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= 040490
(128 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 51.2 bits (121), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 42/69 (60%), Gaps = 4/69 (5%)
Query: 23 PPEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFY--RETDRSTGFGFVTMSTVEE 80
++ KLFVG L +D + + L +F++ G +ISEV+ RET RS GFGFVT +++
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYG--QISEVVVVKDRETQRSRGFGFVTFENIDD 66
Query: 81 AEKVVEMFN 89
A+ + N
Sbjct: 67 AKDAMMAMN 75
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 49.3 bits (116), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 40/65 (61%)
Query: 28 KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEM 87
+L+VG+L +++ + L +F G +E +++ ET RS G+GF+T S E A+K +E
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 88 FNRYE 92
N +E
Sbjct: 88 LNGFE 92
>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 = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/62 (41%), Positives = 34/62 (54%)
Query: 21 SEPPEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEE 80
EP + KLF+G L ++ E L F Q G + V+ T RS GFGFVT +TVEE
Sbjct: 1 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60
Query: 81 AE 82
+
Sbjct: 61 VD 62
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 28 KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEM 87
K+FVG ++ D + L F Q G +E+ E++ R + + GF FVT + +K+V
Sbjct: 99 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-- 156
Query: 88 FNRYETGCSH 97
+Y T H
Sbjct: 157 IQKYHTVNGH 166
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/62 (41%), Positives = 34/62 (54%)
Query: 21 SEPPEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEE 80
EP + KLF+G L ++ E L F Q G + V+ T RS GFGFVT +TVEE
Sbjct: 8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 67
Query: 81 AE 82
+
Sbjct: 68 VD 69
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 28 KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEM 87
K+FVG ++ D + L F Q G +E+ E++ R + + GF FVT + +K+V
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-- 163
Query: 88 FNRYETGCSH 97
+Y T H
Sbjct: 164 IQKYHTVNGH 173
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/62 (41%), Positives = 34/62 (54%)
Query: 21 SEPPEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEE 80
EP + KLF+G L ++ E L F Q G + V+ T RS GFGFVT +TVEE
Sbjct: 6 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 65
Query: 81 AE 82
+
Sbjct: 66 VD 67
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 28 KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEM 87
K+FVG ++ D + L F Q G +E+ E++ R + + GF FVT + +K+V
Sbjct: 104 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-- 161
Query: 88 FNRYETGCSH 97
+Y T H
Sbjct: 162 IQKYHTVNGH 171
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 34/61 (55%)
Query: 22 EPPEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEA 81
EP + KLF+G L ++ E L F Q G + V+ T RS GFGFVT +TVEE
Sbjct: 10 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 69
Query: 82 E 82
+
Sbjct: 70 D 70
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 28 KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEM 87
K+FVG ++ D + L F Q G +E+ E++ R + + GF FVT + +K+V
Sbjct: 107 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-- 164
Query: 88 FNRYETGCSH 97
+Y T H
Sbjct: 165 IQKYHTVNGH 174
>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 = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 34/61 (55%)
Query: 22 EPPEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEA 81
EP + KLF+G L ++ E L F Q G + V+ T RS GFGFVT +TVEE
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 82 E 82
+
Sbjct: 69 D 69
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 28 KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEM 87
K+FVG ++ D + L F Q G +E+ E++ R + + GF FVT + +K+V
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-- 163
Query: 88 FNRYETGCSH 97
+Y T H
Sbjct: 164 IQKYHTVNGH 173
>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 = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 34/61 (55%)
Query: 22 EPPEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEA 81
EP + KLF+G L ++ E L F Q G + V+ T RS GFGFVT +TVEE
Sbjct: 8 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 67
Query: 82 E 82
+
Sbjct: 68 D 68
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 28 KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEM 87
K+FVG ++ D + L F Q G +E+ E++ R + + GF FVT + +K+V
Sbjct: 105 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-- 162
Query: 88 FNRYETGCSH 97
+Y T H
Sbjct: 163 IQKYHTVNGH 172
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 46.2 bits (108), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 37/61 (60%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
++VGNL Y SE++ LF+Q G V ++I+ RET + GFGFV M +E + ++
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKLD 63
Query: 89 N 89
N
Sbjct: 64 N 64
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 35/59 (59%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEM 87
+FVG L + E + H F Q G V+ + ++F + T+R GFGFVT + + EKV E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
L+V NL +D E+L F+ G + ++V+ E RS GFGFV S+ EEA K V
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 89 N 89
N
Sbjct: 76 N 76
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 43.1 bits (100), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 33/62 (53%)
Query: 28 KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEM 87
K+FVG L Y L F G +E + VI R+T +S G+GFVTM+ AE+ +
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 88 FN 89
N
Sbjct: 79 PN 80
>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 = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 36/60 (60%)
Query: 27 AKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVE 86
K+FVG + DV ++ F+Q G + ++++ ++T +S GFGFVT + + ++V +
Sbjct: 88 GKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ 147
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 32/62 (51%)
Query: 25 EDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKV 84
E K+F+G L +D + L F + G V +++ T RS GFGF++ ++V
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 85 VE 86
V+
Sbjct: 62 VK 63
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 40/68 (58%), Gaps = 4/68 (5%)
Query: 27 AKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETD--RSTGFGFVTMSTVEEAEKV 84
+ L+VG+L +++ + L +F G +I ++ +++D RS G+GF+T S E A +
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFG--KIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63
Query: 85 VEMFNRYE 92
+E N +E
Sbjct: 64 LEQLNGFE 71
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
+FV NL Y V +KL +F+ AGVV ++++ ++ +S G G VT EA + + MF
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAISMF 76
Query: 89 N 89
N
Sbjct: 77 N 77
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 35/68 (51%), Gaps = 5/68 (7%)
Query: 27 AKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRE--TDRSTGFGFVTMSTVEEAEKV 84
K+F+G L + E L F Q G E+ E + R+ T RS GFGFVT +KV
Sbjct: 26 CKMFIGGLSWQTTQEGLREYFGQFG--EVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 83
Query: 85 VEMFNRYE 92
+ +R+E
Sbjct: 84 LAQ-SRHE 90
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 33/64 (51%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
+FVGN+ Y+ E+L +F++ G V +++ RET + G+GF E A +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 89 NRYE 92
N E
Sbjct: 71 NGRE 74
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 4/61 (6%)
Query: 27 AKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRE--TDRSTGFGFVTMSTVEEAEKV 84
K+F+G L + E L F Q G E+ E + R+ T RS GFGFVT +KV
Sbjct: 1 CKMFIGGLSWQTTQEGLREYFGQFG--EVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 58
Query: 85 V 85
+
Sbjct: 59 L 59
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 34/68 (50%)
Query: 22 EPPEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEA 81
EP L V + VD +L LF + G +E +++ RET +S G+GFV + A
Sbjct: 38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97
Query: 82 EKVVEMFN 89
++ + N
Sbjct: 98 QQAIAGLN 105
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 13/56 (23%)
Query: 76 STVEEAEKVVEMFNRY------------ETGCSHGFGFFTMSDESKLNDAIAALDG 119
+TV+E + + ++F RY ET S G+GF S AIA L+G
Sbjct: 52 TTVDEVQ-LRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG 106
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 38.9 bits (89), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 30/53 (56%)
Query: 28 KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEE 80
KLF+G L ++ E L + + Q G + V+ + RS GFGFVT S++ E
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE 81
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 4/76 (5%)
Query: 18 VDYSEPP----EDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFV 73
V Y+ P DA L+V L + +++ LF+Q G + S ++ + T S G GF+
Sbjct: 78 VSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFI 137
Query: 74 TMSTVEEAEKVVEMFN 89
EAE+ ++ N
Sbjct: 138 RFDKRIEAEEAIKGLN 153
Score = 33.1 bits (74), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 31/61 (50%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
L V L ++ ++ LF G +E +++ + T +S G+GFV S +A+K +
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 89 N 89
N
Sbjct: 67 N 67
>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 = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 18 VDYSEPPEDA-KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMS 76
++ S+ EDA K FVG L +D + L F + G V + T RS GFGF+
Sbjct: 2 INASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFK 61
Query: 77 TVEEAEKVVEM 87
EKV++
Sbjct: 62 DAASVEKVLDQ 72
>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 = 0.001, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 31/60 (51%)
Query: 27 AKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVE 86
K+FVG L D EK+ F G VE E+ +T++ GF F+T E +K++E
Sbjct: 2 KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
>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 = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 37/73 (50%)
Query: 22 EPPEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEA 81
E PE A LF+ +L + + L +F G V ++V ++T+ S FGFV+ A
Sbjct: 21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 80
Query: 82 EKVVEMFNRYETG 94
+ ++ N ++ G
Sbjct: 81 QAAIQSMNGFQIG 93
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 34/66 (51%)
Query: 24 PEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEK 83
P L V L ++ ++L LF+ G VE +++I + S G+GFV T ++AE+
Sbjct: 2 PGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 61
Query: 84 VVEMFN 89
+ N
Sbjct: 62 AINTLN 67
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 4/76 (5%)
Query: 18 VDYSEPP----EDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFV 73
V Y+ P DA L+V L + ++L LF+Q G + S ++ + T S G GF+
Sbjct: 76 VSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFI 135
Query: 74 TMSTVEEAEKVVEMFN 89
EAE+ ++ N
Sbjct: 136 RFDKRIEAEEAIKGLN 151
Score = 32.7 bits (73), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 31/61 (50%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
L V L ++ E+ LF G +E +++ + T +S G+GFV ++AEK +
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 89 N 89
N
Sbjct: 65 N 65
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 21 SEPPEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEE 80
SE +DA ++VG L V L LF QAG V + + R T + G+GFV + E+
Sbjct: 10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 69
Query: 81 AE---KVVEMFNRY 91
A+ K+++M Y
Sbjct: 70 ADYAIKIMDMIKLY 83
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 39/81 (48%)
Query: 31 VGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMFNR 90
+ + + V + L LF++AG V E T ++ GF FV ++ +A+K+++ F+
Sbjct: 17 IPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG 76
Query: 91 YETGCSHGFGFFTMSDESKLN 111
H +TM D + N
Sbjct: 77 KRLDLKHRLFLYTMKDVERYN 97
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 33/64 (51%)
Query: 26 DAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVV 85
DA L+V L + +++ LF+Q G + S ++ + T S G GF+ EAE+ +
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 86 EMFN 89
+ N
Sbjct: 61 KGLN 64
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%)
Query: 28 KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEM 87
K+FVG + ++ +L F + GVV +I+ E R GFGF+T + ++ V M
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 30/58 (51%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVE 86
+FVG L D EK+ F G VE E+ +T++ GF F+T E +K++E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
>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 = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 33/59 (55%)
Query: 28 KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVE 86
LFVG+L +VD E L + F V++ +T S G+GFV+ ++ ++A+ ++
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Score = 25.8 bits (55), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 18/29 (62%)
Query: 92 ETGCSHGFGFFTMSDESKLNDAIAALDGQ 120
+TG S G+GF + + + +A+ ++ GQ
Sbjct: 38 QTGSSRGYGFVSFTSQDDAQNAMDSMQGQ 66
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 27/49 (55%)
Query: 25 EDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFV 73
E KLFVG L + E L F+Q G V ++ + T++S GFGFV
Sbjct: 15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFV 63
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 35/73 (47%)
Query: 22 EPPEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEA 81
E PE LF+ +L + LA F G V ++V ++T S FGFV+ + A
Sbjct: 36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95
Query: 82 EKVVEMFNRYETG 94
+ ++ N ++ G
Sbjct: 96 QVAIKAMNGFQVG 108
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 3/64 (4%)
Query: 27 AKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRE-TDRSTGFGFVTMSTVEEAEKVV 85
KLF+G L + + + L +F + G ISEV+ ++ T +S GF F+T +A+
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHG--PISEVLLIKDRTSKSRGFAFITFENPADAKNAA 65
Query: 86 EMFN 89
+ N
Sbjct: 66 KDMN 69
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 33/59 (55%)
Query: 28 KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVE 86
LFVG+L +VD E L + F V++ +T S G+GFV+ ++ ++A+ ++
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 147
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 18/29 (62%)
Query: 92 ETGCSHGFGFFTMSDESKLNDAIAALDGQ 120
+TG S G+GF + + + +A+ ++ GQ
Sbjct: 124 QTGSSRGYGFVSFTSQDDAQNAMDSMQGQ 152
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs
Of Human Antigen R
Length = 177
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 33/61 (54%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
L V L ++ ++L LF+ G VE +++I + S G+GFV T ++AE+ +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 89 N 89
N
Sbjct: 65 N 65
Score = 32.3 bits (72), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 4/76 (5%)
Query: 18 VDYSEPP----EDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFV 73
V Y+ P +DA L++ L + + + +F++ G + S V+ + T S G F+
Sbjct: 76 VSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFI 135
Query: 74 TMSTVEEAEKVVEMFN 89
EAE+ + FN
Sbjct: 136 RFDKRSEAEEAITSFN 151
>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 = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 33/61 (54%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
L V L ++ ++L LF+ G VE +++I + S G+GFV T ++AE+ +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 89 N 89
N
Sbjct: 65 N 65
Score = 32.3 bits (72), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 4/76 (5%)
Query: 18 VDYSEPP----EDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFV 73
V Y+ P +DA L++ L + + + +F++ G + S V+ + T S G F+
Sbjct: 76 VSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFI 135
Query: 74 TMSTVEEAEKVVEMFN 89
EAE+ + FN
Sbjct: 136 RFDKRSEAEEAITSFN 151
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 30/58 (51%), Gaps = 6/58 (10%)
Query: 25 EDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAE 82
+ +LFVGNL D+ E LF + G E SEV +R GFGF+ + + AE
Sbjct: 21 QRCRLFVGNLPTDITEEDFKRLFERYG--EPSEVFI----NRDRGFGFIRLESRTLAE 72
Score = 32.7 bits (73), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 27 AKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVE 86
A L V NL V +E L F+Q G VE + V+ + R+TG GFV + A K +E
Sbjct: 97 AALTVKNLSPVVSNELLEQAFSQFGPVEKA-VVVVDDRGRATGKGFVEFAAKPPARKALE 155
>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 = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 33/65 (50%)
Query: 25 EDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKV 84
+ L V L + ++L LF+ G VE +++I + S G+GFV T ++AE+
Sbjct: 18 QGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 77
Query: 85 VEMFN 89
+ N
Sbjct: 78 INTLN 82
>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 = 0.011, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 2/67 (2%)
Query: 23 PPEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAE 82
P +F+ NL +D++ L F+ G + +V+ + + S G+GFV T E AE
Sbjct: 2 PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAE 59
Query: 83 KVVEMFN 89
+ +E N
Sbjct: 60 RAIEKMN 66
>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 = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 6/58 (10%)
Query: 25 EDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAE 82
+ ++LFVGNL D+ E++ LF + G + EV +++ GFGF+ + T AE
Sbjct: 14 QRSRLFVGNLPPDITEEEMRKLFEKYG--KAGEVFIHKD----KGFGFIRLETRTLAE 65
>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 = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 29/58 (50%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVE 86
+F+G L +D + L F++ G V + T RS GFGFV E +KV++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD 59
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 6/58 (10%)
Query: 25 EDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAE 82
+ ++LFVGNL D+ E++ LF + G + EV +++ GFGF+ + T AE
Sbjct: 21 QRSRLFVGNLPPDITEEEMRKLFEKYG--KAGEVFIHKD----KGFGFIRLETRTLAE 72
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 3/73 (4%)
Query: 22 EPPEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETD-RSTGFGFVTMSTVEE 80
+PP KLFVG L + + LF G +E E R D S G FV S+ E
Sbjct: 11 QPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIE--ECTILRGPDGNSKGCAFVKYSSHAE 68
Query: 81 AEKVVEMFNRYET 93
A+ + + +T
Sbjct: 69 AQAAINALHGSQT 81
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 27 AKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVE 86
++FV NL +D + L FN+ G V +++ E +S G G V + E AE+
Sbjct: 9 CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVKFESPEVAERACR 66
Query: 87 MFN 89
M N
Sbjct: 67 MMN 69
>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 = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 30/63 (47%)
Query: 27 AKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVE 86
A L+VG+L DV L F+ AG + V T RS G+ +V +AE+ ++
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 87 MFN 89
N
Sbjct: 76 TMN 78
Score = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
+F+ NL +D++ L F+ G + +V+ + + S G+GFV T E AE+ +E
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIEKM 163
Query: 89 N 89
N
Sbjct: 164 N 164
>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 = 34.3 bits (77), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
+F+ NL +D++ L F+ G + +V+ + + S G+GFV T E AE+ +E
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIEKM 158
Query: 89 N 89
N
Sbjct: 159 N 159
Score = 33.9 bits (76), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 30/63 (47%)
Query: 27 AKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVE 86
A L+VG+L DV L F+ AG + V T RS G+ +V +AE+ ++
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 87 MFN 89
N
Sbjct: 71 TMN 73
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 33.9 bits (76), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVV-EISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEM 87
+F+GNL ++D + L F+ GV+ + +++ +T S G+ F+ ++ + ++ +E
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 88 FN 89
N
Sbjct: 68 MN 69
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 33.9 bits (76), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 34/70 (48%)
Query: 35 RYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMFNRYETG 94
+ V + L LF++AG V E T ++ GF FV ++ +A+K+++ F+
Sbjct: 21 KVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
Query: 95 CSHGFGFFTM 104
H +TM
Sbjct: 81 LKHRLFLYTM 90
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 33.5 bits (75), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
+FV NL +D + L FN+ G V +++ E +S G G V + E AE+ M
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVKFESPEVAERACRMM 65
Query: 89 N 89
N
Sbjct: 66 N 66
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 33.5 bits (75), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
+F+ NL +D++ L F+ G + +V+ + + S G+GFV T E AE+ +E
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIEKM 71
Query: 89 N 89
N
Sbjct: 72 N 72
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 33.5 bits (75), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 28/64 (43%), Gaps = 1/64 (1%)
Query: 26 DAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVV 85
D +FVGNL V E L LF QAG + + RE + FGFV E +
Sbjct: 16 DRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAI 74
Query: 86 EMFN 89
+ N
Sbjct: 75 ALLN 78
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 33.5 bits (75), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 31/61 (50%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
L V L ++ ++ LF G +E +++ + T +S G+GFV S +A+K +
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 89 N 89
N
Sbjct: 67 N 67
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 33.1 bits (74), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 26 DAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRST-GFGFVTMSTVEEAEKV 84
D KLFVG L E + LF GV++ E R D S+ G FV S+ EA+
Sbjct: 15 DRKLFVGMLNKQQSEEDVLRLFQPFGVID--ECTVLRGPDGSSKGCAFVKFSSHTEAQAA 72
Query: 85 VEMFNRYET 93
+ + +T
Sbjct: 73 IHALHGSQT 81
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 32.7 bits (73), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEK-VVEM 87
+FVG+L ++ +E + F G + + V+ T +S G+GFV+ +AE +V M
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 88 FNRYETG 94
++ G
Sbjct: 78 GGQWLGG 84
>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 = 32.3 bits (72), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 31/60 (51%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
+FVG+L ++ +E + F G + + V+ T +S G+GFV+ +AE ++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 32.3 bits (72), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVE---ISEVIFYRETDRSTGFGFVTMSTVEEAEKVV 85
LF+ NL + E L +F++ G ++ IS+ S GFGFV E+A+K +
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 86 EMFNRY 91
+ +
Sbjct: 68 KQLQGH 73
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 32.3 bits (72), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
LFV L D E L F+ G V + ++ RET S GFGFV ++ E+A+ E
Sbjct: 18 LFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
>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 = 32.3 bits (72), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 32/76 (42%), Gaps = 4/76 (5%)
Query: 18 VDYSEPPEDAK----LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFV 73
+ Y PP D + L V NL Y + L +F + G V + R T S GF FV
Sbjct: 35 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 94
Query: 74 TMSTVEEAEKVVEMFN 89
+AE ++ +
Sbjct: 95 RFHDKRDAEDAMDAMD 110
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1
In Complex With Ugcaugu
Length = 109
Score = 31.6 bits (70), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 5/68 (7%)
Query: 19 DYSEPPEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTV 78
+ S+P +L V N+ + L +F Q G + E+IF S GFGFVT
Sbjct: 25 NKSQP---KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENS 79
Query: 79 EEAEKVVE 86
+A++ E
Sbjct: 80 ADADRARE 87
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 28 KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVE 86
+L V N+ + L +F Q G + E+IF S GFGFVT +A++ E
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRARE 73
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 30/64 (46%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
L+VG L +VD + L F G + ++ ET++ GF FV E+A ++
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 89 NRYE 92
N E
Sbjct: 75 NESE 78
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 30.4 bits (67), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 30/64 (46%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
L+VG L +VD + L F G + ++ ET++ GF FV E+A ++
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 89 NRYE 92
N E
Sbjct: 65 NESE 68
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 30/64 (46%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
L+VG L +VD + L F G + ++ ET++ GF FV E+A ++
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 89 NRYE 92
N E
Sbjct: 68 NESE 71
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 30/64 (46%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
L+VG L +VD + L F G + ++ ET++ GF FV E+A ++
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 89 NRYE 92
N E
Sbjct: 126 NESE 129
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 30.4 bits (67), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 30/64 (46%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
L+VG L +VD + L F G + ++ ET++ GF FV E+A ++
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 89 NRYE 92
N E
Sbjct: 70 NESE 73
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 30.4 bits (67), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 24/57 (42%)
Query: 28 KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKV 84
+LFV NL Y E L LF+ G + T + GF FVT E A K
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 30.0 bits (66), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 14/61 (22%), Positives = 27/61 (44%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
L++ L+ + L L G + ++ I + T++ G+GFV + A+K V
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 89 N 89
Sbjct: 68 K 68
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 29.6 bits (65), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 8/65 (12%)
Query: 28 KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEM 87
KLF+GNL + +++ LF Q G V E D +GFV + AE +
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKV--------LECDIIKNYGFVHIEDKTAAEDAIRN 61
Query: 88 FNRYE 92
+ Y+
Sbjct: 62 LHHYK 66
>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 = 29.3 bits (64), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRST--GFGFVTMSTVEEAEKVVE 86
L+VGNL + E++ LF+++G +I ++I + + T GF FV + +AE +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSG--DIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 87 MFN 89
N
Sbjct: 100 YIN 102
>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 = 29.3 bits (64), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 16/76 (21%), Positives = 32/76 (42%)
Query: 19 DYSEPPEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTV 78
DY P KLF+G L ++ +++ L G ++ ++ T S G+ F +
Sbjct: 89 DYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDI 148
Query: 79 EEAEKVVEMFNRYETG 94
++ + N + G
Sbjct: 149 NVTDQAIAGLNGMQLG 164
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 28.9 bits (63), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 16/76 (21%), Positives = 32/76 (42%)
Query: 19 DYSEPPEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTV 78
DY P KLF+G L ++ +++ L G ++ ++ T S G+ F +
Sbjct: 87 DYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDI 146
Query: 79 EEAEKVVEMFNRYETG 94
++ + N + G
Sbjct: 147 NVTDQAIAGLNGMQLG 162
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 28.9 bits (63), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 8/79 (10%)
Query: 19 DYSEPPEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISE--------VIFYRETDRSTGF 70
D E +++ ++V L V + LA F Q GVV++++ + +ET + G
Sbjct: 8 DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 67
Query: 71 GFVTMSTVEEAEKVVEMFN 89
V+ A+ VE F+
Sbjct: 68 ATVSYEDPPTAKAAVEWFD 86
>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 = 28.9 bits (63), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 3/67 (4%)
Query: 24 PEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIF-YRETDRSTGFGFVTMSTVEEAE 82
+ L+VGNL + E++ LF+++G +I ++I + + GF FV + +AE
Sbjct: 16 KKSCTLYVGNLSFYTTEEQIYELFSKSG--DIKKIIMGLDKMKTACGFCFVEYYSRADAE 73
Query: 83 KVVEMFN 89
+ N
Sbjct: 74 NAMRYIN 80
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation
Initiation Factor 4b
Length = 100
Score = 28.9 bits (63), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 26/54 (48%), Gaps = 8/54 (14%)
Query: 23 PPEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRE---TDRSTGFGFV 73
PP A F+GNL YDV E + F + IS V RE +R GFG+
Sbjct: 18 PPYTA--FLGNLPYDVTEESIKEFFRG---LNISAVRLPREPSNPERLKGFGYA 66
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of
Eukaryotic Initiation Factor 4b
Length = 104
Score = 28.9 bits (63), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 26/54 (48%), Gaps = 8/54 (14%)
Query: 23 PPEDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRE---TDRSTGFGFV 73
PP A F+GNL YDV E + F + IS V RE +R GFG+
Sbjct: 14 PPYTA--FLGNLPYDVTEESIKEFFRG---LNISAVRLPREPSNPERLKGFGYA 62
>pdb|3TQS|A Chain A, Structure Of The Dimethyladenosine Transferase (Ksga) From
Coxiella Burnetii
pdb|3TQS|B Chain B, Structure Of The Dimethyladenosine Transferase (Ksga) From
Coxiella Burnetii
pdb|3TQS|C Chain C, Structure Of The Dimethyladenosine Transferase (Ksga) From
Coxiella Burnetii
pdb|3TQS|D Chain D, Structure Of The Dimethyladenosine Transferase (Ksga) From
Coxiella Burnetii
Length = 255
Score = 28.9 bits (63), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 19 DYSEPPEDAKL-FVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDR 66
D+S D L VGNL Y++ + L HLF+Q +E +E R
Sbjct: 88 DFSSVKTDKPLRVVGNLPYNISTPLLFHLFSQIHCIEDXHFXLQKEVVR 136
>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 = 28.5 bits (62), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 11/45 (24%), Positives = 22/45 (48%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFV 73
LFV + YD KL F G ++ +++ + + + G+ F+
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFI 149
>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 = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/67 (22%), Positives = 31/67 (46%)
Query: 28 KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEM 87
+++VG++ Y++ + + F G ++ + + T + GF FV E A+ +E
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 88 FNRYETG 94
N G
Sbjct: 74 XNSVXLG 80
>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 = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/67 (22%), Positives = 32/67 (47%)
Query: 28 KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEM 87
+++VG++ Y++ + + F G ++ ++ + T + GF FV E A+ +E
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 88 FNRYETG 94
N G
Sbjct: 75 MNSVMLG 81
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVE 86
+FVG + +D ++ F + G V+ ++I R T S G+GFV+ + +K+VE
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 69
>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 = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVE 86
+FVG + +D ++ F + G V+ ++I R T S G+GFV+ + +K+VE
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68
>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 = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/68 (22%), Positives = 33/68 (48%)
Query: 27 AKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVE 86
++++VG++ Y++ + + F G ++ ++ + T + GF FV E A+ +E
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 87 MFNRYETG 94
N G
Sbjct: 89 QMNSVMLG 96
>pdb|1WG1|A Chain A, Solution Structure Of Rna Binding Domain In
Bab13405(Homolog Exc-7)
Length = 88
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 61 YRETDRSTGFGFVTMSTVEEAEKVVEMFNRY 91
Y DR+ FVT+ E+A+ ++MF++Y
Sbjct: 33 YCYVDRNKRTAFVTLLNGEQAQNAIQMFHQY 63
>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 = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVE 86
+FVG + +D ++ F + G V+ ++I R T S G+GFV+ + +K+VE
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 28/61 (45%)
Query: 25 EDAKLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKV 84
++A + V NL D L LF G + + + T +S GF F++ E+A +
Sbjct: 14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73
Query: 85 V 85
+
Sbjct: 74 I 74
>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 = 26.9 bits (58), Expect = 2.7, Method: Composition-based stats.
Identities = 11/45 (24%), Positives = 22/45 (48%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFV 73
LFV + YD KL F G ++ +++ + + + G+ F+
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFI 149
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 18 VDYSEPPE-DA-KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETD--RSTGFGFV 73
+D+ + P+ DA K+FVG + + L LF Q G V V+ R + +S G FV
Sbjct: 5 LDHPDQPDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFV 64
Query: 74 TMSTVEEA 81
T T + A
Sbjct: 65 TFYTRKAA 72
>pdb|2A11|A Chain A, Crystal Structure Of Nuclease Domain Of Ribonuclase Iii
From Mycobacterium Tuberculosis
Length = 242
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 3/72 (4%)
Query: 40 SEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMFNRYETGCSHGF 99
+E+L L + + I++ +F+R DRS G ++V + + ++ R C+ G
Sbjct: 42 NERLEFLGDAVLGLTITDALFHRHPDRSEGDLAKLRASVVNTQALADVARRL---CAEGL 98
Query: 100 GFFTMSDESKLN 111
G + + N
Sbjct: 99 GVHVLLGRGEAN 110
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 26/61 (42%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEMF 88
L V NL Y + L +F + G V + R T S GF FV +AE ++
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 89 N 89
+
Sbjct: 133 D 133
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 26.2 bits (56), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 8/65 (12%)
Query: 28 KLFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVVEM 87
K+FVGN+ S++L LF + G VI E D + FV M +A+ +
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRG-----RVI---ECDVVKDYAFVHMEKEADAKAAIAQ 62
Query: 88 FNRYE 92
N E
Sbjct: 63 LNGKE 67
>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 = 25.8 bits (55), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 26 DAK-LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVE 79
DA+ ++VGN+ Y +E+L F+ G V ++ + + GF ++ S E
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE 59
>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 = 25.8 bits (55), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 26 DAK-LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVE 79
DA+ ++VGN+ Y +E+L F+ G V ++ + + GF ++ S E
Sbjct: 4 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE 58
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 25.8 bits (55), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 91 YETGCSHGFGFFTMSDESKLNDAIAALDG 119
Y+TG S+G+ F + E AI L+G
Sbjct: 39 YKTGYSYGYAFVDFTSEMDSQRAIKVLNG 67
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 25.4 bits (54), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 91 YETGCSHGFGFFTMSDESKLNDAIAALDG 119
Y+TG S+G+ F + E AI L+G
Sbjct: 39 YKTGYSYGYAFVDFTSEMDSQRAIKVLNG 67
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 25.4 bits (54), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 26/57 (45%)
Query: 29 LFVGNLRYDVDSEKLAHLFNQAGVVEISEVIFYRETDRSTGFGFVTMSTVEEAEKVV 85
L V L + + L F+ G V + +V +T S GFGFV + E KV+
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 74
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
0.320 0.137 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,205,363
Number of Sequences: 62578
Number of extensions: 112325
Number of successful extensions: 457
Number of sequences better than 100.0: 105
Number of HSP's better than 100.0 without gapping: 84
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 316
Number of HSP's gapped (non-prelim): 157
length of query: 128
length of database: 14,973,337
effective HSP length: 87
effective length of query: 41
effective length of database: 9,529,051
effective search space: 390691091
effective search space used: 390691091
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)