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= 016629
(386 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 = 76.3 bits (186), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 37/80 (46%), Positives = 52/80 (65%), Gaps = 1/80 (1%)
Query: 38 DESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDA 96
DE ++VGGL + NE S+ +VF KYG + V +V DR T R + +GFVTF N A DA
Sbjct: 11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 97 INDMNGRTIDGRVVRVSEVA 116
+ MNG+++DGR +RV +
Sbjct: 71 MMAMNGKSVDGRQIRVDQAG 90
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 65.5 bits (158), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 31/82 (37%), Positives = 51/82 (62%), Gaps = 1/82 (1%)
Query: 41 SVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAIND 99
SV+VG +PY A E+ ++ +F + G VV+ ++V DR T + K YGF + + +A+ A+ +
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 100 MNGRTIDGRVVRVSEVATRGRK 121
+NGR GR +RV A+ K
Sbjct: 70 LNGREFSGRALRVDNAASEKNK 91
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 64.3 bits (155), Expect = 1e-10, Method: Composition-based stats.
Identities = 28/90 (31%), Positives = 52/90 (57%)
Query: 37 DDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDA 96
D +++GGL NE ++ VF K+G + V ++ DR+++ + + F+TF NP A +A
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNA 64
Query: 97 INDMNGRTIDGRVVRVSEVATRGRKSNSGR 126
DMNG+++ G+ ++V + +S R
Sbjct: 65 AKDMNGKSLHGKAIKVEQAKKPSFQSGGRR 94
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 36/92 (39%), Positives = 57/92 (61%), Gaps = 2/92 (2%)
Query: 34 MTIDDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTR-GKCYGFVTFGNPRS 92
M ++ +S+ V L Y + D++R+VF+KYG V V I DR T+ + + FV F + R
Sbjct: 65 MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 124
Query: 93 AVDAINDMNGRTIDGRVVRVSEVATRGRKSNS 124
A DA++ M+G +DGR +RV ++A GR +S
Sbjct: 125 AEDAMDAMDGAVLDGRELRV-QMARYGRPPDS 155
>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 = 57.8 bits (138), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 35/90 (38%), Positives = 56/90 (62%), Gaps = 2/90 (2%)
Query: 36 IDDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTR-GKCYGFVTFGNPRSAV 94
++ +S+ V L Y + D++R+VF+KYG V V I DR T+ + + FV F + R A
Sbjct: 44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 103
Query: 95 DAINDMNGRTIDGRVVRVSEVATRGRKSNS 124
DA++ M+G +DGR +RV ++A GR +S
Sbjct: 104 DAMDAMDGAVLDGRELRV-QMARYGRPPDS 132
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 57.4 bits (137), Expect = 1e-08, Method: Composition-based stats.
Identities = 27/78 (34%), Positives = 47/78 (60%), Gaps = 1/78 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+YVG L ++ ED +R +F+ +G + +++++ D T R K YGF+TF + A A+ +
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 101 NGRTIDGRVVRVSEVATR 118
NG + GR ++V V R
Sbjct: 89 NGFELAGRPMKVGHVTER 106
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAIN 98
S +YVG L ++ ED +R +F+ +G + + ++ D T R K YGF+TF + A A+
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 99 DMNGRTIDGRVVRVSEVATR 118
+NG + GR +RV V R
Sbjct: 66 QLNGFELAGRPMRVGHVTER 85
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 55.1 bits (131), Expect = 6e-08, Method: Composition-based stats.
Identities = 28/76 (36%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 39 ESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTR-GKCYGFVTFGNPRSAVDAI 97
+S+VYV LP+S + + ++F KYG VV V I+ D+ TR K F+ F + SA +
Sbjct: 16 KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCT 75
Query: 98 NDMNGRTIDGRVVRVS 113
+N + + GRV++ S
Sbjct: 76 RAINNKQLFGRVIKAS 91
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 53.9 bits (128), Expect = 1e-07, Method: Composition-based stats.
Identities = 33/91 (36%), Positives = 50/91 (54%), Gaps = 3/91 (3%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAIN 98
+ ++VGGLPY + S+RK F+ +G + ++ DR T + + YGFVT + +A A
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Query: 99 DMNGRTIDGRVVRVSEVATRGRKSNSGRDQF 129
D N IDGR V+ +A G K S + F
Sbjct: 78 DPN-PIIDGRKANVN-LAYLGAKPRSLQTGF 106
>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 = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 50/86 (58%), Gaps = 3/86 (3%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+++GGL + ED++R+ F KYG+V +KI+ D +T R + +GF++F P S + +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 101 NGRTIDGRVVRVSEVATRGRKSNSGR 126
+ +DG+V+ R + +G+
Sbjct: 66 H--ILDGKVIDPKRAIPRDEQDKTGK 89
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 45/75 (60%), Gaps = 2/75 (2%)
Query: 41 SVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAIND 99
++YVG L YSA + V+++F ++G V VK++ DR T + K +GFV S +AI
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIAK 61
Query: 100 MNGRTIDGRVVRVSE 114
++ GR +RV+E
Sbjct: 62 LDNTDFMGRTIRVTE 76
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 46/72 (63%), Gaps = 1/72 (1%)
Query: 47 LPYSANEDSVRKVFDKYGSVVAVKIVNDRSTR-GKCYGFVTFGNPRSAVDAINDMNGRTI 105
+P + +E +R++F++YG + +VKIV DR TR + YGFV F + SA AI +NG I
Sbjct: 50 IPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNI 109
Query: 106 DGRVVRVSEVAT 117
+ ++V+ A+
Sbjct: 110 LNKRLKVALAAS 121
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 51.6 bits (122), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 36/91 (39%), Positives = 53/91 (58%), Gaps = 2/91 (2%)
Query: 36 IDDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRG-KCYGFVTFGNPRSAV 94
+D ++ V L Y + DS+R+VF+KYG V V I + T+ + + FV F + R A
Sbjct: 10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQ 69
Query: 95 DAINDMNGRTIDGRVVRVSEVATRGRKSNSG 125
DA M+G +DGR +RV +VA GR+ SG
Sbjct: 70 DAEAAMDGAELDGRELRV-QVARYGRRDLSG 99
>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 = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 29/88 (32%), Positives = 47/88 (53%), Gaps = 7/88 (7%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
VYVG + Y ED++R+ F +G + ++ + D T + K + FV + P +A A+ M
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 101 NGRTIDGRVVRVSEVATRGRKSNSGRDQ 128
N + GR ++V GR SN G+ Q
Sbjct: 76 NSVMLGGRNIKV------GRPSNIGQAQ 97
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+YV + ++D ++ VF+ +G + + + D +T + K YGF+ + +S+ DA++ M
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 101 NGRTIDGRVVRVSEVAT 117
N + G+ +RV + T
Sbjct: 173 NLFDLGGQYLRVGKAVT 189
>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 = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 48/90 (53%), Gaps = 7/90 (7%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAIN 98
S VYVG + Y ED++R+ F +G + ++ + D T + K + FV + P +A A+
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 99 DMNGRTIDGRVVRVSEVATRGRKSNSGRDQ 128
MN + GR ++V GR SN G+ Q
Sbjct: 89 QMNSVMLGGRNIKV------GRPSNIGQAQ 112
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+YV + ++D ++ VF+ +G + + + D +T + K YGF+ + +S+ DA++ M
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 101 NGRTIDGRVVRVSEVAT 117
N + G+ +RV + T
Sbjct: 188 NLFDLGGQYLRVGKAVT 204
>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 = 50.4 bits (119), Expect = 2e-06, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 45/74 (60%), Gaps = 1/74 (1%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTR-GKCYGFVTFGNPRSAVDAIN 98
+++++ LP + + ++F +G+VV+ K+ D+ T KC+GFV++ NP SA AI
Sbjct: 26 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85
Query: 99 DMNGRTIDGRVVRV 112
MNG I + ++V
Sbjct: 86 SMNGFQIGMKRLKV 99
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 50.4 bits (119), Expect = 2e-06, Method: Composition-based stats.
Identities = 27/84 (32%), Positives = 47/84 (55%), Gaps = 2/84 (2%)
Query: 37 DDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVD 95
D+ ++VGGL +S ++++R F +YG VV I+ D++T + + +GFV F +P + V
Sbjct: 14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP-NCVG 72
Query: 96 AINDMNGRTIDGRVVRVSEVATRG 119
+ T+DGR + RG
Sbjct: 73 TVLASRPHTLDGRNIDPKPCTPRG 96
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 50.1 bits (118), Expect = 2e-06, Method: Composition-based stats.
Identities = 31/89 (34%), Positives = 46/89 (51%), Gaps = 3/89 (3%)
Query: 37 DDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDA 96
+++ +YVG LP + VF KYG++ + + N R G + FV F +PR A DA
Sbjct: 20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG--GPPFAFVEFEDPRDAEDA 77
Query: 97 INDMNGRTIDGRVVRVSEVATRGRKSNSG 125
+ +G DG +RV E GR + SG
Sbjct: 78 VYGRDGYDYDGYRLRV-EFPRSGRGTGSG 105
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/71 (39%), Positives = 42/71 (59%), Gaps = 4/71 (5%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDMN 101
VYVG L + N+ + + F YG + +V + R+ G + FV F +PR A DA+ D++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVA--RNPPG--FAFVEFEDPRDAADAVRDLD 131
Query: 102 GRTIDGRVVRV 112
GRT+ G VRV
Sbjct: 132 GRTLCGCRVRV 142
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 49.3 bits (116), Expect = 4e-06, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 41 SVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTR-GKCYGFVTFGNPRSAVDAIND 99
++++ LP + + F +G+V++ K+ D+ T KC+GFV+F NP SA AI
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 100 MNGRTIDGRVVRV 112
MNG + + ++V
Sbjct: 102 MNGFQVGTKRLKV 114
>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 = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 33/51 (64%)
Query: 39 ESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGN 89
++V+VGG+ +E +R F +YGSV VKI+ DR+ K YGFV+F N
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYN 59
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 48.9 bits (115), Expect = 4e-06, Method: Composition-based stats.
Identities = 27/88 (30%), Positives = 50/88 (56%), Gaps = 4/88 (4%)
Query: 38 DESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAI 97
+ ++ + L YSA E+++++VF+K +K+ +++ + K Y F+ F + A +A+
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKGYAFIEFASFEDAKEAL 70
Query: 98 NDMNGRTIDGRVVRVSEVATRGRKSNSG 125
N N R I+GR +R+ RG NSG
Sbjct: 71 NSCNKREIEGRAIRLELQGPRG-SPNSG 97
>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 = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/50 (46%), Positives = 33/50 (66%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGN 89
++V+VGG+ +E +R F +YGSV VKI+ DR+ K YGFV+F N
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYN 59
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 48.9 bits (115), Expect = 5e-06, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 41/75 (54%)
Query: 39 ESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAIN 98
+ +V+VG L E+ + ++F + G + V I DR + K +GFV F +P S AI
Sbjct: 16 DRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIA 75
Query: 99 DMNGRTIDGRVVRVS 113
+NG + GR + VS
Sbjct: 76 LLNGIRLYGRPINVS 90
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 48.5 bits (114), Expect = 5e-06, Method: Composition-based stats.
Identities = 29/85 (34%), Positives = 46/85 (54%), Gaps = 2/85 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
V+VG L + ++ F +G + ++V D +T + K YGFV+F N A +AI M
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 101 NGRTIDGRVVRVSEVATRGRKSNSG 125
G+ + GR +R + ATR + SG
Sbjct: 78 GGQWLGGRQIR-TNWATRKPPAPSG 101
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 48.5 bits (114), Expect = 6e-06, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 45/79 (56%), Gaps = 1/79 (1%)
Query: 36 IDDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAV 94
+D ++++ V LP + +D + +F G + + K+V D+ T + YGFV + +P A
Sbjct: 1 MDSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 95 DAINDMNGRTIDGRVVRVS 113
AIN +NG + + ++VS
Sbjct: 61 KAINTLNGLKLQTKTIKVS 79
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 45/79 (56%), Gaps = 1/79 (1%)
Query: 36 IDDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAV 94
+D ++++ V LP + +D + +F G + + K+V D+ T + YGFV + +P A
Sbjct: 1 MDSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 95 DAINDMNGRTIDGRVVRVS 113
AIN +NG + + ++VS
Sbjct: 61 KAINTLNGLKLQTKTIKVS 79
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 41/66 (62%), Gaps = 1/66 (1%)
Query: 39 ESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTR-GKCYGFVTFGNPRSAVDAI 97
++++YV GLP + ++ + ++F +YG ++ +I+ D++T + GF+ F A +AI
Sbjct: 90 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 149
Query: 98 NDMNGR 103
+NG+
Sbjct: 150 KGLNGQ 155
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 48.1 bits (113), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 33/51 (64%)
Query: 39 ESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGN 89
++V+VGG+ +E +R F +YGSV VKI+ DR+ K YGFV+F N
Sbjct: 10 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYN 60
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 48.1 bits (113), Expect = 8e-06, Method: Composition-based stats.
Identities = 26/85 (30%), Positives = 46/85 (54%), Gaps = 6/85 (7%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKC----YGFVTFGNPRSAVD 95
S +++ L +S E++++ VF K G++ + I ++ G +GFV + P A
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 96 AINDMNGRTIDGRV--VRVSEVATR 118
A+ + G T+DG VR+SE AT+
Sbjct: 66 ALKQLQGHTVDGHKLEVRISERATK 90
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 48.1 bits (113), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 47/84 (55%), Gaps = 2/84 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVND-RSTRGKCYGFVTFGNPRSAVDAINDM 100
++VGG+P++ E +R+ F K+G V V ++ D R + +GF+TF + +S A+N M
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-M 71
Query: 101 NGRTIDGRVVRVSEVATRGRKSNS 124
+ I G+ V V R KS+
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSKSSG 95
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 47/85 (55%), Gaps = 3/85 (3%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVND-RSTRGKCYGFVTFGNPRSAVDAINDM 100
+++GGL + E+S+R ++++G + ++ D S R + +GFVTF + + VDA
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS-MAEVDAAMAA 88
Query: 101 NGRTIDGRVVRVSEVATRGRKSNSG 125
+IDGRVV R +S SG
Sbjct: 89 RPHSIDGRVVEPKRAVAR-EESGSG 112
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 42/71 (59%), Gaps = 4/71 (5%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDMN 101
VYVG L + N+ + + F YG + +V + R+ G + FV F +PR A DA+ +++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVA--RNPPG--FAFVEFEDPRDAADAVRELD 131
Query: 102 GRTIDGRVVRV 112
GRT+ G VRV
Sbjct: 132 GRTLCGCRVRV 142
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 47.4 bits (111), Expect = 1e-05, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 5/83 (6%)
Query: 29 EERVKMTIDDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFG 88
E+ V + +VY GG+ + +R+ F +G ++ +++ + K Y FV F
Sbjct: 15 EDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFS 69
Query: 89 NPRSAVDAINDMNGRTIDGRVVR 111
SA AI +NG TI+G VV+
Sbjct: 70 THESAAHAIVSVNGTTIEGHVVK 92
>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 = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
V+VG L + ++ F +G + ++V D +T + K YGFV+F N A +AI M
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 101 NGRTIDGRVVRVSEVATR 118
G+ + GR +R + ATR
Sbjct: 78 GGQWLGGRQIR-TNWATR 94
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 42/72 (58%), Gaps = 1/72 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDMN 101
+YV L +++ +RK F +G++ + K++ + R K +GFV F +P A A+ +MN
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 102 GRTIDGRVVRVS 113
GR + + + V+
Sbjct: 77 GRIVATKPLYVA 88
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/85 (30%), Positives = 45/85 (52%), Gaps = 1/85 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRG-KCYGFVTFGNPRSAVDAINDM 100
++V L Y+++E+ + K+F YG + + D T+ K + FVTF P AV A ++
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 101 NGRTIDGRVVRVSEVATRGRKSNSG 125
+G+ GR++ V + S SG
Sbjct: 71 DGQVFQGRMLHVLPSTIKKEASQSG 95
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+++GGL + ++S+R F+++G++ ++ D +T R + +GFVT+ VDA +
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE-VDAAMNA 73
Query: 101 NGRTIDGRVVRVSEVATR 118
+DGRVV +R
Sbjct: 74 RPHKVDGRVVEPKRAVSR 91
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 46/88 (52%), Gaps = 2/88 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDR-STRGKCYGFVTFGNPRSAVDAINDM 100
++VGG+ E +R F++YG + ++I+ DR S + + + FVTF + +VD I
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIVIQ 164
Query: 101 NGRTIDGRVVRVSEVATRGRKSNSGRDQ 128
T++G V + ++ +++ Q
Sbjct: 165 KYHTVNGHNCEVRKALSKQEMASASSSQ 192
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+++GGL + ++S+R F+++G++ ++ D +T R + +GFVT+ VDA +
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE-VDAAMNA 74
Query: 101 NGRTIDGRVVRVSEVATR 118
+DGRVV +R
Sbjct: 75 RPHKVDGRVVEPKRAVSR 92
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 46/88 (52%), Gaps = 2/88 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDR-STRGKCYGFVTFGNPRSAVDAINDM 100
++VGG+ E +R F++YG + ++I+ DR S + + + FVTF + +VD I
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIVIQ 165
Query: 101 NGRTIDGRVVRVSEVATRGRKSNSGRDQ 128
T++G V + ++ +++ Q
Sbjct: 166 KYHTVNGHNCEVRKALSKQEMASASSSQ 193
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 45/88 (51%), Gaps = 7/88 (7%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
VYVG + Y ED++R+ F +G + ++ D T + K + FV + P +A A+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 101 NGRTIDGRVVRVSEVATRGRKSNSGRDQ 128
N + GR ++V GR SN G+ Q
Sbjct: 75 NSVXLGGRNIKV------GRPSNIGQAQ 96
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+YV + ++D ++ VF+ +G + + + D +T + K YGF+ + +S+ DA++
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 101 NGRTIDGRVVRVSEVAT 117
N + G+ +RV + T
Sbjct: 172 NLFDLGGQYLRVGKAVT 188
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+++GGL + ++S+R F+++G++ ++ D +T R + +GFVT+ VDA +
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE-VDAAMNA 72
Query: 101 NGRTIDGRVVRVSEVATR 118
+DGRVV +R
Sbjct: 73 RPHKVDGRVVEPKRAVSR 90
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 38/67 (56%), Gaps = 2/67 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDR-STRGKCYGFVTFGNPRSAVDAINDM 100
++VGG+ E +R F++YG + ++I+ DR S + + + FVTF + +VD I
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIVIQ 163
Query: 101 NGRTIDG 107
T++G
Sbjct: 164 KYHTVNG 170
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+++GGL + ++S+R F+++G++ ++ D +T R + +GFVT+ VDA +
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE-VDAAMNA 74
Query: 101 NGRTIDGRVVRVSEVATR 118
+DGRVV +R
Sbjct: 75 RPHKVDGRVVEPKRAVSR 92
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 38/67 (56%), Gaps = 2/67 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDR-STRGKCYGFVTFGNPRSAVDAINDM 100
++VGG+ E +R F++YG + ++I+ DR S + + + FVTF + +VD I
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIVIQ 165
Query: 101 NGRTIDG 107
T++G
Sbjct: 166 KYHTVNG 172
>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 = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+++GGL + ++S+R F+++G++ ++ D +T R + +GFVT+ VDA +
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE-VDAAMNA 67
Query: 101 NGRTIDGRVVRVSEVATR 118
+DGRVV +R
Sbjct: 68 RPHKVDGRVVEPKRAVSR 85
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 38/67 (56%), Gaps = 2/67 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDR-STRGKCYGFVTFGNPRSAVDAINDM 100
++VGG+ E +R F++YG + ++I+ DR S + + + FVTF + +VD I
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHDSVDKIVIQ 158
Query: 101 NGRTIDG 107
T++G
Sbjct: 159 KYHTVNG 165
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 49/81 (60%), Gaps = 1/81 (1%)
Query: 37 DDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVD 95
DD +++VG L + +++++R F + S ++ ++ D T + YGFV+F + A +
Sbjct: 85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 144
Query: 96 AINDMNGRTIDGRVVRVSEVA 116
A++ M G+ ++GR +R++ A
Sbjct: 145 AMDSMQGQDLNGRPLRINWAA 165
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 47/83 (56%), Gaps = 1/83 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDMN 101
+YVG L + ED +++ F G + +KI+ D++ + Y FV + A A+ +N
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 102 GRTIDGRVVRVSEVATRGRKSNS 124
G+ I+ +V+++ A + ++S+S
Sbjct: 63 GKQIENNIVKINW-AFQSQQSSS 84
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+++GGL + ++S+R F+++G++ ++ D +T R + +GFVT+ VDA +
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE-VDAAMNA 75
Query: 101 NGRTIDGRVVRVSEVATR 118
+DGRVV +R
Sbjct: 76 RPHKVDGRVVEPKRAVSR 93
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 46/88 (52%), Gaps = 2/88 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDR-STRGKCYGFVTFGNPRSAVDAINDM 100
++VGG+ E +R F++YG + ++I+ DR S + + + FVTF + +VD I
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHDSVDKIVIQ 166
Query: 101 NGRTIDGRVVRVSEVATRGRKSNSGRDQ 128
T++G V + ++ +++ Q
Sbjct: 167 KYHTVNGHNCEVRKALSKQEMASASSSQ 194
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 37 DDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVND-RSTRGKCYGFVTFGNPRSAVD 95
D + V GL E +R+VF KYG + V IV D +S R + + FV F N A +
Sbjct: 10 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 69
Query: 96 AINDMNGRTIDGRVVRV 112
A NG +DGR +RV
Sbjct: 70 AKERANGMELDGRRIRV 86
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 47/78 (60%), Gaps = 3/78 (3%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIV-NDRSTRGKCYGFVTFGNPRSAVDAINDM 100
++V +P+ + +R++F ++G ++ V+I+ N+R ++G +GFVTF N A A +
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG--FGFVTFENSADADRAREKL 89
Query: 101 NGRTIDGRVVRVSEVATR 118
+G ++GR + V+ R
Sbjct: 90 HGTVVEGRKIEVNNATAR 107
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 31/82 (37%), Positives = 42/82 (51%), Gaps = 1/82 (1%)
Query: 33 KMTIDDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDR-STRGKCYGFVTFGNPR 91
+ D + V GL E +R+VF KYG + V IV D+ S R + + FV F N
Sbjct: 9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
Query: 92 SAVDAINDMNGRTIDGRVVRVS 113
A +A NG +DGR +RVS
Sbjct: 69 DAKEAKERANGMELDGRRIRVS 90
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 37 DDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVND-RSTRGKCYGFVTFGNPRSAVD 95
D + V GL E +R+VF KYG + V IV D +S R + + FV F N A +
Sbjct: 13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72
Query: 96 AINDMNGRTIDGRVVRV 112
A NG +DGR +RV
Sbjct: 73 AKERANGMELDGRRIRV 89
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 37 DDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVND-RSTRGKCYGFVTFGNPRSAVD 95
D + V GL E +R+VF KYG + V IV D +S R + + FV F N A +
Sbjct: 44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 103
Query: 96 AINDMNGRTIDGRVVRV 112
A NG +DGR +RV
Sbjct: 104 AKERANGMELDGRRIRV 120
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 45.1 bits (105), Expect = 6e-05, Method: Composition-based stats.
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 7/84 (8%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
VY+G +PY E+ + + G V+ +K++ D T R K Y F+ F + S+ A+ ++
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 101 NGRTIDGRVVRVSEVATRGRKSNS 124
NG + R ++ G SNS
Sbjct: 67 NGYQLGSRFLKC------GYSSNS 84
>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 = 45.1 bits (105), Expect = 6e-05, Method: Composition-based stats.
Identities = 18/76 (23%), Positives = 45/76 (59%)
Query: 38 DESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAI 97
++ +++ GLP+S ++ + ++ +G+V +++V +R+ + K +V + N A A+
Sbjct: 16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAV 75
Query: 98 NDMNGRTIDGRVVRVS 113
M+G TI +++V+
Sbjct: 76 MKMDGMTIKENIIKVA 91
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 38 DESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDA 96
++++ V LP + ++ R +F G + + K+V D+ T + YGFV + +P+ A A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 97 INDMNGRTIDGRVVRVS 113
IN +NG + + ++VS
Sbjct: 61 INTLNGLRLQTKTIKVS 77
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 39 ESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTR-GKCYGFVTFGNPRSAVDAI 97
++++YV GLP + + + ++F +YG ++ +I+ D+ T + GF+ F A +AI
Sbjct: 88 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
Query: 98 NDMNGRTIDG 107
+NG+ G
Sbjct: 148 KGLNGQKPSG 157
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 51/85 (60%), Gaps = 4/85 (4%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIV-NDRSTRGKCYGFVTFGNPRSAVDAINDM 100
++V +P+ + +R++F ++G ++ V+I+ N+R ++G +GFVTF N A A +
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG--FGFVTFENSADADRAREKL 75
Query: 101 NGRTIDGRVVRVSEVATRGRKSNSG 125
+G ++GR + V+ R +NSG
Sbjct: 76 HGTVVEGRKIEVNNATAR-VMTNSG 99
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 47/76 (61%), Gaps = 8/76 (10%)
Query: 38 DESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRS-----TRGKCYGFVTFGNPRS 92
D ++VG +P + +E +R++F++YG+V + ++ DRS ++G C FVTF ++
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCC--FVTFYTRKA 59
Query: 93 AVDAINDM-NGRTIDG 107
A++A N + N + + G
Sbjct: 60 ALEAQNALHNMKVLPG 75
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 45.1 bits (105), Expect = 7e-05, Method: Composition-based stats.
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 7/84 (8%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
VY+G +PY E+ + + G V+ +K++ D T R K Y F+ F + S+ A+ ++
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 101 NGRTIDGRVVRVSEVATRGRKSNS 124
NG + R ++ G SNS
Sbjct: 66 NGYQLGSRFLKC------GYSSNS 83
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 44.7 bits (104), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 47/76 (61%), Gaps = 8/76 (10%)
Query: 38 DESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRS-----TRGKCYGFVTFGNPRS 92
D ++VG +P + +E +R++F++YG+V + ++ DRS ++G C FVTF ++
Sbjct: 14 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCC--FVTFYTRKA 71
Query: 93 AVDAINDM-NGRTIDG 107
A++A N + N + + G
Sbjct: 72 ALEAQNALHNMKVLPG 87
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 44.7 bits (104), Expect = 9e-05, Method: Composition-based stats.
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 7/84 (8%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
VY+G +PY E+ + + G V+ +K++ D T R K Y F+ F + S+ A+ ++
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 101 NGRTIDGRVVRVSEVATRGRKSNS 124
NG + R ++ G SNS
Sbjct: 65 NGYQLGSRFLKC------GYSSNS 82
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 30/85 (35%), Positives = 42/85 (49%), Gaps = 4/85 (4%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDMN 101
VYVG L A + + + F YG + V I R+ G + FV F +PR A DA+ ++
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIA--RNPPG--FAFVEFEDPRDAEDAVRGLD 58
Query: 102 GRTIDGRVVRVSEVATRGRKSNSGR 126
G+ I G VRV R+S R
Sbjct: 59 GKVICGSRVRVELSTGMPRRSRFDR 83
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 46/76 (60%), Gaps = 8/76 (10%)
Query: 38 DESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRS-----TRGKCYGFVTFGNPRS 92
D +VG +P + +E +R++F++YG+V + ++ DRS ++G C FVTF ++
Sbjct: 2 DAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCC--FVTFYTRKA 59
Query: 93 AVDAINDM-NGRTIDG 107
A++A N + N + + G
Sbjct: 60 ALEAQNALHNXKVLPG 75
>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 = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDR-STRGKCYGFVTFGNPRSAVDAIN 98
+++ V LP + +D +R +F G V + K++ D+ + YGFV + + A AIN
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 99 DMNGRTIDGRVVRVS 113
+NG + + ++VS
Sbjct: 65 TLNGLRLQSKTIKVS 79
>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 = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDR-STRGKCYGFVTFGNPRSAVDAIN 98
+++ V LP + +D +R +F G V + K++ D+ + YGFV + + A AIN
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 99 DMNGRTIDGRVVRVS 113
+NG + + ++VS
Sbjct: 80 TLNGLRLQSKTIKVS 94
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 45/73 (61%), Gaps = 7/73 (9%)
Query: 38 DESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRS-----TRGKCYGFVTFGNPRS 92
D ++VG +P + +E +R++F++YG+V + ++ DRS ++G C FVTF ++
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCC--FVTFYTRKA 59
Query: 93 AVDAINDMNGRTI 105
A++A N ++ +
Sbjct: 60 ALEAQNALHNMKV 72
>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 = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDR-STRGKCYGFVTFGNPRSAVDAIN 98
+++ V LP + +D +R +F G V + K++ D+ + YGFV + + A AIN
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 99 DMNGRTIDGRVVRVS 113
+NG + + ++VS
Sbjct: 63 TLNGLRLQSKTIKVS 77
Score = 35.4 bits (80), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 39 ESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAI 97
++++Y+ GLP + + V +F ++G ++ +++ D++T + F+ F A +AI
Sbjct: 88 DANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Query: 98 NDMNGRTIDG 107
NG G
Sbjct: 148 TSFNGHKPPG 157
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAIN 98
S +Y+ GL + + K+ YG +V+ K + D++T + K YGFV F +P +A A+
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 99 DMNGRTIDGRVVRVS 113
+ + ++ + S
Sbjct: 66 ALKASGVQAQMAKQS 80
>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 = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 47/77 (61%), Gaps = 1/77 (1%)
Query: 41 SVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAIND 99
+++VG L + +++++R F + S ++ ++ D T + YGFV+F + A +A++
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 100 MNGRTIDGRVVRVSEVA 116
M G+ ++GR +R++ A
Sbjct: 63 MQGQDLNGRPLRINWAA 79
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDR-STRGKCYGFVTFGNPRSAVDAIN 98
+++ V LP + +D +R +F G V + K++ D+ + YGFV + + A AIN
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 99 DMNGRTIDGRVVRVS 113
+NG + + ++VS
Sbjct: 63 TLNGLRLQSKTIKVS 77
Score = 35.0 bits (79), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 39 ESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAI 97
++++Y+ GLP + + V +F ++G ++ +++ D++T + F+ F A +AI
Sbjct: 88 DANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Query: 98 NDMNGRTIDG 107
NG G
Sbjct: 148 TSFNGHKPPG 157
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 45/84 (53%), Gaps = 8/84 (9%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDMN 101
+++G LP A E +R +F++YG V+ I+ K YGFV + +A DAI +++
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLH 63
Query: 102 GRTIDGRVVRVSEVATRGRKSNSG 125
+ G + V E + K++SG
Sbjct: 64 HYKLHGVNINV-EASKNKSKASSG 86
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 41.6 bits (96), Expect = 7e-04, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 41/66 (62%), Gaps = 1/66 (1%)
Query: 39 ESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTR-GKCYGFVTFGNPRSAVDAI 97
++++YV GLP + ++ + ++F +YG ++ +I+ D++T + GF+ F A +AI
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 98 NDMNGR 103
+NG+
Sbjct: 61 KGLNGQ 66
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 41.6 bits (96), Expect = 8e-04, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDR--STRGKCYGFVTFGNPRSAVDAI 97
+ V++G L + +D + ++F YG + + + +R K Y +V F NP A A+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 98 NDMNGRTIDGRVVRVSEV 115
M+G IDG+ + + V
Sbjct: 65 KHMDGGQIDGQEITATAV 82
>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 = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 2/75 (2%)
Query: 37 DDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVD 95
+D +VGGL + ++ ++ F K+G VV I D +T R + +GF+ F + S V+
Sbjct: 9 EDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAAS-VE 67
Query: 96 AINDMNGRTIDGRVV 110
+ D +DGRV+
Sbjct: 68 KVLDQKEHRLDGRVI 82
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 37/73 (50%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAIND 99
S+V+V L Y +++VF G VV I+ D+ + + G VTF AV AI+
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 100 MNGRTIDGRVVRV 112
NG+ + R + V
Sbjct: 76 FNGQLLFDRPMHV 88
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+YVGGL ++ + F +G + ++I D T + + + FV F A AI++M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 101 NGRTIDGRVVRVS 113
N + GR +RV+
Sbjct: 126 NESELFGRTIRVN 138
>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 = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 27/78 (34%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
V+VG L ++ F +G + ++V D +T + K YGFV+F N A +AI M
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 101 NGRTIDGRVVRVSEVATR 118
G+ + GR +R + ATR
Sbjct: 69 GGQWLGGRQIR-TNWATR 85
>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 = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 1/81 (1%)
Query: 41 SVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDM 100
++++ L S + ++ F +G++++ K+V D + K YGFV F +A AI M
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 101 NGRTIDGRVVRVSEVATRGRK 121
NG ++ R V V +R +
Sbjct: 66 NGMLLNDRKVFVGRFKSRKER 86
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 26/85 (30%), Positives = 47/85 (55%), Gaps = 1/85 (1%)
Query: 37 DDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVD 95
+ +++VYVGGL +E + ++F + G VV + DR T + + YGFV F + A
Sbjct: 13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72
Query: 96 AINDMNGRTIDGRVVRVSEVATRGR 120
AI M+ + G+ +RV++ + +
Sbjct: 73 AIKIMDMIKLYGKPIRVNKASAHNK 97
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 35 TIDDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAV 94
T S ++VG LP E+ +RK+F+KYG V I D K +GF+ A
Sbjct: 18 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAE 72
Query: 95 DAINDMNGRTIDGRVVRV 112
A +++ + G+ +RV
Sbjct: 73 IAKVELDNMPLRGKQLRV 90
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/110 (25%), Positives = 54/110 (49%), Gaps = 10/110 (9%)
Query: 29 EERVKMTIDDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKC-YGFVTF 87
EE+ K+ + ++YVG L + E+ + ++F K G + + + D+ + C + FV +
Sbjct: 30 EEQEKL-LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEY 88
Query: 88 GNPRSAVDAINDMNGRTIDGRVVRVSEVA--------TRGRKSNSGRDQF 129
+ A +A+ +NG +D R++R A RGR RD++
Sbjct: 89 YSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEY 138
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAIND 99
++++ L S + ++ F +G++++ K+V D + K YGFV F +A AI
Sbjct: 12 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQEAAERAIEK 70
Query: 100 MNGRTIDGRVVRVSEVATR 118
MNG ++ R V V +R
Sbjct: 71 MNGMLLNDRKVFVGRFKSR 89
>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 = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 42/81 (51%), Gaps = 3/81 (3%)
Query: 41 SVYVGGLPYSANEDSVRKVFDKYGSVVAVKIV-NDRSTRGKCYGFVTFGNPRSAVDAIND 99
+++V + Y E +R+ F+ YG + + +V + RS + + Y F+ + + R A
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 100 MNGRTIDGRVVRVSEVATRGR 120
+G+ IDGR V V RGR
Sbjct: 164 ADGKKIDGRRVLVD--VERGR 182
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 39 ESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAI 97
++++YV LP + +D + +F KYGS+V I+ D+ T R + FV + A +AI
Sbjct: 13 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
Query: 98 NDMNGRTIDG 107
+ +N +G
Sbjct: 73 SALNNVIPEG 82
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 39 ESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAI 97
++++YV LP + +D + +F KYGS+V I+ D+ T R + FV + A +AI
Sbjct: 100 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159
Query: 98 NDMNGRTIDG 107
+ +N +G
Sbjct: 160 SALNNVIPEG 169
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 9/74 (12%)
Query: 42 VYVGGLPYSANEDSVRKVFD--KYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAIND 99
+YV L S +E+ + K F+ K G+V VK + D Y FV F N AV+A+
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD-------YAFVHFSNREDAVEAMKA 70
Query: 100 MNGRTIDGRVVRVS 113
+NG+ +DG + V+
Sbjct: 71 LNGKVLDGSPIEVT 84
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 2/76 (2%)
Query: 38 DESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDR-STRGKCYGFVTFGNPRSAVDA 96
D+ SVYVG + Y + + F GS+ + I+ D+ S K Y ++ F R++VDA
Sbjct: 35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE-RNSVDA 93
Query: 97 INDMNGRTIDGRVVRV 112
M+ GR ++V
Sbjct: 94 AVAMDETVFRGRTIKV 109
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+YVGGL ++ + F +G + ++I D T + + + FV F A AI++M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 101 NGRTIDGRVVRVS 113
N + GR +RV+
Sbjct: 75 NESELFGRTIRVN 87
>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 = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 41 SVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDM 100
++++ L S + ++ F +G++++ K+V D + K YGFV F +A AI M
Sbjct: 100 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 158
Query: 101 NGRTIDGRVVRVSEVATR 118
NG ++ R V V +R
Sbjct: 159 NGMLLNDRKVFVGRFKSR 176
>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 = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+YVGGL ++ + F +G + ++I D T + + + FV F A AI++M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 101 NGRTIDGRVVRVS 113
N + GR +RV+
Sbjct: 70 NESELFGRTIRVN 82
>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 = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 44/84 (52%), Gaps = 1/84 (1%)
Query: 29 EERVKMTIDDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFG 88
EE+ K+ + ++YVG L + E+ + ++F K G + + + D+ + FV +
Sbjct: 9 EEQEKL-LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYY 67
Query: 89 NPRSAVDAINDMNGRTIDGRVVRV 112
+ A +A+ +NG +D R++R
Sbjct: 68 SRADAENAMRYINGTRLDDRIIRT 91
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+YVGGL ++ + F +G + ++I D T + + + FV F A AI++M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 101 NGRTIDGRVVRVS 113
N + GR +RV+
Sbjct: 68 NESELFGRTIRVN 80
>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 = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+YVGGL ++ + F +G + ++I D T + + + FV F A AI++M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 101 NGRTIDGRVVRVS 113
N + GR +RV+
Sbjct: 65 NESELFGRTIRVN 77
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 18/76 (23%), Positives = 34/76 (44%)
Query: 30 ERVKMTIDDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGN 89
+ K D +++Y+ LP S +E + + +G V++ +I+ D S + GF +
Sbjct: 16 QMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMES 75
Query: 90 PRSAVDAINDMNGRTI 105
I NG+ I
Sbjct: 76 TEKCEAVIGHFNGKFI 91
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 39 ESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAI 97
++++YV LP + +D + +F KYGS+V I+ D+ T R + FV + A +AI
Sbjct: 89 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
Query: 98 NDMNGRTIDG 107
+ +N +G
Sbjct: 149 SALNNVIPEG 158
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 20/82 (24%), Positives = 40/82 (48%), Gaps = 1/82 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+++GGLP N+D V+++ +G + A +V D +T K Y F + + AI +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 101 NGRTIDGRVVRVSEVATRGRKS 122
NG + + + V + + +
Sbjct: 64 NGMQLGDKKLLVQRASVGAKNA 85
>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 = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 41 SVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDM 100
++++ L S + ++ F +G++++ K+V D + K YGFV F +A AI M
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQEAAERAIEKM 163
Query: 101 NGRTIDGRVVRVSEVATR 118
NG ++ R V V +R
Sbjct: 164 NGMLLNDRKVFVGRFKSR 181
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+++GGLP N+D V+++ +G + A +V D +T K Y F + + AI +
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 101 NGRTI 105
NG +
Sbjct: 157 NGMQL 161
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 8/80 (10%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDMN 101
++VG + + +R +F++ G V+ +V D Y FV A AI +N
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQLN 64
Query: 102 GRTIDGRVVRVSEVATRGRK 121
G+ + G+ + V E++T+G+K
Sbjct: 65 GKEVKGKRINV-ELSTKGQK 83
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 37 DDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVD 95
D +++GGLP N+D V+++ +G + A +V D +T K Y F + +
Sbjct: 112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 171
Query: 96 AINDMNGRTI 105
AI +NG +
Sbjct: 172 AIAGLNGMQL 181
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 37.4 bits (85), Expect = 0.013, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDMN 101
+Y+ LPY + + +F KYG + +++ N TRG Y V + + A +A++ ++
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAY--VVYEDIFDAKNAVDHLS 68
Query: 102 GRTIDGRVVRV 112
G + R + V
Sbjct: 69 GFNVSNRYLVV 79
>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 = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+++GGL + + ++ F K+G VV + D T R + +GFV F S VD + D
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESES-VDKVMDQ 60
Query: 101 NGRTIDGRVV 110
++G+V+
Sbjct: 61 KEHKLNGKVI 70
>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 = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
+++GGLP N+D V+++ +G + A +V D +T K Y F + + AI +
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 101 NGRTI 105
NG +
Sbjct: 159 NGMQL 163
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 37.4 bits (85), Expect = 0.014, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 8/63 (12%)
Query: 36 IDDESSVYVGGLPY-SANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAV 94
I +S +++G LP + +++ + ++F YG ++ + I N +GF+ F NP+S
Sbjct: 7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVR 59
Query: 95 DAI 97
DAI
Sbjct: 60 DAI 62
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 37.4 bits (85), Expect = 0.014, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 8/60 (13%)
Query: 39 ESSVYVGGLPY-SANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAI 97
+S +++G LP + +++ + ++F YG ++ + I N +GF+ F NP+S DAI
Sbjct: 22 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAI 74
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 1/81 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTR-GKCYGFVTFGNPRSAVDAINDM 100
++V + A ED +++ F YG + + + DR T K Y V + + A+ A +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 101 NGRTIDGRVVRVSEVATRGRK 121
NG I G+ ++V +G K
Sbjct: 89 NGAEIMGQTIQVDWCFVKGPK 109
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 37.0 bits (84), Expect = 0.016, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 8/60 (13%)
Query: 39 ESSVYVGGLPY-SANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAI 97
+S +++G LP + +++ + ++F YG ++ + I N +GF+ F NP+S DAI
Sbjct: 22 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAI 74
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 1/81 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTR-GKCYGFVTFGNPRSAVDAINDM 100
++V + A ED +++ F YG + + + DR T K Y V + + A+ A +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 101 NGRTIDGRVVRVSEVATRGRK 121
NG I G+ ++V +G K
Sbjct: 135 NGAEIMGQTIQVDWCFVKGPK 155
>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 = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 41 SVYVGGLPYSANEDSVRKVFDKYGSVVAVKIV-NDRSTRGKCYGFVTFGNPRSAVDAIND 99
+++V + Y E +R+ F+ YG + + +V + RS + + Y F+ + + R A
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 100 MNGRTIDGRVVRV 112
+G+ IDGR V V
Sbjct: 164 ADGKKIDGRRVLV 176
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 37.0 bits (84), Expect = 0.019, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 8/60 (13%)
Query: 39 ESSVYVGGLPY-SANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAI 97
+S +++G LP + +++ + ++F YG ++ + I N +GF+ F NP+S DAI
Sbjct: 2 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAI 54
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDMN 101
++VG LP E+ +++F++YG V I DR +GF+ + A A +++
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRG-----FGFIRLESRTLAEIAKAELD 79
Query: 102 GRTIDGRVVRVSEVATRG 119
G + R +R+ AT G
Sbjct: 80 GTILKSRPLRIR-FATHG 96
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 36.2 bits (82), Expect = 0.032, Method: Composition-based stats.
Identities = 25/93 (26%), Positives = 50/93 (53%), Gaps = 4/93 (4%)
Query: 32 VKMTIDDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNP 90
V M D ++VG +P +E ++ +F+++G + + ++ DR T K F+T+
Sbjct: 8 VPMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCAR 67
Query: 91 RSAVDAINDMN-GRTIDG--RVVRVSEVATRGR 120
SA+ A + ++ +T+ G R ++V A+ GR
Sbjct: 68 DSALKAQSALHEQKTLPGMNRPIQVKPAASEGR 100
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 36.2 bits (82), Expect = 0.033, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDMN 101
+Y+ LPY + + +F KYG + +++ N TRG Y V + + A +A + ++
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAY--VVYEDIFDAKNACDHLS 72
Query: 102 GRTIDGRVVRV 112
G + R + V
Sbjct: 73 GFNVCNRYLVV 83
>pdb|2DNN|A Chain A, Solution Structure Of Rna Binding Domain In Rna-Binding
Protein 12
Length = 109
Score = 35.8 bits (81), Expect = 0.039, Method: Composition-based stats.
Identities = 27/81 (33%), Positives = 38/81 (46%), Gaps = 2/81 (2%)
Query: 38 DESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAI 97
D+ V V G+P+SA E+ VR F V AV ++ D R G V F +P+ +A+
Sbjct: 15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL 73
Query: 98 NDMNGRTIDGRVVRVSEVATR 118
N + R V VS R
Sbjct: 74 K-RNRMLMIQRYVEVSPATER 93
>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 = 35.8 bits (81), Expect = 0.045, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 35 TIDDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAV 94
T S ++VG LP E+ +RK+F+KYG V I D K +GF+ A
Sbjct: 11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAE 65
Query: 95 DAINDMNGRTIDGRVVRV 112
A +++ + G+ +RV
Sbjct: 66 IAKVELDNMPLRGKQLRV 83
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 35.4 bits (80), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 7/71 (9%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDMN 101
++V L + E+ + K F ++G + VK + D Y F+ F AV A+ +MN
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 66
Query: 102 GRTIDGRVVRV 112
G+ ++G + +
Sbjct: 67 GKDLEGENIEI 77
>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 = 35.0 bits (79), Expect = 0.065, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDMN 101
+Y+ LPY + + +F KYG + +++ N TRG Y V + + A +A + ++
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAY--VVYEDIFDAKNACDHLS 78
Query: 102 GRTIDGRVVRV 112
G + R + V
Sbjct: 79 GFNVCNRYLVV 89
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 35.0 bits (79), Expect = 0.067, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 40 SSVYVGGL-PYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAIN 98
S V++G L + V +F KYG +V + K + FV + N R+A A+
Sbjct: 16 SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVA 68
Query: 99 DMNGRTIDGRVVRVSEVA 116
+GR I G+V+ ++ A
Sbjct: 69 GEDGRMIAGQVLDINLAA 86
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 35.0 bits (79), Expect = 0.068, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAV-KIVNDRST-RGKCYGFVTFGNPRSAVDAI 97
S +++G L +E + F +G ++ KI+ D T K Y F+ F + ++ AI
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 98 NDMNGRTIDGRVVRVS 113
MNG+ + R + VS
Sbjct: 66 EAMNGQYLCNRPITVS 81
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 34.7 bits (78), Expect = 0.090, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 8/75 (10%)
Query: 40 SSVYVGGLPYS-ANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAIN 98
S V++G L + + V +F KYG V + K Y FV + N R A A+
Sbjct: 28 SRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVL 80
Query: 99 DMNGRTIDGRVVRVS 113
NGR + G+ + ++
Sbjct: 81 GENGRVLAGQTLDIN 95
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 34.7 bits (78), Expect = 0.091, Method: Composition-based stats.
Identities = 19/77 (24%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 37 DDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVD 95
DD +++ V L E ++++F +GS+ + + D++T + K + F++F A
Sbjct: 13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 72
Query: 96 AINDMNGRTIDGRVVRV 112
AI ++G D ++ V
Sbjct: 73 AIAGVSGFGYDHLILNV 89
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 34.3 bits (77), Expect = 0.13, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 32/61 (52%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDMN 101
++VG L +ED VR++F+ +G++ I+ K FV + + A AIN ++
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 102 G 102
G
Sbjct: 78 G 78
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRG--KCYGFVTFGNPRSAVDAI 97
S + V +P+ AN+ +R++F +G + V++ + G + +GFV F + A A
Sbjct: 16 SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
Query: 98 NDM 100
N +
Sbjct: 76 NAL 78
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 7/84 (8%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAIND 99
+ ++VG + + +R F++YG V+ IV D Y FV AV+AI
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRG 63
Query: 100 MNGRTIDGRVVRVSEVATRGRKSN 123
++ G+ + V +R R ++
Sbjct: 64 LDNTEFQGKRMHVQLSTSRLRTAS 87
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 33.1 bits (74), Expect = 0.26, Method: Composition-based stats.
Identities = 27/71 (38%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 41 SVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAIND 99
+++V GL E+++++ FD GSV A +IV DR T K +GFV F + A A
Sbjct: 17 TLFVKGLSEDTTEETLKESFD--GSVRA-RIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73
Query: 100 MNGRTIDGRVV 110
M IDG V
Sbjct: 74 MEDGEIDGNKV 84
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 32.7 bits (73), Expect = 0.39, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRG-KCYGFVTFGNPRSAVDAINDM 100
++V G+ A E+ + F +YG + + + DR T K Y V + + A A+ +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 101 NGRTIDGRVVRVSEVATRG 119
NG+ + G+ + V RG
Sbjct: 72 NGQDLMGQPISVDWCFVRG 90
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 32.3 bits (72), Expect = 0.41, Method: Composition-based stats.
Identities = 18/74 (24%), Positives = 36/74 (48%)
Query: 44 VGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDMNGR 103
V L + ++ ++++F ++G++ + DRS R V F A+ A+ NG
Sbjct: 33 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGV 92
Query: 104 TIDGRVVRVSEVAT 117
+DGR + + V +
Sbjct: 93 PLDGRPMNIQLVTS 106
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 32.3 bits (72), Expect = 0.41, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
++V G+ A E+ + F +YG + + + DR T K Y V + + A A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 101 NGRTIDGRVVRVSEVATRG 119
NG+ + G+ + V RG
Sbjct: 70 NGQDLMGQPISVDWCFVRG 88
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 32.3 bits (72), Expect = 0.47, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
++V G+ A E+ + F +YG + + + DR T K Y V + + A A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 101 NGRTIDGRVVRVSEVATRG 119
NG+ + G+ + V RG
Sbjct: 70 NGQDLMGQPISVDWCFVRG 88
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 32.3 bits (72), Expect = 0.48, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 7/62 (11%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDMN 101
++V L + E+ + K F ++G + VK + D Y FV F + +AV A+++MN
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEDRGAAVKAMDEMN 70
Query: 102 GR 103
G+
Sbjct: 71 GK 72
>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 = 32.3 bits (72), Expect = 0.48, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 47 LPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDMNGRTID 106
LPY + + +F KYG + +++ N TRG Y V + + A +A + ++G +
Sbjct: 26 LPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAY--VVYEDIFDAKNACDHLSGFNVC 83
Query: 107 GRVVRV 112
R + V
Sbjct: 84 NRYLVV 89
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 32.0 bits (71), Expect = 0.63, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAIND 99
S ++V LP+ ++ F++ G V+ I + C G V F +P A A
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGC-GVVKFESPEVAERACRM 64
Query: 100 MNGRTIDGRVVRV 112
MNG + GR + V
Sbjct: 65 MNGMKLSGREIDV 77
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 32.0 bits (71), Expect = 0.68, Method: Composition-based stats.
Identities = 18/83 (21%), Positives = 41/83 (49%)
Query: 36 IDDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVD 95
++ + + V L + ++ ++++F ++G++ + DRS R V F A+
Sbjct: 32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALK 91
Query: 96 AINDMNGRTIDGRVVRVSEVATR 118
A+ G +DGR + + VA++
Sbjct: 92 AMKQYKGVPLDGRPMDIQLVASQ 114
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 31.6 bits (70), Expect = 0.78, Method: Composition-based stats.
Identities = 18/83 (21%), Positives = 41/83 (49%)
Query: 36 IDDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVD 95
++ + + V L + ++ ++++F ++G++ + DRS R V F A+
Sbjct: 32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALK 91
Query: 96 AINDMNGRTIDGRVVRVSEVATR 118
A+ G +DGR + + VA++
Sbjct: 92 AMKQYKGVPLDGRPMDIQLVASQ 114
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 31.6 bits (70), Expect = 0.81, Method: Composition-based stats.
Identities = 16/64 (25%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 34 MTIDDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRS 92
M D +++G +P + +E ++ +F+++G + + ++ DR T K F+T+ S
Sbjct: 8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERES 67
Query: 93 AVDA 96
A+ A
Sbjct: 68 ALKA 71
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 31.2 bits (69), Expect = 0.91, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRST-RGKCYGFVTFGNPRSAVDAINDM 100
++V G+ A E+ + F +YG + + + DR T K Y V + + A A+ +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 101 NGRTIDGRVVRVSEVATRG 119
NG+ + G+ + V RG
Sbjct: 86 NGQDLMGQPISVDWCFVRG 104
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 30.8 bits (68), Expect = 1.2, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 38 DESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAI 97
++ ++VG L ++ VRK+F+ +G++ ++ K FV F A AI
Sbjct: 11 EDRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAI 70
Query: 98 NDM-NGRTIDG 107
N + + RT+ G
Sbjct: 71 NTLHSSRTLPG 81
>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 = 1.5, Method: Composition-based stats.
Identities = 18/74 (24%), Positives = 34/74 (45%)
Query: 44 VGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDMNGR 103
V L + ++ ++++F ++G++ + DRS R V F A+ A NG
Sbjct: 34 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYNGV 93
Query: 104 TIDGRVVRVSEVAT 117
+DGR + V +
Sbjct: 94 PLDGRPXNIQLVTS 107
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 30.4 bits (67), Expect = 1.6, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 1/71 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAINDMN 101
++V LP+ ++ F++ G V+ I + C G V F +P A A MN
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGC-GVVKFESPEVAERACRMMN 69
Query: 102 GRTIDGRVVRV 112
G + GR + V
Sbjct: 70 GMKLSGREIDV 80
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 25/84 (29%), Positives = 37/84 (44%), Gaps = 7/84 (8%)
Query: 42 VYVGGLPYSANEDSVRK---VFDKYGSVVAVKIVNDRSTRGK----CYGFVTFGNPRSAV 94
V+V GL + V K F K+G + V I N S G +VT+ A+
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 95 DAINDMNGRTIDGRVVRVSEVATR 118
AI +N +DGR ++ S T+
Sbjct: 78 RAIQCVNNVVVDGRTLKASLGTTK 101
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
Length = 109
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRG-KCYGFVTFGNPRSAVDAINDM 100
++V G+ A E+ + F +YG + + + DR T K Y V + + A A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 101 NGRTIDGRVVRV 112
NG+ + G+ + V
Sbjct: 70 NGQDLMGQPISV 81
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 30.4 bits (67), Expect = 1.9, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSA-VDAIN 98
+++YVGGL + E +R F ++G + + +V R +C F+ F ++A V A
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ----RQQC-AFIQFATRQAAEVAAEK 67
Query: 99 DMNGRTIDGRVVRV 112
N ++GR + V
Sbjct: 68 SFNKLIVNGRRLNV 81
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 18/83 (21%), Positives = 41/83 (49%)
Query: 36 IDDESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVD 95
++ + + V L + ++ ++++F ++G++ + DRS R V F A+
Sbjct: 85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALK 144
Query: 96 AINDMNGRTIDGRVVRVSEVATR 118
A+ G +DGR + + VA++
Sbjct: 145 AMKQYKGVPLDGRPMDIQLVASQ 167
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 29.6 bits (65), Expect = 2.7, Method: Composition-based stats.
Identities = 27/92 (29%), Positives = 44/92 (47%), Gaps = 5/92 (5%)
Query: 39 ESSVYVGGLPYSANEDSVRKVFDK-YGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAI 97
E S++VG L ++ + + F K Y S K+V D++ K YGFV F + A+
Sbjct: 9 EYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRAL 68
Query: 98 NDMNGRT-IDGRVVRVSEV---ATRGRKSNSG 125
+ G + + VR+S A+R + SG
Sbjct: 69 TECQGAVGLGSKPVRLSVAIPKASRVKPVESG 100
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 29.6 bits (65), Expect = 2.9, Method: Composition-based stats.
Identities = 26/86 (30%), Positives = 38/86 (44%), Gaps = 7/86 (8%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAIND 99
S V+VG ED +R+ F +YG V+ V I + + FVTF + + A +
Sbjct: 6 SGVFVGRCTGDMTEDELREFFSQYGDVMDVFI----PKPFRAFAFVTFADDQIAQSLCGE 61
Query: 100 MNGRTIDGRVVRVSEVATRGRKSNSG 125
I G V +S + SNSG
Sbjct: 62 --DLIIKGISVHISNAEPK-HNSNSG 84
>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 = 29.6 bits (65), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 38 DESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDR-STRGKCYGFVTFGNPRS 92
D S+YVG + Y A + + F GSV V I+ D+ S K + ++ F + S
Sbjct: 4 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES 59
>pdb|2PE8|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 (free
Form)
pdb|2PEH|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
pdb|2PEH|B Chain B, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
Length = 105
Score = 29.3 bits (64), Expect = 3.4, Method: Composition-based stats.
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 84 FVTFGNPRSAVDAINDMNGRTIDGRVVR 111
F+ F SA+ A+ D+NGR GRVV+
Sbjct: 60 FLEFERVESAIKAVVDLNGRYFGGRVVK 87
>pdb|2YCB|A Chain A, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
pdb|2YCB|B Chain B, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
Length = 636
Score = 29.3 bits (64), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 10/54 (18%)
Query: 3 CREGGRQGVSTSIVVPI----KARVIFNLIEERVKMTIDDESSVYVGGLPYSAN 52
R GG+ I++P+ +A+ + ++EE ++ I DE VY+ G+ + AN
Sbjct: 405 LRRGGK------ILIPVFAVGRAQELMIVLEEYIRTGIIDEVPVYIDGMIWEAN 452
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 29.3 bits (64), Expect = 4.3, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRG-KCYGFVTFGNPRSAVDAINDM 100
++V G+ A E+ + F +YG + + + DR T K Y V + + A A+ +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 101 NGRTIDGRVVRV 112
NG+ + G+ + V
Sbjct: 85 NGQDLMGQPISV 96
>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 = 28.9 bits (63), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 38 DESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDR-STRGKCYGFVTFGNPRS 92
D S+YVG + Y A + + F GSV V I+ D+ S K + ++ F + S
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES 60
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 28.9 bits (63), Expect = 5.4, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 42 VYVGGLPYSANEDSVRKVFDKYGSVVA---VKIVNDRSTRGKCYGFVTFGNPRSAVDAIN 98
V+VGGLP +ED + F ++G +V K + K Y F+ F S+V A+
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLF-QEESSVQALI 69
Query: 99 D 99
D
Sbjct: 70 D 70
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 28.5 bits (62), Expect = 6.7, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 40 SSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYG--FVTFGNPRSAVDAI 97
+++ V LP + + +F G + +I+ D T G YG FV F + + AI
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKT-GYSYGYAFVDFTSEMDSQRAI 62
Query: 98 NDMNGRTIDGRVVRVS 113
+NG T+ + ++VS
Sbjct: 63 KVLNGITVRNKRLKVS 78
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 28.1 bits (61), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 16/75 (21%), Positives = 34/75 (45%), Gaps = 4/75 (5%)
Query: 38 DESSVYVGGLPYSANEDSVRKVFDKYGSVVAVKIVNDRSTRGKCYGFVTFGNPRSAVDAI 97
D ++ LPY +D +++VF+ +++V+ + + K ++ F A
Sbjct: 92 DARTLLAKNLPYKVTQDELKEVFE---DAAEIRLVS-KDGKSKGIAYIEFKTEADAEKTF 147
Query: 98 NDMNGRTIDGRVVRV 112
+ G IDGR + +
Sbjct: 148 EEKQGTEIDGRSISL 162
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 0.134 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,994,943
Number of Sequences: 62578
Number of extensions: 383747
Number of successful extensions: 1303
Number of sequences better than 100.0: 172
Number of HSP's better than 100.0 without gapping: 115
Number of HSP's successfully gapped in prelim test: 57
Number of HSP's that attempted gapping in prelim test: 1109
Number of HSP's gapped (non-prelim): 210
length of query: 386
length of database: 14,973,337
effective HSP length: 101
effective length of query: 285
effective length of database: 8,652,959
effective search space: 2466093315
effective search space used: 2466093315
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: 52 (24.6 bits)