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= 037075
(806 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 45.8 bits (107), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 67 VDEVILRKAFSPFGEIEKITVFPGRSYAFVQFRSIISACRAKETLQGKLFGNPRVHICFA 126
V E IL KAFS FG++E++ + YAF+ F A +A E + GK + I FA
Sbjct: 23 VTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA 80
Query: 127 K 127
K
Sbjct: 81 K 81
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 43.1 bits (100), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 30/43 (69%)
Query: 71 ILRKAFSPFGEIEKITVFPGRSYAFVQFRSIISACRAKETLQG 113
++R+ FSPFG+I +I VFP + Y+FV+F + SA A ++ G
Sbjct: 41 LMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNG 83
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 2/63 (3%)
Query: 65 LKVDEVILRKAFSPFGEIEKITVFPGRSYAFVQFRSIISACRAKETLQGKLFGNPRVHIC 124
L V E L + F PFG ++++ + G +AFV+F SA +A E + GK F N + +
Sbjct: 41 LDVQESELNEIFGPFGPMKEVKILNG--FAFVEFEEAESAAKAIEEVHGKSFANQPLEVV 98
Query: 125 FAK 127
++K
Sbjct: 99 YSK 101
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 2/63 (3%)
Query: 65 LKVDEVILRKAFSPFGEIEKITVFPGRSYAFVQFRSIISACRAKETLQGKLFGNPRVHIC 124
L V E L + F PFG ++++ + G +AFV+F SA +A E + GK F N + +
Sbjct: 14 LDVQESELNEIFGPFGPMKEVKILNG--FAFVEFEEAESAAKAIEEVHGKSFANQPLEVV 71
Query: 125 FAK 127
++K
Sbjct: 72 YSK 74
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 37/66 (56%)
Query: 70 VILRKAFSPFGEIEKITVFPGRSYAFVQFRSIISACRAKETLQGKLFGNPRVHICFAKSE 129
+LR AFSPFG I +++ P R+ AFV + + SA +A L G + ++ + A+ +
Sbjct: 28 TLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ 87
Query: 130 AGANSG 135
+SG
Sbjct: 88 PMLDSG 93
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 39.7 bits (91), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 34/68 (50%), Gaps = 6/68 (8%)
Query: 67 VDEVILRKAFSPFGEIEKITVF------PGRSYAFVQFRSIISACRAKETLQGKLFGNPR 120
VDEV LR+ F +G IE + + R Y FV+F+S SA +A L G N R
Sbjct: 54 VDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKR 113
Query: 121 VHICFAKS 128
+ + A S
Sbjct: 114 LKVALAAS 121
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 38.5 bits (88), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 4/73 (5%)
Query: 67 VDEVILRKAFSPFGEI--EKITVFPGRS--YAFVQFRSIISACRAKETLQGKLFGNPRVH 122
+D+ LRKAFSPFG I K+ + GRS + FV F S A +A + G++ ++
Sbjct: 27 IDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLY 86
Query: 123 ICFAKSEAGANSG 135
+ A+ + SG
Sbjct: 87 VALAQRKEERQSG 99
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 38.5 bits (88), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 37/67 (55%)
Query: 71 ILRKAFSPFGEIEKITVFPGRSYAFVQFRSIISACRAKETLQGKLFGNPRVHICFAKSEA 130
+LR AFSPFG I +++ P R+ AFV + + SA +A L G + ++ + A+ +
Sbjct: 53 LLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP 112
Query: 131 GANSGRG 137
++ G
Sbjct: 113 MLDAATG 119
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 38.1 bits (87), Expect = 0.018, Method: Composition-based stats.
Identities = 29/87 (33%), Positives = 43/87 (49%), Gaps = 5/87 (5%)
Query: 51 AEPSEVLWIGFPALLKVDEVILRKAFSPFGEIEKITVFPGRSYAFVQFRSIISACRAKET 110
A P+ LW+G L + F FG I I G S+A++Q+ S+ +A A
Sbjct: 14 ANPTTRLWVGGLGP-NTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAK 72
Query: 111 LQGKLFGNP--RVHICFAKSEAGANSG 135
++G G P R+ + FAKS G +SG
Sbjct: 73 MRGFPLGGPDRRLRVDFAKS--GPSSG 97
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 37.4 bits (85), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 29/48 (60%), Gaps = 2/48 (4%)
Query: 67 VDEVILRKAFSPFGEIEKITVFPGRSYAFVQFRSIISACRAKETLQGK 114
V E IL K+FS FG++E++ + YAFV F +A +A + + GK
Sbjct: 27 VTEEILEKSFSEFGKLERVKKL--KDYAFVHFEDRGAAVKAMDEMNGK 72
>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 = 37.0 bits (84), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 37/62 (59%), Gaps = 2/62 (3%)
Query: 68 DEVILRKAFSPFGEIEKITVFPGR-SYAFVQFRSIISACRAKETLQG-KLFGNPRVHICF 125
+E++L F+ F +++ + PGR AFV+F + + A A++ LQG K+ N + I F
Sbjct: 220 NELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISF 279
Query: 126 AK 127
AK
Sbjct: 280 AK 281
Score = 35.0 bits (79), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 5/71 (7%)
Query: 65 LKVDEVI--LRKAFSPFGEIEKITV---FPGRSYAFVQFRSIISACRAKETLQGKLFGNP 119
+K DE+ L FS FG+I I V R AFV F+ + SA A ++QG F +
Sbjct: 21 IKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 80
Query: 120 RVHICFAKSEA 130
+ I +AK+++
Sbjct: 81 PMRIQYAKTDS 91
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 36.6 bits (83), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 45/78 (57%), Gaps = 5/78 (6%)
Query: 53 PSEVLWI-GFPALLKVDEVILRKAFSPFGEIEKITVFPGR-SYAFVQFRSIISACRAKET 110
P+ +L++ P + +E++L F+ F +++ + PGR AFV+F + + A A++
Sbjct: 12 PNHILFLTNLPE--ETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDA 69
Query: 111 LQG-KLFGNPRVHICFAK 127
LQG K+ N + I FAK
Sbjct: 70 LQGFKITQNNAMKISFAK 87
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 42/92 (45%), Gaps = 8/92 (8%)
Query: 42 EKSKMTDKNAEPSEVLWIGFPALLKVDEVILRKAFSPFGEIEKITVFPGR-------SYA 94
EKSK TD + I + +DE +LR++F FG IEKI + G+ A
Sbjct: 198 EKSKRTDSATLEGREIXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCA 257
Query: 95 FVQFRSIISACRAKETLQGKLFGNPRVHICFA 126
F F + SA RA + L GN + + A
Sbjct: 258 FXVFENKDSAERALQX-NRSLLGNREISVSLA 288
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 35.4 bits (80), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 54 SEVLWIGFPALLKVDEVILRKAFSPFGEIEKITVF----PGRS--YAFVQFRSIISACRA 107
S L++G + E +LR F PFG+I+ I + GRS Y F+ F A RA
Sbjct: 5 SSGLYVG-SLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63
Query: 108 KETLQG-KLFGNP 119
E L G +L G P
Sbjct: 64 LEQLNGFELAGRP 76
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 35.4 bits (80), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 6/60 (10%)
Query: 57 LWIGFPALLKVDEVILRKAFSPFGEIEKITVFPG-----RSYAFVQFRSIISACRAKETL 111
L++G + DE + RK F PFG I++ TV G + AFV+F++ A A TL
Sbjct: 15 LFVGMLGKQQTDEDV-RKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTL 73
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 35.0 bits (79), Expect = 0.17, Method: Composition-based stats.
Identities = 22/54 (40%), Positives = 27/54 (50%)
Query: 67 VDEVILRKAFSPFGEIEKITVFPGRSYAFVQFRSIISACRAKETLQGKLFGNPR 120
+ E LR F FGEI ITV + AF+QF + +A A E KL N R
Sbjct: 24 ITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGR 77
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 34.7 bits (78), Expect = 0.20, Method: Composition-based stats.
Identities = 23/62 (37%), Positives = 32/62 (51%), Gaps = 3/62 (4%)
Query: 72 LRKAFSPFGEIEKITVFPG---RSYAFVQFRSIISACRAKETLQGKLFGNPRVHICFAKS 128
L FS FG+I I R AFV F+ I SA A T+QG F + + I ++KS
Sbjct: 27 LYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIGSASNALRTMQGFPFYDKPMQIAYSKS 86
Query: 129 EA 130
++
Sbjct: 87 DS 88
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 34.7 bits (78), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 7/86 (8%)
Query: 50 NAEPSEVLWIGFPALLKVDEVILRKAFSPFGEIEKITVF------PGRSYAFVQFRSIIS 103
N +P+ L + F L E LR+ FS +G I +++ R +AFV F ++
Sbjct: 42 NPDPNCCLGV-FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 100
Query: 104 ACRAKETLQGKLFGNPRVHICFAKSE 129
A AKE G R+ + F+ ++
Sbjct: 101 AKEAKERANGMELDGRRIRVDFSITK 126
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 34.7 bits (78), Expect = 0.22, Method: Composition-based stats.
Identities = 29/90 (32%), Positives = 44/90 (48%), Gaps = 8/90 (8%)
Query: 35 RHFSPDSEKSKMTDKNAEPSEVLWIGFPALLKVDEVILRKAFSPFGEIEKITV------F 88
RH S S + +A VL++G A +VD+ +L AF PFG+I I +
Sbjct: 44 RHVDGGSGGSGGSGGSATTKRVLYVGGLAE-EVDDKVLHAAFIPFGDITDIQIPLDYETE 102
Query: 89 PGRSYAFVQFRSIISACRAKETL-QGKLFG 117
R +AFV+F A A + + + +LFG
Sbjct: 103 KHRGFAFVEFELAEDAAAAIDNMNESELFG 132
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 34.3 bits (77), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 7/83 (8%)
Query: 50 NAEPSEVLWIGFPALLKVDEVILRKAFSPFGEIEKITVF------PGRSYAFVQFRSIIS 103
N +P+ L + F L E LR+ FS +G I +++ R +AFV F ++
Sbjct: 11 NPDPNCCLGV-FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 69
Query: 104 ACRAKETLQGKLFGNPRVHICFA 126
A AKE G R+ + F+
Sbjct: 70 AKEAKERANGMELDGRRIRVDFS 92
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 34.3 bits (77), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 4/68 (5%)
Query: 72 LRKAFSPFGEIEKITVF----PGRSYAFVQFRSIISACRAKETLQGKLFGNPRVHICFAK 127
LR+ F FG+I + + + + FV F + A RA+E L G + ++ + A
Sbjct: 32 LRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT 91
Query: 128 SEAGANSG 135
+ NSG
Sbjct: 92 ARVMTNSG 99
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 33.9 bits (76), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 26/70 (37%), Positives = 34/70 (48%), Gaps = 8/70 (11%)
Query: 57 LWIGFPALLKVDEVILRKAFSPFGEIEKITVF----PGRS--YAFVQFRSIISACRAKET 110
L++G + E +LR F PFG IE I + GRS Y F+ F A +A E
Sbjct: 29 LYVG-SLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 111 LQG-KLFGNP 119
L G +L G P
Sbjct: 88 LNGFELAGRP 97
>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 = 33.9 bits (76), Expect = 0.40, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 8/74 (10%)
Query: 51 AEPSEVLWIGFPALLKVDEVILRKAFSPFGEIEKITV------FPGRSYAFVQFRSIISA 104
A VL++G A +VD+ +L AF PFG+I I + R +AFV+F A
Sbjct: 4 ATTKRVLYVGGLAE-EVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 62
Query: 105 CRAKETL-QGKLFG 117
A + + + +LFG
Sbjct: 63 AAAIDNMNESELFG 76
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 33.9 bits (76), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 7/80 (8%)
Query: 50 NAEPSEVLWIGFPALLKVDEVILRKAFSPFGEIEKITVF------PGRSYAFVQFRSIIS 103
N +P+ L + F L E LR+ FS +G I +++ R +AFV F ++
Sbjct: 11 NPDPNCCLGV-FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 69
Query: 104 ACRAKETLQGKLFGNPRVHI 123
A AKE G R+ +
Sbjct: 70 AKEAKERANGMELDGRRIRV 89
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 33.5 bits (75), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 7/86 (8%)
Query: 50 NAEPSEVLWIGFPALLKVDEVILRKAFSPFGEIEKITVF------PGRSYAFVQFRSIIS 103
N +P+ L + F L E LR+ FS +G I +++ R +AFV F ++
Sbjct: 8 NPDPNCCLGV-FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 66
Query: 104 ACRAKETLQGKLFGNPRVHICFAKSE 129
A AKE G R+ + F+ ++
Sbjct: 67 AKEAKERANGMELDGRRIRVDFSITK 92
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 33.5 bits (75), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 6/84 (7%)
Query: 53 PSEVLWIG-FPALLKVDEVI--LRKAFSPFGEIEKITV---FPGRSYAFVQFRSIISACR 106
P+ ++I +K DE+ L FS FG+I I V R AFV F+ + SA
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 107 AKETLQGKLFGNPRVHICFAKSEA 130
A ++QG F + + I +AK+++
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDS 90
>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 = 33.5 bits (75), Expect = 0.47, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 5/71 (7%)
Query: 65 LKVDEV--ILRKAFSPFGEIEKITV---FPGRSYAFVQFRSIISACRAKETLQGKLFGNP 119
+K DE+ L FS FG+I I V R AFV F+ + SA A ++QG F +
Sbjct: 16 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 75
Query: 120 RVHICFAKSEA 130
+ I +AK+++
Sbjct: 76 PMRIQYAKTDS 86
>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 = 33.5 bits (75), Expect = 0.48, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 5/71 (7%)
Query: 65 LKVDEV--ILRKAFSPFGEIEKITV---FPGRSYAFVQFRSIISACRAKETLQGKLFGNP 119
+K DE+ L FS FG+I I V R AFV F+ + SA A ++QG F +
Sbjct: 15 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 74
Query: 120 RVHICFAKSEA 130
+ I +AK+++
Sbjct: 75 PMRIQYAKTDS 85
>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 = 33.5 bits (75), Expect = 0.48, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 5/71 (7%)
Query: 65 LKVDEV--ILRKAFSPFGEIEKITV---FPGRSYAFVQFRSIISACRAKETLQGKLFGNP 119
+K DE+ L FS FG+I I V R AFV F+ + SA A ++QG F +
Sbjct: 17 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 76
Query: 120 RVHICFAKSEA 130
+ I +AK+++
Sbjct: 77 PMRIQYAKTDS 87
>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 = 33.5 bits (75), Expect = 0.50, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 5/71 (7%)
Query: 65 LKVDEV--ILRKAFSPFGEIEKITV---FPGRSYAFVQFRSIISACRAKETLQGKLFGNP 119
+K DE+ L FS FG+I I V R AFV F+ + SA A ++QG F +
Sbjct: 20 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 79
Query: 120 RVHICFAKSEA 130
+ I +AK+++
Sbjct: 80 PMRIQYAKTDS 90
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 33.1 bits (74), Expect = 0.56, Method: Composition-based stats.
Identities = 31/96 (32%), Positives = 48/96 (50%), Gaps = 13/96 (13%)
Query: 51 AEPSEVLWIGFPALLKVDEVILRKAFSPFGEIEKITV------FPGRSYAFVQFRSIISA 104
A VL++G A +VD+ +L AF PFG+I I + R +AFV+F A
Sbjct: 9 ATTKRVLYVGGLAE-EVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67
Query: 105 CRAKETL-QGKLFGNPRVHICFAK----SEAGANSG 135
A + + + +LFG + + AK E+G +SG
Sbjct: 68 AAAIDNMNESELFGRT-IRVNLAKPMRIKESGPSSG 102
>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 = 33.1 bits (74), Expect = 0.58, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 5/71 (7%)
Query: 65 LKVDEV--ILRKAFSPFGEIEKITV---FPGRSYAFVQFRSIISACRAKETLQGKLFGNP 119
+K DE+ L FS FG+I I V R AFV F+ + SA A ++QG F +
Sbjct: 21 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 80
Query: 120 RVHICFAKSEA 130
+ I +AK+++
Sbjct: 81 PMRIQYAKTDS 91
>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 = 33.1 bits (74), Expect = 0.58, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 5/71 (7%)
Query: 65 LKVDEV--ILRKAFSPFGEIEKITV---FPGRSYAFVQFRSIISACRAKETLQGKLFGNP 119
+K DE+ L FS FG+I I V R AFV F+ + SA A ++QG F +
Sbjct: 21 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 80
Query: 120 RVHICFAKSEA 130
+ I +AK+++
Sbjct: 81 PMRIQYAKTDS 91
>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 = 33.1 bits (74), Expect = 0.63, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 5/71 (7%)
Query: 65 LKVDEV--ILRKAFSPFGEIEKITV---FPGRSYAFVQFRSIISACRAKETLQGKLFGNP 119
+K DE+ L FS FG+I I V R AFV F+ + SA A ++QG F +
Sbjct: 20 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 79
Query: 120 RVHICFAKSEA 130
+ I +AK+++
Sbjct: 80 PMRIQYAKTDS 90
>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 = 33.1 bits (74), Expect = 0.65, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 5/71 (7%)
Query: 65 LKVDEV--ILRKAFSPFGEIEKITV---FPGRSYAFVQFRSIISACRAKETLQGKLFGNP 119
+K DE+ L FS FG+I I V R AFV F+ + SA A ++QG F +
Sbjct: 20 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 79
Query: 120 RVHICFAKSEA 130
+ I +AK+++
Sbjct: 80 PMRIQYAKTDS 90
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 33.1 bits (74), Expect = 0.65, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 8/69 (11%)
Query: 56 VLWIGFPALLKVDEVILRKAFSPFGEIEKITV------FPGRSYAFVQFRSIISACRAKE 109
VL++G A +VD+ +L AF PFG+I I + R +AFV+F A A +
Sbjct: 7 VLYVGGLAE-EVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 110 TL-QGKLFG 117
+ + +LFG
Sbjct: 66 NMNESELFG 74
>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 = 33.1 bits (74), Expect = 0.65, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 8/69 (11%)
Query: 56 VLWIGFPALLKVDEVILRKAFSPFGEIEKITV------FPGRSYAFVQFRSIISACRAKE 109
VL++G A +VD+ +L AF PFG+I I + R +AFV+F A A +
Sbjct: 4 VLYVGGLAE-EVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 110 TL-QGKLFG 117
+ + +LFG
Sbjct: 63 NMNESELFG 71
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 32.7 bits (73), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 64 LLKVDEVILRKAFSPF--GEIEKITVFPGRSYAFVQFRSIISACRAKETLQGKLFGNPRV 121
+L E ++ K F+ G +E++ R YAFV F + A A + L GK+ +
Sbjct: 24 MLSTSEEMIEKEFNNIKPGAVERVKKI--RDYAFVHFSNREDAVEAMKALNGKVLDGSPI 81
Query: 122 HICFAK 127
+ AK
Sbjct: 82 EVTLAK 87
>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 = 32.7 bits (73), Expect = 0.72, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 5/71 (7%)
Query: 65 LKVDEV--ILRKAFSPFGEIEKITV---FPGRSYAFVQFRSIISACRAKETLQGKLFGNP 119
+K DE+ L FS FG+I I V R AFV F+ + SA A ++QG F +
Sbjct: 18 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 77
Query: 120 RVHICFAKSEA 130
+ I +AK+++
Sbjct: 78 PMRIQYAKTDS 88
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 32.7 bits (73), Expect = 0.72, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 5/71 (7%)
Query: 65 LKVDEV--ILRKAFSPFGEIEKITV---FPGRSYAFVQFRSIISACRAKETLQGKLFGNP 119
+K DE+ L FS FG+I I V R AFV F+ + SA A ++QG F +
Sbjct: 21 IKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 80
Query: 120 RVHICFAKSEA 130
+ I +AK+++
Sbjct: 81 PMRIQYAKTDS 91
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 32.3 bits (72), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 40/85 (47%), Gaps = 17/85 (20%)
Query: 40 DSEKSKMTDKNAEPSEVLWIGFPALLKVDEVILRKAFSPFGEIEKITVFPG-----RSYA 94
DSEK+ NA L+IG + K E +R FS FG+IE+ + G R A
Sbjct: 98 DSEKN-----NAVEDRKLFIGMISK-KCTENDIRVMFSSFGQIEECRILRGPDGLSRGCA 151
Query: 95 FVQF------RSIISACRAKETLQG 113
FV F ++ I A +T++G
Sbjct: 152 FVTFTTRAMAQTAIKAMHQAQTMEG 176
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 40/85 (47%), Gaps = 17/85 (20%)
Query: 40 DSEKSKMTDKNAEPSEVLWIGFPALLKVDEVILRKAFSPFGEIEKITVFPG-----RSYA 94
DSEK+ NA L+IG + K E +R FS FG+IE+ + G R A
Sbjct: 86 DSEKN-----NAVEDRKLFIGMISK-KCTENDIRVMFSSFGQIEECRILRGPDGLSRGCA 139
Query: 95 FVQF------RSIISACRAKETLQG 113
FV F ++ I A +T++G
Sbjct: 140 FVTFTTRAMAQTAIKAMHQAQTMEG 164
>pdb|3R27|A Chain A, Crystal Structure Of The First Rrm Domain Of Heterogeneous
Nuclear Ribonucleoprotein L (Hnrnp L)
pdb|3R27|B Chain B, Crystal Structure Of The First Rrm Domain Of Heterogeneous
Nuclear Ribonucleoprotein L (Hnrnp L)
Length = 100
Score = 31.6 bits (70), Expect = 1.7, Method: Composition-based stats.
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 67 VDEVILRKAFSPFGEIEKITVFPGRSYAFVQFRSIISACRA 107
V E L +A FG I + V P + A V+F ++ AC A
Sbjct: 33 VVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNA 73
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 7/70 (10%)
Query: 50 NAEPSEVLWIGFPALLKVDEVILRKAFSPFGEIEKITVFPGRSYAFVQF---RSIISA-- 104
N P L+IG L V + L + FSP+G I +I + ++ F+QF +S+ A
Sbjct: 6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--KNAFGFIQFDNPQSVRDAIE 63
Query: 105 CRAKETLQGK 114
C ++E GK
Sbjct: 64 CESQEMNFGK 73
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 31.2 bits (69), Expect = 2.6, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 65 LKVDEV--ILRKAFSPFGEIEKITV---FPGRSYAFVQFRSIISACRAKETLQGKLFGNP 119
+K DE+ L FS FG+I I V R AFV F+ + SA A + QG F +
Sbjct: 20 IKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDK 79
Query: 120 RVHICFAKSEA 130
I +AK+++
Sbjct: 80 PXRIQYAKTDS 90
>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 = 31.2 bits (69), Expect = 2.6, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 65 LKVDEV--ILRKAFSPFGEIEKITV---FPGRSYAFVQFRSIISACRAKETLQGKLFGNP 119
+K DE+ L FS FG+I I V R AFV F+ + SA A + QG F +
Sbjct: 21 IKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDK 80
Query: 120 RVHICFAKSEA 130
I +AK+++
Sbjct: 81 PXRIQYAKTDS 91
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 30.8 bits (68), Expect = 2.8, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 65 LKVDEV--ILRKAFSPFGEIEKITV---FPGRSYAFVQFRSIISACRAKETLQGKLFGNP 119
+K DE+ L FS FG+I I V R AFV F+ + SA A + QG F +
Sbjct: 18 IKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDK 77
Query: 120 RVHICFAKSEA 130
I +AK+++
Sbjct: 78 PXRIQYAKTDS 88
>pdb|2B0G|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
pdb|2AYM|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
Length = 83
Score = 30.0 bits (66), Expect = 5.3, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 2/64 (3%)
Query: 66 KVDEVILRKAFSPFGEIEKITVFPGR-SYAFVQFRSIISACRAKETLQG-KLFGNPRVHI 123
+ +E++L F+ F +++ + P R AFV+F + + + AKE LQG K+ + I
Sbjct: 19 ETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKI 78
Query: 124 CFAK 127
FAK
Sbjct: 79 TFAK 82
>pdb|1Y7U|A Chain A, Crystal Structure Of Acyl-Coa Hydrolase From Bacillus
Cereus
pdb|1Y7U|B Chain B, Crystal Structure Of Acyl-Coa Hydrolase From Bacillus
Cereus
pdb|1Y7U|C Chain C, Crystal Structure Of Acyl-Coa Hydrolase From Bacillus
Cereus
Length = 174
Score = 29.6 bits (65), Expect = 6.2, Method: Composition-based stats.
Identities = 17/66 (25%), Positives = 32/66 (48%)
Query: 599 VSGNRNIPSQASNSFVDSSIDGHPSVVPKVVQETSSAYTDGISGIPLSENRQLSHQETKP 658
+SG + I + + +FV S + +P VP+V+ +T + +E R + E+K
Sbjct: 108 ISGEKRIAATSFVTFVALSKENNPVPVPRVIPDTEEEKESHRIAVLRAEQRHIRKAESKK 167
Query: 659 SGSLPT 664
+L T
Sbjct: 168 VATLLT 173
>pdb|2O3B|A Chain A, Crystal Structure Complex Of Nuclease A (Nuca) With
Intra-Cellular Inhibitor Nuia
Length = 241
Score = 29.3 bits (64), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 4/77 (5%)
Query: 497 RLEPPGY----NQGPIHHPNELKDANYLSFNADASYLNQSMRSEPFPSRVSFPDMTMSAQ 552
+L P Y NQ + + N AN++++ ++S+L + R + F + P +
Sbjct: 19 KLTPDNYLMVKNQYALSYNNSKGTANWVAWQLNSSWLGNAERQDNFRPDKTLPAGWVRVT 78
Query: 553 SASYPGSVHSMGNISDS 569
+ Y GS ++ G+I+ S
Sbjct: 79 PSMYSGSGYARGHIAPS 95
>pdb|2PE8|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 (free
Form)
pdb|2PEH|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
pdb|2PEH|B Chain B, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
Length = 105
Score = 29.3 bits (64), Expect = 8.4, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 7/64 (10%)
Query: 69 EVILRKAFSPFGEIEKITVF--PGRS-----YAFVQFRSIISACRAKETLQGKLFGNPRV 121
EV ++ +G++ K +F PG F++F + SA +A L G+ FG V
Sbjct: 27 EVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV 86
Query: 122 HICF 125
CF
Sbjct: 87 KACF 90
>pdb|2E5I|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Heterogeneous Nuclear Ribonucleoprotein L-Like
Length = 124
Score = 29.3 bits (64), Expect = 9.8, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 71 ILRKAFSPFGEIEKITVFPGRSY-AFVQFRSIISACRAKETLQG 113
+L +P G++++I +F A V+F S++ A +AK L G
Sbjct: 41 VLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNG 84
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.313 0.131 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,033,794
Number of Sequences: 62578
Number of extensions: 1166921
Number of successful extensions: 1743
Number of sequences better than 100.0: 55
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 43
Number of HSP's that attempted gapping in prelim test: 1725
Number of HSP's gapped (non-prelim): 57
length of query: 806
length of database: 14,973,337
effective HSP length: 107
effective length of query: 699
effective length of database: 8,277,491
effective search space: 5785966209
effective search space used: 5785966209
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (25.8 bits)