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= 030227
(181 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 80.9 bits (198), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 40/92 (43%), Positives = 61/92 (66%), Gaps = 2/92 (2%)
Query: 6 NSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADY 65
N VY+G LDEKVSE +L+++ +QAG VV+ ++P+D+ T + +G+ FVE+ SEE ADY
Sbjct: 13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72
Query: 66 AIKLFSGIVTLYNRTLRF-ALSGQDKNTQNSS 96
AIK+ ++ LY + +R S +KN S
Sbjct: 73 AIKIMD-MIKLYGKPIRVNKASAHNKNLSGPS 103
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 60.5 bits (145), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 30/72 (41%), Positives = 46/72 (63%), Gaps = 2/72 (2%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
V++GNL+ +V E +LY++ +QAG + + I +D+E KPK F FV ++ E YAI L
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIAL 76
Query: 70 FSGIVTLYNRTL 81
+GI LY R +
Sbjct: 77 LNGI-RLYGRPI 87
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 59.7 bits (143), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 34/85 (40%), Positives = 51/85 (60%), Gaps = 1/85 (1%)
Query: 2 SGNSNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 61
SG + + +Y+G L E+V ++VL+ I G + D+ IP D ET+K +GFAFVE+E E
Sbjct: 6 SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 65
Query: 62 IADYAIKLFSGIVTLYNRTLRFALS 86
A AI + L+ RT+R L+
Sbjct: 66 DAAAAIDNMNE-SELFGRTIRVNLA 89
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 58.5 bits (140), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
+Y+G L E+V ++VL+ I G + D+ IP D ET+K +GFAFVE+E E A AI
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 71 SGIVTLYNRTLRFALS 86
+ L+ RT+R L+
Sbjct: 126 NE-SELFGRTIRVNLA 140
>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 = 57.0 bits (136), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
+Y+G L E+V ++VL+ I G + D+ IP D ET+K +GFAFVE+E E A AI
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 71 SGIVTLYNRTLRFALS 86
+ L+ RT+R L+
Sbjct: 70 NE-SELFGRTIRVNLA 84
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 57.0 bits (136), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
+Y+G L E+V ++VL+ I G + D+ IP D ET+K +GFAFVE+E E A AI
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 71 SGIVTLYNRTLRFALS 86
+ L+ RT+R L+
Sbjct: 68 NE-SELFGRTIRVNLA 82
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 56.6 bits (135), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
+Y+G L E+V ++VL+ I G + D+ IP D ET+K +GFAFVE+E E A AI
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 71 SGIVTLYNRTLRFALS 86
+ L+ RT+R L+
Sbjct: 65 NE-SELFGRTIRVNLA 79
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 53.5 bits (127), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 47/84 (55%), Gaps = 1/84 (1%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
+V++GN+ + +E L DI + G VV + D+ET KPKG+ F EY+ +E A A++
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 70 FSGIVTLYNRTLRFALSGQDKNTQ 93
+G R LR + +KN +
Sbjct: 70 LNG-REFSGRALRVDNAASEKNKE 92
>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 = 50.1 bits (118), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
++ + NL + S L + + GRV D+YIPRD+ T + +GFAFV + + A+ A+
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 69 LFSGIVTLYNRTLRFALS 86
G V L R LR ++
Sbjct: 108 AMDGAV-LDGRELRVQMA 124
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 50.1 bits (118), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 32/95 (33%), Positives = 52/95 (54%), Gaps = 4/95 (4%)
Query: 5 SNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDL-YIPRDKETDKPKGFAFVEYESEEIA 63
S+ ++IGNLD ++ E++LYD G ++ I RD +T KG+AF+ + S + +
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 64 DYAIKLFSGIVTLYNR--TLRFALSGQDKNTQNSS 96
D AI+ +G L NR T+ +A K + SS
Sbjct: 62 DAAIEAMNG-QYLCNRPITVSYAFKKDSKGSGPSS 95
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 37/60 (61%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
N+Y+GNL + + ++ Q G+V ++ + D+ET KPKGF FVE + E +++ KL
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKL 62
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
++ + NL + S L + + GRV D+YIPRD+ T + +GFAFV + + A+ A+
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 69 LFSGIVTLYNRTLRFALS 86
G V L R LR ++
Sbjct: 131 AMDGAV-LDGRELRVQMA 147
>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 = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 37/72 (51%)
Query: 3 GNSNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 62
G S N+Y+ NL +++ L I + G +V I RDK T +P+G AFV Y E
Sbjct: 8 GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE 67
Query: 63 ADYAIKLFSGIV 74
A AI + ++
Sbjct: 68 AQEAISALNNVI 79
>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 = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 37/72 (51%)
Query: 3 GNSNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 62
G S N+Y+ NL +++ L I + G +V I RDK T +P+G AFV Y E
Sbjct: 95 GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE 154
Query: 63 ADYAIKLFSGIV 74
A AI + ++
Sbjct: 155 AQEAISALNNVI 166
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 7 SGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYA 66
S N+ + L + ++R LY + G + I RD +T G+AFV++ SE + A
Sbjct: 13 SNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRA 72
Query: 67 IKLFSGIVTLYNRTLRFA 84
IK+ +GI T+ N+ L+ +
Sbjct: 73 IKVLNGI-TVRNKRLKVS 89
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 37/72 (51%)
Query: 3 GNSNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 62
G S N+Y+ NL +++ L I + G +V I RDK T +P+G AFV Y E
Sbjct: 84 GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE 143
Query: 63 ADYAIKLFSGIV 74
A AI + ++
Sbjct: 144 AQEAISALNNVI 155
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 29/98 (29%), Positives = 51/98 (52%), Gaps = 4/98 (4%)
Query: 7 SGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYA 66
S N+ + L + +++R LY + G + I RD +T G+AFV++ SE + A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 67 IKLFSGIVTLYNRTLRFALS---GQDKNTQNSSMTTTP 101
IK+ +GI T+ N+ L+ + + G+ N +T P
Sbjct: 62 IKVLNGI-TVRNKRLKVSYARPGGESIKDTNLYVTNLP 98
>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 = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
N++I NLD+ + + LYD G ++ + D+ + KG+ FV +E++E A+ AI+
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 64
Query: 70 FSGIV 74
+G++
Sbjct: 65 MNGML 69
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
N++I NLD+ + + LYD G ++ + D+ + KG+ FV +E++E A+ AI+
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 70
Query: 70 FSGIV 74
+G++
Sbjct: 71 MNGML 75
>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 = 43.9 bits (102), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
N++I NLD+ + + LYD G ++ + D+ + KG+ FV +E++E A+ AI+
Sbjct: 100 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 157
Query: 70 FSGIV 74
+G++
Sbjct: 158 MNGML 162
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 48/88 (54%), Gaps = 1/88 (1%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
++Y+G+L V+E +LY+ AG ++ + + RD T + G+A+V ++ A+ A+
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 70 FSGIVTLYNRTLRFALSGQDKNTQNSSM 97
+ V + + +R S +D + + S +
Sbjct: 72 MNFDV-IKGKPVRIMWSQRDPSLRKSGV 98
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 43.9 bits (102), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
+ + NL + S L + + GRV D+YIPR+ T P+GFAFV + A A
Sbjct: 14 ITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEA 73
Query: 69 LFSGIVTLYNRTLRFALS 86
G L R LR ++
Sbjct: 74 AMDG-AELDGRELRVQVA 90
>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 = 43.5 bits (101), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
N++I NLD+ + + LYD G ++ + D+ + KG+ FV +E++E A+ AI+
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 162
Query: 70 FSGIV 74
+G++
Sbjct: 163 MNGML 167
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 48/89 (53%), Gaps = 1/89 (1%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
++Y+G+L V+E +LY+ AG ++ + + RD T + G+A+V ++ A+ A+
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 69 LFSGIVTLYNRTLRFALSGQDKNTQNSSM 97
+ V + + +R S +D + + S +
Sbjct: 76 TMNFDV-IKGKPVRIMWSQRDPSLRKSGV 103
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 43.1 bits (100), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 44/88 (50%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
+++G + E E L D Q G++ + I D+ + K +GFAFV ++ + D +
Sbjct: 107 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 166
Query: 70 FSGIVTLYNRTLRFALSGQDKNTQNSSM 97
V +N +R ALS Q+ + +SS
Sbjct: 167 KYHTVNGHNCEVRKALSKQEMASASSSQ 194
Score = 36.2 bits (82), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 29/58 (50%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAI 67
++IG L + ++ L Q G + D + RD T + +GF FV Y + E D A+
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 73
>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 = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 44/88 (50%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
+++G + E E L D Q G++ + I D+ + K +GFAFV ++ + D +
Sbjct: 105 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 164
Query: 70 FSGIVTLYNRTLRFALSGQDKNTQNSSM 97
V +N +R ALS Q+ + +SS
Sbjct: 165 KYHTVNGHNCEVRKALSKQEMASASSSQ 192
Score = 35.8 bits (81), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 29/58 (50%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAI 67
++IG L + ++ L Q G + D + RD T + +GF FV Y + E D A+
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 71
>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 = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 44/87 (50%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
+++G + E E L D Q G++ + I D+ + K +GFAFV ++ + D +
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
Query: 70 FSGIVTLYNRTLRFALSGQDKNTQNSS 96
V +N +R ALS Q+ + +SS
Sbjct: 166 KYHTVNGHNCEVRKALSKQEMASASSS 192
Score = 35.8 bits (81), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 29/58 (50%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAI 67
++IG L + ++ L Q G + D + RD T + +GF FV Y + E D A+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 72
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 32/65 (49%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
+ + NL E E L ++ G + +Y+ +DK T + KGFAF+ + E A AI
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75
Query: 69 LFSGI 73
SG
Sbjct: 76 GVSGF 80
>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 = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
C +Y+GNL +E +Y++ ++G + + + DK GF FVEY S A+ A++
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 69 LFSGIVTLYNRTLR 82
+G L +R +R
Sbjct: 100 YING-TRLDDRIIR 112
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 29/49 (59%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYE 58
+++G LD ++ L Q G VVD I +DK T++ +GF FV+++
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK 66
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%)
Query: 5 SNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIAD 64
+SGC ++IG L + ++ L + Q G V + + RD T + +GF FV + + D
Sbjct: 22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVD 81
Query: 65 YAI 67
+
Sbjct: 82 KVL 84
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 2/72 (2%)
Query: 2 SGNSNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 61
S S+ C +++ NL + ++L D + G V LY E K KG V++ES E
Sbjct: 2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPE 59
Query: 62 IADYAIKLFSGI 73
+A+ A ++ +G+
Sbjct: 60 VAERACRMMNGM 71
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 4 NSNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIA 63
S+ +Y+G+L ++E +L I G++ ++ + +D +T + KG+ F+ + E A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 64 DYAIKLFSGIVTLYNRTLR 82
A++ +G L R +R
Sbjct: 61 RRALEQLNGF-ELAGRPMR 78
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 36/66 (54%)
Query: 8 GCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAI 67
GCN++I +L ++ ++ L + G V+ + DK+T K F FV +++ + A AI
Sbjct: 40 GCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAI 99
Query: 68 KLFSGI 73
K +G
Sbjct: 100 KAMNGF 105
>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 = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 4/88 (4%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
VY+G++ +E + D+ G V++L + D +T + KG+AF+E+ E + A++
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 71 SGIVTLYNRTLRFALSGQDKNTQNSSMT 98
+G Y RF G N+ S ++
Sbjct: 66 NG----YQLGSRFLKCGYSSNSDISGVS 89
>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 = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 4/82 (4%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
VY+G++ +E + D+ G V++L + D +T + KG+AF+E+ E + A++
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 71 SGIVTLYNRTLRFALSGQDKNT 92
+G Y RF G N+
Sbjct: 67 NG----YQLGSRFLKCGYSSNS 84
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 34/63 (53%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
+Y+G+L ++E +L I GR+ + + D ET + KG+ F+ + E A A++
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 71 SGI 73
+G
Sbjct: 89 NGF 91
>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 = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 40/80 (50%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
+++G + E E L D Q G++ + I D+ + K +GFAFV ++ + D +
Sbjct: 99 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 158
Query: 70 FSGIVTLYNRTLRFALSGQD 89
V +N +R ALS Q+
Sbjct: 159 KYHTVNGHNCEVRKALSKQE 178
Score = 35.4 bits (80), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 29/58 (50%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAI 67
++IG L + ++ L Q G + D + RD T + +GF FV Y + E D A+
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 4/88 (4%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
VY+G++ +E + D+ G V++L + D +T + KG+AF+E+ E + A++
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 71 SGIVTLYNRTLRFALSGQDKNTQNSSMT 98
+G Y RF G N+ S ++
Sbjct: 65 NG----YQLGSRFLKCGYSSNSDISGVS 88
>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 = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 35/66 (53%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
C VY+G++ ++ E + G + + + D T K KGFAFVEYE E A A++
Sbjct: 14 CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 73
Query: 69 LFSGIV 74
+ ++
Sbjct: 74 QMNSVM 79
Score = 33.1 bits (74), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 31/57 (54%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAI 67
+Y+ ++ + +S+ + + G++ + RD T K KG+ F+EYE + + A+
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 169
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 8 GCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAI 67
G V++ NLD KV + L ++ AG VV I DK+ K +G V +E A AI
Sbjct: 15 GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDG-KSRGIGTVTFEQSIEAVQAI 73
Query: 68 KLFSGIVTLYNRTL 81
+F+G + L++R +
Sbjct: 74 SMFNGQL-LFDRPM 86
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
+++G + E E L D Q G++ + I D+ + K +GFAFV ++ + D +
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
Query: 70 FSGIVTLYNRTLRFALSGQ 88
V +N +R ALS Q
Sbjct: 166 KYHTVNGHNCEVRKALSKQ 184
Score = 35.4 bits (80), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 29/58 (50%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAI 67
++IG L + ++ L Q G + D + RD T + +GF FV Y + E D A+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 72
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 40.0 bits (92), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
+++G + E E L D Q G++ + I D+ + K +GFAFV ++ + D +
Sbjct: 104 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 163
Query: 70 FSGIVTLYNRTLRFALSGQ 88
V +N +R ALS Q
Sbjct: 164 KYHTVNGHNCEVRKALSKQ 182
Score = 35.4 bits (80), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 29/58 (50%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAI 67
++IG L + ++ L Q G + D + RD T + +GF FV Y + E D A+
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 70
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 30/53 (56%)
Query: 20 VSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLFSG 72
V ++ L + +AG+VV++ P D+ T K KGF FVE S A IK F G
Sbjct: 24 VLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG 76
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 7 SGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYA 66
S N+ + L + +++R LY + G + I RD +T G+AFV++ SE + A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 67 IKLFSGIVTLYNRTLR 82
IK+ +GI T+ N+ L+
Sbjct: 62 IKVLNGI-TVRNKRLK 76
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 30/53 (56%)
Query: 20 VSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLFSG 72
V ++ L + +AG+VV++ P D+ T K KGF FVE S A IK F G
Sbjct: 24 VLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG 76
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 31/60 (51%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
C VY+G++ ++ E + G + + D T K KGFAFVEYE E A A++
Sbjct: 13 CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALE 72
Score = 33.1 bits (74), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 31/57 (54%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAI 67
+Y+ ++ + +S+ + + G++ + RD T K KG+ F+EYE + + A+
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 33/57 (57%)
Query: 7 SGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIA 63
S VY+ NL ++ LY I + G+VV + I +DK+T K KG AF+ + ++ A
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 53/95 (55%), Gaps = 3/95 (3%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
++IG L+ + +E++L + + G + ++ + +D+ T K +GFAF+ +E+ A A K
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 71 SGIVTLYNRTLRFALSGQDKNTQNSSMTTTPLSSR 105
+G +L+ + ++ + + + Q+ P SSR
Sbjct: 69 NG-KSLHGKAIKVEQA-KKPSFQSGGRRRPPASSR 101
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 12/72 (16%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRV----------VDLYIPRDKETDKPKGFAFVEYESE 60
+Y+ L++ V+ L D Q G V + +Y+ DKET KPKG A V YE
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYL--DKETGKPKGDATVSYEDP 75
Query: 61 EIADYAIKLFSG 72
A A++ F G
Sbjct: 76 PTAKAAVEWFDG 87
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 45/78 (57%), Gaps = 1/78 (1%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
+++G L +E+ L + + G++ ++ + +D+ET + +GF FV +E+ + A A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 71 SGIVTLYNRTLRFALSGQ 88
+G ++ R +R +G+
Sbjct: 75 NG-KSVDGRQIRVDQAGK 91
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
+Y+GNLD+ ++E +L G + ++ I DK +K +AFVEY A+ A++
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61
Query: 71 SG 72
+G
Sbjct: 62 NG 63
Score = 28.5 bits (62), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 15/68 (22%), Positives = 33/68 (48%)
Query: 5 SNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIAD 64
S+ N+++G+L+ V + L + + ++ D +T +G+ FV + S++ A
Sbjct: 84 SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQ 143
Query: 65 YAIKLFSG 72
A+ G
Sbjct: 144 NAMDSMQG 151
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition
In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
C ++IG L+ +E L + + G V DL I +D T + +GF F+ +E D +K
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 29/55 (52%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIAD 64
+++G + V + + Q G ++D + DK+T + +GF FV Y+S + D
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVD 143
>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 = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
++I L ++ L +I G V DL + ++ KPKG A+VEYE+E A A+
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKM 78
Query: 71 SGIVTLYNRTLRFALS 86
G+ T+ ++ A+S
Sbjct: 79 DGM-TIKENIIKVAIS 93
>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 = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
C +Y+GNL +E +Y++ ++G + + + DK GF FVEY S A+ A++
Sbjct: 19 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-MKTACGFCFVEYYSRADAENAMR 77
Query: 69 LFSGIVTLYNRTLR 82
+G L +R +R
Sbjct: 78 YING-TRLDDRIIR 90
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 31/60 (51%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
+++G + E L + + G V ++ + D E +P+GF F+ +E E+ D A+ +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 43/90 (47%), Gaps = 9/90 (10%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
C +++GNL ++E + + G +++I RD +GF F+ ES +A+ A
Sbjct: 23 CRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKA 76
Query: 69 LFSGIVTLYNRTL--RFALSGQDKNTQNSS 96
G + L +R L RFA G +N S
Sbjct: 77 ELDGTI-LKSRPLRIRFATHGAALTVKNLS 105
>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 = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
+V++G+L +++ + GR+ D + +D T K KG+ FV + ++ A+ AI+
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 70 FSGIVTLYNRTLR 82
G L R +R
Sbjct: 77 MGG-QWLGGRQIR 88
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 47/102 (46%), Gaps = 3/102 (2%)
Query: 2 SGNSNSGCNVYIGNLDE-KVSERVLYDILIQAGRVVDLYI-PRDKETDKPKGFAFVEYES 59
S S+ C ++IG + + K E +L +I V+D+ + + K +GFAFVEYES
Sbjct: 2 SSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYES 61
Query: 60 EEIADYA-IKLFSGIVTLYNRTLRFALSGQDKNTQNSSMTTT 100
A A KL G + L+ + + + + M T
Sbjct: 62 HRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETV 103
>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 = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 36/66 (54%)
Query: 8 GCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAI 67
G N++I +L ++ ++ L + + G VV + DK+T+ K F FV Y++ A AI
Sbjct: 25 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 84
Query: 68 KLFSGI 73
+ +G
Sbjct: 85 QSMNGF 90
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 36/64 (56%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
N+YI L ++++ + D+ + GR+++ + D+ T +G AF+ ++ A+ AI
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 69 LFSG 72
F+G
Sbjct: 149 SFNG 152
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
N+ + L + +++ L + G V + RDK G+ FV Y + + A+ AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 69 LFSGIVTLYNRTLR 82
+G+ L ++T++
Sbjct: 63 TLNGL-RLQSKTIK 75
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 36/64 (56%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
N+YI L ++++ + D+ + GR+++ + D+ T +G AF+ ++ A+ AI
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 69 LFSG 72
F+G
Sbjct: 149 SFNG 152
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
N+ + L + +++ L + G V + RDK G+ FV Y + + A+ AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 69 LFSGIVTLYNRTLR 82
+G+ L ++T++
Sbjct: 63 TLNGL-RLQSKTIK 75
>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 = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 34/64 (53%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
VY+G++ ++ E + G + + + D T K KGFAFVEYE E A A++
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 71 SGIV 74
+ ++
Sbjct: 91 NSVM 94
Score = 33.5 bits (75), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 31/57 (54%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAI 67
+Y+ ++ + +S+ + + G++ + RD T K KG+ F+EYE + + A+
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV 184
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 30/58 (51%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAI 67
++IG L + +E L + Q G++ D + RD + + +GF FV + S D A+
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 36.6 bits (83), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 4 NSNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIA 63
N + C + + L +ER L ++ + G + D+ I D+++ + +GFAFV +E+ + A
Sbjct: 42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 101
Query: 64 DYAIKLFSGIVTLYNRTLRFALS 86
A + +G+ L R +R S
Sbjct: 102 KEAKERANGM-ELDGRRIRVDFS 123
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 3/63 (4%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
+++ NL SE L + G + +L+ P D T KPKGFAFV + ++A+K +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF---MFPEHAVKAY 67
Query: 71 SGI 73
+ +
Sbjct: 68 AEV 70
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 7/57 (12%)
Query: 8 GCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKP-KGFAFVEYESEEIA 63
G V++G E ++ L Q G VVD++IP KP + FAFV + +++A
Sbjct: 11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIP------KPFRAFAFVTFADDKVA 61
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 36.2 bits (82), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 29/59 (49%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAI 67
C ++IG L + ++ L + Q G V + + RD T + +GF FV + + D +
Sbjct: 1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 35.8 bits (81), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
+++ NL + ++L D + G V LY E K KG V++ES E+A+ A ++
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVAERACRMM 65
Query: 71 SGI 73
+G+
Sbjct: 66 NGM 68
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 35.8 bits (81), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 4 NSNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIA 63
N + C + + L +ER L ++ + G + D+ I D+++ + +GFAFV +E+ + A
Sbjct: 11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 70
Query: 64 DYAIKLFSGIVTLYNRTLRFALS 86
A + +G+ L R +R S
Sbjct: 71 KEAKERANGM-ELDGRRIRVDFS 92
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 35.4 bits (80), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 44/84 (52%), Gaps = 1/84 (1%)
Query: 3 GNSNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 62
N + C + + L +ER L ++ + G + D+ I D+++ + +GFAFV +E+ +
Sbjct: 7 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 66
Query: 63 ADYAIKLFSGIVTLYNRTLRFALS 86
A A + +G+ L R +R S
Sbjct: 67 AKEAKERANGM-ELDGRRIRVDFS 89
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 35.4 bits (80), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 45/93 (48%), Gaps = 4/93 (4%)
Query: 5 SNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIAD 64
N+ C +Y+GNL + + + D+ + G + D+ + +++ P FAFVE+E A+
Sbjct: 19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-KNRRGGPP--FAFVEFEDPRDAE 75
Query: 65 YAIKLFSGI-VTLYNRTLRFALSGQDKNTQNSS 96
A+ G Y + F SG+ + SS
Sbjct: 76 DAVYGRDGYDYDGYRLRVEFPRSGRGTGSGPSS 108
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 35.4 bits (80), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 39/82 (47%), Gaps = 6/82 (7%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
C VY+GNL ++ L G + +++ R+ P GFAFVE+E A A++
Sbjct: 74 CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVR 128
Query: 69 LFSGIVTLYNRTLRFALSGQDK 90
G TL +R LS +K
Sbjct: 129 ELDG-RTLCGCRVRVELSNGEK 149
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 35.4 bits (80), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 34/64 (53%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
N+Y+ L + +S++ + + Q GR++ I D+ T +G F+ ++ A+ AIK
Sbjct: 91 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150
Query: 69 LFSG 72
+G
Sbjct: 151 GLNG 154
Score = 30.0 bits (66), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 1/79 (1%)
Query: 6 NSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADY 65
+S N+ + L + +++ + G + + RDK T + G+ FV Y AD
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 66 AIKLFSGIVTLYNRTLRFA 84
AI +G+ L +T++ +
Sbjct: 62 AINTLNGL-KLQTKTIKVS 79
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 35.4 bits (80), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 34/64 (53%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
N+Y+ L + +S++ + + Q GR++ I D+ T +G F+ ++ A+ AIK
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 69 LFSG 72
+G
Sbjct: 62 GLNG 65
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 32/59 (54%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
+++G L + + Q G+V D + DK T++ +GF FV +ESE+I + ++
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 35.0 bits (79), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 39/82 (47%), Gaps = 6/82 (7%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
C VY+GNL ++ L G + +++ R+ P GFAFVE+E A A++
Sbjct: 74 CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVR 128
Query: 69 LFSGIVTLYNRTLRFALSGQDK 90
G TL +R LS +K
Sbjct: 129 DLDG-RTLCGCRVRVELSNGEK 149
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 35.0 bits (79), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
+V++G+L +++ + G++ D + +D T K KG+ FV + ++ A+ AI +
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAI-V 75
Query: 70 FSGIVTLYNRTLR 82
G L R +R
Sbjct: 76 HMGGQWLGGRQIR 88
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 35.0 bits (79), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
N+ + + V E L + + G + + I D+ET + +G+ FV+++S A AI
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 70 FSGIVTLYNRTLRFALS 86
+G + N+ L+ AL+
Sbjct: 104 LNGF-NILNKRLKVALA 119
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 35.0 bits (79), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 4 NSNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIA 63
N + C + + L +ER L ++ + G + D+ I D+++ + +GFAFV +E+ + A
Sbjct: 11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 70
Query: 64 DYAIKLFSGIVTLYNRTLR 82
A + +G+ L R +R
Sbjct: 71 KEAKERANGM-ELDGRRIR 88
>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 = 35.0 bits (79), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 41/87 (47%), Gaps = 6/87 (6%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
+VY+GN+D + + L G + + I DK + PKG+A++E+ D A+ +
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAM 97
Query: 70 ----FSG--IVTLYNRTLRFALSGQDK 90
F G I L RT +S D+
Sbjct: 98 DETVFRGRTIKVLPKRTNMPGISSTDR 124
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 34.7 bits (78), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
N+YI NL + E+ L ++L G+V+ I RD + +G F ES E + I
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGH 85
Query: 70 FSG 72
F+G
Sbjct: 86 FNG 88
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 34.7 bits (78), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 30/58 (51%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAI 67
+YI L +++ L + G++V DK T+K KG+ FV+++S A A+
Sbjct: 7 GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
>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 = 34.7 bits (78), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 38/68 (55%)
Query: 5 SNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIAD 64
S G +++ + E+ +E ++D + G + ++++ D+ T KG+ VEYE+ + A
Sbjct: 4 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
Query: 65 YAIKLFSG 72
A++ +G
Sbjct: 64 AAMEGLNG 71
>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 = 34.7 bits (78), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 38/68 (55%)
Query: 5 SNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIAD 64
S G +++ + E+ +E ++D + G + ++++ D+ T KG+ VEYE+ + A
Sbjct: 6 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 65
Query: 65 YAIKLFSG 72
A++ +G
Sbjct: 66 AAMEGLNG 73
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 34.7 bits (78), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 38/68 (55%)
Query: 5 SNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIAD 64
S G +++ + E+ +E ++D + G + ++++ D+ T KG+ VEYE+ + A
Sbjct: 4 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
Query: 65 YAIKLFSG 72
A++ +G
Sbjct: 64 AAMEGLNG 71
>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 = 34.3 bits (77), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 27/57 (47%)
Query: 2 SGNSNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYE 58
S N ++G L S++ L D + G VVD I D T + +GF F+ ++
Sbjct: 5 SKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFK 61
>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 = 34.3 bits (77), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 34/64 (53%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
N+Y+ L + ++++ L + Q GR++ I D+ T +G F+ ++ A+ AIK
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
Query: 69 LFSG 72
+G
Sbjct: 149 GLNG 152
Score = 27.3 bits (59), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 7 SGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYA 66
S N+ + L + +++ + G + + RDK T + G+ FV Y + A+ A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 67 IKLFSGIVTLYNRTLRFA 84
I +G+ L +T++ +
Sbjct: 61 INTLNGL-RLQTKTIKVS 77
>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 = 34.3 bits (77), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 38/68 (55%)
Query: 5 SNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIAD 64
S G +++ + E+ +E ++D + G + ++++ D+ T KG+ VEYE+ + A
Sbjct: 20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 79
Query: 65 YAIKLFSG 72
A++ +G
Sbjct: 80 AAMEGLNG 87
>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 = 34.3 bits (77), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 38/68 (55%)
Query: 5 SNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIAD 64
S G +++ + E+ +E ++D + G + ++++ D+ T KG+ VEYE+ + A
Sbjct: 4 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
Query: 65 YAIKLFSG 72
A++ +G
Sbjct: 64 AAMEGLNG 71
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 34.3 bits (77), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 3/72 (4%)
Query: 4 NSNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDK---PKGFAFVEYESE 60
S+ ++I NL+ +E L + + G + I + K GF FVEY+
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 61 EIADYAIKLFSG 72
E A A+K G
Sbjct: 61 EQAQKALKQLQG 72
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 33.9 bits (76), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 51/92 (55%), Gaps = 14/92 (15%)
Query: 11 VYIGNLD----EKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYA 66
Y+GNL + + + D+ I++ R+V RDK+TDK KGF +VE++ + A
Sbjct: 18 AYVGNLPFNTVQGDIDAIFKDLSIRSVRLV-----RDKDTDKFKGFCYVEFDEVDSLKEA 72
Query: 67 IKLFSGIVTLYNRTLRFALS---GQDKNTQNS 95
+ + G + L +R+LR ++ QDK+ +S
Sbjct: 73 LT-YDGAL-LGDRSLRVDIAEGRKQDKSGPSS 102
>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 = 33.9 bits (76), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 28/52 (53%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 61
++Y+GN+D + L G V + I DK + PKGFA++E+ +E
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE 59
>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 = 33.9 bits (76), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 38/68 (55%)
Query: 5 SNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIAD 64
S G +++ + E+ +E ++D + G + ++++ D+ T KG+ VEYE+ + A
Sbjct: 19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 78
Query: 65 YAIKLFSG 72
A++ +G
Sbjct: 79 AAMEGLNG 86
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 33.9 bits (76), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 23/91 (25%), Positives = 42/91 (46%), Gaps = 9/91 (9%)
Query: 2 SGNSNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 61
SG+S + +++GN+ + + L + + GRV++ + +D +AFV E E
Sbjct: 3 SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEA 54
Query: 62 IADYAIKLFSGIVTLYNR-TLRFALSGQDKN 91
A AI +G R + + GQ K+
Sbjct: 55 DAKAAIAQLNGKEVKGKRINVELSTKGQKKS 85
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 33.5 bits (75), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
VY+GNL + L G + ++I R+ P GFAFVE+E A+ A++
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56
Query: 70 FSGIVTLYNRT 80
G V +R
Sbjct: 57 LDGKVICGSRV 67
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 33.5 bits (75), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 7/55 (12%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKP-KGFAFVEYESEEIA 63
V++G ++E L + Q G V+D++IP KP + FAFV + ++IA
Sbjct: 7 GVFVGRCTGDMTEDELREFFSQYGDVMDVFIP------KPFRAFAFVTFADDQIA 55
>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 = 33.5 bits (75), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
+V++G+L +++ + GR+ D + +D T K KG+ FV + ++ A+ AI+
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 70 FSGIVTLYNRTLR 82
G L R +R
Sbjct: 68 MGG-QWLGGRQIR 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 = 33.5 bits (75), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 29/57 (50%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAI 67
++IG L +++ L D + G VVD + D T + +GF FV ++ E D +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM 58
>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 = 33.5 bits (75), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 28/52 (53%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 61
++Y+GN+D + L G V + I DK + PKGFA++E+ +E
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE 58
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 33.1 bits (74), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 7/79 (8%)
Query: 4 NSNSGCN-VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 62
+ +SG N +YIGNL V+ L + D +P + G+AFV+Y +
Sbjct: 3 SGSSGMNKLYIGNLSPAVTADDLRQLF------GDRKLPLAGQVLLKSGYAFVDYPDQNW 56
Query: 63 ADYAIKLFSGIVTLYNRTL 81
A AI+ SG V L+ + +
Sbjct: 57 AIRAIETLSGKVELHGKIM 75
>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 = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 34/68 (50%)
Query: 6 NSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADY 65
+S ++IG L +++ + ++L G + + +D T KG+AF EY + D
Sbjct: 112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 171
Query: 66 AIKLFSGI 73
AI +G+
Sbjct: 172 AIAGLNGM 179
>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 = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 14/56 (25%), Positives = 31/56 (55%), Gaps = 6/56 (10%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYA 66
+++GNL ++E + + + G+ +++I +D KGF F+ E+ +A+ A
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIA 67
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 32.3 bits (72), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 9/59 (15%)
Query: 11 VYIGNLDEKVSERVL---YDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYA 66
+++ L E +E L +D ++A R+V D+ET KGF FV++ SEE A A
Sbjct: 18 LFVKGLSEDTTEETLKESFDGSVRA-RIV-----TDRETGSSKGFGFVDFNSEEDAKAA 70
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 27/52 (51%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 61
+++G L E + + G V + +P D +T+K +GF F+ ++ EE
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 54
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 27/51 (52%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 61
+++G L E + + G V + +P D +T+K +GF F+ ++ EE
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 52
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 29/59 (49%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
V+ L ++ R L D G+V D+ I D+ + + KG A+VE+ + AI L
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGL 86
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 32.3 bits (72), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 43/85 (50%), Gaps = 2/85 (2%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
+Y+ NL +V+ER L + + I T + +G AF+ + ++EIA A+ L
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 71 SGIVTLYNRTLRFALSGQDKNTQNS 95
+G LY + L G++K ++S
Sbjct: 88 NG-YKLYGKILVIEF-GKNKKQRSS 110
>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 = 32.0 bits (71), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 32/63 (50%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
++IG L +++ + ++L G + + +D T KG+AF EY + D AI
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 71 SGI 73
+G+
Sbjct: 159 NGM 161
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif In Trna Selenocysteine Associated Protein
Length = 104
Score = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 45/91 (49%), Gaps = 12/91 (13%)
Query: 2 SGNSNSGCNVYIGNLDEKVSERVLYDILIQ------AGRVVDLYIPRDKETDKPKGFAFV 55
SG+S ++++G+L V + +LY+ ++ G+VV +T KG+ FV
Sbjct: 3 SGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVV------LDQTGVSKGYGFV 56
Query: 56 EYESEEIADYAIKLFSGIVTLYNRTLRFALS 86
++ E A+ G V L ++ +R +++
Sbjct: 57 KFTDELEQKRALTECQGAVGLGSKPVRLSVA 87
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 31.6 bits (70), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 32/63 (50%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
++IG L +++ + ++L G + + +D T KG+AF EY + D AI
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 71 SGI 73
+G+
Sbjct: 157 NGM 159
>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 = 0.26, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 29/54 (53%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIA 63
++IG + + E+ L + + G++ +L + +D+ T KG AF+ Y E A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA 68
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 31.6 bits (70), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 32/63 (50%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
++IG L +++ + ++L G + + +D T KG+AF EY + D AI
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 71 SGI 73
+G+
Sbjct: 64 NGM 66
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 31.6 bits (70), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 36/68 (52%)
Query: 5 SNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIAD 64
S G +++ ++ E+ E + + G + ++++ D+ T KG+A VEYE+ + A
Sbjct: 23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 82
Query: 65 YAIKLFSG 72
A + +G
Sbjct: 83 AAKEALNG 90
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 31.6 bits (70), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 10/81 (12%)
Query: 11 VYIGNLDEKVSERV-LYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
V+IGNL+ + ++ + I + GRV + KG+AFV+Y +E A A+
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAAVLG 81
Query: 70 FSGIVTLYNRTLRFALSGQDK 90
+G V L +TL ++G+ K
Sbjct: 82 ENGRV-LAGQTLDINMAGEPK 101
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 31.2 bits (69), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDK-ETDKPKGFAFVEYESEEIADYAI 67
V+IG L V++ + +I G++ + +P ++ KG+A+VE+E+ + A+ A+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 68 KLFSG 72
K G
Sbjct: 65 KHMDG 69
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 31.2 bits (69), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 34/64 (53%), Gaps = 3/64 (4%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
+++G + + E+ L + + GR+ +L + +D+ T KG AF+ Y + D A+K
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCAR---DSALKA 73
Query: 70 FSGI 73
S +
Sbjct: 74 QSAL 77
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 31.2 bits (69), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 14/56 (25%), Positives = 31/56 (55%), Gaps = 6/56 (10%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYA 66
+++GNL ++E + + + G+ +++I +D KGF F+ E+ +A+ A
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIA 74
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 31.2 bits (69), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 13/59 (22%), Positives = 32/59 (54%), Gaps = 6/59 (10%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAI 67
C VY G + ++++++ G+++++ + +K G++FV + + E A +AI
Sbjct: 26 CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAI 78
>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 = 31.2 bits (69), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 36/68 (52%)
Query: 5 SNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIAD 64
S G +++ ++ E+ E + + G + ++++ D+ T KG+A VEYE+ + A
Sbjct: 69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 128
Query: 65 YAIKLFSG 72
A + +G
Sbjct: 129 AAKEALNG 136
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 30.8 bits (68), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
+++G L+++ SE + + G + + I R + + KG AFV+Y S A AI
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNS-KGCAFVKYSSHAEAQAAINAL 76
Query: 71 SGIVTL 76
G T+
Sbjct: 77 HGSQTM 82
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 30.4 bits (67), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 1/79 (1%)
Query: 6 NSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADY 65
+S N+ + L + +++ + G + + RDK T + G+ FV Y AD
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 66 AIKLFSGIVTLYNRTLRFA 84
AI +G+ L +T++ +
Sbjct: 62 AINTLNGL-KLQTKTIKVS 79
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 30.4 bits (67), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 3/85 (3%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
N+Y+ NLD+ + + L G + + E + KGF FV + S E A A+
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSKGFGFVCFSSPEEATKAVTE 74
Query: 70 FSGIVTLYNRTLRFALSGQDKNTQN 94
+G + + + L AL+ + + Q+
Sbjct: 75 MNGRI-VATKPLYVALAQRKEERQS 98
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 29.6 bits (65), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKP--KGFAFVEYESEEIA 63
+++G + SE+ L ++ Q G V ++ + RD+ + P KG FV + + + A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
>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 = 29.6 bits (65), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKL 69
N+++G+L+ V + L + + ++ D +T +G+ FV + S++ A A+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 70 FSGIVTLYNRTLR 82
G L R LR
Sbjct: 63 MQG-QDLNGRPLR 74
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 29.6 bits (65), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKP--KGFAFVEYESEEIA 63
+++G + SE+ L ++ Q G V ++ + RD+ + P KG FV + + + A
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 72
>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 = 29.6 bits (65), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKP--KGFAFVEYESEEIA 63
+++G + SE+ L ++ Q G V ++ + RD+ + P KG FV + + + A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 6/55 (10%)
Query: 18 EKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLFSG 72
E ++ +L G ++DL + D P+ AFV YE E AD A+ +G
Sbjct: 23 EDMTPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVAELNG 71
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 8/67 (11%)
Query: 2 SGNSNSGCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 61
S S+ ++IGNL + +E+ + + Q G+V+ E D K + FV E +
Sbjct: 2 SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVL--------ECDIIKNYGFVHIEDKT 53
Query: 62 IADYAIK 68
A+ AI+
Sbjct: 54 AAEDAIR 60
>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 = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 12 YIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKP--KGFAFVEYESEEIA 63
++G + SE+ L ++ Q G V ++ + RD+ + P KG FV + + + A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 29.3 bits (64), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 6/55 (10%)
Query: 18 EKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLFSG 72
E ++ +L G ++DL + D P+ AFV YE E AD A+ +G
Sbjct: 47 EDMTPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVAELNG 95
>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 = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 1/77 (1%)
Query: 8 GCNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAI 67
G N+ + L + ++ L + G V + RDK G+ FV Y + + A+ AI
Sbjct: 19 GTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 78
Query: 68 KLFSGIVTLYNRTLRFA 84
+G+ L ++T++ +
Sbjct: 79 NTLNGL-RLQSKTIKVS 94
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 28.5 bits (62), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 15/64 (23%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGR-VVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
++++G+L+ + E + G V+ + I R++ T P G+ FVE+ A+ +
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 69 LFSG 72
+G
Sbjct: 71 KING 74
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 28.5 bits (62), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 19/38 (50%)
Query: 44 KETDKPKGFAFVEYESEEIADYAIKLFSGIVTLYNRTL 81
K + KP+G+AF+EYE E A K G R L
Sbjct: 138 KRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVL 175
>pdb|3GQI|B Chain B, Crystal Structure Of Activated Receptor Tyrosine Kinase In
Complex With Substrates
Length = 226
Score = 28.5 bits (62), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 40/100 (40%), Gaps = 7/100 (7%)
Query: 45 ETDKPKGFAFVEYESEE-IADYAIKLFSGIVTLYNRTLRFALSGQDKNTQNSSMTTTPLS 103
ET P G +F+ ESE + DY + + + R +G K ++ L
Sbjct: 31 ETGAPDG-SFLVRESETFVGDYTLSFWRNGKVQHCRIHSRQDAGTPKFFLTDNLVFDSLY 89
Query: 104 SRKSRSDPVPVPVNGMEISHHSMRISEPPPPGVTHESNGY 143
+ VP+ N E MR+SEP P HES +
Sbjct: 90 DLITHYQQVPLRCNEFE-----MRLSEPVPQTNAHESKEW 124
>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 = 28.5 bits (62), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 1/76 (1%)
Query: 9 CNVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
N+ + L + +++ L + G V + RDK G+ FV Y + + A+ AI
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 69 LFSGIVTLYNRTLRFA 84
+G+ L ++T++ +
Sbjct: 65 TLNGL-RLQSKTIKVS 79
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 28.5 bits (62), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 33 GRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLFSG 72
G + +++ K + KP+G+AF+EYE E A K G
Sbjct: 127 GPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADG 166
>pdb|3IFU|A Chain A, The Crystal Structure Of Porcine Reproductive And
Respiratory Syndrome Virus (Prrsv) Leader Protease Nsp1
Length = 180
Score = 28.1 bits (61), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 29/100 (29%), Positives = 44/100 (44%), Gaps = 14/100 (14%)
Query: 49 PKGFAFVEYESEEIADYAIKLF------SGIVTLYNRTLRFAL----SGQDKNTQNSSMT 98
P+ F VE S A + +F SG + R +R A +GQ T +
Sbjct: 62 PRAFPTVEC-SPAGACWLSAIFPIARMTSGNLNFQQRMVRVAAEIYRAGQLTPT---VLK 117
Query: 99 TTPLSSRKSRSDPVPVPVNGMEISHHSMRISEPPPPGVTH 138
T + R R P+ PV G+ + +S+ +S+ P PG TH
Sbjct: 118 TLQVYERGCRWYPIVGPVPGVGVYANSLHVSDKPFPGATH 157
>pdb|4FBN|A Chain A, Insights Into Structural Integration Of The Plcgamma
Regulatory Region And Mechanism Of Autoinhibition And
Activation Based On Key Roles Of Sh2 Domains
Length = 246
Score = 28.1 bits (61), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 40/100 (40%), Gaps = 7/100 (7%)
Query: 45 ETDKPKGFAFVEYESEE-IADYAIKLFSGIVTLYNRTLRFALSGQDKNTQNSSMTTTPLS 103
ET P G +F+ ESE + DY + + + R +G K ++ L
Sbjct: 31 ETGAPDG-SFLVRESETFVGDYTLSFWRNGKVQHCRIHSRQDAGTPKFFLTDNLVFDSLY 89
Query: 104 SRKSRSDPVPVPVNGMEISHHSMRISEPPPPGVTHESNGY 143
+ VP+ N E MR+SEP P HES +
Sbjct: 90 DLITHYQQVPLRCNEFE-----MRLSEPVPQTNAHESKEW 124
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 27.7 bits (60), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 5/77 (6%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
+ + NL +E L ++ +A + +P++ + K KG+AF+E+ S E A A+
Sbjct: 18 LVLSNLSYSATEETLQEVFEKA---TFIKVPQN-QNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 71 SGIVTLYNRTLRFALSG 87
+ + R +R L G
Sbjct: 74 NK-REIEGRAIRLELQG 89
>pdb|4EY0|A Chain A, Structure Of Tandem Sh2 Domains From Plcgamma1
pdb|4EY0|B Chain B, Structure Of Tandem Sh2 Domains From Plcgamma1
pdb|4EY0|C Chain C, Structure Of Tandem Sh2 Domains From Plcgamma1
pdb|4EY0|D Chain D, Structure Of Tandem Sh2 Domains From Plcgamma1
Length = 246
Score = 27.7 bits (60), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 40/100 (40%), Gaps = 7/100 (7%)
Query: 45 ETDKPKGFAFVEYESEE-IADYAIKLFSGIVTLYNRTLRFALSGQDKNTQNSSMTTTPLS 103
ET P G +F+ ESE + DY + + + R +G K ++ L
Sbjct: 31 ETGAPDG-SFLVRESETFVGDYTLSFWRNGKVQHCRIHSRQDAGTPKFFLTDNLVFDSLY 89
Query: 104 SRKSRSDPVPVPVNGMEISHHSMRISEPPPPGVTHESNGY 143
+ VP+ N E MR+SEP P HES +
Sbjct: 90 DLITHYQQVPLRCNEFE-----MRLSEPVPQTNAHESKEW 124
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 27.3 bits (59), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
+YI NL K++ +YDI + G + + + ET +G A+V YE A A+
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAVDHL 67
Query: 71 SGI 73
SG
Sbjct: 68 SGF 70
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 26.9 bits (58), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 12/72 (16%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRV----------VDLYIPRDKETDKPKGFAFVEYESE 60
+++ L E V+ + D Q G + ++LY D+ET K KG A V ++
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLY--TDRETGKLKGEATVSFDDP 73
Query: 61 EIADYAIKLFSG 72
A AI F G
Sbjct: 74 PSAKAAIDWFDG 85
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 26.6 bits (57), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
+YI NL K++ +YDI + G + + + ET +G A+V YE A A
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNACDHL 71
Query: 71 SGI 73
SG
Sbjct: 72 SGF 74
>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 = 26.6 bits (57), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIKLF 70
+YI NL K++ +YDI + G + + + ET +G A+V YE A A
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNACDHL 77
Query: 71 SGIVTLYNRTL 81
SG + NR L
Sbjct: 78 SGF-NVCNRYL 87
>pdb|2AD9|A Chain A, Solution Structure Of Polypyrimidine Tract Binding
Protein Rbd1 Complexed With Cucucu Rna
Length = 119
Score = 26.2 bits (56), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 4/50 (8%)
Query: 28 ILIQAGRVVDLYIPRDKETD----KPKGFAFVEYESEEIADYAIKLFSGI 73
I + G V+ L +P K T+ K K AF+E +EE A+ + ++ +
Sbjct: 41 IDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSV 90
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 26.2 bits (56), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 13/59 (22%), Positives = 26/59 (44%)
Query: 10 NVYIGNLDEKVSERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIADYAIK 68
+++G L ++ L G + + + D++T K +G+ FV A+ A K
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 26.2 bits (56), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 12/72 (16%)
Query: 11 VYIGNLDEKVSERVLYDILIQAGRV----------VDLYIPRDKETDKPKGFAFVEYESE 60
+++ L E V+ + D Q G + ++LY D+ET K KG A V ++
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYT--DRETGKLKGEATVSFDDP 67
Query: 61 EIADYAIKLFSG 72
A AI F G
Sbjct: 68 PSAKAAIDWFDG 79
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
0.313 0.131 0.373
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,618,267
Number of Sequences: 62578
Number of extensions: 227599
Number of successful extensions: 505
Number of sequences better than 100.0: 148
Number of HSP's better than 100.0 without gapping: 112
Number of HSP's successfully gapped in prelim test: 36
Number of HSP's that attempted gapping in prelim test: 368
Number of HSP's gapped (non-prelim): 167
length of query: 181
length of database: 14,973,337
effective HSP length: 93
effective length of query: 88
effective length of database: 9,153,583
effective search space: 805515304
effective search space used: 805515304
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)