Search to RefSeqBP_Rel44
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= 20070806C-000022
(1075 letters)
Database: RefSeq44_BP.fasta
33,615 sequences; 18,071,151 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001012693.1| major histocompatibility complex, class II, ... 326 2e-89
Alignment gi|NP_001013619.3| major histocompatibility complex, class II, ... 325 3e-89
Alignment gi|XP_002702914.1| PREDICTED: BOLA-DQA2 protein-like [Bos tauru... 322 5e-88
Alignment gi|NP_001073045.1| major histocompatibility complex, class II, ... 312 4e-85
Alignment gi|NP_001012699.1| major histocompatibility complex, class II, ... 295 5e-80
Alignment gi|NP_001012696.1| major histocompatibility complex, class II, ... 269 3e-72
Alignment gi|NP_001012695.1| major histocompatibility complex, class II, ... 228 7e-60
Alignment gi|XP_002697222.1| PREDICTED: MHC class II antigen-like [Bos ta... 221 7e-58
Alignment gi|XP_604082.2| PREDICTED: MHC class II antigen-like isoform 1 ... 221 7e-58
Alignment gi|XP_002702869.1| PREDICTED: MHC class II antigen-like [Bos ta... 209 5e-54
>ref|NP_001012693.1| major histocompatibility complex, class II, DQ alpha 5 [Bos
taurus].
Length = 255
Score = 326 bits (836), Expect = 2e-89
Identities = 158/216 (73%), Positives = 172/216 (79%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ +GPSG YTHEFDGDE+FYVDL KKET WQLPLFS+ SFDPQ ALRNIA K +++ L
Sbjct: 40 QSYGPSGQYTHEFDGDEQFYVDLEKKETAWQLPLFSRMLSFDPQLALRNIAIMKLHVDFL 99
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
K SN+TAA N+VPEVTVF KSPVMLGQPNTLICHVDNIFPPVINITWL+NGHSVTEG S
Sbjct: 100 TKFSNSTAATNKVPEVTVFSKSPVMLGQPNTLICHVDNIFPPVINITWLRNGHSVTEGVS 159
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETX 585
ETSFL ++D+SFLKI YL FLPSDDD YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET
Sbjct: 160 ETSFLIRSDYSFLKIKYLAFLPSDDDIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETV 219
Query: 586 XXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 693
QGLRSG PSRHQG L
Sbjct: 220 VCTLGLTMGLVGITVGTIFIIQGLRSGDPSRHQGPL 255
>ref|NP_001013619.3| major histocompatibility complex, class II, DQ alpha, type 1 [Bos
taurus].
Length = 255
Score = 325 bits (834), Expect = 3e-89
Identities = 155/216 (71%), Positives = 170/216 (78%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ HGPSG Y HEFDGDE FYVDLGKKETVWQLP+F + SF+ Q AL IA AKH L++L
Sbjct: 40 QSHGPSGQYIHEFDGDELFYVDLGKKETVWQLPMFGELTSFEAQDALNEIAKAKHTLDVL 99
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
KRSN T +N+VPEVTVF KSP+MLGQPNTLICHVDNIFPPVINITWL+NGH+VTEG S
Sbjct: 100 TKRSNFTPVINEVPEVTVFSKSPMMLGQPNTLICHVDNIFPPVINITWLRNGHAVTEGVS 159
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETX 585
ETSFL K+D+SFLKI YLTFLPSDDD YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET
Sbjct: 160 ETSFLPKSDYSFLKIGYLTFLPSDDDVYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETV 219
Query: 586 XXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 693
+GLRSGG SRHQG L
Sbjct: 220 VCALGLTVGLVGIVVGTVLIIRGLRSGGASRHQGPL 255
>ref|XP_002702914.1| PREDICTED: BOLA-DQA2 protein-like [Bos taurus].
Length = 254
Score = 322 bits (824), Expect = 5e-88
Identities = 155/216 (71%), Positives = 171/216 (79%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ HGPS YT EFDGD+ FYVDL KKETVW+LP+FS+F SFDPQ LRNIA +KHNLNI+
Sbjct: 40 QSHGPSDQYTQEFDGDKLFYVDLEKKETVWRLPMFSQFASFDPQAILRNIAISKHNLNIM 99
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
IK SN A+N+VPEVTVF KSP++LGQPNTLICH+DN FPPVINITWLKNGH+VTEG S
Sbjct: 100 IKYSNFIPAINEVPEVTVFSKSPMVLGQPNTLICHMDN-FPPVINITWLKNGHAVTEGVS 158
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETX 585
ETSFL K+DHSFLKI YLTFLPSDDD YDCKVEHW LD+PLLKHWEPE+PAPMSELTET
Sbjct: 159 ETSFLPKDDHSFLKIGYLTFLPSDDDVYDCKVEHWSLDEPLLKHWEPEVPAPMSELTETV 218
Query: 586 XXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 693
QGLRSGG SRHQG L
Sbjct: 219 VCALRLTVGLVGIVVGTIFIIQGLRSGGASRHQGPL 254
>ref|NP_001073045.1| major histocompatibility complex, class II, DQ alpha, type 3 [Bos
taurus].
Length = 254
Score = 312 bits (799), Expect = 4e-85
Identities = 151/216 (69%), Positives = 167/216 (77%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ HGPSG Y H+FDGDEEFYVDL K+E VW+LP+F K R F PQGALRNIA AKHNL++L
Sbjct: 40 QSHGPSGQYIHQFDGDEEFYVDLEKEEAVWRLPMFDKLR-FHPQGALRNIAIAKHNLDVL 98
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
K N T +N+VPEVTVF KSPVML QPNTLICHVDNIFPPVINITWL+NGHSVTE S
Sbjct: 99 TKLYNFTPVINEVPEVTVFSKSPVMLSQPNTLICHVDNIFPPVINITWLRNGHSVTEHVS 158
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETX 585
ETSFL ++D+S+LKISYL F PSDDD YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET
Sbjct: 159 ETSFLLRSDYSYLKISYLPFRPSDDDVYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETV 218
Query: 586 XXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 693
+GLRS G SRHQG L
Sbjct: 219 VCALGLTVGLVGIVVGTVLITRGLRSSGASRHQGPL 254
>ref|NP_001012699.1| major histocompatibility complex, class II, DQ alpha 2 [Bos
taurus].
Length = 268
Score = 295 bits (755), Expect = 5e-80
Identities = 135/165 (81%), Positives = 147/165 (89%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ HGPSG YT EFDGDE FYVDLGKKETVW+LP+FS+F FDPQ AL IATAKHNL++L
Sbjct: 40 QSHGPSGQYTQEFDGDEMFYVDLGKKETVWRLPMFSQFAGFDPQAALSEIATAKHNLDVL 99
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
KRSN T +N+VPEVTVF KSPVMLGQPNTLICHVDNIFPPVINITWLKNGH+VTEG S
Sbjct: 100 TKRSNFTPVINEVPEVTVFSKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHAVTEGVS 159
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHW 540
ETSFL K+DHSFLKI YLTFLPSD+D YDCKVEHWGLD+PLLKHW
Sbjct: 160 ETSFLPKDDHSFLKIGYLTFLPSDNDIYDCKVEHWGLDEPLLKHW 204
>ref|NP_001012696.1| major histocompatibility complex, class II, DY alpha [Bos taurus].
Length = 253
Score = 269 bits (688), Expect = 3e-72
Identities = 124/179 (69%), Positives = 146/179 (81%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ +G SG +T EFDGDE FYVDLGKKETVW+LP FS F+ Q ALRNI +K NL+IL
Sbjct: 38 QTYGASGQFTFEFDGDELFYVDLGKKETVWRLPEFSNITKFEVQSALRNIVMSKRNLDIL 97
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
IK S+ T A +++PEV VFPKS V+LG PNTLIC VDNIFPPVINITW NGH V EG +
Sbjct: 98 IKNSSFTPATSEIPEVAVFPKSSVVLGIPNTLICQVDNIFPPVINITWFYNGHFVAEGIA 157
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 582
ET+F K+DHSFLK SYLTFLP+++DFYDC+VEHWGL++PL+KHWEPEIP P SELTET
Sbjct: 158 ETTFYPKSDHSFLKFSYLTFLPTNEDFYDCRVEHWGLEEPLVKHWEPEIPTPTSELTET 216
>ref|NP_001012695.1| major histocompatibility complex, class II, DR alpha [Bos taurus].
Length = 253
Score = 228 bits (581), Expect = 7e-60
Identities = 106/173 (61%), Positives = 129/173 (74%)
Frame = +1
Query: 61 SGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSN 240
S + +FDGDE F+VD+GKKETVW+LP F F SF+ QGAL N+A K NL+I+IKRSN
Sbjct: 43 SAEFMFDFDGDEIFHVDMGKKETVWRLPEFGHFASFEAQGALANMAVMKANLDIMIKRSN 102
Query: 241 NTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFL 420
NT N PEVT+ P PV LG+PNTLIC +D PPVI++TWL+NG VT+G S+T FL
Sbjct: 103 NTPNTNVPPEVTLLPNKPVELGEPNTLICFIDKFSPPVISVTWLRNGKPVTDGVSQTVFL 162
Query: 421 SKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 579
+NDH F K YL FLP+ +D YDCKVEH GL++PLLKHWE E PAP+ E TE
Sbjct: 163 PRNDHLFRKFHYLPFLPTTEDVYDCKVEHLGLNEPLLKHWEYEAPAPLPETTE 215
>ref|XP_002697222.1| PREDICTED: MHC class II antigen-like [Bos taurus].
Length = 250
Score = 221 bits (564), Expect = 7e-58
Identities = 101/179 (56%), Positives = 129/179 (72%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ + +G +T++FDG++ F VDL K+E VW+LP F F FDPQ L +IA K +L L
Sbjct: 40 QSYDGAGQFTYDFDGEQLFSVDLKKREAVWRLPEFGNFAYFDPQSGLVSIAMIKAHLEDL 99
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
+KRSN T A N P V V PKS V LG+PN LIC VD IFPPVINITWL+NGH VT+G +
Sbjct: 100 VKRSNGTRAPNVSPRVAVLPKSHVQLGEPNVLICIVDKIFPPVINITWLRNGHPVTQGVT 159
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 582
++SF ++ DH F K YLTF+P DDFYDCKVEHWGLD+PL +HWEP++P + + T T
Sbjct: 160 QSSFYAQPDHLFRKFHYLTFVPLVDDFYDCKVEHWGLDQPLFQHWEPQVPTALPDTTGT 218
>ref|XP_604082.2| PREDICTED: MHC class II antigen-like isoform 1 [Bos taurus].
Length = 250
Score = 221 bits (564), Expect = 7e-58
Identities = 101/179 (56%), Positives = 129/179 (72%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ + +G +T++FDG++ F VDL K+E VW+LP F F FDPQ L +IA K +L L
Sbjct: 40 QSYDGAGQFTYDFDGEQLFSVDLKKREAVWRLPEFGNFAYFDPQSGLVSIAMIKAHLEDL 99
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
+KRSN T A N P V V PKS V LG+PN LIC VD IFPPVINITWL+NGH VT+G +
Sbjct: 100 VKRSNGTRAPNVSPRVAVLPKSHVQLGEPNVLICIVDKIFPPVINITWLRNGHPVTQGVT 159
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 582
++SF ++ DH F K YLTF+P DDFYDCKVEHWGLD+PL +HWEP++P + + T T
Sbjct: 160 QSSFYAQPDHLFRKFHYLTFVPLVDDFYDCKVEHWGLDQPLFQHWEPQVPTALPDTTGT 218
>ref|XP_002702869.1| PREDICTED: MHC class II antigen-like [Bos taurus].
Length = 224
Score = 209 bits (531), Expect = 5e-54
Identities = 96/165 (58%), Positives = 120/165 (72%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ + +G +T++FDG++ F VDL K+E VW+LP F F FDPQ L +IA K +L L
Sbjct: 40 QSYDGAGQFTYDFDGEQLFSVDLKKREAVWRLPEFGNFAYFDPQSGLVSIAMIKAHLEDL 99
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
+KRSN T A N P V V PKS V LG+PN LIC VD IFPPVINITWL+NGH VT+G +
Sbjct: 100 VKRSNGTRAPNVSPRVAVLPKSHVQLGEPNVLICIVDKIFPPVINITWLRNGHPVTQGVT 159
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHW 540
++SF ++ DH F K YLTF+P DDFYDCKVEHWGLD+PL +HW
Sbjct: 160 QSSFYAQPDHLFRKFHYLTFVPLVDDFYDCKVEHWGLDQPLFQHW 204
Database: RefSeq44_BP.fasta
Posted date: Nov 15, 2010 4:36 PM
Number of letters in database: 18,071,151
Number of sequences in database: 33,615
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: 33615
Number of Hits to DB: 37,366,667
Number of extensions: 910814
Number of successful extensions: 2587
Number of sequences better than 1.0e-05: 52
Number of HSP's gapped: 2568
Number of HSP's successfully gapped: 52
Length of query: 358
Length of database: 18,071,151
Length adjustment: 104
Effective length of query: 254
Effective length of database: 14,575,191
Effective search space: 3702098514
Effective search space used: 3702098514
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 RefSeqCP_Rel44
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= 20070806C-000022
(1075 letters)
Database: RefSeq44_CP.fasta
33,359 sequences; 18,921,627 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001011726.1| major histocompatibility complex, class II, ... 333 1e-91
Alignment gi|NP_001011723.1| MHC class II DR alpha chain [Canis lupus fam... 226 2e-59
Alignment gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati... 221 7e-58
Alignment gi|XP_532104.2| PREDICTED: similar to HLA class II histocompati... 80 4e-15
Alignment gi|NP_001014403.1| major histocompatibility complex, class II, ... 68 1e-11
Alignment gi|NP_001014768.1| DLA class II histocompatibility antigen, DR-... 68 2e-11
Alignment gi|NP_001041564.1| major histocompatibility complex, class II, ... 68 2e-11
Alignment gi|XP_535458.1| PREDICTED: similar to beta-2-microglobulin prec... 65 9e-11
Alignment gi|XP_850148.1| PREDICTED: similar to beta-2-microglobulin prec... 65 9e-11
Alignment gi|NP_001041592.1| major histocompatibility complex, class II, ... 60 3e-09
>ref|NP_001011726.1| major histocompatibility complex, class II, DQ alpha [Canis lupus
familiaris].
Length = 255
Score = 333 bits (855), Expect = 1e-91
Identities = 160/216 (74%), Positives = 172/216 (79%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ +GPSG YTHEFDGDEEFYVDL KKETVW+LP+FS FRSFDPQGALRN+A K NLNI+
Sbjct: 40 QSYGPSGQYTHEFDGDEEFYVDLEKKETVWRLPVFSTFRSFDPQGALRNLAIIKQNLNIM 99
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
KRSN TAA N+VPEVTVF KSPVMLGQPNTLIC VDNIFPPVIN+TWLKN HSVTEG S
Sbjct: 100 TKRSNQTAATNEVPEVTVFSKSPVMLGQPNTLICLVDNIFPPVINVTWLKNRHSVTEGVS 159
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETX 585
ETSF +K DHSF KISYLTFLPS +D YDCKVEHWGLD+PLLKHWEPE+P PMSELTET
Sbjct: 160 ETSFFAKGDHSFSKISYLTFLPSAEDIYDCKVEHWGLDEPLLKHWEPEVPTPMSELTETV 219
Query: 586 XXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 693
QGLRSGG SRHQG L
Sbjct: 220 VCALGLAVGLVGIVMGTVFIIQGLRSGGTSRHQGPL 255
>ref|NP_001011723.1| MHC class II DR alpha chain [Canis lupus familiaris].
Length = 254
Score = 226 bits (577), Expect = 2e-59
Identities = 107/174 (61%), Positives = 127/174 (72%)
Frame = +1
Query: 58 PSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNILIKRS 237
PSG + +FDGDE F+VD+ KKETVW+L F +F SF+ QGAL NIA K NL+ +IKRS
Sbjct: 43 PSGEFMFDFDGDEIFHVDMEKKETVWRLEEFGRFASFEAQGALANIAVDKANLDTMIKRS 102
Query: 238 NNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSF 417
N+T N PEVTV +PV LG+PN LIC +D PPVIN+TWL+NG+ VT G SET F
Sbjct: 103 NHTPNTNVPPEVTVLSNTPVELGEPNILICFIDKFSPPVINVTWLRNGNPVTTGVSETIF 162
Query: 418 LSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 579
L + DH F K YL FLPS +D YDCKVEHWGLD+PLLKHWE E P P+ E TE
Sbjct: 163 LPREDHLFRKFHYLPFLPSAEDVYDCKVEHWGLDEPLLKHWEFEPPTPLPETTE 216
>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 = 221 bits (564), Expect = 7e-58
Identities = 101/186 (54%), Positives = 132/186 (70%), Gaps = 7/186 (3%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ +G SG + HEFDG++ F V+L K++ VW+LP F FDPQ L +IA K +L++L
Sbjct: 10 QSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEFGNLAHFDPQNGLASIAVIKAHLDVL 69
Query: 226 IKRSNNTAAVNQV-------PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGH 384
++RSN T A+N P V V PK V LGQPN LIC VDNIFPPVINITWL+NG
Sbjct: 70 VERSNRTRAINGTHLSSPLPPRVAVLPKFRVELGQPNVLICIVDNIFPPVINITWLRNGQ 129
Query: 385 SVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPM 564
++EG ++TSF S+ DH F K YLTF+PS +D YDCKVEHWGL++PLL+HWEP++P P+
Sbjct: 130 IISEGVAQTSFYSQPDHLFRKFCYLTFVPSAEDMYDCKVEHWGLEEPLLRHWEPQVPIPV 189
Query: 565 SELTET 582
+ ET
Sbjct: 190 PDTIET 195
>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 = 79.7 bits (195), Expect = 4e-15
Identities = 39/94 (41%), Positives = 59/94 (62%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ +G SG + HEFDG++ F V+L K++ VW+LP F FDPQ L +IA K +L++L
Sbjct: 26 QSYGSSGQFAHEFDGEQLFSVELKKRQAVWRLPEFGNLAHFDPQNGLASIAVIKAHLDVL 85
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLIC 327
++RSN T A+N+ P+V + + TLIC
Sbjct: 86 VERSNRTRAINE-PQVPIPVPDTI-----ETLIC 113
>ref|NP_001014403.1| major histocompatibility complex, class II, DQ beta 1 [Canis lupus
familiaris].
Length = 269
Score = 68.2 bits (165), Expect = 1e-11
Identities = 31/103 (30%), Positives = 46/103 (44%)
Frame = +1
Query: 265 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 444
P VT+FP +L N L+C V + +P I + W +N T G T + D +F
Sbjct: 129 PTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLIRNGDWTFQ 188
Query: 445 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 573
+ L P D Y C VEH L P+ W + + S++
Sbjct: 189 ILVMLEMTPQRGDVYTCHVEHASLQSPITVQWRAQSESAQSKM 231
>ref|NP_001014768.1| DLA class II histocompatibility antigen, DR-1 beta chain precursor
[Canis lupus familiaris].
Length = 266
Score = 67.8 bits (164), Expect = 2e-11
Identities = 34/123 (27%), Positives = 55/123 (44%)
Frame = +1
Query: 205 KHNLNILIKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGH 384
+HN ++ + T P VTV+P L N L+C V+ +P I + WL+NG
Sbjct: 109 RHNYGVI---ESFTVQRRVEPTVTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQ 165
Query: 385 SVTEGFSETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPM 564
G T + D +F + L +P + Y C+VEH L P+ W + +
Sbjct: 166 EEEAGVVSTGLIRNGDWTFQILVMLEIVPQSGEVYTCQVEHPSLTSPVTVEWRAQSDSAQ 225
Query: 565 SEL 573
S++
Sbjct: 226 SKM 228
>ref|NP_001041564.1| major histocompatibility complex, class II, DM alpha [Canis lupus
familiaris].
Length = 170
Score = 67.8 bits (164), Expect = 2e-11
Identities = 36/105 (34%), Positives = 52/105 (49%)
Frame = +1
Query: 265 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 444
P V VF P+ G+PN L+C + N+FPP + + W + V EG T + + SF
Sbjct: 38 PMVDVFTLKPLEFGKPNMLVCFISNLFPPTLTVNWWHHLDPV-EGIGPTFVSAVDGFSFQ 96
Query: 445 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 579
SYL F P+ D + C V H + + +W P P S+L E
Sbjct: 97 AFSYLNFTPAPSDLFSCVVTHEIDNYTAIAYWVPHDALP-SDLLE 140
>ref|XP_535458.1| PREDICTED: similar to beta-2-microglobulin precursor isoform 2
[Canis familiaris].
Length = 125
Score = 65.5 bits (158), Expect = 9e-11
Identities = 32/98 (32%), Positives = 52/98 (53%)
Frame = +1
Query: 250 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN 429
AV P++ V+ + P G+PN L C+V PP I I LKNG + ++ SF
Sbjct: 27 AVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSF--SK 84
Query: 430 DHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 543
D +F + + F P++ D + C+V+H L +P + W+
Sbjct: 85 DWTFYLLVHTEFTPNEQDEFSCRVKHVTLSEPQIVKWD 122
>ref|XP_850148.1| PREDICTED: similar to beta-2-microglobulin precursor isoform 3
[Canis familiaris].
Length = 125
Score = 65.5 bits (158), Expect = 9e-11
Identities = 32/98 (32%), Positives = 52/98 (53%)
Frame = +1
Query: 250 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN 429
AV P++ V+ + P G+PN L C+V PP I I LKNG + ++ SF
Sbjct: 27 AVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSF--SK 84
Query: 430 DHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 543
D +F + + F P++ D + C+V+H L +P + W+
Sbjct: 85 DWTFYLLVHTEFTPNEQDEFSCRVKHVTLSEPQIVKWD 122
>ref|NP_001041592.1| major histocompatibility complex, class II, DO beta [Canis lupus
familiaris].
Length = 270
Score = 60.5 bits (145), Expect = 3e-09
Identities = 30/95 (31%), Positives = 41/95 (43%)
Frame = +1
Query: 265 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 444
PEVTV+P+ + N L+C V +P I I W +NG G T + D +F
Sbjct: 123 PEVTVYPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQ 182
Query: 445 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPE 549
+ L P D Y C V H L P+ W +
Sbjct: 183 TMVMLEMTPELGDVYTCLVNHPSLLSPVSVEWRAQ 217
Database: RefSeq44_CP.fasta
Posted date: Nov 15, 2010 4:36 PM
Number of letters in database: 18,921,627
Number of sequences in database: 33,359
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: 33359
Number of Hits to DB: 38,203,093
Number of extensions: 918939
Number of successful extensions: 2620
Number of sequences better than 1.0e-05: 21
Number of HSP's gapped: 2606
Number of HSP's successfully gapped: 21
Length of query: 358
Length of database: 18,921,627
Length adjustment: 104
Effective length of query: 254
Effective length of database: 15,452,291
Effective search space: 3924881914
Effective search space used: 3924881914
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_Rel44
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= 20070806C-000022
(1075 letters)
Database: RefSeq44_HP.fasta
33,950 sequences; 18,324,212 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|XP_003121105.1| PREDICTED: HLA class II histocompatibility a... 334 9e-92
Alignment gi|XP_003121104.1| PREDICTED: HLA class II histocompatibility a... 334 9e-92
Alignment gi|XP_003121103.1| PREDICTED: HLA class II histocompatibility a... 334 9e-92
Alignment gi|XP_003119376.1| PREDICTED: HLA class II histocompatibility a... 332 3e-91
Alignment gi|XP_003119375.1| PREDICTED: HLA class II histocompatibility a... 332 3e-91
Alignment gi|XP_003119374.1| PREDICTED: HLA class II histocompatibility a... 332 3e-91
Alignment gi|XP_003119478.1| PREDICTED: HLA class II histocompatibility a... 329 2e-90
Alignment gi|XP_003119477.1| PREDICTED: HLA class II histocompatibility a... 329 2e-90
Alignment gi|XP_003119476.1| PREDICTED: HLA class II histocompatibility a... 329 2e-90
Alignment gi|NP_064440.1| HLA class II histocompatibility antigen, DQ alp... 327 2e-89
>ref|XP_003121105.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 3 [Homo sapiens].
Length = 250
Score = 334 bits (856), Expect = 9e-92
Identities = 161/216 (74%), Positives = 174/216 (80%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ +GPSG Y+HEFDGDEEFYVDL +KETVWQLPLF +FR FDPQ AL NIA KHNLNI+
Sbjct: 35 QSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIV 94
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
IKRSN+TAA N+VPEVTVF KSPV LGQPNTLIC VDNIFPPV+NITWL NGHSVTEG S
Sbjct: 95 IKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVS 154
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETX 585
ETSFLSK+DHSF KISYLTFLPSDD+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET
Sbjct: 155 ETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETV 214
Query: 586 XXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 693
+GLRS G SRHQG L
Sbjct: 215 VCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 250
>ref|XP_003121104.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 2 [Homo sapiens].
Length = 255
Score = 334 bits (856), Expect = 9e-92
Identities = 161/216 (74%), Positives = 174/216 (80%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ +GPSG Y+HEFDGDEEFYVDL +KETVWQLPLF +FR FDPQ AL NIA KHNLNI+
Sbjct: 40 QSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIV 99
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
IKRSN+TAA N+VPEVTVF KSPV LGQPNTLIC VDNIFPPV+NITWL NGHSVTEG S
Sbjct: 100 IKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVS 159
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETX 585
ETSFLSK+DHSF KISYLTFLPSDD+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET
Sbjct: 160 ETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETV 219
Query: 586 XXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 693
+GLRS G SRHQG L
Sbjct: 220 VCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 255
>ref|XP_003121103.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 1 [Homo sapiens].
Length = 255
Score = 334 bits (856), Expect = 9e-92
Identities = 161/216 (74%), Positives = 174/216 (80%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ +GPSG Y+HEFDGDEEFYVDL +KETVWQLPLF +FR FDPQ AL NIA KHNLNI+
Sbjct: 40 QSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIV 99
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
IKRSN+TAA N+VPEVTVF KSPV LGQPNTLIC VDNIFPPV+NITWL NGHSVTEG S
Sbjct: 100 IKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVS 159
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETX 585
ETSFLSK+DHSF KISYLTFLPSDD+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET
Sbjct: 160 ETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETV 219
Query: 586 XXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 693
+GLRS G SRHQG L
Sbjct: 220 VCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 255
>ref|XP_003119376.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 3 [Homo sapiens].
Length = 250
Score = 332 bits (852), Expect = 3e-91
Identities = 160/216 (74%), Positives = 173/216 (80%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ +GPSG Y+HEFDGDEEFYVDL +KETVWQLPLF +FR FDPQ AL NIA KHNLNI+
Sbjct: 35 QSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIV 94
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
IKRSN+TAA N+VPEVTVF KSPV LGQPNTLIC VDNIFPPV+NITWL NGHSVTEG S
Sbjct: 95 IKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVS 154
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETX 585
ETSFLSK+DHSF KISYLTFLPSDD+ YDCKVEHWGLD+PLLKHWEPEIP PMSELTET
Sbjct: 155 ETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWEPEIPTPMSELTETV 214
Query: 586 XXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 693
+GLRS G SRHQG L
Sbjct: 215 VCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 250
>ref|XP_003119375.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 2 [Homo sapiens].
Length = 255
Score = 332 bits (852), Expect = 3e-91
Identities = 160/216 (74%), Positives = 173/216 (80%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ +GPSG Y+HEFDGDEEFYVDL +KETVWQLPLF +FR FDPQ AL NIA KHNLNI+
Sbjct: 40 QSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIV 99
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
IKRSN+TAA N+VPEVTVF KSPV LGQPNTLIC VDNIFPPV+NITWL NGHSVTEG S
Sbjct: 100 IKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVS 159
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETX 585
ETSFLSK+DHSF KISYLTFLPSDD+ YDCKVEHWGLD+PLLKHWEPEIP PMSELTET
Sbjct: 160 ETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWEPEIPTPMSELTETV 219
Query: 586 XXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 693
+GLRS G SRHQG L
Sbjct: 220 VCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 255
>ref|XP_003119374.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 1 [Homo sapiens].
Length = 255
Score = 332 bits (852), Expect = 3e-91
Identities = 160/216 (74%), Positives = 173/216 (80%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ +GPSG Y+HEFDGDEEFYVDL +KETVWQLPLF +FR FDPQ AL NIA KHNLNI+
Sbjct: 40 QSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIV 99
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
IKRSN+TAA N+VPEVTVF KSPV LGQPNTLIC VDNIFPPV+NITWL NGHSVTEG S
Sbjct: 100 IKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVS 159
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETX 585
ETSFLSK+DHSF KISYLTFLPSDD+ YDCKVEHWGLD+PLLKHWEPEIP PMSELTET
Sbjct: 160 ETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWEPEIPTPMSELTETV 219
Query: 586 XXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 693
+GLRS G SRHQG L
Sbjct: 220 VCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 255
>ref|XP_003119478.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 3 [Homo sapiens].
Length = 250
Score = 329 bits (844), Expect = 2e-90
Identities = 159/216 (73%), Positives = 172/216 (79%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ +GPSG Y+HEFDGDEEFYVDL +KETVWQLPLF +FR FDPQ AL NIA KHNLNI+
Sbjct: 35 QSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIV 94
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
IKRSN+TAA N+VPEVTVF KSPV LGQPNTLIC VDNIFPPV+NITWL NGHSVTEG S
Sbjct: 95 IKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVS 154
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETX 585
ETSFLSK+DHSF KISYLTFLPS D+ YDCKVEHWGLD+PLLKHWEPEIP PMSELTET
Sbjct: 155 ETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWEPEIPTPMSELTETV 214
Query: 586 XXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 693
+GLRS G SRHQG L
Sbjct: 215 VCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 250
>ref|XP_003119477.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 2 [Homo sapiens].
Length = 255
Score = 329 bits (844), Expect = 2e-90
Identities = 159/216 (73%), Positives = 172/216 (79%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ +GPSG Y+HEFDGDEEFYVDL +KETVWQLPLF +FR FDPQ AL NIA KHNLNI+
Sbjct: 40 QSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIV 99
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
IKRSN+TAA N+VPEVTVF KSPV LGQPNTLIC VDNIFPPV+NITWL NGHSVTEG S
Sbjct: 100 IKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVS 159
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETX 585
ETSFLSK+DHSF KISYLTFLPS D+ YDCKVEHWGLD+PLLKHWEPEIP PMSELTET
Sbjct: 160 ETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWEPEIPTPMSELTETV 219
Query: 586 XXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 693
+GLRS G SRHQG L
Sbjct: 220 VCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 255
>ref|XP_003119476.1| PREDICTED: HLA class II histocompatibility antigen, DQ alpha 1
chain-like isoform 1 [Homo sapiens].
Length = 255
Score = 329 bits (844), Expect = 2e-90
Identities = 159/216 (73%), Positives = 172/216 (79%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ +GPSG Y+HEFDGDEEFYVDL +KETVWQLPLF +FR FDPQ AL NIA KHNLNI+
Sbjct: 40 QSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIV 99
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
IKRSN+TAA N+VPEVTVF KSPV LGQPNTLIC VDNIFPPV+NITWL NGHSVTEG S
Sbjct: 100 IKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVS 159
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETX 585
ETSFLSK+DHSF KISYLTFLPS D+ YDCKVEHWGLD+PLLKHWEPEIP PMSELTET
Sbjct: 160 ETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWEPEIPTPMSELTETV 219
Query: 586 XXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 693
+GLRS G SRHQG L
Sbjct: 220 VCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL 255
>ref|NP_064440.1| HLA class II histocompatibility antigen, DQ alpha 2 chain precursor
[Homo sapiens].
Length = 255
Score = 327 bits (837), Expect = 2e-89
Identities = 157/216 (72%), Positives = 170/216 (78%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ HGPSG YTHEFDGDEEFYVDL KETVWQLP+FSKF SFDPQ ALRN+A KH L +
Sbjct: 40 QSHGPSGQYTHEFDGDEEFYVDLETKETVWQLPMFSKFISFDPQSALRNMAVGKHTLEFM 99
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
+++SN+TAA N+VPEVTVF K PV LGQPNTLIC VDNIFPPV+NITWL NGHSVTEG S
Sbjct: 100 MRQSNSTAATNEVPEVTVFSKFPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVS 159
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETX 585
ETSFLSK+DHSF KISYLTFLPS D+ YDCKVEHWGLD+PLLKHWEPEIPAPMSELTET
Sbjct: 160 ETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETL 219
Query: 586 XXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 693
QGLRS G SRHQG L
Sbjct: 220 VCALGLSVGLMGIVVGTVFIIQGLRSVGASRHQGLL 255
Database: RefSeq44_HP.fasta
Posted date: Nov 15, 2010 4:36 PM
Number of letters in database: 18,324,212
Number of sequences in database: 33,950
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: 33950
Number of Hits to DB: 37,788,931
Number of extensions: 918967
Number of successful extensions: 2820
Number of sequences better than 1.0e-05: 117
Number of HSP's gapped: 2762
Number of HSP's successfully gapped: 118
Length of query: 358
Length of database: 18,324,212
Length adjustment: 104
Effective length of query: 254
Effective length of database: 14,793,412
Effective search space: 3757526648
Effective search space used: 3757526648
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 RefSeqMP_Rel44
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= 20070806C-000022
(1075 letters)
Database: RefSeq44_MP.fasta
29,866 sequences; 15,452,059 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_034508.2| histocompatibility 2, class II antigen A, alpha... 295 4e-80
Alignment gi|NP_034511.2| histocompatibility 2, class II antigen E alpha ... 217 1e-56
Alignment gi|XP_003085197.1| PREDICTED: h-2 class II histocompatibility a... 215 5e-56
Alignment gi|NP_032232.2| histocompatibility 2, O region alpha locus [Mus... 210 1e-54
Alignment gi|NP_034516.3| class II histocompatibility antigen, M alpha ch... 79 6e-15
Alignment gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ... 71 2e-12
Alignment gi|NP_033865.2| beta-2-microglobulin precursor [Mus musculus]. 67 2e-11
Alignment gi|NP_034512.2| H-2 class II histocompatibility antigen, I-E be... 64 2e-10
Alignment gi|NP_001029150.1| histocompatibility 2, class II antigen E bet... 64 3e-10
Alignment gi|NP_996988.2| histocompatibility 2, class II antigen A, beta ... 64 3e-10
>ref|NP_034508.2| histocompatibility 2, class II antigen A, alpha precursor [Mus
musculus].
Length = 256
Score = 295 bits (755), Expect = 4e-80
Identities = 141/213 (66%), Positives = 156/213 (73%)
Frame = +1
Query: 55 GPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNILIKR 234
G G YT EFDGDE FYVDL KKETVW LP F + SFDPQG L+NIA KHNL +L KR
Sbjct: 44 GDIGQYTFEFDGDELFYVDLDKKETVWMLPEFGQLASFDPQGGLQNIAVVKHNLGVLTKR 103
Query: 235 SNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETS 414
SN+T A N+ P+ TVFPKSPV+LGQPNTLIC VDNIFPPVINITWL+N SV +G ETS
Sbjct: 104 SNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETS 163
Query: 415 FLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETXXXX 594
F D+SF K+SYLTF+PSDDD YDCKVEHWGL++P+LKHWEPEIPAPMSELTET
Sbjct: 164 FFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEPEIPAPMSELTETVVCA 223
Query: 595 XXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 693
QGLRSGG SRH G L
Sbjct: 224 LGLSVGLVGIVVGTIFIIQGLRSGGTSRHPGPL 256
>ref|NP_034511.2| histocompatibility 2, class II antigen E alpha precursor [Mus
musculus].
Length = 255
Score = 217 bits (553), Expect = 1e-56
Identities = 100/172 (58%), Positives = 125/172 (72%)
Frame = +1
Query: 64 GYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNN 243
G + +FDGDE F+VD+ K ET+W+L F+KF SF+ QGAL NIA K NL+++ +RSNN
Sbjct: 45 GEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLDVMKERSNN 104
Query: 244 TAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLS 423
T N PEVTV +SPV LG+PN LIC +D PPV+N+TW +NG VTEG SET FL
Sbjct: 105 TPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWFRNGRPVTEGVSETVFLP 164
Query: 424 KNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 579
++DH F K YLTFLPS DDFYDC+V+HWGL++PL KHWE E + E TE
Sbjct: 165 RDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEEPLRKHWEFEEKTLLPETTE 216
>ref|XP_003085197.1| PREDICTED: h-2 class II histocompatibility antigen, E-K alpha
chain-like [Mus musculus].
Length = 276
Score = 215 bits (547), Expect = 5e-56
Identities = 99/172 (57%), Positives = 125/172 (72%)
Frame = +1
Query: 64 GYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSNN 243
G + +FDGDE F+VD+ K ET+W+L F+KF SF+ QGAL NIA K NL+++ +RSNN
Sbjct: 66 GEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLDVMKERSNN 125
Query: 244 TAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLS 423
T N PEVTV +SPV LG+PN LIC +D PPV+N+TWL+NG VTEG SET FL
Sbjct: 126 TPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWLRNGRPVTEGVSETVFLP 185
Query: 424 KNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 579
++DH F K +LTFLPS DDFYDC+V+HWGL++PL KHWE E + E E
Sbjct: 186 RDDHLFRKFHFLTFLPSTDDFYDCEVDHWGLEEPLRKHWEFEEKTLLPETKE 237
>ref|NP_032232.2| histocompatibility 2, O region alpha locus [Mus musculus].
Length = 250
Score = 210 bits (535), Expect = 1e-54
Identities = 97/179 (54%), Positives = 128/179 (71%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ + SG +THEFDG++ F VDL +E VW+LP F F D Q L +I+ K +L+IL
Sbjct: 40 QSYDASGQFTHEFDGEQIFSVDLKNEEVVWRLPEFGDFAHSDFQSGLMSISMIKAHLDIL 99
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
++RSN T AV+ P VTV PK+ V LG+PN LIC VD+IFPPVIN+TWL+N +T+G +
Sbjct: 100 VERSNRTRAVSVPPRVTVLPKTRVELGKPNVLICIVDDIFPPVINVTWLRNSQPITKGVA 159
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 582
+TSF S+ +H F K YLTF+PS +D YDCKVEHWGLD PLL+HWEP++ P + ET
Sbjct: 160 QTSFYSQPNHRFRKFHYLTFVPSAEDVYDCKVEHWGLDTPLLQHWEPQVLTPPPDTIET 218
>ref|NP_034516.3| class II histocompatibility antigen, M alpha chain precursor [Mus
musculus].
Length = 261
Score = 79.0 bits (193), Expect = 6e-15
Identities = 54/171 (31%), Positives = 78/171 (45%), Gaps = 5/171 (2%)
Frame = +1
Query: 82 FDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNILI-----KRSNNT 246
+D DE F D + V +LP F+++ QG IA K +L+ K
Sbjct: 63 YDEDELFSFDFSQNTRVPRLPDFAEWAQ--GQGDASAIAFDKSFCEMLMREVSPKLEGQI 120
Query: 247 AAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSK 426
+P VF P+ G+PNTL+C + N+FPP + + W + V EG S TS +
Sbjct: 121 PVSRGLPVAEVFTLKPLEFGKPNTLVCFISNLFPPTLTVNWQLHSAPV-EGASPTSISAV 179
Query: 427 NDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 579
+ +F SYL F P D Y C V H + +W P+ P S+L E
Sbjct: 180 DGLTFQAFSYLNFTPEPFDLYSCTVTHEIDRYTAIAYWVPQNALP-SDLLE 229
>ref|NP_034519.2| histocompatibility 2, O region beta locus [Mus musculus].
Length = 271
Score = 70.9 bits (172), Expect = 2e-12
Identities = 35/99 (35%), Positives = 48/99 (48%)
Frame = +1
Query: 244 TAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLS 423
T N PEVTV+P+ +L Q N L+C V +P I++ W +NG G T +
Sbjct: 116 TVERNVPPEVTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVR 175
Query: 424 KNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHW 540
D +F L +P D Y C VEH GL +P+ W
Sbjct: 176 NGDWTFQTTVMLEMIPELGDIYSCLVEHPGLLRPVSVAW 214
>ref|NP_033865.2| beta-2-microglobulin precursor [Mus musculus].
Length = 119
Score = 67.4 bits (163), Expect = 2e-11
Identities = 33/102 (32%), Positives = 57/102 (55%), Gaps = 1/102 (0%)
Frame = +1
Query: 250 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTE-GFSETSFLSK 426
A+ + P++ V+ + P G+PN L C+V PP I I LKNG + + S+ SF
Sbjct: 20 AIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSF--S 77
Query: 427 NDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEI 552
D SF +++ F P++ D Y C+V+H + +P +W+ ++
Sbjct: 78 KDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM 119
>ref|NP_034512.2| H-2 class II histocompatibility antigen, I-E beta chain precursor
[Mus musculus].
Length = 264
Score = 63.9 bits (154), Expect = 2e-10
Identities = 29/103 (28%), Positives = 48/103 (46%)
Frame = +1
Query: 265 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 444
P VTV+P L N L+C V + +P I + W +NG G T + D +F
Sbjct: 124 PTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQ 183
Query: 445 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 573
+ L +P + Y C+VEH L P+ W+ + + +++
Sbjct: 184 TLVMLETVPQSGEVYTCQVEHPSLTDPVTVEWKAQSTSAQNKM 226
>ref|NP_001029150.1| histocompatibility 2, class II antigen E beta2 [Mus musculus].
Length = 287
Score = 63.5 bits (153), Expect = 3e-10
Identities = 29/103 (28%), Positives = 47/103 (45%)
Frame = +1
Query: 265 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 444
P+VTV+P L N L+C V + +P I + W +NG G T + D ++
Sbjct: 125 PKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNRDWTYQ 184
Query: 445 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 573
+ L +P + Y C+VEH L P+ W + ++L
Sbjct: 185 TLVMLEMVPRGGEVYTCQVEHPSLTSPVTVEWRARSTSAQNKL 227
>ref|NP_996988.2| histocompatibility 2, class II antigen A, beta 1 precursor [Mus
musculus].
Length = 265
Score = 63.5 bits (153), Expect = 3e-10
Identities = 30/103 (29%), Positives = 45/103 (43%)
Frame = +1
Query: 265 PEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSFL 444
P V + L NTL+C V + +P I + W +NG T G S T + D +F
Sbjct: 125 PNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQ 184
Query: 445 KISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSEL 573
+ L P + Y C VEH L P+ W + + S++
Sbjct: 185 VLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRAQSESAWSKM 227
Database: RefSeq44_MP.fasta
Posted date: Nov 15, 2010 4:36 PM
Number of letters in database: 15,452,059
Number of sequences in database: 29,866
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: 29866
Number of Hits to DB: 31,703,423
Number of extensions: 765157
Number of successful extensions: 2221
Number of sequences better than 1.0e-05: 24
Number of HSP's gapped: 2211
Number of HSP's successfully gapped: 24
Length of query: 358
Length of database: 15,452,059
Length adjustment: 102
Effective length of query: 256
Effective length of database: 12,405,727
Effective search space: 3175866112
Effective search space used: 3175866112
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 RefSeqSP_Rel44
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= 20070806C-000022
(1075 letters)
Database: RefSeq44_SP.fasta
20,576 sequences; 9,542,844 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001123696.1| SLA class II histocompatibility antigen, DQ ... 391 e-109
Alignment gi|NP_001107534.2| SLA class II histocompatibility antigen, DQ ... 364 e-101
Alignment gi|NP_001172072.1| MHC class II antigen [Sus scrofa]. 240 7e-64
Alignment gi|NP_001107178.1| MHC class II DR-alpha [Sus scrofa]. 224 5e-59
Alignment gi|NP_001107177.1| major histocompatibility complex, class II, ... 74 1e-13
Alignment gi|NP_001004039.1| SLA-DM alpha chain [Sus scrofa]. 74 1e-13
Alignment gi|XP_003121588.1| PREDICTED: beta-2-microglobulin-like isoform... 71 8e-13
Alignment gi|XP_003121587.1| PREDICTED: beta-2-microglobulin-like isoform... 71 8e-13
Alignment gi|XP_003121585.1| PREDICTED: beta-2-microglobulin-like isoform... 71 8e-13
Alignment gi|XP_003121584.1| PREDICTED: beta-2-microglobulin-like isoform... 71 8e-13
>ref|NP_001123696.1| SLA class II histocompatibility antigen, DQ haplotype D alpha chain
precursor [Sus scrofa].
Length = 255
Score = 391 bits (1005), Expect = e-109
Identities = 189/216 (87%), Positives = 191/216 (88%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ +GPSGYYTHEFDGDEEFYVDL KKETVWQLPLFSKF SFDPQGALRNIATAKHNLNIL
Sbjct: 40 QSYGPSGYYTHEFDGDEEFYVDLEKKETVWQLPLFSKFTSFDPQGALRNIATAKHNLNIL 99
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS
Sbjct: 100 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 159
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETX 585
ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET
Sbjct: 160 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETV 219
Query: 586 XXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 693
QGLRSGGPSRHQGSL
Sbjct: 220 VCALGLIVGLVGIVVGTVFIIQGLRSGGPSRHQGSL 255
>ref|NP_001107534.2| SLA class II histocompatibility antigen, DQ haplotype C alpha chain
precursor [Sus scrofa].
Length = 254
Score = 364 bits (935), Expect = e-101
Identities = 177/216 (81%), Positives = 186/216 (86%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ +GPSGY+THEFDGDEEFYVDL KKETVW+LPLFS+F SFDPQGALRNIAT KHNLNI+
Sbjct: 40 QSYGPSGYFTHEFDGDEEFYVDLEKKETVWRLPLFSEFTSFDPQGALRNIATLKHNLNIV 99
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
KRSNNTAAVNQVPEVTVF KSPV+LGQPNTLICHVD+IFPPVINITWLKNGHSV +GFS
Sbjct: 100 TKRSNNTAAVNQVPEVTVFSKSPVILGQPNTLICHVDSIFPPVINITWLKNGHSV-KGFS 158
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETX 585
ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET
Sbjct: 159 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETV 218
Query: 586 XXXXXXXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 693
QGL SGGPSRHQGSL
Sbjct: 219 VCALGLIVGLVGIVVGTVFIIQGLLSGGPSRHQGSL 254
>ref|NP_001172072.1| MHC class II antigen [Sus scrofa].
Length = 250
Score = 240 bits (613), Expect = 7e-64
Identities = 109/179 (60%), Positives = 136/179 (75%)
Frame = +1
Query: 46 EEHGPSGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNIL 225
+ + SG +T++FDG++ F VDL K+E VW+LP FS F FDPQ LR IA + +L++L
Sbjct: 40 QSYDGSGQFTYDFDGEQLFSVDLKKREAVWRLPEFSNFADFDPQNGLRGIALIRAHLDVL 99
Query: 226 IKRSNNTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFS 405
++RSN+T A N P VTV PKSPV LGQPN LIC VDNIFPPVINITWL NG +VTEG +
Sbjct: 100 VERSNHTRATNVPPRVTVLPKSPVALGQPNVLICIVDNIFPPVINITWLHNGQTVTEGVT 159
Query: 406 ETSFLSKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTET 582
+TSF ++ DHSF K YLTF+PS DFYDCKVEHWGLD+PL HWEP++ P+ + TET
Sbjct: 160 QTSFYAQPDHSFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWEPQVTMPLPDTTET 218
>ref|NP_001107178.1| MHC class II DR-alpha [Sus scrofa].
Length = 252
Score = 224 bits (571), Expect = 5e-59
Identities = 110/211 (52%), Positives = 131/211 (62%)
Frame = +1
Query: 61 SGYYTHEFDGDEEFYVDLGKKETVWQLPLFSKFRSFDPQGALRNIATAKHNLNILIKRSN 240
SG + +FDGDE F+VD+ K+ETVW+L F F SF+ QGAL NIA K NL ILIKRSN
Sbjct: 42 SGEFMFDFDGDEIFHVDMEKRETVWRLEEFGHFASFEAQGALANIAVDKANLEILIKRSN 101
Query: 241 NTAAVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFL 420
NT N PEVTV PV LG+PN LIC +D PPV+N+TWL+NG VT G SET FL
Sbjct: 102 NTPNTNVPPEVTVLSDKPVELGEPNILICFIDKFSPPVVNVTWLRNGSPVTRGVSETVFL 161
Query: 421 SKNDHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTETXXXXXX 600
+ DH F K YL F+PS +D YDC+VEHWGLDKPLLKHWE E P+ E TE
Sbjct: 162 PREDHLFRKFHYLPFMPSTEDVYDCQVEHWGLDKPLLKHWEFEAQTPLPETTENTVCALG 221
Query: 601 XXXXXXXXXXXXXXXXQGLRSGGPSRHQGSL 693
+G+R G + +G L
Sbjct: 222 LIVALVGIIVGTVLIIKGVRKGNATERRGPL 252
>ref|NP_001107177.1| major histocompatibility complex, class II, DO alpha [Sus scrofa].
Length = 260
Score = 73.9 bits (180), Expect = 1e-13
Identities = 38/106 (35%), Positives = 56/106 (52%)
Frame = +1
Query: 262 VPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSF 441
+P VF P+ G+PNTL+C V N+FPP + +TW ++ + EG T + +D SF
Sbjct: 126 LPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTW-EHHSAPVEGIGPTFVSATDDLSF 184
Query: 442 LKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 579
SYL F P+ D + C V H + +W P+ P S+L E
Sbjct: 185 QAFSYLNFTPTPSDLFSCVVTHELDGYVAISYWVPQNALP-SDLLE 229
>ref|NP_001004039.1| SLA-DM alpha chain [Sus scrofa].
Length = 260
Score = 73.9 bits (180), Expect = 1e-13
Identities = 38/106 (35%), Positives = 56/106 (52%)
Frame = +1
Query: 262 VPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKNDHSF 441
+P VF P+ G+PNTL+C V N+FPP + +TW ++ + EG T + +D SF
Sbjct: 126 LPIAEVFTLKPLEFGKPNTLVCFVSNLFPPALTVTW-EHHSAPVEGIGPTFVSATDDLSF 184
Query: 442 LKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWEPEIPAPMSELTE 579
SYL F P+ D + C V H + +W P+ P S+L E
Sbjct: 185 QAFSYLNFTPTPSDLFSCVVTHELDGYVAISYWVPQNALP-SDLLE 229
>ref|XP_003121588.1| PREDICTED: beta-2-microglobulin-like isoform 5 [Sus scrofa].
Length = 118
Score = 71.2 bits (173), Expect = 8e-13
Identities = 38/98 (38%), Positives = 53/98 (54%)
Frame = +1
Query: 250 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN 429
AV + P+V V+ + P G+PN L C+V PP I I LKNG + S+ SF
Sbjct: 20 AVARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SK 77
Query: 430 DHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 543
D SF + + F P+ D Y C+V+H LDKP + W+
Sbjct: 78 DWSFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 115
>ref|XP_003121587.1| PREDICTED: beta-2-microglobulin-like isoform 4 [Sus scrofa].
Length = 118
Score = 71.2 bits (173), Expect = 8e-13
Identities = 38/98 (38%), Positives = 53/98 (54%)
Frame = +1
Query: 250 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN 429
AV + P+V V+ + P G+PN L C+V PP I I LKNG + S+ SF
Sbjct: 20 AVARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SK 77
Query: 430 DHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 543
D SF + + F P+ D Y C+V+H LDKP + W+
Sbjct: 78 DWSFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 115
>ref|XP_003121585.1| PREDICTED: beta-2-microglobulin-like isoform 2 [Sus scrofa].
Length = 118
Score = 71.2 bits (173), Expect = 8e-13
Identities = 38/98 (38%), Positives = 53/98 (54%)
Frame = +1
Query: 250 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN 429
AV + P+V V+ + P G+PN L C+V PP I I LKNG + S+ SF
Sbjct: 20 AVARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SK 77
Query: 430 DHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 543
D SF + + F P+ D Y C+V+H LDKP + W+
Sbjct: 78 DWSFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 115
>ref|XP_003121584.1| PREDICTED: beta-2-microglobulin-like isoform 1 [Sus scrofa].
Length = 118
Score = 71.2 bits (173), Expect = 8e-13
Identities = 38/98 (38%), Positives = 53/98 (54%)
Frame = +1
Query: 250 AVNQVPEVTVFPKSPVMLGQPNTLICHVDNIFPPVINITWLKNGHSVTEGFSETSFLSKN 429
AV + P+V V+ + P G+PN L C+V PP I I LKNG + S+ SF
Sbjct: 20 AVARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SK 77
Query: 430 DHSFLKISYLTFLPSDDDFYDCKVEHWGLDKPLLKHWE 543
D SF + + F P+ D Y C+V+H LDKP + W+
Sbjct: 78 DWSFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWD 115
Database: RefSeq44_SP.fasta
Posted date: Nov 15, 2010 4:36 PM
Number of letters in database: 9,542,844
Number of sequences in database: 20,576
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: 20576
Number of Hits to DB: 19,797,957
Number of extensions: 481855
Number of successful extensions: 1270
Number of sequences better than 1.0e-05: 30
Number of HSP's gapped: 1251
Number of HSP's successfully gapped: 30
Length of query: 358
Length of database: 9,542,844
Length adjustment: 99
Effective length of query: 259
Effective length of database: 7,505,820
Effective search space: 1944007380
Effective search space used: 1944007380
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)