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-012104
(1227 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_001012695.1| major histocompatibility complex, class II, ... 355 6e-98
Alignment gi|NP_001192849.1| HLA class II histocompatibility antigen, DO ... 233 2e-61
Alignment gi|XP_002697222.1| PREDICTED: MHC class II antigen-like [Bos ta... 233 2e-61
Alignment gi|NP_001013619.3| major histocompatibility complex, class II, ... 222 6e-58
Alignment gi|XP_002702869.1| PREDICTED: MHC class II antigen-like [Bos ta... 217 2e-56
Alignment gi|XP_002702914.1| PREDICTED: BOLA-DQA2 protein-like [Bos tauru... 215 7e-56
Alignment gi|NP_001012693.1| major histocompatibility complex, class II, ... 205 8e-53
Alignment gi|NP_001012696.1| major histocompatibility complex, class II, ... 204 1e-52
Alignment gi|NP_001073045.1| major histocompatibility complex, class II, ... 202 4e-52
Alignment gi|NP_001012699.1| major histocompatibility complex, class II, ... 201 1e-51
>ref|NP_001012695.1| major histocompatibility complex, class II, DR alpha [Bos taurus].
Length = 253
Score = 355 bits (910), Expect = 6e-98
Identities = 175/253 (69%), Positives = 193/253 (76%), Gaps = 1/253 (0%)
Frame = +1
Query: 88 MTILGVPVLGFVITIL-NLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDM 264
M I VP+LG IT+L LQ+SWAI ENHVIIQAEFYL P++S EFMFDFDGDEIFHVDM
Sbjct: 1 MAITRVPILGLFITVLIGLQESWAIKENHVIIQAEFYLKPEESAEFMFDFDGDEIFHVDM 60
Query: 265 EKRETVWRLEEFGHFASFEAQGALANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSDKP 444
K+ETVWRL EFGHFASFEAQGALAN+AV KANL+IMIKRS L +KP
Sbjct: 61 GKKETVWRLPEFGHFASFEAQGALANMAVMKANLDIMIKRSNNTPNTNVPPEVTLLPNKP 120
Query: 445 VELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPS 624
VELGEPN LICFIDKFSPPV++VTWLRNG PVT GVS+TVFLPR DHLFRKFHYLPF+P+
Sbjct: 121 VELGEPNTLICFIDKFSPPVISVTWLRNGKPVTDGVSQTVFLPRNDHLFRKFHYLPFLPT 180
Query: 625 TEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXX 804
TEDVYDC+VEH GL++PLLKHWE+EA PLPETTEN VCA
Sbjct: 181 TEDVYDCKVEHLGLNEPLLKHWEYEAPAPLPETTENAVCALGLIVALVGIIAGTIFIIKG 240
Query: 805 XRKGNATERRGPL 843
RK N ERRGPL
Sbjct: 241 VRKANTVERRGPL 253
>ref|NP_001192849.1| HLA class II histocompatibility antigen, DO alpha chain [Bos
taurus].
Length = 250
Score = 233 bits (595), Expect = 2e-61
Identities = 113/222 (50%), Positives = 153/222 (68%), Gaps = 3/222 (1%)
Frame = +1
Query: 88 MTILGVPVLGF--VITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHV 258
M + G VLG ++T+L+LQ+ AI +H+ FY S D +G+F +DFDG+++F V
Sbjct: 1 MVLRGRLVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSV 60
Query: 259 DMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSD 438
D++KRE VWRL EFG+FA F+ Q L +IA+ KA+LE ++KRS L
Sbjct: 61 DLKKREAVWRLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNVSPRVAVLPK 120
Query: 439 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFM 618
V+LGEPN+LIC +DK PPV+N+TWLRNG PVT+GV+++ F + DHLFRKFHYL F+
Sbjct: 121 SHVQLGEPNVLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTFV 180
Query: 619 PSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCA 744
P +D YDC+VEHWGLD+PL +HWE + T LP+TT VCA
Sbjct: 181 PLVDDFYDCKVEHWGLDQPLFQHWEPQVPTALPDTTGTLVCA 222
>ref|XP_002697222.1| PREDICTED: MHC class II antigen-like [Bos taurus].
Length = 250
Score = 233 bits (595), Expect = 2e-61
Identities = 113/222 (50%), Positives = 153/222 (68%), Gaps = 3/222 (1%)
Frame = +1
Query: 88 MTILGVPVLGF--VITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHV 258
M + G VLG ++T+L+LQ+ AI +H+ FY S D +G+F +DFDG+++F V
Sbjct: 1 MVLRGRLVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSV 60
Query: 259 DMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSD 438
D++KRE VWRL EFG+FA F+ Q L +IA+ KA+LE ++KRS L
Sbjct: 61 DLKKREAVWRLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNVSPRVAVLPK 120
Query: 439 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFM 618
V+LGEPN+LIC +DK PPV+N+TWLRNG PVT+GV+++ F + DHLFRKFHYL F+
Sbjct: 121 SHVQLGEPNVLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTFV 180
Query: 619 PSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCA 744
P +D YDC+VEHWGLD+PL +HWE + T LP+TT VCA
Sbjct: 181 PLVDDFYDCKVEHWGLDQPLFQHWEPQVPTALPDTTGTLVCA 222
>ref|NP_001013619.3| major histocompatibility complex, class II, DQ alpha, type 1 [Bos
taurus].
Length = 255
Score = 222 bits (565), Expect = 6e-58
Identities = 110/230 (47%), Positives = 139/230 (60%), Gaps = 1/230 (0%)
Frame = +1
Query: 157 IVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 333
IV +H+ A+FY S SG+++ +FDGDE+F+VD+ K+ETVW+L FG SFEAQ A
Sbjct: 26 IVADHIGTYGADFYQSHGPSGQYIHEFDGDELFYVDLGKKETVWQLPMFGELTSFEAQDA 85
Query: 334 LANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 513
L IA K L+++ KRS S P+ LG+PN LIC +D PPV+N+
Sbjct: 86 LNEIAKAKHTLDVLTKRSNFTPVINEVPEVTVFSKSPMMLGQPNTLICHVDNIFPPVINI 145
Query: 514 TWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 693
TWLRNG VT GVSET FLP+ D+ F K YL F+PS +DVYDC+VEHWGLD+PLLKHWE
Sbjct: 146 TWLRNGHAVTEGVSETSFLPKSDYSFLKIGYLTFLPSDDDVYDCKVEHWGLDEPLLKHWE 205
Query: 694 FEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 843
E P+ E TE VCA R G A+ +GPL
Sbjct: 206 PEIPAPMSELTETVVCALGLTVGLVGIVVGTVLIIRGLRSGGASRHQGPL 255
>ref|XP_002702869.1| PREDICTED: MHC class II antigen-like [Bos taurus].
Length = 224
Score = 217 bits (552), Expect = 2e-56
Identities = 104/204 (50%), Positives = 142/204 (69%), Gaps = 3/204 (1%)
Frame = +1
Query: 88 MTILGVPVLGF--VITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHV 258
M + G VLG ++T+L+LQ+ AI +H+ FY S D +G+F +DFDG+++F V
Sbjct: 1 MVLRGRLVLGLHTLMTLLSLQEVGAIKADHMGSYGPAFYQSYDGAGQFTYDFDGEQLFSV 60
Query: 259 DMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSD 438
D++KRE VWRL EFG+FA F+ Q L +IA+ KA+LE ++KRS L
Sbjct: 61 DLKKREAVWRLPEFGNFAYFDPQSGLVSIAMIKAHLEDLVKRSNGTRAPNVSPRVAVLPK 120
Query: 439 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFM 618
V+LGEPN+LIC +DK PPV+N+TWLRNG PVT+GV+++ F + DHLFRKFHYL F+
Sbjct: 121 SHVQLGEPNVLICIVDKIFPPVINITWLRNGHPVTQGVTQSSFYAQPDHLFRKFHYLTFV 180
Query: 619 PSTEDVYDCQVEHWGLDKPLLKHW 690
P +D YDC+VEHWGLD+PL +HW
Sbjct: 181 PLVDDFYDCKVEHWGLDQPLFQHW 204
>ref|XP_002702914.1| PREDICTED: BOLA-DQA2 protein-like [Bos taurus].
Length = 254
Score = 215 bits (547), Expect = 7e-56
Identities = 105/211 (49%), Positives = 130/211 (61%)
Frame = +1
Query: 211 SGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEIMIKRSX 390
S ++ +FDGD++F+VD+EK+ETVWRL F FASF+ Q L NIA+ K NL IMIK S
Sbjct: 45 SDQYTQEFDGDKLFYVDLEKKETVWRLPMFSQFASFDPQAILRNIAISKHNLNIMIKYSN 104
Query: 391 XXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFL 570
S P+ LG+PN LIC +D F PPV+N+TWL+NG VT GVSET FL
Sbjct: 105 FIPAINEVPEVTVFSKSPMVLGQPNTLICHMDNF-PPVINITWLKNGHAVTEGVSETSFL 163
Query: 571 PREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCAXX 750
P++DH F K YL F+PS +DVYDC+VEHW LD+PLLKHWE E P+ E TE VCA
Sbjct: 164 PKDDHSFLKIGYLTFLPSDDDVYDCKVEHWSLDEPLLKHWEPEVPAPMSELTETVVCALR 223
Query: 751 XXXXXXXXXXXXXXXXXXXRKGNATERRGPL 843
R G A+ +GPL
Sbjct: 224 LTVGLVGIVVGTIFIIQGLRSGGASRHQGPL 254
>ref|NP_001012693.1| major histocompatibility complex, class II, DQ alpha 5 [Bos
taurus].
Length = 255
Score = 205 bits (521), Expect = 8e-53
Identities = 104/230 (45%), Positives = 132/230 (57%), Gaps = 1/230 (0%)
Frame = +1
Query: 157 IVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 333
IV +HV I Y S SG++ +FDGDE F+VD+EK+ET W+L F SF+ Q A
Sbjct: 26 IVADHVGIYGISIYQSYGPSGQYTHEFDGDEQFYVDLEKKETAWQLPLFSRMLSFDPQLA 85
Query: 334 LANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 513
L NIA+ K +++ + K S S PV LG+PN LIC +D PPV+N+
Sbjct: 86 LRNIAIMKLHVDFLTKFSNSTAATNKVPEVTVFSKSPVMLGQPNTLICHVDNIFPPVINI 145
Query: 514 TWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 693
TWLRNG VT GVSET FL R D+ F K YL F+PS +D+YDC+VEHWGLD+PLLKHWE
Sbjct: 146 TWLRNGHSVTEGVSETSFLIRSDYSFLKIKYLAFLPSDDDIYDCKVEHWGLDEPLLKHWE 205
Query: 694 FEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 843
E P+ E TE VC R G+ + +GPL
Sbjct: 206 PEIPAPMSELTETVVCTLGLTMGLVGITVGTIFIIQGLRSGDPSRHQGPL 255
>ref|NP_001012696.1| major histocompatibility complex, class II, DY alpha [Bos taurus].
Length = 253
Score = 204 bits (520), Expect = 1e-52
Identities = 98/197 (49%), Positives = 122/197 (61%), Gaps = 1/197 (0%)
Frame = +1
Query: 157 IVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 333
IV +HV Y + SG+F F+FDGDE+F+VD+ K+ETVWRL EF + FE Q A
Sbjct: 24 IVADHVGTYGTNVYQTYGASGQFTFEFDGDELFYVDLGKKETVWRLPEFSNITKFEVQSA 83
Query: 334 LANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 513
L NI + K NL+I+IK S V LG PN LIC +D PPV+N+
Sbjct: 84 LRNIVMSKRNLDILIKNSSFTPATSEIPEVAVFPKSSVVLGIPNTLICQVDNIFPPVINI 143
Query: 514 TWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 693
TW NG V G++ET F P+ DH F KF YL F+P+ ED YDC+VEHWGL++PL+KHWE
Sbjct: 144 TWFYNGHFVAEGIAETTFYPKSDHSFLKFSYLTFLPTNEDFYDCRVEHWGLEEPLVKHWE 203
Query: 694 FEAQTPLPETTENTVCA 744
E TP E TE VCA
Sbjct: 204 PEIPTPTSELTETVVCA 220
>ref|NP_001073045.1| major histocompatibility complex, class II, DQ alpha, type 3 [Bos
taurus].
Length = 254
Score = 202 bits (515), Expect = 4e-52
Identities = 106/230 (46%), Positives = 129/230 (56%), Gaps = 1/230 (0%)
Frame = +1
Query: 157 IVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 333
IV +HV +FY S SG+++ FDGDE F+VD+EK E VWRL F F QGA
Sbjct: 26 IVADHVGTYGTDFYQSHGPSGQYIHQFDGDEEFYVDLEKEEAVWRLPMFDKLR-FHPQGA 84
Query: 334 LANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 513
L NIA+ K NL+++ K S PV L +PN LIC +D PPV+N+
Sbjct: 85 LRNIAIAKHNLDVLTKLYNFTPVINEVPEVTVFSKSPVMLSQPNTLICHVDNIFPPVINI 144
Query: 514 TWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 693
TWLRNG VT VSET FL R D+ + K YLPF PS +DVYDC+VEHWGLD+PLLKHWE
Sbjct: 145 TWLRNGHSVTEHVSETSFLLRSDYSYLKISYLPFRPSDDDVYDCKVEHWGLDEPLLKHWE 204
Query: 694 FEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 843
E P+ E TE VCA R A+ +GPL
Sbjct: 205 PEIPAPMSELTETVVCALGLTVGLVGIVVGTVLITRGLRSSGASRHQGPL 254
>ref|NP_001012699.1| major histocompatibility complex, class II, DQ alpha 2 [Bos
taurus].
Length = 268
Score = 201 bits (510), Expect = 1e-51
Identities = 95/179 (53%), Positives = 119/179 (66%), Gaps = 1/179 (0%)
Frame = +1
Query: 157 IVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 333
IV +HV E Y S SG++ +FDGDE+F+VD+ K+ETVWRL F FA F+ Q A
Sbjct: 26 IVADHVGSYGTEIYQSHGPSGQYTQEFDGDEMFYVDLGKKETVWRLPMFSQFAGFDPQAA 85
Query: 334 LANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 513
L+ IA K NL+++ KRS S PV LG+PN LIC +D PPV+N+
Sbjct: 86 LSEIATAKHNLDVLTKRSNFTPVINEVPEVTVFSKSPVMLGQPNTLICHVDNIFPPVINI 145
Query: 514 TWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHW 690
TWL+NG VT GVSET FLP++DH F K YL F+PS D+YDC+VEHWGLD+PLLKHW
Sbjct: 146 TWLKNGHAVTEGVSETSFLPKDDHSFLKIGYLTFLPSDNDIYDCKVEHWGLDEPLLKHW 204
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: 47,509,040
Number of extensions: 1315268
Number of successful extensions: 4181
Number of sequences better than 1.0e-05: 35
Number of HSP's gapped: 4162
Number of HSP's successfully gapped: 35
Length of query: 409
Length of database: 17,681,374
Length adjustment: 105
Effective length of query: 304
Effective length of database: 14,207,134
Effective search space: 4318968736
Effective search space used: 4318968736
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-012104
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-012104
(1227 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_001011723.1| MHC class II DR alpha chain [Canis lupus fam... 372 e-103
Alignment gi|NP_001011726.1| major histocompatibility complex, class II, ... 223 3e-58
Alignment gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati... 206 3e-53
Alignment gi|XP_532104.2| PREDICTED: similar to HLA class II histocompati... 77 3e-14
Alignment gi|NP_001041564.1| major histocompatibility complex, class II, ... 64 2e-10
Alignment gi|NP_001014768.1| DLA class II histocompatibility antigen, DR-... 60 3e-09
Alignment gi|NP_001014403.1| major histocompatibility complex, class II, ... 59 7e-09
Alignment gi|XP_535458.1| PREDICTED: similar to beta-2-microglobulin prec... 55 1e-07
Alignment gi|XP_850148.1| PREDICTED: similar to beta-2-microglobulin prec... 55 1e-07
Alignment gi|XP_849737.1| PREDICTED: similar to HLA class II histocompati... 54 2e-07
>ref|NP_001011723.1| MHC class II DR alpha chain [Canis lupus familiaris].
Length = 254
Score = 372 bits (956), Expect = e-103
Identities = 184/254 (72%), Positives = 198/254 (77%), Gaps = 2/254 (0%)
Frame = +1
Query: 88 MTILGVPVLGFVIT--ILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVD 261
MTI GVPVLGF I ++ Q+SWA+ E HVIIQAEFYL+PD SGEFMFDFDGDEIFHVD
Sbjct: 1 MTISGVPVLGFFIMAFLMGPQESWAVKEEHVIIQAEFYLTPDPSGEFMFDFDGDEIFHVD 60
Query: 262 MEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSDK 441
MEK+ETVWRLEEFG FASFEAQGALANIAVDKANL+ MIKRS LS+
Sbjct: 61 MEKKETVWRLEEFGRFASFEAQGALANIAVDKANLDTMIKRSNHTPNTNVPPEVTVLSNT 120
Query: 442 PVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMP 621
PVELGEPNILICFIDKFSPPV+NVTWLRNG+PVT GVSET+FLPREDHLFRKFHYLPF+P
Sbjct: 121 PVELGEPNILICFIDKFSPPVINVTWLRNGNPVTTGVSETIFLPREDHLFRKFHYLPFLP 180
Query: 622 STEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXX 801
S EDVYDC+VEHWGLD+PLLKHWEFE TPLPETTEN VCA
Sbjct: 181 SAEDVYDCKVEHWGLDEPLLKHWEFEPPTPLPETTENVVCALGLIVGLVGIITGTIFIIK 240
Query: 802 XXRKGNATERRGPL 843
RK A ERRGPL
Sbjct: 241 GMRKVKAGERRGPL 254
>ref|NP_001011726.1| major histocompatibility complex, class II, DQ alpha [Canis lupus
familiaris].
Length = 255
Score = 223 bits (568), Expect = 3e-58
Identities = 118/255 (46%), Positives = 145/255 (56%), Gaps = 3/255 (1%)
Frame = +1
Query: 88 MTILGVPVLGFVITILNLQKSWA--IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHV 258
M + V +LG +I + + S IV +HV Y S SG++ +FDGDE F+V
Sbjct: 1 MILNRVLILGTLILTIMMSPSGGEEIVADHVANYGINVYQSYGPSGQYTHEFDGDEEFYV 60
Query: 259 DMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSD 438
D+EK+ETVWRL F F SF+ QGAL N+A+ K NL IM KRS S
Sbjct: 61 DLEKKETVWRLPVFSTFRSFDPQGALRNLAIIKQNLNIMTKRSNQTAATNEVPEVTVFSK 120
Query: 439 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFM 618
PV LG+PN LIC +D PPV+NVTWL+N VT GVSET F + DH F K YL F+
Sbjct: 121 SPVMLGQPNTLICLVDNIFPPVINVTWLKNRHSVTEGVSETSFFAKGDHSFSKISYLTFL 180
Query: 619 PSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXX 798
PS ED+YDC+VEHWGLD+PLLKHWE E TP+ E TE VCA
Sbjct: 181 PSAEDIYDCKVEHWGLDEPLLKHWEPEVPTPMSELTETVVCALGLAVGLVGIVMGTVFII 240
Query: 799 XXXRKGNATERRGPL 843
R G + +GPL
Sbjct: 241 QGLRSGGTSRHQGPL 255
>ref|XP_850803.1| PREDICTED: similar to HLA class II histocompatibility antigen, DO
alpha chain precursor (MHC class II antigen DOA) (MHC DZ
alpha) (MHC DN-alpha) isoform 11 [Canis familiaris].
Length = 227
Score = 206 bits (525), Expect = 3e-53
Identities = 93/192 (48%), Positives = 132/192 (68%), Gaps = 7/192 (3%)
Frame = +1
Query: 190 FYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLE 369
FY S SG+F +FDG+++F V+++KR+ VWRL EFG+ A F+ Q LA+IAV KA+L+
Sbjct: 8 FYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEFGNLAHFDPQNGLASIAVIKAHLD 67
Query: 370 IMIKRSXXXXXXXXXXXXXXLSDKP-------VELGEPNILICFIDKFSPPVVNVTWLRN 528
++++RS L + VELG+PN+LIC +D PPV+N+TWLRN
Sbjct: 68 VLVERSNRTRAINGTHLSSPLPPRVAVLPKFRVELGQPNVLICIVDNIFPPVINITWLRN 127
Query: 529 GSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWEFEAQT 708
G ++ GV++T F + DHLFRKF YL F+PS ED+YDC+VEHWGL++PLL+HWE +
Sbjct: 128 GQIISEGVAQTSFYSQPDHLFRKFCYLTFVPSAEDMYDCKVEHWGLEEPLLRHWEPQVPI 187
Query: 709 PLPETTENTVCA 744
P+P+T E +CA
Sbjct: 188 PVPDTIETLICA 199
>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 = 77.4 bits (189), Expect = 3e-14
Identities = 37/89 (41%), Positives = 63/89 (70%), Gaps = 1/89 (1%)
Frame = +1
Query: 124 ITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEF 300
+++L+ ++ AI +H+ FY S SG+F +FDG+++F V+++KR+ VWRL EF
Sbjct: 1 MSLLSPHETGAIEADHMGSYGPAFYQSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEF 60
Query: 301 GHFASFEAQGALANIAVDKANLEIMIKRS 387
G+ A F+ Q LA+IAV KA+L+++++RS
Sbjct: 61 GNLAHFDPQNGLASIAVIKAHLDVLVERS 89
>ref|NP_001041564.1| major histocompatibility complex, class II, DM alpha [Canis lupus
familiaris].
Length = 170
Score = 64.3 bits (155), Expect = 2e-10
Identities = 33/101 (32%), Positives = 50/101 (49%)
Frame = +1
Query: 439 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFM 618
KP+E G+PN+L+CFI PP + V W + PV G+ T + F+ F YL F
Sbjct: 46 KPLEFGKPNMLVCFISNLFPPTLTVNWWHHLDPV-EGIGPTFVSAVDGFSFQAFSYLNFT 104
Query: 619 PSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVC 741
P+ D++ C V H + + +W P + EN +C
Sbjct: 105 PAPSDLFSCVVTHEIDNYTAIAYWVPHDALP-SDLLENVLC 144
>ref|NP_001014768.1| DLA class II histocompatibility antigen, DR-1 beta chain precursor
[Canis lupus familiaris].
Length = 266
Score = 60.5 bits (145), Expect = 3e-09
Identities = 30/90 (33%), Positives = 44/90 (48%)
Frame = +1
Query: 439 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFM 618
K L N+L+C ++ F P + V WLRNG GV T + D F+ L +
Sbjct: 134 KTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNGDWTFQILVMLEIV 193
Query: 619 PSTEDVYDCQVEHWGLDKPLLKHWEFEAQT 708
P + +VY CQVEH L P+ W ++ +
Sbjct: 194 PQSGEVYTCQVEHPSLTSPVTVEWRAQSDS 223
>ref|NP_001014403.1| major histocompatibility complex, class II, DQ beta 1 [Canis lupus
familiaris].
Length = 269
Score = 59.3 bits (142), Expect = 7e-09
Identities = 28/86 (32%), Positives = 39/86 (45%)
Frame = +1
Query: 451 LGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTE 630
L N+L+C + F P + V W RN T GV T + D F+ L P
Sbjct: 141 LNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLIRNGDWTFQILVMLEMTPQRG 200
Query: 631 DVYDCQVEHWGLDKPLLKHWEFEAQT 708
DVY C VEH L P+ W ++++
Sbjct: 201 DVYTCHVEHASLQSPITVQWRAQSES 226
>ref|XP_535458.1| PREDICTED: similar to beta-2-microglobulin precursor isoform 2
[Canis familiaris].
Length = 125
Score = 55.5 bits (132), Expect = 1e-07
Identities = 26/87 (29%), Positives = 45/87 (51%)
Frame = +1
Query: 433 SDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLP 612
S P E G+PN L C++ F PP + + L+NG + ++ F +D F +
Sbjct: 38 SRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSF--SKDWTFYLLVHTE 95
Query: 613 FMPSTEDVYDCQVEHWGLDKPLLKHWE 693
F P+ +D + C+V+H L +P + W+
Sbjct: 96 FTPNEQDEFSCRVKHVTLSEPQIVKWD 122
>ref|XP_850148.1| PREDICTED: similar to beta-2-microglobulin precursor isoform 3
[Canis familiaris].
Length = 125
Score = 55.5 bits (132), Expect = 1e-07
Identities = 26/87 (29%), Positives = 45/87 (51%)
Frame = +1
Query: 433 SDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLP 612
S P E G+PN L C++ F PP + + L+NG + ++ F +D F +
Sbjct: 38 SRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSF--SKDWTFYLLVHTE 95
Query: 613 FMPSTEDVYDCQVEHWGLDKPLLKHWE 693
F P+ +D + C+V+H L +P + W+
Sbjct: 96 FTPNEQDEFSCRVKHVTLSEPQIVKWD 122
>ref|XP_849737.1| PREDICTED: similar to HLA class II histocompatibility antigen, DM
beta chain precursor (MHC class II antigen DMB) [Canis
familiaris].
Length = 263
Score = 54.3 bits (129), Expect = 2e-07
Identities = 28/84 (33%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
Frame = +1
Query: 442 PVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSE-TVFLPREDHLFRKFHYLPFM 618
P E +L C++ F P V ++W +NG PV S + P D ++ +L
Sbjct: 124 PFNTKESVMLACYVWGFYPADVTISWRKNGQPVPSHSSALNMAQPNGDWTYQTVSHLATT 183
Query: 619 PSTEDVYDCQVEHWGLDKPLLKHW 690
PS ED Y C VEH G +P+ + W
Sbjct: 184 PSYEDTYTCVVEHIGAPEPVCEDW 207
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: 49,710,964
Number of extensions: 1365834
Number of successful extensions: 4434
Number of sequences better than 1.0e-05: 11
Number of HSP's gapped: 4419
Number of HSP's successfully gapped: 11
Length of query: 409
Length of database: 18,874,504
Length adjustment: 105
Effective length of query: 304
Effective length of database: 15,374,224
Effective search space: 4673764096
Effective search space used: 4673764096
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-012104
(1227 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_001107178.1| MHC class II DR-alpha [Sus scrofa]. 436 e-122
Alignment gi|NP_001172072.1| src-like-adapter [Sus scrofa]. 227 9e-60
Alignment gi|NP_001123696.1| SLA class II histocompatibility antigen, DQ ... 211 9e-55
Alignment gi|NP_001107534.2| SLA class II histocompatibility antigen, DQ ... 206 2e-53
Alignment gi|NP_001004039.1| SLA-DM alpha chain [Sus scrofa]. 74 1e-13
Alignment gi|NP_001107177.1| major histocompatibility complex, class II, ... 74 1e-13
Alignment gi|NP_001107167.1| MHC class II histocompatibility antigen SLA-... 61 1e-09
Alignment gi|XP_003128397.1| PREDICTED: DLA class II histocompatibility a... 60 2e-09
Alignment gi|XP_003128372.1| PREDICTED: DLA class II histocompatibility a... 60 2e-09
Alignment gi|NP_999143.1| beta-2-microglobulin precursor [Sus scrofa]. 60 2e-09
>ref|NP_001107178.1| MHC class II DR-alpha [Sus scrofa].
Length = 252
Score = 436 bits (1121), Expect = e-122
Identities = 216/252 (85%), Positives = 217/252 (86%)
Frame = +1
Query: 88 MTILGVPVLGFVITILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDME 267
MTILGVPVLGFVITILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDME
Sbjct: 1 MTILGVPVLGFVITILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDME 60
Query: 268 KRETVWRLEEFGHFASFEAQGALANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSDKPV 447
KRETVWRLEEFGHFASFEAQGALANIAVDKANLEI+IKRS LSDKPV
Sbjct: 61 KRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSNNTPNTNVPPEVTVLSDKPV 120
Query: 448 ELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPST 627
ELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPST
Sbjct: 121 ELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPST 180
Query: 628 EDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXX 807
EDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCA
Sbjct: 181 EDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCALGLIVALVGIIVGTVLIIKGV 240
Query: 808 RKGNATERRGPL 843
RKGNATERRGPL
Sbjct: 241 RKGNATERRGPL 252
>ref|NP_001172072.1| src-like-adapter [Sus scrofa].
Length = 250
Score = 227 bits (579), Expect = 9e-60
Identities = 109/222 (49%), Positives = 147/222 (66%), Gaps = 3/222 (1%)
Frame = +1
Query: 88 MTILGVPVLGF--VITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHV 258
M + G VLG ++T+L+ QK+ AI +H+ FY S D SG+F +DFDG+++F V
Sbjct: 1 MVLHGGLVLGLHILMTLLSPQKAGAIKADHMGSYGPAFYQSYDGSGQFTYDFDGEQLFSV 60
Query: 259 DMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSD 438
D++KRE VWRL EF +FA F+ Q L IA+ +A+L+++++RS L
Sbjct: 61 DLKKREAVWRLPEFSNFADFDPQNGLRGIALIRAHLDVLVERSNHTRATNVPPRVTVLPK 120
Query: 439 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFM 618
PV LG+PN+LIC +D PPV+N+TWL NG VT GV++T F + DH FRKFHYL F+
Sbjct: 121 SPVALGQPNVLICIVDNIFPPVINITWLHNGQTVTEGVTQTSFYAQPDHSFRKFHYLTFV 180
Query: 619 PSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCA 744
PS D YDC+VEHWGLD+PL HWE + PLP+TTE VCA
Sbjct: 181 PSAGDFYDCKVEHWGLDEPLFTHWEPQVTMPLPDTTETLVCA 222
>ref|NP_001123696.1| SLA class II histocompatibility antigen, DQ haplotype D alpha chain
precursor [Sus scrofa].
Length = 255
Score = 211 bits (536), Expect = 9e-55
Identities = 101/184 (54%), Positives = 119/184 (64%)
Frame = +1
Query: 193 YLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEI 372
Y S SG + +FDGDE F+VD+EK+ETVW+L F F SF+ QGAL NIA K NL I
Sbjct: 39 YQSYGPSGYYTHEFDGDEEFYVDLEKKETVWQLPLFSKFTSFDPQGALRNIATAKHNLNI 98
Query: 373 MIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGV 552
+IKRS PV LG+PN LIC +D PPV+N+TWL+NG VT G
Sbjct: 99 LIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGF 158
Query: 553 SETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTEN 732
SET FL + DH F K YL F+PS +D YDC+VEHWGLDKPLLKHWE E P+ E TE
Sbjct: 159 SETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 218
Query: 733 TVCA 744
VCA
Sbjct: 219 VVCA 222
>ref|NP_001107534.2| SLA class II histocompatibility antigen, DQ haplotype C alpha chain
precursor [Sus scrofa].
Length = 254
Score = 206 bits (525), Expect = 2e-53
Identities = 102/184 (55%), Positives = 119/184 (64%)
Frame = +1
Query: 193 YLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEI 372
Y S SG F +FDGDE F+VD+EK+ETVWRL F F SF+ QGAL NIA K NL I
Sbjct: 39 YQSYGPSGYFTHEFDGDEEFYVDLEKKETVWRLPLFSEFTSFDPQGALRNIATLKHNLNI 98
Query: 373 MIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGV 552
+ KRS S PV LG+PN LIC +D PPV+N+TWL+NG V +G
Sbjct: 99 VTKRSNNTAAVNQVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSV-KGF 157
Query: 553 SETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTEN 732
SET FL + DH F K YL F+PS +D YDC+VEHWGLDKPLLKHWE E P+ E TE
Sbjct: 158 SETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 217
Query: 733 TVCA 744
VCA
Sbjct: 218 VVCA 221
>ref|NP_001004039.1| SLA-DM alpha chain [Sus scrofa].
Length = 260
Score = 74.3 bits (181), Expect = 1e-13
Identities = 52/176 (29%), Positives = 80/176 (45%), Gaps = 6/176 (3%)
Frame = +1
Query: 232 FDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEIMIKR-----SXXX 396
+DGD++F + + V RL EF +A + + A I DK MI++
Sbjct: 63 YDGDQLFSFNFSQNIRVPRLPEFADWAH-QIEDTPA-IFFDKGFCREMIEKVGPLFEGKI 120
Query: 397 XXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPR 576
+ KP+E G+PN L+CF+ PP + VTW + +PV G+ T
Sbjct: 121 PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSAT 179
Query: 577 EDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLP-ETTENTVC 741
+D F+ F YL F P+ D++ C V H + +W Q LP + EN +C
Sbjct: 180 DDLSFQAFSYLNFTPTPSDLFSCVVTHELDGYVAISYW--VPQNALPSDLLENVLC 233
>ref|NP_001107177.1| major histocompatibility complex, class II, DO alpha [Sus scrofa].
Length = 260
Score = 74.3 bits (181), Expect = 1e-13
Identities = 52/176 (29%), Positives = 80/176 (45%), Gaps = 6/176 (3%)
Frame = +1
Query: 232 FDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEIMIKR-----SXXX 396
+DGD++F + + V RL EF +A + + A I DK MI++
Sbjct: 63 YDGDQLFSFNFSQNIRVPRLPEFADWAH-QIEDTPA-IFFDKGFCREMIEKVGPLFEGKI 120
Query: 397 XXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPR 576
+ KP+E G+PN L+CF+ PP + VTW + +PV G+ T
Sbjct: 121 PVSRGLPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTWEHHSAPV-EGIGPTFVSAT 179
Query: 577 EDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLP-ETTENTVC 741
+D F+ F YL F P+ D++ C V H + +W Q LP + EN +C
Sbjct: 180 DDLSFQAFSYLNFTPTPSDLFSCVVTHELDGYVAISYW--VPQNALPSDLLENVLC 233
>ref|NP_001107167.1| MHC class II histocompatibility antigen SLA-DRB1 [Sus scrofa].
Length = 266
Score = 61.2 bits (147), Expect = 1e-09
Identities = 30/90 (33%), Positives = 43/90 (47%)
Frame = +1
Query: 439 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFM 618
K L N+L+C + F P V V W RNG GV T +P D F+ L +
Sbjct: 134 KTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLETV 193
Query: 619 PSTEDVYDCQVEHWGLDKPLLKHWEFEAQT 708
P + +VY C+VEH L P+ W +++
Sbjct: 194 PQSGEVYSCRVEHPSLTSPVTVEWRARSES 223
>ref|XP_003128397.1| PREDICTED: DLA class II histocompatibility antigen, DR-1 beta
chain-like [Sus scrofa].
Length = 321
Score = 60.5 bits (145), Expect = 2e-09
Identities = 30/84 (35%), Positives = 40/84 (47%)
Frame = +1
Query: 439 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFM 618
K L N+L+C + F P V V W RNG GV T +P D F+ L +
Sbjct: 134 KTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLETV 193
Query: 619 PSTEDVYDCQVEHWGLDKPLLKHW 690
P + +VY C+VEH L P+ W
Sbjct: 194 PQSGEVYSCRVEHPSLTSPVTVEW 217
>ref|XP_003128372.1| PREDICTED: DLA class II histocompatibility antigen, DR-1 beta
chain-like [Sus scrofa].
Length = 261
Score = 60.5 bits (145), Expect = 2e-09
Identities = 30/84 (35%), Positives = 40/84 (47%)
Frame = +1
Query: 439 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFM 618
K L N+L+C + F P V V W RNG GV T +P D F+ L +
Sbjct: 129 KTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVMLETV 188
Query: 619 PSTEDVYDCQVEHWGLDKPLLKHW 690
P + +VY C+VEH L P+ W
Sbjct: 189 PQSGEVYSCRVEHPSLTSPVTVEW 212
>ref|NP_999143.1| beta-2-microglobulin precursor [Sus scrofa].
Length = 118
Score = 60.5 bits (145), Expect = 2e-09
Identities = 30/87 (34%), Positives = 45/87 (51%)
Frame = +1
Query: 433 SDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLP 612
S P E G+PN L C++ F PP + + L+NG + S+ F +D F +
Sbjct: 31 SRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFYLLVHTE 88
Query: 613 FMPSTEDVYDCQVEHWGLDKPLLKHWE 693
F P+ D Y C+V+H LDKP + W+
Sbjct: 89 FTPNAVDQYSCRVKHVTLDKPKIVKWD 115
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: 30,548,555
Number of extensions: 844059
Number of successful extensions: 2641
Number of sequences better than 1.0e-05: 24
Number of HSP's gapped: 2632
Number of HSP's successfully gapped: 24
Length of query: 409
Length of database: 11,343,932
Length adjustment: 101
Effective length of query: 308
Effective length of database: 8,829,335
Effective search space: 2719435180
Effective search space used: 2719435180
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-012104
(1227 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_034511.2| histocompatibility 2, class II antigen E alpha ... 330 1e-90
Alignment gi|NP_032232.2| histocompatibility 2, O region alpha locus [Mus... 215 6e-56
Alignment gi|NP_034508.2| histocompatibility 2, class II antigen A, alpha... 212 4e-55
Alignment gi|NP_034516.3| class II histocompatibility antigen, M alpha ch... 82 1e-15
Alignment gi|NP_996988.2| histocompatibility 2, class II antigen A, beta ... 60 3e-09
Alignment gi|NP_034517.2| class II histocompatibility antigen, M beta 1 c... 58 2e-08
Alignment gi|XP_003086107.1| PREDICTED: class II histocompatibility antig... 58 2e-08
Alignment gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ... 58 2e-08
Alignment gi|NP_034512.2| H-2 class II histocompatibility antigen, I-E be... 58 2e-08
Alignment gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ... 57 3e-08
>ref|NP_034511.2| histocompatibility 2, class II antigen E alpha precursor [Mus
musculus].
Length = 255
Score = 330 bits (846), Expect = 1e-90
Identities = 159/239 (66%), Positives = 177/239 (74%)
Frame = +1
Query: 118 FVITILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEE 297
F+ +++ QKSWAI E H IIQAEFYL PDK GEFMFDFDGDEIFHVD+EK ET+WRLEE
Sbjct: 13 FIAVLMSSQKSWAIKEEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEE 72
Query: 298 FGHFASFEAQGALANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILIC 477
F FASFEAQGALANIAVDKANL++M +RS LS PV LGEPNILIC
Sbjct: 73 FAKFASFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPNILIC 132
Query: 478 FIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEH 657
FIDKFSPPVVNVTW RNG PVT GVSETVFLPR+DHLFRKFHYL F+PST+D YDC+V+H
Sbjct: 133 FIDKFSPPVVNVTWFRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDH 192
Query: 658 WGLDKPLLKHWEFEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERR 834
WGL++PL KHWEFE +T LPETTEN VCA +K N ERR
Sbjct: 193 WGLEEPLRKHWEFEEKTLLPETTENVVCALGLFVGLVGIVVGIILIMKGIKKRNVVERR 251
>ref|NP_032232.2| histocompatibility 2, O region alpha locus [Mus musculus].
Length = 250
Score = 215 bits (547), Expect = 6e-56
Identities = 104/214 (48%), Positives = 141/214 (65%), Gaps = 1/214 (0%)
Frame = +1
Query: 103 VPVLGFVITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRET 279
VPVL ++ L+ + AI +H+ FY S D SG+F +FDG++IF VD++ E
Sbjct: 8 VPVLLTAMSFLSPRGVRAIKADHMGSYGPAFYQSYDASGQFTHEFDGEQIFSVDLKNEEV 67
Query: 280 VWRLEEFGHFASFEAQGALANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSDKPVELGE 459
VWRL EFG FA + Q L +I++ KA+L+I+++RS L VELG+
Sbjct: 68 VWRLPEFGDFAHSDFQSGLMSISMIKAHLDILVERSNRTRAVSVPPRVTVLPKTRVELGK 127
Query: 460 PNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVY 639
PN+LIC +D PPV+NVTWLRN P+T+GV++T F + +H FRKFHYL F+PS EDVY
Sbjct: 128 PNVLICIVDDIFPPVINVTWLRNSQPITKGVAQTSFYSQPNHRFRKFHYLTFVPSAEDVY 187
Query: 640 DCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVC 741
DC+VEHWGLD PLL+HWE + TP P+T E +C
Sbjct: 188 DCKVEHWGLDTPLLQHWEPQVLTPPPDTIETLIC 221
>ref|NP_034508.2| histocompatibility 2, class II antigen A, alpha precursor [Mus
musculus].
Length = 256
Score = 212 bits (540), Expect = 4e-55
Identities = 109/256 (42%), Positives = 142/256 (55%), Gaps = 1/256 (0%)
Frame = +1
Query: 79 KEKMTILGVPVLGFVITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFH 255
+ + ILGV L ++++ + I +HV Y SP G++ F+FDGDE+F+
Sbjct: 3 RSRALILGVLALTTMLSLCGGEDD--IEADHVGTYGISVYQSPGDIGQYTFEFDGDELFY 60
Query: 256 VDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLS 435
VD++K+ETVW L EFG ASF+ QG L NIAV K NL ++ KRS
Sbjct: 61 VDLDKKETVWMLPEFGQLASFDPQGGLQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFP 120
Query: 436 DKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPF 615
PV LG+PN LICF+D PPV+N+TWLRN V GV ET F D+ F K YL F
Sbjct: 121 KSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTF 180
Query: 616 MPSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXX 795
+PS +D+YDC+VEHWGL++P+LKHWE E P+ E TE VCA
Sbjct: 181 IPSDDDIYDCKVEHWGLEEPVLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTIFI 240
Query: 796 XXXXRKGNATERRGPL 843
R G + GPL
Sbjct: 241 IQGLRSGGTSRHPGPL 256
>ref|NP_034516.3| class II histocompatibility antigen, M alpha chain precursor [Mus
musculus].
Length = 261
Score = 81.6 bits (200), Expect = 1e-15
Identities = 65/231 (28%), Positives = 96/231 (41%), Gaps = 17/231 (7%)
Frame = +1
Query: 100 GVPVLGFVITILNLQKSWAIVE-----------NHVIIQAEFYLSPDKSGEFMFDFDGDE 246
G +L + + L SWA++E NH F + +D DE
Sbjct: 8 GAVLLRLLRLLWLLPHSWAVLEASTPVFWDDPQNHTFRHTLFCQDGIPNIGLSETYDEDE 67
Query: 247 IFHVDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEIMI-----KRSXXXXXXXX 411
+F D + V RL +F +A + QG + IA DK+ E+++ K
Sbjct: 68 LFSFDFSQNTRVPRLPDFAEWA--QGQGDASAIAFDKSFCEMLMREVSPKLEGQIPVSRG 125
Query: 412 XXXXXXLSDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLF 591
+ KP+E G+PN L+CFI PP + V W + +PV G S T + F
Sbjct: 126 LPVAEVFTLKPLEFGKPNTLVCFISNLFPPTLTVNWQLHSAPV-EGASPTSISAVDGLTF 184
Query: 592 RKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLP-ETTENTVC 741
+ F YL F P D+Y C V H + +W Q LP + EN +C
Sbjct: 185 QAFSYLNFTPEPFDLYSCTVTHEIDRYTAIAYW--VPQNALPSDLLENALC 233
>ref|NP_996988.2| histocompatibility 2, class II antigen A, beta 1 precursor [Mus
musculus].
Length = 265
Score = 60.5 bits (145), Expect = 3e-09
Identities = 29/86 (33%), Positives = 40/86 (46%)
Frame = +1
Query: 451 LGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTE 630
L N L+C + F P + V W RNG T GVS T + D F+ L P
Sbjct: 137 LNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRG 196
Query: 631 DVYDCQVEHWGLDKPLLKHWEFEAQT 708
+VY C VEH L P+ W ++++
Sbjct: 197 EVYTCHVEHPSLKSPITVEWRAQSES 222
>ref|NP_034517.2| class II histocompatibility antigen, M beta 1 chain precursor [Mus
musculus].
Length = 261
Score = 57.8 bits (138), Expect = 2e-08
Identities = 29/84 (34%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
Frame = +1
Query: 442 PVELGEPNILICFIDKFSPPVVNVTWLRNGSPV-TRGVSETVFLPREDHLFRKFHYLPFM 618
P EP +L C++ F P V +TW++NG V + E P D ++ YL
Sbjct: 124 PFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPNGDWTYQTVSYLALT 183
Query: 619 PSTEDVYDCQVEHWGLDKPLLKHW 690
PS DVY C V+H G +P+ W
Sbjct: 184 PSYGDVYTCVVQHSGTSEPIRGDW 207
>ref|XP_003086107.1| PREDICTED: class II histocompatibility antigen, M beta 1 chain-like
[Mus musculus].
Length = 261
Score = 57.8 bits (138), Expect = 2e-08
Identities = 29/84 (34%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
Frame = +1
Query: 442 PVELGEPNILICFIDKFSPPVVNVTWLRNGSPV-TRGVSETVFLPREDHLFRKFHYLPFM 618
P EP +L C++ F P V +TW++NG V + E P D ++ YL
Sbjct: 124 PFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPNGDWTYQTVSYLALT 183
Query: 619 PSTEDVYDCQVEHWGLDKPLLKHW 690
PS DVY C V+H G +P+ W
Sbjct: 184 PSYGDVYTCVVQHSGTSEPIRGDW 207
>ref|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus musculus].
Length = 261
Score = 57.8 bits (138), Expect = 2e-08
Identities = 29/84 (34%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
Frame = +1
Query: 442 PVELGEPNILICFIDKFSPPVVNVTWLRNGSPV-TRGVSETVFLPREDHLFRKFHYLPFM 618
P EP +L C++ F P V +TW++NG V + E P D ++ YL
Sbjct: 124 PFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPNGDWTYQTVSYLALT 183
Query: 619 PSTEDVYDCQVEHWGLDKPLLKHW 690
PS DVY C V+H G +P+ W
Sbjct: 184 PSYGDVYTCVVQHSGTSEPIRGDW 207
>ref|NP_034512.2| H-2 class II histocompatibility antigen, I-E beta chain precursor
[Mus musculus].
Length = 264
Score = 57.8 bits (138), Expect = 2e-08
Identities = 28/88 (31%), Positives = 42/88 (47%)
Frame = +1
Query: 439 KPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFM 618
K L N+L+C + F P + V W RNG G+ T + D F+ L +
Sbjct: 132 KTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETV 191
Query: 619 PSTEDVYDCQVEHWGLDKPLLKHWEFEA 702
P + +VY CQVEH L P+ W+ ++
Sbjct: 192 PQSGEVYTCQVEHPSLTDPVTVEWKAQS 219
>ref|NP_034519.2| histocompatibility 2, O region beta locus [Mus musculus].
Length = 271
Score = 57.0 bits (136), Expect = 3e-08
Identities = 28/85 (32%), Positives = 43/85 (50%)
Frame = +1
Query: 451 LGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTE 630
L + N+L+C + F P ++V W RNG GV T + D F+ L +P
Sbjct: 135 LQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVRNGDWTFQTTVMLEMIPELG 194
Query: 631 DVYDCQVEHWGLDKPLLKHWEFEAQ 705
D+Y C VEH GL +P+ W +++
Sbjct: 195 DIYSCLVEHPGLLRPVSVAWMAQSE 219
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: 41,533,538
Number of extensions: 1135161
Number of successful extensions: 3664
Number of sequences better than 1.0e-05: 17
Number of HSP's gapped: 3652
Number of HSP's successfully gapped: 17
Length of query: 409
Length of database: 15,617,559
Length adjustment: 104
Effective length of query: 305
Effective length of database: 12,493,815
Effective search space: 3810613575
Effective search space used: 3810613575
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-012104
(1227 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_061984.2| HLA class II histocompatibility antigen, DR alp... 372 e-103
Alignment gi|NP_001229454.1| HLA class II histocompatibility antigen, DP ... 239 3e-63
Alignment gi|NP_001229453.1| HLA class II histocompatibility antigen, DP ... 239 3e-63
Alignment gi|NP_291032.2| HLA class II histocompatibility antigen, DP alp... 239 3e-63
Alignment gi|NP_002110.1| HLA class II histocompatibility antigen, DO alp... 229 3e-60
Alignment gi|NP_002113.2| HLA class II histocompatibility antigen, DQ alp... 213 3e-55
Alignment gi|XP_003119375.1| PREDICTED: HLA class II histocompatibility a... 213 4e-55
Alignment gi|XP_003119374.1| PREDICTED: HLA class II histocompatibility a... 213 4e-55
Alignment gi|XP_003119376.1| PREDICTED: HLA class II histocompatibility a... 211 1e-54
Alignment gi|XP_003120319.1| PREDICTED: HLA class II histocompatibility a... 209 5e-54
>ref|NP_061984.2| HLA class II histocompatibility antigen, DR alpha chain precursor
[Homo sapiens].
Length = 254
Score = 372 bits (956), Expect = e-103
Identities = 183/254 (72%), Positives = 199/254 (78%), Gaps = 2/254 (0%)
Frame = +1
Query: 88 MTILGVPVLGFVI--TILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVD 261
M I GVPVLGF I +++ Q+SWAI E HVIIQAEFYL+PD+SGEFMFDFDGDEIFHVD
Sbjct: 1 MAISGVPVLGFFIIAVLMSAQESWAIKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVD 60
Query: 262 MEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSDK 441
M K+ETVWRLEEFG FASFEAQGALANIAVDKANLEIM KRS L++
Sbjct: 61 MAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNS 120
Query: 442 PVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMP 621
PVEL EPN+LICFIDKF+PPVVNVTWLRNG PVT GVSETVFLPREDHLFRKFHYLPF+P
Sbjct: 121 PVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLP 180
Query: 622 STEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXX 801
STEDVYDC+VEHWGLD+PLLKHWEF+A +PLPETTEN VCA
Sbjct: 181 STEDVYDCRVEHWGLDEPLLKHWEFDAPSPLPETTENVVCALGLTVGLVGIIIGTIFIIK 240
Query: 802 XXRKGNATERRGPL 843
RK NA ERRGPL
Sbjct: 241 GLRKSNAAERRGPL 254
>ref|NP_001229454.1| HLA class II histocompatibility antigen, DP alpha 1 chain precursor
[Homo sapiens].
Length = 260
Score = 239 bits (611), Expect = 3e-63
Identities = 115/205 (56%), Positives = 144/205 (70%)
Frame = +1
Query: 130 ILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHF 309
+L+L+ + AI +HV A F + +GEFMF+FD DE+F+VD++K+ETVW LEEFG
Sbjct: 23 LLSLRGAGAIKADHVSTYAAFVQTHRPTGEFMFEFDEDEMFYVDLDKKETVWHLEEFGQA 82
Query: 310 ASFEAQGALANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDK 489
SFEAQG LANIA+ NL +I+RS +PVELG+PN LIC IDK
Sbjct: 83 FSFEAQGGLANIAILNNNLNTLIQRSNHTQATNDPPEVTVFPKEPVELGQPNTLICHIDK 142
Query: 490 FSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLD 669
F PPV+NVTWL NG VT GV+E++FLPR D+ F KFHYL F+PS ED YDC+VEHWGLD
Sbjct: 143 FFPPVLNVTWLCNGELVTEGVAESLFLPRTDYSFHKFHYLTFVPSAEDFYDCRVEHWGLD 202
Query: 670 KPLLKHWEFEAQTPLPETTENTVCA 744
+PLLKHWE + +PETTE +CA
Sbjct: 203 QPLLKHWEAQEPIQMPETTETVLCA 227
>ref|NP_001229453.1| HLA class II histocompatibility antigen, DP alpha 1 chain precursor
[Homo sapiens].
Length = 260
Score = 239 bits (611), Expect = 3e-63
Identities = 115/205 (56%), Positives = 144/205 (70%)
Frame = +1
Query: 130 ILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHF 309
+L+L+ + AI +HV A F + +GEFMF+FD DE+F+VD++K+ETVW LEEFG
Sbjct: 23 LLSLRGAGAIKADHVSTYAAFVQTHRPTGEFMFEFDEDEMFYVDLDKKETVWHLEEFGQA 82
Query: 310 ASFEAQGALANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDK 489
SFEAQG LANIA+ NL +I+RS +PVELG+PN LIC IDK
Sbjct: 83 FSFEAQGGLANIAILNNNLNTLIQRSNHTQATNDPPEVTVFPKEPVELGQPNTLICHIDK 142
Query: 490 FSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLD 669
F PPV+NVTWL NG VT GV+E++FLPR D+ F KFHYL F+PS ED YDC+VEHWGLD
Sbjct: 143 FFPPVLNVTWLCNGELVTEGVAESLFLPRTDYSFHKFHYLTFVPSAEDFYDCRVEHWGLD 202
Query: 670 KPLLKHWEFEAQTPLPETTENTVCA 744
+PLLKHWE + +PETTE +CA
Sbjct: 203 QPLLKHWEAQEPIQMPETTETVLCA 227
>ref|NP_291032.2| HLA class II histocompatibility antigen, DP alpha 1 chain precursor
[Homo sapiens].
Length = 260
Score = 239 bits (611), Expect = 3e-63
Identities = 115/205 (56%), Positives = 144/205 (70%)
Frame = +1
Query: 130 ILNLQKSWAIVENHVIIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHF 309
+L+L+ + AI +HV A F + +GEFMF+FD DE+F+VD++K+ETVW LEEFG
Sbjct: 23 LLSLRGAGAIKADHVSTYAAFVQTHRPTGEFMFEFDEDEMFYVDLDKKETVWHLEEFGQA 82
Query: 310 ASFEAQGALANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDK 489
SFEAQG LANIA+ NL +I+RS +PVELG+PN LIC IDK
Sbjct: 83 FSFEAQGGLANIAILNNNLNTLIQRSNHTQATNDPPEVTVFPKEPVELGQPNTLICHIDK 142
Query: 490 FSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLD 669
F PPV+NVTWL NG VT GV+E++FLPR D+ F KFHYL F+PS ED YDC+VEHWGLD
Sbjct: 143 FFPPVLNVTWLCNGELVTEGVAESLFLPRTDYSFHKFHYLTFVPSAEDFYDCRVEHWGLD 202
Query: 670 KPLLKHWEFEAQTPLPETTENTVCA 744
+PLLKHWE + +PETTE +CA
Sbjct: 203 QPLLKHWEAQEPIQMPETTETVLCA 227
>ref|NP_002110.1| HLA class II histocompatibility antigen, DO alpha chain precursor
[Homo sapiens].
Length = 250
Score = 229 bits (585), Expect = 3e-60
Identities = 112/215 (52%), Positives = 144/215 (66%), Gaps = 3/215 (1%)
Frame = +1
Query: 109 VLGF--VITILNLQKSWAIVENHV-IIQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRET 279
VLGF ++T+L+ Q++ A +H+ FY S SG+F +FD +++F VD++K E
Sbjct: 8 VLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEA 67
Query: 280 VWRLEEFGHFASFEAQGALANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSDKPVELGE 459
VWRL EFG FA F+ QG LA IA KA+L+I+++RS L VELG+
Sbjct: 68 VWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQ 127
Query: 460 PNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVY 639
PNILIC +D PPV+N+TWLRNG VT GV++T F + DHLFRKFHYLPF+PS EDVY
Sbjct: 128 PNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVY 187
Query: 640 DCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCA 744
DCQVEHWGLD PLL+HWE + P P+ E VCA
Sbjct: 188 DCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCA 222
>ref|NP_002113.2| HLA class II histocompatibility antigen, DQ alpha 1 chain precursor
[Homo sapiens].
Length = 255
Score = 213 bits (542), Expect = 3e-55
Identities = 108/230 (46%), Positives = 131/230 (56%), Gaps = 1/230 (0%)
Frame = +1
Query: 157 IVENHVI-IQAEFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 333
IV +HV Y SG++ +FDGDE F+VD+E++ET WR EF F F+ QGA
Sbjct: 26 IVADHVASCGVNLYQFYGPSGQYTHEFDGDEQFYVDLERKETAWRWPEFSKFGGFDPQGA 85
Query: 334 LANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 513
L N+AV K NL IMIKR S PV LG+PN LIC +D PPVVN+
Sbjct: 86 LRNMAVAKHNLNIMIKRYNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNI 145
Query: 514 TWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 693
TWL NG VT GVSET FL + DH F K YL F+PS +++YDC+VEHWGLD+PLLKHWE
Sbjct: 146 TWLSNGQSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDQPLLKHWE 205
Query: 694 FEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 843
E P+ E TE VCA R A+ +GPL
Sbjct: 206 PEIPAPMSELTETVVCALGLSVGLMGIVVGTVFIIQGLRSVGASRHQGPL 255
>ref|XP_003119375.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 2 [Homo sapiens].
Length = 255
Score = 213 bits (541), Expect = 4e-55
Identities = 110/230 (47%), Positives = 134/230 (58%), Gaps = 1/230 (0%)
Frame = +1
Query: 157 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 333
IV +HV Y S SG++ +FDGDE F+VD+E++ETVW+L F F F+ Q A
Sbjct: 26 IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFA 85
Query: 334 LANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 513
L NIAV K NL I+IKRS S PV LG+PN LIC +D PPVVN+
Sbjct: 86 LTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNI 145
Query: 514 TWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 693
TWL NG VT GVSET FL + DH F K YL F+PS +++YDC+VEHWGLD+PLLKHWE
Sbjct: 146 TWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWE 205
Query: 694 FEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 843
E TP+ E TE VCA R A+ +GPL
Sbjct: 206 PEIPTPMSELTETVVCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 255
>ref|XP_003119374.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 1 [Homo sapiens].
Length = 255
Score = 213 bits (541), Expect = 4e-55
Identities = 110/230 (47%), Positives = 134/230 (58%), Gaps = 1/230 (0%)
Frame = +1
Query: 157 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 333
IV +HV Y S SG++ +FDGDE F+VD+E++ETVW+L F F F+ Q A
Sbjct: 26 IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFA 85
Query: 334 LANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 513
L NIAV K NL I+IKRS S PV LG+PN LIC +D PPVVN+
Sbjct: 86 LTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNI 145
Query: 514 TWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 693
TWL NG VT GVSET FL + DH F K YL F+PS +++YDC+VEHWGLD+PLLKHWE
Sbjct: 146 TWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWE 205
Query: 694 FEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 843
E TP+ E TE VCA R A+ +GPL
Sbjct: 206 PEIPTPMSELTETVVCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 255
>ref|XP_003119376.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 3 [Homo sapiens].
Length = 250
Score = 211 bits (537), Expect = 1e-54
Identities = 106/217 (48%), Positives = 129/217 (59%)
Frame = +1
Query: 193 YLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEI 372
Y S SG++ +FDGDE F+VD+E++ETVW+L F F F+ Q AL NIAV K NL I
Sbjct: 34 YQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNI 93
Query: 373 MIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGV 552
+IKRS S PV LG+PN LIC +D PPVVN+TWL NG VT GV
Sbjct: 94 VIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGV 153
Query: 553 SETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTEN 732
SET FL + DH F K YL F+PS +++YDC+VEHWGLD+PLLKHWE E TP+ E TE
Sbjct: 154 SETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWEPEIPTPMSELTET 213
Query: 733 TVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 843
VCA R A+ +GPL
Sbjct: 214 VVCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 250
>ref|XP_003120319.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 3 [Homo sapiens].
Length = 254
Score = 209 bits (531), Expect = 5e-54
Identities = 110/230 (47%), Positives = 133/230 (57%), Gaps = 1/230 (0%)
Frame = +1
Query: 157 IVENHVIIQA-EFYLSPDKSGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGA 333
IV +HV Y S SG+F +FDGDE F+VD+E++ETVW+L F H F+ Q A
Sbjct: 26 IVADHVASYGVNLYQSYGPSGQFTHEFDGDEEFYVDLERKETVWKLPLF-HRLRFDPQFA 84
Query: 334 LANIAVDKANLEIMIKRSXXXXXXXXXXXXXXLSDKPVELGEPNILICFIDKFSPPVVNV 513
L NIAV K NL I+IKRS S PV LG+PN LIC +D PPVVN+
Sbjct: 85 LTNIAVLKHNLNILIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNI 144
Query: 514 TWLRNGSPVTRGVSETVFLPREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWE 693
TWL NG VT GVSET FL + DH F K YL F+PS +++YDC+VEHWGLD+PLLKHWE
Sbjct: 145 TWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWE 204
Query: 694 FEAQTPLPETTENTVCAXXXXXXXXXXXXXXXXXXXXXRKGNATERRGPL 843
E P+ E TE VCA R A+ +GPL
Sbjct: 205 PEIPAPMSELTETVVCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 254
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: 48,884,930
Number of extensions: 1348615
Number of successful extensions: 4282
Number of sequences better than 1.0e-05: 44
Number of HSP's gapped: 4259
Number of HSP's successfully gapped: 44
Length of query: 409
Length of database: 18,297,164
Length adjustment: 105
Effective length of query: 304
Effective length of database: 14,835,944
Effective search space: 4510126976
Effective search space used: 4510126976
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-012104
(1227 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 702 0.0
>Sscrofa_Chr07
|| Length = 134764511
Score = 702 bits (354), Expect = 0.0
Identities = 370/374 (98%), Gaps = 1/374 (0%)
Strand = Plus / Plus
Query: 855 cagggaatggactttgttaaagatcaatgaagatatttcctcttgaacagctttacaaac 914
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29041742 cagggaatggactttgttaaagatcaatgaagatatttcctcttgaacagctttacaaac 29041801
Query: 915 ccagcgatactccagctgttcacctccgtgaagacaactctccttcagcactttccagcc 974
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29041802 ccagcgatactccagctgttcacctccgtgaagacaactctccttcagcactttccagcc 29041861
Query: 975 ctgaagccactctaagtgttgatgccttctttaatcttcaaattctaacatctggttatt 1034
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29041862 ctgaagccactctaagtgttgatgccttctttaatcttcaaattctaacatctggttatt 29041921
Query: 1035 ccctgtttgttaccccttcttgtgctggctttccctccatttccacagcctttttattat 1094
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29041922 ccctgtttgttaccccttcttgtgctggctttccctccatttccacagcctttttattat 29041981
Query: 1095 caccgtgtaatgcctttggaagagatcccatgggatcctttctctgctatgaaacctttc 1154
|||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||
Sbjct: 29041982 caccatgtaatgcctttggaagagatcccataggatcctttctctgctatgaaacctttc 29042041
Query: 1155 gaatggtctatggaggcatctactgtatacttattacttggagtttcttcc-actgtgat 1213
||||| ||||||||||||||||||||||||||||||||||||||||||||| ||||||||
Sbjct: 29042042 gaatgttctatggaggcatctactgtatacttattacttggagtttcttccaactgtgat 29042101
Query: 1214 tgtgatttttctga 1227
||||||||||||||
Sbjct: 29042102 tgtgatttttctga 29042115
Score = 561 bits (283), Expect = e-157
Identities = 283/283 (100%)
Strand = Plus / Plus
Query: 409 gtacctccagaagtgactgtgctctcagacaagcctgttgaactgggagagcccaacatc 468
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29040050 gtacctccagaagtgactgtgctctcagacaagcctgttgaactgggagagcccaacatc 29040109
Query: 469 ctcatctgtttcatcgacaagttctccccgccagtggtcaatgtcacctggcttcgaaat 528
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29040110 ctcatctgtttcatcgacaagttctccccgccagtggtcaatgtcacctggcttcgaaat 29040169
Query: 529 ggctcccctgtcaccagaggagtgtcagagacagtcttcctgccccgggaggaccacctt 588
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29040170 ggctcccctgtcaccagaggagtgtcagagacagtcttcctgccccgggaggaccacctt 29040229
Query: 589 ttccgcaagttccactatctccccttcatgccctcaaccgaggatgtctatgactgccag 648
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29040230 ttccgcaagttccactatctccccttcatgccctcaaccgaggatgtctatgactgccag 29040289
Query: 649 gtggagcactggggtttggacaagcctcttctcaagcactggg 691
|||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29040290 gtggagcactggggtttggacaagcctcttctcaagcactggg 29040332
Score = 492 bits (248), Expect = e-136
Identities = 248/248 (100%)
Strand = Plus / Plus
Query: 162 agagaatcacgtgatcatccaggctgagttctatctgagccctgacaaatctggcgagtt 221
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29039360 agagaatcacgtgatcatccaggctgagttctatctgagccctgacaaatctggcgagtt 29039419
Query: 222 tatgtttgactttgacggtgatgagattttccacgtggatatggaaaagagggagacggt 281
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29039420 tatgtttgactttgacggtgatgagattttccacgtggatatggaaaagagggagacggt 29039479
Query: 282 ctggcgacttgaagaatttggacattttgccagctttgaggctcagggtgcactggccaa 341
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29039480 ctggcgacttgaagaatttggacattttgccagctttgaggctcagggtgcactggccaa 29039539
Query: 342 catagctgtggacaaagccaacctggaaatcatgatcaagcgctccaacaacaccccgaa 401
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29039540 catagctgtggacaaagccaacctggaaatcatgatcaagcgctccaacaacaccccgaa 29039599
Query: 402 caccaatg 409
||||||||
Sbjct: 29039600 caccaatg 29039607
Score = 325 bits (164), Expect = 3e-86
Identities = 167/168 (99%)
Strand = Plus / Plus
Query: 691 gagtttgaagctcaaacccccctcccagagactacagagaacaccgtgtgtgctctgggc 750
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29040632 gagtttgaagctcaaacccccctcccagagactacagagaacaccgtgtgtgctctgggc 29040691
Query: 751 ctgattgtggctctggtgggcatcatcgtcgggaccgtcctcatcatcaagggtgtgcgc 810
|||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||
Sbjct: 29040692 ctgattgtggctctggtgggcatcatcgtcggaaccgtcctcatcatcaagggtgtgcgc 29040751
Query: 811 aaaggcaacgccactgaacgccgagggcctctgtgaggtgcttgcagg 858
||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29040752 aaaggcaacgccactgaacgccgagggcctctgtgaggtgcttgcagg 29040799
Score = 323 bits (163), Expect = 1e-85
Identities = 163/163 (100%)
Strand = Plus / Plus
Query: 1 gacaccctgcattctctttgcttgtattgctgtccatcctgacccaccatagctctacag 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29036542 gacaccctgcattctctttgcttgtattgctgtccatcctgacccaccatagctctacag 29036601
Query: 61 accctcatcgaggcatctaaggagaaaatgaccatacttggggtcccagtcctgggattt 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29036602 accctcatcgaggcatctaaggagaaaatgaccatacttggggtcccagtcctgggattt 29036661
Query: 121 gtcatcaccatcttgaaccttcagaaatcatgggctatcgtag 163
|||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29036662 gtcatcaccatcttgaaccttcagaaatcatgggctatcgtag 29036704
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: 36,327,163
Number of extensions: 172
Number of successful extensions: 172
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 171
Number of HSP's successfully gapped: 5
Length of query: 1227
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 1206
Effective length of database: 2,808,413,156
Effective search space: 3386946266136
Effective search space used: 3386946266136
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)