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= 015974
(397 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 31/54 (57%), Gaps = 6/54 (11%)
Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP-HMRVGKGIAYVLFK 390
T F+GNLP+DV +E I + F GLN + AVR+ R P + KG Y F+
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLN-----ISAVRLPREPSNPERLKGFGYAEFE 65
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 31/105 (29%), Positives = 52/105 (49%), Gaps = 16/105 (15%)
Query: 287 AYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPF 346
Y+ F+S + E AL + GN I+L++ KG+D+ +T+ NLP+
Sbjct: 51 GYVDFESAEDLEKALELTGLKVFGNEIKLEKP-------KGKDSKKERDARTLLAKNLPY 103
Query: 347 DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
V +E+ ++F E + E +R++ KGIAY+ FKT
Sbjct: 104 KVTQDELKEVF------EDAAE-IRLVSKDGKS--KGIAYIEFKT 139
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 31/54 (57%), Gaps = 6/54 (11%)
Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP-HMRVGKGIAYVLFK 390
T F+GNLP+DV +E I + F GLN + AVR+ R P + KG Y F+
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLN-----ISAVRLPREPSNPERLKGFGYAEFE 69
>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 = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 30/105 (28%), Positives = 53/105 (50%), Gaps = 16/105 (15%)
Query: 287 AYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPF 346
Y+ F+S + E AL + GN I+L+ K KG D+ +T+ NL F
Sbjct: 57 GYVDFESAEDLEKALELTGLKVFGNEIKLE-------KPKGRDSKKVRAARTLLAKNLSF 109
Query: 347 DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKT 391
++ ++E+ ++F E ++E +R++ KGIAY+ FK+
Sbjct: 110 NITEDELKEVF------EDALE-IRLVSQDGKS--KGIAYIEFKS 145
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 40/181 (22%), Positives = 80/181 (44%), Gaps = 35/181 (19%)
Query: 222 GKLLRTIFVGNLPLKVKKKTLIKEF---IKFGEIDSVRIRSVPIIDTKIPRKGAILQKQI 278
G + R ++VGN+P + ++ ++ F ++ G + T+ P +L QI
Sbjct: 1 GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGL------------TQAPGN-PVLAVQI 47
Query: 279 NENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKG--EDAPLY--- 333
N+ D A++ F+S T A+AF+ + G +++ R + L G E+ +Y
Sbjct: 48 NQ--DKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPH-DYQPLPGMSENPSVYVPG 104
Query: 334 -------DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAY 386
D +F+G LP + D+++ +L L +A +++ + KG A+
Sbjct: 105 VVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPL----KAFNLVKDSATGLSKGYAF 160
Query: 387 V 387
Sbjct: 161 C 161
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 4/59 (6%)
Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRDN 394
K TV+V NLPF + + ++Y++F V V +++ R KG+A++LF +D+
Sbjct: 16 KSTVYVSNLPFSLTNNDLYRIFSKY----GKVVKVTIMKDKDTRKSKGVAFILFLDKDS 70
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 38/162 (23%), Positives = 75/162 (46%), Gaps = 25/162 (15%)
Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
R ++VGN+P + ++ ++ F +R+ + T+ P +L QIN+ D
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNA-----QMRLGGL----TQAPGN-PVLAVQINQ--DKN 54
Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLP 345
A++ F+S T A+AF+ + G +++ R P + PL K +F+G LP
Sbjct: 55 FAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR---PH-----DYQPLPGAHK-LFIGGLP 105
Query: 346 FDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYV 387
+ D+++ +L L +A +++ + KG A+
Sbjct: 106 NYLNDDQVKELLTSFGPL----KAFNLVKDSATGLSKGYAFC 143
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 38/162 (23%), Positives = 75/162 (46%), Gaps = 25/162 (15%)
Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV 285
R ++VGN+P + ++ ++ F +R+ + T+ P +L QIN+ D
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNA-----QMRLGGL----TQAPGN-PVLAVQINQ--DKN 52
Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLP 345
A++ F+S T A+AF+ + G +++ R P + PL K +F+G LP
Sbjct: 53 FAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR---PH-----DYQPLPGAHK-LFIGGLP 103
Query: 346 FDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYV 387
+ D+++ +L L +A +++ + KG A+
Sbjct: 104 NYLNDDQVKELLTSFGPL----KAFNLVKDSATGLSKGYAFC 141
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 4/57 (7%)
Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRD 393
KTVF+ NL FD ++E + ++ DL+ VRV+ HP KG A+ F T++
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKY----VRVVLHPDTEHSKGCAFAQFMTQE 68
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 35.0 bits (79), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 46/100 (46%), Gaps = 22/100 (22%)
Query: 220 DEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQIN 279
DEGKL FVG L +++L + F K+G+I V V + D + R
Sbjct: 11 DEGKL----FVGGLSFDTNEQSLEQVFSKYGQISEV----VVVKDRETQRSRGF------ 56
Query: 280 ENADSVHAYIVFKS-EQSTEAALAFNMAVIGGNHIRLDRA 318
++ F++ + + +A +A N + G IR+D+A
Sbjct: 57 -------GFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA 89
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 14/56 (25%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRDN 394
+FVG L FD ++ + Q+F + V V++ + +G +V F+ D+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYG----QISEVVVVKDRETQRSRGFGFVTFENIDD 66
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 34.7 bits (78), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRDNWIE 397
T +VGNLPF+ +I +F L S+ +VR++R KG YV F D+ E
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDL-----SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKE 71
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 32.7 bits (73), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 40/100 (40%), Gaps = 17/100 (17%)
Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSVHA 287
IFVG +P + L + F KFG + V V I D + R
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEV----VMIYDAEKQRPRGF-------------G 55
Query: 288 YIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKG 327
+I F+ EQS + A+ + I G + + RA P K G
Sbjct: 56 FITFEDEQSVDQAVNMHFHDIMGKKVEVKRAEPRDSKSSG 95
>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 = 0.54, Method: Composition-based stats.
Identities = 23/95 (24%), Positives = 46/95 (48%), Gaps = 18/95 (18%)
Query: 226 RTIFVGNLPLKVKKKTLIKEF---IKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENA 282
R ++VGN+P + ++ ++ F ++ G + T+ P +L QIN+
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGL------------TQAP-GNPVLAVQINQ-- 51
Query: 283 DSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDR 317
D A++ F+S T A+AF+ + G +++ R
Sbjct: 52 DKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR 86
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 32.0 bits (71), Expect = 0.59, Method: Composition-based stats.
Identities = 23/95 (24%), Positives = 46/95 (48%), Gaps = 18/95 (18%)
Query: 226 RTIFVGNLPLKVKKKTLIKEF---IKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENA 282
R ++VGN+P + ++ ++ F ++ G + T+ P +L QIN+
Sbjct: 2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGL------------TQAP-GNPVLAVQINQ-- 46
Query: 283 DSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDR 317
D A++ F+S T A+AF+ + G +++ R
Sbjct: 47 DKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR 81
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 31.2 bits (69), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPI-IDTKIPRKGAILQKQINENA 282
R ++VG L +V K L FI FG+I ++I P+ +T+ R A ++ ++ E+A
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI---PLDYETEKHRGFAFVEFELAEDA 118
>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 = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 5/55 (9%)
Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
T++VGNL F +E+IY+LF D++ + + M+ G +V + +R
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGL-----DKMKTACGFCFVEYYSR 69
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 7/57 (12%)
Query: 334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK 390
++ + +++ NLP+ + EE+Y +F + +RV P R G AYV+++
Sbjct: 6 EVNRILYIRNLPYKITAEEMYDIFGKY----GPIRQIRVGNTPETR---GTAYVVYE 55
Score = 29.3 bits (64), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 21/36 (58%)
Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVP 261
R +++ NLP K+ + + F K+G I +R+ + P
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP 44
>pdb|3E9A|A Chain A, Crystal Structure Of 2-dehydro-3-deoxyphosphooctonate
Aldolase From Vibrio Cholerae O1 Biovar Eltor Str.
N16961
Length = 286
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 35/59 (59%), Gaps = 5/59 (8%)
Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGK--GIAYVLFKTRD 393
K V VG++P V +++ + LF G+N LES A+++ H +++V GI YV + D
Sbjct: 7 KIVHVGDIP--VANDKPFTLFAGMNVLESRDLAMQICEH-YVKVTDKLGIPYVFKASFD 62
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 7/57 (12%)
Query: 334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK 390
++ + +++ NLP+ + EE+Y +F + +RV P R G AYV+++
Sbjct: 10 EVNRILYIRNLPYKITAEEMYDIFGKY----GPIRQIRVGNTPETR---GTAYVVYE 59
Score = 29.6 bits (65), Expect = 3.2, Method: Composition-based stats.
Identities = 11/36 (30%), Positives = 21/36 (58%)
Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVP 261
R +++ NLP K+ + + F K+G I +R+ + P
Sbjct: 13 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP 48
>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 = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 30/55 (54%), Gaps = 4/55 (7%)
Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
T++VGNL F +E+IY+LF D++ + + ++ + G +V + +R
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMK----KTACGFCFVEYYSR 91
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPI-IDTKIPRKGAILQKQINENA 282
R ++VG L +V K L FI FG+I ++I P+ +T+ R A ++ ++ E+A
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI---PLDYETEKHRGFAFVEFELAEDA 67
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 30.0 bits (66), Expect = 2.1, Method: Composition-based stats.
Identities = 24/101 (23%), Positives = 43/101 (42%), Gaps = 25/101 (24%)
Query: 217 GFDDEGKLLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQK 276
G E K + T++VG L + + L F +FGEI ++ ++Q+
Sbjct: 4 GSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTI----------------TVVQR 47
Query: 277 QINENADSVHAYIVFKSEQSTEAAL--AFNMAVIGGNHIRL 315
Q A+I F + Q+ E A +FN ++ G + +
Sbjct: 48 Q-------QCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV 81
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 22/32 (68%)
Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRI 257
RT+FVGNL +V+++ L + F++ G + V I
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTI 48
Score = 28.9 bits (63), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 12/21 (57%), Positives = 17/21 (80%)
Query: 337 KTVFVGNLPFDVKDEEIYQLF 357
+TVFVGNL V++E +Y+LF
Sbjct: 17 RTVFVGNLEARVREEILYELF 37
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 228 IFVGNLPLK-VKKKTLIKEFIKFGEIDSVRIRSV 260
+F+GNLPLK V K+ L + F +G I + I++
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA 46
>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 = 29.6 bits (65), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 10/60 (16%)
Query: 333 YDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
+ + +FVGNLP D+ +EE+ +LF E +A V H KG ++ +TR
Sbjct: 12 FTQRSRLFVGNLPPDITEEEMRKLF------EKYGKAGEVFIHKD----KGFGFIRLETR 61
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 10/57 (17%)
Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR 392
+ +FVGNLP D+ +EE+ +LF E +A V H KG ++ +TR
Sbjct: 22 RSRLFVGNLPPDITEEEMRKLF------EKYGKAGEVFIHKD----KGFGFIRLETR 68
>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 = 29.3 bits (64), Expect = 4.2, Method: Composition-based stats.
Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 7/57 (12%)
Query: 334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK 390
++ + +++ NLP+ + EE+Y +F + +RV P R G AYV+++
Sbjct: 16 EVNRILYIRNLPYKITAEEMYDIFGKY----GPIRQIRVGNTPETR---GTAYVVYE 65
Score = 28.5 bits (62), Expect = 6.8, Method: Composition-based stats.
Identities = 11/36 (30%), Positives = 21/36 (58%)
Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVP 261
R +++ NLP K+ + + F K+G I +R+ + P
Sbjct: 19 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP 54
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 228 IFVGNLPLK-VKKKTLIKEFIKFGEIDSVRIRS 259
+F+GNLPLK V K+ L + F +G I + I++
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN 57
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 28.9 bits (63), Expect = 4.8, Method: Composition-based stats.
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSV 367
+FVG LP+ D + + F G D+E +V
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAV 48
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 228 IFVGNLPLK-VKKKTLIKEFIKFGEIDSVRIRS 259
+F+GNLPLK V K+ L + F +G I + I++
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN 57
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 28.9 bits (63), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 228 IFVGNLPLK-VKKKTLIKEFIKFGEIDSVRIRS 259
+F+GNLPLK V K+ L + F +G I + I++
Sbjct: 5 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN 37
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 28.5 bits (62), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 38/173 (21%), Positives = 72/173 (41%), Gaps = 37/173 (21%)
Query: 225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADS 284
+ +++VG+L V + L ++F G I S+R+ + I ++ +
Sbjct: 15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRV-----------CRDMITRRSLG----- 58
Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRL---DRACPPRKKLKGEDAPLYDIKKTVF 340
+AY+ F+ E AL N VI G +R+ R RK G +F
Sbjct: 59 -YAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVG----------NIF 107
Query: 341 VGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRD 393
+ NL + ++ +Y F ++ S +V+ + KG +V F+T++
Sbjct: 108 IKNLDKSIDNKALYDTFSAFGNILS----CKVVCDENG--SKGYGFVHFETQE 154
>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 = 7.2, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPI-IDTKIPRKGAILQKQINENA 282
R ++VG L +V K L FI FG+I ++I P+ +T+ R A ++ ++ E+A
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI---PLDYETEKHRGFAFVEFELAEDA 62
>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 = 28.5 bits (62), Expect = 7.4, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPI-IDTKIPRKGAILQKQINENA 282
R ++VG L +V K L FI FG+I ++I P+ +T+ R A ++ ++ E+A
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI---PLDYETEKHRGFAFVEFELAEDA 57
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 28.5 bits (62), Expect = 7.6, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 226 RTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPI-IDTKIPRKGAILQKQINENA 282
R ++VG L +V K L FI FG+I ++I P+ +T+ R A ++ ++ E+A
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI---PLDYETEKHRGFAFVEFELAEDA 60
>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 = 28.1 bits (61), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 38/173 (21%), Positives = 72/173 (41%), Gaps = 37/173 (21%)
Query: 225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADS 284
+ +++VG+L V + L ++F G I S+R+ + I ++ +
Sbjct: 10 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRV-----------CRDMITRRSLG----- 53
Query: 285 VHAYIVFKSEQSTEAAL-AFNMAVIGGNHIRL---DRACPPRKKLKGEDAPLYDIKKTVF 340
+AY+ F+ E AL N VI G +R+ R RK G +F
Sbjct: 54 -YAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVG----------NIF 102
Query: 341 VGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTRD 393
+ NL + ++ +Y F ++ S +V+ + KG +V F+T++
Sbjct: 103 IKNLDKSIDNKALYDTFSAFGNILS----CKVVCDENG--SKGYGFVHFETQE 149
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 28.1 bits (61), Expect = 9.2, Method: Composition-based stats.
Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 7/57 (12%)
Query: 334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK 390
++ + + + NLP+ + EE+Y +F + +RV P R G AYV+++
Sbjct: 16 EVNRILMIRNLPYKITAEEMYDIFGKY----GPIRQIRVGNTPETR---GTAYVVYE 65
>pdb|3HI7|A Chain A, Crystal Structure Of Human Diamine Oxidase
pdb|3HI7|B Chain B, Crystal Structure Of Human Diamine Oxidase
pdb|3HIG|A Chain A, Crystal Structure Of Human Diamine Oxidase In Complex With
The Inhibitor Berenil
pdb|3HIG|B Chain B, Crystal Structure Of Human Diamine Oxidase In Complex With
The Inhibitor Berenil
pdb|3HII|A Chain A, Crystal Structure Of Human Diamine Oxidase In Complex With
The Inhibitor Pentamidine
pdb|3HII|B Chain B, Crystal Structure Of Human Diamine Oxidase In Complex With
The Inhibitor Pentamidine
pdb|3K5T|A Chain A, Crystal Structure Of Human Diamine Oxidase In Space Group
C2221
pdb|3MPH|A Chain A, The Structure Of Human Diamine Oxidase Complexed With An
Inhibitor Aminoguanidine
pdb|3MPH|B Chain B, The Structure Of Human Diamine Oxidase Complexed With An
Inhibitor Aminoguanidine
Length = 731
Score = 28.1 bits (61), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 9/83 (10%)
Query: 267 IPRKGAILQKQINENADSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKL- 325
+PRK + N+ +VH+++ K E + + MA N + L P+K
Sbjct: 6 LPRKAGVFSDLSNQELKAVHSFLWSKKELRLQPSSTTTMA---KNTVFLIEMLLPKKYHV 62
Query: 326 -----KGEDAPLYDIKKTVFVGN 343
KGE P+ + + +F G+
Sbjct: 63 LRFLDKGERHPVREARAVIFFGD 85
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
0.314 0.133 0.370
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,785,444
Number of Sequences: 62578
Number of extensions: 352275
Number of successful extensions: 678
Number of sequences better than 100.0: 38
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 632
Number of HSP's gapped (non-prelim): 57
length of query: 397
length of database: 14,973,337
effective HSP length: 101
effective length of query: 296
effective length of database: 8,652,959
effective search space: 2561275864
effective search space used: 2561275864
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: 52 (24.6 bits)