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= psy3346
(79 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 101 bits (251), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 47/63 (74%), Positives = 52/63 (82%)
Query: 17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
KQT SKILVRNIPFQA Q E+ ELF FGELK VRLPKKM G+G HRGFGFV+FITK +A
Sbjct: 12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 71
Query: 77 KRV 79
K+
Sbjct: 72 KKA 74
>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 = 8e-05, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
G+ ++V +P Q E+ LF + GE++ +L + V +G G+GFV ++T +A+R
Sbjct: 19 GTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKV-AGHSLGYGFVNYVTAKDAER 76
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 35/55 (63%), Gaps = 1/55 (1%)
Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
A Q S ++V +P++ + +++E F FGE+ V++ KK + +G +GFGFV F
Sbjct: 11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQV-KKDLKTGHSKGFGFVRF 64
>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 = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ ++V +P Q E+ LF + GE++ +L + V +G G+GFV ++T +A+R
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKV-AGHSLGYGFVNYVTAKDAER 61
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs
Of Human Antigen R
Length = 177
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ ++V +P Q E+ LF + GE++ +L + V +G G+GFV ++T +A+R
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKV-AGHSLGYGFVNYVTAKDAER 59
Score = 34.7 bits (78), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
R SS V K + + + +P Q +VE++F FG + R+ +GL RG F+
Sbjct: 80 RPSSEVIKD--ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQT-TGLSRGVAFIR 136
Query: 70 FITKNEAK 77
F ++EA+
Sbjct: 137 FDKRSEAE 144
>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 = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+ ++V +P Q E+ LF + GE++ +L + V +G G+GFV ++T +A+R
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKV-AGHSLGYGFVNYVTAKDAER 59
Score = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
R SS V K + + + +P Q +VE++F FG + R+ +GL RG F+
Sbjct: 80 RPSSEVIKD--ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQT-TGLSRGVAFIR 136
Query: 70 FITKNEAK 77
F ++EA+
Sbjct: 137 FDKRSEAE 144
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 37.7 bits (86), Expect = 0.001, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 9 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFG 66
+R+ S + T + + V N+P Q + EEL + FG L+ F+ ++ +G +G+G
Sbjct: 84 ERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER---TGQSKGYG 140
Query: 67 FVEFITKNEAKR 78
F E++ K+ A R
Sbjct: 141 FAEYMKKDSAAR 152
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 37.7 bits (86), Expect = 0.001, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 9 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFG 66
+R+ S + T + + V N+P Q + EEL + FG L+ F+ ++ +G +G+G
Sbjct: 84 ERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER---TGQSKGYG 140
Query: 67 FVEFITKNEAKR 78
F E++ K+ A R
Sbjct: 141 FAEYMKKDSAAR 152
>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 = 37.7 bits (86), Expect = 0.002, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 9 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFG 66
+R+ S + T + + V N+P Q + EEL + FG L+ F+ ++ +G +G+G
Sbjct: 82 ERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER---TGQSKGYG 138
Query: 67 FVEFITKNEAKR 78
F E++ K+ A R
Sbjct: 139 FAEYMKKDSAAR 150
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 32/55 (58%), Gaps = 4/55 (7%)
Query: 24 LVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
L RN+ + + E+F +G++K + +P + + L +G+ +VEF +EA++
Sbjct: 12 LTRNV----TKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62
>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 = 0.002, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
I V N+ ++++++ELF+ FG + + L K +G +GF F+ F + +A R
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKT-TGQSKGFAFISFHRREDAARA 73
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 36/66 (54%), Gaps = 13/66 (19%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLH------RGFGFVEFITK 73
G + +RN+ F +++ + E+ + FG+LK+VR+ LH +G F +F+T+
Sbjct: 15 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVV-------LHPDTEHSKGCAFAQFMTQ 67
Query: 74 NEAKRV 79
A++
Sbjct: 68 EAAQKC 73
>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 = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 3 SEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLH 62
S ++ V R S+++ K K+ + +PF + E+EE+ KA G +K +RL G
Sbjct: 3 SGSSGVFRYSTSLEKH---KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGK--P 57
Query: 63 RGFGFVEFITKNEAKRV 79
+G +VE+ +++A +
Sbjct: 58 KGLAYVEYENESQASQA 74
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 43/79 (54%), Gaps = 7/79 (8%)
Query: 2 GSEATTVKRKSSNVAKQTGSK-ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSG 60
G+E K K + K+ ++ +L +N+P++ Q E++E+F+ E++ V G
Sbjct: 74 GNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVS------KDG 127
Query: 61 LHRGFGFVEFITKNEAKRV 79
+G ++EF T+ +A++
Sbjct: 128 KSKGIAYIEFKTEADAEKT 146
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 22/31 (70%)
Query: 18 QTGSKILVRNIPFQAKQSEVEELFKAFGELK 48
+TG+K+LV N+ F ++++ELF FG LK
Sbjct: 33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLK 63
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 22/31 (70%)
Query: 18 QTGSKILVRNIPFQAKQSEVEELFKAFGELK 48
+TG+K+LV N+ F ++++ELF FG LK
Sbjct: 33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLK 63
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 4/77 (5%)
Query: 2 GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
G +A+ V+ + + +Q + + + N+P + E+E + K FG++ R+ + SG
Sbjct: 7 GLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD--SSGT 64
Query: 62 HRGFGF--VEFITKNEA 76
RG GF +E K EA
Sbjct: 65 SRGVGFARMESTEKCEA 81
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 35.4 bits (80), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 10/58 (17%)
Query: 21 SKILVRNI-PFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
S++ + N+ K+S+VE +F +G K+VG +H+GF FV+++ + A+
Sbjct: 16 SRVFIGNLNTLVVKKSDVEAIFSKYG---------KIVGCSVHKGFAFVQYVNERNAR 64
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 22/31 (70%)
Query: 18 QTGSKILVRNIPFQAKQSEVEELFKAFGELK 48
+TG+K+LV N+ F ++++ELF FG LK
Sbjct: 86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLK 116
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 19/81 (23%)
Query: 17 KQTGSKILVRNIPFQAKQSEVEELFKAF-GELK-----------FVRLPKKMVG------ 58
KQ + I+ N FQ++QS ++ F F G+L F P + G
Sbjct: 64 KQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDM 123
Query: 59 -SGLHRGFGFVEFITKNEAKR 78
+G RG+GFV F ++++A+
Sbjct: 124 QTGSSRGYGFVSFTSQDDAQN 144
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
T ++ V NIPF+ + ++ ++F FG++ V + GS +GFGFV F +A R
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS---KGFGFVTFENSADADR 70
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 34.7 bits (78), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 39 ELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
ELF G + +PK V +G H+G+GFVEF+++ +A
Sbjct: 34 ELFLQAGPVVNTHMPKDRV-TGQHQGYGFVEFLSEEDAD 71
>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 = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
++I V ++ +++ +F+AFG++K L + +G H+G+GF+E+
Sbjct: 110 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPT-TGKHKGYGFIEY 158
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1
In Complex With Ugcaugu
Length = 109
Score = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
++ V NIPF+ + ++ ++F FG++ V + GS +GFGFV F +A R
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS---KGFGFVTFENSADADR 84
>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 = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
++I V ++ +++ +F+AFG++K L + +G H+G+GF+E+
Sbjct: 126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPT-TGKHKGYGFIEY 174
>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 = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
++I V ++ +++ +F+AFG++K L + +G H+G+GF+E+
Sbjct: 111 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPT-TGKHKGYGFIEY 159
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 13/67 (19%)
Query: 8 VKRKSSNVAKQTG----SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHR 63
V R S +Q G +++ VR P ++SE+ E+F FG +K V+ +
Sbjct: 15 VPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVK---------ILN 65
Query: 64 GFGFVEF 70
GF FVEF
Sbjct: 66 GFAFVEF 72
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 34.3 bits (77), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
++ VRN+ + + + ++E+LF A+G L + P + + +GF FV F+ A
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSL-TKKPKGFAFVTFMFPEHA 63
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 33.5 bits (75), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
+ + V +P Q E+E+LF +G + R+ V +G+ RG GF+ F + EA+
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV-TGVSRGVGFIRFDKRIEAE 144
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 33.5 bits (75), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 9/52 (17%)
Query: 19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
+ +++ VR P ++SE+ E+F FG +K V+ + GF FVEF
Sbjct: 3 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVK---------ILNGFAFVEF 45
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 32.7 bits (73), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+G K+ + + +Q Q + E F FGE+K + + + + RGFGFV F+ + +
Sbjct: 24 SGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL-TKRSRGFGFVTFMDQAGVDK 82
Query: 79 V 79
V
Sbjct: 83 V 83
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation
Initiation Factor 4b
Length = 100
Score = 32.3 bits (72), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 13 SNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
S + K + N+P+ + ++E F+ + VRLP++ +GFG+ EF
Sbjct: 12 SRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF 68
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 32.3 bits (72), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 12/75 (16%)
Query: 4 EATTVKRKSSNVAKQTGSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLH 62
+A+ V K N K S++ + N+ K+S+VE +F +G ++ G +H
Sbjct: 13 QASNVTNK--NDPKSINSRVFIGNLNTALVKKSDVETIFSKYG---------RVAGCSVH 61
Query: 63 RGFGFVEFITKNEAK 77
+G+ FV++ + A+
Sbjct: 62 KGYAFVQYSNERHAR 76
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 32.0 bits (71), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
+ + V +P Q E+E+LF +G + R+ +G+ RG GF+ F + EA+
Sbjct: 91 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQ-ATGVSRGVGFIRFDKRIEAE 146
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 32.0 bits (71), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGEL-KFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
+KI V +P+ + + + F+ FG++ + V + + G RG+GFV + A+R
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGK--SRGYGFVTMADRAAAERA 75
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
+ + V +P Q E+E+LF +G + R+ +G+ RG GF+ F + EA+
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQA-TGVSRGVGFIRFDKRIEAE 57
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of
Eukaryotic Initiation Factor 4b
Length = 104
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 27 NIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
N+P+ + ++E F+ + VRLP++ +GFG+ EF
Sbjct: 22 NLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF 64
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
K+ V IP + +++ LF+ FG + + + K + +GLH+G F+ + ++ A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRL-TGLHKGCAFLTYCARDSA 70
>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 = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
+ V ++ + +++ F FG + R+ K M +G +G+GFV F K +A+
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMA-TGKSKGYGFVSFFNKWDAENA 73
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
+ V ++ + +++ F FG++ R+ K M +G +G+GFV F K +A+
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMA-TGKSKGYGFVSFYNKLDAENA 73
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 30.8 bits (68), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSG--LHRGFGFVEFITKNEAKR 78
S + ++N+ F + ++ +F G +K + KK +G L GFGFVE+ +A++
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 79 V 79
Sbjct: 66 A 66
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
K+ V + F + +E++F +G++ V + K + RGFGFV F ++AK
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRE-TQRSRGFGFVTFENIDDAK 68
>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From
Hypothetical Protein Bab23448
Length = 111
Score = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 7/57 (12%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
IL +N+P +E++E F FG L V LP+ + + VEF+ EA++
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITA-------IVEFLEPLEARKA 62
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 30.4 bits (67), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELK 48
K+LV N+ F ++++ELF FG LK
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLK 56
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELK 48
K+LV N+ F ++++ELF FG LK
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLK 57
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 15/65 (23%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 71
SS + K+ + IP + +++ LF+ FG++ + + K +G+H+G F+ +
Sbjct: 5 SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRF-TGMHKGCAFLTYC 63
Query: 72 TKNEA 76
+ A
Sbjct: 64 ERESA 68
>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 = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
A T KI V I ++ + + F+ +G+++ + + GSG RGF FV F +
Sbjct: 93 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTFDDHDS 151
Query: 76 AKRV 79
++
Sbjct: 152 VDKI 155
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 30.0 bits (66), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
A T KI V I ++ + + F+ +G+++ + + GSG RGF FV F +
Sbjct: 100 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTFDDHDS 158
Query: 76 AKRV 79
++
Sbjct: 159 VDKI 162
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 30.0 bits (66), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
A T KI V I ++ + + F+ +G+++ + + GSG RGF FV F +
Sbjct: 98 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTFDDHDS 156
Query: 76 AKRV 79
++
Sbjct: 157 VDKI 160
>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 = 30.0 bits (66), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
A T KI V I ++ + + F+ +G+++ + + GSG RGF FV F +
Sbjct: 99 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTFDDHDS 157
Query: 76 AKRV 79
++
Sbjct: 158 VDKI 161
>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 = 30.0 bits (66), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
A T KI V I ++ + + F+ +G+++ + + GSG RGF FV F +
Sbjct: 100 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTFDDHDS 158
Query: 76 AKRV 79
++
Sbjct: 159 VDKI 162
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 30.0 bits (66), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
A T KI V I ++ + + F+ +G+++ + + GSG RGF FV F +
Sbjct: 101 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTFDDHDS 159
Query: 76 AKRV 79
++
Sbjct: 160 VDKI 163
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 30.0 bits (66), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
K+ + + +Q Q + E F FGE+K + + + + RGFGFV F+ + +V
Sbjct: 1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL-TKRSRGFGFVTFMDQAGVDKV 58
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 29.6 bits (65), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
+++R +P A + ++ ++ G + + VRL + SG RGF FVEF +A R
Sbjct: 4 VMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNK-SSGQSRGFAFVEFSHLQDATR 59
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 29.6 bits (65), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 35/60 (58%), Gaps = 6/60 (10%)
Query: 21 SKILV-RNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
SK LV N+ + A + ++E+F+ + F+++P+ +G +G+ F+EF + +AK
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFE---KATFIKVPQNQ--NGKSKGYAFIEFASFEDAKEA 69
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 29.3 bits (64), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
+ V I + ++E+ F +G +K V++ +G+ +G+GFV F + +++
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR--TGVSKGYGFVSFYNDVDVQKI 67
>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 = 29.3 bits (64), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVG--SGLHRGFGFVEFITKNEAKRV 79
KI V I + E EE F +G + +L M+ +G RGFGFV + + + RV
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQL---MLDKDTGQSRGFGFVTYDSADAVDRV 145
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 29.3 bits (64), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 7/53 (13%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFG---ELKFVRLPKKMVGSGLHRGFGFVEF 70
+KI V IP ++E+ E FK FG E+ + +K RGFGF+ F
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQ----RPRGFGFITF 59
>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 = 29.3 bits (64), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 9/44 (20%), Positives = 26/44 (59%)
Query: 9 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRL 52
KR + + + +++RN+P++ E+ ++F +G ++ +R+
Sbjct: 7 KRANIRLPPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQIRV 50
>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 = 29.3 bits (64), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
+ V I + ++E+ F +G +K V++ +G+ +G+GFV F + +++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR--TGVSKGYGFVSFYNDVDVQKI 66
>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 = 28.9 bits (63), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
I ++N+ + + F AFG + ++ GS +G+GFV F T+ A+R
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS---KGYGFVHFETQEAAERA 61
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 28.9 bits (63), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
I ++N+ + + F AFG + ++ GS +G+GFV F T+ A+R
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS---KGYGFVHFETQEAAERA 67
>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 = 1.0, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
+ V I + ++E+ F +G +K V++ +G+ +G+GFV F + +++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR--TGVSKGYGFVSFYNDVDVQKI 66
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 22/44 (50%)
Query: 36 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
+ E L KAF + K M+ G +GFGFV F + EA +
Sbjct: 28 DDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKA 71
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 28.1 bits (61), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
I V N+ + A +V+ELF FG++ V+L + +GFGFVE
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDR-ETKKPKGFGFVE 49
>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 = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
I ++N+ + + F AFG + ++ GS +G+GFV F T+ A+R
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS---KGYGFVHFETQEAAER 158
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 9/44 (20%), Positives = 25/44 (56%)
Query: 9 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRL 52
KR + + + + +RN+P++ E+ ++F +G ++ +R+
Sbjct: 7 KRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV 50
>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 = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
I ++N+ + + F AFG + ++ GS +G+GFV F T+ A+R
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS---KGYGFVHFETQEAAER 153
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 25 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
V N+PF Q +++ +FK ++ VRL + + +GF +VEF
Sbjct: 20 VGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDK-DTDKFKGFCYVEF 63
>pdb|3L7Y|A Chain A, The Crystal Structure Of Smu.1108c From Streptococcus
Mutans Ua159
Length = 304
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 5/46 (10%)
Query: 28 IPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK 73
+ Q K+ E ++ KA + K +++VG+ GFG+++ ITK
Sbjct: 185 LTLQVKEEESAQIMKAIADYK---TSQRLVGTA--SGFGYIDIITK 225
>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 = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
KI V + + ++ E F FGE++ + LP + RGF F+ F + K++
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDN-KTNKRRGFCFITFKEEEPVKKI 59
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 10/71 (14%)
Query: 12 SSNVAKQTGS--KILVRNIPFQAKQSEVEELFKAFG---ELKFVRLPKKMVGSGLHRGFG 66
SS +Q S K+ V + Q + +V LF+AFG E +R P G +G
Sbjct: 5 SSGCLRQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPD-----GNSKGCA 59
Query: 67 FVEFITKNEAK 77
FV++ + EA+
Sbjct: 60 FVKYSSHAEAQ 70
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 8/43 (18%), Positives = 24/43 (55%)
Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRL 52
R + + + + +RN+P++ E+ ++F +G ++ +R+
Sbjct: 2 RANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV 44
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/56 (25%), Positives = 28/56 (50%), Gaps = 9/56 (16%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
K+ + N+P +A + E+ LF+ +G K++ + + +GFV K A+
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYG---------KVLECDIIKNYGFVHIEDKTAAE 56
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 29/69 (42%), Gaps = 6/69 (8%)
Query: 11 KSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
+ S+ GSK+ V E+++ F +GE+ V +PK R F FV F
Sbjct: 2 RGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF------RAFAFVTF 55
Query: 71 ITKNEAKRV 79
A+ +
Sbjct: 56 ADDKVAQSL 64
>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 = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 7/57 (12%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
S++ V N+P + E+ +LF+ +G+ V + K +GFGF+ T+ A+
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-------KGFGFIRLETRTLAE 65
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
S I VRN+PF +++ F G + + + + +G +G G V+F + A+R
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME---NGKSKGCGVVKFESPEVAERA 61
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 26.2 bits (56), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
+I VRN+PF +++ F G + + + + +G +G G V+F + A+R
Sbjct: 9 CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME---NGKSKGCGVVKFESPEVAERA 64
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 7/30 (23%), Positives = 20/30 (66%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRL 52
+ +RN+P++ E+ ++F +G ++ +R+
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRV 40
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 26.2 bits (56), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
I V + + ++ E F FGE++ + LP + RGF F+ F + K++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDN-KTNKRRGFCFITFKEEEPVKKI 57
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 25.8 bits (55), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKN 74
K+ V + + Q + F +GE+ + K + RGFGFV+F N
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKT-TNQSRGFGFVKFKDPN 69
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 25.8 bits (55), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 7/70 (10%)
Query: 9 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFG 66
KR S + G + ++ +PF+A+ V + FK +L V + +G G G
Sbjct: 14 KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFK---KLDIVEDSIYIAYGPNGKATGEG 70
Query: 67 FVEFITKNEA 76
FVEF +NEA
Sbjct: 71 FVEF--RNEA 78
>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 = 25.8 bits (55), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 44 FGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
FG + R+ K M +G +G+GFV F K +A+
Sbjct: 30 FGRISDARVVKDMA-TGKSKGYGFVSFFNKWDAE 62
>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 = 25.8 bits (55), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
+ + + + + ++++ F FGE+ L + +G RGFGFV F
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPI-TGRSRGFGFVLF 48
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 25.8 bits (55), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 7/57 (12%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
S++ V N+P + E+ +LF+ +G+ V + K +GFGF+ T+ A+
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-------KGFGFIRLETRTLAE 72
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
0.317 0.133 0.358
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,905,542
Number of Sequences: 62578
Number of extensions: 59704
Number of successful extensions: 278
Number of sequences better than 100.0: 90
Number of HSP's better than 100.0 without gapping: 33
Number of HSP's successfully gapped in prelim test: 57
Number of HSP's that attempted gapping in prelim test: 230
Number of HSP's gapped (non-prelim): 99
length of query: 79
length of database: 14,973,337
effective HSP length: 48
effective length of query: 31
effective length of database: 11,969,593
effective search space: 371057383
effective search space used: 371057383
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)