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= 008851
(551 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 130 bits (327), Expect = 2e-30, Method: Composition-based stats.
Identities = 65/94 (69%), Positives = 74/94 (78%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
R VFVGNIPY+ATEEQL +I EVGPVVSFRLV DRETGKPKGYGFCEY+D+ETALSA R
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 67 NLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
NL G E +GR LRVD A ++K + + G G P
Sbjct: 69 NLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 102
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 92.0 bits (227), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 36/79 (45%), Positives = 59/79 (74%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
R V++G+IPYD TEEQ++++C VGPV++ +++ D +TG+ KGY F E++D E++ SA R
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 67 NLQGYEINGRQLRVDFAEN 85
NL GY++ R L+ ++ N
Sbjct: 63 NLNGYQLGSRFLKCGYSSN 81
>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 = 92.0 bits (227), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 36/79 (45%), Positives = 59/79 (74%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
R V++G+IPYD TEEQ++++C VGPV++ +++ D +TG+ KGY F E++D E++ SA R
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 67 NLQGYEINGRQLRVDFAEN 85
NL GY++ R L+ ++ N
Sbjct: 65 NLNGYQLGSRFLKCGYSSN 83
>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 = 89.4 bits (220), Expect = 5e-18, Method: Composition-based stats.
Identities = 36/79 (45%), Positives = 59/79 (74%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
R V++G+IPYD TEEQ++++C VGPV++ +++ D +TG+ KGY F E++D E++ SA R
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 67 NLQGYEINGRQLRVDFAEN 85
NL GY++ R L+ ++ N
Sbjct: 64 NLNGYQLGSRFLKCGYSSN 82
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 63.5 bits (153), Expect = 3e-10, Method: Composition-based stats.
Identities = 34/81 (41%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
R ++VGN+ Y AT EQ+ E+ + G V + +L+ DRET KPKG+GF E + EE+ A
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIA 60
Query: 67 NLQGYEINGRQLRVDFAENDK 87
L + GR +RV A K
Sbjct: 61 KLDNTDFMGRTIRVTEANPKK 81
>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 = 60.8 bits (146), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 43/75 (57%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
+ +FV + YD TE +L GP+ +V + +GKP+GY F EY+ E SA +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 67 NLQGYEINGRQLRVD 81
+ G +I+GR++ VD
Sbjct: 163 HADGKKIDGRRVLVD 177
>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 = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 43/75 (57%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
+ +FV + YD TE +L GP+ +V + +GKP+GY F EY+ E SA +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 67 NLQGYEINGRQLRVD 81
+ G +I+GR++ VD
Sbjct: 163 HADGKKIDGRRVLVD 177
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 59.7 bits (143), Expect = 4e-09, Method: Composition-based stats.
Identities = 28/72 (38%), Positives = 45/72 (62%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
++VG++ ++ TE+ L I G + S +L++D ETG+ KGYGF + D E A A L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 69 QGYEINGRQLRV 80
G+E+ GR ++V
Sbjct: 89 NGFELAGRPMKV 100
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 57.4 bits (137), Expect = 2e-08, Method: Composition-based stats.
Identities = 34/99 (34%), Positives = 50/99 (50%), Gaps = 7/99 (7%)
Query: 2 ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
SS ++VG++ ++ TE+ L I G + + L+ D +TG+ KGYGF + D E A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 62 LSARRNLQGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
A L G+E+ GR +RV G R G GP
Sbjct: 61 RRALEQLNGFELAGRPMRV-------GHVTERLDGGSGP 92
>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 = 57.4 bits (137), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
S H+ +F+G +P ++Q+ E+ GP+ +F LV D TG KGY FCEY D
Sbjct: 112 DSAHK-LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 170
Query: 63 SARRNLQGYEINGRQLRV 80
A L G ++ ++L V
Sbjct: 171 QAIAGLNGMQLGDKKLLV 188
>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 = 56.2 bits (134), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 39/72 (54%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+F+G +P ++Q+ E+ GP+ +F LV D TG KGY FCEY D A L
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 69 QGYEINGRQLRV 80
G ++ ++L V
Sbjct: 159 NGMQLGDKKLLV 170
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 56.2 bits (134), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 39/72 (54%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+F+G +P ++Q+ E+ GP+ +F LV D TG KGY FCEY D A L
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 69 QGYEINGRQLRV 80
G ++ ++L V
Sbjct: 157 NGMQLGDKKLLV 168
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In
Cytotoxic Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 55.5 bits (132), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 45/81 (55%)
Query: 3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
+S H VFVG++ + T E + G + R+V D TGK KGYGF + ++ A
Sbjct: 12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 71
Query: 63 SARRNLQGYEINGRQLRVDFA 83
+A + + G + GRQ+R ++A
Sbjct: 72 NAIQQMGGQWLGGRQIRTNWA 92
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 54.3 bits (129), Expect = 2e-07, Method: Composition-based stats.
Identities = 28/83 (33%), Positives = 50/83 (60%), Gaps = 1/83 (1%)
Query: 1 MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
MAS + + +FVG + +D E+ L ++ + G + +V DRET + +G+GF +++ +
Sbjct: 8 MASDEGK-LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDD 66
Query: 61 ALSARRNLQGYEINGRQLRVDFA 83
A A + G ++GRQ+RVD A
Sbjct: 67 AKDAMMAMNGKSVDGRQIRVDQA 89
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 43/77 (55%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
R + V IP E QL ++ GP+ S ++V DRET + +GYGF +++ +A A
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 67 NLQGYEINGRQLRVDFA 83
L G+ I ++L+V A
Sbjct: 103 GLNGFNILNKRLKVALA 119
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 53.9 bits (128), Expect = 2e-07, Method: Composition-based stats.
Identities = 27/75 (36%), Positives = 40/75 (53%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+F+G +P ++Q+ E+ GP+ +F LV D TG KGY FCEY D A L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 69 QGYEINGRQLRVDFA 83
G ++ ++L V A
Sbjct: 64 NGMQLGDKKLLVQRA 78
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 53.1 bits (126), Expect = 4e-07, Method: Composition-based stats.
Identities = 30/82 (36%), Positives = 47/82 (57%), Gaps = 3/82 (3%)
Query: 3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
S + +FV + D TEE L E V R+V DRETG KG+GF ++ EE A
Sbjct: 12 SQPSKTLFVKGLSEDTTEETLKE---SFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAK 68
Query: 63 SARRNLQGYEINGRQLRVDFAE 84
+A+ ++ EI+G ++ +D+A+
Sbjct: 69 AAKEAMEDGEIDGNKVTLDWAK 90
>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 = 52.8 bits (125), Expect = 5e-07, Method: Composition-based stats.
Identities = 30/91 (32%), Positives = 52/91 (57%), Gaps = 2/91 (2%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+FV +I +A E+++ E + G + + L +DR TG KGY EY+ + AL+A+ L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 69 QGYEINGRQLRVD--FAENDKGADRNREQGR 97
G EI G+ ++VD F + K ++ ++ R
Sbjct: 135 NGAEIMGQTIQVDWCFVKGPKRVKKSEKRRR 165
>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 = 52.4 bits (124), Expect = 6e-07, Method: Composition-based stats.
Identities = 27/72 (37%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+F+ +P+ T+E+L EIC+ G V RLV +R GKPKG + EY++E A A +
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKM 78
Query: 69 QGYEINGRQLRV 80
G I ++V
Sbjct: 79 DGMTIKENIIKV 90
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 52.4 bits (124), Expect = 7e-07, Method: Composition-based stats.
Identities = 27/74 (36%), Positives = 45/74 (60%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+FV +I +A E+++ E + G + + L +DR TG KGY EY+ + AL+A+ L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 69 QGYEINGRQLRVDF 82
G EI G+ ++VD+
Sbjct: 89 NGAEIMGQTIQVDW 102
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 46/80 (57%)
Query: 4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
+Q V+VG + +E L E+ + GPVV+ + DR TG+ +GYGF E+ EE A
Sbjct: 13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72
Query: 64 ARRNLQGYEINGRQLRVDFA 83
A + + ++ G+ +RV+ A
Sbjct: 73 AIKIMDMIKLYGKPIRVNKA 92
>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 = 51.2 bits (121), Expect = 2e-06, Method: Composition-based stats.
Identities = 28/93 (30%), Positives = 47/93 (50%), Gaps = 3/93 (3%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
++VGN+ + TEEQ+ E+ + G + + +D+ G+ F EY A +A R +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 69 QGYEINGRQLRVDFAENDKGADRNREQGRGGPG 101
G ++ R +R D+ D G R+ GRG G
Sbjct: 102 NGTRLDDRIIRTDW---DAGFKEGRQYGRGRSG 131
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 51.2 bits (121), Expect = 2e-06, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 44/76 (57%)
Query: 8 CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
C+ V + TE L E+ + GP+ +V D+++ + +G+ F +++ + A A+
Sbjct: 14 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 73
Query: 68 LQGYEINGRQLRVDFA 83
G E++GR++RVDF+
Sbjct: 74 ANGMELDGRRIRVDFS 89
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 51.2 bits (121), Expect = 2e-06, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 44/76 (57%)
Query: 8 CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
C+ V + TE L E+ + GP+ +V D+++ + +G+ F +++ + A A+
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 68 LQGYEINGRQLRVDFA 83
G E++GR++RVDF+
Sbjct: 77 ANGMELDGRRIRVDFS 92
>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 = 51.2 bits (121), Expect = 2e-06, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 46/75 (61%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+FVG++ + +E L ++ +S ++ D +TG +GYGF + ++ A +A ++
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 69 QGYEINGRQLRVDFA 83
QG ++NGR LR+++A
Sbjct: 64 QGQDLNGRPLRINWA 78
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 50.8 bits (120), Expect = 2e-06, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+FVG IP++ E +L E ++ G V ++ D E +P+G+GF ++DE++ A N+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQA-VNM 71
Query: 69 QGYEINGRQLRVDFAE 84
++I G+++ V AE
Sbjct: 72 HFHDIMGKKVEVKRAE 87
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 50.4 bits (119), Expect = 2e-06, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 46/75 (61%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+FVG++ + +E L ++ +S ++ D +TG +GYGF + ++ A +A ++
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 69 QGYEINGRQLRVDFA 83
QG ++NGR LR+++A
Sbjct: 150 QGQDLNGRPLRINWA 164
Score = 38.9 bits (89), Expect = 0.008, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
R ++VGN+ TE+ L + + GP+ + +++ID+ K Y F EY A A +
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNN-KNVNYAFVEYHQSHDANIALQ 59
Query: 67 NLQGYEINGRQLRVDFA 83
L G +I +++++A
Sbjct: 60 TLNGKQIENNIVKINWA 76
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 50.1 bits (118), Expect = 3e-06, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 44/76 (57%)
Query: 8 CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
C+ V + TE L E+ + GP+ +V D+++ + +G+ F +++ + A A+
Sbjct: 48 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
Query: 68 LQGYEINGRQLRVDFA 83
G E++GR++RVDF+
Sbjct: 108 ANGMELDGRRIRVDFS 123
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 49.3 bits (116), Expect = 5e-06, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 42/75 (56%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+ V +P D T+ +L + R +GP+ + R++ D +TG GY F ++ E + A + L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 69 QGYEINGRQLRVDFA 83
G + ++L+V +A
Sbjct: 66 NGITVRNKRLKVSYA 80
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From
Drosophila Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From
Drosophila Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From
Drosophila Melanogaster
Length = 184
Score = 48.9 bits (115), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 41/75 (54%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+ V +P D T+ +L + R +GP+ + R+ D +TG GY F ++ E + A + L
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 69 QGYEINGRQLRVDFA 83
G + ++L+V +A
Sbjct: 77 NGITVRNKRLKVSYA 91
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 31/56 (55%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
++V N+P T++QL I + G +V ++ D+ TG+P+G F Y E A A
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 158
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 48.9 bits (115), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 36/72 (50%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+FV N+ Y ++EE L ++ GP+ ID T KPKG+ F + E A+ A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 69 QGYEINGRQLRV 80
G GR L V
Sbjct: 71 DGQVFQGRMLHV 82
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 48.5 bits (114), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 41/76 (53%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+ V N+P T++Q E+ R G + LV TG+ KGYGF EY +++A A+ +L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 69 QGYEINGRQLRVDFAE 84
G + R L V + +
Sbjct: 158 LGKPLGPRTLYVHWTD 173
Score = 32.7 bits (73), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 4/79 (5%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVS--FRLVIDRETGKPKGYGFCEYKDEETALSA 64
RC+ V +P + + +CR + V S F + + G+ KG+ EY+ E A A
Sbjct: 185 RCLCVDRLPPGFND--VDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEA 242
Query: 65 RRNLQGYEINGRQLRVDFA 83
++ G + G LRV F
Sbjct: 243 QQQADGLSLGGSHLRVSFC 261
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 48.5 bits (114), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 41/76 (53%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+ V N+P T++Q E+ R G + LV TG+ KGYGF EY +++A A+ +L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 69 QGYEINGRQLRVDFAE 84
G + R L V + +
Sbjct: 158 LGKPLGPRTLYVHWTD 173
Score = 32.7 bits (73), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 4/79 (5%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVS--FRLVIDRETGKPKGYGFCEYKDEETALSA 64
RC+ V +P + + +CR + V S F + + G+ KG+ EY+ E A A
Sbjct: 185 RCLCVDRLPPGFND--VDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEA 242
Query: 65 RRNLQGYEINGRQLRVDFA 83
++ G + G LRV F
Sbjct: 243 QQQADGLSLGGSHLRVSFC 261
>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 = 48.5 bits (114), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 41/76 (53%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+ V N+P T++Q E+ R G + LV TG+ KGYGF EY +++A A+ +L
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 69 QGYEINGRQLRVDFAE 84
G + R L V + +
Sbjct: 156 LGKPLGPRTLYVHWTD 171
Score = 32.7 bits (73), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 4/79 (5%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVS--FRLVIDRETGKPKGYGFCEYKDEETALSA 64
RC+ V +P + + +CR + V S F + + G+ KG+ EY+ E A A
Sbjct: 183 RCLCVDRLPPGFND--VDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEA 240
Query: 65 RRNLQGYEINGRQLRVDFA 83
++ G + G LRV F
Sbjct: 241 QQQADGLSLGGSHLRVSFC 259
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 48.5 bits (114), Expect = 1e-05, Method: Composition-based stats.
Identities = 29/74 (39%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
R VFVGN+ EE L E+ + GP+ + DRE GKPK +GF +K E+ A
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIA 75
Query: 67 NLQGYEINGRQLRV 80
L G + GR + V
Sbjct: 76 LLNGIRLYGRPINV 89
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 48.1 bits (113), Expect = 1e-05, Method: Composition-based stats.
Identities = 28/81 (34%), Positives = 45/81 (55%)
Query: 3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
+S H VFVG++ + T E + G + R+V D TGK KGYGF + ++ A
Sbjct: 12 TSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAE 71
Query: 63 SARRNLQGYEINGRQLRVDFA 83
+A ++ G + GRQ+R ++A
Sbjct: 72 NAIVHMGGQWLGGRQIRTNWA 92
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 47.8 bits (112), Expect = 1e-05, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 42/75 (56%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+ V +P D T+ +L + R +GP+ + R++ D +TG GY F ++ E + A + L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 69 QGYEINGRQLRVDFA 83
G + ++L+V +A
Sbjct: 66 NGITVRNKRLKVSYA 80
Score = 39.7 bits (91), Expect = 0.004, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 31/56 (55%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
++V N+P T++QL I + G +V ++ D+ TG+P+G F Y E A A
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 147
>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 = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 41/72 (56%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
++V ++ D +++ + + G + S L D TGK KGYGF EY+ +++ A ++
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 69 QGYEINGRQLRV 80
+++ G+ LRV
Sbjct: 188 NLFDLGGQYLRV 199
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 37/72 (51%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
V+VG+I Y+ E+ + + GP+ S + D T K KG+ F EY+ E A A +
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 69 QGYEINGRQLRV 80
+ GR ++V
Sbjct: 91 NSVMLGGRNIKV 102
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug
Triplet Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 46/72 (63%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+F+ ++P + ++ L+++ G VVS ++ ID++T K +GF Y + +A +A +++
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 69 QGYEINGRQLRV 80
G++I ++L+V
Sbjct: 88 NGFQIGMKRLKV 99
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 30/91 (32%), Positives = 49/91 (53%), Gaps = 9/91 (9%)
Query: 10 FVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ 69
+VGN+P++ + + I +++ + S RLV D++T K KG+ + E+ DE +L
Sbjct: 19 YVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEF-DEVDSLKEALTYD 76
Query: 70 GYEINGRQLRVDFAENDKGADRNREQGRGGP 100
G + R LRVD AE R+Q + GP
Sbjct: 77 GALLGDRSLRVDIAE-------GRKQDKSGP 100
>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 = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 41/74 (55%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+FV + +ATEE + + E G + + L +DR TG KGY EY+ + A +A L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 69 QGYEINGRQLRVDF 82
G ++ G+ + VD+
Sbjct: 70 NGQDLMGQPISVDW 83
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 7/77 (9%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEE---TALS 63
R ++VGN+ Y AT E+L G V ++ D+ +G PKG+ + E+ D+E T+L+
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 65
Query: 64 ARRNLQGYEINGRQLRV 80
+L GRQ++V
Sbjct: 66 LDESL----FRGRQIKV 78
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of
Hypothetical Polyadenylate-Binding Protein (Pabpn1)
From Homo Sapiens At 1.95 A Resolution
Length = 89
Score = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 7/77 (9%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEE---TALS 63
R ++VGN+ Y AT E+L G V ++ D+ +G PKG+ + E+ D+E T+L+
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
Query: 64 ARRNLQGYEINGRQLRV 80
+L GRQ++V
Sbjct: 67 LDESL----FRGRQIKV 79
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 47.0 bits (110), Expect = 3e-05, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 41/74 (55%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+FV + +ATEE + + E G + + L +DR TG KGY EY+ + A +A L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 69 QGYEINGRQLRVDF 82
G ++ G+ + VD+
Sbjct: 70 NGQDLMGQPISVDW 83
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 46.6 bits (109), Expect = 3e-05, Method: Composition-based stats.
Identities = 26/92 (28%), Positives = 48/92 (52%), Gaps = 15/92 (16%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+F+GN+P +ATE+++ + + G V+ ++ K YGF +D+ A A RNL
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNL 62
Query: 69 QGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
Y+++G + V+ A +N+ + GP
Sbjct: 63 HHYKLHGVNINVE-------ASKNKSKASSGP 87
>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 = 46.6 bits (109), Expect = 4e-05, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 41/74 (55%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+FV + +ATEE + + E G + + L +DR TG KGY EY+ + A +A L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 69 QGYEINGRQLRVDF 82
G ++ G+ + VD+
Sbjct: 85 NGQDLMGQPISVDW 98
>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 = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 41/72 (56%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
++V ++ D +++ + + G + S L D TGK KGYGF EY+ +++ A ++
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 69 QGYEINGRQLRV 80
+++ G+ LRV
Sbjct: 173 NLFDLGGQYLRV 184
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 37/72 (51%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
V+VG+I Y+ E+ + + GP+ S + D T K KG+ F EY+ E A A +
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 69 QGYEINGRQLRV 80
+ GR ++V
Sbjct: 76 NSVMLGGRNIKV 87
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 40/75 (53%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+ V +P + T+++ + +G + S +LV D+ TG+ GYGF Y D A A L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 69 QGYEINGRQLRVDFA 83
G ++ + ++V +A
Sbjct: 67 NGLKLQTKTIKVSYA 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 = 46.2 bits (108), Expect = 5e-05, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 41/74 (55%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+FV + +ATEE + + E G + + L +DR TG KGY EY+ + A +A L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 69 QGYEINGRQLRVDF 82
G ++ G+ + VD+
Sbjct: 70 NGQDLMGQPISVDW 83
>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 = 46.2 bits (108), Expect = 5e-05, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 41/74 (55%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+FV + +ATEE + + E G + + L +DR TG KGY EY+ + A +A L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 69 QGYEINGRQLRVDF 82
G ++ G+ + VD+
Sbjct: 72 NGQDLMGQPISVDW 85
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 46.2 bits (108), Expect = 5e-05, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 40/75 (53%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
V+V N+P+ T L I + G VV ++ D++T K KG F + D+++A + R +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 69 QGYEINGRQLRVDFA 83
++ GR ++ A
Sbjct: 79 NNKQLFGRVIKASIA 93
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 45.8 bits (107), Expect = 6e-05, Method: Composition-based stats.
Identities = 29/87 (33%), Positives = 44/87 (50%), Gaps = 2/87 (2%)
Query: 2 ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
SS +FV N+P+D T + L + E G V+ I E GK KG G +++ E A
Sbjct: 1 GSSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYAD--IKMENGKSKGCGVVKFESPEVA 58
Query: 62 LSARRNLQGYEINGRQLRVDFAENDKG 88
A R + G +++GR++ V N G
Sbjct: 59 ERACRMMNGMKLSGREIDVRIDRNASG 85
>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 = 45.4 bits (106), Expect = 7e-05, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 41/74 (55%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+FV + +ATEE + + E G + + L +DR TG KGY EY+ + A +A L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 69 QGYEINGRQLRVDF 82
G ++ G+ + VD+
Sbjct: 86 NGQDLMGQPISVDW 99
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 45.4 bits (106), Expect = 8e-05, Method: Composition-based stats.
Identities = 27/86 (31%), Positives = 50/86 (58%), Gaps = 6/86 (6%)
Query: 4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
++ + VF+ N+ +D+ EE L E+ ++ G + R+V+ +T KG F ++ +E A
Sbjct: 13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72
Query: 64 --ARRNLQ----GYEINGRQLRVDFA 83
A +L+ G +++GRQL+VD A
Sbjct: 73 CLAAASLEAEGGGLKLDGRQLKVDLA 98
>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 = 45.4 bits (106), Expect = 8e-05, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 43/84 (51%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+ V +P + T+E+ + +G + S +LV D+ TG+ GYGF Y D + A A L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 69 QGYEINGRQLRVDFAENDKGADRN 92
G + + ++V +A + R+
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIRD 88
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 45.1 bits (105), Expect = 9e-05, Method: Composition-based stats.
Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 5/82 (6%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
R + N+PY T+++L E+ + + RLV + GK KG + E+K E A
Sbjct: 94 RTLLAKNLPYKVTQDELKEVFEDAAEI---RLV--SKDGKSKGIAYIEFKTEADAEKTFE 148
Query: 67 NLQGYEINGRQLRVDFAENDKG 88
QG EI+GR + + + KG
Sbjct: 149 EKQGTEIDGRSISLYYTGEPKG 170
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 41/73 (56%)
Query: 8 CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRN 67
C+ V + TE L E+ + GP+ +V D+++ + +G+ F +++ + A A+
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 68 LQGYEINGRQLRV 80
G E++GR++RV
Sbjct: 77 ANGMELDGRRIRV 89
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 42/83 (50%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+ V +P + T+++ + +G + S +LV D+ TG+ GYGF Y D A A L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 69 QGYEINGRQLRVDFAENDKGADR 91
G ++ + ++V +A + R
Sbjct: 67 NGLKLQTKTIKVSYARPSSASIR 89
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+FVG +PY T+ L + G + ++ DR+TGK +GYGF D A A ++
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 69 QGYEINGRQLRVDFA 83
I+GR+ V+ A
Sbjct: 80 NPI-IDGRKANVNLA 93
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+FV N+P+D T + L + E G V+ I E GK KG G +++ E A A R +
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYAD--IKMENGKSKGCGVVKFESPEVAERACRMM 68
Query: 69 QGYEINGRQLRVDFAENDKG 88
G +++GR++ V N G
Sbjct: 69 NGMKLSGREIDVRIDRNASG 88
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 42/72 (58%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+F+ ++P + T+ L G V+S ++ ID++T K +GF + + ++A A + +
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 69 QGYEINGRQLRV 80
G+++ ++L+V
Sbjct: 103 NGFQVGTKRLKV 114
>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 = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
++V ++ D +++ + + G + S L D TGK KGYGF EY+ +++ A +
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 69 QGYEINGRQLRV 80
+++ G+ LRV
Sbjct: 172 NLFDLGGQYLRV 183
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 35/72 (48%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
V+VG+I Y+ E+ + + GP+ S D T K KG+ F EY+ E A A
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 69 QGYEINGRQLRV 80
+ GR ++V
Sbjct: 75 NSVXLGGRNIKV 86
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 44/83 (53%)
Query: 2 ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
S+ R ++VG + + ++ L G + ++ +D ET K +G+ F E++ E A
Sbjct: 1 GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60
Query: 62 LSARRNLQGYEINGRQLRVDFAE 84
+A N+ E+ GR +RV+ A+
Sbjct: 61 AAAIDNMNESELFGRTIRVNLAK 83
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
+ + + + N+ Y ATEE L +EV +F V + GK KGY F E+ E A A
Sbjct: 14 ESKTLVLSNLSYSATEETL----QEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEA 69
Query: 65 RRNLQGYEINGRQLRVD 81
+ EI GR +R++
Sbjct: 70 LNSCNKREIEGRAIRLE 86
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 29/88 (32%), Positives = 45/88 (51%), Gaps = 7/88 (7%)
Query: 2 ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKP-----KGYGFCEYK 56
SS +F+ N+ + TEE L + +VG + S I ++ K G+GF EYK
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKS--CTISKKKNKAGVLLSMGFGFVEYK 58
Query: 57 DEETALSARRNLQGYEINGRQLRVDFAE 84
E A A + LQG+ ++G +L V +E
Sbjct: 59 KPEQAQKALKQLQGHTVDGHKLEVRISE 86
>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 = 43.5 bits (101), Expect = 3e-04, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 47/84 (55%), Gaps = 1/84 (1%)
Query: 1 MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
MA+++ R ++VG + + ++ L G + ++ +D ET K +G+ F E++ E
Sbjct: 3 MATTK-RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61
Query: 61 ALSARRNLQGYEINGRQLRVDFAE 84
A +A N+ E+ GR +RV+ A+
Sbjct: 62 AAAAIDNMNESELFGRTIRVNLAK 85
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 42.7 bits (99), Expect = 5e-04, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 43/81 (53%)
Query: 3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETAL 62
++ R ++VG + + ++ L G + ++ +D ET K +G+ F E++ E A
Sbjct: 60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 119
Query: 63 SARRNLQGYEINGRQLRVDFA 83
+A N+ E+ GR +RV+ A
Sbjct: 120 AAIDNMNESELFGRTIRVNLA 140
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 45/86 (52%), Gaps = 8/86 (9%)
Query: 6 HRCVFVGNIPYDATEEQLIEICREV----GPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
++ +++ N+ TE L+ + GP + FR++ TG+ +G F + ++E A
Sbjct: 25 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM----TGRMRGQAFITFPNKEIA 80
Query: 62 LSARRNLQGYEINGRQLRVDFAENDK 87
A + GY++ G+ L ++F +N K
Sbjct: 81 WQALHLVNGYKLYGKILVIEFGKNKK 106
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+F+G + + E+ L + + GP+ L+ DR T K +G+ F +++ A +A +++
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 69 QGYEINGRQLRVD 81
G ++G+ ++V+
Sbjct: 69 NGKSLHGKAIKVE 81
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 42.4 bits (98), Expect = 6e-04, Method: Composition-based stats.
Identities = 26/78 (33%), Positives = 42/78 (53%)
Query: 6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
H VFVG++ + T + G + R+V D TGK KGYGF + ++ A +A
Sbjct: 6 HFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 65
Query: 66 RNLQGYEINGRQLRVDFA 83
+ + G + GRQ+R ++A
Sbjct: 66 QQMGGQWLGGRQIRTNWA 83
>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 = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 38/76 (50%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+ V +P + T+++L + +G V S +L+ D+ G GYGF Y + A A L
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 69 QGYEINGRQLRVDFAE 84
G + + ++V +A
Sbjct: 67 NGLRLQSKTIKVSYAR 82
>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 = 42.4 bits (98), Expect = 7e-04, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 41/77 (53%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
R ++VG + + ++ L G + ++ +D ET K +G+ F E++ E A +A
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 67 NLQGYEINGRQLRVDFA 83
N+ E+ GR +RV+ A
Sbjct: 63 NMNESELFGRTIRVNLA 79
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
+Q +FVGN+P D TEE++ ++ + G + K KG+GF + A
Sbjct: 20 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEI 73
Query: 64 ARRNLQGYEINGRQLRVDFA 83
A+ L + G+QLRV FA
Sbjct: 74 AKVELDNMPLRGKQLRVRFA 93
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 42.4 bits (98), Expect = 8e-04, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 47/84 (55%), Gaps = 1/84 (1%)
Query: 1 MASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
MA+++ R ++VG + + ++ L G + ++ +D ET K +G+ F E++ E
Sbjct: 8 MATTK-RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 66
Query: 61 ALSARRNLQGYEINGRQLRVDFAE 84
A +A N+ E+ GR +RV+ A+
Sbjct: 67 AAAAIDNMNESELFGRTIRVNLAK 90
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 42.0 bits (97), Expect = 9e-04, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 47/79 (59%), Gaps = 2/79 (2%)
Query: 5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
Q R ++VGN+ D TE ++++ ++GP S +++ + + P Y F E+ + A +A
Sbjct: 14 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAA 71
Query: 65 RRNLQGYEINGRQLRVDFA 83
+ G +I G++++V++A
Sbjct: 72 LAAMNGRKILGKEVKVNWA 90
>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 = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 38/75 (50%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+ V +P + T+++L + +G V S +L+ D+ G GYGF Y + A A L
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 69 QGYEINGRQLRVDFA 83
G + + ++V +A
Sbjct: 82 NGLRLQSKTIKVSYA 96
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition
Motif Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition
Motif Of Nono
Length = 99
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
+Q +FVGN+P D TEE++ ++ + G + K KG+GF + A
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEI 66
Query: 64 ARRNLQGYEINGRQLRVDFA 83
A+ L + G+QLRV FA
Sbjct: 67 AKVELDNMPLRGKQLRVRFA 86
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs
Of Human Antigen R
Length = 177
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 38/75 (50%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+ V +P + T+++L + +G V S +L+ D+ G GYGF Y + A A L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 69 QGYEINGRQLRVDFA 83
G + + ++V +A
Sbjct: 65 NGLRLQSKTIKVSYA 79
>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 = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 38/75 (50%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+ V +P + T+++L + +G V S +L+ D+ G GYGF Y + A A L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 69 QGYEINGRQLRVDFA 83
G + + ++V +A
Sbjct: 65 NGLRLQSKTIKVSYA 79
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 24/88 (27%), Positives = 43/88 (48%), Gaps = 3/88 (3%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
++VGN+P D + + ++ + G + L +R G P + F E++D A A
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLK-NRRGGPP--FAFVEFEDPRDAEDAVYGR 81
Query: 69 QGYEINGRQLRVDFAENDKGADRNREQG 96
GY+ +G +LRV+F + +G G
Sbjct: 82 DGYDYDGYRLRVEFPRSGRGTGSGPSSG 109
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The
Second Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 31/56 (55%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
++V N+P T++QL I + G +V ++ D+ TG+P+G F Y E A A
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 71
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 26/85 (30%), Positives = 43/85 (50%), Gaps = 6/85 (7%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
R + N+ ++ TE++L E+ + + RLV + GK KG + E+K E A
Sbjct: 17 RTLLAKNLSFNITEDELKEVFEDA---LEIRLV--SQDGKSKGIAYIEFKSEADAEKNLE 71
Query: 67 NLQGYEINGRQLRVDFAENDKGADR 91
QG EI+GR + + + +KG R
Sbjct: 72 EKQGAEIDGRSVSL-YYTGEKGGTR 95
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 39/79 (49%), Gaps = 9/79 (11%)
Query: 7 RC-VFVGNIPYDATEEQLIEICREVG-PVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
RC +FVGN+P D TEE + G P F I+R+ +G+GF + A A
Sbjct: 22 RCRLFVGNLPTDITEEDFKRLFERYGEPSEVF---INRD----RGFGFIRLESRTLAEIA 74
Query: 65 RRNLQGYEINGRQLRVDFA 83
+ L G + R LR+ FA
Sbjct: 75 KAELDGTILKSRPLRIRFA 93
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 38/80 (47%)
Query: 11 VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG 70
V N+ Y + + L + + G V + DR T + +G+ F + D+ A A + G
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 71 YEINGRQLRVDFAENDKGAD 90
++GR+LRV A + D
Sbjct: 135 AVLDGRELRVQMARYGRPPD 154
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 29/98 (29%), Positives = 46/98 (46%), Gaps = 8/98 (8%)
Query: 9 VFVGNIPYDATEEQLIE----ICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
+F+G IP E+++E + V V+ + D+ K +G+ F EY+ A A
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKM--KNRGFAFVEYESHRAAAMA 68
Query: 65 RRNLQGYEIN--GRQLRVDFAENDKGADRNREQGRGGP 100
RR L I G Q+ VD+AE + D + + GP
Sbjct: 69 RRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSGP 106
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 41/68 (60%), Gaps = 1/68 (1%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+F+G + +D T++ L + + G VV L +D TG+ +G+GF +K+ E+ + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESES-VDKVMDQ 60
Query: 69 QGYEINGR 76
+ +++NG+
Sbjct: 61 KEHKLNGK 68
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 30/61 (49%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+FVG IP E+ L + E G + ++ DR TG KG F Y ++AL A+ L
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSAL 77
Query: 69 Q 69
Sbjct: 78 H 78
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 35/73 (47%)
Query: 11 VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG 70
V N+ Y + + L + + G V + + T P+G+ F + D A A + G
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 71 YEINGRQLRVDFA 83
E++GR+LRV A
Sbjct: 78 AELDGRELRVQVA 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 = 0.006, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
++VGN+ + TEEQ+ E+ + G + + +D+ G+ F EY A +A R +
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-MKTACGFCFVEYYSRADAENAMRYI 79
Query: 69 QGYEINGRQLRVDF 82
G ++ R +R D+
Sbjct: 80 NGTRLDDRIIRTDW 93
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 39.3 bits (90), Expect = 0.006, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 32/61 (52%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+F+G IP + E+ L + E G + ++ DR TG KG F Y + E+AL A+ L
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 69 Q 69
Sbjct: 76 H 76
>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 = 38.9 bits (89), Expect = 0.007, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 42/82 (51%), Gaps = 6/82 (7%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
R + N+ ++ TE++L E+ + + RLV + GK KG + E+K E A
Sbjct: 100 RTLLAKNLSFNITEDELKEVFEDA---LEIRLV--SQDGKSKGIAYIEFKSEADAEKNLE 154
Query: 67 NLQGYEINGRQLRVDFAENDKG 88
QG EI+GR + + + +KG
Sbjct: 155 EKQGAEIDGRSVSL-YYTGEKG 175
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 2/75 (2%)
Query: 8 CVFVGNIPYDATEEQLIEICREVG--PVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
V+VG+ + T++QLI++ R +G VV + +R G+ KGY E +
Sbjct: 57 AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116
Query: 66 RNLQGYEINGRQLRV 80
L G +NG ++ V
Sbjct: 117 ELLPGKVLNGEKVDV 131
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 27/53 (50%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
+FVG I D E L + + G + ++ DR +GK +G+ F + D ++
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 158
Score = 33.9 bits (76), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
Q R +F+G + ++ T+E L + G + ++ D T + +G+GF Y E + A
Sbjct: 11 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDA 69
Query: 65 RRNLQGYEINGR 76
N + ++++GR
Sbjct: 70 AMNARPHKVDGR 81
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 27/53 (50%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
+FVG I D E L + + G + ++ DR +GK +G+ F + D ++
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 159
Score = 33.9 bits (76), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
Q R +F+G + ++ T+E L + G + ++ D T + +G+GF Y E + A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDA 70
Query: 65 RRNLQGYEINGR 76
N + ++++GR
Sbjct: 71 AMNARPHKVDGR 82
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 38.9 bits (89), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 27/53 (50%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
+FVG I D E L + + G + ++ DR +GK +G+ F + D ++
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 160
Score = 33.5 bits (75), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
Q R +F+G + ++ T+E L + G + ++ D T + +G+GF Y E + A
Sbjct: 13 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDA 71
Query: 65 RRNLQGYEINGR 76
N + ++++GR
Sbjct: 72 AMNARPHKVDGR 83
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 38.5 bits (88), Expect = 0.009, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 29/47 (61%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEY 55
+FVG I D ++ E + G ++ +L++D++TG+ +G+GF Y
Sbjct: 90 IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY 136
Score = 38.5 bits (88), Expect = 0.010, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 29/48 (60%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYK 56
+F+G + +D TE+ L E + G V +++ D TG+ +G+GF ++
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFE 53
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 38.5 bits (88), Expect = 0.009, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
+R +++ N+PY T E++ +I + GP+ R+ ET +G + Y+D A +A
Sbjct: 8 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAV 64
Query: 66 RNLQGYEINGRQLRV 80
+L G+ ++ R L V
Sbjct: 65 DHLSGFNVSNRYLVV 79
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 38.5 bits (88), Expect = 0.010, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 29/51 (56%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEE 59
+FVG + D EE++ E G V S L +D +T K +G+ F +K+EE
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 52
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 38.5 bits (88), Expect = 0.010, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 29/51 (56%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEE 59
+FVG + D EE++ E G V S L +D +T K +G+ F +K+EE
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 54
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 38.1 bits (87), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 27/53 (50%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
+FVG I D E L + + G + ++ DR +GK +G+ F + D ++
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 159
Score = 33.1 bits (74), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
Q R +F+G + ++ T+E L + G + ++ D T + +G+GF Y E + A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDA 70
Query: 65 RRNLQGYEINGR 76
N + ++++GR
Sbjct: 71 AMNARPHKVDGR 82
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 38.1 bits (87), Expect = 0.012, Method: Composition-based stats.
Identities = 19/78 (24%), Positives = 40/78 (51%)
Query: 2 ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
SS +++ + T++ L+++C+ G +VS + ++D+ T K KGYGF ++ A
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 62 LSARRNLQGYEINGRQLR 79
A L+ + + +
Sbjct: 61 QKAVTALKASGVQAQMAK 78
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 38.1 bits (87), Expect = 0.013, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 2/80 (2%)
Query: 4 SQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALS 63
SQ + + V NIP+ + L ++ + G ++ ++ + E G KG+GF +++ A
Sbjct: 27 SQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGS-KGFGFVTFENSADADR 84
Query: 64 ARRNLQGYEINGRQLRVDFA 83
AR L G + GR++ V+ A
Sbjct: 85 AREKLHGTVVEGRKIEVNNA 104
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 38.1 bits (87), Expect = 0.014, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
+R +++ N+PY T E++ +I + GP+ R+ ET +G + Y+D A +A
Sbjct: 12 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAC 68
Query: 66 RNLQGYEINGRQLRV 80
+L G+ + R L V
Sbjct: 69 DHLSGFNVCNRYLVV 83
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 37.7 bits (86), Expect = 0.016, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARR 66
R V+VGN+ Y +T + L G + ++ D+ +G PKGY + E+ E ++ A
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFA-ERNSVDAAV 95
Query: 67 NLQGYEINGRQLRV 80
+ GR ++V
Sbjct: 96 AMDETVFRGRTIKV 109
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 37.7 bits (86), Expect = 0.016, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 5/79 (6%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
V+VGN+ + + +L GP+ S + + P G+ F E++D A A R+L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRDL 130
Query: 69 QGYEINGRQLRVDFAENDK 87
G + G ++RV+ + +K
Sbjct: 131 DGRTLCGCRVRVELSNGEK 149
>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 = 37.7 bits (86), Expect = 0.017, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 38/80 (47%)
Query: 11 VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG 70
V N+ Y + + L + + G V + DR T + +G+ F + D+ A A + G
Sbjct: 52 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111
Query: 71 YEINGRQLRVDFAENDKGAD 90
++GR+LRV A + D
Sbjct: 112 AVLDGRELRVQMARYGRPPD 131
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 37.4 bits (85), Expect = 0.022, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 35/74 (47%)
Query: 11 VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG 70
V N+ D E L E+ R G + L D+ TG+ KG+ F + E A A + G
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
Query: 71 YEINGRQLRVDFAE 84
+ + L V++A+
Sbjct: 80 FGYDHLILNVEWAK 93
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 37.0 bits (84), Expect = 0.025, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 5/79 (6%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
V+VGN+ + + +L GP+ S + + P G+ F E++D A A R L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVREL 130
Query: 69 QGYEINGRQLRVDFAENDK 87
G + G ++RV+ + +K
Sbjct: 131 DGRTLCGCRVRVELSNGEK 149
>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 = 37.0 bits (84), Expect = 0.029, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
+R +++ N+PY T E++ +I + GP+ R+ ET +G + Y+D A +A
Sbjct: 18 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAC 74
Query: 66 RNLQGYEINGRQLRV 80
+L G+ + R L V
Sbjct: 75 DHLSGFNVCNRYLVV 89
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation
Initiation Factor 4b
Length = 100
Score = 37.0 bits (84), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 46/80 (57%), Gaps = 7/80 (8%)
Query: 8 CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKP---KGYGFCEYKDEETALSA 64
F+GN+PYD TEE + E R + + + RL RE P KG+G+ E++D ++ LSA
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRL--PREPSNPERLKGFGYAEFEDLDSLLSA 77
Query: 65 RRNLQGYEINGRQLRVDFAE 84
+ + R++RVD A+
Sbjct: 78 LSLNEE-SLGNRRIRVDVAD 96
>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 = 36.6 bits (83), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+F+ N+ + L + G ++S ++V D E G KGYGF ++ +E A A +
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAIEKM 158
Query: 69 QGYEINGRQLRV 80
G +N R++ V
Sbjct: 159 NGMLLNDRKVFV 170
Score = 35.8 bits (81), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 39/78 (50%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
++VG++ D TE L E GP++S R+ D T + GY + ++ A A +
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 69 QGYEINGRQLRVDFAEND 86
I G+ +R+ +++ D
Sbjct: 73 NFDVIKGKPVRIMWSQRD 90
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 36.6 bits (83), Expect = 0.037, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 28/48 (58%)
Query: 10 FVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKD 57
FVG + +D +++ L + + G VV + D TG+ +G+GF +KD
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKD 62
>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 = 36.6 bits (83), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+F+ N+ + L + G ++S ++V D E G KGYGF ++ +E A A +
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGS-KGYGFVHFETQEAAERAIEKM 163
Query: 69 QGYEINGRQLRV 80
G +N R++ V
Sbjct: 164 NGMLLNDRKVFV 175
Score = 36.2 bits (82), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 39/78 (50%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
++VG++ D TE L E GP++S R+ D T + GY + ++ A A +
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 69 QGYEINGRQLRVDFAEND 86
I G+ +R+ +++ D
Sbjct: 78 NFDVIKGKPVRIMWSQRD 95
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 36.6 bits (83), Expect = 0.041, Method: Composition-based stats.
Identities = 15/52 (28%), Positives = 27/52 (51%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
+FVG I D E L + + G + ++ DR +GK +G+ F + D ++
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 151
Score = 34.7 bits (78), Expect = 0.12, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
Q R +F+G + ++ T+E L + G + ++ D T + +G+GF Y E + A
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDA 63
Query: 65 RRNLQGYEINGR 76
N + ++++GR
Sbjct: 64 AMNARPHKVDGR 75
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 36.2 bits (82), Expect = 0.045, Method: Composition-based stats.
Identities = 15/52 (28%), Positives = 27/52 (51%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEET 60
+FVG I D E L + + G + ++ DR +GK +G+ F + D ++
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 156
Score = 34.7 bits (78), Expect = 0.15, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSA 64
Q R +F+G + ++ T+E L + G + ++ D T + +G+GF Y E + A
Sbjct: 10 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE-EVDA 68
Query: 65 RRNLQGYEINGR 76
N + ++++GR
Sbjct: 69 AMNARPHKVDGR 80
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 36.2 bits (82), Expect = 0.046, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 2/73 (2%)
Query: 11 VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG 70
V NIP+ + L ++ + G ++ ++ + E G KG+GF +++ A AR L G
Sbjct: 20 VSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGS-KGFGFVTFENSADADRAREKLHG 77
Query: 71 YEINGRQLRVDFA 83
+ GR++ V+ A
Sbjct: 78 TVVEGRKIEVNNA 90
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 36.2 bits (82), Expect = 0.049, Method: Composition-based stats.
Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 8/89 (8%)
Query: 3 SSQHRCVFVGNIPYDATEEQLIEICREVGPVVS--------FRLVIDRETGKPKGYGFCE 54
+S + +FV + + T E + + +++G + + L DRETGK KG
Sbjct: 4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63
Query: 55 YKDEETALSARRNLQGYEINGRQLRVDFA 83
+ D +A +A G E +G ++V FA
Sbjct: 64 FDDPPSAKAAIDWFDGKEFSGNPIKVSFA 92
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 35.8 bits (81), Expect = 0.061, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 4/70 (5%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEE---TALSAR 65
+FVG + + T+E L + G VV ++ D+ T + +G+GF ++KD T L++R
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 66 -RNLQGYEIN 74
L G I+
Sbjct: 79 PHTLDGRNID 88
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 35.4 bits (80), Expect = 0.077, Method: Composition-based stats.
Identities = 23/88 (26%), Positives = 39/88 (44%), Gaps = 2/88 (2%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+ V +P+ TE+ L E G V+ ++ D +TG KG+GF + + ET +
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-- 75
Query: 69 QGYEINGRQLRVDFAENDKGADRNREQG 96
Q + I+GR + + D G
Sbjct: 76 QRHMIDGRWCDCKLPNSKQSQDSGPSSG 103
>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 = 35.4 bits (80), Expect = 0.079, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 6 HRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSAR 65
+R + + N+PY T E++ +I + GP+ R+ ET +G + Y+D A +A
Sbjct: 18 NRILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAC 74
Query: 66 RNLQGYEINGRQLRV 80
+L G+ + R L V
Sbjct: 75 DHLSGFNVCNRYLVV 89
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 35.4 bits (80), Expect = 0.079, Method: Composition-based stats.
Identities = 18/46 (39%), Positives = 26/46 (56%)
Query: 38 LVIDRETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQLRVDFA 83
+ +D+ETGKPKG Y+D TA +A G + G +L+V A
Sbjct: 55 IYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA 100
>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 = 35.0 bits (79), Expect = 0.10, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+F+ N+ + L + G ++S ++V D E G KGYGF ++ +E A A +
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGS-KGYGFVHFETQEAAERAIEKM 65
Query: 69 QGYEINGRQLRV 80
G +N R++ V
Sbjct: 66 NGMLLNDRKVFV 77
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 35.0 bits (79), Expect = 0.10, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+F+ N+ + L + G ++S ++V D E G KGYGF ++ +E A A +
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGS-KGYGFVHFETQEAAERAIEKM 71
Query: 69 QGYEINGRQLRV 80
G +N R++ V
Sbjct: 72 NGMLLNDRKVFV 83
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 35.0 bits (79), Expect = 0.10, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 8/83 (9%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVS--------FRLVIDRETGKPKGYGFCEYKDEET 60
+FV + + T E + + +++G + + L DRETGK KG + D +
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 61 ALSARRNLQGYEINGRQLRVDFA 83
A +A G E +G ++V FA
Sbjct: 76 AKAAIDWFDGKEFSGNPIKVSFA 98
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
Length = 88
Score = 34.3 bits (77), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 2/67 (2%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKP--KGYGFCEYKDEETALSARR 66
+FVG +P +E+ L E+ + G V ++ DR P KG F + + AL A+
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 67 NLQGYEI 73
L ++
Sbjct: 66 ALHNMKV 72
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 34.3 bits (77), Expect = 0.21, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 33/79 (41%), Gaps = 5/79 (6%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
V+VGN+P DA L RE+G V RL P+ F Y D A A L
Sbjct: 22 VYVGNLPRDARVSDLKRALRELGS-VPLRLTWQ----GPRRRAFLHYPDSAAAQQAVSCL 76
Query: 69 QGYEINGRQLRVDFAENDK 87
QG + LRV A +
Sbjct: 77 QGLRLGTDTLRVALARQQR 95
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 33.9 bits (76), Expect = 0.27, Method: Composition-based stats.
Identities = 30/90 (33%), Positives = 49/90 (54%), Gaps = 7/90 (7%)
Query: 10 FVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKP---KGYGFCEYKDEETALSARR 66
F+GN+PYD TEE + E R + + + RL RE P KG+G+ E++D ++ LSA
Sbjct: 19 FLGNLPYDVTEESIKEFFRGLN-ISAVRL--PREPSNPERLKGFGYAEFEDLDSLLSALS 75
Query: 67 NLQGYEINGRQLRVDFAENDKGADRNREQG 96
+ + +++RVD A+ + D G
Sbjct: 76 LNE-ESLGNKRIRVDVADQAQDKDSGPSSG 104
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 33.5 bits (75), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 2/67 (2%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKP--KGYGFCEYKDEETALSARR 66
+FVG +P +E+ L E+ + G V ++ DR P KG F + + AL A+
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 67 NLQGYEI 73
L ++
Sbjct: 78 ALHNMKV 84
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 33.5 bits (75), Expect = 0.31, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 6/75 (8%)
Query: 10 FVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQ 69
++GNIP+ ATE LI + + G ++ F+ + KG F +Y E A L
Sbjct: 31 YIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVALA 84
Query: 70 GYEINGRQLRVDFAE 84
+ GR LR + +
Sbjct: 85 NFPFQGRNLRTGWGK 99
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 33.5 bits (75), Expect = 0.31, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
V+VGN+ A + +L GP+ + + + P G+ F E++D A A R L
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 69 QGYEINGRQLRVDFA 83
G I G ++RV+ +
Sbjct: 58 DGKVICGSRVRVELS 72
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 33.1 bits (74), Expect = 0.37, Method: Composition-based stats.
Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 43 ETGKPKGYGFCEYKDEETALSARRNLQGYEINGRQ-LRVD-FAENDK 87
E GK KGY F EY A+ A +N GY+++ + RV+ F + DK
Sbjct: 56 EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDFDK 102
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 33.1 bits (74), Expect = 0.40, Method: Composition-based stats.
Identities = 22/69 (31%), Positives = 32/69 (46%)
Query: 2 ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
+S +FVG++ D + L E +V P V+ +TG KGYGF ++ DE
Sbjct: 5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQ 64
Query: 62 LSARRNLQG 70
A QG
Sbjct: 65 KRALTECQG 73
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 33.1 bits (74), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 2/67 (2%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKP--KGYGFCEYKDEETALSARR 66
+FVG +P +E+ L E+ + G V ++ DR P KG F + + AL A+
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 67 NLQGYEI 73
L ++
Sbjct: 66 ALHNMKV 72
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 33.1 bits (74), Expect = 0.46, Method: Composition-based stats.
Identities = 14/51 (27%), Positives = 27/51 (52%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEE 59
+FVG + + T E + + G V L+ D+ T + +G+GF ++ E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 32.7 bits (73), Expect = 0.49, Method: Composition-based stats.
Identities = 23/92 (25%), Positives = 40/92 (43%), Gaps = 16/92 (17%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+FVGN+ T ++L + G V+ +V K Y F + E A +A L
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQL 63
Query: 69 QGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
G E+ G+++ V+ + + Q + GP
Sbjct: 64 NGKEVKGKRINVELS--------TKGQKKSGP 87
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 32.3 bits (72), Expect = 0.61, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 32/73 (43%), Gaps = 8/73 (10%)
Query: 11 VGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQG 70
VGNI T ++L E GPV+ +V K Y F + E A+ A R L
Sbjct: 15 VGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLDN 66
Query: 71 YEINGRQLRVDFA 83
E G+++ V +
Sbjct: 67 TEFQGKRMHVQLS 79
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 32.3 bits (72), Expect = 0.71, Method: Composition-based stats.
Identities = 16/71 (22%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDR-ETGKPKGYGFCEYKDEETALSARRN 67
V +G + + T++ ++EI G + + ++R KGY + E+++ + A A ++
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 68 LQGYEINGRQL 78
+ G +I+G+++
Sbjct: 67 MDGGQIDGQEI 77
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 32.3 bits (72), Expect = 0.77, Method: Composition-based stats.
Identities = 22/91 (24%), Positives = 45/91 (49%), Gaps = 3/91 (3%)
Query: 2 ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSF-RLVIDRETGKPKGYGFCEYKDEET 60
SS +F+GN+ + E+ L + G ++ +++ D +TG KGY F + +
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 61 ALSARRNLQGYEINGRQLRVDFA--ENDKGA 89
+ +A + G + R + V +A ++ KG+
Sbjct: 61 SDAAIEAMNGQYLCNRPITVSYAFKKDSKGS 91
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 31.6 bits (70), Expect = 1.2, Method: Composition-based stats.
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 43 ETGKPKGYGFCEYKDEETALSARRNLQGYEIN 74
E GK KGY F EY A+ A +N GY+++
Sbjct: 42 EDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 73
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 31.6 bits (70), Expect = 1.2, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDE 58
VFVG I E ++ G V +++ DR TG KGYGF + ++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYND 60
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 31.6 bits (70), Expect = 1.3, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDE 58
VFVG I E ++ G V +++ DR TG KGYGF + ++
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYND 61
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 31.6 bits (70), Expect = 1.3, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 10 FVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFC--EYKDEETALSARRN 67
FVG +P +E+ L E+ + G V ++ DR P+ G C + + AL A+
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 68 LQGYEI 73
L ++
Sbjct: 67 LHNXKV 72
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 31.2 bits (69), Expect = 1.4, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 12/61 (19%)
Query: 7 RCVFVGNIPYDATEEQLIEICREVGPVVSFRLVID-------RETGKPKGYGFCEYKDEE 59
R VFVG +P D E+++ R GP LV+D + PKGY F +++E
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGP-----LVVDWPHKAESKSYFPPKGYAFLLFQEES 63
Query: 60 T 60
+
Sbjct: 64 S 64
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+++ N+P E++L + + G V+S R++ D +G +G GF + E + +
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 69 QGYEI 73
G I
Sbjct: 87 NGKFI 91
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 49 GYGFCEYKDEETALSARRNLQG-YEINGRQLRVDFAENDK 87
GY F +Y D+ A+ A L G E++G+ + VD++ + K
Sbjct: 45 GYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK 84
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 30.8 bits (68), Expect = 2.1, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDE 58
VFVG I E ++ G V +++ DR TG KGYGF + ++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYND 60
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 30.8 bits (68), Expect = 2.2, Method: Composition-based stats.
Identities = 14/50 (28%), Positives = 27/50 (54%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDE 58
+F+G + + T+E L E + G V ++ D T + +G+GF + D+
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 2/82 (2%)
Query: 2 ASSQHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETA 61
+S + R GN Y E+ + R G F +ID P+ F Y+ E+A
Sbjct: 5 SSGERRAPRKGNTLYVYGEDMTPTLLR--GAFSPFGNIIDLSMDPPRNCAFVTYEKMESA 62
Query: 62 LSARRNLQGYEINGRQLRVDFA 83
A L G ++ QL+V+ A
Sbjct: 63 DQAVAELNGTQVESVQLKVNIA 84
>pdb|1M3E|A Chain A, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
(Selenomethionine)
pdb|1M3E|B Chain B, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
(Selenomethionine)
pdb|1M3E|C Chain C, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
(Selenomethionine)
pdb|1M3E|D Chain D, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
(Selenomethionine)
Length = 481
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 9/88 (10%)
Query: 294 QLPQNAKNQALQQASLPGQSG--------IPMLPSMHPSVRPQIQLANSSSLNQQVHPPS 345
+L N + + +++A+L + G IP+L S S + L + + + + P
Sbjct: 257 KLGDNVRERIIKRAALEFEDGXYANLGIGIPLLASNFISPNXTVHLQSENGI-LGLGPYP 315
Query: 346 LENQVQVSASNLGQNTWTKLPNSAMRSS 373
L+N+V N G+ T T LP ++ SS
Sbjct: 316 LQNEVDADLINAGKETVTVLPGASYFSS 343
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 8/76 (10%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+FV P D E +L EI GP+ +++ G+ F E+++ E+A A +
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEV 85
Query: 69 QGYEINGRQLRVDFAE 84
G + L V +++
Sbjct: 86 HGKSFANQPLEVVYSK 101
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 30.4 bits (67), Expect = 2.7, Method: Composition-based stats.
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 8/76 (10%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
+FV P D E +L EI GP+ +++ G+ F E+++ E+A A +
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEV 58
Query: 69 QGYEINGRQLRVDFAE 84
G + L V +++
Sbjct: 59 HGKSFANQPLEVVYSK 74
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 30.4 bits (67), Expect = 2.9, Method: Composition-based stats.
Identities = 13/51 (25%), Positives = 28/51 (54%)
Query: 8 CVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDE 58
CV++ +P++A + +I+ +++ V + GK G GF E+++E
Sbjct: 27 CVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNE 77
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 30.4 bits (67), Expect = 3.0, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 7/75 (9%)
Query: 5 QHRCVFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYK---DEETA 61
Q R +F+G + ++ TEE L + G + ++ D + + +G+GF + + + A
Sbjct: 26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 85
Query: 62 LSARRNLQGYEINGR 76
++AR + I+GR
Sbjct: 86 MAARP----HSIDGR 96
>pdb|1O9L|A Chain A, Succinate:coenzyme-A Transferase (Pig Heart)
pdb|1O9L|B Chain B, Succinate:coenzyme-A Transferase (Pig Heart)
pdb|1O9L|C Chain C, Succinate:coenzyme-A Transferase (Pig Heart)
pdb|1O9L|D Chain D, Succinate:coenzyme-A Transferase (Pig Heart)
pdb|1OOY|A Chain A, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
pdb|1OOY|B Chain B, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
pdb|3K6M|A Chain A, Dynamic Domains Of Succinyl-Coa:3-Ketoacid-Coenzyme A
Transferase From Pig Heart.
pdb|3K6M|D Chain D, Dynamic Domains Of Succinyl-Coa:3-Ketoacid-Coenzyme A
Transferase From Pig Heart.
pdb|3K6M|C Chain C, Dynamic Domains Of Succinyl-Coa:3-Ketoacid-Coenzyme A
Transferase From Pig Heart.
pdb|3K6M|B Chain B, Dynamic Domains Of Succinyl-Coa:3-Ketoacid-Coenzyme A
Transferase From Pig Heart
Length = 481
Score = 30.0 bits (66), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 9/88 (10%)
Query: 294 QLPQNAKNQALQQASLPGQSG--------IPMLPSMHPSVRPQIQLANSSSLNQQVHPPS 345
+L N + + +++A+L + G IP+L S S + L + + + + P
Sbjct: 257 KLGDNVRERIIKRAALEFEDGMYANLGIGIPLLASNFISPNMTVHLQSENGI-LGLGPYP 315
Query: 346 LENQVQVSASNLGQNTWTKLPNSAMRSS 373
L+N+V N G+ T T LP ++ SS
Sbjct: 316 LQNEVDADLINAGKETVTVLPGASYFSS 343
>pdb|3OXO|A Chain A, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
Covalently Bound To Coa
pdb|3OXO|B Chain B, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
Covalently Bound To Coa
pdb|3OXO|C Chain C, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
Covalently Bound To Coa
pdb|3OXO|D Chain D, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
Covalently Bound To Coa
pdb|3OXO|E Chain E, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
Covalently Bound To Coa
pdb|3OXO|F Chain F, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
Covalently Bound To Coa
pdb|3OXO|G Chain G, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
Covalently Bound To Coa
pdb|3OXO|H Chain H, Succinyl-Coa:3-Ketoacid Coa Transferase From Pig Heart
Covalently Bound To Coa
Length = 488
Score = 30.0 bits (66), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 9/88 (10%)
Query: 294 QLPQNAKNQALQQASLPGQSG--------IPMLPSMHPSVRPQIQLANSSSLNQQVHPPS 345
+L N + + +++A+L + G IP+L S S + L + + + + P
Sbjct: 257 KLGDNVRERIIKRAALEFEDGMYANLGIGIPLLASNFISPNMTVHLQSENGI-LGLGPYP 315
Query: 346 LENQVQVSASNLGQNTWTKLPNSAMRSS 373
L+N+V N G+ T T LP ++ SS
Sbjct: 316 LQNEVDADLINAGKETVTVLPGASYFSS 343
>pdb|2NRB|A Chain A, C28s Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
pdb|2NRB|B Chain B, C28s Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
pdb|2NRB|C Chain C, C28s Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
pdb|2NRB|D Chain D, C28s Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
Length = 481
Score = 30.0 bits (66), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 9/88 (10%)
Query: 294 QLPQNAKNQALQQASLPGQSG--------IPMLPSMHPSVRPQIQLANSSSLNQQVHPPS 345
+L N + + +++A+L + G IP+L S S + L + + + + P
Sbjct: 257 KLGDNVRERIIKRAALEFEDGMYANLGIGIPLLASNFISPNMTVHLQSENGI-LGLGPYP 315
Query: 346 LENQVQVSASNLGQNTWTKLPNSAMRSS 373
L+N+V N G+ T T LP ++ SS
Sbjct: 316 LQNEVDADLINAGKETVTVLPGASYFSS 343
>pdb|2NRC|A Chain A, C28a Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
pdb|2NRC|B Chain B, C28a Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
pdb|2NRC|C Chain C, C28a Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
pdb|2NRC|D Chain D, C28a Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
Length = 481
Score = 30.0 bits (66), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 9/88 (10%)
Query: 294 QLPQNAKNQALQQASLPGQSG--------IPMLPSMHPSVRPQIQLANSSSLNQQVHPPS 345
+L N + + +++A+L + G IP+L S S + L + + + + P
Sbjct: 257 KLGDNVRERIIKRAALEFEDGMYANLGIGIPLLASNFISPNMTVHLQSENGI-LGLGPYP 315
Query: 346 LENQVQVSASNLGQNTWTKLPNSAMRSS 373
L+N+V N G+ T T LP ++ SS
Sbjct: 316 LQNEVDADLINAGKETVTVLPGASYFSS 343
>pdb|1OOZ|A Chain A, Deletion Mutant Of Succinyl-coa:3-ketoacid Coa Transferase
From Pig Heart
pdb|1OOZ|B Chain B, Deletion Mutant Of Succinyl-coa:3-ketoacid Coa Transferase
From Pig Heart
pdb|1OPE|A Chain A, Deletion Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
pdb|1OPE|B Chain B, Deletion Mutant Of Succinyl-Coa:3-Ketoacid Coa Transferase
From Pig Heart
Length = 475
Score = 30.0 bits (66), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 9/88 (10%)
Query: 294 QLPQNAKNQALQQASLPGQSG--------IPMLPSMHPSVRPQIQLANSSSLNQQVHPPS 345
+L N + + +++A+L + G IP+L S S + L + + + + P
Sbjct: 251 KLGDNVRERIIKRAALEFEDGMYANLGIGIPLLASNFISPNMTVHLQSENGI-LGLGPYP 309
Query: 346 LENQVQVSASNLGQNTWTKLPNSAMRSS 373
L+N+V N G+ T T LP ++ SS
Sbjct: 310 LQNEVDADLINAGKETVTVLPGASYFSS 337
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 29.6 bits (65), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 2/72 (2%)
Query: 12 GNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNLQGY 71
GN Y E+ + R G F +ID P+ F Y+ E+A A L G
Sbjct: 39 GNTLYVYGEDMTPTLLR--GAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGT 96
Query: 72 EINGRQLRVDFA 83
++ QL+V+ A
Sbjct: 97 QVESVQLKVNIA 108
>pdb|4HPV|A Chain A, Crystal Structure Of S-Adenosylmethionine Synthetase From
Sulfolobus Solfataricus 982
pdb|4HPV|B Chain B, Crystal Structure Of S-Adenosylmethionine Synthetase From
Sulfolobus Solfataricus 982
Length = 407
Score = 29.3 bits (64), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 9/84 (10%)
Query: 440 LDSISHPSKIVKTEDGSGTSFSVGALNVSKPIGSAPSQAFGAGLVPVNQVPKV---EEVQ 496
LD+ H IV + G G+S VG SK + + +FG G P+ ++ K+ E
Sbjct: 129 LDAERHV--IVDYKIGKGSSDLVGIFEASKRVPLSNDTSFGVGFAPLTKLEKLVYETERH 186
Query: 497 YSEKQ----IPQISPDVESALLQQ 516
+ KQ +P++ D++ L++
Sbjct: 187 LNSKQFKAKLPEVGEDIKVXGLRR 210
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 28.9 bits (63), Expect = 7.1, Method: Composition-based stats.
Identities = 14/50 (28%), Positives = 27/50 (54%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDE 58
+F+G + + T+E L E + G V ++ D T + +G+GF + D+
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 28.9 bits (63), Expect = 7.1, Method: Composition-based stats.
Identities = 22/92 (23%), Positives = 43/92 (46%), Gaps = 9/92 (9%)
Query: 9 VFVGNIPYDATEEQLIEICREVGPVVSFRLVIDRETGKPKGYGFCEYKDEETALSARRNL 68
++V N+ +E+L + G + S ++++ E G+ KG+GF + E A A +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 69 QGYEINGRQLRVDFAENDKGADRNREQGRGGP 100
G + + L V A+ +E+ + GP
Sbjct: 76 NGRIVATKPLYVALAQ-------RKEERQSGP 100
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
0.312 0.128 0.365
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,905,405
Number of Sequences: 62578
Number of extensions: 581560
Number of successful extensions: 997
Number of sequences better than 100.0: 168
Number of HSP's better than 100.0 without gapping: 131
Number of HSP's successfully gapped in prelim test: 37
Number of HSP's that attempted gapping in prelim test: 825
Number of HSP's gapped (non-prelim): 190
length of query: 551
length of database: 14,973,337
effective HSP length: 104
effective length of query: 447
effective length of database: 8,465,225
effective search space: 3783955575
effective search space used: 3783955575
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 54 (25.4 bits)