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= 001976
(987 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 52.0 bits (123), Expect = 2e-06, Method: Composition-based stats.
Identities = 43/151 (28%), Positives = 68/151 (45%), Gaps = 14/151 (9%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMKAL 334
L V + ++ D EL ALF G I T Y G+ + + ++ A+K L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 335 QNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE--- 391
+R ++L + Y+ P S KD N L V NL +++ ++L IFG YG I +
Sbjct: 66 NGITVRNKRLKVSYARP-GGESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
Query: 392 IRD--TQHKHNHKFIEFYDIRAAETALRTLN 420
+RD T F+ + A+ A+ LN
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Score = 40.0 bits (92), Expect = 0.007, Method: Composition-based stats.
Identities = 25/84 (29%), Positives = 45/84 (53%), Gaps = 5/84 (5%)
Query: 360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEI---REIRD--TQHKHNHKFIEFYDIRAAET 414
A+ L+V L ++ EL+ +F G I R +RD T + + + F++F ++
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 415 ALRTLNRSDVAGKQIKLEASRPGG 438
A++ LN V K++K+ +RPGG
Sbjct: 61 AIKVLNGITVRNKRLKVSYARPGG 84
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 50.8 bits (120), Expect = 3e-06, Method: Composition-based stats.
Identities = 38/141 (26%), Positives = 63/141 (44%), Gaps = 15/141 (10%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 339
LFV N+ ++ + E++ LFE++G ++ K +GF I A A L N PL
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPL 83
Query: 340 RRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE----IRDT 395
R ++L + ++ + +L V NL VS E L + F ++G++ + D
Sbjct: 84 RGKQLRVRFA----------CHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDR 133
Query: 396 QHKHNHKFIEFYDIRAAETAL 416
+EF AA AL
Sbjct: 134 GRPSGKGIVEFSGKPAARKAL 154
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 50.4 bits (119), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 275 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 328
P+ T+++ N+N ++ ELK A+F QFG I I + K RG + + ++ +A
Sbjct: 7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 329 NAMKALQNKPLRRRKLDIHYS 349
NA++++Q P + + I Y+
Sbjct: 67 NALRSMQGFPFYDKPMRIQYA 87
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 49.7 bits (117), Expect = 8e-06, Method: Composition-based stats.
Identities = 43/151 (28%), Positives = 67/151 (44%), Gaps = 14/151 (9%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMKAL 334
L V + + D EL ALF G I T Y G+ + + ++ A+K L
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 335 QNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE--- 391
+R ++L + Y+ P S KD N L V NL +++ ++L IFG YG I +
Sbjct: 77 NGITVRNKRLKVSYARP-GGESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSIVQKNI 132
Query: 392 IRD--TQHKHNHKFIEFYDIRAAETALRTLN 420
+RD T F+ + A+ A+ LN
Sbjct: 133 LRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
Score = 36.6 bits (83), Expect = 0.062, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAET 414
A+ L+V L + EL+ +F G I R T + + F++F ++
Sbjct: 12 ASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQR 71
Query: 415 ALRTLNRSDVAGKQIKLEASRPGG 438
A++ LN V K++K+ +RPGG
Sbjct: 72 AIKVLNGITVRNKRLKVSYARPGG 95
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 48.5 bits (114), Expect = 2e-05, Method: Composition-based stats.
Identities = 46/160 (28%), Positives = 69/160 (43%), Gaps = 15/160 (9%)
Query: 280 LFVRNINSNVEDSELK-ALFEQFG-------DIRTIYTACKHRGFVMISYYDIRAARNAM 331
LFV N+N N ELK + + F D+R T R F Y D +A +
Sbjct: 10 LFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMT----RKF---GYVDFESAEDLE 62
Query: 332 KALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE 391
KAL+ L+ +I PK S+K+ + TL+ NL V+ +EL ++F EIR
Sbjct: 63 KALELTGLKVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRL 122
Query: 392 IRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKL 431
+ +IEF AE +++ G+ I L
Sbjct: 123 VSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISL 162
Score = 38.5 bits (88), Expect = 0.021, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 36/82 (43%)
Query: 268 GEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAA 327
G+ E +RTL +N+ V ELK +FE +IR + K +G I + A
Sbjct: 84 GKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEADA 143
Query: 328 RNAMKALQNKPLRRRKLDIHYS 349
+ Q + R + ++Y+
Sbjct: 144 EKTFEEKQGTEIDGRSISLYYT 165
>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 = 48.5 bits (114), Expect = 2e-05, Method: Composition-based stats.
Identities = 46/160 (28%), Positives = 72/160 (45%), Gaps = 15/160 (9%)
Query: 280 LFVRNINSNVEDSELK-ALFEQFG-------DIRTIYTACKHRGFVMISYYDIRAARNAM 331
LF+ N+N N +ELK A+ E F D+RT +R F Y D +A +
Sbjct: 16 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT----GTNRKF---GYVDFESAEDLE 68
Query: 332 KALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE 391
KAL+ L+ +I PK S+K TL+ NL +++ +EL ++F EIR
Sbjct: 69 KALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL 128
Query: 392 IRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKL 431
+ +IEF AE L +++ G+ + L
Sbjct: 129 VSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL 168
Score = 38.5 bits (88), Expect = 0.018, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 37/73 (50%)
Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 336
+RTL +N++ N+ + ELK +FE +IR + K +G I + A ++ Q
Sbjct: 99 ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQG 158
Query: 337 KPLRRRKLDIHYS 349
+ R + ++Y+
Sbjct: 159 AEIDGRSVSLYYT 171
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 48.1 bits (113), Expect = 2e-05, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 276 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAARN 329
P+ T+++ N+N ++ ELK A+F QFG I I + K RG + + ++ +A N
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 330 AMKALQNKPLRRRKLDIHYS 349
A++++Q P + + I Y+
Sbjct: 67 ALRSMQGFPFYDKPMRIQYA 86
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 47.8 bits (112), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 275 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 328
P+ T+++ N+N ++ ELK A+F QFG I I + K RG + + ++ +A
Sbjct: 7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 329 NAMKALQNKPLRRRKLDIHYS 349
NA++++Q P + + I Y+
Sbjct: 67 NALRSMQGFPFYDKPMRIQYA 87
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 47.4 bits (111), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 5/78 (6%)
Query: 360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAET 414
+++G L V L + + L Q+F YG+I E+ R+TQ F+ F +I A+
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 415 ALRTLNRSDVAGKQIKLE 432
A+ +N V G+QI+++
Sbjct: 70 AMMAMNGKSVDGRQIRVD 87
>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 = 47.0 bits (110), Expect = 5e-05, Method: Composition-based stats.
Identities = 45/161 (27%), Positives = 72/161 (44%), Gaps = 22/161 (13%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACK---------HRGFVMISYYDIRAARNA 330
L V + N+ E ++LF G+I + CK G+ ++Y D + A A
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIES----CKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 331 MKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI- 389
+ L L+ + + + Y+ P + S +DAN L V L +++ +EL Q+F YG I
Sbjct: 61 INTLNGLRLQTKTIKVSYARPS-SASIRDAN---LYVSGLPKTMTQKELEQLFSQYGRII 116
Query: 390 --REIRD--TQHKHNHKFIEFYDIRAAETALRTLNRSDVAG 426
R + D T FI F AE A++ LN +G
Sbjct: 117 TSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSG 157
Score = 43.5 bits (101), Expect = 6e-04, Method: Composition-based stats.
Identities = 32/107 (29%), Positives = 49/107 (45%), Gaps = 17/107 (15%)
Query: 361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRD--TQHKHNHKFIEFYDIRAAETA 415
++ L+V L +++ EE +FG GEI +RD T + F+ + D + AE A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 416 LRTLNRSDVAGKQIKLEASRPGGAR------------RFMVQSEQEQ 450
+ TLN + K IK+ +RP A + M Q E EQ
Sbjct: 61 INTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQ 107
>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 = 47.0 bits (110), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 34/155 (21%), Positives = 72/155 (46%), Gaps = 12/155 (7%)
Query: 275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHR------GFVMISYYDIRAAR 328
+P +L+V +++ +V ++ L F G I +I C+ G+ +++ A
Sbjct: 13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSI-RVCRDMITRRSLGYAYVNFQQPADAE 71
Query: 329 NAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE 388
A+ + ++ + + I +S + +PS + + G + + NLD S+ + L+ F +G
Sbjct: 72 RALDTMNFDVIKGKPVRIMWS--QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 129
Query: 389 I---REIRDTQHKHNHKFIEFYDIRAAETALRTLN 420
I + + D + F+ F AAE A+ +N
Sbjct: 130 ILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 164
Score = 39.3 bits (90), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 54/218 (24%), Positives = 90/218 (41%), Gaps = 33/218 (15%)
Query: 354 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYG---EIREIRD--TQHKHNHKFIEFYD 408
NPS +L V +L V+ L++ F G IR RD T+ + ++ F
Sbjct: 7 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66
Query: 409 IRAAETALRTLNRSDVAGKQIKLEAS-------RPGGARRFMVQSEQEQDDLNLCQIPFD 461
AE AL T+N + GK +++ S + G F+ ++ D+ L +D
Sbjct: 67 PADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKAL----YD 122
Query: 462 DLSS-GQMVSSGVITSTCMDNGS--IQVLHSATRSPAIALTESHQTSSVPNGLPSLARVG 518
S+ G ++S V+ C +NGS +H T+ A E NG+ R
Sbjct: 123 TFSAFGNILSCKVV---CDENGSKGYGFVHFETQEAAERAIEKM------NGMLLNDRKV 173
Query: 519 SIGKQFGHYEPNLSLDEMKFGNQHPSFHPHSLPEYHDS 556
+G+ E E + G + F+P+ +P+Y S
Sbjct: 174 FVGRFKSRKE-----REAELGARAKEFYPYDVPDYAGS 206
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 46.6 bits (109), Expect = 6e-05, Method: Composition-based stats.
Identities = 43/151 (28%), Positives = 66/151 (43%), Gaps = 14/151 (9%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIY-----TACKHRGFVMISYYDIRAARNAMKAL 334
L V + N+ E K+LF GDI + + G+ ++Y D A A+ L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 335 QNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR- 393
L+ + + + Y+ P + S +DAN L V L ++S +E+ Q+F YG I R
Sbjct: 67 NGLKLQTKTIKVSYARPS-SASIRDAN---LYVSGLPKTMSQKEMEQLFSQYGRIITSRI 122
Query: 394 ----DTQHKHNHKFIEFYDIRAAETALRTLN 420
T FI F AE A++ LN
Sbjct: 123 LLDQATGVSRGVGFIRFDKRIEAEEAIKGLN 153
Score = 37.0 bits (84), Expect = 0.052, Method: Composition-based stats.
Identities = 29/107 (27%), Positives = 48/107 (44%), Gaps = 17/107 (15%)
Query: 361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRD--TQHKHNHKFIEFYDIRAAETA 415
++ L+V L +++ +E +FG G+I +RD T + F+ + D A+ A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 416 LRTLNRSDVAGKQIKLEASRPGGAR------------RFMVQSEQEQ 450
+ TLN + K IK+ +RP A + M Q E EQ
Sbjct: 63 INTLNGLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQ 109
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 45.8 bits (107), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 275 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 328
P+ T+++ N+N ++ ELK A+F +FG I I + K RG + + ++ +A
Sbjct: 7 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 329 NAMKALQNKPLRRRKLDIHYS 349
NA++++Q P + + I Y+
Sbjct: 67 NALRSMQGFPFYDKPMRIQYA 87
>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 = 45.8 bits (107), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 38/169 (22%), Positives = 84/169 (49%), Gaps = 17/169 (10%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMKAL 334
++V +I + + ++ F FG I++I KH+GF + Y AA+ A++ +
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 335 QNKPLRRRKL------DIHYSIP-KDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYG 387
+ L R + +I + P D +E+ + V ++ +S +++ +F +G
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 150
Query: 388 EIRE---IRD-TQHKHN-HKFIEFYDIRAAETALRTLNRSDVAGKQIKL 431
+I+ RD T KH + FIE+ ++++ A+ ++N D+ G+ +++
Sbjct: 151 KIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 45.8 bits (107), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 275 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 328
P+ T+++ N+N ++ ELK A+F +FG I I + K RG + + ++ +A
Sbjct: 6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 65
Query: 329 NAMKALQNKPLRRRKLDIHYS 349
NA++++Q P + + I Y+
Sbjct: 66 NALRSMQGFPFYDKPMRIQYA 86
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 275 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 328
P+ T+++ N+N ++ ELK A+F +FG I I + K RG + + ++ +A
Sbjct: 7 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 329 NAMKALQNKPLRRRKLDIHYS 349
NA++++Q P + + I Y+
Sbjct: 67 NALRSMQGFPFYDKPMRIQYA 87
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 275 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 328
P+ T+++ N+N ++ ELK A+F +FG I I + K RG + + ++ +A
Sbjct: 6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 65
Query: 329 NAMKALQNKPLRRRKLDIHYS 349
NA++++Q P + + I Y+
Sbjct: 66 NALRSMQGFPFYDKPMRIQYA 86
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 275 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 328
P+ T+++ N+N ++ ELK A+F +FG I I + K RG + + ++ +A
Sbjct: 4 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 63
Query: 329 NAMKALQNKPLRRRKLDIHYS 349
NA++++Q P + + I Y+
Sbjct: 64 NALRSMQGFPFYDKPMRIQYA 84
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 45.4 bits (106), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 275 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 328
P+ T+++ N+N ++ ELK A+F +FG I I + K RG + + ++ +A
Sbjct: 6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 65
Query: 329 NAMKALQNKPLRRRKLDIHYS 349
NA++++Q P + + I Y+
Sbjct: 66 NALRSMQGFPFYDKPMRIQYA 86
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 275 HPSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAAR 328
P+ T+++ N+N ++ ELK A+F +FG I I + K RG + + ++ +A
Sbjct: 3 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 62
Query: 329 NAMKALQNKPLRRRKLDIHYS 349
NA++++Q P + + I Y+
Sbjct: 63 NALRSMQGFPFYDKPMRIQYA 83
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 276 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAARN 329
P+ T+++ N+N ++ ELK A+F +FG I I + K RG + + ++ +A N
Sbjct: 3 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 62
Query: 330 AMKALQNKPLRRRKLDIHYS 349
A++++Q P + + I Y+
Sbjct: 63 ALRSMQGFPFYDKPMRIQYA 82
>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 = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 34/155 (21%), Positives = 72/155 (46%), Gaps = 12/155 (7%)
Query: 275 HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHR------GFVMISYYDIRAAR 328
+P +L+V +++ +V ++ L F G I +I C+ G+ +++ A
Sbjct: 8 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSI-RVCRDMITRRSLGYAYVNFQQPADAE 66
Query: 329 NAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGE 388
A+ + ++ + + I +S + +PS + + G + + NLD S+ + L+ F +G
Sbjct: 67 RALDTMNFDVIKGKPVRIMWS--QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 124
Query: 389 I---REIRDTQHKHNHKFIEFYDIRAAETALRTLN 420
I + + D + F+ F AAE A+ +N
Sbjct: 125 ILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 159
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 276 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYTA--CKHRGFVMISYYDIRAARN 329
P+ T+++ N+N ++ ELK A+F +FG I I + K RG + + ++ +A N
Sbjct: 2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61
Query: 330 AMKALQNKPLRRRKLDIHYS 349
A++++Q P + + I Y+
Sbjct: 62 ALRSMQGFPFYDKPMRIQYA 81
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 44.3 bits (103), Expect = 3e-04, Method: Composition-based stats.
Identities = 38/141 (26%), Positives = 59/141 (41%), Gaps = 15/141 (10%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 339
LFV N+ +++ + + K LFE++G+ ++ + RGF I A A L L
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFIN-RDRGFGFIRLESRTLAEIAKAELDGTIL 83
Query: 340 RRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIRE----IRDT 395
+ R L I ++ + L V NL VS E L Q F +G + + + D
Sbjct: 84 KSRPLRIRFA----------THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDR 133
Query: 396 QHKHNHKFIEFYDIRAAETAL 416
F+EF A AL
Sbjct: 134 GRATGKGFVEFAAKPPARKAL 154
>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 = 44.3 bits (103), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 38/169 (22%), Positives = 84/169 (49%), Gaps = 17/169 (10%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMKAL 334
++V +I + + ++ F FG I++I KH+GF + Y AA+ A++ +
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 335 QNKPLRRRKL------DIHYSIP-KDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYG 387
+ L R + +I + P D +E+ + V ++ +S +++ +F +G
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 135
Query: 388 EIREI---RD-TQHKHN-HKFIEFYDIRAAETALRTLNRSDVAGKQIKL 431
+I+ RD T KH + FIE+ ++++ A+ ++N D+ G+ +++
Sbjct: 136 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 43.9 bits (102), Expect = 4e-04, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 276 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARN 329
P+ T+++ N+N ++ ELK A+F +FG I I + K RG + + ++ +A N
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATN 66
Query: 330 AMKALQNKPLRRRKLDIHYS 349
A+++ Q P + I Y+
Sbjct: 67 ALRSXQGFPFYDKPXRIQYA 86
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 43.9 bits (102), Expect = 4e-04, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 276 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARN 329
P+ T+++ N+N ++ ELK A+F +FG I I + K RG + + ++ +A N
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATN 67
Query: 330 AMKALQNKPLRRRKLDIHYS 349
A+++ Q P + I Y+
Sbjct: 68 ALRSXQGFPFYDKPXRIQYA 87
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 43.9 bits (102), Expect = 5e-04, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 276 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARN 329
P+ T+++ N+N ++ ELK A+F +FG I I + K RG + + ++ +A N
Sbjct: 5 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATN 64
Query: 330 AMKALQNKPLRRRKLDIHYS 349
A+++ Q P + I Y+
Sbjct: 65 ALRSXQGFPFYDKPXRIQYA 84
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 43.5 bits (101), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 276 PSRTLFVRNINSNVEDSELK----ALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARN 329
P+ T+++ N+N ++ ELK ALF QFG + I K RG + + ++ ++ N
Sbjct: 5 PNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGSSTN 64
Query: 330 AMKALQNKPLRRRKLDIHYS 349
A++ LQ P + + I Y+
Sbjct: 65 ALRQLQGFPFYGKPMRIQYA 84
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 42.0 bits (97), Expect = 0.002, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 276 PSRTLFVRNIN----SNVEDSELKALFEQFGDIRTIYT--ACKHRGFVMISYYDIRAARN 329
P++T+++ N+N L A+F QFG I I K RG + + +I +A N
Sbjct: 5 PNQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIGSASN 64
Query: 330 AMKALQNKPLRRRKLDIHYS 349
A++ +Q P + + I YS
Sbjct: 65 ALRTMQGFPFYDKPMQIAYS 84
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 41.6 bits (96), Expect = 0.002, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 367 VFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG 426
V NL + EL + F YG +R + ++ F+EF D R AE A+R L+ + G
Sbjct: 5 VGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICG 64
Query: 427 KQIKLEASRPGGARR 441
++++E S G RR
Sbjct: 65 SRVRVELS-TGMPRR 78
Score = 38.5 bits (88), Expect = 0.019, Method: Composition-based stats.
Identities = 23/94 (24%), Positives = 49/94 (52%), Gaps = 4/94 (4%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 339
++V N+ + EL+ F +G +RT++ A GF + + D R A +A++ L K +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 340 --RRRKLDIHYSIPKDNPSEKDANQGTL--VVFN 369
R ++++ +P+ + ++ + L V+FN
Sbjct: 63 CGSRVRVELSTGMPRRSRFDRPPARRKLLEVLFN 96
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 41.2 bits (95), Expect = 0.003, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 38/68 (55%)
Query: 367 VFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG 426
V NL ++ + EL + FG YG +R + ++ F+EF D R A A+R L+ + G
Sbjct: 78 VGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCG 137
Query: 427 KQIKLEAS 434
++++E S
Sbjct: 138 CRVRVELS 145
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 41.2 bits (95), Expect = 0.003, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 38/68 (55%)
Query: 367 VFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAG 426
V NL ++ + EL + FG YG +R + ++ F+EF D R A A+R L+ + G
Sbjct: 78 VGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRTLCG 137
Query: 427 KQIKLEAS 434
++++E S
Sbjct: 138 CRVRVELS 145
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 355 PSEKDANQGTLVVFNLD-SSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAE 413
P A L+V NL+ V+ + L +FG+YG+++ ++ +K + ++ D A+
Sbjct: 27 PGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQ 86
Query: 414 TALRTLNRSDVAGKQIKLEASR 435
A+ LN + GK I++ S+
Sbjct: 87 LAMSHLNGHKLHGKPIRITLSK 108
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 40.8 bits (94), Expect = 0.004, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETA 415
++ T+ V NL S++ +L++IF YG++ ++ +DT+ FI F D +A+
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Query: 416 LRTLNRSDVAGKQIK 430
R +N + G+ IK
Sbjct: 75 TRAINNKQLFGRVIK 89
Score = 32.3 bits (72), Expect = 1.5, Method: Composition-based stats.
Identities = 20/81 (24%), Positives = 42/81 (51%), Gaps = 6/81 (7%)
Query: 276 PSR-TLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARN 329
PS+ T++V N+ ++ +++L +F ++G + + K +G I + D +A+N
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
Query: 330 AMKALQNKPLRRRKLDIHYSI 350
+A+ NK L R + +I
Sbjct: 74 CTRAINNKQLFGRVIKASIAI 94
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 40.4 bits (93), Expect = 0.005, Method: Composition-based stats.
Identities = 25/84 (29%), Positives = 45/84 (53%), Gaps = 5/84 (5%)
Query: 360 ANQGTLVVFNLDSSVSTEELHQIFGIYGEI---REIRD--TQHKHNHKFIEFYDIRAAET 414
A+ L+V L ++ EL+ +F G I R +RD T + + + F++F ++
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 415 ALRTLNRSDVAGKQIKLEASRPGG 438
A++ LN V K++K+ +RPGG
Sbjct: 61 AIKVLNGITVRNKRLKVSYARPGG 84
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 40.4 bits (93), Expect = 0.005, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHN-HKFIEFYDIRAAETALRTLNRS 422
TLV+ NL S + E L ++F I+ ++ K + FIEF A+ AL + N+
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKR 76
Query: 423 DVAGKQIKLEASRPGGA 439
++ G+ I+LE P G+
Sbjct: 77 EIEGRAIRLELQGPRGS 93
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 40.0 bits (92), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 32/157 (20%), Positives = 66/157 (42%), Gaps = 17/157 (10%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTA-------CKHRGFVMISYYDIRAARNAMK 332
+FV + + +L+ LFEQ+G + I + +G +++Y +AA A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 333 ALQNKPLRRRKLDIHYSI---PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI 389
AL N + +H+ I P D+ L + + + ++ +F +G+I
Sbjct: 78 ALHNMKVLP---GMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 134
Query: 390 REIRDTQ----HKHNHKFIEFYDIRAAETALRTLNRS 422
E R + F+ F A+TA++ ++++
Sbjct: 135 EECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA 171
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 40.0 bits (92), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 280 LFVRNINSNVEDSELKALFEQF-----GDIRTIYTACKHRGFVMISYYDIRAARNAMKAL 334
LFV ++N NV+D L+ F+ F G + RG+ +S+ A+NAM ++
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 335 QNKPLRRRKLDIHYS 349
Q + L R L I+++
Sbjct: 64 QGQDLNGRPLRINWA 78
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 40.0 bits (92), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 45/80 (56%), Gaps = 7/80 (8%)
Query: 280 LFVRNINS-NVEDSELKALFEQFGDIRTIYTACK-HRGFVMISYYDIRAARNAMKALQNK 337
+F+ N+N+ V+ S+++A+F ++G I C H+GF + Y + R AR A+ +
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKI----VGCSVHKGFAFVQYVNERNARAAVAGEDGR 73
Query: 338 PLRRRKLDIHYSI-PKDNPS 356
+ + LDI+ + PK N S
Sbjct: 74 MIAGQVLDINLAAEPKVNRS 93
>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 = 40.0 bits (92), Expect = 0.007, Method: Composition-based stats.
Identities = 38/169 (22%), Positives = 82/169 (48%), Gaps = 17/169 (10%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMKAL 334
++V +I + + ++ F FG I++I KH+GF + Y AA+ A++
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 335 QNKPLRRRKL------DIHYSIP-KDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYG 387
+ L R + +I + P D +E+ + V ++ +S +++ +F +G
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 134
Query: 388 EIREI---RD-TQHKHN-HKFIEFYDIRAAETALRTLNRSDVAGKQIKL 431
+I+ RD T KH + FIE+ ++++ A+ + N D+ G+ +++
Sbjct: 135 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRV 183
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 40.0 bits (92), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 32/96 (33%), Positives = 47/96 (48%), Gaps = 11/96 (11%)
Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIR---DTQHKH-NHKFIEFYDIRAAETALRTL 419
L V NLD +++ + L Q F + G I I+ D +K+ N+ F+E++ A AL+TL
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 420 NRSDVAGKQIKLEASRPGGARRFMVQSEQEQDDLNL 455
N GKQI+ + A F Q D NL
Sbjct: 62 N-----GKQIENNIVKINWA--FQSQQSSSDDTFNL 90
Score = 38.9 bits (89), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 280 LFVRNINSNVEDSELKALFEQF-----GDIRTIYTACKHRGFVMISYYDIRAARNAMKAL 334
LFV ++N NV+D L+ F+ F G + RG+ +S+ A+NAM ++
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 335 QNKPLRRRKLDIHYS 349
Q + L R L I+++
Sbjct: 150 QGQDLNGRPLRINWA 164
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 39.7 bits (91), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 32/157 (20%), Positives = 66/157 (42%), Gaps = 17/157 (10%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC-------KHRGFVMISYYDIRAARNAMK 332
+FV + + +L+ LFEQ+G + I + +G +++Y +AA A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 333 ALQNKPLRRRKLDIHYSI---PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI 389
AL N + +H+ I P D+ L + + + ++ +F +G+I
Sbjct: 66 ALHNMKVLP---GMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 122
Query: 390 REIRDTQ----HKHNHKFIEFYDIRAAETALRTLNRS 422
E R + F+ F A+TA++ ++++
Sbjct: 123 EECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA 159
>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 = 39.3 bits (90), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 8/84 (9%)
Query: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKA 333
+L V N+ L+ +FE++G + +Y + RGF + ++D R A +AM A
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 334 LQNKPLRRRKLDIH---YSIPKDN 354
+ L R+L + Y P D+
Sbjct: 109 MDGAVLDGRELRVQMARYGRPPDS 132
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 39.3 bits (90), Expect = 0.012, Method: Composition-based stats.
Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 6/86 (6%)
Query: 353 DNPSEKDANQG-TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEF 406
D P + + +G L V + + E++H F YGEI+ I R T + + +E+
Sbjct: 12 DEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 71
Query: 407 YDIRAAETALRTLNRSDVAGKQIKLE 432
+ A+ A+ LN D+ G+ I ++
Sbjct: 72 ETYKEAQAAMEGLNGQDLMGQPISVD 97
Score = 31.6 bits (70), Expect = 2.2, Method: Composition-based stats.
Identities = 15/74 (20%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHR-----GFVMISYYDIRAARNAMKAL 334
LFV ++ + ++ F ++G+I+ I+ R G+ ++ Y + A+ AM+ L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 335 QNKPLRRRKLDIHY 348
+ L + + + +
Sbjct: 85 NGQDLMGQPISVDW 98
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 38.5 bits (88), Expect = 0.018, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 37/73 (50%)
Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQN 336
+RTL +N++ N+ + ELK +FE +IR + K +G I + A ++ Q
Sbjct: 16 ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQG 75
Query: 337 KPLRRRKLDIHYS 349
+ R + ++Y+
Sbjct: 76 AEIDGRSVSLYYT 88
Score = 31.2 bits (69), Expect = 3.3, Method: Composition-based stats.
Identities = 22/86 (25%), Positives = 38/86 (44%)
Query: 356 SEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETA 415
S+K TL+ NL +++ +EL ++F EIR + +IEF AE
Sbjct: 10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKN 69
Query: 416 LRTLNRSDVAGKQIKLEASRPGGARR 441
L +++ G+ + L + G R
Sbjct: 70 LEEKQGAEIDGRSVSLYYTGEKGGTR 95
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 38.5 bits (88), Expect = 0.018, Method: Composition-based stats.
Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 6/86 (6%)
Query: 353 DNPSEKDANQG-TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEF 406
D P + + +G L V + + E++H F YGEI+ I R T + + +E+
Sbjct: 13 DEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 72
Query: 407 YDIRAAETALRTLNRSDVAGKQIKLE 432
+ A+ A+ LN D+ G+ I ++
Sbjct: 73 ETYKEAQAAMEGLNGQDLMGQPISVD 98
Score = 32.3 bits (72), Expect = 1.3, Method: Composition-based stats.
Identities = 16/81 (19%), Positives = 38/81 (46%), Gaps = 5/81 (6%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHR-----GFVMISYYDIRAARNAMKAL 334
LFV ++ + ++ F ++G+I+ I+ R G+ ++ Y + A+ AM+ L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 335 QNKPLRRRKLDIHYSIPKDNP 355
+ L + + + + + P
Sbjct: 86 NGQDLMGQPISVDWCFVRGPP 106
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 38.5 bits (88), Expect = 0.018, Method: Composition-based stats.
Identities = 27/81 (33%), Positives = 41/81 (50%), Gaps = 6/81 (7%)
Query: 362 QGT-LVVFNLDSSVSTEELHQIFGIYGEIRE---IRD--TQHKHNHKFIEFYDIRAAETA 415
QGT L+V L + + +EL +F GE+ IRD H + F+ + + AE A
Sbjct: 18 QGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 77
Query: 416 LRTLNRSDVAGKQIKLEASRP 436
+ TLN + K IK+ +RP
Sbjct: 78 INTLNGLRLQSKTIKVSYARP 98
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 38.5 bits (88), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 364 TLVVFNLD-SSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRS 422
L+V NL+ V+ + L +FG+YG+++ ++ +K + ++ D A+ A+ LN
Sbjct: 5 VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGH 64
Query: 423 DVAGKQIKLEASR 435
+ GK I++ S+
Sbjct: 65 KLHGKPIRITLSK 77
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 38.5 bits (88), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 5/80 (6%)
Query: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIY----TACKHRGFVMISYYDIRAARN 329
+HP + LF+ +N + LKA+F + G I + K RGF I++ + A+N
Sbjct: 5 DHPGK-LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKN 63
Query: 330 AMKALQNKPLRRRKLDIHYS 349
A K + K L + + + +
Sbjct: 64 AAKDMNGKSLHGKAIKVEQA 83
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 38.1 bits (87), Expect = 0.023, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 38/67 (56%), Gaps = 2/67 (2%)
Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIR--DTQHKHNHKFIEFYDIRAAETALRTLNRS 422
L + NL ++ EE++ IFG YG IR+IR +T ++ + DI A+ A+ L+
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGF 70
Query: 423 DVAGKQI 429
+V+ + +
Sbjct: 71 NVSNRYL 77
Score = 36.2 bits (82), Expect = 0.095, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC--KHRGFVMISYYDIRAARNAMKAL 334
+R L++RN+ + E+ +F ++G IR I + RG + Y DI A+NA+ L
Sbjct: 8 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 335 QNKPLRRRKLDIHY 348
+ R L + Y
Sbjct: 68 SGFNVSNRYLVVLY 81
>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 = 37.7 bits (86), Expect = 0.028, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 339
LFV N+ ++ + E++ LFE++G ++ K +GF I A A L N PL
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-KDKGFGFIRLETRTLAEIAKVELDNMPL 76
Query: 340 RRRKLDIHYS 349
R ++L + ++
Sbjct: 77 RGKQLRVRFA 86
>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 = 37.7 bits (86), Expect = 0.029, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 2/67 (2%)
Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIR--DTQHKHNHKFIEFYDIRAAETALRTLNRS 422
L++ NL ++ EE++ IFG YG IR+IR +T ++ + DI A+ A L+
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF 80
Query: 423 DVAGKQI 429
+V + +
Sbjct: 81 NVCNRYL 87
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 37.7 bits (86), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK 332
GE + LFVR +V++SEL +F FG ++ + GF + + + +A A++
Sbjct: 27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIE 83
Query: 333 ALQNKPLRRRKLDIHYS 349
+ K + L++ YS
Sbjct: 84 EVHGKSFANQPLEVVYS 100
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
Length = 109
Score = 37.7 bits (86), Expect = 0.030, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTL 419
L V + + E++H F YGEI+ I R T + + +E+ + A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 420 NRSDVAGKQIKLE 432
N D+ G+ I ++
Sbjct: 70 NGQDLMGQPISVD 82
Score = 32.3 bits (72), Expect = 1.4, Method: Composition-based stats.
Identities = 15/74 (20%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHR-----GFVMISYYDIRAARNAMKAL 334
LFV ++ + ++ F ++G+I+ I+ R G+ ++ Y + A+ AM+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 335 QNKPLRRRKLDIHY 348
+ L + + + +
Sbjct: 70 NGQDLMGQPISVDW 83
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 37.7 bits (86), Expect = 0.031, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAA 327
G R L+V + V+D L A F FGDI I Y KHRGF + + A
Sbjct: 1 GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELA 57
Query: 328 RNAMKALQN 336
+A A+ N
Sbjct: 58 EDAAAAIDN 66
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 37.7 bits (86), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 3/78 (3%)
Query: 357 EKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-DTQHKHN--HKFIEFYDIRAAE 413
E D TL V NL V+ + Q+F G + + T+H N + F+EFY+ R A
Sbjct: 10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAA 69
Query: 414 TALRTLNRSDVAGKQIKL 431
AL +N + GK++K+
Sbjct: 70 AALAAMNGRKILGKEVKV 87
Score = 31.2 bits (69), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/75 (21%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRG---FVMISYYDIRAARNAMKAL 334
RTL+V N++ +V + + LF Q G ++ +H + + +Y+ R A A+ A+
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAM 75
Query: 335 QNKPLRRRKLDIHYS 349
+ + +++ ++++
Sbjct: 76 NGRKILGKEVKVNWA 90
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 37.7 bits (86), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 3/71 (4%)
Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDV 424
L + NL + +E+ +F YG++ E + N+ F+ D AAE A+R L+ +
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIK---NYGFVHIEDKTAAEDAIRNLHHYKL 67
Query: 425 AGKQIKLEASR 435
G I +EAS+
Sbjct: 68 HGVNINVEASK 78
Score = 35.0 bits (79), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 339
LF+ N+ + E+++LFEQ+G + K+ GFV I D AA +A++ L + L
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLEC-DIIKNYGFVHIE--DKTAAEDAIRNLHHYKL 67
Query: 340 RRRKLDIHYSIPKDNPS 356
+++ S K S
Sbjct: 68 HGVNINVEASKNKSKAS 84
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 37.4 bits (85), Expect = 0.038, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTL 419
L V + + E++H F YGEI+ I R T + + +E+ + A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 420 NRSDVAGKQIKLE 432
N D+ G+ I ++
Sbjct: 70 NGQDLMGQPISVD 82
Score = 32.0 bits (71), Expect = 1.8, Method: Composition-based stats.
Identities = 15/74 (20%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHR-----GFVMISYYDIRAARNAMKAL 334
LFV ++ + ++ F ++G+I+ I+ R G+ ++ Y + A+ AM+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 335 QNKPLRRRKLDIHY 348
+ L + + + +
Sbjct: 70 NGQDLMGQPISVDW 83
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 37.4 bits (85), Expect = 0.040, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIR--DTQHKHNHKFIEFYDIRAAETALRTLNRS 422
L + NL ++ EE++ IFG YG IR+IR +T ++ + DI A+ A L+
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF 74
Query: 423 DVAGKQI 429
+V + +
Sbjct: 75 NVCNRYL 81
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 37.4 bits (85), Expect = 0.040, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 8/84 (9%)
Query: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAARNAMKA 333
+L V N+ L+ +FE++G + +Y + RGF + ++D R A +AM A
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 334 LQNKPLRRRKLDIH---YSIPKDN 354
+ L R+L + Y P D+
Sbjct: 132 MDGAVLDGRELRVQMARYGRPPDS 155
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 37.4 bits (85), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 4/77 (5%)
Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMK 332
G S +FV ++ + EL+ F Q+GD+ ++ R F +++ D + A +
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIA----Q 56
Query: 333 ALQNKPLRRRKLDIHYS 349
+L + L + + +H S
Sbjct: 57 SLCGEDLIIKGISVHIS 73
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 37.4 bits (85), Expect = 0.043, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIRE---IRD--TQHKHNHKFIEFYDIRAAETALRTL 419
L+V L +++ +EL +F GE+ IRD H + F+ + + AE A+ TL
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 420 NRSDVAGKQIKLEASRP 436
N + K IK+ +RP
Sbjct: 67 NGLRLQSKTIKVSYARP 83
Score = 31.2 bits (69), Expect = 3.1, Method: Composition-based stats.
Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 6/82 (7%)
Query: 276 PSRT-LFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARN 329
P RT L V + N+ EL++LF G++ + A G+ ++Y + A
Sbjct: 2 PGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 61
Query: 330 AMKALQNKPLRRRKLDIHYSIP 351
A+ L L+ + + + Y+ P
Sbjct: 62 AINTLNGLRLQSKTIKVSYARP 83
>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 = 0.043, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 5/79 (6%)
Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYT-----ACKHRGFVMISYYDIRAA 327
G S L+V +++ N+ + L+ +FE FG I I + +G+ I++ D A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 328 RNAMKALQNKPLRRRKLDI 346
R A++ L L R + +
Sbjct: 61 RRALEQLNGFELAGRPMRV 79
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 37.4 bits (85), Expect = 0.044, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTL 419
L V + + E++H F YGEI+ I R T + + +E+ + A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 420 NRSDVAGKQIKLE 432
N D+ G+ I ++
Sbjct: 70 NGQDLMGQPISVD 82
Score = 32.7 bits (73), Expect = 0.90, Method: Composition-based stats.
Identities = 16/81 (19%), Positives = 38/81 (46%), Gaps = 5/81 (6%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHR-----GFVMISYYDIRAARNAMKAL 334
LFV ++ + ++ F ++G+I+ I+ R G+ ++ Y + A+ AM+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 335 QNKPLRRRKLDIHYSIPKDNP 355
+ L + + + + + P
Sbjct: 70 NGQDLMGQPISVDWCFVRGPP 90
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 37.4 bits (85), Expect = 0.045, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIREI--RDTQHKHNHKFIEFYDIRAAETALRT 418
N + V NL + T+++ +F YG IR+I ++ + F+EF D R AE A+
Sbjct: 21 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYG 80
Query: 419 LNRSDVAGKQIKLEASRPG 437
+ D G ++++E R G
Sbjct: 81 RDGYDYDGYRLRVEFPRSG 99
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 37.4 bits (85), Expect = 0.045, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTL 419
L V + + E++H F YGEI+ I R T + + +E+ + A+ A+ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 420 NRSDVAGKQIKLE 432
N D+ G+ I ++
Sbjct: 72 NGQDLMGQPISVD 84
Score = 31.6 bits (70), Expect = 2.0, Method: Composition-based stats.
Identities = 15/74 (20%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHR-----GFVMISYYDIRAARNAMKAL 334
LFV ++ + ++ F ++G+I+ I+ R G+ ++ Y + A+ AM+ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 335 QNKPLRRRKLDIHY 348
+ L + + + +
Sbjct: 72 NGQDLMGQPISVDW 85
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 37.4 bits (85), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 5/77 (6%)
Query: 365 LVVFNLDSSVSTEELHQIFGIYGEI---REIRDTQHKHN--HKFIEFYDIRAAETALRTL 419
L+V L +++ +EL +F GE+ + IRD H+ + F+ + + AE A+ TL
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 420 NRSDVAGKQIKLEASRP 436
N + K IK+ +RP
Sbjct: 65 NGLRLQSKTIKVSYARP 81
Score = 37.0 bits (84), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 36/151 (23%), Positives = 65/151 (43%), Gaps = 14/151 (9%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMKAL 334
L V + N+ EL++LF G++ + A G+ ++Y + A A+ L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 335 QNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI---RE 391
L+ + + + Y+ P KDAN L + L +++ +++ +F +G I R
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVI-KDAN---LYISGLPRTMTQKDVEDMFSRFGRIINSRV 120
Query: 392 IRD--TQHKHNHKFIEFYDIRAAETALRTLN 420
+ D T FI F AE A+ + N
Sbjct: 121 LVDQTTGLSRGVAFIRFDKRSEAEEAITSFN 151
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 37.4 bits (85), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 5/77 (6%)
Query: 365 LVVFNLDSSVSTEELHQIFGIYGEI---REIRDTQHKHN--HKFIEFYDIRAAETALRTL 419
L+V L +++ +EL +F GE+ + IRD H+ + F+ + + AE A+ TL
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 420 NRSDVAGKQIKLEASRP 436
N + K IK+ +RP
Sbjct: 65 NGLRLQSKTIKVSYARP 81
Score = 36.6 bits (83), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 36/151 (23%), Positives = 65/151 (43%), Gaps = 14/151 (9%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMKAL 334
L V + N+ EL++LF G++ + A G+ ++Y + A A+ L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 335 QNKPLRRRKLDIHYSIPKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI---RE 391
L+ + + + Y+ P KDAN L + L +++ +++ +F +G I R
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVI-KDAN---LYISGLPRTMTQKDVEDMFSRFGRIINSRV 120
Query: 392 IRD--TQHKHNHKFIEFYDIRAAETALRTLN 420
+ D T FI F AE A+ + N
Sbjct: 121 LVDQTTGLSRGVAFIRFDKRSEAEEAITSFN 151
>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 = 37.0 bits (84), Expect = 0.048, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREIR--DTQHKHNHKFIEFYDIRAAETALRTLNRS 422
L + NL ++ EE++ IFG YG IR+IR +T ++ + DI A+ A L+
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF 80
Query: 423 DVAGKQI 429
+V + +
Sbjct: 81 NVCNRYL 87
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 37.0 bits (84), Expect = 0.049, Method: Composition-based stats.
Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 15/86 (17%)
Query: 274 EHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK------HRGFVMISYYDIRAA 327
+H + LF+ I N+++ +LK LFE+FG I + T K H+G ++Y + +A
Sbjct: 10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYEL-TVLKDRFTGMHKGCAFLTYCERESA 68
Query: 328 RNAMKALQ--------NKPLRRRKLD 345
A AL N+P++ + D
Sbjct: 69 LKAQSALHEQKTLPGMNRPIQVKPAD 94
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 37.0 bits (84), Expect = 0.050, Method: Composition-based stats.
Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 8/92 (8%)
Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHR--------GFVMISYYDI 324
G S LF++N+N + + LK +F + G I++ + K GF + Y
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 325 RAARNAMKALQNKPLRRRKLDIHYSIPKDNPS 356
A+ A+K LQ + KL++ S P+
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEVRISERATKPA 92
>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 = 37.0 bits (84), Expect = 0.051, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 10/73 (13%)
Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIY-------TACKHRGFVMISYYDIRAARN 329
S TL+V N++ + ++ LF + GDI+ I TAC GF + YY A N
Sbjct: 18 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTAC---GFCFVEYYSRADAEN 74
Query: 330 AMKALQNKPLRRR 342
AM+ + L R
Sbjct: 75 AMRYINGTRLDDR 87
Score = 32.0 bits (71), Expect = 1.6, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 4/73 (5%)
Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK----FIEFYDIRAAETALRTL 419
TL V NL + E+++++F G+I++I K F+E+Y AE A+R +
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYI 79
Query: 420 NRSDVAGKQIKLE 432
N + + + I+ +
Sbjct: 80 NGTRLDDRIIRTD 92
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 37.0 bits (84), Expect = 0.054, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 30/64 (46%), Gaps = 8/64 (12%)
Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMK 332
R L+V + V+D L A F FGDI I Y KHRGF + + A +A
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELAEDAAA 120
Query: 333 ALQN 336
A+ N
Sbjct: 121 AIDN 124
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 37.0 bits (84), Expect = 0.054, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 3/85 (3%)
Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK 337
+ LFVRN+ + V + L+ F QFG + + K + + I + + A AM+ + K
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVK---KLKDYAFIHFDERDGAVKAMEEMNGK 68
Query: 338 PLRRRKLDIHYSIPKDNPSEKDANQ 362
L ++I ++ P D ++ Q
Sbjct: 69 DLEGENIEIVFAKPPDQKRKERKAQ 93
>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 = 37.0 bits (84), Expect = 0.061, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 30/64 (46%), Gaps = 8/64 (12%)
Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMK 332
R L+V + V+D L A F FGDI I Y KHRGF + + A +A
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELAEDAAA 64
Query: 333 ALQN 336
A+ N
Sbjct: 65 AIDN 68
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 36.6 bits (83), Expect = 0.063, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 5/79 (6%)
Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMK 332
R L+V + V+D L A F FGDI I Y KHRGF + + A A+
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 333 ALQNKPLRRRKLDIHYSIP 351
+ L R + ++ + P
Sbjct: 73 NMNESELFGRTIRVNLAKP 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 = 36.6 bits (83), Expect = 0.063, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 30/64 (46%), Gaps = 8/64 (12%)
Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMK 332
R L+V + V+D L A F FGDI I Y KHRGF + + A +A
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELAEDAAA 59
Query: 333 ALQN 336
A+ N
Sbjct: 60 AIDN 63
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 36.6 bits (83), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 42/81 (51%), Gaps = 5/81 (6%)
Query: 365 LVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRTL 419
L+V + ++V +L Q+F YG I + R+T+ + F++F +A+ A+ L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 420 NRSDVAGKQIKLEASRPGGAR 440
N ++ K++K+ + G R
Sbjct: 105 NGFNILNKRLKVALAASGHQR 125
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 36.6 bits (83), Expect = 0.065, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 40/79 (50%), Gaps = 8/79 (10%)
Query: 262 SAGSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK------HRG 315
S+GS G+ P + S+ L VRNI E++ LF FG+++T+ K HRG
Sbjct: 2 SSGSS-GQVPKKQTTSKIL-VRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG 59
Query: 316 FVMISYYDIRAARNAMKAL 334
F + + + A+ A AL
Sbjct: 60 FGFVDFITKQDAKKAFNAL 78
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 36.6 bits (83), Expect = 0.069, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 42/84 (50%), Gaps = 5/84 (5%)
Query: 361 NQGTLVVFNLDSSVSTEELHQIFGIYGEIRE---IRD--TQHKHNHKFIEFYDIRAAETA 415
++ L+V L +++ +E +FG G+I +RD T + F+ + D A+ A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 416 LRTLNRSDVAGKQIKLEASRPGGA 439
+ TLN + K IK+ +RP A
Sbjct: 63 INTLNGLKLQTKTIKVSYARPSSA 86
Score = 29.6 bits (65), Expect = 9.3, Method: Composition-based stats.
Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 5/77 (6%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTI-----YTACKHRGFVMISYYDIRAARNAMKAL 334
L V + N+ E K+LF GDI + + G+ ++Y D A A+ L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 335 QNKPLRRRKLDIHYSIP 351
L+ + + + Y+ P
Sbjct: 67 NGLKLQTKTIKVSYARP 83
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 36.6 bits (83), Expect = 0.080, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 3/70 (4%)
Query: 354 NPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEI---REIRDTQHKHNHKFIEFYDIR 410
+PS + + G + + NLD S+ + L+ F +G I + + D + F+ F
Sbjct: 3 DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQE 62
Query: 411 AAETALRTLN 420
AAE A+ +N
Sbjct: 63 AAERAIEKMN 72
Score = 31.6 bits (70), Expect = 2.5, Method: Composition-based stats.
Identities = 15/68 (22%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKH---RGFVMISYYDIRAARNAMKALQN 336
+F++N++ ++++ L F FG+I + C +G+ + + AA A++ +
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 337 KPLRRRKL 344
L RK+
Sbjct: 74 MLLNDRKV 81
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 36.2 bits (82), Expect = 0.081, Method: Composition-based stats.
Identities = 28/85 (32%), Positives = 42/85 (49%), Gaps = 6/85 (7%)
Query: 272 YGE-HPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNA 330
YG+ +P+ L+V + N + L F++FG IRTI K F I Y + AA+ A
Sbjct: 11 YGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTI-DHVKGDSFAYIQYESLDAAQAA 69
Query: 331 MKALQNKPL----RRRKLDIHYSIP 351
++ PL RR ++D S P
Sbjct: 70 CAKMRGFPLGGPDRRLRVDFAKSGP 94
>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 = 36.2 bits (82), Expect = 0.094, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 11/74 (14%)
Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIY--------TACKHRGFVMISYYDIRAAR 328
S TL+V N++ + ++ LF + GDI+ I TAC GF + YY A
Sbjct: 39 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTAC---GFCFVEYYSRADAE 95
Query: 329 NAMKALQNKPLRRR 342
NAM+ + L R
Sbjct: 96 NAMRYINGTRLDDR 109
Score = 31.6 bits (70), Expect = 2.0, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHK-----FIEFYDIRAAETALRT 418
TL V NL + E+++++F G+I++I K F+E+Y AE A+R
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 419 LNRSDVAGKQIKLE 432
+N + + + I+ +
Sbjct: 101 INGTRLDDRIIRTD 114
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 35.4 bits (80), Expect = 0.17, Method: Composition-based stats.
Identities = 39/161 (24%), Positives = 59/161 (36%), Gaps = 31/161 (19%)
Query: 269 EHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHRGFVMI 319
E P R LF+ ++ D L++ FEQ+G + T C + RGF +
Sbjct: 3 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFV 58
Query: 320 SYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ-------GTLVVFNLDS 372
+Y + AM A R K+D PK S +D+ + + V +
Sbjct: 59 TYATVEEVDAAMNA------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE 112
Query: 373 SVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYD 408
L F YG+I I R + K F+ F D
Sbjct: 113 DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 153
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 35.0 bits (79), Expect = 0.18, Method: Composition-based stats.
Identities = 39/161 (24%), Positives = 59/161 (36%), Gaps = 31/161 (19%)
Query: 269 EHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHRGFVMI 319
E P R LF+ ++ D L++ FEQ+G + T C + RGF +
Sbjct: 5 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFV 60
Query: 320 SYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ-------GTLVVFNLDS 372
+Y + AM A R K+D PK S +D+ + + V +
Sbjct: 61 TYATVEEVDAAMNA------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE 114
Query: 373 SVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYD 408
L F YG+I I R + K F+ F D
Sbjct: 115 DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 155
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 35.0 bits (79), Expect = 0.19, Method: Composition-based stats.
Identities = 40/166 (24%), Positives = 60/166 (36%), Gaps = 31/166 (18%)
Query: 264 GSVVGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHR 314
G E P R LF+ ++ D L++ FEQ+G + T C + R
Sbjct: 1 GGSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSR 56
Query: 315 GFVMISYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ-------GTLVV 367
GF ++Y + AM A R K+D PK S +D+ + + V
Sbjct: 57 GFGFVTYATVEEVDAAMNA------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFV 110
Query: 368 FNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYD 408
+ L F YG+I I R + K F+ F D
Sbjct: 111 GGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 156
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 35.0 bits (79), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 45/82 (54%), Gaps = 6/82 (7%)
Query: 280 LFVRNINSNVEDSELKALFEQFG---DIRTIYTACKH--RGFVMISYYDIRAARNAMKAL 334
+FV I N ++EL+ F++FG ++ IY A K RGF I++ D ++ A+ +
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-M 71
Query: 335 QNKPLRRRKLDIHYSIPKDNPS 356
+ +K+++ + P+D+ S
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSKS 93
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 35.0 bits (79), Expect = 0.21, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKPL 339
LFVR +V++SEL +F FG ++ + GF + + + +A A++ + K
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSF 63
Query: 340 RRRKLDIHYS 349
+ L++ YS
Sbjct: 64 ANQPLEVVYS 73
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 35.0 bits (79), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 5/71 (7%)
Query: 365 LVVFNLDSSVSTEELHQIFGIYGEI---REIRD--TQHKHNHKFIEFYDIRAAETALRTL 419
+ V +L ++TE++ F +G+I R ++D T + F+ FY+ AE A+ +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 420 NRSDVAGKQIK 430
+ G+QI+
Sbjct: 78 GGQWLGGRQIR 88
>pdb|2A3J|A Chain A, Structure Of Urndesign, A Complete Computational Redesign
Of Human U1a Protein
Length = 127
Score = 35.0 bits (79), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 28/105 (26%), Positives = 45/105 (42%), Gaps = 9/105 (8%)
Query: 267 VGEHPYGEHPSRTLFVRNINSNVEDSELKALFEQF----GDIRTIYTACK--HRGFVMIS 320
+G P PS+ + + NIN V +L+AL GDI I + G I
Sbjct: 19 LGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIV 78
Query: 321 YYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQGTL 365
+ +A+ ++A Q P + L I +S + P + A G+L
Sbjct: 79 FATQESAQAFVEAFQGYPFQGNPLVITFS---ETPQSQVAEDGSL 120
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 35.0 bits (79), Expect = 0.23, Method: Composition-based stats.
Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 5/92 (5%)
Query: 271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDI---RTIY--TACKHRGFVMISYYDIR 325
P + R++FV NI + +LK +F + G + R +Y K +G+ Y D
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 326 AARNAMKALQNKPLRRRKLDIHYSIPKDNPSE 357
A +AM+ L + R L + + + N E
Sbjct: 62 TALSAMRNLNGREFSGRALRVDNAASEKNKEE 93
Score = 31.6 bits (70), Expect = 2.4, Method: Composition-based stats.
Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 5/79 (6%)
Query: 359 DANQGTLVVFNLDSSVSTEELHQIFGIYGEIREIR-----DTQHKHNHKFIEFYDIRAAE 413
D + ++ V N+ + E+L IF G + R +T + F E+ D A
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64
Query: 414 TALRTLNRSDVAGKQIKLE 432
+A+R LN + +G+ ++++
Sbjct: 65 SAMRNLNGREFSGRALRVD 83
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 34.7 bits (78), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 40/72 (55%), Gaps = 6/72 (8%)
Query: 280 LFVRNINSN-VEDSELKALFEQFGDIRTIYTACK-HRGFVMISYYDIRAARNAMKALQNK 337
+F+ N+N+ V+ S+++ +F ++G + C H+G+ + Y + R AR A+ +
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRV----AGCSVHKGYAFVQYSNERHARAAVLGENGR 85
Query: 338 PLRRRKLDIHYS 349
L + LDI+ +
Sbjct: 86 VLAGQTLDINMA 97
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 34.7 bits (78), Expect = 0.25, Method: Composition-based stats.
Identities = 39/161 (24%), Positives = 59/161 (36%), Gaps = 31/161 (19%)
Query: 269 EHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHRGFVMI 319
E P R LF+ ++ D L++ FEQ+G + T C + RGF +
Sbjct: 4 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFV 59
Query: 320 SYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ-------GTLVVFNLDS 372
+Y + AM A R K+D PK S +D+ + + V +
Sbjct: 60 TYATVEEVDAAMNA------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE 113
Query: 373 SVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYD 408
L F YG+I I R + K F+ F D
Sbjct: 114 DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 154
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 34.7 bits (78), Expect = 0.25, Method: Composition-based stats.
Identities = 39/161 (24%), Positives = 59/161 (36%), Gaps = 31/161 (19%)
Query: 269 EHPYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHRGFVMI 319
E P R LF+ ++ D L++ FEQ+G + T C + RGF +
Sbjct: 5 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFV 60
Query: 320 SYYDIRAARNAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ-------GTLVVFNLDS 372
+Y + AM A R K+D PK S +D+ + + V +
Sbjct: 61 TYATVEEVDAAMNA------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE 114
Query: 373 SVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYD 408
L F YG+I I R + K F+ F D
Sbjct: 115 DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 155
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 34.7 bits (78), Expect = 0.27, Method: Composition-based stats.
Identities = 32/156 (20%), Positives = 62/156 (39%), Gaps = 17/156 (10%)
Query: 281 FVRNINSNVEDSELKALFEQFGDIRTI-------YTACKHRGFVMISYYDIRAARNAMKA 333
FV + + +L+ LFEQ+G + I + +G +++Y +AA A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 334 LQNKPLRRRKLDIHYSI---PKDNPSEKDANQGTLVVFNLDSSVSTEELHQIFGIYGEIR 390
L N + H+ I P D+ L + + + ++ F +G+I
Sbjct: 67 LHNXKVLP---GXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIE 123
Query: 391 EIRDTQH----KHNHKFIEFYDIRAAETALRTLNRS 422
E R + F+ F A+TA++ +++
Sbjct: 124 ECRILRGPDGLSRGCAFVTFTTRAXAQTAIKAXHQA 159
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 34.7 bits (78), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTAC-----KHRGFVMISYYDIRAARNAMKAL 334
L+V +++ N+ + L+ +FE FG I +I + +G+ I++ D A+ A++ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 335 QNKPLRRRKLDI 346
L R + +
Sbjct: 89 NGFELAGRPMKV 100
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 34.7 bits (78), Expect = 0.28, Method: Composition-based stats.
Identities = 37/152 (24%), Positives = 57/152 (37%), Gaps = 31/152 (20%)
Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTAC---------KHRGFVMISYYDIRAAR 328
R LF+ ++ D L++ FEQ+G + T C + RGF ++Y +
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTL----TDCVVMRDPNTKRSRGFGFVTYATVEEVD 62
Query: 329 NAMKALQNKPLRRRKLDIHYSIPKDNPSEKDANQ-------GTLVVFNLDSSVSTEELHQ 381
AM A R K+D PK S +D+ + + V + L
Sbjct: 63 AAMNA------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRD 116
Query: 382 IFGIYGEIREI-----RDTQHKHNHKFIEFYD 408
F YG+I I R + K F+ F D
Sbjct: 117 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 148
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 33.5 bits (75), Expect = 0.53, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK------HRGFVMISYYDI 324
P +H + LFV I +++ +LK LFE+FG I + T K H+G ++Y
Sbjct: 9 PMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYEL-TVLKDRLTGLHKGCAFLTYCAR 67
Query: 325 RAARNAMKALQNK 337
+A A AL +
Sbjct: 68 DSALKAQSALHEQ 80
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 33.5 bits (75), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 19/88 (21%), Positives = 40/88 (45%), Gaps = 6/88 (6%)
Query: 273 GEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACK------HRGFVMISYYDIRA 326
G S +F+ N++ +++ L F FG I + +G+ I++ A
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 327 ARNAMKALQNKPLRRRKLDIHYSIPKDN 354
+ A++A+ + L R + + Y+ KD+
Sbjct: 61 SDAAIEAMNGQYLCNRPITVSYAFKKDS 88
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 33.5 bits (75), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 43/90 (47%), Gaps = 5/90 (5%)
Query: 268 GEHPYGEHPS--RTLFVRNINSNVEDSELKALFEQFG---DIRTIYTACKHRGFVMISYY 322
G H E+ S + L V NI D +L+ +F QFG D+ I+ +GF +++
Sbjct: 18 GSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFE 77
Query: 323 DIRAARNAMKALQNKPLRRRKLDIHYSIPK 352
+ A A + L + RK++++ + +
Sbjct: 78 NSADADRAREKLHGTVVEGRKIEVNNATAR 107
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 33.5 bits (75), Expect = 0.65, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH-----RGFVMISYYDIRAARNAMKA 333
TL V N+ L+ +FE++G + +Y + RGF + ++D R A++A A
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 334 LQNKPLRRRKLDIH 347
+ L R+L +
Sbjct: 75 MDGAELDGRELRVQ 88
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 33.1 bits (74), Expect = 0.83, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 279 TLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNKP 338
TL+V + + +++L+ F QFG+IRTI T + + I + +AA A + NK
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTI-TVVQRQQCAFIQFATRQAAEVAAEKSFNKL 72
Query: 339 L-RRRKLDIHY 348
+ R+L++ +
Sbjct: 73 IVNGRRLNVKW 83
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 33.1 bits (74), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 3/78 (3%)
Query: 278 RTLFVRNINSNVEDSELKALFEQFG---DIRTIYTACKHRGFVMISYYDIRAARNAMKAL 334
+ L V NI D +L+ +F QFG D+ I+ +GF +++ + A A + L
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 75
Query: 335 QNKPLRRRKLDIHYSIPK 352
+ RK++++ + +
Sbjct: 76 HGTVVEGRKIEVNNATAR 93
>pdb|2GCJ|A Chain A, Crystal Structure Of The Pob3 Middle Domain
pdb|2GCJ|B Chain B, Crystal Structure Of The Pob3 Middle Domain
pdb|2GCJ|C Chain C, Crystal Structure Of The Pob3 Middle Domain
pdb|2GCJ|D Chain D, Crystal Structure Of The Pob3 Middle Domain
Length = 261
Score = 32.0 bits (71), Expect = 1.6, Method: Composition-based stats.
Identities = 29/114 (25%), Positives = 45/114 (39%), Gaps = 17/114 (14%)
Query: 763 PMMSMQTSFDSSNERMRNLSYRRNESNSNHADKKQYE----LDIDRILRGDDSRTTLMIK 818
P + +Q D E NL E N KKQY+ + + +L+G R +
Sbjct: 97 PFLVLQFQKDEETEVQLNLEDEDYEENYKDKLKKQYDAKTHIVLSHVLKGLTDRRVI--- 153
Query: 819 NIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPF 872
+P +Y SK A+ + ++Y P+D AF + P IPF
Sbjct: 154 -VPGEYKSKYDQCAVSCSFKANEGYLY-PLD--------NAFFFLTKPTLYIPF 197
>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 = 32.0 bits (71), Expect = 1.7, Method: Composition-based stats.
Identities = 16/71 (22%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 277 SRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH---RGFVMISYYDIRAARNAMKA 333
S +F++N++ ++++ L F FG+I + C +G+ + + AA A++
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK 64
Query: 334 LQNKPLRRRKL 344
+ L RK+
Sbjct: 65 MNGMLLNDRKV 75
>pdb|2GCL|A Chain A, Structure Of The Pob3 Middle Domain
pdb|2GCL|B Chain B, Structure Of The Pob3 Middle Domain
Length = 261
Score = 32.0 bits (71), Expect = 1.8, Method: Composition-based stats.
Identities = 29/114 (25%), Positives = 45/114 (39%), Gaps = 17/114 (14%)
Query: 763 PMMSMQTSFDSSNERMRNLSYRRNESNSNHADKKQYE----LDIDRILRGDDSRTTLMIK 818
P + +Q D E NL E N KKQY+ + + +L+G R +
Sbjct: 97 PFLVLQFQKDEETEVQLNLEDEDYEENYKDKLKKQYDAKTHIVLSHVLKGLTDRRVI--- 153
Query: 819 NIPNKYTSKMLLAAIDEHCRGTYDFIYLPIDFKNKCNVGYAFINMIDPRQIIPF 872
+P +Y SK A+ + ++Y P+D AF + P IPF
Sbjct: 154 -VPGEYKSKYDQCAVSCSFKANEGYLY-PLD--------NAFFFLTKPTLYIPF 197
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 32.0 bits (71), Expect = 2.0, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 6/70 (8%)
Query: 370 LDSSVSTEELHQIFGIYGEIREIR---DTQHKH---NHKFIEFYDIRAAETALRTLNRSD 423
L +V+ + + +IF YG+I+ I + H H + ++EF + AE AL+ ++
Sbjct: 12 LTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQ 71
Query: 424 VAGKQIKLEA 433
+ G++I A
Sbjct: 72 IDGQEITATA 81
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 31.2 bits (69), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSD 423
T+ + S ++ + + Q F +G+I EIR K + F+ F +A A+ ++N +
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK-GYSFVRFSTHESAAHAIVSVNGTT 85
Query: 424 VAGKQIKL 431
+ G +K
Sbjct: 86 IEGHVVKC 93
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 31.2 bits (69), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 7/64 (10%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTA-------CKHRGFVMISYYDIRAARNAMK 332
+FV + + +L+ LFEQ+G + I + +G +++Y +AA A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 333 ALQN 336
AL N
Sbjct: 66 ALHN 69
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 30.8 bits (68), Expect = 3.6, Method: Composition-based stats.
Identities = 10/30 (33%), Positives = 22/30 (73%)
Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTI 307
+T+F+RN++ + E+ L + +QFGD++ +
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYV 45
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 30.8 bits (68), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 418
L VF L + +L ++F YG I ++ + ++ F+ F ++ A+ A
Sbjct: 48 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
Query: 419 LNRSDVAGKQIKLEAS 434
N ++ G++I+++ S
Sbjct: 108 ANGMELDGRRIRVDFS 123
Score = 30.8 bits (68), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 41/82 (50%), Gaps = 5/82 (6%)
Query: 276 PSRTLFVRNINSNVEDSELKALFEQFG---DIRTIY--TACKHRGFVMISYYDIRAARNA 330
P+ L V ++ + +L+ +F ++G D+ +Y + + RGF + + ++ A+ A
Sbjct: 45 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104
Query: 331 MKALQNKPLRRRKLDIHYSIPK 352
+ L R++ + +SI K
Sbjct: 105 KERANGMELDGRRIRVDFSITK 126
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 30.8 bits (68), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 373 SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE 432
+VS E+L +IF YG I +I K+ FI+F + ++ A+ ++ GK++ LE
Sbjct: 22 NVSKEDLFRIFSPYGHIMQINI---KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE 78
Query: 433 ASRPGGARRF 442
S +F
Sbjct: 79 VSSSNARPQF 88
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 30.8 bits (68), Expect = 4.3, Method: Composition-based stats.
Identities = 20/82 (24%), Positives = 41/82 (50%), Gaps = 6/82 (7%)
Query: 275 HPSRTLFVRNINSNVEDSELKALFEQFGDIR----TIYTACKHRGFVMISYYDIRAARNA 330
PS+TLFV+ ++ + + LK F+ G +R T +GF + + A+ A
Sbjct: 13 QPSKTLFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAA 70
Query: 331 MKALQNKPLRRRKLDIHYSIPK 352
+A+++ + K+ + ++ PK
Sbjct: 71 KEAMEDGEIDGNKVTLDWAKPK 92
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 30.4 bits (67), Expect = 4.7, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 278 RTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKHRGFVMISYYDIRAARNAMKALQNK 337
+ LFVRN+ + V + L+ F +FG + + K + + + + D AA AM + K
Sbjct: 16 KVLFVRNLATTVTEEILEKSFSEFGKLERVK---KLKDYAFVHFEDRGAAVKAMDEMNGK 72
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 30.4 bits (67), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 418
L VF L + +L ++F YG I ++ + ++ F+ F ++ A+ A
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 419 LNRSDVAGKQIKLEASRPG 437
N ++ G++I++ G
Sbjct: 77 ANGMELDGRRIRVSGPSSG 95
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 30.4 bits (67), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 364 TLVVFNLDSSVSTEELHQIFGIYGEIREI-----RDTQHKHNHKFIEFYDIRAAETALRT 418
L VF L + +L ++F YG I ++ + ++ F+ F ++ A+ A
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 419 LNRSDVAGKQIKLEAS 434
N ++ G++I+++ S
Sbjct: 77 ANGMELDGRRIRVDFS 92
Score = 30.4 bits (67), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 41/82 (50%), Gaps = 5/82 (6%)
Query: 276 PSRTLFVRNINSNVEDSELKALFEQFG---DIRTIY--TACKHRGFVMISYYDIRAARNA 330
P+ L V ++ + +L+ +F ++G D+ +Y + + RGF + + ++ A+ A
Sbjct: 14 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73
Query: 331 MKALQNKPLRRRKLDIHYSIPK 352
+ L R++ + +SI K
Sbjct: 74 KERANGMELDGRRIRVDFSITK 95
>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 = 30.0 bits (66), Expect = 6.5, Method: Composition-based stats.
Identities = 12/57 (21%), Positives = 32/57 (56%), Gaps = 4/57 (7%)
Query: 271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH----RGFVMISYYD 323
P G+ T+FV I+ ++++E+++ F ++G ++ + +G+ +S+Y+
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYN 59
>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 = 30.0 bits (66), Expect = 6.6, Method: Composition-based stats.
Identities = 19/90 (21%), Positives = 46/90 (51%), Gaps = 6/90 (6%)
Query: 271 PYGEHPSRTLFVRNINSNVEDSELKALFEQFGDIRTIYTACKH----RGFVMISYYDIRA 326
P G+ T+FV I+ ++++E+++ F ++G ++ + +G+ +S+Y+
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVD 62
Query: 327 ARNAMKALQNKPLRRRKLDIHYSIPKDNPS 356
+ +++ N +KL + +I K N S
Sbjct: 63 VQKIVESQIN--FHGKKLKLGPAIRKQNLS 90
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 30.0 bits (66), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 373 SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE 432
+VS E+L +IF YG I +I K+ FI+F + ++ A+ ++ GK++ LE
Sbjct: 34 NVSKEDLFRIFSPYGHIMQI---NIKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE 90
Query: 433 AS 434
S
Sbjct: 91 VS 92
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 30.0 bits (66), Expect = 7.3, Method: Composition-based stats.
Identities = 17/78 (21%), Positives = 37/78 (47%), Gaps = 5/78 (6%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHR-----GFVMISYYDIRAARNAMKAL 334
LFV +I+ ++ E++ F +G+I+ I+ R G+ ++ Y + A A +AL
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 335 QNKPLRRRKLDIHYSIPK 352
+ + + + + K
Sbjct: 89 NGAEIMGQTIQVDWCFVK 106
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 29.6 bits (65), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 373 SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE 432
+VS E+L +IF YG I +I K+ FI+F + ++ A+ ++ GK++ LE
Sbjct: 14 NVSKEDLFRIFSPYGHIMQI---NIKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE 70
Query: 433 AS 434
S
Sbjct: 71 VS 72
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 29.6 bits (65), Expect = 9.7, Method: Composition-based stats.
Identities = 17/78 (21%), Positives = 37/78 (47%), Gaps = 5/78 (6%)
Query: 280 LFVRNINSNVEDSELKALFEQFGDIRTIYTACKHR-----GFVMISYYDIRAARNAMKAL 334
LFV +I+ ++ E++ F +G+I+ I+ R G+ ++ Y + A A +AL
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 335 QNKPLRRRKLDIHYSIPK 352
+ + + + + K
Sbjct: 135 NGAEIMGQTIQVDWCFVK 152
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 29.3 bits (64), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 373 SVSTEELHQIFGIYGEIREIRDTQHKHNHKFIEFYDIRAAETALRTLNRSDVAGKQIKLE 432
+VS E+L +IF YG I +I K+ FI+F + ++ A+ ++ GK++ LE
Sbjct: 34 NVSKEDLFRIFSPYGHIMQI---NIKNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE 90
Query: 433 AS 434
S
Sbjct: 91 VS 92
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
0.316 0.133 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 29,746,346
Number of Sequences: 62578
Number of extensions: 1262762
Number of successful extensions: 3038
Number of sequences better than 100.0: 139
Number of HSP's better than 100.0 without gapping: 27
Number of HSP's successfully gapped in prelim test: 112
Number of HSP's that attempted gapping in prelim test: 2881
Number of HSP's gapped (non-prelim): 216
length of query: 987
length of database: 14,973,337
effective HSP length: 108
effective length of query: 879
effective length of database: 8,214,913
effective search space: 7220908527
effective search space used: 7220908527
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: 56 (26.2 bits)