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= psy1928
(105 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 102 bits (254), Expect = 6e-23, Method: Compositional matrix adjust.
Identities = 46/59 (77%), Positives = 53/59 (89%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KAMKQYNGVPLDGRPM IQL
Sbjct: 45 IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 103
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 99.4 bits (246), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 48/67 (71%), Positives = 54/67 (80%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
I ELF+EFG LK A + YDRSGRSLGTAD+ +ERR+DA+KAMKQY GVPLDGRPM IQL
Sbjct: 52 IQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV 111
Query: 62 ADVSVLE 68
A LE
Sbjct: 112 ASQIDLE 118
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 99.4 bits (246), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 48/67 (71%), Positives = 54/67 (80%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
I ELF+EFG LK A + YDRSGRSLGTAD+ +ERR+DA+KAMKQY GVPLDGRPM IQL
Sbjct: 52 IQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV 111
Query: 62 ADVSVLE 68
A LE
Sbjct: 112 ASQIDLE 118
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 98.2 bits (243), Expect = 9e-22, Method: Compositional matrix adjust.
Identities = 48/67 (71%), Positives = 54/67 (80%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
I ELF+EFG LK A + YDRSGRSLGTAD+ +ERR+DA+KAMKQY GVPLDGRPM IQL
Sbjct: 105 IQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV 164
Query: 62 ADVSVLE 68
A LE
Sbjct: 165 ASQIDLE 171
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 97.1 bits (240), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 44/59 (74%), Positives = 51/59 (86%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I ELF+EFG LK A +HYDRSGRSLGTAD+ +ER++DA+KA KQYNGVPLDGRP IQL
Sbjct: 46 IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYNGVPLDGRPXNIQL 104
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 38/59 (64%), Gaps = 1/59 (1%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
E+FS++GP+ + YD+ S RS G A + +E DA +A ++ NG+ LDGR +++ +
Sbjct: 34 EVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 92
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 38/59 (64%), Gaps = 1/59 (1%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
E+FS++GP+ + YD+ S RS G A + +E DA +A ++ NG+ LDGR +++ +
Sbjct: 31 EVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 89
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 38/59 (64%), Gaps = 1/59 (1%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
E+FS++GP+ + YD+ S RS G A + +E DA +A ++ NG+ LDGR +++ +
Sbjct: 65 EVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 123
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 42.4 bits (98), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 37/57 (64%), Gaps = 1/57 (1%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
E+FS++GP+ + YD+ S RS G A + +E DA +A ++ NG+ LDGR +++
Sbjct: 34 EVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS 90
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 42.0 bits (97), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
++FSE GP+ S +L YDR +G+ G Y+ + A+ AM+ NG GR +++ AA
Sbjct: 27 DIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA 86
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 37/74 (50%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
M+ +F + GP+ L DR+ +S G A + +E +DA A K NG L G+ ++++
Sbjct: 23 MLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ 82
Query: 61 AADVSVLENTVPRP 74
A S RP
Sbjct: 83 AKKPSFQSGGRRRP 96
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
M+ +F FG ++S +L D +GRS G + + A KA++Q NG L GRPM++
Sbjct: 42 MLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV 100
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 35/59 (59%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ E+FS G + A + D+ G+S G + +E+ +A++A+ +NG L RPM +++
Sbjct: 32 LKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM 90
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 39.3 bits (90), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 32/61 (52%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
IYELFS+ G +K + D+ + G + Y R+DA AM+ NG LD R ++
Sbjct: 35 IYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD 94
Query: 62 A 62
A
Sbjct: 95 A 95
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+Y +FS+FG + + RS + G A +I++ S A A++ G P +PM+IQ A
Sbjct: 30 LYAIFSQFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 87
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 14/66 (21%)
Query: 2 IYELFSEFG------PLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRP 55
+Y LFS+FG LK+ K+ G A +I++ + A++Q G P G+P
Sbjct: 27 LYALFSQFGHVVDIVALKTMKMR--------GQAFVIFKELGSSTNALRQLQGFPFYGKP 78
Query: 56 MQIQLA 61
M+IQ A
Sbjct: 79 MRIQYA 84
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+Y +FS+FG + + RS + G A +I++ S A A++ G P +PM+IQ A
Sbjct: 29 LYAIFSQFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+Y +FS+FG + + RS + G A +I++ S A A++ G P +PM+IQ A
Sbjct: 30 LYAIFSQFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 87
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 42/66 (63%), Gaps = 3/66 (4%)
Query: 2 IYELFSEFGPLKSAKLHYDRS-GRSLGTADLIYERRSDAIKAMKQYNGV--PLDGRPMQI 58
+ ++FS FG + ++++ D++ G S G A + +++RS+A +A+ +NG P P+ +
Sbjct: 105 VEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITV 164
Query: 59 QLAADV 64
+ AA++
Sbjct: 165 KFAANL 170
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 5 LFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
LFS G ++SAKL D+ +G SLG + Y DA +A+ NG+ L + +++ A
Sbjct: 22 LFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA 79
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I E F ++G +K+ L+ DR +G S G A + YE A+ A + NG + G+ +Q+
Sbjct: 43 IQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW 102
Query: 61 A 61
Sbjct: 103 C 103
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 5 LFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
LFS G ++SAKL D+ +G SLG + Y DA +A+ NG+ L + +++ A
Sbjct: 24 LFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA 81
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 5 LFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
LFS G ++SAKL D+ +G SLG + Y DA +A+ NG+ L + +++ A
Sbjct: 39 LFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA 96
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs
Of Human Antigen R
Length = 177
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 5 LFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
LFS G ++SAKL D+ +G SLG + Y DA +A+ NG+ L + +++ A
Sbjct: 22 LFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA 79
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 41/66 (62%), Gaps = 3/66 (4%)
Query: 2 IYELFSEFGPLKSAKLHYDRS-GRSLGTADLIYERRSDAIKAMKQYNGV--PLDGRPMQI 58
+ ++FS FG + ++++ D++ G S G A + +++RS+A +A+ +NG P P+ +
Sbjct: 105 VEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITV 164
Query: 59 QLAADV 64
AA++
Sbjct: 165 XFAANL 170
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 29/58 (50%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
++YELF + GPL + DR G+ + ++ A+ NG+ L GRP+ +
Sbjct: 32 ILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINV 89
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 33 YERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+ R DA++AMK NG LDG P+++ LA
Sbjct: 58 FSNREDAVEAMKALNGKVLDGSPIEVTLA 86
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I E F ++G +K+ L+ DR +G S G A + YE A+ A + NG + G+ +Q+
Sbjct: 89 IQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW 148
Query: 61 A 61
Sbjct: 149 C 149
>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 = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I++ F+E+G +K+ L+ DR +G G + YE +A AM+ NG L G+P+ +
Sbjct: 26 IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 85
Query: 61 A 61
Sbjct: 86 C 86
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
LF G ++S KL D+ +G+SLG + Y +DA KA+ NG+ L + +++ A
Sbjct: 23 SLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYA 81
>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 = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I++ F+E+G +K+ L+ DR +G G + YE +A AM+ NG L G+P+ +
Sbjct: 24 IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 83
Query: 61 A 61
Sbjct: 84 C 84
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I++ F+E+G +K+ L+ DR +G G + YE +A AM+ NG L G+P+ +
Sbjct: 24 IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 83
Query: 61 A 61
Sbjct: 84 C 84
>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 = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I++ F+E+G +K+ L+ DR +G G + YE +A AM+ NG L G+P+ +
Sbjct: 24 IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 83
Query: 61 A 61
Sbjct: 84 C 84
>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 = 0.007, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
M+YE FS GP+ S ++ D + RSLG A + +++ +DA +A+ N + G+P++I
Sbjct: 31 MLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIM 90
Query: 60 LA 61
+
Sbjct: 91 WS 92
Score = 32.3 bits (72), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+Y+ FS FG + S K+ D +G S G + +E + A +A+++ NG+ L+ R + +
Sbjct: 120 LYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 175
>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 = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
M+YE FS GP+ S ++ D + RSLG A + +++ +DA +A+ N + G+P++I
Sbjct: 26 MLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIM 85
Query: 60 LA 61
+
Sbjct: 86 WS 87
Score = 32.3 bits (72), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+Y+ FS FG + S K+ D +G S G + +E + A +A+++ NG+ L+ R + +
Sbjct: 115 LYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 170
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
M+ +F FG + + L D +GRS G + + A +A++Q NG L GRPM++
Sbjct: 21 MLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRV 79
>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 = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I++ F+E+G +K+ L+ DR +G G + YE +A AM+ NG L G+P+ +
Sbjct: 39 IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98
Query: 61 A 61
Sbjct: 99 C 99
>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 = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I++ F+E+G +K+ L+ DR +G G + YE +A AM+ NG L G+P+ +
Sbjct: 40 IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 99
Query: 61 A 61
Sbjct: 100 C 100
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 5 LFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
LF G ++S KL D+ +G+SLG + Y +DA KA+ NG+ L + +++ A
Sbjct: 24 LFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYA 81
>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 = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
++ +FS FG + + RS + G A +I++ S A A++ G P +PM+IQ A
Sbjct: 29 LHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRS-LGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
IYELFS+ G +K + D+ ++ G + Y R+DA AM+ NG LD R ++
Sbjct: 56 IYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW 115
Query: 61 AA 62
A
Sbjct: 116 DA 117
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In
Imidazole And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With
C75u Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
++ +FS FG + + RS + G A +I++ S A A++ G P +PM+IQ A
Sbjct: 30 LHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 87
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
++ +FS FG + + RS + G A +I++ S A A++ G P +PM+IQ A
Sbjct: 30 LHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 87
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 34.7 bits (78), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
++ +FS FG + + RS + G A +I++ S A A++ G P +PM+IQ A
Sbjct: 29 LHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86
>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 = 34.7 bits (78), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
++ +FS FG + + RS + G A +I++ S A A++ G P +PM+IQ A
Sbjct: 29 LHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86
>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 = 34.7 bits (78), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
++ +FS FG + + RS + G A +I++ S A A++ G P +PM+IQ A
Sbjct: 27 LHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 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 = 34.7 bits (78), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
++ +FS FG + + RS + G A +I++ S A A++ G P +PM+IQ A
Sbjct: 25 LHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 82
>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 = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
++ +FS FG + + RS + G A +I++ S A A++ G P +PM+IQ A
Sbjct: 24 LHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 81
>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 = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
++ +FS FG + + RS + G A +I++ S A A++ G P +PM+IQ A
Sbjct: 26 LHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 83
>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 = 33.9 bits (76), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 6 FSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
F +F S + +D ++G S G + + + DA AM G L+GRP++I AA
Sbjct: 22 FKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA 79
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 33.9 bits (76), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ ++FS++G + + DR + RS G + +E DA AM NG +DGR +++
Sbjct: 29 LEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ 88
Query: 61 AA 62
A
Sbjct: 89 AG 90
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 33.9 bits (76), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 6 FSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
F +GP+K + Y RSG+ G A + YE D A K +G +DGR
Sbjct: 123 FEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGR 172
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 33.5 bits (75), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 6 FSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
F +F S + +D ++G S G + + + DA AM G L+GRP++I AA
Sbjct: 108 FKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA 165
Score = 30.0 bits (66), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 14/61 (22%), Positives = 33/61 (54%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
++ + F GP+ + K+ D++ +++ A + Y + DA A++ NG ++ ++I
Sbjct: 16 ILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINW 75
Query: 61 A 61
A
Sbjct: 76 A 76
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 33.5 bits (75), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 4 ELFSEFGPLKSAKLHYDRSGR-SLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
+LF +GP++S K+ DR R S G + ++ S A +A+ NG + + +++ LAA
Sbjct: 61 QLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA 120
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 33.5 bits (75), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+ ++F +FG + ++ ++ G S G + +E +DA +A ++ +G ++GR +++
Sbjct: 32 LRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN-N 89
Query: 62 ADVSVLENTVP 72
A V+ N+ P
Sbjct: 90 ATARVMTNSGP 100
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The
C-Fos Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The
Tumor Necrosis Factor Alpha Rna
Length = 167
Score = 33.5 bits (75), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 5 LFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
LF G ++S KL D+ +G+SLG + Y DA KA+ NG+ L + +++ A
Sbjct: 22 LFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYA 79
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir
In The Complex With Fbp Nbox Peptide
Length = 199
Score = 33.5 bits (75), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
I + F+ FGP+KS + +D + + G A + YE A A++Q N V L GR +++
Sbjct: 30 IRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV 87
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 33.1 bits (74), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 6 FSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
FS FG + SAK+ + GRS G + + +A KA+ + NG + +P+ + LA
Sbjct: 36 FSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA 90
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 33.1 bits (74), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 7/61 (11%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
++ + FS+FG L+ K D A + ++ R A+KAM++ NG L+G ++I
Sbjct: 27 ILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMNGKDLEGENIEIVF 79
Query: 61 A 61
A
Sbjct: 80 A 80
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 33.1 bits (74), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
I + F+ FGP+KS +D + + G A + YE A A++Q N V L GR +++
Sbjct: 29 IRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKV 86
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 33.1 bits (74), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
I + F+ FGP+KS + +D + + G A + YE A A++Q N V L GR +++
Sbjct: 45 IRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV 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 = 32.3 bits (72), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+Y+ FS FG + S K+ D +G S G + +E + A +A+++ NG+ L+ R + +
Sbjct: 22 LYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 77
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 32.3 bits (72), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+Y+ FS FG + S K+ D +G S G + +E + A +A+++ NG+ L+ R + +
Sbjct: 28 LYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 83
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 32.3 bits (72), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 6 FSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
F +GP+K + Y RSG+ G A + YE D A K +G +DGR
Sbjct: 123 FEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGR 172
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 32.0 bits (71), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 5 LFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+F ++G + + DR + S G A + + + DA AM +G LDGR +++Q+A
Sbjct: 90 VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 147
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 32.0 bits (71), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 14/61 (22%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+ ++F +FG + ++ ++ G S G + +E +DA +A ++ +G ++GR +++ A
Sbjct: 46 LRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA 104
Query: 62 A 62
Sbjct: 105 T 105
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 32.0 bits (71), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDRS-GRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ ELF FG + L D++ G+S G A + + RR DA +A+ +G D + ++
Sbjct: 32 LQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW 91
Query: 61 A 61
A
Sbjct: 92 A 92
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 32.0 bits (71), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 4 ELFSEFGPLKSAKLH----YDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
E F +FG + ++ Y S +A + Y R DA++A++ N V +DGR ++
Sbjct: 37 EYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS 96
Query: 60 LA 61
L
Sbjct: 97 LG 98
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 5 LFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+F ++G + + DR + S G A + + + DA AM +G LDGR +++Q+A
Sbjct: 67 VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 124
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 30.8 bits (68), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 15/75 (20%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
++ + FS+FGP++ A + D GR+ G + + + A KA+++
Sbjct: 112 LLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALER--------------- 156
Query: 61 AADVSVLENTVPRPV 75
D + L T PRPV
Sbjct: 157 CGDGAFLLTTTPRPV 171
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 34/61 (55%), Gaps = 4/61 (6%)
Query: 5 LFSEFGPLKSAKLHYDRSGR----SLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+FS+ G +KS + ++ S+G + Y++ A KA+KQ G +DG +++++
Sbjct: 25 VFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRI 84
Query: 61 A 61
+
Sbjct: 85 S 85
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 30.4 bits (67), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRS---LGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+ ELFS+FG + + KL YDR + G ++ E S+AI + + GR +++
Sbjct: 18 VKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKL---DNTDFMGRTIRV 74
Query: 59 QLA 61
A
Sbjct: 75 TEA 77
>pdb|4HFS|A Chain A, Crystal Structure Of An Uncharacterized Protein (Yncm)
From Bacillus Subtilis Subsp. Subtilis Str. 168 At 1.55
A Resolution
pdb|4HFS|B Chain B, Crystal Structure Of An Uncharacterized Protein (Yncm)
From Bacillus Subtilis Subsp. Subtilis Str. 168 At 1.55
A Resolution
Length = 212
Score = 30.4 bits (67), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 24 RSLGTADLIYERRSDAIKAM--KQYNGVPLDGRP----MQIQLAADVSVLENTVPRPV 75
++L TA + YE + DAIKA +N + +D + + Q A VSV N V V
Sbjct: 153 KTLATAAVSYESQRDAIKATFSTSFNNITIDNKAVTPVVDTQDFAKVSVAGNNVTISV 210
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 30.4 bits (67), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 14/63 (22%)
Query: 2 IYELFSEFG------PLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRP 55
+Y +FS+FG LK+ K+ G A +I++ A A++ G P +P
Sbjct: 27 LYAIFSQFGQILDIVALKTLKMR--------GQAFVIFKEIGSASNALRTMQGFPFYDKP 78
Query: 56 MQI 58
MQI
Sbjct: 79 MQI 81
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 30.0 bits (66), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 2 IYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I +L S GP+ + K+ +D ++GRS G A + + + A++ NG L R ++
Sbjct: 19 ILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGY 78
Query: 61 AADVSV 66
+++ +
Sbjct: 79 SSNSDI 84
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 30.0 bits (66), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 2 IYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I +L S GP+ + K+ +D ++GRS G A + + + A++ NG L R ++
Sbjct: 20 ILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGY 79
Query: 61 AADVSV 66
+++ +
Sbjct: 80 SSNSDI 85
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition
In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 30.0 bits (66), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 2 IYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I +L S GP+ + K+ +D ++GRS G A + + + A++ NG L R ++
Sbjct: 21 ILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGY 80
Query: 61 AAD 63
+++
Sbjct: 81 SSN 83
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 29.6 bits (65), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+I +LFS+ GP KS K+ + + YE R DA A+ NG + G+ +++
Sbjct: 31 LILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHR-DAAAALAAMNGRKILGKEVKVNW 89
Query: 61 AA 62
A
Sbjct: 90 AT 91
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 29.6 bits (65), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 5 LFSEFGPLKSAKLHYDRSGRSLGTADLIYERRS---DAIKAMKQYNGVPLDGRPMQIQLA 61
+FS FG ++ ++ G S G A + + R+ AIKAM Q + PM ++ A
Sbjct: 115 MFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 29.6 bits (65), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 30/53 (56%), Gaps = 2/53 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
+Y++F ++GP++ ++ + + GTA ++YE DA A+ +G + R
Sbjct: 25 MYDIFGKYGPIRQIRV--GNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNR 75
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 29.3 bits (64), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSL--GTADLIYERRSDAIKAMKQYNGVPLDGR 54
I E+FS +G +K + +R L G A + +E +A KA+K +G +DG+
Sbjct: 21 IMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQ 75
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 29.3 bits (64), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
M+ + F+E G + A + + +G+S G + +E A +A + NG+ L GR + +++
Sbjct: 21 MLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI 79
Query: 61 AADVS 65
+ S
Sbjct: 80 DRNAS 84
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 29.3 bits (64), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRS---DAIKAMKQYNGVPLDGRPMQI 58
I +FS FG ++ ++ G S G A + + R+ AIKAM Q + PM +
Sbjct: 124 IRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV 183
Query: 59 QLA 61
+ A
Sbjct: 184 KFA 186
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 29.3 bits (64), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
M+ + F+E G + A + + +G+S G + +E A +A + NG+ L GR + +++
Sbjct: 24 MLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI 82
Query: 61 AADVS 65
+ S
Sbjct: 83 DRNAS 87
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 29.3 bits (64), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 28/55 (50%), Gaps = 7/55 (12%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
E+F FGP+K K+ G A + +E A KA+++ +G +P+++
Sbjct: 23 EIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEVHGKSFANQPLEV 70
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 29.3 bits (64), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+Y++F ++GP++ ++ + + GTA ++YE DA A +G + R + +
Sbjct: 29 MYDIFGKYGPIRQIRV--GNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVV 83
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 29.3 bits (64), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 8/71 (11%)
Query: 2 IYELFSEFGPLKSAKLHYDRSG----RSLGTADLIYERRSDAIKAMKQ-YNGVPLDGRPM 56
I ELFS FG LK+ +L +G R G D I ++ DA KA + L GR +
Sbjct: 32 IRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ--DAKKAFNALCHSTHLYGRRL 89
Query: 57 QIQLA-ADVSV 66
++ A ++V+V
Sbjct: 90 VLEWADSEVTV 100
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 28.9 bits (63), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 28/55 (50%), Gaps = 7/55 (12%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
E+F FGP+K K+ G A + +E A KA+++ +G +P+++
Sbjct: 50 EIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEVHGKSFANQPLEV 97
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 28.5 bits (62), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ EL + FGPLK+ L D +G S G A Y + +A+ NG+ L + + +Q
Sbjct: 131 VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 190
Query: 61 AA 62
A+
Sbjct: 191 AS 192
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
Length = 125
Score = 28.5 bits (62), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
+Y++F ++GP++ ++ + + GTA ++YE DA A +G + R
Sbjct: 35 MYDIFGKYGPIRQIRV--GNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNR 85
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 28.5 bits (62), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
+Y++F ++GP++ ++ + + GTA ++YE DA A +G + R
Sbjct: 35 MYDIFGKYGPIRQIRV--GNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNR 85
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 7/56 (12%)
Query: 6 FSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
F E+GP+ + D A + ER DA++A++ + G+ M +QL+
Sbjct: 31 FEEYGPVIECDIVKDY-------AFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS 79
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 22/38 (57%)
Query: 21 RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+ G+S G A + ++ +DA K ++ G +DGR + +
Sbjct: 125 KDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISL 162
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ EL + FGPLK+ L D +G S G A Y + +A+ NG+ L + + +Q
Sbjct: 18 VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 77
Query: 61 AA 62
A+
Sbjct: 78 AS 79
>pdb|1WEZ|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein H'
Length = 102
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQ 45
IY FS P++ + GR G AD+ + DA+ AM +
Sbjct: 32 IYNFFSPLNPMR-VHIEIGPDGRVTGEADVEFATHEDAVAAMAK 74
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ EL + FGPLK+ L D +G S G A Y + +A+ NG+ L + + +Q
Sbjct: 113 VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 172
Query: 61 AA 62
A+
Sbjct: 173 AS 174
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ EL + FGPLK+ L D +G S G A Y + +A+ NG+ L + + +Q
Sbjct: 111 VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 170
Query: 61 AA 62
A+
Sbjct: 171 AS 172
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 23/38 (60%)
Query: 21 RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+ G+S G A + ++ +DA K +++ G +DGR + +
Sbjct: 131 QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL 168
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/58 (24%), Positives = 32/58 (55%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
E+ G +K +L +R+G+ G A + YE S A +A+ + +G+ + +++ ++
Sbjct: 36 EICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS 93
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 23/38 (60%)
Query: 21 RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+ G+S G A + ++ +DA K +++ G +DGR + +
Sbjct: 48 QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL 85
>pdb|2WVV|A Chain A, Crystal Structure Of An Alpha-L-Fucosidase Gh29 From
Bacteroides Thetaiotaomicron
pdb|2WVV|C Chain C, Crystal Structure Of An Alpha-L-Fucosidase Gh29 From
Bacteroides Thetaiotaomicron
pdb|2WVV|D Chain D, Crystal Structure Of An Alpha-L-Fucosidase Gh29 From
Bacteroides Thetaiotaomicron
Length = 450
Score = 26.9 bits (58), Expect = 2.8, Method: Composition-based stats.
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 15 AKLHYDRSGRSLGTADLIYERR-SDAIKAMK 44
K H+D +GR +G + YERR D +K +K
Sbjct: 235 GKRHFDSNGRLMGDYESGYERRLPDPVKDLK 265
>pdb|2WVV|B Chain B, Crystal Structure Of An Alpha-L-Fucosidase Gh29 From
Bacteroides Thetaiotaomicron
Length = 450
Score = 26.9 bits (58), Expect = 2.8, Method: Composition-based stats.
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 15 AKLHYDRSGRSLGTADLIYERR-SDAIKAMK 44
K H+D +GR +G + YERR D +K +K
Sbjct: 235 GKRHFDSNGRLMGDYESGYERRLPDPVKDLK 265
>pdb|2XIB|A Chain A, Crystal Structure Of An Alpha-L-Fucosidase Gh29 From
Bacteroides Thetaiotaomicron In Complex With
Deoxyfuconojirimycin
pdb|2XIB|B Chain B, Crystal Structure Of An Alpha-L-Fucosidase Gh29 From
Bacteroides Thetaiotaomicron In Complex With
Deoxyfuconojirimycin
pdb|2XIB|C Chain C, Crystal Structure Of An Alpha-L-Fucosidase Gh29 From
Bacteroides Thetaiotaomicron In Complex With
Deoxyfuconojirimycin
pdb|2XIB|D Chain D, Crystal Structure Of An Alpha-L-Fucosidase Gh29 From
Bacteroides Thetaiotaomicron In Complex With
Deoxyfuconojirimycin
pdb|2XII|A Chain A, Crystal Structure Of An Alpha-L-Fucosidase Gh29 From
Bacteroides Thetaiotaomicron In Complex With An Extended
9- Fluorenone Iminosugar Inhibitor
pdb|2XII|B Chain B, Crystal Structure Of An Alpha-L-Fucosidase Gh29 From
Bacteroides Thetaiotaomicron In Complex With An Extended
9- Fluorenone Iminosugar Inhibitor
Length = 453
Score = 26.9 bits (58), Expect = 2.8, Method: Composition-based stats.
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 15 AKLHYDRSGRSLGTADLIYERR-SDAIKAMK 44
K H+D +GR +G + YERR D +K +K
Sbjct: 238 GKRHFDSNGRLMGDYESGYERRLPDPVKDLK 268
>pdb|2WVT|A Chain A, Crystal Structure Of An Alpha-L-Fucosidase Gh29 From
Bacteroides Thetaiotaomicron In Complex With A Novel
Iminosugar Fucosidase Inhibitor
pdb|2WVT|B Chain B, Crystal Structure Of An Alpha-L-Fucosidase Gh29 From
Bacteroides Thetaiotaomicron In Complex With A Novel
Iminosugar Fucosidase Inhibitor
pdb|2WVU|A Chain A, Crystal Structure Of A Michaelis Complex Of Alpha-L-
Fucosidase Gh29 From Bacteroides Thetaiotaomicron With
The Synthetic Substrate 4-Nitrophenyl-Alpha-L-Fucose
pdb|2WVU|B Chain B, Crystal Structure Of A Michaelis Complex Of Alpha-L-
Fucosidase Gh29 From Bacteroides Thetaiotaomicron With
The Synthetic Substrate 4-Nitrophenyl-Alpha-L-Fucose
pdb|2WVU|C Chain C, Crystal Structure Of A Michaelis Complex Of Alpha-L-
Fucosidase Gh29 From Bacteroides Thetaiotaomicron With
The Synthetic Substrate 4-Nitrophenyl-Alpha-L-Fucose
pdb|2WVU|D Chain D, Crystal Structure Of A Michaelis Complex Of Alpha-L-
Fucosidase Gh29 From Bacteroides Thetaiotaomicron With
The Synthetic Substrate 4-Nitrophenyl-Alpha-L-Fucose
Length = 443
Score = 26.9 bits (58), Expect = 2.8, Method: Composition-based stats.
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 15 AKLHYDRSGRSLGTADLIYERR-SDAIKAMK 44
K H+D +GR +G + YERR D +K +K
Sbjct: 239 GKRHFDSNGRLMGDYESGYERRLPDPVKDLK 269
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 26.9 bits (58), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 7/48 (14%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNG 48
++ + FSEFG L+ K D A + +E R A+KAM + NG
Sbjct: 31 ILEKSFSEFGKLERVKKLKD-------YAFVHFEDRGAAVKAMDEMNG 71
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 27/45 (60%)
Query: 16 KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
K+ +++G+S G A + + DA +A+ N ++GR ++++L
Sbjct: 43 KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL 87
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 6/66 (9%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSL-GTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
++ LF +G ++ K+ +++ +L AD + A AM NG L G+P++I L
Sbjct: 21 LFILFGVYGDVQRVKILFNKKENALVQMAD-----GNQAQLAMSHLNGHKLHGKPIRITL 75
Query: 61 AADVSV 66
+ +V
Sbjct: 76 SKHQNV 81
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 26.2 bits (56), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
++ LF +G ++ K+ +++ +L + + A AM NG L G+P++I L+
Sbjct: 52 LFILFGVYGDVQRVKILFNKKENAL----VQMADGNQAQLAMSHLNGHKLHGKPIRITLS 107
Query: 62 ADVSV 66
+V
Sbjct: 108 KHQNV 112
>pdb|2WVS|A Chain A, Crystal Structure Of An Alpha-L-Fucosidase Gh29 Trapped
Covalent Intermediate From Bacteroides Thetaiotaomicron
In Complex With 2-Fluoro-Fucosyl Fluoride Using An E288q
Mutant
pdb|2WVS|B Chain B, Crystal Structure Of An Alpha-L-Fucosidase Gh29 Trapped
Covalent Intermediate From Bacteroides Thetaiotaomicron
In Complex With 2-Fluoro-Fucosyl Fluoride Using An E288q
Mutant
pdb|2WVS|C Chain C, Crystal Structure Of An Alpha-L-Fucosidase Gh29 Trapped
Covalent Intermediate From Bacteroides Thetaiotaomicron
In Complex With 2-Fluoro-Fucosyl Fluoride Using An E288q
Mutant
pdb|2WVS|D Chain D, Crystal Structure Of An Alpha-L-Fucosidase Gh29 Trapped
Covalent Intermediate From Bacteroides Thetaiotaomicron
In Complex With 2-Fluoro-Fucosyl Fluoride Using An E288q
Mutant
Length = 443
Score = 25.8 bits (55), Expect = 6.7, Method: Composition-based stats.
Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 15 AKLHYDRSGRSLGTADLIYERR-SDAIKAMK 44
K H+D +GR +G + Y+RR D +K +K
Sbjct: 239 GKRHFDSNGRLMGDYESGYQRRLPDPVKDLK 269
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 25.4 bits (54), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 4 ELFSEFGPLKSAKLHY-DRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
EL FG L+ L Y +R+G+S G Y ++ A +A G PL R + +
Sbjct: 114 ELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVH 170
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 25.4 bits (54), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 4 ELFSEFGPLKSAKLHY-DRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
EL FG L+ L Y +R+G+S G Y ++ A +A G PL R + +
Sbjct: 112 ELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVH 168
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 25.4 bits (54), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 4 ELFSEFGPLKSAKLHY-DRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
EL FG L+ L Y +R+G+S G Y ++ A +A G PL R + +
Sbjct: 114 ELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVH 170
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
0.318 0.137 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,516,027
Number of Sequences: 62578
Number of extensions: 72908
Number of successful extensions: 282
Number of sequences better than 100.0: 113
Number of HSP's better than 100.0 without gapping: 57
Number of HSP's successfully gapped in prelim test: 56
Number of HSP's that attempted gapping in prelim test: 207
Number of HSP's gapped (non-prelim): 118
length of query: 105
length of database: 14,973,337
effective HSP length: 70
effective length of query: 35
effective length of database: 10,592,877
effective search space: 370750695
effective search space used: 370750695
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)