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-027492
(983 letters)
Database: RefSeqSP
1040 sequences; 434,620 total letters
Searching...done
***** No hits found ******
Database: RefSeqSP
Posted date: Aug 1, 2006 7:14 PM
Number of letters in database: 434,620
Number of sequences in database: 1040
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 775,610
Number of Sequences: 1040
Number of extensions: 16193
Number of successful extensions: 33
Number of sequences better than 1.0e-05: 0
Number of HSP's better than 0.0 without gapping: 32
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): 33
length of database: 434,620
effective HSP length: 77
effective length of database: 354,540
effective search space used: 88635000
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
Search to RefSeqBP
BLASTX 2.2.10 [Oct-19-2004]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20060611S-027492
(983 letters)
Database: RefSeqBP
33,508 sequences; 16,112,626 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001029840.2| MHC class II antigen [Bos taurus] 116 1e-27
Alignment gi|NP_001012694.1| major histocompatibility complex, class II, ... 116 2e-26
Alignment gi|NP_001030383.1| ribosomal protein L5 [Bos taurus] 67 1e-14
Alignment gi|NP_001012698.2| major histocompatibility complex, class II, ... 78 1e-14
Alignment gi|NP_001012697.1| major histocompatibility complex, class II, ... 72 9e-13
Alignment gi|XP_582099.2| PREDICTED: similar to major histocompatibility ... 70 3e-12
Alignment gi|NP_001013618.1| major histocompatibility complex, class II, ... 69 4e-12
Alignment gi|XP_587461.2| PREDICTED: similar to 60S ribosomal protein L5 ... 59 2e-10
Alignment gi|XP_869064.1| PREDICTED: similar to 60S ribosomal protein L5 ... 59 2e-10
Alignment gi|XP_582668.2| PREDICTED: similar to 60S ribosomal protein L5 ... 39 9e-06
>ref|NP_001029840.2| MHC class II antigen [Bos taurus]
Length = 261
Score = 116 bits (291), Expect(2) = 1e-27
Identities = 55/75 (73%), Positives = 63/75 (84%)
Frame = +1
Query: 49 MSGMVALRLPRGLWTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVT 228
MSGMVAL +PRGLWTA + V LV+L P AEGRDSP+DFV QFKG CY NGT+RVR+VT
Sbjct: 1 MSGMVALWIPRGLWTAVVMVTLVMLSTPGAEGRDSPKDFVVQFKGLCYFTNGTERVRYVT 60
Query: 229 RYIYNQNEHVRYDSD 273
RYIYNQ E+VR+DSD
Sbjct: 61 RYIYNQEEYVRFDSD 75
Score = 25.4 bits (54), Expect(2) = 1e-27
Identities = 9/19 (47%), Positives = 13/19 (68%)
Frame = +2
Query: 275 WVDFQEMTPLGQPDKHYRN 331
W ++ +TPLG+PD Y N
Sbjct: 76 WDLYRALTPLGRPDAEYWN 94
>ref|NP_001012694.1| major histocompatibility complex, class II, DQ beta [Bos taurus]
Length = 261
Score = 116 bits (291), Expect = 2e-26
Identities = 56/77 (72%), Positives = 61/77 (79%)
Frame = +1
Query: 49 MSGMVALRLPRGLWTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVT 228
MSGMVALR+PRGLWTAA+ V L VL P AEGRDSPQD V F G+CY NGT+RVR+VT
Sbjct: 1 MSGMVALRIPRGLWTAAVMVTLAVLSTPGAEGRDSPQDTVVHFMGQCYFTNGTERVRYVT 60
Query: 229 RYIYNQNEHVRYDSDVG 279
RYIYNQ E YDSDVG
Sbjct: 61 RYIYNQEETAYYDSDVG 77
>ref|NP_001030383.1| ribosomal protein L5 [Bos taurus]
Length = 297
Score = 67.4 bits (163), Expect(2) = 1e-14
Identities = 40/85 (47%), Positives = 47/85 (55%)
Frame = +2
Query: 332 GVMVGLTKYCAPHSIVLMLAHTFLNRFSMHHINERNSEVTGDENDEYRIKSQPDSPNC*M 511
GV VGLT Y A + L+LA LNRF M I E EVTGDE + I QP + C +
Sbjct: 87 GVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYL 146
Query: 512 HT*LAQITTSKKVFETLTVAKNGGL 586
LA+ TT KVF L A +GGL
Sbjct: 147 DAGLARTTTGNKVFGALKGAVDGGL 171
Score = 30.8 bits (68), Expect(2) = 1e-14
Identities = 15/33 (45%), Positives = 20/33 (60%)
Frame = +1
Query: 604 TKRCPEYDSKITDSTAELHRKSDQEHIDSDYKR 702
TKR P YDS+ + +AE+HRK +DY R
Sbjct: 177 TKRFPGYDSESKEFSAEVHRKHIMGQNVADYMR 209
>ref|NP_001012698.2| major histocompatibility complex, class II, DRB3 [Bos taurus]
Length = 266
Score = 77.8 bits (190), Expect = 1e-14
Identities = 39/74 (52%), Positives = 48/74 (64%)
Frame = +1
Query: 58 MVALRLPRGLWTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVTRYI 237
MV L G W AAL VML+VL PLA R+ F+ +KGEC+ FNGT+RVR + R+
Sbjct: 1 MVCLYFSGGSWMAALIVMLMVLCPPLAWAREIQPHFLEYYKGECHFFNGTERVRFLDRHF 60
Query: 238 YNQNEHVRYDSDVG 279
YN E VR+DSD G
Sbjct: 61 YNGEEFVRFDSDWG 74
>ref|NP_001012697.1| major histocompatibility complex, class II, DY beta [Bos taurus]
Length = 259
Score = 71.6 bits (174), Expect = 9e-13
Identities = 38/71 (53%), Positives = 47/71 (66%), Gaps = 2/71 (2%)
Frame = +1
Query: 73 LPRGLWTAALTVMLV--VLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVTRYIYNQ 246
+PR T A VM V VL P A RD+P++FVYQFKG CY NGT+ VR V R IYN+
Sbjct: 5 IPRNPGTVAGMVMAVFLVLRIPEAHCRDAPKNFVYQFKGMCYFTNGTEHVRLVARQIYNK 64
Query: 247 NEHVRYDSDVG 279
E + +DSD+G
Sbjct: 65 EEILHFDSDLG 75
>ref|XP_582099.2| PREDICTED: similar to major histocompatibility complex, class II,
DR beta 5 precursor [Bos taurus]
Length = 255
Score = 70.1 bits (170), Expect = 3e-12
Identities = 32/62 (51%), Positives = 42/62 (67%)
Frame = +1
Query: 94 AALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVTRYIYNQNEHVRYDSD 273
AAL V+L+VL P + R++ F++QFKGEC NG +R+R RYIYN E V +DSD
Sbjct: 2 AALAVLLMVLSLPFSWARETQPHFIHQFKGECRFSNGLERMRFFARYIYNTQEDVHFDSD 61
Query: 274 VG 279
VG
Sbjct: 62 VG 63
>ref|NP_001013618.1| major histocompatibility complex, class II, DO beta [Bos taurus]
Length = 271
Score = 69.3 bits (168), Expect = 4e-12
Identities = 29/64 (45%), Positives = 42/64 (65%)
Frame = +1
Query: 88 WTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVTRYIYNQNEHVRYD 267
W + L A + +GRDSP+DFV Q K +CY NGT++VR V R+I+N ++ R+D
Sbjct: 8 WVVTFLSTALRLDASVTQGRDSPEDFVTQAKADCYFTNGTEKVRFVVRFIFNLEDYARFD 67
Query: 268 SDVG 279
SD+G
Sbjct: 68 SDLG 71
>ref|XP_587461.2| PREDICTED: similar to 60S ribosomal protein L5 isoform 2 [Bos
taurus]
Length = 217
Score = 58.5 bits (140), Expect(2) = 2e-10
Identities = 37/84 (44%), Positives = 45/84 (53%)
Frame = +2
Query: 335 VMVGLTKYCAPHSIVLMLAHTFLNRFSMHHINERNSEVTGDENDEYRIKSQPDSPNC*MH 514
V VGLT Y A + L+LA LNRF + I E EVTGDE + I QP + C +
Sbjct: 16 VKVGLTNYAAAYCTGLLLACRLLNRFGIDKIYEGQVEVTGDEYNVEIIDGQPGAFTCYLD 75
Query: 515 T*LAQITTSKKVFETLTVAKNGGL 586
LA+ TT KVF L A + GL
Sbjct: 76 AGLARTTTGNKVFGALKGAVDEGL 99
Score = 25.0 bits (53), Expect(2) = 2e-10
Identities = 13/31 (41%), Positives = 17/31 (54%)
Frame = +1
Query: 604 TKRCPEYDSKITDSTAELHRKSDQEHIDSDY 696
TK P YDS+ +AE+HRK +DY
Sbjct: 105 TKWFPGYDSESKKFSAEVHRKHIMGQNVADY 135
>ref|XP_869064.1| PREDICTED: similar to 60S ribosomal protein L5 isoform 3 [Bos
taurus]
Length = 217
Score = 58.5 bits (140), Expect(2) = 2e-10
Identities = 37/84 (44%), Positives = 45/84 (53%)
Frame = +2
Query: 335 VMVGLTKYCAPHSIVLMLAHTFLNRFSMHHINERNSEVTGDENDEYRIKSQPDSPNC*MH 514
V VGLT Y A + L+LA LNRF + I E EVTGDE + I QP + C +
Sbjct: 16 VKVGLTNYAAAYCTGLLLACRLLNRFGIDKIYEGQVEVTGDEYNVEIIDGQPGAFTCYLD 75
Query: 515 T*LAQITTSKKVFETLTVAKNGGL 586
LA+ TT KVF L A + GL
Sbjct: 76 AGLARTTTGNKVFGALKGAVDEGL 99
Score = 25.0 bits (53), Expect(2) = 2e-10
Identities = 13/31 (41%), Positives = 17/31 (54%)
Frame = +1
Query: 604 TKRCPEYDSKITDSTAELHRKSDQEHIDSDY 696
TK P YDS+ +AE+HRK +DY
Sbjct: 105 TKWFPGYDSESKKFSAEVHRKHIMGQNVADY 135
>ref|XP_582668.2| PREDICTED: similar to 60S ribosomal protein L5 [Bos taurus]
Length = 170
Score = 38.5 bits (88), Expect(2) = 9e-06
Identities = 22/59 (37%), Positives = 30/59 (50%)
Frame = +2
Query: 416 MHHINERNSEVTGDENDEYRIKSQPDSPNC*MHT*LAQITTSKKVFETLTVAKNGGLVL 592
M + E +VTGDE + + QP + C + LA+ TT KV L A NGGL +
Sbjct: 1 MDKVYEGQVKVTGDEYNVESVDGQPGAFTCYLDAGLARTTTGNKVLGALKGAVNGGLFI 59
Score = 29.3 bits (64), Expect(2) = 9e-06
Identities = 14/31 (45%), Positives = 19/31 (61%)
Frame = +1
Query: 604 TKRCPEYDSKITDSTAELHRKSDQEHIDSDY 696
TKR P YDS+ + +AE+HRK +DY
Sbjct: 63 TKRFPGYDSESKEFSAEVHRKHIMGQNIADY 93
Database: RefSeqBP
Posted date: Aug 1, 2006 7:14 PM
Number of letters in database: 16,112,626
Number of sequences in database: 33,508
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 28,210,726
Number of Sequences: 33508
Number of extensions: 581067
Number of successful extensions: 1278
Number of sequences better than 1.0e-05: 10
Number of HSP's better than 0.0 without gapping: 1239
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): 1278
length of database: 16,112,626
effective HSP length: 102
effective length of database: 12,694,810
effective search space used: 2856332250
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
Search to RefSeqHP
BLASTX 2.2.10 [Oct-19-2004]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 20060611S-027492
(983 letters)
Database: RefSeqHP
39,411 sequences; 17,774,539 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_872355.1| major histocompatibility complex, class II, DQ ... 104 1e-22
Alignment gi|NP_002114.2| major histocompatibility complex, class II, DQ ... 102 5e-22
Alignment gi|XP_945926.1| PREDICTED: similar to HLA class II histocompati... 84 2e-16
Alignment gi|XP_949921.1| PREDICTED: similar to HLA class II histocompati... 84 2e-16
Alignment gi|NP_002115.1| major histocompatibility complex, class II, DR ... 82 5e-16
Alignment gi|NP_002116.2| major histocompatibility complex, class II, DR ... 80 3e-15
Alignment gi|XP_945196.1| PREDICTED: similar to HLA class II histocompati... 79 5e-15
Alignment gi|NP_068818.4| major histocompatibility complex, class II, DR ... 79 5e-15
Alignment gi|NP_000960.2| ribosomal protein L5 [Homo sapiens] 67 2e-14
Alignment gi|NP_072049.2| major histocompatibility complex, class II, DR ... 77 3e-14
>ref|NP_872355.1| major histocompatibility complex, class II, DQ beta 2 [Homo
sapiens]
Length = 231
Score = 104 bits (259), Expect = 1e-22
Identities = 48/77 (62%), Positives = 60/77 (77%)
Frame = +1
Query: 49 MSGMVALRLPRGLWTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVT 228
MS +AL++P G W AA+TVMLV+L P+AE RD P+DF+ QFKG CY NGT+RVR V
Sbjct: 1 MSWKMALQIPGGFWAAAVTVMLVMLSTPVAEARDFPKDFLVQFKGMCYFTNGTERVRGVA 60
Query: 229 RYIYNQNEHVRYDSDVG 279
RYIYN+ E+ R+DSDVG
Sbjct: 61 RYIYNREEYGRFDSDVG 77
>ref|NP_002114.2| major histocompatibility complex, class II, DQ beta 1 precursor
[Homo sapiens]
Length = 261
Score = 102 bits (254), Expect = 5e-22
Identities = 50/77 (64%), Positives = 60/77 (77%)
Frame = +1
Query: 49 MSGMVALRLPRGLWTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVT 228
MS ALR+P GL A +T+ML +L P+AEGRDSP+DFVYQFKG CY NGT+RVR V+
Sbjct: 1 MSWKKALRIPGGLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVS 60
Query: 229 RYIYNQNEHVRYDSDVG 279
R IYN+ E VR+DSDVG
Sbjct: 61 RSIYNREEIVRFDSDVG 77
>ref|XP_945926.1| PREDICTED: similar to HLA class II histocompatibility antigen,
DRB1-9 beta chain precursor (MHC class I antigen DRB1*9)
(DR-9) (DR9) isoform 1 [Homo sapiens]
Length = 266
Score = 83.6 bits (205), Expect = 2e-16
Identities = 43/74 (58%), Positives = 54/74 (72%)
Frame = +1
Query: 58 MVALRLPRGLWTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVTRYI 237
MV L+LP G AALTV L+VL +PLA D+ F+ Q K EC+ FNGT+RVR++ R I
Sbjct: 1 MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60
Query: 238 YNQNEHVRYDSDVG 279
YNQ E+VR+DSDVG
Sbjct: 61 YNQEENVRFDSDVG 74
>ref|XP_949921.1| PREDICTED: similar to HLA class II histocompatibility antigen,
DRB1-9 beta chain precursor (MHC class I antigen DRB1*9)
(DR-9) (DR9) isoform 3 [Homo sapiens]
Length = 325
Score = 83.6 bits (205), Expect = 2e-16
Identities = 43/74 (58%), Positives = 54/74 (72%)
Frame = +1
Query: 58 MVALRLPRGLWTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVTRYI 237
MV L+LP G AALTV L+VL +PLA D+ F+ Q K EC+ FNGT+RVR++ R I
Sbjct: 1 MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLKQDKFECHFFNGTERVRYLHRGI 60
Query: 238 YNQNEHVRYDSDVG 279
YNQ E+VR+DSDVG
Sbjct: 61 YNQEENVRFDSDVG 74
>ref|NP_002115.1| major histocompatibility complex, class II, DR beta 1 precursor
[Homo sapiens]
Length = 266
Score = 82.4 bits (202), Expect = 5e-16
Identities = 42/74 (56%), Positives = 52/74 (70%)
Frame = +1
Query: 58 MVALRLPRGLWTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVTRYI 237
MV L+LP G ALTV L+VL +PLA D+ F++Q K EC+ FNGT+RVR + R I
Sbjct: 1 MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVRLLERCI 60
Query: 238 YNQNEHVRYDSDVG 279
YNQ E VR+DSDVG
Sbjct: 61 YNQEESVRFDSDVG 74
>ref|NP_002116.2| major histocompatibility complex, class II, DR beta 5 precursor
[Homo sapiens]
Length = 266
Score = 80.1 bits (196), Expect = 3e-15
Identities = 41/74 (55%), Positives = 52/74 (70%)
Frame = +1
Query: 58 MVALRLPRGLWTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVTRYI 237
MV L+LP G + A LTV L+VL +PLA D+ F+ Q K EC+ FNGT+RVR + R I
Sbjct: 1 MVCLKLPGGSYMAKLTVTLMVLSSPLALAGDTRPRFLQQDKYECHFFNGTERVRFLHRDI 60
Query: 238 YNQNEHVRYDSDVG 279
YNQ E +R+DSDVG
Sbjct: 61 YNQEEDLRFDSDVG 74
>ref|XP_945196.1| PREDICTED: similar to HLA class II histocompatibility antigen,
DR-W53 beta chain precursor [Homo sapiens]
Length = 140
Score = 79.3 bits (194), Expect = 5e-15
Identities = 40/74 (54%), Positives = 51/74 (68%)
Frame = +1
Query: 58 MVALRLPRGLWTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVTRYI 237
MV L+LP G AALTV L VL +PLA D+ F+ Q K EC+ NGT+RV ++ RYI
Sbjct: 1 MVCLKLPGGSCMAALTVTLTVLSSPLALAGDTQPRFLEQAKCECHFLNGTERVWNLIRYI 60
Query: 238 YNQNEHVRYDSDVG 279
YNQ E+ RY+SD+G
Sbjct: 61 YNQEEYARYNSDLG 74
>ref|NP_068818.4| major histocompatibility complex, class II, DR beta 4 precursor
[Homo sapiens]
Length = 266
Score = 79.3 bits (194), Expect = 5e-15
Identities = 40/74 (54%), Positives = 51/74 (68%)
Frame = +1
Query: 58 MVALRLPRGLWTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVTRYI 237
MV L+LP G AALTV L VL +PLA D+ F+ Q K EC+ NGT+RV ++ RYI
Sbjct: 1 MVCLKLPGGSCMAALTVTLTVLSSPLALAGDTQPRFLEQAKCECHFLNGTERVWNLIRYI 60
Query: 238 YNQNEHVRYDSDVG 279
YNQ E+ RY+SD+G
Sbjct: 61 YNQEEYARYNSDLG 74
>ref|NP_000960.2| ribosomal protein L5 [Homo sapiens]
Length = 297
Score = 67.4 bits (163), Expect(2) = 2e-14
Identities = 40/85 (47%), Positives = 47/85 (55%)
Frame = +2
Query: 332 GVMVGLTKYCAPHSIVLMLAHTFLNRFSMHHINERNSEVTGDENDEYRIKSQPDSPNC*M 511
GV VGLT Y A + L+LA LNRF M I E EVTGDE + I QP + C +
Sbjct: 87 GVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYL 146
Query: 512 HT*LAQITTSKKVFETLTVAKNGGL 586
LA+ TT KVF L A +GGL
Sbjct: 147 DAGLARTTTGNKVFGALKGAVDGGL 171
Score = 30.4 bits (67), Expect(2) = 2e-14
Identities = 15/33 (45%), Positives = 19/33 (57%)
Frame = +1
Query: 604 TKRCPEYDSKITDSTAELHRKSDQEHIDSDYKR 702
TKR P YDS+ + AE+HRK +DY R
Sbjct: 177 TKRFPGYDSESKEFNAEVHRKHIMGQNVADYMR 209
>ref|NP_072049.2| major histocompatibility complex, class II, DR beta 3 precursor
[Homo sapiens]
Length = 266
Score = 76.6 bits (187), Expect = 3e-14
Identities = 39/74 (52%), Positives = 51/74 (68%)
Frame = +1
Query: 58 MVALRLPRGLWTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVTRYI 237
MV L+LP G AALTV L+VL + LA D+ F+ K EC+ FNGT+RVR++ RY
Sbjct: 1 MVCLKLPGGSSLAALTVTLMVLSSRLAFAGDTRPRFLELRKSECHFFNGTERVRYLDRYF 60
Query: 238 YNQNEHVRYDSDVG 279
+NQ E +R+DSDVG
Sbjct: 61 HNQEEFLRFDSDVG 74
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: 31,559,549
Number of Sequences: 39411
Number of extensions: 657980
Number of successful extensions: 1581
Number of sequences better than 1.0e-05: 10
Number of HSP's better than 0.0 without gapping: 1500
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): 1579
length of database: 17,774,539
effective HSP length: 102
effective length of database: 13,754,617
effective search space used: 3094788825
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-027492
(983 letters)
Database: RefSeqMP
45,328 sequences; 21,768,885 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_996988.1| histocompatibility 2, class II antigen A, beta ... 94 3e-19
Alignment gi|NP_058676.1| ribosomal protein L5 [Mus musculus] 63 4e-13
Alignment gi|NP_001029150.1| H-2 class II histocompatibility antigen E-a/... 73 5e-13
Alignment gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ... 70 3e-12
Alignment gi|NP_034512.1| histocompatibility 2, class II antigen E beta [... 70 4e-12
Alignment gi|XP_981783.1| PREDICTED: similar to 60S ribosomal protein L5 ... 63 5e-12
Alignment gi|XP_001004898.1| PREDICTED: similar to 60S ribosomal protein ... 59 6e-12
>ref|NP_996988.1| histocompatibility 2, class II antigen A, beta 1 [Mus musculus]
Length = 265
Score = 93.6 bits (231), Expect = 3e-19
Identities = 46/73 (63%), Positives = 59/73 (80%)
Frame = +1
Query: 61 VALRLPRGLWTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVTRYIY 240
+AL++P L +AA+ V+L+VL +P EG DS + FVYQF GECY NGTQR+R+VTRYIY
Sbjct: 1 MALQIPSLLLSAAV-VVLMVLSSPGTEGGDSERHFVYQFMGECYFTNGTQRIRYVTRYIY 59
Query: 241 NQNEHVRYDSDVG 279
N+ E+VRYDSDVG
Sbjct: 60 NREEYVRYDSDVG 72
>ref|NP_058676.1| ribosomal protein L5 [Mus musculus]
Length = 297
Score = 62.8 bits (151), Expect(2) = 4e-13
Identities = 38/85 (44%), Positives = 45/85 (52%)
Frame = +2
Query: 332 GVMVGLTKYCAPHSIVLMLAHTFLNRFSMHHINERNSEVTGDENDEYRIKSQPDSPNC*M 511
GV VGLT Y A + L+LA LNRF M I E EV G E + I QP + C +
Sbjct: 87 GVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVNGGEYNVESIDGQPGAFTCYL 146
Query: 512 HT*LAQITTSKKVFETLTVAKNGGL 586
LA+ TT KVF L A +GGL
Sbjct: 147 DAGLARTTTGNKVFGALKGAVDGGL 171
Score = 30.4 bits (67), Expect(2) = 4e-13
Identities = 15/33 (45%), Positives = 19/33 (57%)
Frame = +1
Query: 604 TKRCPEYDSKITDSTAELHRKSDQEHIDSDYKR 702
TKR P YDS+ + AE+HRK +DY R
Sbjct: 177 TKRFPGYDSESKEFNAEVHRKHIMGQNVADYMR 209
>ref|NP_001029150.1| H-2 class II histocompatibility antigen E-a/k beta-2 [Mus musculus]
Length = 287
Score = 72.8 bits (177), Expect = 5e-13
Identities = 37/74 (50%), Positives = 49/74 (66%)
Frame = +1
Query: 58 MVALRLPRGLWTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVTRYI 237
MV+L LPRGL AA+ + L++L P+ RD F+ Q K EC+ FNG +RV VTR+I
Sbjct: 1 MVSLWLPRGLCVAAVILSLMMLTPPVILVRDPRPRFLEQLKAECHYFNGKERVWSVTRFI 60
Query: 238 YNQNEHVRYDSDVG 279
YNQ E R++SD G
Sbjct: 61 YNQEEFARFNSDFG 74
>ref|NP_034519.2| histocompatibility 2, O region beta locus [Mus musculus]
Length = 271
Score = 70.1 bits (170), Expect = 3e-12
Identities = 31/67 (46%), Positives = 46/67 (68%)
Frame = +1
Query: 79 RGLWTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVTRYIYNQNEHV 258
R W AL V L+ L + + EGRDSP++FV Q K +CY NGT++V + R+I+N E++
Sbjct: 5 RAPWVVALLVNLMRLDSFMIEGRDSPENFVIQAKADCYFTNGTEKVHLLVRFIFNLEEYL 64
Query: 259 RYDSDVG 279
+DSD+G
Sbjct: 65 HFDSDLG 71
>ref|NP_034512.1| histocompatibility 2, class II antigen E beta [Mus musculus]
Length = 264
Score = 69.7 bits (169), Expect = 4e-12
Identities = 35/69 (50%), Positives = 46/69 (66%)
Frame = +1
Query: 73 LPRGLWTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVTRYIYNQNE 252
LPR AA+ ++L VL P+A RDS F+ K EC+ +NGTQRVR + RY YN E
Sbjct: 4 LPRVPCVAAVILLLTVLSPPVALVRDSRPWFLEYCKSECHFYNGTQRVRFLKRYFYNLEE 63
Query: 253 HVRYDSDVG 279
++R+DSDVG
Sbjct: 64 NLRFDSDVG 72
>ref|XP_981783.1| PREDICTED: similar to 60S ribosomal protein L5 [Mus musculus]
Length = 297
Score = 62.8 bits (151), Expect(2) = 5e-12
Identities = 38/85 (44%), Positives = 45/85 (52%)
Frame = +2
Query: 332 GVMVGLTKYCAPHSIVLMLAHTFLNRFSMHHINERNSEVTGDENDEYRIKSQPDSPNC*M 511
GV VGLT Y A + L+LA LNRF M I E EV G E + I QP + C +
Sbjct: 87 GVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVNGGEYNVESIDGQPGAFTCYL 146
Query: 512 HT*LAQITTSKKVFETLTVAKNGGL 586
LA+ TT KVF L A +GGL
Sbjct: 147 DAGLARTTTGNKVFGALKGAVDGGL 171
Score = 26.9 bits (58), Expect(2) = 5e-12
Identities = 14/31 (45%), Positives = 17/31 (54%)
Frame = +1
Query: 604 TKRCPEYDSKITDSTAELHRKSDQEHIDSDY 696
TKR P YDS+ AE+HRK +DY
Sbjct: 177 TKRFPGYDSESKVFNAEVHRKHIMGQNVADY 207
>ref|XP_001004898.1| PREDICTED: similar to 60S ribosomal protein L5 [Mus musculus]
Length = 368
Score = 58.9 bits (141), Expect(2) = 6e-12
Identities = 37/85 (43%), Positives = 44/85 (51%)
Frame = +2
Query: 332 GVMVGLTKYCAPHSIVLMLAHTFLNRFSMHHINERNSEVTGDENDEYRIKSQPDSPNC*M 511
GV VGL Y A + L+LA LNRF M I E EV G E + I QP + C +
Sbjct: 158 GVKVGLKHYTAAYCTGLLLAPRLLNRFGMDKIYEGQVEVNGGEYNVESIDGQPGAFTCYL 217
Query: 512 HT*LAQITTSKKVFETLTVAKNGGL 586
LA+ TT KVF L A +GGL
Sbjct: 218 DAGLARTTTGNKVFGALKGAVDGGL 242
Score = 30.4 bits (67), Expect(2) = 6e-12
Identities = 15/33 (45%), Positives = 19/33 (57%)
Frame = +1
Query: 604 TKRCPEYDSKITDSTAELHRKSDQEHIDSDYKR 702
TKR P YDS+ + AE+HRK +DY R
Sbjct: 248 TKRFPGYDSESKEFNAEVHRKHIMGQDVADYMR 280
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: 38,232,249
Number of Sequences: 45328
Number of extensions: 791269
Number of successful extensions: 1842
Number of sequences better than 1.0e-05: 7
Number of HSP's better than 0.0 without gapping: 1763
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): 1842
length of database: 21,768,885
effective HSP length: 104
effective length of database: 17,054,773
effective search space used: 3803214379
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-027492
(983 letters)
Database: RefSeqCP
33,732 sequences; 19,266,565 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Ca... 113 2e-25
Alignment gi|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis fami... 79 9e-15
Alignment gi|XP_537074.2| PREDICTED: similar to 60S ribosomal protein L5 ... 67 2e-14
Alignment gi|XP_861384.1| PREDICTED: similar to HLA class II histocompati... 72 6e-13
Alignment gi|XP_850395.1| PREDICTED: similar to HLA class II histocompati... 72 6e-13
Alignment gi|XP_863594.1| PREDICTED: similar to ribosomal protein L5 isof... 65 8e-11
Alignment gi|XP_863572.1| PREDICTED: similar to ribosomal protein L5 isof... 65 8e-11
Alignment gi|XP_851333.1| PREDICTED: similar to ribosomal protein L5 isof... 65 8e-11
Alignment gi|XP_867018.1| PREDICTED: similar to 60S ribosomal protein L5 ... 41 1e-06
>ref|NP_001014403.1| MHC class II DLA-DQ beta chain b1 domain [Canis familiaris]
Length = 269
Score = 113 bits (283), Expect = 2e-25
Identities = 51/77 (66%), Positives = 64/77 (83%)
Frame = +1
Query: 49 MSGMVALRLPRGLWTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVT 228
MSG + L +PRG WTAA+ ++LVVL P+AEGRDSPQDFV+Q+K ECY NGT+RVR +T
Sbjct: 1 MSGKMTLCIPRGFWTAAVMMILVVLSIPVAEGRDSPQDFVFQYKAECYFTNGTERVRLLT 60
Query: 229 RYIYNQNEHVRYDSDVG 279
+YIYN+ E VR+DSDVG
Sbjct: 61 KYIYNREEFVRFDSDVG 77
>ref|NP_001014768.1| MHC class II DLA DRB1 beta chain [Canis familiaris]
Length = 266
Score = 78.6 bits (192), Expect = 9e-15
Identities = 39/74 (52%), Positives = 48/74 (64%)
Frame = +1
Query: 58 MVALRLPRGLWTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVTRYI 237
MV L G W AL ++L+VL P A RD+P F+ K ECY NGT+RVR V RYI
Sbjct: 1 MVCLCFLGGSWMTALMLILMVLNPPFAWARDTPPHFLEVAKSECYFTNGTERVRFVERYI 60
Query: 238 YNQNEHVRYDSDVG 279
+N+ E VR+DSDVG
Sbjct: 61 HNREEFVRFDSDVG 74
>ref|XP_537074.2| PREDICTED: similar to 60S ribosomal protein L5 isoform 1 [Canis
familiaris]
Length = 247
Score = 67.4 bits (163), Expect(2) = 2e-14
Identities = 40/85 (47%), Positives = 47/85 (55%)
Frame = +2
Query: 332 GVMVGLTKYCAPHSIVLMLAHTFLNRFSMHHINERNSEVTGDENDEYRIKSQPDSPNC*M 511
GV VGLT Y A + L+LA LNRF M I E EVTGDE + I QP + C +
Sbjct: 37 GVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYL 96
Query: 512 HT*LAQITTSKKVFETLTVAKNGGL 586
LA+ TT KVF L A +GGL
Sbjct: 97 DAGLARTTTGNKVFGALKGAVDGGL 121
Score = 30.4 bits (67), Expect(2) = 2e-14
Identities = 15/33 (45%), Positives = 19/33 (57%)
Frame = +1
Query: 604 TKRCPEYDSKITDSTAELHRKSDQEHIDSDYKR 702
TKR P YDS+ + AE+HRK +DY R
Sbjct: 127 TKRFPGYDSESKEFNAEVHRKHIMGQNVADYMR 159
>ref|XP_861384.1| PREDICTED: similar to HLA class II histocompatibility antigen, DO
beta chain precursor (MHC class II antigen DOB) isoform
2 [Canis familiaris]
Length = 228
Score = 72.4 bits (176), Expect = 6e-13
Identities = 31/64 (48%), Positives = 44/64 (68%)
Frame = +1
Query: 88 WTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVTRYIYNQNEHVRYD 267
W AL V + L + + +GRDSP+DFV Q K +CY NGT++V+ V R+I+N E+ R+D
Sbjct: 8 WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67
Query: 268 SDVG 279
S VG
Sbjct: 68 SHVG 71
>ref|XP_850395.1| PREDICTED: similar to HLA class II histocompatibility antigen, DO
beta chain precursor (MHC class II antigen DOB) isoform
1 [Canis familiaris]
Length = 270
Score = 72.4 bits (176), Expect = 6e-13
Identities = 31/64 (48%), Positives = 44/64 (68%)
Frame = +1
Query: 88 WTAALTVMLVVLGAPLAEGRDSPQDFVYQFKGECYIFNGTQRVRHVTRYIYNQNEHVRYD 267
W AL V + L + + +GRDSP+DFV Q K +CY NGT++V+ V R+I+N E+ R+D
Sbjct: 8 WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67
Query: 268 SDVG 279
S VG
Sbjct: 68 SHVG 71
>ref|XP_863594.1| PREDICTED: similar to ribosomal protein L5 isoform 4 [Canis
familiaris]
Length = 179
Score = 65.5 bits (158), Expect = 8e-11
Identities = 39/85 (45%), Positives = 46/85 (54%)
Frame = +2
Query: 332 GVMVGLTKYCAPHSIVLMLAHTFLNRFSMHHINERNSEVTGDENDEYRIKSQPDSPNC*M 511
GV VGLT Y A + L+LA LNRF M I E EVTGDE + I P + C +
Sbjct: 87 GVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGHPGAFTCYL 146
Query: 512 HT*LAQITTSKKVFETLTVAKNGGL 586
LA+ TT KVF L A +GGL
Sbjct: 147 DAGLARTTTGNKVFGALKGAVDGGL 171
>ref|XP_863572.1| PREDICTED: similar to ribosomal protein L5 isoform 3 [Canis
familiaris]
Length = 129
Score = 65.5 bits (158), Expect = 8e-11
Identities = 39/85 (45%), Positives = 46/85 (54%)
Frame = +2
Query: 332 GVMVGLTKYCAPHSIVLMLAHTFLNRFSMHHINERNSEVTGDENDEYRIKSQPDSPNC*M 511
GV VGLT Y A + L+LA LNRF M I E EVTGDE + I P + C +
Sbjct: 37 GVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGHPGAFTCYL 96
Query: 512 HT*LAQITTSKKVFETLTVAKNGGL 586
LA+ TT KVF L A +GGL
Sbjct: 97 DAGLARTTTGNKVFGALKGAVDGGL 121
>ref|XP_851333.1| PREDICTED: similar to ribosomal protein L5 isoform 1 [Canis
familiaris]
Length = 179
Score = 65.5 bits (158), Expect = 8e-11
Identities = 39/85 (45%), Positives = 46/85 (54%)
Frame = +2
Query: 332 GVMVGLTKYCAPHSIVLMLAHTFLNRFSMHHINERNSEVTGDENDEYRIKSQPDSPNC*M 511
GV VGLT Y A + L+LA LNRF M I E EVTGDE + I P + C +
Sbjct: 87 GVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGHPGAFTCYL 146
Query: 512 HT*LAQITTSKKVFETLTVAKNGGL 586
LA+ TT KVF L A +GGL
Sbjct: 147 DAGLARTTTGNKVFGALKGAVDGGL 171
>ref|XP_867018.1| PREDICTED: similar to 60S ribosomal protein L5 isoform 2 [Canis
familiaris]
Length = 183
Score = 40.8 bits (94), Expect(2) = 1e-06
Identities = 25/57 (43%), Positives = 30/57 (52%)
Frame = +2
Query: 416 MHHINERNSEVTGDENDEYRIKSQPDSPNC*MHT*LAQITTSKKVFETLTVAKNGGL 586
M I E EVTGDE + I QP + C + LA+ TT KVF L A +GGL
Sbjct: 1 MDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGL 57
Score = 30.4 bits (67), Expect(2) = 1e-06
Identities = 15/33 (45%), Positives = 19/33 (57%)
Frame = +1
Query: 604 TKRCPEYDSKITDSTAELHRKSDQEHIDSDYKR 702
TKR P YDS+ + AE+HRK +DY R
Sbjct: 63 TKRFPGYDSESKEFNAEVHRKHIMGQNVADYMR 95
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: 33,229,197
Number of Sequences: 33732
Number of extensions: 686650
Number of successful extensions: 1641
Number of sequences better than 1.0e-05: 9
Number of HSP's better than 0.0 without gapping: 1566
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): 1641
length of database: 19,266,565
effective HSP length: 103
effective length of database: 15,792,169
effective search space used: 3537445856
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)