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= 008920
(548 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 = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 48/95 (50%), Gaps = 10/95 (10%)
Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP-HMRVGKGIAYVLFKTREAAN 396
T F+GNLP+DV +E I + F GLN + AVR+ R P + KG Y F+ ++
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLN-----ISAVRLPREPSNPERLKGFGYAEFEDLDSLL 71
Query: 397 LVIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPA 431
+ L ++ +R+ A Q ++ KD P+
Sbjct: 72 SALSLNEESLGNKRIRVDVADQ----AQDKDSGPS 102
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 30/95 (31%), Positives = 47/95 (49%), Gaps = 4/95 (4%)
Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
KTVF+ NL FD ++E + ++ DL+ VRV+ HP KG A+ F T+EAA
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKY----VRVVLHPDTEHSKGCAFAQFMTQEAAQ 71
Query: 397 LVIKRRNLKLRDRELRLSHAQQNCTPSKRKDVAPA 431
+ +L+ L+L Q + +D A +
Sbjct: 72 KCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAAS 106
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 42/82 (51%), Gaps = 6/82 (7%)
Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHP-HMRVGKGIAYVLFKTREAAN 396
T F+GNLP+DV +E I + F GLN + AVR+ R P + KG Y F+ ++
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLN-----ISAVRLPREPSNPERLKGFGYAEFEDLDSLL 75
Query: 397 LVIKRRNLKLRDRELRLSHAQQ 418
+ L +R +R+ A Q
Sbjct: 76 SALSLNEESLGNRRIRVDVADQ 97
>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 = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 46/211 (21%), Positives = 93/211 (44%), Gaps = 36/211 (17%)
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 VLFKTREAANLVIKRRN-LKLRDRELRLSHA 416
+ + I N ++L D++L + A
Sbjct: 161 CEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 191
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 4/60 (6%)
Query: 336 KKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
K TV+V NLPF + + ++Y++F V V +++ R KG+A++LF +++A
Sbjct: 16 KSTVYVSNLPFSLTNNDLYRIFSK----YGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 43/195 (22%), Positives = 87/195 (44%), Gaps = 32/195 (16%)
Query: 226 RTIFVGNLPLKVKKKTLIKEF---IKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENA 282
R ++VGN+P + ++ ++ F ++ G + T+ P +L QIN+
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGL------------TQAP-GNPVLAVQINQ-- 49
Query: 283 DSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVG 342
D A++ F+S T A+AF+ + G +++ R + PL K +F+G
Sbjct: 50 DKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRP--------HDYQPLPGAHK-LFIG 100
Query: 343 NLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR 402
LP + D+++ +L L +A +++ + KG A+ + + I
Sbjct: 101 GLPNYLNDDQVKELLTSFGPL----KAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 403 N-LKLRDRELRLSHA 416
N ++L D++L + A
Sbjct: 157 NGMQLGDKKLLVQRA 171
>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 = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 43/195 (22%), Positives = 87/195 (44%), Gaps = 32/195 (16%)
Query: 226 RTIFVGNLPLKVKKKTLIKEF---IKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENA 282
R ++VGN+P + ++ ++ F ++ G + T+ P +L QIN+
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGL------------TQAP-GNPVLAVQINQ-- 51
Query: 283 DSVHAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVG 342
D A++ F+S T A+AF+ + G +++ R + PL K +F+G
Sbjct: 52 DKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRP--------HDYQPLPGAHK-LFIG 102
Query: 343 NLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRR 402
LP + D+++ +L L +A +++ + KG A+ + + I
Sbjct: 103 GLPNYLNDDQVKELLTSFGPL----KAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 403 N-LKLRDRELRLSHA 416
N ++L D++L + A
Sbjct: 159 NGMQLGDKKLLVQRA 173
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 32/110 (29%), Positives = 53/110 (48%), Gaps = 16/110 (14%)
Query: 286 HAYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLP 345
Y+ F+S + E AL + GN I+L++ KG+D+ +T+ NLP
Sbjct: 50 FGYVDFESAEDLEKALELTGLKVFGNEIKLEKP-------KGKDSKKERDARTLLAKNLP 102
Query: 346 FDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
+ V +E+ ++F E + E +R++ KGIAY+ FKT A
Sbjct: 103 YKVTQDELKEVF------EDAAE-IRLVSKDGKS--KGIAYIEFKTEADA 143
>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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 30/109 (27%), Positives = 54/109 (49%), Gaps = 16/109 (14%)
Query: 287 AYIVFKSEQSTEAALAFNMAVIGGNHIRLDRACPPRKKLKGEDAPLYDIKKTVFVGNLPF 346
Y+ F+S + E AL + GN I+L++ KG D+ +T+ NL F
Sbjct: 57 GYVDFESAEDLEKALELTGLKVFGNEIKLEKP-------KGRDSKKVRAARTLLAKNLSF 109
Query: 347 DVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAA 395
++ ++E+ ++F E ++E +R++ KGIAY+ FK+ A
Sbjct: 110 NITEDELKEVF------EDALE-IRLVSQDGKS--KGIAYIEFKSEADA 149
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 5/80 (6%)
Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
T +VGNLPF+ +I +F L S+ +VR++R KG YV F ++
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDL-----SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKE 71
Query: 398 VIKRRNLKLRDRELRLSHAQ 417
+ L DR LR+ A+
Sbjct: 72 ALTYDGALLGDRSLRVDIAE 91
>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 = 38.5 bits (88), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 44/84 (52%), Gaps = 11/84 (13%)
Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
+FVGNLP D+ +EE+ +LF E +A V H KG ++ +TR A +
Sbjct: 18 LFVGNLPPDITEEEMRKLF------EKYGKAGEVFIHKD----KGFGFIRLETRTLAEIA 67
Query: 399 -IKRRNLKLRDRELRLSHAQQNCT 421
++ N+ LR ++LR+ A + +
Sbjct: 68 KVELDNMPLRGKQLRVRFACHSAS 91
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.5 bits (88), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 46/88 (52%), Gaps = 11/88 (12%)
Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
+FVGNLP D+ +EE+ +LF E +A V H KG ++ +TR A +
Sbjct: 25 LFVGNLPPDITEEEMRKLF------EKYGKAGEVFIHKD----KGFGFIRLETRTLAEIA 74
Query: 399 -IKRRNLKLRDRELRLSHAQQNCTPSKR 425
++ N+ LR ++LR+ A + + + R
Sbjct: 75 KVELDNMPLRGKQLRVRFACHSASLTVR 102
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 37.7 bits (86), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 46/192 (23%), Positives = 84/192 (43%), Gaps = 38/192 (19%)
Query: 225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADS 284
+ +++VG+L V + L ++F G I S+R+ + I ++ +
Sbjct: 15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVC-----------RDMITRRSLG----- 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 VGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIK 400
+ NL + ++ +Y F ++ S +V+ + KG +V F+T+EAA I+
Sbjct: 108 IKNLDKSIDNKALYDTFSAFGNILS----CKVVCDENG--SKGYGFVHFETQEAAERAIE 161
Query: 401 RRN-LKLRDREL 411
+ N + L DR++
Sbjct: 162 KMNGMLLNDRKV 173
>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 = 37.4 bits (85), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 46/192 (23%), Positives = 84/192 (43%), Gaps = 38/192 (19%)
Query: 225 LRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADS 284
+ +++VG+L V + L ++F G I S+R+ + I ++ +
Sbjct: 10 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVC-----------RDMITRRSLG----- 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 VGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIK 400
+ NL + ++ +Y F ++ S +V+ + KG +V F+T+EAA I+
Sbjct: 103 IKNLDKSIDNKALYDTFSAFGNILS----CKVVCDENG--SKGYGFVHFETQEAAERAIE 156
Query: 401 RRN-LKLRDREL 411
+ N + L DR++
Sbjct: 157 KMNGMLLNDRKV 168
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 35.0 bits (79), Expect = 0.11, 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 = 32.3 bits (72), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 5/79 (6%)
Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
+FVG L FD ++ + Q+F + V V++ + +G +V F+ + A
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYG----QISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 399 IKRRNLKLRD-RELRLSHA 416
+ N K D R++R+ A
Sbjct: 71 MMAMNGKSVDGRQIRVDQA 89
>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 = 35.0 bits (79), Expect = 0.11, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
T++VGNL F +E+IY+LF D++ + + M+ G +V + +R A
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGL-----DKMKTACGFCFVEYYSRADAEN 74
Query: 398 VIKRRN-LKLRDRELR 412
++ N +L DR +R
Sbjct: 75 AMRYINGTRLDDRIIR 90
>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 = 33.9 bits (76), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 42/207 (20%), Positives = 92/207 (44%), Gaps = 45/207 (21%)
Query: 224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENAD 283
++ ++VG++ ++ + T+ + F FG I K I+ + D
Sbjct: 27 IMSRVYVGSIYYELGEDTIRQAFAPFGPI-----------------------KSIDMSWD 63
Query: 284 SV------HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDR------ACPPRKKLKGEDA 330
SV A++ ++ ++ + AL N ++GG +I++ R A P +L E+A
Sbjct: 64 SVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLA-EEA 122
Query: 331 PLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK 390
++ ++V ++ D+ D++I +F ++S+ A R P KG ++ ++
Sbjct: 123 RAFN---RIYVASVHQDLSDDDIKSVFEAFGKIKSATLA----RDPTTGKHKGYGFIEYE 175
Query: 391 TREAANLVIKRRNL-KLRDRELRLSHA 416
+++ + NL L + LR+ A
Sbjct: 176 KAQSSQDAVSSMNLFDLGGQYLRVGKA 202
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 33.5 bits (75), Expect = 0.27, Method: Composition-based stats.
Identities = 27/98 (27%), Positives = 41/98 (41%), Gaps = 5/98 (5%)
Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
+FVG LP+ D + + F G D+E +V VI +G +V R AA
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAV----VITDRQTGKSRGYGFVTMADRAAAERA 75
Query: 399 IKRRNLKLRDRELRLSHAQQNCTP-SKRKDVAPAVNSP 435
K N + R+ ++ A P S + A V+ P
Sbjct: 76 CKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGP 113
>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 = 33.1 bits (74), Expect = 0.40, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 338 TVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANL 397
T++VGNL F +E+IY+LF D++ + + ++ + G +V + +R A
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMK----KTACGFCFVEYYSRADAEN 96
Query: 398 VIKRRN-LKLRDRELR 412
++ N +L DR +R
Sbjct: 97 AMRYINGTRLDDRIIR 112
>pdb|3E9A|A Chain A, Crystal Structure Of 2-dehydro-3-deoxyphosphooctonate
Aldolase From Vibrio Cholerae O1 Biovar Eltor Str.
N16961
Length = 286
Score = 32.7 bits (73), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 37/62 (59%), Gaps = 5/62 (8%)
Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGK--GIAYVLFKTREA 394
K V VG++P V +++ + LF G+N LES A+++ H +++V GI YV + +
Sbjct: 7 KIVHVGDIP--VANDKPFTLFAGMNVLESRDLAMQICEH-YVKVTDKLGIPYVFKASFDK 63
Query: 395 AN 396
AN
Sbjct: 64 AN 65
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 32.3 bits (72), Expect = 0.68, 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|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 32.0 bits (71), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 43/83 (51%), Gaps = 9/83 (10%)
Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
++VFVGN+P++ +E++ +F + V + R++ KG + ++ +E A
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVG----PVVSFRLVYDRETGKPKGYGFCEYQDQETA- 63
Query: 397 LVIKRRNLKLRD---RELRLSHA 416
+ RNL R+ R LR+ +A
Sbjct: 64 -LSAMRNLNGREFSGRALRVDNA 85
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 32.0 bits (71), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 41/87 (47%), Gaps = 8/87 (9%)
Query: 334 DIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK-TR 392
++ + +++ NLP+ + EE+Y +F + +RV P R G AYV+++
Sbjct: 6 EVNRILYIRNLPYKITAEEMYDIFGKY----GPIRQIRVGNTPETR---GTAYVVYEDIF 58
Query: 393 EAANLVIKRRNLKLRDRELRLSHAQQN 419
+A N V + +R L + + N
Sbjct: 59 DAKNAVDHLSGFNVSNRYLVVLYYNAN 85
Score = 29.3 bits (64), Expect = 6.5, 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|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 32.0 bits (71), Expect = 1.00, Method: Composition-based stats.
Identities = 19/79 (24%), Positives = 44/79 (55%), Gaps = 4/79 (5%)
Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
+F+GNL ++ ++ +Y F + ++ +++R P KG A++ F + +A++
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVI---LQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64
Query: 399 IKRRNLK-LRDRELRLSHA 416
I+ N + L +R + +S+A
Sbjct: 65 IEAMNGQYLCNRPITVSYA 83
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 32.0 bits (71), Expect = 1.0, 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|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 = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 42/81 (51%), Gaps = 5/81 (6%)
Query: 335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
I V+VG++ +++ ++ I Q F ++S + + H KG A+V ++ EA
Sbjct: 11 IXCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKH----KGFAFVEYEVPEA 66
Query: 395 ANLVIKRRN-LKLRDRELRLS 414
A L +++ N + L R +++
Sbjct: 67 AQLALEQXNSVXLGGRNIKVG 87
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 46/203 (22%), Positives = 86/203 (42%), Gaps = 45/203 (22%)
Query: 228 IFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENADSV-- 285
++VG++ ++ + T+ + F FG I K I+ + DSV
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPI-----------------------KSIDXSWDSVTX 51
Query: 286 -HAYIVFKSEQSTEAA-LAF---NMAVIGGNHIRLDR------ACPPRKKLKGEDAPLYD 334
H F + EAA LA N +GG +I++ R A P +L E+A ++
Sbjct: 52 KHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQL-AEEARAFN 110
Query: 335 IKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREA 394
++V ++ D+ D++I +F ++S A R P KG ++ ++ ++
Sbjct: 111 ---RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLA----RDPTTGKHKGYGFIEYEKAQS 163
Query: 395 ANLVIKRRNL-KLRDRELRLSHA 416
+ + NL L + LR+ A
Sbjct: 164 SQDAVSSXNLFDLGGQYLRVGKA 186
>pdb|2EK6|A Chain A, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|B Chain B, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|C Chain C, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|D Chain D, Crystal Structure Of Human Rna-Binding Protein 12
Length = 95
Score = 31.6 bits (70), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 341 VGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR-EAANLVI 399
V N+PF V +EI F G + SV +++ + G A V F++R EA VI
Sbjct: 20 VQNMPFTVSIDEILDFFYGYQVIPGSV----CLKYNEKGMPTGEAMVAFESRDEATAAVI 75
Query: 400 KRRNLKLRDRELRLS 414
+ + R+++LS
Sbjct: 76 DLNDRPIGSRKVKLS 90
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 31.6 bits (70), Expect = 1.1, 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|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 31.6 bits (70), Expect = 1.2, 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|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 = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 42/207 (20%), Positives = 91/207 (43%), Gaps = 45/207 (21%)
Query: 224 LLRTIFVGNLPLKVKKKTLIKEFIKFGEIDSVRIRSVPIIDTKIPRKGAILQKQINENAD 283
++ ++VG++ ++ + T+ + F FG I K I+ + D
Sbjct: 12 IMCRVYVGSIYYELGEDTIRQAFAPFGPI-----------------------KSIDMSWD 48
Query: 284 SV------HAYIVFKSEQSTEAAL-AFNMAVIGGNHIRLDR------ACPPRKKLKGEDA 330
SV A++ ++ ++ + AL N ++GG +I++ R A P +L E+A
Sbjct: 49 SVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQL-AEEA 107
Query: 331 PLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFK 390
++ ++V ++ D+ D++I +F ++S A R P KG ++ ++
Sbjct: 108 RAFN---RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLA----RDPTTGKHKGYGFIEYE 160
Query: 391 TREAANLVIKRRNL-KLRDRELRLSHA 416
+++ + NL L + LR+ A
Sbjct: 161 KAQSSQDAVSSMNLFDLGGQYLRVGKA 187
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 31.2 bits (69), Expect = 1.7, 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 = 4.3, 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|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 = 30.8 bits (68), Expect = 2.1, 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: 16 EVNRILYIRNLPYKITAEEMYDIFGKY----GPIRQIRVGNTPETR---GTAYVVYE 65
Score = 29.6 bits (65), Expect = 4.1, 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: 19 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP 54
>pdb|3S8S|A Chain A, Crystal Structure Of The Rrm Domain Of Human Setd1a
Length = 110
Score = 30.4 bits (67), Expect = 2.5, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 367 VEAVRVIRHPHMRVGKGIAYVLFKTREAANLVIKRRNLKLRDRELRLSHAQQNCTPSKR 425
VE V ++ HP R G+A VLF + A +K NL L + HAQ + +R
Sbjct: 33 VEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK--NLHLTSVMGNIIHAQLDIKGQQR 89
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 30.0 bits (66), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 4/80 (5%)
Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
+ ++VGNL + E++ +LF V V++I + KG +V + +
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQF----GKVFNVKLIYDRETKKPKGFGFVEMQEESVSE 57
Query: 397 LVIKRRNLKLRDRELRLSHA 416
+ K N R +R++ A
Sbjct: 58 AIAKLDNTDFMGRTIRVTEA 77
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 30.0 bits (66), Expect = 3.0, 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: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN 45
>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 = 3.2, 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 = 30.0 bits (66), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 40/81 (49%), Gaps = 10/81 (12%)
Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVG--KGIAYVLFKTREA 394
+TVFVGNL V++E +Y+LF L V + + R G K +V FK E+
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTK----VTICKD---REGKPKSFGFVCFKHPES 69
Query: 395 ANLVIKRRN-LKLRDRELRLS 414
+ I N ++L R + +S
Sbjct: 70 VSYAIALLNGIRLYGRPINVS 90
>pdb|2CQP|A Chain A, Solution Structure Of The Rna Binding Domain Of
Rna-Binding Protein 12
Length = 98
Score = 29.6 bits (65), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 341 VGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR-EAANLVI 399
V N+PF V +EI F G + SV +++ + G A V F++R EA VI
Sbjct: 20 VQNMPFTVSIDEILDFFYGYQVIPGSV----CLKYNEKGMPTGEAMVAFESRDEATAAVI 75
Query: 400 KRRNLKLRDRELRL 413
+ + R+++L
Sbjct: 76 DLNDRPIGSRKVKL 89
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 29.6 bits (65), Expect = 4.3, 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: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI---PLDYETEKHRGFAFVEFELAEDA 118
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 29.6 bits (65), Expect = 4.7, 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|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 29.6 bits (65), 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|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 29.6 bits (65), 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: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN 57
>pdb|2EK1|A Chain A, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|B Chain B, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|C Chain C, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|D Chain D, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|E Chain E, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|F Chain F, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|G Chain G, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|H Chain H, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
Length = 95
Score = 29.6 bits (65), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 341 VGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTR-EAANLVI 399
V N PF V +EI F G + SV +++ G A V F++R EA VI
Sbjct: 20 VQNXPFTVSIDEILDFFYGYQVIPGSV----CLKYNEKGXPTGEAXVAFESRDEATAAVI 75
Query: 400 KRRNLKLRDRELRLS 414
+ + R+++LS
Sbjct: 76 DLNDRPIGSRKVKLS 90
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 29.3 bits (64), Expect = 5.3, 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|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 29.3 bits (64), Expect = 5.4, Method: Compositional matrix adjust.
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|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 = 29.3 bits (64), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 7/74 (9%)
Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
+F+ NL + ++ +Y F ++ S +V+ + KG +V F+T+EAA
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILS----CKVVCDENGS--KGYGFVHFETQEAAERA 61
Query: 399 IKRRN-LKLRDREL 411
I++ N + L DR++
Sbjct: 62 IEKMNGMLLNDRKV 75
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 29.3 bits (64), Expect = 5.9, Method: Composition-based stats.
Identities = 18/84 (21%), Positives = 43/84 (51%), Gaps = 5/84 (5%)
Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
+ V++G++P+D +E+I L + V ++++ P KG A++ F+ E++
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNV----GPVINLKMMFDPQTGRSKGYAFIEFRDLESSA 59
Query: 397 LVIKRRN-LKLRDRELRLSHAQQN 419
++ N +L R L+ ++ +
Sbjct: 60 SAVRNLNGYQLGSRFLKCGYSSNS 83
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 29.3 bits (64), Expect = 6.2, Method: Composition-based stats.
Identities = 25/92 (27%), Positives = 41/92 (44%), Gaps = 5/92 (5%)
Query: 327 GEDAPLYDIKKTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAY 386
G P D T+ V NL + + + ++F + V V + R PH + +G A+
Sbjct: 4 GSSGPDVDGMITLKVDNLTYRTSPDSLRRVF----EKYGRVGDVYIPREPHTKAPRGFAF 59
Query: 387 VLFKT-REAANLVIKRRNLKLRDRELRLSHAQ 417
V F R+A + +L RELR+ A+
Sbjct: 60 VRFHDRRDAQDAEAAMDGAELDGRELRVQVAR 91
>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 = 29.3 bits (64), Expect = 6.5, 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|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 = 28.9 bits (63), Expect = 6.7, 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|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 28.9 bits (63), Expect = 6.9, Method: Composition-based stats.
Identities = 18/84 (21%), Positives = 43/84 (51%), Gaps = 5/84 (5%)
Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
+ V++G++P+D +E+I L + V ++++ P KG A++ F+ E++
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNV----GPVINLKMMFDPQTGRSKGYAFIEFRDLESSA 58
Query: 397 LVIKRRN-LKLRDRELRLSHAQQN 419
++ N +L R L+ ++ +
Sbjct: 59 SAVRNLNGYQLGSRFLKCGYSSNS 82
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 28.9 bits (63), Expect = 7.3, 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|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 28.9 bits (63), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 7/74 (9%)
Query: 339 VFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAANLV 398
+F+ NL + ++ +Y F ++ S +V+ + KG +V F+T+EAA
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILS----CKVVCDENGS--KGYGFVHFETQEAAERA 67
Query: 399 IKRRN-LKLRDREL 411
I++ N + L DR++
Sbjct: 68 IEKMNGMLLNDRKV 81
>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 = 28.5 bits (62), Expect = 8.9, Method: Composition-based stats.
Identities = 15/67 (22%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 337 KTVFVGNLPFDVKDEEIYQLFCGLNDLESSVEAVRVIRHPHMRVGKGIAYVLFKTREAAN 396
+ V++G++P+D +E+I L + V ++++ P KG A++ F+ E++
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNV----GPVINLKMMFDPQTGRSKGYAFIEFRDLESSA 60
Query: 397 LVIKRRN 403
++ N
Sbjct: 61 SAVRNLN 67
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 0.130 0.358
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,040,679
Number of Sequences: 62578
Number of extensions: 463982
Number of successful extensions: 829
Number of sequences better than 100.0: 57
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 43
Number of HSP's that attempted gapping in prelim test: 778
Number of HSP's gapped (non-prelim): 82
length of query: 548
length of database: 14,973,337
effective HSP length: 104
effective length of query: 444
effective length of database: 8,465,225
effective search space: 3758559900
effective search space used: 3758559900
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: 54 (25.4 bits)