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= psy13181
(137 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 109 bits (273), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 52/97 (53%), Positives = 72/97 (74%), Gaps = 1/97 (1%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEF 73
G + K LPTEPPYTA+VGNLP QGD++ F + + SVRLV+DK+TD+FKGFCYVEF
Sbjct: 4 GSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEF 63
Query: 74 VDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKG 110
+V++L++AL DG + D +R+DIA+G++ D G
Sbjct: 64 DEVDSLKEALTYDGALLGD-RSLRVDIAEGRKQDKSG 99
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 55.1 bits (131), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 53/92 (57%), Gaps = 2/92 (2%)
Query: 20 LPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKE-TDRFKGFCYVEFVDVEN 78
LP PPYTAF+GNLP +T+ ++ FF + +VRL ++ +R KGF Y EF + +
Sbjct: 10 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEF-EDLD 68
Query: 79 LRQALLKDGRITVDGLQVRLDIADGKRNDNKG 110
+ L ++ ++R+D+AD ++ + G
Sbjct: 69 SLLSALSLNEESLGNKRIRVDVADQAQDKDSG 100
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 49/84 (58%), Gaps = 2/84 (2%)
Query: 20 LPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKE-TDRFKGFCYVEFVDVEN 78
LP PPYTAF+GNLP +T+ ++ FF + +VRL ++ +R KGF Y EF + +
Sbjct: 14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEF-EDLD 72
Query: 79 LRQALLKDGRITVDGLQVRLDIAD 102
+ L ++ ++R+D+AD
Sbjct: 73 SLLSALSLNEESLGNRRIRVDVAD 96
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 53.1 bits (126), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 31/84 (36%), Positives = 52/84 (61%), Gaps = 2/84 (2%)
Query: 29 FVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 87
FVG L + +E+ F + +S V +VKD+ET R +GF +V F ++++ + A++
Sbjct: 16 FVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMN 75
Query: 88 RITVDGLQVRLDIADGKRNDNKGG 111
+VDG Q+R+D A GK +DN+ G
Sbjct: 76 GKSVDGRQIRVDQA-GKSSDNRSG 98
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 26 YTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 84
+ FVG+L IT D++ F P K+ R+VKD T + KG+ +V F + + A++
Sbjct: 16 FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 75
Query: 85 KDGRITVDGLQVRLDIA 101
G + G Q+R + A
Sbjct: 76 HMGGQWLGGRQIRTNWA 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 = 42.4 bits (98), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 26 YTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 84
+ FVG+L IT D++ F P ++ R+VKD T + KG+ +V F + + A+
Sbjct: 16 FHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 75
Query: 85 KDGRITVDGLQVRLDIA 101
+ G + G Q+R + A
Sbjct: 76 QMGGQWLGGRQIRTNWA 92
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 1/81 (1%)
Query: 27 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 85
+ FVGN+P T+ ++ F E +VS RLV D+ET + KG+ + E+ D E A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 86 DGRITVDGLQVRLDIADGKRN 106
G +R+D A ++N
Sbjct: 70 LNGREFSGRALRVDNAASEKN 90
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 32/50 (64%), Gaps = 1/50 (2%)
Query: 27 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVD 75
T +V NLP +T D+ R F + K+V V ++KDK+T + KG ++ F+D
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLD 67
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 43/82 (52%), Gaps = 6/82 (7%)
Query: 22 TEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 81
++P T FV L T+ ++ F V R+V D+ET KGF +V+F E+ +
Sbjct: 12 SQPSKTLFVKGLSEDTTEETLKESF--DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKA 69
Query: 82 A--LLKDGRITVDGLQVRLDIA 101
A ++DG I DG +V LD A
Sbjct: 70 AKEAMEDGEI--DGNKVTLDWA 89
>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 = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 48/102 (47%), Gaps = 1/102 (0%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDV-ERFFPEQKLVSVRLVKDKETDRFKGFCYVE 72
G + P+ P + +VG+L +T+ + E+F P ++S+R+ +D T R G+ YV
Sbjct: 4 GSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVN 63
Query: 73 FVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNN 114
F + +AL + G VR+ + + K G N
Sbjct: 64 FQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN 105
>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 = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 47/97 (48%), Gaps = 1/97 (1%)
Query: 19 TLPTEPPYTAFVGNLPNGITQGDV-ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVE 77
+ P+ P + +VG+L +T+ + E+F P ++S+R+ +D T R G+ YV F
Sbjct: 4 SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 63
Query: 78 NLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNN 114
+ +AL + G VR+ + + K G N
Sbjct: 64 DAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN 100
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 39.3 bits (90), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 25 PYTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 83
P +VG+L IT+ + F P ++ S++L+ D ET R KG+ ++ F D E ++AL
Sbjct: 26 PMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 85
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 27 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 83
T F L I D+E FF K+ VR++ D+ + R KG YVEF +++++ A+
Sbjct: 27 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 84
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 36/57 (63%), Gaps = 3/57 (5%)
Query: 29 FVGNLPNGITQGDVER--FFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 83
+VG+L IT+ D+ R F P K+ ++ L+KD +T R KG+ ++ F D E R+AL
Sbjct: 9 YVGSLHFNITE-DMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
>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 = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 27 TAFVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLK 85
+ +VGN+ G T ++E F V+ V ++ DK + KGF Y+EF D E++R +L
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLAL 67
Query: 86 D 86
D
Sbjct: 68 D 68
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 45/79 (56%), Gaps = 2/79 (2%)
Query: 29 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 87
+VGNL T V+ F + K+ +V+L+ D+ET + KGF +VE + E++ +A+ K
Sbjct: 5 YVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKLD 63
Query: 88 RITVDGLQVRLDIADGKRN 106
G +R+ A+ K++
Sbjct: 64 NTDFMGRTIRVTEANPKKS 82
>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 = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 27 TAFVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLK 85
+ +VGN+ G T ++E F V+ V ++ DK + KGF Y+EF D E++R +L
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLAL 66
Query: 86 D 86
D
Sbjct: 67 D 67
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 41/69 (59%), Gaps = 1/69 (1%)
Query: 38 TQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQV 96
T+ D+ F + + V +V D+++ R +GF +V F +V++ ++A + + +DG ++
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87
Query: 97 RLDIADGKR 105
R+D + KR
Sbjct: 88 RVDFSITKR 96
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 41/69 (59%), Gaps = 1/69 (1%)
Query: 38 TQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQV 96
T+ D+ F + + V +V D+++ R +GF +V F +V++ ++A + + +DG ++
Sbjct: 59 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 118
Query: 97 RLDIADGKR 105
R+D + KR
Sbjct: 119 RVDFSITKR 127
>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 = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 21 PTEPPYTAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENL 79
P + F+G LPN + V+ L + LVKD T KG+ + E+VD+
Sbjct: 92 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 151
Query: 80 RQAL 83
QA+
Sbjct: 152 DQAI 155
Score = 32.7 bits (73), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 18/73 (24%)
Query: 29 FVGNLPNGITQGDVERFF------------PEQKLVSVRLVKDKETDRFKGFCYVEFVDV 76
+VGN+P GIT+ + FF P +++V++ +DK F ++EF V
Sbjct: 10 YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------FAFLEFRSV 63
Query: 77 ENLRQALLKDGRI 89
+ QA+ DG I
Sbjct: 64 DETTQAMAFDGII 76
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 35.4 bits (80), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 21 PTEPPYTAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENL 79
P + F+G LPN + V+ L + LVKD T KG+ + E+VD+
Sbjct: 90 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 149
Query: 80 RQAL 83
QA+
Sbjct: 150 DQAI 153
Score = 32.3 bits (72), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 18/73 (24%)
Query: 29 FVGNLPNGITQGDVERFF------------PEQKLVSVRLVKDKETDRFKGFCYVEFVDV 76
+VGN+P GIT+ + FF P +++V++ +DK F ++EF V
Sbjct: 8 YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------FAFLEFRSV 61
Query: 77 ENLRQALLKDGRI 89
+ QA+ DG I
Sbjct: 62 DETTQAMAFDGII 74
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 35.4 bits (80), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 7/59 (11%)
Query: 54 VRLVKDKETDRFKGFCYVEFVDVE-----NLRQALLKDGRITVDGLQVRLDIADGKRND 107
VR++KDK+T +GF +++ +E + QAL +T+DG + ++ A G + D
Sbjct: 55 VRVIKDKQTQLNRGFAFIQLSTIEAAQLLQILQAL--HPPLTIDGKTINVEFAKGSKRD 111
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 41/69 (59%), Gaps = 1/69 (1%)
Query: 38 TQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQV 96
T+ D+ F + + V +V D+++ R +GF +V F +V++ ++A + + +DG ++
Sbjct: 25 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 84
Query: 97 RLDIADGKR 105
R+D + KR
Sbjct: 85 RVDFSITKR 93
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 18 KTLPTEPPYTAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDV 76
T+ + + F+G LPN + V+ L + LVKD T KG+ + E+VD+
Sbjct: 107 STVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDI 166
Query: 77 ENLRQAL 83
QA+
Sbjct: 167 NVTDQAI 173
Score = 32.7 bits (73), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 18/73 (24%)
Query: 29 FVGNLPNGITQGDVERFF------------PEQKLVSVRLVKDKETDRFKGFCYVEFVDV 76
+VGN+P GIT+ + FF P +++V++ +DK F ++EF V
Sbjct: 8 YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------FAFLEFRSV 61
Query: 77 ENLRQALLKDGRI 89
+ QA+ DG I
Sbjct: 62 DETTQAMAFDGII 74
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 35.0 bits (79), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 29 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 83
F+G LPN + V+ L + LVKD T KG+ + E+VD+ QA+
Sbjct: 5 FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60
>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 = 34.7 bits (78), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 21 PTEPPYTAFVGNL-PNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENL 79
P + FVG+L P T F P ++ R+VKD T + KG+ +V F + +
Sbjct: 2 PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 61
Query: 80 RQALLKDGRITVDGLQVRLDIA 101
A+ + G + G Q+R + A
Sbjct: 62 ENAIQQMGGQWLGGRQIRTNWA 83
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 33.9 bits (76), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 18/84 (21%), Positives = 40/84 (47%), Gaps = 3/84 (3%)
Query: 27 TAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
T + NL T+ ++ F + + V + + KG+ ++EF E+ ++AL
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKATFIKV---PQNQNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 87 GRITVDGLQVRLDIADGKRNDNKG 110
+ ++G +RL++ + + N G
Sbjct: 74 NKREIEGRAIRLELQGPRGSPNSG 97
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 33.1 bits (74), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 29 FVGNLPNGITQGDVERFFPE--QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 85
++G+L + + + R F + ++SV++++++ T G+C+VEF D+ + L K
Sbjct: 13 WMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 32.7 bits (73), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 2/69 (2%)
Query: 29 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 87
FVG L TQ + +F + ++V ++KDK T++ +GF +V+F D N +L
Sbjct: 20 FVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD-PNCVGTVLASR 78
Query: 88 RITVDGLQV 96
T+DG +
Sbjct: 79 PHTLDGRNI 87
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 32.3 bits (72), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 18/73 (24%)
Query: 29 FVGNLPNGITQGDVERFF------------PEQKLVSVRLVKDKETDRFKGFCYVEFVDV 76
+VGN+P GIT+ + FF P +++V++ +DK F ++EF V
Sbjct: 5 YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------FAFLEFRSV 58
Query: 77 ENLRQALLKDGRI 89
+ QA+ DG I
Sbjct: 59 DETTQAMAFDGII 71
>pdb|2DGW|A Chain A, Solution Structure Of The Second Rna Recognition Motif
In Rna-Binding Protein 19
Length = 91
Score = 32.3 bits (72), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 34 PNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 83
P +T+ +V F K V++R+V++ ++ G+ +V+F + E ++QAL
Sbjct: 19 PFNVTEKNVMEFLAPLKPVAIRIVRNAHGNK-TGYIFVDFSNEEEVKQAL 67
>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 = 32.3 bits (72), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 27 TAFVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLK 85
+ +VGN+ G T D+E F ++ + ++ DK + KG+ Y+EF + ++ A+
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAM 97
Query: 86 D 86
D
Sbjct: 98 D 98
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af
Large Subunit
Length = 87
Score = 32.3 bits (72), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 18/73 (24%)
Query: 29 FVGNLPNGITQGDVERFF------------PEQKLVSVRLVKDKETDRFKGFCYVEFVDV 76
+VGN+P GIT+ + FF P +++V++ +DK F ++EF V
Sbjct: 10 YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------FAFLEFRSV 63
Query: 77 ENLRQALLKDGRI 89
+ QA+ DG I
Sbjct: 64 DETTQAMAFDGII 76
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 32.0 bits (71), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 46/79 (58%), Gaps = 8/79 (10%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-D 86
+VGNL N + ++ER F L SV + ++ GF +VEF D + A+ + D
Sbjct: 77 YVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVRELD 131
Query: 87 GRITVDGLQVRLDIADGKR 105
GR T+ G +VR+++++G++
Sbjct: 132 GR-TLCGCRVRVELSNGEK 149
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 31.6 bits (70), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 21/85 (24%), Positives = 42/85 (49%), Gaps = 1/85 (1%)
Query: 27 TAFVGNLPNGITQGDV-ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 85
T +VG L +++ + E F +V+ + KD+ T + +G+ +VEF+ E+ A+
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 86 DGRITVDGLQVRLDIADGKRNDNKG 110
I + G +R++ A + G
Sbjct: 77 MDMIKLYGKPIRVNKASAHNKNLSG 101
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 31.6 bits (70), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 38 TQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQV 96
T+ D+ F + + V +V D+++ R +GF +V F +V++ ++A + + +DG ++
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87
Query: 97 RL 98
R+
Sbjct: 88 RV 89
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 31.6 bits (70), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 29 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 87
++ L G T D+ + P K+VS + + DK T++ KG+ +V+F ++A+
Sbjct: 9 YIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT--- 65
Query: 88 RITVDGLQVRL 98
+ G+Q ++
Sbjct: 66 ALKASGVQAQM 76
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 31.6 bits (70), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 30 VGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 83
V NL + D++ F P + + L KDK T + KGF ++ F E+ +A+
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 31.2 bits (69), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 43/78 (55%), Gaps = 8/78 (10%)
Query: 28 AFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK- 85
+VGNL G +G++ER F L +V + ++ GF +VEF D + A+
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRGL 57
Query: 86 DGRITVDGLQVRLDIADG 103
DG++ + G +VR++++ G
Sbjct: 58 DGKV-ICGSRVRVELSTG 74
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 45/79 (56%), Gaps = 8/79 (10%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-D 86
+VGNL N + ++ER F L SV + ++ GF +VEF D + A+ D
Sbjct: 77 YVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVRDLD 131
Query: 87 GRITVDGLQVRLDIADGKR 105
GR T+ G +VR+++++G++
Sbjct: 132 GR-TLCGCRVRVELSNGEK 149
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 30.8 bits (68), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 2/82 (2%)
Query: 29 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR 88
+VGNLP I D+E F K ++R + K F +VEF D + A+
Sbjct: 26 YVGNLPPDIRTKDIEDVF--YKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDG 83
Query: 89 ITVDGLQVRLDIADGKRNDNKG 110
DG ++R++ R G
Sbjct: 84 YDYDGYRLRVEFPRSGRGTGSG 105
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 30.8 bits (68), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 32/66 (48%)
Query: 45 FFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADGK 104
F P + +++ D ET++ +GF +VEF E+ A+ + G +R+++A
Sbjct: 33 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPM 92
Query: 105 RNDNKG 110
R G
Sbjct: 93 RIKESG 98
>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 = 30.8 bits (68), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 7/73 (9%)
Query: 29 FVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 87
F+ LP T+ ++E V +RLV ++ + KG YVE+ + QA++K
Sbjct: 21 FISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMK-- 77
Query: 88 RITVDGLQVRLDI 100
+DG+ ++ +I
Sbjct: 78 ---MDGMTIKENI 87
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 30.8 bits (68), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 6/82 (7%)
Query: 29 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR 88
FVG +T+ ++ FF + V + F+ F +V F D + + Q+L +
Sbjct: 9 FVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFAD-DQIAQSLCGEDL 63
Query: 89 ITVDGLQVRLDIADGKRNDNKG 110
I + G+ V + A+ K N N G
Sbjct: 64 I-IKGISVHISNAEPKHNSNSG 84
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 30.8 bits (68), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 34 PNGITQGDVERFFPEQKLV--SVRLVKDKETDRFKGFCYVEF---VDVENLRQAL 83
P+ + + P L ++RL+KDK+T + +GF +V+ +D L Q L
Sbjct: 19 PHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQIL 73
>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 = 30.0 bits (66), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 29 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEF 73
++ LP +TQ DVE F ++++ R++ D+ T +G ++ F
Sbjct: 92 YISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRF 137
>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 = 30.0 bits (66), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 14/61 (22%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 24 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 82
P ++G++P T+ + +++++++ D +T R KG+ ++EF D+E+ A
Sbjct: 2 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
Query: 83 L 83
+
Sbjct: 62 V 62
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 30.0 bits (66), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 29 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEF 73
++ LP +TQ DVE F ++++ R++ D+ T +G ++ F
Sbjct: 92 YISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRF 137
>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 = 30.0 bits (66), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 14/61 (22%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 24 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 82
P ++G++P T+ + +++++++ D +T R KG+ ++EF D+E+ A
Sbjct: 3 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
Query: 83 L 83
+
Sbjct: 63 V 63
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 30.0 bits (66), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 14/61 (22%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 24 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 82
P ++G++P T+ + +++++++ D +T R KG+ ++EF D+E+ A
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 83 L 83
+
Sbjct: 61 V 61
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 29.3 bits (64), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 29 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 82
FVG +P G+ + D++ F E ++ + ++KD+ T KG ++ + ++ +A
Sbjct: 19 FVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKA 73
>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 = 29.3 bits (64), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEF 73
+V LP +TQ ++E+ F + ++++ R++ D+ T +G ++ F
Sbjct: 92 YVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRF 137
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 83
V LP +TQ + F ++ S +LV+DK T + G+ +V ++D ++ +A+
Sbjct: 6 IVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 28.9 bits (63), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 29 FVGNLPNGITQGDV-ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 83
F+ +LP T D+ F P ++S ++ DK+T K F +V F + ++ + A+
Sbjct: 44 FIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAI 99
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 28.9 bits (63), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 30/57 (52%)
Query: 45 FFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA 101
F P + +++ D ET++ +GF +VEF E+ A+ + G +R+++A
Sbjct: 26 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 82
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 29 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEF 73
FVG L T DV+ +F + K+ L+ DK T+R +GF +V F
Sbjct: 3 FVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48
>pdb|3DJL|A Chain A, Crystal Structure Of Alkylation Response Protein E. Coli
Aidb
pdb|3U33|A Chain A, Crystal Structure Of The E. Coli Adaptive Response Protein
Aidb In The Space Group P3(2)
pdb|3U33|B Chain B, Crystal Structure Of The E. Coli Adaptive Response Protein
Aidb In The Space Group P3(2)
pdb|3U33|C Chain C, Crystal Structure Of The E. Coli Adaptive Response Protein
Aidb In The Space Group P3(2)
pdb|3U33|D Chain D, Crystal Structure Of The E. Coli Adaptive Response Protein
Aidb In The Space Group P3(2)
pdb|3U33|E Chain E, Crystal Structure Of The E. Coli Adaptive Response Protein
Aidb In The Space Group P3(2)
pdb|3U33|F Chain F, Crystal Structure Of The E. Coli Adaptive Response Protein
Aidb In The Space Group P3(2)
pdb|3U33|G Chain G, Crystal Structure Of The E. Coli Adaptive Response Protein
Aidb In The Space Group P3(2)
pdb|3U33|H Chain H, Crystal Structure Of The E. Coli Adaptive Response Protein
Aidb In The Space Group P3(2)
pdb|3U33|I Chain I, Crystal Structure Of The E. Coli Adaptive Response Protein
Aidb In The Space Group P3(2)
pdb|3U33|J Chain J, Crystal Structure Of The E. Coli Adaptive Response Protein
Aidb In The Space Group P3(2)
pdb|3U33|K Chain K, Crystal Structure Of The E. Coli Adaptive Response Protein
Aidb In The Space Group P3(2)
pdb|3U33|L Chain L, Crystal Structure Of The E. Coli Adaptive Response Protein
Aidb In The Space Group P3(2)
Length = 541
Score = 28.5 bits (62), Expect = 1.1, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 42 VERFFPEQKLVSVRL--VKDKETDRFKGFCYVEFVD 75
V RF P+ + ++RL +KDK +R C VEF D
Sbjct: 240 VPRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQD 275
>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 = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 30/57 (52%)
Query: 45 FFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA 101
F P + +++ D ET++ +GF +VEF E+ A+ + G +R+++A
Sbjct: 28 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 84
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 43/91 (47%), Gaps = 8/91 (8%)
Query: 24 PPYTAFVGNLPNGITQGDVERFF----PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENL 79
P Y+ FVG+L + G + FF P + V L +T KG+ +V+F D
Sbjct: 8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVL---DQTGVSKGYGFVKFTDELEQ 64
Query: 80 RQALLK-DGRITVDGLQVRLDIADGKRNDNK 109
++AL + G + + VRL +A K + K
Sbjct: 65 KRALTECQGAVGLGSKPVRLSVAIPKASRVK 95
>pdb|3I6X|A Chain A, Crystal Structure Of The Calponin Homology Domain Of
Iqgap1
pdb|3I6X|B Chain B, Crystal Structure Of The Calponin Homology Domain Of
Iqgap1
pdb|3I6X|C Chain C, Crystal Structure Of The Calponin Homology Domain Of
Iqgap1
pdb|3I6X|D Chain D, Crystal Structure Of The Calponin Homology Domain Of
Iqgap1
Length = 193
Score = 28.5 bits (62), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 3/66 (4%)
Query: 4 YSYGGYPERYGRNQKTLPTE--PPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKE 61
Y Y + E R + E PP T L NG+ + FF K+VS++ + D+E
Sbjct: 43 YEYLCHLEEAKRWMEACLGEDLPPTTELEEGLRNGVYLAKLGNFF-SPKVVSLKKIYDRE 101
Query: 62 TDRFKG 67
R+K
Sbjct: 102 QTRYKA 107
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 27/41 (65%), Gaps = 3/41 (7%)
Query: 43 ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 83
ER+ P + SV++V D+ET + +G+ +V+F + +QA+
Sbjct: 64 ERYGP---IESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
>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 = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 30/57 (52%)
Query: 45 FFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA 101
F P + +++ D ET++ +GF +VEF E+ A+ + G +R+++A
Sbjct: 23 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 79
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 17/30 (56%), Gaps = 4/30 (13%)
Query: 21 PTEPPYT----AFVGNLPNGITQGDVERFF 46
P E YT FVGNLP IT+ D +R F
Sbjct: 14 PGEKTYTQRCRLFVGNLPTDITEEDFKRLF 43
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 33 LPNGITQGDVERFFPEQKLVS--VRLVKDKETDRFKGFCYVEFVDVEN 78
LP T+ D+ + + VRL+++K + + +GF +VEF +++
Sbjct: 9 LPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQD 56
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 27 TAFVGNLPNGIT-QGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 85
T + G + +G+T Q + F P +++ +R+ +K G+ +V F E+ A++
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIVS 80
Query: 86 DGRITVDGLQVRL 98
T++G V+
Sbjct: 81 VNGTTIEGHVVKC 93
>pdb|2RR8|A Chain A, Solution Structure Of Calponin Homology Domain Of Iqgap1
Length = 190
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 3/66 (4%)
Query: 4 YSYGGYPERYGRNQKTLPTE--PPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKE 61
Y Y + E R + E PP T L NG+ + FF K+VS++ + D+E
Sbjct: 21 YEYLCHLEEAKRWMEACLGEDLPPTTELEEGLRNGVYLAKLGNFF-SPKVVSLKKIYDRE 79
Query: 62 TDRFKG 67
R+K
Sbjct: 80 QTRYKA 85
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 30/57 (52%)
Query: 45 FFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA 101
F P + +++ D ET++ +GF +VEF E+ A+ + G +R+++A
Sbjct: 84 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
>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 = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 46/86 (53%), Gaps = 6/86 (6%)
Query: 29 FVGNLPNGITQGDV-ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL--LK 85
F+ +LP D+ + F P +VS ++ DK+T+ K F +V + + + + A+ +
Sbjct: 29 FIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMN 88
Query: 86 DGRITVDGLQVRLDIADGKRNDNKGG 111
+I + L+V+L + +ND+K G
Sbjct: 89 GFQIGMKRLKVQLKRS---KNDSKSG 111
>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 = 26.9 bits (58), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 14/56 (25%), Positives = 28/56 (50%)
Query: 43 ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRL 98
+ F P + S+ + D T + KGF +VE+ E + AL + + + G +++
Sbjct: 47 QAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV 102
Score = 25.4 bits (54), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 12/56 (21%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 29 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 83
+V ++ ++ D++ F K+ S L +D T + KG+ ++E+ ++ + A+
Sbjct: 129 YVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV 184
>pdb|2FR7|A Chain A, Crystal Structure Of Cytochrome P450 Cyp199a2
pdb|4DNJ|A Chain A, The Crystal Structures Of 4-Methoxybenzoate Bound Cyp199a2
Length = 412
Score = 26.9 bits (58), Expect = 3.3, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 22/53 (41%), Gaps = 3/53 (5%)
Query: 4 YSYGGYPERYGRNQKTLPTEPPYTAFVGNL---PNGITQGDVERFFPEQKLVS 53
Y +P+ G Q+ PY V N PN + Q +ER P Q V+
Sbjct: 158 YPLSVFPDAMGLKQEGRENLLPYAGLVFNAFGPPNELRQSAIERSAPHQAYVA 210
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 26.9 bits (58), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 29 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 85
FVG L + + +F ++ S+ L D +T++ +GFC++ F + E +++ + K
Sbjct: 3 FVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>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 = 26.9 bits (58), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 29 FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 85
FVG L + + +F ++ S+ L D +T++ +GFC++ F + E +++ + K
Sbjct: 5 FVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
>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 = 26.9 bits (58), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 25/48 (52%)
Query: 54 VRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA 101
V + +D+ T +GF +V F D + A+ +DG ++R+ +A
Sbjct: 77 VYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 124
>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 = 26.9 bits (58), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 27 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEF---VDVEN 78
T +VGNL T+ + F + + + + DK GFC+VE+ D EN
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 26.6 bits (57), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 16/79 (20%), Positives = 36/79 (45%), Gaps = 1/79 (1%)
Query: 27 TAFVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLK 85
T FV + T+ + R F + + +V K + + +G+ ++E+ ++ A
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 86 DGRITVDGLQVRLDIADGK 104
+DG +V +D+ G+
Sbjct: 164 ADGKKIDGRRVLVDVERGR 182
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 26.6 bits (57), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 29 FVGNLPNGITQGDVERFFPEQKLVSVRLV-KDKETDRFKGFCYVEFVDVENLRQALLKD 86
F+G L TQ + +F + V LV +D T R +GF +V F+D + + L +
Sbjct: 29 FIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 26.6 bits (57), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 44/86 (51%), Gaps = 10/86 (11%)
Query: 25 PYTAFVGNLPNGITQGDVERFFPEQKLV-SVRLVKDKETDRFKGFCYVEF---VDVENLR 80
P T FVG + + + ++ FF V V+++ D+ T KG+ +V F VDV+ +
Sbjct: 10 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 68
Query: 81 QALLKDGRITVDGLQVRLDIADGKRN 106
++ +I G +++L A K+N
Sbjct: 69 ES-----QINFHGKKLKLGPAIRKQN 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 = 26.6 bits (57), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 16/79 (20%), Positives = 36/79 (45%), Gaps = 1/79 (1%)
Query: 27 TAFVGNLPNGITQGDVERFFPEQKLVS-VRLVKDKETDRFKGFCYVEFVDVENLRQALLK 85
T FV + T+ + R F + + +V K + + +G+ ++E+ ++ A
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 86 DGRITVDGLQVRLDIADGK 104
+DG +V +D+ G+
Sbjct: 164 ADGKKIDGRRVLVDVERGR 182
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 26.2 bits (56), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 4/72 (5%)
Query: 27 TAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
T NL IT+ +++ F + + +RLV + + KG Y+EF + + L +
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDA--LEIRLVS--QDGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 87 GRITVDGLQVRL 98
+DG V L
Sbjct: 74 QGAEIDGRSVSL 85
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 26.2 bits (56), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 30 VGNLPNGITQGDVERFFPEQKLV-SVRLVKDKETDRFKGFCYVEFVDVENLRQAL-LKDG 87
V NL + + R F + V V + +D+ T +GF +V F D + A+ DG
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 88 RITVDGLQVRLDIA 101
+ +DG ++R+ +A
Sbjct: 135 AV-LDGRELRVQMA 147
>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 = 26.2 bits (56), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 44/86 (51%), Gaps = 10/86 (11%)
Query: 25 PYTAFVGNLPNGITQGDVERFFPEQKLV-SVRLVKDKETDRFKGFCYVEF---VDVENLR 80
P T FVG + + + ++ FF V V+++ D+ T KG+ +V F VDV+ +
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 67
Query: 81 QALLKDGRITVDGLQVRLDIADGKRN 106
++ +I G +++L A K+N
Sbjct: 68 ES-----QINFHGKKLKLGPAIRKQN 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 = 26.2 bits (56), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 14/56 (25%), Positives = 28/56 (50%)
Query: 43 ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRL 98
+ F P + S+ + D T + KGF +VE+ E + AL + + + G +++
Sbjct: 32 QAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV 87
>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 = 26.2 bits (56), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 14/56 (25%), Positives = 27/56 (48%)
Query: 43 ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRL 98
+ F P + S+ D T + KGF +VE+ E + AL + + + G +++
Sbjct: 31 QAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKV 86
>pdb|2YMV|A Chain A, Structure Of Reduced M Smegmatis 5246, A Homologue Of M.
Tuberculosis Acg
Length = 330
Score = 25.8 bits (55), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 60 KETDRFKGFCYVEFVDVENLRQALLKDGRITVDGL--QVRLDIADGK 104
+ TDR YV++ E L +A L DG + D L VR ++A+
Sbjct: 121 RRTDRLPXSAYVDWDAFETLLRARLGDGPVHXDTLGEDVREEVAEAA 167
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 25.8 bits (55), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 6/85 (7%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEF 73
GR+ K + T NL IT+ +++ F + + +RLV + + KG Y+EF
Sbjct: 90 GRDSKKV--RAARTLLAKNLSFNITEDELKEVFEDA--LEIRLVS--QDGKSKGIAYIEF 143
Query: 74 VDVENLRQALLKDGRITVDGLQVRL 98
+ + L + +DG V L
Sbjct: 144 KSEADAEKNLEEKQGAEIDGRSVSL 168
>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 = 25.8 bits (55), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEF 73
FVG + + + E FF + ++ +L+ DK+T + +GF +V +
Sbjct: 91 FVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY 136
>pdb|1LTL|A Chain A, The Dodecamer Structure Of Mcm From Archaeal M.
Thermoautotrophicum
pdb|1LTL|B Chain B, The Dodecamer Structure Of Mcm From Archaeal M.
Thermoautotrophicum
pdb|1LTL|C Chain C, The Dodecamer Structure Of Mcm From Archaeal M.
Thermoautotrophicum
pdb|1LTL|D Chain D, The Dodecamer Structure Of Mcm From Archaeal M.
Thermoautotrophicum
pdb|1LTL|E Chain E, The Dodecamer Structure Of Mcm From Archaeal M.
Thermoautotrophicum
pdb|1LTL|F Chain F, The Dodecamer Structure Of Mcm From Archaeal M.
Thermoautotrophicum
Length = 279
Score = 25.8 bits (55), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 5/39 (12%)
Query: 32 NLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCY 70
+L + +T GD+ R ++R V+D+ T RFK F Y
Sbjct: 207 DLVDTLTPGDIVRVTG-----TLRTVRDERTKRFKNFIY 240
>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 = 25.4 bits (54), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 25 PYTAFVGNLPNGITQGDVERFFPEQKLV-SVRLVKDKETDRFKGFCYVEF---VDVENLR 80
P T FVG + + + ++ FF V V+++ D+ T KG+ +V F VDV+ +
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 67
Query: 81 QA 82
++
Sbjct: 68 ES 69
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 0.139 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,406,303
Number of Sequences: 62578
Number of extensions: 176146
Number of successful extensions: 401
Number of sequences better than 100.0: 94
Number of HSP's better than 100.0 without gapping: 57
Number of HSP's successfully gapped in prelim test: 37
Number of HSP's that attempted gapping in prelim test: 324
Number of HSP's gapped (non-prelim): 102
length of query: 137
length of database: 14,973,337
effective HSP length: 89
effective length of query: 48
effective length of database: 9,403,895
effective search space: 451386960
effective search space used: 451386960
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 46 (22.3 bits)