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= 033227
(124 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 160 bits (405), Expect = 2e-40, Method: Compositional matrix adjust.
Identities = 72/121 (59%), Positives = 91/121 (75%)
Query: 1 MATIPLRKGNARLPPEVNRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTA 60
MA ++ N RLPPEVNR+LY+RNLP+ I++EEMYDIFGKYG IRQIR+G++ +TRGTA
Sbjct: 1 MAMQAAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTA 60
Query: 61 FVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQTXXXXXXXXXXXXXELAKMQEKYGVS 120
+VVYEDI+DAK A DHLSGFNV NRYL+VLYY +L ++EKYG++
Sbjct: 61 YVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGIN 120
Query: 121 T 121
T
Sbjct: 121 T 121
>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 = 157 bits (398), Expect = 1e-39, Method: Compositional matrix adjust.
Identities = 71/121 (58%), Positives = 90/121 (74%)
Query: 1 MATIPLRKGNARLPPEVNRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTA 60
MA ++ N RLPPEVNR+L +RNLP+ I++EEMYDIFGKYG IRQIR+G++ +TRGTA
Sbjct: 1 MAMQAAKRANIRLPPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTA 60
Query: 61 FVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQTXXXXXXXXXXXXXELAKMQEKYGVS 120
+VVYEDI+DAK A DHLSGFNV NRYL+VLYY +L ++EKYG++
Sbjct: 61 YVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGIN 120
Query: 121 T 121
T
Sbjct: 121 T 121
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 156 bits (394), Expect = 3e-39, Method: Compositional matrix adjust.
Identities = 70/110 (63%), Positives = 88/110 (80%)
Query: 12 RLPPEVNRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAK 71
RLPPEVNR+LY+RNLP+ I++EEMYDIFGKYG IRQIR+G++ +TRGTA+VVYEDI+DAK
Sbjct: 2 RLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAK 61
Query: 72 TAVDHLSGFNVANRYLIVLYYQQTXXXXXXXXXXXXXELAKMQEKYGVST 121
AVDHLSGFNV+NRYL+VLYY +L ++EKYG++T
Sbjct: 62 NAVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINT 111
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 146 bits (369), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 64/86 (74%), Positives = 77/86 (89%)
Query: 8 KGNARLPPEVNRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDI 67
+ N RLPPEVNR+LY+RNLP+ I++EEMYDIFGKYG IRQIR+G++ +TRGTA+VVYEDI
Sbjct: 2 RANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDI 61
Query: 68 YDAKTAVDHLSGFNVANRYLIVLYYQ 93
+DAK A DHLSGFNV NRYL+VLYY
Sbjct: 62 FDAKNACDHLSGFNVCNRYLVVLYYN 87
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 5/74 (6%)
Query: 18 NRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHL 77
N L+VR P ++ E+ +IFG +G +++++I G AFV +E+ A A++ +
Sbjct: 31 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI-----LNGFAFVEFEEAESAAKAIEEV 85
Query: 78 SGFNVANRYLIVLY 91
G + AN+ L V+Y
Sbjct: 86 HGKSFANQPLEVVY 99
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 5/74 (6%)
Query: 18 NRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHL 77
N L+VR P ++ E+ +IFG +G +++++I G AFV +E+ A A++ +
Sbjct: 4 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI-----LNGFAFVEFEEAESAAKAIEEV 58
Query: 78 SGFNVANRYLIVLY 91
G + AN+ L V+Y
Sbjct: 59 HGKSFANQPLEVVY 72
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 48.9 bits (115), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 37/57 (64%), Gaps = 4/57 (7%)
Query: 13 LPPEVNRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTR---GTAFVVYED 66
L P + V YV NLPF++++ ++Y IF KYG + ++ I KDTR G AF+++ D
Sbjct: 12 LAPSKSTV-YVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLD 67
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 47.0 bits (110), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 3/78 (3%)
Query: 15 PEVNRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAK 71
P+V R L V +P + ++ +F +YG I ++I ++T RG FV ++ A+
Sbjct: 39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQ 98
Query: 72 TAVDHLSGFNVANRYLIV 89
A+ L+GFN+ N+ L V
Sbjct: 99 QAIAGLNGFNILNKRLKV 116
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 39/61 (63%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHLSGF 80
+YV NLP +I ++++ D+F KYGAIR I + + + AFV +ED DA+ AV G+
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 84
Query: 81 N 81
+
Sbjct: 85 D 85
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 46.2 bits (108), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 3/72 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVDHL 77
LYV +L FNI+ + + IF +G I I++ +T +G F+ + D AK A++ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 78 SGFNVANRYLIV 89
+GF +A R + V
Sbjct: 89 NGFELAGRPMKV 100
>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 = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 4/78 (5%)
Query: 18 NRVLYVRNLPFNISSEEM----YDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTA 73
N +Y+ NL I +E+ Y IF ++G I I + S RG AFV+++++ A A
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 68
Query: 74 VDHLSGFNVANRYLIVLY 91
+ + GF ++ + + Y
Sbjct: 69 LRSMQGFPFYDKPMRIQY 86
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 45.4 bits (106), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 6/83 (7%)
Query: 15 PEV--NRVLYVRNLPFNISSEEM----YDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIY 68
PE N +Y+ NL I +E+ Y IF ++G I I + S RG AFV+++++
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVS 62
Query: 69 DAKTAVDHLSGFNVANRYLIVLY 91
A A+ + GF ++ + + Y
Sbjct: 63 SATNALRSMQGFPFYDKPMRIQY 85
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 45.1 bits (105), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 42/72 (58%), Gaps = 3/72 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVDHL 77
L+V L F+ + + + +F KYG I ++ + ++T RG FV +E+I DAK A+ +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 78 SGFNVANRYLIV 89
+G +V R + V
Sbjct: 75 NGKSVDGRQIRV 86
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 15 PEV--NRVLYVRNLPFNISSEEM----YDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIY 68
PE N +Y+ NL I +E+ Y IF ++G I I + S RG AFV+++++
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVS 63
Query: 69 DAKTAVDHLSGF 80
A A+ + GF
Sbjct: 64 SATNALRSMQGF 75
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The
Second Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/61 (44%), Positives = 36/61 (59%), Gaps = 3/61 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVDHL 77
LYV NLP I+ +++ IFGKYG+I Q I K T RG AFV Y +A+ A+ L
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 78 S 78
+
Sbjct: 76 N 76
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/61 (44%), Positives = 36/61 (59%), Gaps = 3/61 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVDHL 77
LYV NLP I+ +++ IFGKYG+I Q I K T RG AFV Y +A+ A+ L
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 78 S 78
+
Sbjct: 152 N 152
Score = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 37/77 (48%), Gaps = 3/77 (3%)
Query: 18 NRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTR---GTAFVVYEDIYDAKTAV 74
N L V LP +++ E+Y +F G I RI T G AFV + D++ A+
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 75 DHLSGFNVANRYLIVLY 91
L+G V N+ L V Y
Sbjct: 63 KVLNGITVRNKRLKVSY 79
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/61 (44%), Positives = 36/61 (59%), Gaps = 3/61 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVDHL 77
LYV NLP I+ +++ IFGKYG+I Q I K T RG AFV Y +A+ A+ L
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 162
Query: 78 S 78
+
Sbjct: 163 N 163
Score = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 37/81 (45%), Gaps = 3/81 (3%)
Query: 14 PPEVNRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTR---GTAFVVYEDIYDA 70
P N L V LP + + E+Y +F G I RI T G AFV + D+
Sbjct: 10 PRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDS 69
Query: 71 KTAVDHLSGFNVANRYLIVLY 91
+ A+ L+G V N+ L V Y
Sbjct: 70 QRAIKVLNGITVRNKRLKVSY 90
>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 = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 45/84 (53%), Gaps = 5/84 (5%)
Query: 11 ARLPPEVNRV--LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGS---SKDTRGTAFVVYE 65
R PP+V + L V NL + S + + +F KYG + + I +K++RG AFV +
Sbjct: 38 GRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFH 97
Query: 66 DIYDAKTAVDHLSGFNVANRYLIV 89
D DA+ A+D + G + R L V
Sbjct: 98 DKRDAEDAMDAMDGAVLDGRELRV 121
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 44/84 (52%), Gaps = 3/84 (3%)
Query: 11 ARLPPEVNRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRI---GSSKDTRGTAFVVYEDI 67
+R P+ N L V L + ++ ++F KYG I + I S+ +RG AFV +E++
Sbjct: 5 SRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 64
Query: 68 YDAKTAVDHLSGFNVANRYLIVLY 91
DAK A + +G + R + V +
Sbjct: 65 DDAKEAKERANGMELDGRRIRVDF 88
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 3/77 (3%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVDHL 77
LYV +L FNI+ + + IF +G I I + DT +G F+ + D A+ A++ L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 78 SGFNVANRYLIVLYYQQ 94
+GF +A R + V + +
Sbjct: 68 NGFELAGRPMRVGHVTE 84
>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 = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 6/83 (7%)
Query: 15 PEV--NRVLYVRNLPFNISSEEM----YDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIY 68
PE N +Y+ NL I +E+ + IF ++G I I + S RG AFV+++++
Sbjct: 1 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 60
Query: 69 DAKTAVDHLSGFNVANRYLIVLY 91
A A+ + GF ++ + + Y
Sbjct: 61 SATNALRSMQGFPFYDKPMRIQY 83
>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 = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 6/83 (7%)
Query: 15 PEV--NRVLYVRNLPFNISSEEM----YDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIY 68
PE N +Y+ NL I +E+ + IF ++G I I + S RG AFV+++++
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 63
Query: 69 DAKTAVDHLSGFNVANRYLIVLY 91
A A+ + GF ++ + + Y
Sbjct: 64 SATNALRSMQGFPFYDKPMRIQY 86
>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 = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 6/83 (7%)
Query: 15 PEV--NRVLYVRNLPFNISSEEM----YDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIY 68
PE N +Y+ NL I +E+ + IF ++G I I + S RG AFV+++++
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 62
Query: 69 DAKTAVDHLSGFNVANRYLIVLY 91
A A+ + GF ++ + + Y
Sbjct: 63 SATNALRSMQGFPFYDKPMRIQY 85
>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 = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 15 PEV--NRVLYVRNLPFNISSEEM----YDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIY 68
PE N +Y+ NL I +E+ + IF ++G I I + S RG AFV+++++
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 63
Query: 69 DAKTAVDHLSGF 80
A A+ + GF
Sbjct: 64 SATNALRSMQGF 75
>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 = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 6/83 (7%)
Query: 15 PEV--NRVLYVRNLPFNISSEEM----YDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIY 68
PE N +Y+ NL I +E+ + IF ++G I I + S RG AFV+++++
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 62
Query: 69 DAKTAVDHLSGFNVANRYLIVLY 91
A A+ + GF ++ + + Y
Sbjct: 63 SATNALRSMQGFPFYDKPMRIQY 85
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 3/83 (3%)
Query: 12 RLPPEVNRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRI---GSSKDTRGTAFVVYEDIY 68
R P+ N L V L + ++ ++F KYG I + I S+ +RG AFV +E++
Sbjct: 40 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 99
Query: 69 DAKTAVDHLSGFNVANRYLIVLY 91
DAK A + +G + R + V +
Sbjct: 100 DAKEAKERANGMELDGRRIRVDF 122
>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 = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 6/83 (7%)
Query: 15 PEV--NRVLYVRNLPFNISSEEM----YDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIY 68
PE N +Y+ NL I +E+ + IF ++G I I + S RG AFV+++++
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 62
Query: 69 DAKTAVDHLSGFNVANRYLIVLY 91
A A+ + GF ++ + + Y
Sbjct: 63 SATNALRSMQGFPFYDKPMRIQY 85
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 3/83 (3%)
Query: 12 RLPPEVNRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRI---GSSKDTRGTAFVVYEDIY 68
R P+ N L V L + ++ ++F KYG I + I S+ +RG AFV +E++
Sbjct: 9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
Query: 69 DAKTAVDHLSGFNVANRYLIVLY 91
DAK A + +G + R + V +
Sbjct: 69 DAKEAKERANGMELDGRRIRVDF 91
>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 = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 4/67 (5%)
Query: 18 NRVLYVRNLPFNISSEEM----YDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTA 73
N +Y+ NL I +E+ + IF ++G I I + S RG AFV+++++ A A
Sbjct: 5 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 64
Query: 74 VDHLSGF 80
+ + GF
Sbjct: 65 LRSMQGF 71
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 3/81 (3%)
Query: 12 RLPPEVNRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRI---GSSKDTRGTAFVVYEDIY 68
R P+ N L V L + ++ ++F KYG I + I S+ +RG AFV +E++
Sbjct: 9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
Query: 69 DAKTAVDHLSGFNVANRYLIV 89
DAK A + +G + R + V
Sbjct: 69 DAKEAKERANGMELDGRRIRV 89
>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 = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 4/67 (5%)
Query: 18 NRVLYVRNLPFNISSEEM----YDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTA 73
N +Y+ NL I +E+ + IF ++G I I + S RG AFV+++++ A A
Sbjct: 4 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 63
Query: 74 VDHLSGF 80
+ + GF
Sbjct: 64 LRSMQGF 70
>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 = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 4/67 (5%)
Query: 18 NRVLYVRNLPFNISSEEM----YDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTA 73
N +Y+ NL I +E+ + IF ++G I I + S RG AFV+++++ A A
Sbjct: 3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62
Query: 74 VDHLSGF 80
+ + GF
Sbjct: 63 LRSMQGF 69
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition
In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 48/81 (59%), Gaps = 5/81 (6%)
Query: 14 PPEVNRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDA 70
PP +RV+Y+ ++P++ + E++ D+ G + +++ T +G AF+ + D+ +
Sbjct: 2 PP--SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESS 59
Query: 71 KTAVDHLSGFNVANRYLIVLY 91
+AV +L+G+ + +R+L Y
Sbjct: 60 ASAVRNLNGYQLGSRFLKCGY 80
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 42.0 bits (97), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 6/72 (8%)
Query: 15 PEV--NRVLYVRNLPFNISSEEM----YDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIY 68
PE N +Y+ NL I +E+ + IF ++G I I + S RG AFV+++++
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVS 62
Query: 69 DAKTAVDHLSGF 80
A A+ GF
Sbjct: 63 SATNALRSXQGF 74
>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 = 42.0 bits (97), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 6/72 (8%)
Query: 15 PEV--NRVLYVRNLPFNISSEEM----YDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIY 68
PE N +Y+ NL I +E+ + IF ++G I I + S RG AFV+++++
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVS 63
Query: 69 DAKTAVDHLSGF 80
A A+ GF
Sbjct: 64 SATNALRSXQGF 75
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 6/72 (8%)
Query: 15 PEV--NRVLYVRNLPFNISSEEM----YDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIY 68
PE N +Y+ NL I +E+ + IF ++G I I + S RG AFV+++++
Sbjct: 1 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVS 60
Query: 69 DAKTAVDHLSGF 80
A A+ GF
Sbjct: 61 SATNALRSXQGF 72
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 46/77 (59%), Gaps = 3/77 (3%)
Query: 18 NRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAV 74
+RV+Y+ ++P++ + E++ D+ G + +++ T +G AF+ + D+ + +AV
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 75 DHLSGFNVANRYLIVLY 91
+L+G+ + +R+L Y
Sbjct: 62 RNLNGYQLGSRFLKCGY 78
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIR-IGSSKDTRGTAFVVYEDIYDAKTAVDHLSG 79
L+V N+PF ++ +FG++G I + I + + ++G FV +E+ DA A + L G
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 91
Query: 80 FNVANRYLIV 89
V R + V
Sbjct: 92 TVVEGRKIEV 101
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 39/68 (57%), Gaps = 2/68 (2%)
Query: 20 VLYVRNLPFNISSEEMYDIFGKYGAIRQIRIG--SSKDTRGTAFVVYEDIYDAKTAVDHL 77
LYV NL F + E++Y++F K G I++I +G K G FV Y DA+ A+ ++
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYI 79
Query: 78 SGFNVANR 85
+G + +R
Sbjct: 80 NGTRLDDR 87
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 15 PEVNRVL---YVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIY 68
P V+R L +V N+P+ + E++ DIF + G + R+ ++T +G F Y+D
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 69 DAKTAVDHLSGFNVANRYLIV 89
A +A+ +L+G + R L V
Sbjct: 62 TALSAMRNLNGREFSGRALRV 82
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 46/77 (59%), Gaps = 3/77 (3%)
Query: 18 NRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAV 74
+RV+Y+ ++P++ + E++ D+ G + +++ T +G AF+ + D+ + +AV
Sbjct: 3 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 62
Query: 75 DHLSGFNVANRYLIVLY 91
+L+G+ + +R+L Y
Sbjct: 63 RNLNGYQLGSRFLKCGY 79
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIR-IGSSKDTRGTAFVVYEDIYDAKTAVDHLSG 79
L+V N+PF ++ +FG++G I + I + + ++G FV +E+ DA A + L G
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 77
Query: 80 FNVANRYLIV 89
V R + V
Sbjct: 78 TVVEGRKIEV 87
>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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 40/69 (57%), Gaps = 3/69 (4%)
Query: 20 VLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTR---GTAFVVYEDIYDAKTAVDH 76
LYV NL F + E++Y++F K G I++I +G K + G FV Y DA+ A+ +
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 77 LSGFNVANR 85
++G + +R
Sbjct: 101 INGTRLDDR 109
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 6/75 (8%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGT------AFVVYEDIYDAKTAV 74
L+++NL F+ + E + +F K GAI+ I K+ G FV Y+ A+ A+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 75 DHLSGFNVANRYLIV 89
L G V L V
Sbjct: 68 KQLQGHTVDGHKLEV 82
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSK--DTRGTAFVVYEDIYDAKTAVDHLS 78
L++ LPF+ + EE+ +I +G ++ +R+ +++ +G A+V YE+ A AV +
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 79 GFNVANRYLIV 89
G + + V
Sbjct: 80 GMTIKENIIKV 90
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGS---SKDTRGTAFVVYEDIYDAKTAVDHL 77
L V NL + S + + +F KYG + + I +K++RG AFV + D DA+ A+D +
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 78 SGFNVANRYLIV 89
G + R L V
Sbjct: 133 DGAVLDGRELRV 144
>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 = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTR---GTAFVVYEDIYDAKTAVDHL 77
L V LP N++ EE +FG G I ++ K T G FV Y D DA+ A++ L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 78 SGFNVANRYLIVLY 91
+G + + + V Y
Sbjct: 65 NGLRLQTKTIKVSY 78
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVDHL 77
LYV LP ++ +E+ +F +YG I RI + T RG F+ ++ +A+ A+ L
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 78 SG 79
+G
Sbjct: 151 NG 152
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHLSG 79
+YV NL N + E+ FG YG +R + + +++ G AFV +ED DA AV L G
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWV--ARNPPGFAFVEFEDPRDAADAVRELDG 132
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHLSG 79
+YV NL N + E+ FG YG +R + + +++ G AFV +ED DA AV L G
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWV--ARNPPGFAFVEFEDPRDAADAVRDLDG 132
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTR---GTAFVVYEDIYDAKTAVDHL 77
L V LP N++ +E +FG G I ++ K T G FV Y D DA A++ L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 78 SGFNVANRYLIVLY 91
+G + + + V Y
Sbjct: 67 NGLKLQTKTIKVSY 80
Score = 37.7 bits (86), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVDHL 77
LYV LP +S +EM +F +YG I RI + T RG F+ ++ +A+ A+ L
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 78 SG 79
+G
Sbjct: 153 NG 154
>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 = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 18 NRVLYVRNLPFNISSEEM----YDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTA 73
N +Y+ N+ I EE+ Y +F ++G + I + RG AFV+++++ + A
Sbjct: 6 NHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGSSTNA 65
Query: 74 VDHLSGF 80
+ L GF
Sbjct: 66 LRQLQGF 72
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTR---GTAFVVYEDIYDAKTAVDHL 77
L V LP N++ +E +FG G I ++ K T G FV Y D DA A++ L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 78 SGFNVANRYLIVLY 91
+G + + + V Y
Sbjct: 67 NGLKLQTKTIKVSY 80
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVDHL 77
LYV LP +S +EM +F +YG I RI + T RG F+ ++ +A+ A+ L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 78 SG 79
+G
Sbjct: 64 NG 65
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRI--GSSKDTRGTAFVVYEDIYDAKTAVDHLS 78
LY+ NLP ++ +E+ ++ +G + RI SS +RG F E + + H +
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFN 87
Query: 79 G 79
G
Sbjct: 88 G 88
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 7/76 (9%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKD--TRGTAFVVYEDIYDAKTAVDH 76
R L +NLP+ ++ +E+ ++F IR + SKD ++G A++ ++ DA+ +
Sbjct: 94 RTLLAKNLPYKVTQDELKEVFEDAAEIRLV----SKDGKSKGIAYIEFKTEADAEKTFEE 149
Query: 77 LSGFNVANRYLIVLYY 92
G + R I LYY
Sbjct: 150 KQGTEIDGRS-ISLYY 164
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 45/82 (54%), Gaps = 5/82 (6%)
Query: 14 PPEVNRVLYVRNLPFNISSEEMYDIFGKY----GAIRQIRIGSSKDTRGTAFVVYEDIYD 69
P E N+VLY++NL ++ ++ +F ++ G Q R+ + + RG AF+ + +
Sbjct: 21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGR-MRGQAFITFPNKEI 79
Query: 70 AKTAVDHLSGFNVANRYLIVLY 91
A A+ ++G+ + + L++ +
Sbjct: 80 AWQALHLVNGYKLYGKILVIEF 101
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 4/78 (5%)
Query: 18 NRVLYVRNL----PFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTA 73
N+ +Y+ NL + +Y IF ++G I I + RG AFV++++I A A
Sbjct: 6 NQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIGSASNA 65
Query: 74 VDHLSGFNVANRYLIVLY 91
+ + GF ++ + + Y
Sbjct: 66 LRTMQGFPFYDKPMQIAY 83
>pdb|2E44|A Chain A, Solution Structure Of Rna Binding Domain In Insulin-Like
Growth Factor 2 Mrna Binding Protein 3
Length = 96
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 34/73 (46%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHLS 78
R L +RN+P ++ E + + +YG + ++ V Y A+ A+D L+
Sbjct: 16 RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLN 75
Query: 79 GFNVANRYLIVLY 91
GF + N L V Y
Sbjct: 76 GFQLENFTLKVAY 88
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 7/76 (9%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKD--TRGTAFVVYEDIYDAKTAVDH 76
R L +NL FNI+ +E+ ++F IR + S+D ++G A++ ++ DA+ ++
Sbjct: 17 RTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEE 72
Query: 77 LSGFNVANRYLIVLYY 92
G + R + LYY
Sbjct: 73 KQGAEIDGRS-VSLYY 87
>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 = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 47/93 (50%), Gaps = 9/93 (9%)
Query: 4 IPLRKGNARLPPEVN--RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKD--TRGT 59
I L K R +V R L +NL FNI+ +E+ ++F IR + S+D ++G
Sbjct: 83 IKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGI 138
Query: 60 AFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYY 92
A++ ++ DA+ ++ G + R + LYY
Sbjct: 139 AYIEFKSEADAEKNLEEKQGAEIDGRS-VSLYY 170
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHLSG 79
+YV NL E+ F YG +R + I +++ G AFV +ED DA+ AV L G
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWI--ARNPPGFAFVEFEDPRDAEDAVRGLDG 59
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRI--GSSKDTRGTAFVVYEDIYDAKTAVDHLS 78
L++ L + + + +FGK+G I ++ + + +RG AF+ +E+ DAK A ++
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 79 GFNVANRYLIV 89
G ++ + + V
Sbjct: 70 GKSLHGKAIKV 80
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 37/63 (58%), Gaps = 3/63 (4%)
Query: 18 NRVLYVRNL-PFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDH 76
N VL V NL P ++ + ++ +FG YG +++++I +K + A V D A+ A+ H
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--KENALVQMADGNQAQLAMSH 60
Query: 77 LSG 79
L+G
Sbjct: 61 LNG 63
>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 = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKD-TRGTAFVVYEDIYDAKTAVDHLSG 79
++++NL +I ++ +YD F +G I ++ ++ ++G FV +E A+ A++ ++G
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 160
Query: 80 FNVANRYLIV 89
+ +R + V
Sbjct: 161 MLLNDRKVFV 170
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 3/77 (3%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTR---GTAFVVYEDIYDAKTAVDHL 77
LYV +L +++ +Y+ F G I IR+ TR G A+V ++ DA+ A+D +
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 78 SGFNVANRYLIVLYYQQ 94
+ + + + +++ Q+
Sbjct: 73 NFDVIKGKPVRIMWSQR 89
>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 = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/91 (23%), Positives = 47/91 (51%), Gaps = 11/91 (12%)
Query: 5 PLRKGNARLPPEVNRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKD-TRGTAFVV 63
PL GN ++++NL +I ++ +YD F +G I ++ ++ ++G FV
Sbjct: 2 PLGSGN----------IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVH 51
Query: 64 YEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 94
+E A+ A++ ++G + +R + V ++
Sbjct: 52 FETQEAAERAIEKMNGMLLNDRKVFVGRFKS 82
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 15 PEVNRV--LYVRNLPFNISSEEMYDIFGKYGAIRQI---RIGSSKDTRGTAFVVYEDIYD 69
P+V+ + L V NL + S + + +F KYG + + R +K RG AFV + D D
Sbjct: 8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRD 67
Query: 70 AKTAVDHLSGFNVANRYLIV 89
A+ A + G + R L V
Sbjct: 68 AQDAEAAMDGAELDGRELRV 87
>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 = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 37/63 (58%), Gaps = 3/63 (4%)
Query: 18 NRVLYVRNL-PFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDH 76
N VL V NL P ++ + ++ +FG YG +++++I +K + A V D A+ A+ H
Sbjct: 34 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--KENALVQMADGNQAQLAMSH 91
Query: 77 LSG 79
L+G
Sbjct: 92 LNG 94
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKD-TRGTAFVVYEDIYDAKTAVDHLSG 79
++++NL +I ++ +YD F +G I ++ ++ ++G FV +E A+ A++ ++G
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 80 FNVANRYLIVLYYQQ 94
+ +R + V ++
Sbjct: 74 MLLNDRKVFVGRFKS 88
>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 = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKD-TRGTAFVVYEDIYDAKTAVDHLSG 79
++++NL +I ++ +YD F +G I ++ ++ ++G FV +E A+ A++ ++G
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 165
Query: 80 FNVANRYLIV 89
+ +R + V
Sbjct: 166 MLLNDRKVFV 175
Score = 33.5 bits (75), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 45/93 (48%), Gaps = 3/93 (3%)
Query: 5 PLRKGNARLPPEVNRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTR---GTAF 61
PL N P LYV +L +++ +Y+ F G I IR+ TR G A+
Sbjct: 2 PLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAY 61
Query: 62 VVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 94
V ++ DA+ A+D ++ + + + +++ Q+
Sbjct: 62 VNFQQPADAERALDTMNFDVIKGKPVRIMWSQR 94
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 35.4 bits (80), Expect = 0.008, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 3/74 (4%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVD 75
+ L+V + ++ + ++ F YG I++I + SK + RG AF+ YE D +A
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 76 HLSGFNVANRYLIV 89
H G + R ++V
Sbjct: 163 HADGKKIDGRRVLV 176
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRI----GSSKDTRGTAFVVYEDIYDAKTAVDH 76
+ VRN+PF + E+ ++F +G ++ +R+ + RG FV + DAK A +
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA 77
Query: 77 LS 78
L
Sbjct: 78 LC 79
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 37/77 (48%), Gaps = 3/77 (3%)
Query: 18 NRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTR---GTAFVVYEDIYDAKTAV 74
N L V LP +++ E+Y +F G I RI T G AFV + D++ A+
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 75 DHLSGFNVANRYLIVLY 91
L+G V N+ L V Y
Sbjct: 63 KVLNGITVRNKRLKVSY 79
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 7/78 (8%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRI----GSSKDTRGTAFVVYEDIYDAKTAVDH 76
LYV+NL I E + F +G I ++ G SK G FV + +A AV
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSK---GFGFVCFSSPEEATKAVTE 74
Query: 77 LSGFNVANRYLIVLYYQQ 94
++G VA + L V Q+
Sbjct: 75 MNGRIVATKPLYVALAQR 92
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 35.0 bits (79), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 3/74 (4%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVD 75
+ L+V + ++ + ++ F YG I++I + SK + RG AF+ YE D +A
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 76 HLSGFNVANRYLIV 89
H G + R ++V
Sbjct: 163 HADGKKIDGRRVLV 176
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 20 VLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVDH 76
+L+V + + E+++D F +YG I+ I + + T +G V YE +A+ A++
Sbjct: 25 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84
Query: 77 LSGFNVANRYLIVLY 91
L+G ++ + + V +
Sbjct: 85 LNGQDLMGQPISVDW 99
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 8/68 (11%)
Query: 15 PEVN---RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAK 71
PEV +VL+VRNL ++ E + F ++G + ++ K + AFV +ED A
Sbjct: 9 PEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERV-----KKLKDYAFVHFEDRGAAV 63
Query: 72 TAVDHLSG 79
A+D ++G
Sbjct: 64 KAMDEMNG 71
>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 = 34.7 bits (78), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 3/62 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVDHL 77
LY+ LP ++ +++ D+F ++G I R+ + T RG AF+ ++ +A+ A+
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 78 SG 79
+G
Sbjct: 151 NG 152
Score = 32.7 bits (73), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQ---IRIGSSKDTRGTAFVVYEDIYDAKTAVDHL 77
L V LP N++ +E+ +F G + IR + + G FV Y DA+ A++ L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 78 SGFNVANRYLIVLY 91
+G + ++ + V Y
Sbjct: 65 NGLRLQSKTIKVSY 78
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 34.7 bits (78), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 3/62 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVDHL 77
LY+ LP ++ +++ D+F ++G I R+ + T RG AF+ ++ +A+ A+
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 78 SG 79
+G
Sbjct: 151 NG 152
Score = 32.7 bits (73), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQ---IRIGSSKDTRGTAFVVYEDIYDAKTAVDHL 77
L V LP N++ +E+ +F G + IR + + G FV Y DA+ A++ L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 78 SGFNVANRYLIVLY 91
+G + ++ + V Y
Sbjct: 65 NGLRLQSKTIKVSY 78
>pdb|2XB2|D Chain D, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
Length = 90
Score = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 20 VLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVDH 76
+L+V + + E+++D F +YG I+ I + + T +G V YE +A+ A++
Sbjct: 9 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 77 LSGFNVANRYLIVLY 91
L+G ++ + + V +
Sbjct: 69 LNGQDLMGQPISVDW 83
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 37/64 (57%), Gaps = 8/64 (12%)
Query: 13 LPPEVNRVLYVRNLPF-NISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAK 71
+PP+ L++ NLP N+S E+++ IF YG I QI I K+ G F+ +++ +
Sbjct: 7 IPPKSR--LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFG--FIQFDNPQSVR 59
Query: 72 TAVD 75
A++
Sbjct: 60 DAIE 63
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 20 VLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVDH 76
+L+V + + E+++D F +YG I+ I + + T +G V YE +A+ A++
Sbjct: 11 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 70
Query: 77 LSGFNVANRYLIVLY 91
L+G ++ + + V +
Sbjct: 71 LNGQDLMGQPISVDW 85
>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 = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 20 VLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVDH 76
+L+V + + E+++D F +YG I+ I + + T +G V YE +A+ A++
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83
Query: 77 LSGFNVANRYLIVLY 91
L+G ++ + + V +
Sbjct: 84 LNGQDLMGQPISVDW 98
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 34.7 bits (78), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 3/63 (4%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVD 75
RVLYV L + + ++ F +G I I+I +T RG AFV +E DA A+D
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 76 HLS 78
+++
Sbjct: 124 NMN 126
>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 = 34.7 bits (78), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 3/63 (4%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVD 75
RVLYV L + + ++ F +G I I+I +T RG AFV +E DA A+D
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 76 HLS 78
+++
Sbjct: 68 NMN 70
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 34.3 bits (77), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 20 VLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVDH 76
+L+V + + E+++D F +YG I+ I + + T +G V YE +A+ A++
Sbjct: 9 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 77 LSGFNVANRYLIVLY 91
L+G ++ + + V +
Sbjct: 69 LNGQDLMGQPISVDW 83
>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 = 34.3 bits (77), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 3/63 (4%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVD 75
RVLYV L + + ++ F +G I I+I +T RG AFV +E DA A+D
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 76 HLS 78
+++
Sbjct: 63 NMN 65
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHLSGF 80
L+V NLP +I+ EEM +F KYG ++ I K G F+ E A+ A L
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK---GFGFIRLETRTLAEIAKVELDNM 81
Query: 81 NVANRYLIVLY 91
+ + L V +
Sbjct: 82 PLRGKQLRVRF 92
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 3/63 (4%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVD 75
RVLYV L + + ++ F +G I I+I +T RG AFV +E DA A+D
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 76 HLS 78
+++
Sbjct: 66 NMN 68
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 5/80 (6%)
Query: 13 LPPEVNRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYD 69
LP E YV NLPFN ++ IF K +IR +R+ KDT +G +V ++++
Sbjct: 10 LPTEPPYTAYVGNLPFNTVQGDIDAIF-KDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDS 68
Query: 70 AKTAVDHLSGFNVANRYLIV 89
K A+ + G + +R L V
Sbjct: 69 LKEALTY-DGALLGDRSLRV 87
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 2/79 (2%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGT--AFVVYEDIYDAKTAVDH 76
RVLYV NL I+ + + F G I I+I K+ + AFV Y +DA A+
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 77 LSGFNVANRYLIVLYYQQT 95
L+G + N + + + Q+
Sbjct: 61 LNGKQIENNIVKINWAFQS 79
Score = 28.9 bits (63), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 9/77 (11%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGA------IRQIRIGSSKDTRGTAFVVYEDIYDAKTAV 74
L+V +L N+ E + + F + + + ++ GSS RG FV + DA+ A+
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSS---RGYGFVSFTSQDDAQNAM 146
Query: 75 DHLSGFNVANRYLIVLY 91
D + G ++ R L + +
Sbjct: 147 DSMQGQDLNGRPLRINW 163
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
Length = 109
Score = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 3/63 (4%)
Query: 20 VLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVDH 76
+L+V + + E+++D F +YG I+ I + + T +G V YE +A+ A++
Sbjct: 9 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 77 LSG 79
L+G
Sbjct: 69 LNG 71
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 4/75 (5%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQ----IRIGSSKDTRGTAFVVYEDIYDAKTAVDH 76
+++ NL I + +YD F +G I Q +R + +++G AF+ + + A++
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 77 LSGFNVANRYLIVLY 91
++G + NR + V Y
Sbjct: 68 MNGQYLCNRPITVSY 82
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 34.3 bits (77), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 3/63 (4%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVD 75
RVLYV L + + ++ F +G I I+I +T RG AFV +E DA A+D
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 76 HLS 78
+++
Sbjct: 73 NMN 75
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 33.9 bits (76), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 33/56 (58%), Gaps = 6/56 (10%)
Query: 21 LYVRNLPF-NISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVD 75
L++ NLP N+S E+++ IF YG I QI I K+ G F+ +++ + A++
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFG--FIQFDNPQSVRDAIE 75
>pdb|1OPI|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
pdb|2M0G|B Chain B, Structure, Phosphorylation And U2af65 Binding Of The
Nterminal Domain Of Splicing Factor 1 During 3 Splice
Site Recognition
Length = 104
Score = 33.9 bits (76), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 33 EEMYDIFGKYGAIRQIRI-----GSSKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYL 87
E++ D KYG ++ I I G G FV + ++D + A+ L+G ANR +
Sbjct: 29 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 88
Query: 88 IVLY 91
+ Y
Sbjct: 89 VTKY 92
>pdb|1O0P|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
Length = 104
Score = 33.9 bits (76), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 33 EEMYDIFGKYGAIRQIRI-----GSSKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYL 87
E++ D KYG ++ I I G G FV + ++D + A+ L+G ANR +
Sbjct: 29 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 88
Query: 88 IVLY 91
+ Y
Sbjct: 89 VTKY 92
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 33.9 bits (76), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 33/56 (58%), Gaps = 6/56 (10%)
Query: 21 LYVRNLPF-NISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVD 75
L++ NLP N+S E+++ IF YG I QI I K+ G F+ +++ + A++
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFG--FIQFDNPQSVRDAIE 75
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 33.9 bits (76), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 33/56 (58%), Gaps = 6/56 (10%)
Query: 21 LYVRNLPF-NISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVD 75
L++ NLP N+S E+++ IF YG I QI I K+ G F+ +++ + A++
Sbjct: 5 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KNAFG--FIQFDNPQSVRDAIE 55
>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 = 33.5 bits (75), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 40/75 (53%), Gaps = 4/75 (5%)
Query: 18 NRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAV 74
NR+ YV ++ ++S +++ +F +G I+ + T +G F+ YE ++ AV
Sbjct: 111 NRI-YVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 169
Query: 75 DHLSGFNVANRYLIV 89
++ F++ +YL V
Sbjct: 170 SSMNLFDLGGQYLRV 184
>pdb|4FXW|A Chain A, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
pdb|4FXW|C Chain C, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
Length = 106
Score = 33.5 bits (75), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 33 EEMYDIFGKYGAIRQIRI-----GSSKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYL 87
E++ D KYG ++ I I G G FV + ++D + A L+G ANR +
Sbjct: 31 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVV 90
Query: 88 IVLY 91
+ Y
Sbjct: 91 VTKY 94
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 33.5 bits (75), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIR--IGS-SKDTRGTAFVVYEDIYDAKTAVDHL 77
L+VRNL + S E++ +F YG + ++ I S +K +G AFV + A A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 78 SGFNVANRYLIVL 90
G R L VL
Sbjct: 71 DGQVFQGRMLHVL 83
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 33.5 bits (75), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 44/94 (46%), Gaps = 6/94 (6%)
Query: 5 PLRKGNARLPPEVN--RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTR---GT 59
P+R+ L PE R ++ L I ++ D F G +R +RI S +++R G
Sbjct: 10 PVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGI 69
Query: 60 AFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQ 93
A+V + +I A+ L+G + +IV Q
Sbjct: 70 AYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ 102
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 33.5 bits (75), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHLSGF 80
L+V NLP +I+ E+ +F +YG ++ I RG F+ E A+ A L G
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRD---RGFGFIRLESRTLAEIAKAELDGT 81
Query: 81 NVANRYLIVLY 91
+ +R L + +
Sbjct: 82 ILKSRPLRIRF 92
>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 = 33.5 bits (75), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHLSGF 80
L+V NLP +I+ EEM +F KYG ++ I K G F+ E A+ A L
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK---GFGFIRLETRTLAEIAKVELDNM 74
Query: 81 NVANRYLIVLY 91
+ + L V +
Sbjct: 75 PLRGKQLRVRF 85
>pdb|3V4M|A Chain A, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af)
From Mus Musculus At 1.80 A Resolution
pdb|3V4M|B Chain B, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af)
From Mus Musculus At 1.80 A Resolution
Length = 105
Score = 33.1 bits (74), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 33 EEMYDIFGKYGAIRQIRI-----GSSKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYL 87
E++ D KYG ++ I I G G FV + ++D + A L+G ANR +
Sbjct: 30 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVV 89
Query: 88 IVLY 91
+ Y
Sbjct: 90 VTKY 93
>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 = 33.1 bits (74), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 3/74 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAI---RQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHL 77
L V LP N++ +E+ +F G + + IR + + G FV Y DA+ A++ L
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 78 SGFNVANRYLIVLY 91
+G + ++ + V Y
Sbjct: 67 NGLRLQSKTIKVSY 80
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 33.1 bits (74), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 32/57 (56%), Gaps = 5/57 (8%)
Query: 13 LPPEV--NRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVY 64
LP +V + +++RNL F+ E + ++ ++G ++ +R+ DT +G AF +
Sbjct: 8 LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQF 64
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 33.1 bits (74), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 4/86 (4%)
Query: 7 RKGNARLPPEVNRVLYVRNLPFNISSEEMYDIFGKYGAIRQ---IRIGSSKDTRGTAFVV 63
++ +R P E +Y++ LPF ++ + D F K + I G + G FV
Sbjct: 14 KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVE 73
Query: 64 YEDIYDAKTAVDHLSGFNVANRYLIV 89
+ + D K A+ + + NR++ V
Sbjct: 74 FRNEADYKAALCRHKQY-MGNRFIQV 98
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 33.1 bits (74), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 37/66 (56%), Gaps = 4/66 (6%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKD----TRGTAFVVYEDIYDAKTAVDH 76
+++ L N++ + + +IF YG I+ I + + ++G A+V +E+ +A+ A+ H
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 77 LSGFNV 82
+ G +
Sbjct: 67 MDGGQI 72
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 33.1 bits (74), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 40/75 (53%), Gaps = 4/75 (5%)
Query: 18 NRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAV 74
NR+ YV ++ ++S +++ +F +G I+ + T +G F+ YE ++ AV
Sbjct: 126 NRI-YVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV 184
Query: 75 DHLSGFNVANRYLIV 89
++ F++ +YL V
Sbjct: 185 SSMNLFDLGGQYLRV 199
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 32.7 bits (73), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAI--RQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHLS 78
++VRNLPF+ + + + D F + G + I++ + K ++G V +E A+ A ++
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGK-SKGCGVVKFESPEVAERACRMMN 69
Query: 79 GFNVANRYLIV 89
G ++ R + V
Sbjct: 70 GMKLSGREIDV 80
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 32.7 bits (73), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAI--RQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHLS 78
++VRNLPF+ + + + D F + G + I++ + K ++G V +E A+ A ++
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGK-SKGCGVVKFESPEVAERACRMMN 66
Query: 79 GFNVANRYLIV 89
G ++ R + V
Sbjct: 67 GMKLSGREIDV 77
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 32.3 bits (72), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 4/75 (5%)
Query: 18 NRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAV 74
NR+ YV ++ ++S +++ +F +G I+ + T +G F+ YE ++ AV
Sbjct: 110 NRI-YVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
Query: 75 DHLSGFNVANRYLIV 89
+ F++ +YL V
Sbjct: 169 SSXNLFDLGGQYLRV 183
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 32.0 bits (71), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 16/78 (20%), Positives = 41/78 (52%), Gaps = 3/78 (3%)
Query: 15 PEVNRVLYVRNLPFNISSEEMYDIFGKYGAIRQ---IRIGSSKDTRGTAFVVYEDIYDAK 71
P+ L++ LP ++ +++ ++ +G ++ ++ ++ ++G AF Y DI
Sbjct: 111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTD 170
Query: 72 TAVDHLSGFNVANRYLIV 89
A+ L+G + ++ L+V
Sbjct: 171 QAIAGLNGMQLGDKKLLV 188
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYE 65
R LYV N+PF I+ E M D F Q+R+G G + +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNA-----QMRLGGLTQAPGNPVLAVQ 46
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 32.0 bits (71), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 3/81 (3%)
Query: 18 NRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAV 74
N + V NL + ++ ++F +G+I +I + K T +G AF+ + DA A+
Sbjct: 15 NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
Query: 75 DHLSGFNVANRYLIVLYYQQT 95
+SGF + L V + + +
Sbjct: 75 AGVSGFGYDHLILNVEWAKPS 95
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 32.0 bits (71), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRI---GSSKDTRGTAFVVYEDIYDAKTAVDHL 77
++V +L I++E++ F +G I R+ ++ ++G FV + + DA+ A+ H+
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 78 SGFNVANRYL 87
G + R +
Sbjct: 78 GGQWLGGRQI 87
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 31.6 bits (70), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 11/83 (13%)
Query: 18 NRVLYVRNLPFNISSEEMYDIFGKYGAIR--------QIRIGSSKDT---RGTAFVVYED 66
N +YV+ L +++ +++ D F + G ++ I I K+T +G A V YED
Sbjct: 15 NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 74
Query: 67 IYDAKTAVDHLSGFNVANRYLIV 89
AK AV+ G + L V
Sbjct: 75 PPTAKAAVEWFDGKDFQGSKLKV 97
>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 = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAI---RQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHL 77
L V LP N + +E+ +F G + + IR + + G FV Y DA+ A++ L
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 78 SGFNVANRYLIVLY 91
+G + ++ + V Y
Sbjct: 82 NGLRLQSKTIKVSY 95
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYE 65
R LYV N+PF I+ E M D F Q+R+G G + +
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNA-----QMRLGGLTQAPGNPVLAVQ 48
Score = 30.8 bits (68), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 21 LYVRNLPFNISSEEMYDI---FGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHL 77
L++ LP ++ +++ ++ FG A ++ ++ ++G AF Y DI A+ L
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 78 SGFNVANRYLIV 89
+G + ++ L+V
Sbjct: 159 NGMQLGDKKLLV 170
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 15/75 (20%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHLS 78
+VL+VRNL ++ E + F ++G + ++ K + AF+ +++ A A++ ++
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERV-----KKLKDYAFIHFDERDGAVKAMEEMN 66
Query: 79 GFNVANRYLIVLYYQ 93
G ++ + +++ +
Sbjct: 67 GKDLEGENIEIVFAK 81
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYE 65
R LYV N+PF I+ E M D F Q+R+G G + +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNA-----QMRLGGLTQAPGNPVLAVQ 46
Score = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 21 LYVRNLPFNISSEEMYDI---FGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHL 77
L++ LP ++ +++ ++ FG A ++ ++ ++G AF Y DI A+ L
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 78 SGFNVANRYLIV 89
+G + ++ L+V
Sbjct: 157 NGMQLGDKKLLV 168
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In
Cytotoxic Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 16/70 (22%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRI---GSSKDTRGTAFVVYEDIYDAKTAVDHL 77
++V +L I++E++ F +G I R+ ++ ++G FV + + +DA+ A+ +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 78 SGFNVANRYL 87
G + R +
Sbjct: 78 GGQWLGGRQI 87
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYE 65
R LYV N+PF I+ E M D F Q+R+G G + +
Sbjct: 2 RRLYVGNIPFGITEEAMMDFFNA-----QMRLGGLTQAPGNPVLAVQ 43
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af
Large Subunit
Length = 87
Score = 30.8 bits (68), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYE 65
R LYV N+PF I+ E M D F Q+R+G G + +
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNA-----QMRLGGLTQAPGNPVLAVQ 48
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 30.8 bits (68), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 14/58 (24%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRI---GSSKDTRGTAFVVYEDIYDAKTAVD 75
++V +P N E+ + F K+G + ++ + + RG F+ +ED AV+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 15/72 (20%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQ---IRIGSSKDTRGTAFVVYEDIYDAKTAVDHL 77
L++ LP ++ +++ ++ +G ++ ++ ++ ++G AF Y DI A+ L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 78 SGFNVANRYLIV 89
+G + ++ L+V
Sbjct: 64 NGMQLGDKKLLV 75
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 30.0 bits (66), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 11/73 (15%)
Query: 18 NRVLYVRNLPFNISSEEMYDIFGKYGAIR--------QIRIGSSKDT---RGTAFVVYED 66
N ++V+ L N++ E + D F + G I+ I + + ++T +G A V ++D
Sbjct: 13 NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 72
Query: 67 IYDAKTAVDHLSG 79
AK A+D G
Sbjct: 73 PPSAKAAIDWFDG 85
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 30.0 bits (66), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 5/77 (6%)
Query: 1 MATIPLRKGNARLPPEVNRVLYVRNLPFNISSEEM---YDIFGKYGAIRQIRIGSSKDTR 57
+ T+PL + + E R L++ L F + E + Y+ +GK +R +SK +R
Sbjct: 12 LETVPLER--KKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSR 69
Query: 58 GTAFVVYEDIYDAKTAV 74
G FV + + + A+
Sbjct: 70 GFGFVTFSSMAEVDAAM 86
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 30.0 bits (66), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 11/73 (15%)
Query: 18 NRVLYVRNLPFNISSEEMYDIFGKYGAIR--------QIRIGSSKDT---RGTAFVVYED 66
N ++V+ L N++ E + D F + G I+ I + + ++T +G A V ++D
Sbjct: 7 NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 66
Query: 67 IYDAKTAVDHLSG 79
AK A+D G
Sbjct: 67 PPSAKAAIDWFDG 79
>pdb|2EK6|A Chain A, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|B Chain B, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|C Chain C, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|D Chain D, Crystal Structure Of Human Rna-Binding Protein 12
Length = 95
Score = 30.0 bits (66), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 20 VLYVRNLPFNISSEEMYDIFGKYGAIRQ---IRIGSSKDTRGTAFVVYEDIYDAKTAVDH 76
V+ V+N+PF +S +E+ D F Y I ++ G A V +E +A AV
Sbjct: 17 VIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76
Query: 77 LSGFNVANR 85
L+ + +R
Sbjct: 77 LNDRPIGSR 85
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 29.6 bits (65), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 7/63 (11%)
Query: 19 RVLYVRNLPFNISSEEMYDIFG--KYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDH 76
++LYVRNL + S E + F K GA+ ++ K R AFV + + DA A+
Sbjct: 16 KILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEAMKA 70
Query: 77 LSG 79
L+G
Sbjct: 71 LNG 73
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 29.3 bits (64), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 3/75 (4%)
Query: 20 VLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVDH 76
+L+V ++ +E+ + F YG I+ I + + T +G A V YE A A +
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 77 LSGFNVANRYLIVLY 91
L+G + + + V +
Sbjct: 88 LNGAEIMGQTIQVDW 102
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 29.3 bits (64), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 9/77 (11%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGA------IRQIRIGSSKDTRGTAFVVYEDIYDAKTAV 74
L+V +L N+ E + + F + + + ++ GSS RG FV + DA+ A+
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSS---RGYGFVSFTSQDDAQNAM 60
Query: 75 DHLSGFNVANRYLIVLY 91
D + G ++ R L + +
Sbjct: 61 DSMQGQDLNGRPLRINW 77
>pdb|2CQP|A Chain A, Solution Structure Of The Rna Binding Domain Of
Rna-Binding Protein 12
Length = 98
Score = 29.3 bits (64), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 20 VLYVRNLPFNISSEEMYDIFGKYGAIRQ---IRIGSSKDTRGTAFVVYEDIYDAKTAVDH 76
++ V+N+PF +S +E+ D F Y I ++ G A V +E +A AV
Sbjct: 17 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76
Query: 77 LSGFNVANR 85
L+ + +R
Sbjct: 77 LNDRPIGSR 85
>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 = 29.3 bits (64), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 3/75 (4%)
Query: 20 VLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYEDIYDAKTAVDH 76
+L+V ++ +E+ + F YG I+ I + + T +G A V YE A A +
Sbjct: 74 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133
Query: 77 LSGFNVANRYLIVLY 91
L+G + + + V +
Sbjct: 134 LNGAEIMGQTIQVDW 148
>pdb|2VOD|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VOD|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VON|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VON|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VOO|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOO|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOP|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auuuu
Length = 193
Score = 29.3 bits (64), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 11/81 (13%)
Query: 6 LRKGNARLPPEV---------NRVLYVRNLPFNISSEEMYDIFGKYGAIR--QIRIGSSK 54
+R+ ++ PEV NR +Y++ P + + +++ + G + Q+R K
Sbjct: 88 IRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHK 147
Query: 55 DTRGTAFVVYEDIYDAKTAVD 75
+G+ FVV++ I AK V+
Sbjct: 148 AFKGSIFVVFDSIESAKKFVE 168
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 29.3 bits (64), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHLSGF 80
++V N+ +S+E+ +F + G + + + + AFV E DAK A+ L+G
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDV-----VKDYAFVHMEKEADAKAAIAQLNGK 66
Query: 81 NVANRYLIV 89
V + + V
Sbjct: 67 EVKGKRINV 75
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 28.5 bits (62), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 37/63 (58%), Gaps = 5/63 (7%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVY--EDIYDAKTA 73
R +YV NL ++ +SE++ ++F ++G + +++ ++T +G FV E + +A
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61
Query: 74 VDH 76
+D+
Sbjct: 62 LDN 64
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 28.5 bits (62), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 10 NARLPPEVNRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYED 66
NA E +V L ++ S +++ D F K+G + I +T RG F++++D
Sbjct: 3 NASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKD 62
Query: 67 IYDAKTAVDH 76
+ +D
Sbjct: 63 AASVEKVLDQ 72
>pdb|2EK1|A Chain A, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|B Chain B, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|C Chain C, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|D Chain D, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|E Chain E, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|F Chain F, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|G Chain G, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|H Chain H, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
Length = 95
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 20 VLYVRNLPFNISSEEMYDIFGKYGAIRQ---IRIGSSKDTRGTAFVVYEDIYDAKTAVDH 76
V+ V+N PF +S +E+ D F Y I ++ G A V +E +A AV
Sbjct: 17 VIKVQNXPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGXPTGEAXVAFESRDEATAAVID 76
Query: 77 LSGFNVANR 85
L+ + +R
Sbjct: 77 LNDRPIGSR 85
>pdb|2DHA|A Chain A, Solution Structure Of The Second Rna Recognition Motif
In Hypothetical Protein Flj201171
Length = 123
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 7/54 (12%)
Query: 13 LPPEVNRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYED 66
L E ++ +R LPF ++EE+ FG++ I + G FV Y D
Sbjct: 18 LSKENQVIVRMRGLPFTATAEEVVAFFGQHCPI-------TGGKEGILFVTYPD 64
>pdb|1UKX|A Chain A, Solution Structure Of The Rwd Domain Of Mouse Gcn2
Length = 137
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 4/32 (12%)
Query: 5 PLRKGNARLPPEVNRVLYVRNLPFNISSEEMY 36
P +G R PPE+N VLY P ++ EE+Y
Sbjct: 35 PDARGRVREPPEINLVLY----PQGLAGEEVY 62
>pdb|1S79|A Chain A, Solution Structure Of The Central Rrm Of Human La
Protein
Length = 103
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 18 NRVLYVRNLPFNISSEEMYDIFGKYGAIR--QIRIGSSKDTRGTAFVVYEDIYDAKTAVD 75
NR +Y++ P + + +++ + G + Q+R K +G+ FVV++ I AK V+
Sbjct: 11 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE 70
>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From
Hypothetical Protein Bab23448
Length = 111
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 32/59 (54%), Gaps = 3/59 (5%)
Query: 20 VLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHLS 78
V+ +NLP + E+ + F ++G++ ++ + + TA V + + +A+ A HL+
Sbjct: 12 VILAKNLPAGTLAAEIQETFSRFGSLGRVLL---PEGGITAIVEFLEPLEARKAFRHLA 67
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHL 77
L++ NLP + +E+ +F +YG + + I + FV ED A+ A+ +L
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDI-----IKNYGFVHIEDKTAAEDAIRNL 62
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 2/75 (2%)
Query: 17 VNRVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKD--TRGTAFVVYEDIYDAKTAV 74
+ ++V NL + + +++ ++F G + + I KD +RG V +E +A A+
Sbjct: 14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAI 73
Query: 75 DHLSGFNVANRYLIV 89
+G + +R + V
Sbjct: 74 SMFNGQLLFDRPMHV 88
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition
In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 11/48 (22%), Positives = 28/48 (58%), Gaps = 3/48 (6%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRI---GSSKDTRGTAFVVYE 65
+++ L ++ + + + + FGKYG + ++I ++ +RG F+ +E
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFE 53
>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 = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRI----GSSKDTRGTAFVVYED 66
++V + + + D F +YG I I I GS K RG AFV ++D
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK-KRGFAFVTFDD 148
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRI----GSSKDTRGTAFVVYED 66
++V + + + D F +YG I I I GS K RG AFV ++D
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK-KRGFAFVTFDD 155
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 27.3 bits (59), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRI----GSSKDTRGTAFVVYED 66
++V + + + D F +YG I I I GS K RG AFV ++D
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK-KRGFAFVTFDD 153
>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 = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRI----GSSKDTRGTAFVVYED 66
++V + + + D F +YG I I I GS K RG AFV ++D
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK-KRGFAFVTFDD 155
>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 = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRI----GSSKDTRGTAFVVYED 66
++V + + + D F +YG I I I GS K RG AFV ++D
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK-KRGFAFVTFDD 154
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRI----GSSKDTRGTAFVVYED 66
++V + + + D F +YG I I I GS K RG AFV ++D
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK-KRGFAFVTFDD 156
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 26.2 bits (56), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSK---DTRGTAFVVYEDIYDAKTAV 74
R +YV N+ + ++EE+ F G++ ++ I K +G A++ + D +T++
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 64
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of
Hypothetical Polyadenylate-Binding Protein (Pabpn1)
From Homo Sapiens At 1.95 A Resolution
Length = 89
Score = 26.2 bits (56), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 14/59 (23%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 19 RVLYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSK---DTRGTAFVVYEDIYDAKTAV 74
R +YV N+ + ++EE+ F G++ ++ I K +G A++ + D +T++
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 25.8 bits (55), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 20/86 (23%), Positives = 41/86 (47%), Gaps = 8/86 (9%)
Query: 14 PPEVNRVLYVRNLPFNISSEEMYDIFGKY--------GAIRQIRIGSSKDTRGTAFVVYE 65
P E N +YV+NL ++ +++ IFG+Y + IR+ +G AF+
Sbjct: 41 PGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLP 100
Query: 66 DIYDAKTAVDHLSGFNVANRYLIVLY 91
+ A A+ +G+ + + ++V +
Sbjct: 101 NEKAAAKALKEANGYVLFGKPMVVQF 126
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 25.8 bits (55), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 11/49 (22%), Positives = 26/49 (53%)
Query: 39 FGKYGAIRQIRIGSSKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYL 87
FG+ R ++ ++ ++G FV + + +DA+ A+ + G + R +
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 25.8 bits (55), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 21 LYVRNLPFNISSEEMYDIFGKYGAIRQIRIGSSKDT---RGTAFVVYED 66
L+V L ++ + E + F +YG + I K T RG FV ++D
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
>pdb|2IIR|A Chain A, Acetate Kinase From A Hypothermophile Thermotoga Maritima
pdb|2IIR|B Chain B, Acetate Kinase From A Hypothermophile Thermotoga Maritima
pdb|2IIR|C Chain C, Acetate Kinase From A Hypothermophile Thermotoga Maritima
pdb|2IIR|D Chain D, Acetate Kinase From A Hypothermophile Thermotoga Maritima
pdb|2IIR|E Chain E, Acetate Kinase From A Hypothermophile Thermotoga Maritima
pdb|2IIR|F Chain F, Acetate Kinase From A Hypothermophile Thermotoga Maritima
pdb|2IIR|G Chain G, Acetate Kinase From A Hypothermophile Thermotoga Maritima
pdb|2IIR|H Chain H, Acetate Kinase From A Hypothermophile Thermotoga Maritima
pdb|2IIR|I Chain I, Acetate Kinase From A Hypothermophile Thermotoga Maritima
pdb|2IIR|J Chain J, Acetate Kinase From A Hypothermophile Thermotoga Maritima
Length = 403
Score = 25.4 bits (54), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 29 NISSEEMYDIFGKYGAIRQIRIGSSKDTR 57
IS +EMYDI K + + G S D R
Sbjct: 257 GISPQEMYDILNKKSGVYGLSKGFSSDMR 285
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
0.319 0.137 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,017,808
Number of Sequences: 62578
Number of extensions: 98468
Number of successful extensions: 399
Number of sequences better than 100.0: 162
Number of HSP's better than 100.0 without gapping: 112
Number of HSP's successfully gapped in prelim test: 50
Number of HSP's that attempted gapping in prelim test: 250
Number of HSP's gapped (non-prelim): 174
length of query: 124
length of database: 14,973,337
effective HSP length: 85
effective length of query: 39
effective length of database: 9,654,207
effective search space: 376514073
effective search space used: 376514073
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)