Search to RefSeqHP
BLASTX 2.2.10 [Oct-19-2004]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20060611S-000638
(1339 letters)
Database: RefSeqHP
39,411 sequences; 17,774,539 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_004039.1| beta-2-microglobulin precursor [Homo sapiens] 120 5e-31
Alignment gi|NP_291032.2| major histocompatibility complex, class II, DP ... 53 5e-07
Alignment gi|NP_002113.2| major histocompatibility complex, class II, DQ ... 53 5e-07
Alignment gi|NP_064440.1| major histocompatibility complex, class II, DQ ... 52 9e-07
Alignment gi|XP_941306.1| PREDICTED: similar to HLA class II histocompati... 52 2e-06
Alignment gi|XP_941305.1| PREDICTED: similar to HLA class II histocompati... 52 2e-06
Alignment gi|XP_941304.1| PREDICTED: similar to HLA class II histocompati... 52 2e-06
Alignment gi|XP_941255.1| PREDICTED: similar to HLA class II histocompati... 52 2e-06
Alignment gi|XP_941303.1| PREDICTED: similar to HLA class II histocompati... 52 2e-06
Alignment gi|XP_941302.1| PREDICTED: similar to HLA class II histocompati... 52 2e-06
>ref|NP_004039.1| beta-2-microglobulin precursor [Homo sapiens]
Length = 119
Score = 120 bits (301), Expect(2) = 5e-31
Identities = 55/70 (78%), Positives = 61/70 (87%), Gaps = 1/70 (1%)
Frame = +1
Query: 94 RPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKM-NAEQSDLSFSKDWSF 270
R PK+QVYSRHPAENGK N+LNCYVSGFHP IE+DLLKNGE++ E SDLSFSKDWSF
Sbjct: 23 RTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSF 82
Query: 271 YLLVHTEFTP 300
YLL +TEFTP
Sbjct: 83 YLLYYTEFTP 92
Score = 33.5 bits (75), Expect(2) = 5e-31
Identities = 13/15 (86%), Positives = 14/15 (93%)
Frame = +2
Query: 314 HVTLDKPKIVKWDRD 358
HVTL +PKIVKWDRD
Sbjct: 104 HVTLSQPKIVKWDRD 118
>ref|NP_291032.2| major histocompatibility complex, class II, DP alpha 1 precursor
[Homo sapiens]
Length = 260
Score = 53.1 bits (126), Expect = 5e-07
Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Frame = +1
Query: 97 PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSF 270
PP+V V+ + P E G+PN L C++ F PP + + L NGE + ++ F D+SF
Sbjct: 117 PPEVTVFPKEPVELGQPNTLICHIDKFFPPVLNVTWLCNGELVTEGVAESLFLPRTDYSF 176
Query: 271 YLLVHTEFTPNAVEARDSR 327
+ + F P+A + D R
Sbjct: 177 HKFHYLTFVPSAEDFYDCR 195
>ref|NP_002113.2| major histocompatibility complex, class II, DQ alpha 1 precursor
[Homo sapiens]
Length = 255
Score = 53.1 bits (126), Expect = 5e-07
Identities = 28/78 (35%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Frame = +1
Query: 100 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 273
P+V V+S+ P G+PN L C V PP + I L NG+ + S+ SF D SF+
Sbjct: 113 PEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGQSVTEGVSETSFLSKSDHSFF 172
Query: 274 LLVHTEFTPNAVEARDSR 327
+ + F P+A E D +
Sbjct: 173 KISYLTFLPSADEIYDCK 190
>ref|NP_064440.1| major histocompatibility complex, class II, DQ alpha 2 [Homo
sapiens]
Length = 255
Score = 52.4 bits (124), Expect = 9e-07
Identities = 28/78 (35%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Frame = +1
Query: 100 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 273
P+V V+S+ P G+PN L C V PP + I L NG + S+ SF D SF+
Sbjct: 113 PEVTVFSKFPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 172
Query: 274 LLVHTEFTPNAVEARDSR 327
+ + F P+A E D +
Sbjct: 173 KISYLTFLPSADEIYDCK 190
>ref|XP_941306.1| PREDICTED: similar to HLA class II histocompatibility antigen,
DQ(3) alpha chain precursor (DC-alpha) (HLA-DCA)
(HLA-DQA1*05011) (HLA-DQA1*0502) isoform 10 [Homo
sapiens]
Length = 254
Score = 51.6 bits (122), Expect = 2e-06
Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Frame = +1
Query: 100 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 273
P+V V+S+ P G+PN L C V PP + I L NG + S+ SF D SF+
Sbjct: 112 PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 171
Query: 274 LLVHTEFTPNAVEARDSR 327
+ + P+A E+ D +
Sbjct: 172 KISYLTLLPSAEESYDCK 189
>ref|XP_941305.1| PREDICTED: similar to HLA class II histocompatibility antigen,
DQ(3) alpha chain precursor (DC-alpha) (HLA-DCA)
(HLA-DQA1*05011) (HLA-DQA1*0502) isoform 9 [Homo
sapiens]
Length = 254
Score = 51.6 bits (122), Expect = 2e-06
Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Frame = +1
Query: 100 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 273
P+V V+S+ P G+PN L C V PP + I L NG + S+ SF D SF+
Sbjct: 112 PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 171
Query: 274 LLVHTEFTPNAVEARDSR 327
+ + P+A E+ D +
Sbjct: 172 KISYLTLLPSAEESYDCK 189
>ref|XP_941304.1| PREDICTED: similar to HLA class II histocompatibility antigen,
DQ(3) alpha chain precursor (DC-alpha) (HLA-DCA)
(HLA-DQA1*05011) (HLA-DQA1*0502) isoform 8 [Homo
sapiens]
Length = 254
Score = 51.6 bits (122), Expect = 2e-06
Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Frame = +1
Query: 100 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 273
P+V V+S+ P G+PN L C V PP + I L NG + S+ SF D SF+
Sbjct: 112 PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 171
Query: 274 LLVHTEFTPNAVEARDSR 327
+ + P+A E+ D +
Sbjct: 172 KISYLTLLPSAEESYDCK 189
>ref|XP_941255.1| PREDICTED: similar to HLA class II histocompatibility antigen,
DQ(3) alpha chain precursor (DC-alpha) (HLA-DCA)
(HLA-DQA1*05011) (HLA-DQA1*0502) isoform 1 [Homo
sapiens]
Length = 254
Score = 51.6 bits (122), Expect = 2e-06
Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Frame = +1
Query: 100 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 273
P+V V+S+ P G+PN L C V PP + I L NG + S+ SF D SF+
Sbjct: 112 PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 171
Query: 274 LLVHTEFTPNAVEARDSR 327
+ + P+A E+ D +
Sbjct: 172 KISYLTLLPSAEESYDCK 189
>ref|XP_941303.1| PREDICTED: similar to HLA class II histocompatibility antigen,
DQ(3) alpha chain precursor (DC-alpha) (HLA-DCA)
(HLA-DQA1*05011) (HLA-DQA1*0502) isoform 7 [Homo
sapiens]
Length = 172
Score = 51.6 bits (122), Expect = 2e-06
Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Frame = +1
Query: 100 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 273
P+V V+S+ P G+PN L C V PP + I L NG + S+ SF D SF+
Sbjct: 30 PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 89
Query: 274 LLVHTEFTPNAVEARDSR 327
+ + P+A E+ D +
Sbjct: 90 KISYLTLLPSAEESYDCK 107
>ref|XP_941302.1| PREDICTED: similar to HLA class II histocompatibility antigen,
DQ(3) alpha chain precursor (DC-alpha) (HLA-DCA)
(HLA-DQA1*05011) (HLA-DQA1*0502) isoform 6 [Homo
sapiens]
Length = 172
Score = 51.6 bits (122), Expect = 2e-06
Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Frame = +1
Query: 100 PKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSFY 273
P+V V+S+ P G+PN L C V PP + I L NG + S+ SF D SF+
Sbjct: 30 PEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFF 89
Query: 274 LLVHTEFTPNAVEARDSR 327
+ + P+A E+ D +
Sbjct: 90 KISYLTLLPSAEESYDCK 107
Database: RefSeqHP
Posted date: Aug 2, 2006 12:57 AM
Number of letters in database: 17,774,539
Number of sequences in database: 39,411
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 45,100,245
Number of Sequences: 39411
Number of extensions: 1030950
Number of successful extensions: 3004
Number of sequences better than 1.0e-05: 10
Number of HSP's better than 0.0 without gapping: 2783
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 2999
length of database: 17,774,539
effective HSP length: 105
effective length of database: 13,636,384
effective search space used: 4636370560
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
Search to RefSeqCP
BLASTX 2.2.10 [Oct-19-2004]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20060611S-000638
(1339 letters)
Database: RefSeqCP
33,732 sequences; 19,266,565 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|XP_535458.1| PREDICTED: similar to beta-2-microglobulin prec... 140 3e-37
Alignment gi|XP_850148.1| PREDICTED: similar to beta-2-microglobulin prec... 140 3e-37
Alignment gi|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris] 50 4e-06
>ref|XP_535458.1| PREDICTED: similar to beta-2-microglobulin precursor isoform 2
[Canis familiaris]
Length = 125
Score = 140 bits (354), Expect(2) = 3e-37
Identities = 61/69 (88%), Positives = 68/69 (98%)
Frame = +1
Query: 97 PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWSFYL 276
PPK+QVYSRHPAENGKPN+LNCYVSGFHPP+IEIDLLKNG++M AEQ+DLSFSKDW+FYL
Sbjct: 31 PPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSFSKDWTFYL 90
Query: 277 LVHTEFTPN 303
LVHTEFTPN
Sbjct: 91 LVHTEFTPN 99
Score = 34.3 bits (77), Expect(2) = 3e-37
Identities = 13/17 (76%), Positives = 16/17 (94%)
Frame = +2
Query: 311 KHVTLDKPKIVKWDRDH 361
KHVTL +P+IVKWDRD+
Sbjct: 109 KHVTLSEPQIVKWDRDN 125
>ref|XP_850148.1| PREDICTED: similar to beta-2-microglobulin precursor isoform 3
[Canis familiaris]
Length = 125
Score = 140 bits (354), Expect(2) = 3e-37
Identities = 61/69 (88%), Positives = 68/69 (98%)
Frame = +1
Query: 97 PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWSFYL 276
PPK+QVYSRHPAENGKPN+LNCYVSGFHPP+IEIDLLKNG++M AEQ+DLSFSKDW+FYL
Sbjct: 31 PPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMKAEQTDLSFSKDWTFYL 90
Query: 277 LVHTEFTPN 303
LVHTEFTPN
Sbjct: 91 LVHTEFTPN 99
Score = 34.3 bits (77), Expect(2) = 3e-37
Identities = 13/17 (76%), Positives = 16/17 (94%)
Frame = +2
Query: 311 KHVTLDKPKIVKWDRDH 361
KHVTL +P+IVKWDRD+
Sbjct: 109 KHVTLSEPQIVKWDRDN 125
>ref|NP_001011723.1| MHC class II DR alpha chain [Canis familiaris]
Length = 254
Score = 50.4 bits (119), Expect = 4e-06
Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 2/79 (2%)
Frame = +1
Query: 97 PPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSF--SKDWSF 270
PP+V V S P E G+PN L C++ F PP I + L+NG + S+ F +D F
Sbjct: 111 PPEVTVLSNTPVELGEPNILICFIDKFSPPVINVTWLRNGNPVTTGVSETIFLPREDHLF 170
Query: 271 YLLVHTEFTPNAVEARDSR 327
+ F P+A + D +
Sbjct: 171 RKFHYLPFLPSAEDVYDCK 189
Database: RefSeqCP
Posted date: Aug 1, 2006 9:25 PM
Number of letters in database: 19,266,565
Number of sequences in database: 33,732
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 47,710,806
Number of Sequences: 33732
Number of extensions: 1077181
Number of successful extensions: 3016
Number of sequences better than 1.0e-05: 3
Number of HSP's better than 0.0 without gapping: 2832
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 3007
length of database: 19,266,565
effective HSP length: 106
effective length of database: 15,690,973
effective search space used: 5319239847
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
Search to RefSeqMP
BLASTX 2.2.10 [Oct-19-2004]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20060611S-000638
(1339 letters)
Database: RefSeqMP
45,328 sequences; 21,768,885 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_033865.2| beta-2-microglobulin [Mus musculus] 114 5e-27
>ref|NP_033865.2| beta-2-microglobulin [Mus musculus]
Length = 119
Score = 114 bits (286), Expect(2) = 5e-27
Identities = 50/74 (67%), Positives = 60/74 (81%), Gaps = 1/74 (1%)
Frame = +1
Query: 94 RPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKM-NAEQSDLSFSKDWSF 270
+ P++QVYSRHP ENGKPN LNCYV+ FHPP IEI +LKNG+K+ E SD+SFSKDWSF
Sbjct: 23 KTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSF 82
Query: 271 YLLVHTEFTPNAVE 312
Y+L HTEFTP +
Sbjct: 83 YILAHTEFTPTETD 96
Score = 26.2 bits (56), Expect(2) = 5e-27
Identities = 9/16 (56%), Positives = 12/16 (75%)
Frame = +2
Query: 311 KHVTLDKPKIVKWDRD 358
KH ++ +PK V WDRD
Sbjct: 103 KHASMAEPKTVYWDRD 118
Database: RefSeqMP
Posted date: Aug 2, 2006 12:58 AM
Number of letters in database: 21,768,885
Number of sequences in database: 45,328
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 54,560,045
Number of Sequences: 45328
Number of extensions: 1229451
Number of successful extensions: 3288
Number of sequences better than 1.0e-05: 1
Number of HSP's better than 0.0 without gapping: 3060
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 3285
length of database: 21,768,885
effective HSP length: 107
effective length of database: 16,918,789
effective search space used: 5718550682
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)