF+ P+ G+PNTL+
Sbjct: 80 -------FDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLI 132
Query: 531 CFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSATDDLSFQAFSYLNFTPTPSDLFSCVVT 707
C V N+FPP + +TW + V EG+ T + D SF SYL F P+ +++ C V
Sbjct: 133 CLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVE 192
Query: 708 HELDGYIAISYWVPQNALP-SDLLENVLCGV 797
H + +W P+ P S+L E V+C +
Sbjct: 193 HWGLDEPLLKHWEPEIPTPMSELTETVVCAL 223
>ref|XP_003120318.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 2 [Homo sapiens].
Length = 249
Score = 82.8 bits (203), Expect = 5e-16
Identities = 52/187 (27%), Positives = 84/187 (44%), Gaps = 2/187 (1%)
Frame = +3
Query: 243 QDGNPEVGLSEVYDGDQLFSFNFSQNIRVPRLPEFADWAHQIEDTPAIFFDKGFCREMIE 422
Q P + +DGD+ F + + V +LP F H++ P +
Sbjct: 35 QSYGPSGQFTHEFDGDEEFYVDLERKETVWKLPLF----HRLRFDPQFALTNIAVLKHNL 90
Query: 423 KVGPLFEGKIPVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPV-E 599
+ + +P VF+ P+ G+PNTL+C V N+FPP + +TW + V E
Sbjct: 91 NILIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTE 150
Query: 600 GIGPTFVSATDDLSFQAFSYLNFTPTPSDLFSCVVTHELDGYIAISYWVPQNALP-SDLL 776
G+ T + D SF SYL F P+ +++ C V H + +W P+ P S+L
Sbjct: 151 GVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELT 210
Query: 777 ENVLCGV 797
E V+C +
Sbjct: 211 ETVVCAL 217
>ref|NP_002113.2| HLA class II histocompatibility antigen, DQ alpha 1 chain precursor
[Homo sapiens].
Length = 255
Score = 82.8 bits (203), Expect = 5e-16
Identities = 53/180 (29%), Positives = 82/180 (45%), Gaps = 7/180 (3%)
Frame = +3
Query: 279 YDGDQLFSFNFSQNIRVPRLPEFADWAHQIEDTPAIFFDKGFCREMIEKVGPLF-----E 443
+DGD+ F + + R PEF+ + F +G R M L
Sbjct: 52 FDGDEQFYVDLERKETAWRWPEFSKFGG--------FDPQGALRNMAVAKHNLNIMIKRY 103
Query: 444 GKIPVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFV 620
+ +P VF+ P+ G+PNTL+C V N+FPP + +TW + V EG+ T
Sbjct: 104 NSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGQSVTEGVSETSF 163
Query: 621 SATDDLSFQAFSYLNFTPTPSDLFSCVVTHELDGYIAISYWVPQNALP-SDLLENVLCGV 797
+ D SF SYL F P+ +++ C V H + +W P+ P S+L E V+C +
Sbjct: 164 LSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDQPLLKHWEPEIPAPMSELTETVVCAL 223
>ref|NP_064440.1| HLA class II histocompatibility antigen, DQ alpha 2 chain precursor
[Homo sapiens].
Length = 255
Score = 82.4 bits (202), Expect = 7e-16
Identities = 58/213 (27%), Positives = 98/213 (46%), Gaps = 3/213 (1%)
Frame = +3
Query: 168 TAPEAPAPGWRDELQNHTFQYTM-YCQDGNPEVGLSEVYDGDQLFSFNFSQNIRVPRLPE 344
TA +P G D + +H Y + + Q P + +DGD+ F + V +LP
Sbjct: 15 TAVMSPCGG-EDIVADHVASYGVNFYQSHGPSGQYTHEFDGDEEFYVDLETKETVWQLPM 73
Query: 345 FADWAHQIEDTPAIFFDKGFCREMIEKVGPLFEGKIPVSRGLPIAEVFTLKPLEFGKPNT 524
F+ + D + + + +E + + +P VF+ P+ G+PNT
Sbjct: 74 FSKFISF--DPQSALRNMAVGKHTLEFMMRQ-SNSTAATNEVPEVTVFSKFPVTLGQPNT 130
Query: 525 LVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSATDDLSFQAFSYLNFTPTPSDLFSCV 701
L+C V N+FPP + +TW + V EG+ T + D SF SYL F P+ +++ C
Sbjct: 131 LICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCK 190
Query: 702 VTHELDGYIAISYWVPQNALP-SDLLENVLCGV 797
V H + +W P+ P S+L E ++C +
Sbjct: 191 VEHWGLDEPLLKHWEPEIPAPMSELTETLVCAL 223
>ref|XP_003119376.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 3 [Homo sapiens].
Length = 250
Score = 81.6 bits (200), Expect = 1e-15
Identities = 57/193 (29%), Positives = 85/193 (44%), Gaps = 8/193 (4%)
Frame = +3
Query: 243 QDGNPEVGLSEVYDGDQLFSFNFSQNIRVPRLPEFADWAHQIEDTPAIFFDKGFCREMIE 422
Q P S +DGD+ F + + V +LP F + FD F I
Sbjct: 35 QSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRR---------FDPQFALTNIA 85
Query: 423 KVGPLFEGKIPVSRG------LPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHH 584
+ I S +P VF+ P+ G+PNTL+C V N+FPP + +TW +
Sbjct: 86 VLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSN 145
Query: 585 SAPV-EGIGPTFVSATDDLSFQAFSYLNFTPTPSDLFSCVVTHELDGYIAISYWVPQNAL 761
V EG+ T + D SF SYL F P+ +++ C V H + +W P+
Sbjct: 146 GHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWEPEIPT 205
Query: 762 P-SDLLENVLCGV 797
P S+L E V+C +
Sbjct: 206 PMSELTETVVCAL 218
>ref|NP_002110.1| HLA class II histocompatibility antigen, DO alpha chain precursor
[Homo sapiens].
Length = 250
Score = 81.6 bits (200), Expect = 1e-15
Identities = 55/178 (30%), Positives = 86/178 (48%), Gaps = 5/178 (2%)
Frame = +3
Query: 279 YDGDQLFSFNFSQNIRVPRLPEFADWAHQIED--TPAIFFDKGFCREMIEKVGPLFEGKI 452
+D +QLFS + ++ V RLPEF D+A I K ++E+ +
Sbjct: 52 FDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINV 111
Query: 453 PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSAT 629
P P V +E G+PN L+C V N+FPP + +TW + V EG+ T +
Sbjct: 112 P-----PRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQ 166
Query: 630 DDLSFQAFSYLNFTPTPSDLFSCVVTH-ELDGYIAISYWVPQNAL-PSDLLENVLCGV 797
D F+ F YL F P+ D++ C V H LD + + +W Q + P D +E ++C +
Sbjct: 167 PDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPL-LRHWELQVPIPPPDAMETLVCAL 223
Database: RefSeq49_HP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 18,297,164
Number of sequences in database: 32,964
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 Sequences: 32964
Number of Hits to DB: 45,491,148
Number of extensions: 1252238
Number of successful extensions: 4926
Number of sequences better than 1.0e-05: 18
Number of HSP's gapped: 4874
Number of HSP's successfully gapped: 18
Length of query: 371
Length of database: 18,297,164
Length adjustment: 104
Effective length of query: 267
Effective length of database: 14,868,908
Effective search space: 3969998436
Effective search space used: 3969998436
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 35 (18.1 bits)
Search to Sscrofa10_2
BLASTN 2.2.24 [Aug-08-2010]
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= 20110601C-012854
(1115 letters)
Database: Sscrofa_10.2.fasta
4582 sequences; 2,808,509,378 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Sscrofa_Chr07 571 e-160
>Sscrofa_Chr07
|| Length = 134764511
Score = 571 bits (288), Expect = e-160
Identities = 288/288 (100%)
Strand = Plus / Minus
Query: 179 agctcctgctccagggtggagggatgagctgcaaaaccacacgttccagtacacaatgta 238
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29502246 agctcctgctccagggtggagggatgagctgcaaaaccacacgttccagtacacaatgta 29502187
Query: 239 ctgccaggatgggaatcccgaagtgggactctccgaggtctatgatggggaccagctttt 298
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29502186 ctgccaggatgggaatcccgaagtgggactctccgaggtctatgatggggaccagctttt 29502127
Query: 299 ctccttcaacttttcccagaacatccgagtgcctcgcctgcctgaatttgcggactgggc 358
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29502126 ctccttcaacttttcccagaacatccgagtgcctcgcctgcctgaatttgcggactgggc 29502067
Query: 359 tcaccagattgaagacactcctgccattttctttgacaaaggattctgccgagagatgat 418
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29502066 tcaccagattgaagacactcctgccattttctttgacaaaggattctgccgagagatgat 29502007
Query: 419 cgaaaaagttggcccactgtttgaagggaaaatcccagtgtctagagg 466
||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29502006 cgaaaaagttggcccactgtttgaagggaaaatcccagtgtctagagg 29501959
Score = 541 bits (273), Expect = e-151
Identities = 279/281 (99%)
Strand = Plus / Minus
Query: 464 agggttacccatcgctgaggtgttcacgctgaagcccctggagtttggcaaacccaacac 523
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29501393 agggttacccatcgctgaggtgttcacgctgaagcccctggagtttggcaaacccaacac 29501334
Query: 524 actggtctgttttgtcagtaaccttttcccacccgcactgacggtgacctgggagcatca 583
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29501333 actggtctgttttgtcagtaaccttttcccacccgcactgacggtgacctgggagcatca 29501274
Query: 584 ctctgctcctgtggaaggaatcgggcccactttcgtctccgccacggatgacctcagctt 643
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29501273 ctctgctcctgtggaaggaatcgggcccactttcgtctccgccacggatgacctcagctt 29501214
Query: 644 ccaggccttttcttatttaaacttcacaccgacaccctctgaccttttctcctgcgtcgt 703
||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||
Sbjct: 29501213 ccaggccttttcttatttaaacttcacaccgacaccctctgaccttttctcttgcgtcgt 29501154
Query: 704 gactcatgagctcgacggctacatagcaatctcttactggg 744
|||||||||||||||||||||| ||||||||||||||||||
Sbjct: 29501153 gactcatgagctcgacggctacgtagcaatctcttactggg 29501113
Score = 432 bits (218), Expect = e-118
Identities = 225/226 (99%), Gaps = 1/226 (0%)
Strand = Plus / Minus
Query: 866 ctcagcctgattctccctgaccagagtccggtgccagcagctgcagtcatccaagcagga 925
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29500341 ctcagcctgattctccctgaccagagtccggtgccagcagctgcagtcatccaagcagga 29500282
Query: 926 ggcattcagctttctcacctcctgcctaggatctctccttctcagagcagaagtccttgg 985
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29500281 ggcattcagctttctcacctcctgcctaggatctctccttctcagagcagaagtccttgg 29500222
Query: 986 gacgctgcgcgcgcctgctctgctctccgtggtactggatccaggggacccccgagtggc 1045
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29500221 gacgctgcgcgcgcctgctctgctctccgtggtactggatccaggggacccccgagtggc 29500162
Query: 1046 cttcctatccctacgacatcactgccatgtcaaggc-ataaatctc 1090
|||||||||||||||||||||||||||||||||||| |||||||||
Sbjct: 29500161 cttcctatccctacgacatcactgccatgtcaaggcaataaatctc 29500116
Score = 345 bits (174), Expect = 3e-92
Identities = 174/174 (100%)
Strand = Plus / Minus
Query: 7 ggaagtgagctggtgaaccatgatctgggaagggacctgggggacctgggttagctagtt 66
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29504570 ggaagtgagctggtgaaccatgatctgggaagggacctgggggacctgggttagctagtt 29504511
Query: 67 agtagctcctaacccactgtgaggatatggatcatgagctgagccagggagctgcactgc 126
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29504510 agtagctcctaacccactgtgaggatatggatcatgagctgagccagggagctgcactgc 29504451
Query: 127 tacggctgctacaccttctgtggctgctgccccactcctggactgcccccgaag 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29504450 tacggctgctacaccttctgtggctgctgccccactcctggactgcccccgaag 29504397
Score = 244 bits (123), Expect = 9e-62
Identities = 126/127 (99%)
Strand = Plus / Minus
Query: 744 gtgccccagaatgcgctgccctcagacctcctggagaacgtgctgtgtggcgtggccttt 803
|||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||
Sbjct: 29500827 gtgccccagaatgcgctgccctcagacctccttgagaacgtgctgtgtggcgtggccttt 29500768
Query: 804 ggcctgggtgtgctgggaatcattgttggcttagtcctcatcatctactctcggaagcct 863
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29500767 ggcctgggtgtgctgggaatcattgttggcttagtcctcatcatctactctcggaagcct 29500708
Query: 864 tgctcag 870
|||||||
Sbjct: 29500707 tgctcag 29500701
Database: Sscrofa_10.2.fasta
Posted date: Nov 16, 2011 10:34 AM
Number of letters in database: 2,808,509,378
Number of sequences in database: 4582
Lambda K H
1.37 0.711 1.31
Gapped
Lambda K H
1.37 0.711 1.31
Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Sequences: 4582
Number of Hits to DB: 31,869,811
Number of extensions: 187
Number of successful extensions: 187
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 187
Number of HSP's successfully gapped: 5
Length of query: 1115
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 1094
Effective length of database: 2,808,413,156
Effective search space: 3072403992664
Effective search space used: 3072403992664
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
X3: 50 (99.1 bits)
S1: 18 (36.2 bits)
S2: 30 (60.0 bits)