BLASTP 2.2.26 [Sep-21-2011]
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.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 004905
(724 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 2/80 (2%)
Query: 3 EQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSS 62
E++L A FG++ER+K ++Y+F+ F D A +A E + G+ I I+F+
Sbjct: 25 EEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKP 82
Query: 63 ELAPGKDYPGSYSGTKGPRS 82
K+ GP S
Sbjct: 83 PDQKRKERKAQRQAASGPSS 102
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 35.8 bits (81), Expect = 0.079, Method: Composition-based stats.
Identities = 29/93 (31%), Positives = 43/93 (46%), Gaps = 11/93 (11%)
Query: 1 MDEQMLHNAMILFGEIERIK----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRIT 56
+D + L++ FG I K S+ Y FV F + + A RA E + G L ND ++
Sbjct: 17 IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 76
Query: 57 I-MFSS-----SEL-APGKDYPGSYSGTKGPRS 82
+ F S +EL A K++ Y GP S
Sbjct: 77 VGRFKSRKEREAELGARAKEFTNVYIKNFGPGS 109
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 1 MDEQMLHNAMILFGEIERIKSYPSRN----YSFVEFRSVDEARRAKEGLQGRLFNDPRIT 56
+D + L++ FG I K N Y FV F + + A RA E + G L ND ++
Sbjct: 115 IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 174
Query: 57 I 57
+
Sbjct: 175 V 175
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 35.4 bits (80), Expect = 0.13, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 1 MDEQMLHNAMILFGEIERIK----SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRIT 56
+D + L++ FG I K S+ Y FV F + + A RA E + G L ND ++
Sbjct: 23 IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 82
Query: 57 I 57
+
Sbjct: 83 V 83
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 35.0 bits (79), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 1 MDEQMLHNAMILFGEIERIKSYPSRN----YSFVEFRSVDEARRAKEGLQGRLFNDPRIT 56
+D + L++ FG I K N Y FV F + + A RA E + G L ND ++
Sbjct: 110 IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 169
Query: 57 I 57
+
Sbjct: 170 V 170
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 33.9 bits (76), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 27/44 (61%)
Query: 20 KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSE 63
+S SR ++FV F +VD+A+ AKE G + RI + FS ++
Sbjct: 83 QSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK 126
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 33.9 bits (76), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 6/68 (8%)
Query: 1 MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPR 54
+DE L +G IE +K + SR Y FV+F+S A++A GL G + R
Sbjct: 54 VDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKR 113
Query: 55 ITIMFSSS 62
+ + ++S
Sbjct: 114 LKVALAAS 121
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 33.5 bits (75), Expect = 0.38, Method: Composition-based stats.
Identities = 17/41 (41%), Positives = 25/41 (60%)
Query: 20 KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
+S SR ++FV F +VD+A+ AKE G + RI + FS
Sbjct: 49 QSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 89
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 33.5 bits (75), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 25/47 (53%)
Query: 1 MDEQMLHNAMILFGEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQG 47
+ +Q++ FG+I I+ +P + YSFV F + + A A + G
Sbjct: 37 LTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNG 83
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 33.5 bits (75), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 25/41 (60%)
Query: 20 KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFS 60
+S SR ++FV F +VD+A+ AKE G + RI + FS
Sbjct: 52 QSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 92
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 33.1 bits (74), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 7/67 (10%)
Query: 1 MDEQMLHNAMILFGEI---ERIKSYP----SRNYSFVEFRSVDEARRAKEGLQGRLFNDP 53
+DE++L++ FG I +I P S+ Y+F+ F S D + A E + G+ +
Sbjct: 17 IDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNR 76
Query: 54 RITIMFS 60
IT+ ++
Sbjct: 77 PITVSYA 83
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 32.3 bits (72), Expect = 0.92, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 31/51 (60%), Gaps = 3/51 (5%)
Query: 16 IERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAP 66
+ER+ + S+ Y++VEF + DEA +A + + G + IT +++ LAP
Sbjct: 38 VERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEIT---ATAVLAP 85
>pdb|1MU2|B Chain B, Crystal Structure Of Hiv-2 Reverse Transcriptase
Length = 426
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 617 QGTEASTLYGSSVFQQPNNPTAVSNQ-VNLSQPQNVMTVSVDKVNLEHPNHVQQLQSVLS 675
QG + S +Q P +N+ V + Q + + ++ D+ +LEH V QL+ +L+
Sbjct: 146 QGWKGSPAIFQHTMRQVLEPFRKANKDVIIIQYMDDILIASDRTDLEHDRVVLQLKELLN 205
Query: 676 GAGQGTSDGEVDKNQRY 692
G G T D + K+ Y
Sbjct: 206 GLGFSTPDEKFQKDPPY 222
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
Length = 109
Score = 31.2 bits (69), Expect = 2.1, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 3 EQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEARRAKEGLQGR 48
E+ +H+ +GEI+ I ++ + Y+ VE+ + EA+ A EGL G+
Sbjct: 21 EEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQ 72
>pdb|1G6E|A Chain A, Antifungal Protein From Streptomyces Tendae Tu901, 30-
Conformers Ensemble
pdb|1GH5|A Chain A, Antifungal Protein From Streptomyces Tendae Tu901, Nmr
Average Structure
Length = 87
Score = 31.2 bits (69), Expect = 2.4, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 618 GTEASTLYGSSVFQQPNNPTAVSNQVNLSQPQNVMTVSVDKVNLEHPNHVQQLQSV 673
GT +YG + + NN + Q NLS P+ + T+++ K +P H+ ++ S+
Sbjct: 30 GTMPVAIYGVNWVESGNNVVTLQFQRNLSDPR-LETITLQKWGSWNPGHIHEILSI 84
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 30.8 bits (68), Expect = 2.4, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 3 EQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEARRAKEGLQGR 48
E+ +H+ +GEI+ I ++ + Y+ VE+ + EA+ A EGL G+
Sbjct: 21 EEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQ 72
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 30.8 bits (68), Expect = 2.5, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 7/57 (12%)
Query: 1 MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGL-QGRLF 50
+D+++LH A I FG+I I+ + R ++FVEF ++A A + + + LF
Sbjct: 17 VDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF 73
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 30.8 bits (68), Expect = 2.5, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 7/57 (12%)
Query: 1 MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGL-QGRLF 50
+D+++LH A I FG+I I+ + R ++FVEF ++A A + + + LF
Sbjct: 14 VDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF 70
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 30.8 bits (68), Expect = 2.5, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 7/57 (12%)
Query: 1 MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGL-QGRLF 50
+D+++LH A I FG+I I+ + R ++FVEF ++A A + + + LF
Sbjct: 75 VDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF 131
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 30.8 bits (68), Expect = 2.5, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 7/57 (12%)
Query: 1 MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGL-QGRLF 50
+D+++LH A I FG+I I+ + R ++FVEF ++A A + + + LF
Sbjct: 19 VDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF 75
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 30.8 bits (68), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 23/38 (60%)
Query: 20 KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITI 57
+S SR ++FV F +VD+A+ AKE G + RI +
Sbjct: 52 QSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
>pdb|1MU2|A Chain A, Crystal Structure Of Hiv-2 Reverse Transcriptase
Length = 555
Score = 30.8 bits (68), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 617 QGTEASTLYGSSVFQQPNNPTAVSNQ-VNLSQPQNVMTVSVDKVNLEHPNHVQQLQSVLS 675
QG + S +Q P +N+ V + Q + + ++ D+ +LEH V QL+ +L+
Sbjct: 151 QGWKGSPAIFQHTMRQVLEPFRKANKDVIIIQYMDDILIASDRTDLEHDRVVLQLKELLN 210
Query: 676 GAGQGTSDGEVDKNQRY 692
G G T D + K+ Y
Sbjct: 211 GLGFSTPDEKFQKDPPY 227
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 30.8 bits (68), Expect = 2.8, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 3 EQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEARRAKEGLQGR 48
E+ +H+ +GEI+ I ++ + Y+ VE+ + EA+ A EGL G+
Sbjct: 36 EEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQ 87
>pdb|1NHC|A Chain A, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|B Chain B, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|C Chain C, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|D Chain D, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|E Chain E, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
pdb|1NHC|F Chain F, Structural Insights Into The Processivity Of
Endopolygalacturonase I From Aspergillus Niger
Length = 336
Score = 30.8 bits (68), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 40/83 (48%), Gaps = 8/83 (9%)
Query: 222 IDDHGLVLDQSYGLGSITGGPASG---AFVNVQG-RNRLSPVASKV-TAGGFGRNPIDSD 276
I D+G+V++Q Y GS TG P++G V V G L A++V G G SD
Sbjct: 254 ITDYGIVIEQDYENGSPTGTPSTGIPITDVTVDGVTGTLEDDATQVYILCGDGSC---SD 310
Query: 277 FIWRGIIAKGGTPVCRARCVPFG 299
+ W G+ GG + VP G
Sbjct: 311 WTWSGVDLSGGKTSDKCENVPSG 333
>pdb|2XB2|D Chain D, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
Length = 90
Score = 30.8 bits (68), Expect = 3.1, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 3 EQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEARRAKEGLQGR 48
E+ +H+ +GEI+ I ++ + Y+ VE+ + EA+ A EGL G+
Sbjct: 21 EEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQ 72
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 30.4 bits (67), Expect = 3.3, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 3 EQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEARRAKEGLQGR 48
E+ +H+ +GEI+ I ++ + Y+ VE+ + EA+ A EGL G+
Sbjct: 23 EEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQ 74
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 30.0 bits (66), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 1 MDEQMLHNAMILF-----GEI-ERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFN 51
+D++ L NA F G + +++ SR Y FV F S D+A+ A + +QG+ N
Sbjct: 13 VDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLN 69
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 30.0 bits (66), Expect = 4.9, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 3 EQMLHNAMILFGEIERI------KSYPSRNYSFVEFRSVDEARRAKEGLQGR 48
E+ +H+ +GEI+ I ++ + Y+ VE+ + EA+ A EGL G+
Sbjct: 37 EEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQ 88
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 29.6 bits (65), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 1 MDEQMLHNAM-----ILFGEI-ERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFN 51
+D++ L NA L G + +++ SR Y FV F S D+A+ A + +QG+ N
Sbjct: 99 VDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLN 155
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
Length = 94
Score = 29.6 bits (65), Expect = 6.0, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 3 EQMLHNAMILFGEIERI---KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF 59
++ LH FG+I I +S R +FV F+ V A A +QG F D + I +
Sbjct: 23 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 82
Query: 60 SSSE 63
+ ++
Sbjct: 83 AKTD 86
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
Length = 90
Score = 29.6 bits (65), Expect = 6.3, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 3 EQMLHNAMILFGEIERI---KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF 59
++ LH FG+I I +S R +FV F+ V A A +QG F D + I +
Sbjct: 21 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 80
Query: 60 SSSE 63
+ ++
Sbjct: 81 AKTD 84
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 29.6 bits (65), Expect = 6.3, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 3 EQMLHNAMILFGEIERI---KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF 59
++ LH FG+I I +S R +FV F+ V A A +QG F D + I +
Sbjct: 22 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 81
Query: 60 SSSE 63
+ ++
Sbjct: 82 AKTD 85
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 29.6 bits (65), Expect = 6.6, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 14 GEIERIKSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMFSSSELAPGKDYPGS 73
G +ER+K R+Y+FV F + ++A A + L G++ + I + + KD G
Sbjct: 42 GAVERVKKI--RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK---PVDKDSSGP 96
Query: 74 YSG 76
SG
Sbjct: 97 SSG 99
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna
Complex Reveals The Basis Of Cooperativity In
Regulation Of Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna
Complex Reveals The Basis Of Cooperativity In
Regulation Of Polyadenylation By Human U1a Protein
Length = 101
Score = 29.6 bits (65), Expect = 6.7, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 3 EQMLHNAMILFGEIERI---KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF 59
++ LH FG+I I +S R +FV F+ V A A +QG F D + I +
Sbjct: 26 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 85
Query: 60 SSSE 63
+ ++
Sbjct: 86 AKTD 89
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX
THAT Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V.
Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 29.3 bits (64), Expect = 7.1, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 3 EQMLHNAMILFGEIERI---KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF 59
++ LH FG+I I +S R +FV F+ V A A +QG F D + I +
Sbjct: 27 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 86
Query: 60 SSSE 63
+ ++
Sbjct: 87 AKTD 90
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution
Reveals A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution
Reveals A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme
Self-Ligation Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme
Self-Ligation Product, In Complex With U1a Rbd
Length = 97
Score = 29.3 bits (64), Expect = 7.2, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 3 EQMLHNAMILFGEIERI---KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF 59
++ LH FG+I I +S R +FV F+ V A A +QG F D + I +
Sbjct: 26 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 85
Query: 60 SSSE 63
+ ++
Sbjct: 86 AKTD 89
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group
I Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group
I Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group
I Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 29.3 bits (64), Expect = 7.9, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 3 EQMLHNAMILFGEIERI---KSYPSRNYSFVEFRSVDEARRAKEGLQGRLFNDPRITIMF 59
++ LH FG+I I +S R +FV F+ V A A +QG F D + I +
Sbjct: 24 KKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 83
Query: 60 SSSE 63
+ ++
Sbjct: 84 AKTD 87
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 29.3 bits (64), Expect = 8.4, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 6/51 (11%)
Query: 1 MDEQMLHNAMILFGEIERIK------SYPSRNYSFVEFRSVDEARRAKEGL 45
+D+++LH A I FG+I I+ + R ++FVEF ++A A + +
Sbjct: 24 VDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
>pdb|3R7K|A Chain A, Crystal Structure Of A Probable Acyl Coa Dehydrogenase
From Mycobacterium Abscessus Atcc 19977 DSM 44196
pdb|3R7K|B Chain B, Crystal Structure Of A Probable Acyl Coa Dehydrogenase
From Mycobacterium Abscessus Atcc 19977 DSM 44196
pdb|3R7K|C Chain C, Crystal Structure Of A Probable Acyl Coa Dehydrogenase
From Mycobacterium Abscessus Atcc 19977 DSM 44196
pdb|3R7K|D Chain D, Crystal Structure Of A Probable Acyl Coa Dehydrogenase
From Mycobacterium Abscessus Atcc 19977 DSM 44196
Length = 403
Score = 28.9 bits (63), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 29/61 (47%), Gaps = 10/61 (16%)
Query: 266 GGFGRNPIDSDFIWRGIIAKGG-TPVCRARCVPFGKGIESELPEVVNCSARTGLDMLAKH 324
GG G N IDS + I+A GG T VC A F GI LP + A G D L +
Sbjct: 84 GGSGGNAIDSALVTEAILAAGGSTGVCAA---LFTHGI--ALPHI----AANGSDALIER 134
Query: 325 Y 325
Y
Sbjct: 135 Y 135
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.314 0.131 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,053,334
Number of Sequences: 62578
Number of extensions: 927274
Number of successful extensions: 1472
Number of sequences better than 100.0: 45
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 28
Number of HSP's that attempted gapping in prelim test: 1451
Number of HSP's gapped (non-prelim): 46
length of query: 724
length of database: 14,973,337
effective HSP length: 106
effective length of query: 618
effective length of database: 8,340,069
effective search space: 5154162642
effective search space used: 5154162642
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 bits)