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= 046223
(408 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 = 45.4 bits (106), Expect = 5e-05, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 46/78 (58%), Gaps = 3/78 (3%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
+ V NL + V+ L++ F FG ++ +++ K FI F + A KA++EMNG+++
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKDL 70
Query: 291 YGKHVVIEFSRPGGHSKK 308
G+++ I F++P +K
Sbjct: 71 EGENIEIVFAKPPDQKRK 88
>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 = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 44/86 (51%), Gaps = 5/86 (5%)
Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRD 277
PD ++ V NL S TL+ +F+ +G V ++ R T + F+ F+D RD
Sbjct: 42 PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 101
Query: 278 AAKALKEMNGQEIYGKHVVIEFSRPG 303
A A+ M+G + G+ + ++ +R G
Sbjct: 102 AEDAMDAMDGAVLDGRELRVQMARYG 127
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 49/92 (53%), Gaps = 7/92 (7%)
Query: 218 TCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR------FIE 271
+ ++ PD + T+ V NL S +L+ +F+ +G V ++ P + H + F+
Sbjct: 3 SGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDV-YIPREPHTKAPRGFAFVR 61
Query: 272 FYDVRDAAKALKEMNGQEIYGKHVVIEFSRPG 303
F+D RDA A M+G E+ G+ + ++ +R G
Sbjct: 62 FHDRRDAQDAEAAMDGAELDGRELRVQVARYG 93
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 5/83 (6%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEM 285
++V L ++ L +F+A GP+ R +T F++F D+ +A+K +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 286 NGQEIYGKHVVIEFSRPGGHSKK 308
NG + K + + ++RPGG S K
Sbjct: 66 NGITVRNKRLKVSYARPGGESIK 88
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
+ V NL +G L+ F +GP++ + F+EF D RDA A++ ++G+ I
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 291 YGKHVVIEFS 300
G V +E S
Sbjct: 63 CGSRVRVELS 72
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 40/74 (54%), Gaps = 4/74 (5%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR----FIEFYDVRDAAKALKEMN 286
+ V NLD ++ LK+ FQ GP+ ++ K ++ F+E++ DA AL+ +N
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 287 GQEIYGKHVVIEFS 300
G++I V I ++
Sbjct: 63 GKQIENNIVKINWA 76
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 5/79 (6%)
Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
++ V NL S TL+ +F+ +G V ++ R T + F+ F+D RDA A+
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 285 MNGQEIYGKHVVIEFSRPG 303
M+G + G+ + ++ +R G
Sbjct: 132 MDGAVLDGRELRVQMARYG 150
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 5/73 (6%)
Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKEMNG 287
VF L + L+E+F +GP+ ++ ++ +R F+ F +V DA +A + NG
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 288 QEIYGKHVVIEFS 300
E+ G+ + ++FS
Sbjct: 111 MELDGRRIRVDFS 123
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 45/85 (52%), Gaps = 7/85 (8%)
Query: 221 AVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDV 275
A PD N + VF L + L+E+F +GP+ ++ ++ +R F+ F +V
Sbjct: 7 ANPDPN--CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 64
Query: 276 RDAAKALKEMNGQEIYGKHVVIEFS 300
DA +A + NG E+ G+ + ++FS
Sbjct: 65 DDAKEAKERANGMELDGRRIRVDFS 89
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 5/73 (6%)
Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKEMNG 287
VF L + L+E+F +GP+ ++ ++ +R F+ F +V DA +A + NG
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 288 QEIYGKHVVIEFS 300
E+ G+ + ++FS
Sbjct: 80 MELDGRRIRVDFS 92
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 41.6 bits (96), Expect = 8e-04, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 5/83 (6%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEM 285
++V L ++ L +F+A GP+ R +T F++F D+ +A+K +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 286 NGQEIYGKHVVIEFSRPGGHSKK 308
NG + K + + ++RPGG S K
Sbjct: 66 NGITVRNKRLKVSYARPGGESIK 88
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 27/86 (31%), Positives = 43/86 (50%), Gaps = 8/86 (9%)
Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQ-----RFIEFYDVRD 277
P GNN I V NL + + ++++F +G + R+ LK + F+EF D RD
Sbjct: 17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAI---RDIDLKNRRGGPPFAFVEFEDPRD 73
Query: 278 AAKALKEMNGQEIYGKHVVIEFSRPG 303
A A+ +G + G + +EF R G
Sbjct: 74 AEDAVYGRDGYDYDGYRLRVEFPRSG 99
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 39/70 (55%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
+ V NL + + + L+ F +GP++ + F+EF D RDAA A++E++G+ +
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTL 135
Query: 291 YGKHVVIEFS 300
G V +E S
Sbjct: 136 CGCRVRVELS 145
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 19/79 (24%), Positives = 42/79 (53%), Gaps = 5/79 (6%)
Query: 225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAA 279
+++G + V L + +L+++F +G + E+ RET + F+ F ++ DA
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 280 KALKEMNGQEIYGKHVVIE 298
A+ MNG+ + G+ + ++
Sbjct: 69 DAMMAMNGKSVDGRQIRVD 87
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 44/91 (48%), Gaps = 6/91 (6%)
Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRD 277
P +N IV + L + L +F+A GP+ R +T F++F D
Sbjct: 10 PRASNTNLIVNY-LPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXD 68
Query: 278 AAKALKEMNGQEIYGKHVVIEFSRPGGHSKK 308
+ +A+K +NG + K + + ++RPGG S K
Sbjct: 69 SQRAIKVLNGITVRNKRLKVSYARPGGESIK 99
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKE-LRETPLKKHQRFIEFYDVRDAAKALKEMNGQ 288
T+V+ NL + TL+E+F+ +K + K FIEF DA +AL N +
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKR 76
Query: 289 EIYGKHVVIEFSRPGG 304
EI G+ + +E P G
Sbjct: 77 EIEGRAIRLELQGPRG 92
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 39/70 (55%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
+ V NL + + + L+ F +GP++ + F+EF D RDAA A+++++G+ +
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRTL 135
Query: 291 YGKHVVIEFS 300
G V +E S
Sbjct: 136 CGCRVRVELS 145
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 28/80 (35%), Positives = 41/80 (51%), Gaps = 3/80 (3%)
Query: 224 DGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR---ETPLKKHQRFIEFYDVRDAAK 280
D T+ V NL V+ + ++F GP K + E F+EFY+ RDAA
Sbjct: 11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAA 70
Query: 281 ALKEMNGQEIYGKHVVIEFS 300
AL MNG++I GK V + ++
Sbjct: 71 ALAAMNGRKILGKEVKVNWA 90
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMN 286
N I V N+ + +S L+ +F+ G V E + K F+ DA A+ ++N
Sbjct: 8 NTWKIFVGNVSAACTSQELRSLFERRGRVIE---CDVVKDYAFVHMEKEADAKAAIAQLN 64
Query: 287 GQEIYGKHVVIEFSRPG 303
G+E+ GK + +E S G
Sbjct: 65 GKEVKGKRINVELSTKG 81
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 44/93 (47%), Gaps = 7/93 (7%)
Query: 222 VPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL---RETPLKKHQ--RFIEFYDVR 276
+ + N T+ V LD VS L E+F GPV ++ +HQ F+EF
Sbjct: 9 ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 68
Query: 277 DAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKF 309
DA A+K M+ ++YGK I ++ H+K
Sbjct: 69 DADYAIKIMDMIKLYGK--PIRVNKASAHNKNL 99
>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 = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 44/87 (50%), Gaps = 6/87 (6%)
Query: 221 AVPDGNNQGTIVVFNLDSGVSSSTLKE----IFQAFGPVKE-LRETPLK-KHQRFIEFYD 274
AVP+ TI + NL+ + LK+ IF FG + + L LK + Q F+ F +
Sbjct: 2 AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKE 61
Query: 275 VRDAAKALKEMNGQEIYGKHVVIEFSR 301
V A AL+ M G Y K + I++++
Sbjct: 62 VSSATNALRSMQGFPFYDKPMRIQYAK 88
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 40/78 (51%)
Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
T++ NL ++ LKE+F+ ++ + + K +IEF DA K L+E G E
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAE 77
Query: 290 IYGKHVVIEFSRPGGHSK 307
I G+ V + ++ G ++
Sbjct: 78 IDGRSVSLYYTGEKGGTR 95
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 40/68 (58%), Gaps = 5/68 (7%)
Query: 234 FNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGK 293
F LD V S L EIF FGP+KE++ + F+EF + AAKA++E++G+ +
Sbjct: 39 FPLD--VQESELNEIFGPFGPMKEVK---ILNGFAFVEFEEAESAAKAIEEVHGKSFANQ 93
Query: 294 HVVIEFSR 301
+ + +S+
Sbjct: 94 PLEVVYSK 101
>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 = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 44/87 (50%), Gaps = 6/87 (6%)
Query: 221 AVPDGNNQGTIVVFNLDSGVSSSTLKE----IFQAFGPVKE-LRETPLK-KHQRFIEFYD 274
AVP+ TI + NL+ + LK+ IF FG + + L LK + Q F+ F +
Sbjct: 1 AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKE 60
Query: 275 VRDAAKALKEMNGQEIYGKHVVIEFSR 301
V A AL+ M G Y K + I++++
Sbjct: 61 VSSATNALRSMQGFPFYDKPMRIQYAK 87
>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 = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 44/87 (50%), Gaps = 6/87 (6%)
Query: 221 AVPDGNNQGTIVVFNLDSGVSSSTLKE----IFQAFGPVKE-LRETPLK-KHQRFIEFYD 274
AVP+ TI + NL+ + LK+ IF FG + + L LK + Q F+ F +
Sbjct: 2 AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKE 61
Query: 275 VRDAAKALKEMNGQEIYGKHVVIEFSR 301
V A AL+ M G Y K + I++++
Sbjct: 62 VSSATNALRSMQGFPFYDKPMRIQYAK 88
>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 = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 44/87 (50%), Gaps = 6/87 (6%)
Query: 221 AVPDGNNQGTIVVFNLDSGVSSSTLKE----IFQAFGPVKE-LRETPLK-KHQRFIEFYD 274
AVP+ TI + NL+ + LK+ IF FG + + L LK + Q F+ F +
Sbjct: 2 AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKE 61
Query: 275 VRDAAKALKEMNGQEIYGKHVVIEFSR 301
V A AL+ M G Y K + I++++
Sbjct: 62 VSSATNALRSMQGFPFYDKPMRIQYAK 88
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 4/82 (4%)
Query: 224 DGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL----RETPLKKHQRFIEFYDVRDAA 279
+ ++ G + + L+ + LK +F GP+ E+ T + FI F + DA
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAK 62
Query: 280 KALKEMNGQEIYGKHVVIEFSR 301
A K+MNG+ ++GK + +E ++
Sbjct: 63 NAAKDMNGKSLHGKAIKVEQAK 84
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 44/87 (50%), Gaps = 6/87 (6%)
Query: 221 AVPDGNNQGTIVVFNLDSGVSSSTLKE----IFQAFGPVKE-LRETPLK-KHQRFIEFYD 274
AVP+ TI + NL+ + LK+ IF FG + + L LK + Q F+ F +
Sbjct: 2 AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKE 61
Query: 275 VRDAAKALKEMNGQEIYGKHVVIEFSR 301
V A AL+ M G Y K + I++++
Sbjct: 62 VSSATNALRSMQGFPFYDKPMRIQYAK 88
>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 = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 44/87 (50%), Gaps = 6/87 (6%)
Query: 221 AVPDGNNQGTIVVFNLDSGVSSSTLKE----IFQAFGPVKE-LRETPLK-KHQRFIEFYD 274
AVP+ TI + NL+ + LK+ IF FG + + L LK + Q F+ F +
Sbjct: 1 AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKE 60
Query: 275 VRDAAKALKEMNGQEIYGKHVVIEFSR 301
V A AL+ M G Y K + I++++
Sbjct: 61 VSSATNALRSMQGFPFYDKPMRIQYAK 87
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 44/87 (50%), Gaps = 6/87 (6%)
Query: 221 AVPDGNNQGTIVVFNLDSGVSSSTLKE----IFQAFGPVKE-LRETPLK-KHQRFIEFYD 274
AVP+ TI + NL+ + LK+ IF FG + + L LK + Q F+ F +
Sbjct: 1 AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKE 60
Query: 275 VRDAAKALKEMNGQEIYGKHVVIEFSR 301
V A AL+ M G Y K + I++++
Sbjct: 61 VSSATNALRSMQGFPFYDKPMRIQYAK 87
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 40/68 (58%), Gaps = 5/68 (7%)
Query: 234 FNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGK 293
F LD V S L EIF FGP+KE++ + F+EF + AAKA++E++G+ +
Sbjct: 12 FPLD--VQESELNEIFGPFGPMKEVK---ILNGFAFVEFEEAESAAKAIEEVHGKSFANQ 66
Query: 294 HVVIEFSR 301
+ + +S+
Sbjct: 67 PLEVVYSK 74
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 38.1 bits (87), Expect = 0.010, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 44/87 (50%), Gaps = 6/87 (6%)
Query: 221 AVPDGNNQGTIVVFNLDSGVSSSTLKE----IFQAFGPVKE-LRETPLK-KHQRFIEFYD 274
AVP+ TI + NL+ + LK+ IF FG + + L LK + Q F+ F +
Sbjct: 1 AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKE 60
Query: 275 VRDAAKALKEMNGQEIYGKHVVIEFSR 301
V A AL+ M G Y K + I++++
Sbjct: 61 VSSATNALRSMQGFPFYDKPMRIQYAK 87
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 2/67 (2%)
Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
T+ + SG++ +++ F FG + E+R P K + F+ F AA A+ +NG
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYS-FVRFSTHESAAHAIVSVNGTT 85
Query: 290 IYGKHVV 296
I G HVV
Sbjct: 86 IEG-HVV 91
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 233 VFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAKALKEMNG 287
VF L + L+E+F +GP+ ++ ++ +R F+ F +V DA +A + NG
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 288 QEIYGKHVVI 297
E+ G+ + +
Sbjct: 80 MELDGRRIRV 89
>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 = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 38/75 (50%)
Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
T++ NL ++ LKE+F+ ++ + + K +IEF DA K L+E G E
Sbjct: 101 TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAE 160
Query: 290 IYGKHVVIEFSRPGG 304
I G+ V + ++ G
Sbjct: 161 IDGRSVSLYYTGEKG 175
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 36.6 bits (83), Expect = 0.024, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 5/68 (7%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEM 285
+ V +L ++ L+ IF+ FG ++ ++ ET K FI F D A KAL+++
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 286 NGQEIYGK 293
NG E+ G+
Sbjct: 89 NGFELAGR 96
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 36.6 bits (83), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKE 284
++ V N+ + LK+IF GPV R ET K F E+ D A A++
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 285 MNGQEIYGKHVVIE 298
+NG+E G+ + ++
Sbjct: 70 LNGREFSGRALRVD 83
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 36.6 bits (83), Expect = 0.029, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 7/78 (8%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPL----KKHQ--RFIEFYDVRDAAKALKE 284
+ V L V L F FG + ++ + PL +KH+ F+EF DAA A+
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDI-QIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73
Query: 285 MNGQEIYGKHVVIEFSRP 302
MN E++G+ + + ++P
Sbjct: 74 MNESELFGRTIRVNLAKP 91
>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 = 36.6 bits (83), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 236 LDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEIY 291
L GV + L E Q FGP+ + P KK Q +EF DV A A+ +IY
Sbjct: 29 LIDGVVEADLVEALQEFGPISYVVVMP-KKRQALVEFEDVLGACNAVNYAADNQIY 83
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 36.2 bits (82), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 15/71 (21%), Positives = 41/71 (57%), Gaps = 2/71 (2%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR--ETPLKKHQRFIEFYDVRDAAKALKEMNGQ 288
+ + NL +++ + +IF +GP++++R TP + ++ + D+ DA A+ ++G
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGF 70
Query: 289 EIYGKHVVIEF 299
+ +++V+ +
Sbjct: 71 NVSNRYLVVLY 81
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 36.2 bits (82), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 44/91 (48%), Gaps = 5/91 (5%)
Query: 216 VPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAF----GPVKELRE-TPLKKHQRFI 270
+P ++ G + + NL V+ L +F F GP + R T + Q FI
Sbjct: 13 IPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFI 72
Query: 271 EFYDVRDAAKALKEMNGQEIYGKHVVIEFSR 301
F + A +AL +NG ++YGK +VIEF +
Sbjct: 73 TFPNKEIAWQALHLVNGYKLYGKILVIEFGK 103
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 36.2 bits (82), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVR-----DAAKALKEM 285
++V NLD GVS + ++E+F FG +K+ + R + DV DA KA+K+
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKA-AVDYDRSGRSLGTADVHFERRADALKAMKQY 149
Query: 286 NGQEIYGKHVVIEF 299
G + G+ + I+
Sbjct: 150 KGVPLDGRPMDIQL 163
>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 = 35.8 bits (81), Expect = 0.040, Method: Composition-based stats.
Identities = 15/71 (21%), Positives = 41/71 (57%), Gaps = 2/71 (2%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR--ETPLKKHQRFIEFYDVRDAAKALKEMNGQ 288
+++ NL +++ + +IF +GP++++R TP + ++ + D+ DA A ++G
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF 80
Query: 289 EIYGKHVVIEF 299
+ +++V+ +
Sbjct: 81 NVCNRYLVVLY 91
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 35.8 bits (81), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPV---KELRETPLKKHQRFIEFYDVRDAAKALKEMNG 287
+ V NLD G+ L++ F FG + K + E K F+ F +A KA+ EMNG
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 288 QEIYGKHVVIEFSR 301
+ + K + + ++
Sbjct: 78 RIVATKPLYVALAQ 91
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 35.8 bits (81), Expect = 0.048, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVR-----DAAKALKEM 285
++V NLD GVS + ++E+F FG +K+ + R + DV DA KA+K+
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKK-AAVHYDRSGRSLGTADVHFERKADALKAMKQY 89
Query: 286 NGQEIYGKHVVIEF 299
NG + G+ + I+
Sbjct: 90 NGVPLDGRPMNIQL 103
>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 = 35.4 bits (80), Expect = 0.061, Method: Composition-based stats.
Identities = 26/85 (30%), Positives = 42/85 (49%), Gaps = 6/85 (7%)
Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKE----IFQAFGPVKE-LRETPLK-KHQRFIEFYDVR 276
P+ TI + NL+ + LK+ IF FG + + L LK + Q F+ F +V
Sbjct: 1 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 60
Query: 277 DAAKALKEMNGQEIYGKHVVIEFSR 301
A AL+ M G Y K + I++++
Sbjct: 61 SATNALRSMQGFPFYDKPMRIQYAK 85
>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 = 35.4 bits (80), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 26/112 (23%), Positives = 53/112 (47%), Gaps = 9/112 (8%)
Query: 200 PARGLVAGRPVWAQFIVPTCNAVPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR 259
P G+ V+ +V T VPD ++ + + L + ++ +KE+ +FGP+K
Sbjct: 90 PLPGMSENPSVYVPGVVSTV--VPDSAHK--LFIGGLPNYLNDDQVKELLTSFGPLKAFN 145
Query: 260 -----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHS 306
T L K F E+ D+ +A+ +NG ++ K ++++ + G +
Sbjct: 146 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKN 197
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 35.0 bits (79), Expect = 0.071, Method: Composition-based stats.
Identities = 25/90 (27%), Positives = 47/90 (52%), Gaps = 11/90 (12%)
Query: 225 GNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAA 279
++ TI V NL + L+E+F+ FG + + + T K FI F+ DAA
Sbjct: 12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 71
Query: 280 KALKEMNGQEIYG-KHVV--IEFSRPGGHS 306
+A+ ++G +G H++ +E+++P +S
Sbjct: 72 RAIAGVSG---FGYDHLILNVEWAKPSTNS 98
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 35.0 bits (79), Expect = 0.073, Method: Composition-based stats.
Identities = 15/71 (21%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR--ETPLKKHQRFIEFYDVRDAAKALKEMNGQ 288
+ + NL +++ + +IF +GP++++R TP + ++ + D+ DA A ++G
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF 74
Query: 289 EIYGKHVVIEF 299
+ +++V+ +
Sbjct: 75 NVCNRYLVVLY 85
>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 = 35.0 bits (79), Expect = 0.073, Method: Composition-based stats.
Identities = 15/71 (21%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELR--ETPLKKHQRFIEFYDVRDAAKALKEMNGQ 288
+ + NL +++ + +IF +GP++++R TP + ++ + D+ DA A ++G
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF 80
Query: 289 EIYGKHVVIEF 299
+ +++V+ +
Sbjct: 81 NVCNRYLVVLY 91
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 35.0 bits (79), Expect = 0.074, Method: Composition-based stats.
Identities = 27/87 (31%), Positives = 42/87 (48%), Gaps = 6/87 (6%)
Query: 221 AVPDGNNQGTIVVFNLDSGVSSSTLKE----IFQAFGPVKE-LRETPLK-KHQRFIEFYD 274
AVP+ TI + NL+ + LK+ IF FG + + L LK + Q F+ F +
Sbjct: 1 AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKE 60
Query: 275 VRDAAKALKEMNGQEIYGKHVVIEFSR 301
V A AL+ G Y K I++++
Sbjct: 61 VSSATNALRSXQGFPFYDKPXRIQYAK 87
>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 = 35.0 bits (79), Expect = 0.074, Method: Composition-based stats.
Identities = 27/87 (31%), Positives = 42/87 (48%), Gaps = 6/87 (6%)
Query: 221 AVPDGNNQGTIVVFNLDSGVSSSTLKE----IFQAFGPVKE-LRETPLK-KHQRFIEFYD 274
AVP+ TI + NL+ + LK+ IF FG + + L LK + Q F+ F +
Sbjct: 2 AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKE 61
Query: 275 VRDAAKALKEMNGQEIYGKHVVIEFSR 301
V A AL+ G Y K I++++
Sbjct: 62 VSSATNALRSXQGFPFYDKPXRIQYAK 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 = 35.0 bits (79), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPV---KELRETPLKKHQRFIEFYDVRDAAKALKEM 285
G I + NLD + + L + F AFG + K + + K F+ F A +A+++M
Sbjct: 104 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 163
Query: 286 NGQEIYGKHVVI 297
NG + + V +
Sbjct: 164 NGMLLNDRKVFV 175
>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 = 35.0 bits (79), Expect = 0.082, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 230 TIVVFNLDSGVSSSTLKE----IFQAFGPVKE-LRETPLK-KHQRFIEFYDVRDAAKALK 283
TI + NL+ + LK+ IF FG + + L LK + Q F+ F +V A AL+
Sbjct: 7 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 66
Query: 284 EMNGQEIYGKHVVIEFSR 301
M G Y K + I++++
Sbjct: 67 SMQGFPFYDKPMRIQYAK 84
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 35.0 bits (79), Expect = 0.085, Method: Composition-based stats.
Identities = 22/86 (25%), Positives = 42/86 (48%), Gaps = 7/86 (8%)
Query: 222 VPDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR------ETPLKKHQRFIEFYDV 275
VP I+V N+ + ++E+F FG +K +R T + F++F
Sbjct: 9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 68
Query: 276 RDAAKALKEM-NGQEIYGKHVVIEFS 300
+DA KA + + +YG+ +V+E++
Sbjct: 69 QDAKKAFNALCHSTHLYGRRLVLEWA 94
>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 = 35.0 bits (79), Expect = 0.086, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 230 TIVVFNLDSGVSSSTLKE----IFQAFGPVKE-LRETPLK-KHQRFIEFYDVRDAAKALK 283
TI + NL+ + LK+ IF FG + + L LK + Q F+ F +V A AL+
Sbjct: 5 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64
Query: 284 EMNGQEIYGKHVVIEFSR 301
M G Y K + I++++
Sbjct: 65 SMQGFPFYDKPMRIQYAK 82
>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 = 34.7 bits (78), Expect = 0.087, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 230 TIVVFNLDSGVSSSTLKE----IFQAFGPVKE-LRETPLK-KHQRFIEFYDVRDAAKALK 283
TI + NL+ + LK+ IF FG + + L LK + Q F+ F +V A AL+
Sbjct: 6 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 65
Query: 284 EMNGQEIYGKHVVIEFSR 301
M G Y K + I++++
Sbjct: 66 SMQGFPFYDKPMRIQYAK 83
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 34.7 bits (78), Expect = 0.089, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 5/77 (6%)
Query: 224 DGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDA 278
D +N + V +L +++ +K F FG + + R T K F+ FY+ DA
Sbjct: 11 DTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDA 70
Query: 279 AKALKEMNGQEIYGKHV 295
A+ M GQ + G+ +
Sbjct: 71 ENAIVHMGGQWLGGRQI 87
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 34.7 bits (78), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 36/71 (50%)
Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
T++ NL V+ LKE+F+ ++ + + K +IEF DA K +E G E
Sbjct: 95 TLLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTE 154
Query: 290 IYGKHVVIEFS 300
I G+ + + ++
Sbjct: 155 IDGRSISLYYT 165
>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 = 34.7 bits (78), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPV---KELRETPLKKHQRFIEFYDVRDAAKALKEM 285
G I + NLD + + L + F AFG + K + + K F+ F A +A+++M
Sbjct: 99 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 158
Query: 286 NGQEIYGKHVVI 297
NG + + V +
Sbjct: 159 NGMLLNDRKVFV 170
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 7/77 (9%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPL----KKHQ--RFIEFYDVRDAAKALKE 284
+ V L V L F FG + ++ + PL +KH+ F+EF DAA A+
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDI-QIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66
Query: 285 MNGQEIYGKHVVIEFSR 301
MN E++G+ + + ++
Sbjct: 67 MNESELFGRTIRVNLAK 83
>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 = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 7/77 (9%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPL----KKHQ--RFIEFYDVRDAAKALKE 284
+ V L V L F FG + ++ + PL +KH+ F+EF DAA A+
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDI-QIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68
Query: 285 MNGQEIYGKHVVIEFSR 301
MN E++G+ + + ++
Sbjct: 69 MNESELFGRTIRVNLAK 85
>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 = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 240 VSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKH 294
++ +KE+ +FGP+K T L K F E+ D+ +A+ +NG ++ K
Sbjct: 108 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 167
Query: 295 VVIE 298
++++
Sbjct: 168 LLVQ 171
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 6/66 (9%)
Query: 236 LDSGVSSSTLKEIFQAFGPVKEL-----RETP-LKKHQRFIEFYDVRDAAKALKEMNGQE 289
L V+ + EIF +G +K + R P L K ++EF + +A KALK M+G +
Sbjct: 12 LTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQ 71
Query: 290 IYGKHV 295
I G+ +
Sbjct: 72 IDGQEI 77
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVR-----DAAKALKEM 285
++V NLD GVS + ++E+F FG +K+ + R + DV DA KA+K+
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKK-AAVDYDRSGRSLGTADVHFERRADALKAMKQY 96
Query: 286 NGQEIYGKHVVIEF 299
G + G+ + I+
Sbjct: 97 KGVPLDGRPMDIQL 110
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVR-----DAAKALKEM 285
++V NLD GVS + ++E+F FG +K+ + R + DV DA KA+K+
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKK-AAVDYDRSGRSLGTADVHFERRADALKAMKQY 96
Query: 286 NGQEIYGKHVVIEF 299
G + G+ + I+
Sbjct: 97 KGVPLDGRPMDIQL 110
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 240 VSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKH 294
++ +KE+ +FGP+K T L K F E+ D+ +A+ +NG ++ K
Sbjct: 106 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 165
Query: 295 VVIE 298
++++
Sbjct: 166 LLVQ 169
>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 = 33.9 bits (76), Expect = 0.17, Method: Composition-based stats.
Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 228 QGTIVVFN-LDSGVSSSTLKEIFQAFGPVK--ELRETPLKKHQR---FIEFYDVRDAAKA 281
QGT ++ N L + L+ +F + G V+ +L + H F+ + +DA +A
Sbjct: 18 QGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 77
Query: 282 LKEMNGQEIYGKHVVIEFSRP 302
+ +NG + K + + ++RP
Sbjct: 78 INTLNGLRLQSKTIKVSYARP 98
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 33.9 bits (76), Expect = 0.19, Method: Composition-based stats.
Identities = 27/86 (31%), Positives = 40/86 (46%), Gaps = 8/86 (9%)
Query: 223 PDGNNQ--GTIVVFNLDSGVSSSTLKEIFQAFGPVKEL----RETPLKKHQRFIEFYDVR 276
P+ +Q T+ V L + TLKE F G V+ RET K F++F
Sbjct: 8 PNARSQPSKTLFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEE 65
Query: 277 DAAKALKEMNGQEIYGKHVVIEFSRP 302
DA A + M EI G V +++++P
Sbjct: 66 DAKAAKEAMEDGEIDGNKVTLDWAKP 91
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 33.5 bits (75), Expect = 0.22, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPL----KKHQ--RFIEFYDVRDAAKALKE 284
+ V L V L F FG + ++ + PL +KH+ F+EF DAA A+
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDI-QIPLDYETEKHRGFAFVEFELAEDAAAAIDN 63
Query: 285 MNGQEIYGKHVVIEFS 300
MN E++G+ + + +
Sbjct: 64 MNESELFGRTIRVNLA 79
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 33.5 bits (75), Expect = 0.22, Method: Composition-based stats.
Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 6/68 (8%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVR-----DAAKALKEM 285
++V NLD GVS + ++E+F FG +K+ + R + DV DA KA K+
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKK-AAVHYDRSGRSLGTADVHFERKADALKAXKQY 90
Query: 286 NGQEIYGK 293
NG + G+
Sbjct: 91 NGVPLDGR 98
>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 = 33.5 bits (75), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 8/71 (11%)
Query: 244 TLKEIFQAFGPVKELRETPLKKHQ--------RFIEFYDVRDAAKALKEMNGQEIYGKHV 295
T +E FG + E+ L + + F+ + D +DA KA+ +NG + K +
Sbjct: 15 TQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTI 74
Query: 296 VIEFSRPGGHS 306
+ ++RP S
Sbjct: 75 KVSYARPSSAS 85
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 3/58 (5%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQ 288
+ V NL + V+ L++ F FG ++ +++ K F+ F D A KA+ EMNG+
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKL---KDYAFVHFEDRGAAVKAMDEMNGK 72
>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 = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPV---KELRETPLKKHQRFIEFYDVRDAAKALKEM 285
G I + NLD + + L + F AFG + K + + K F+ F A +A+++M
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 65
Query: 286 NGQEIYGKHVVI 297
NG + + V +
Sbjct: 66 NGMLLNDRKVFV 77
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 229 GTIVVFNLDSGVSSSTLKEIFQAFGPV---KELRETPLKKHQRFIEFYDVRDAAKALKEM 285
G I + NLD + + L + F AFG + K + + K F+ F A +A+++M
Sbjct: 12 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 71
Query: 286 NGQEIYGKHVVI 297
NG + + V +
Sbjct: 72 NGMLLNDRKVFV 83
>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 = 33.1 bits (74), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 225 GNNQGTIVVFNLD-SGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALK 283
G ++V NL+ V+ +L +F +G V+ ++ KK ++ D A A+
Sbjct: 31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMS 90
Query: 284 EMNGQEIYGKHVVIEFSR 301
+NG +++GK + I S+
Sbjct: 91 HLNGHKLHGKPIRITLSK 108
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 33.1 bits (74), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 18/79 (22%), Positives = 39/79 (49%), Gaps = 5/79 (6%)
Query: 230 TIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKE 284
++V + + V L+++F+ +GP++ + RET + F++F A +A+
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 285 MNGQEIYGKHVVIEFSRPG 303
+NG I K + + + G
Sbjct: 104 LNGFNILNKRLKVALAASG 122
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 32.7 bits (73), Expect = 0.36, Method: Composition-based stats.
Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 240 VSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKH 294
++ +KE+ +FGP+K T L K F E+ D+ +A+ +NG ++ K
Sbjct: 13 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 72
Query: 295 VVIEFSRPGG 304
++++ + G
Sbjct: 73 LLVQRASVGA 82
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 32.7 bits (73), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 39/82 (47%), Gaps = 3/82 (3%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPV-KELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
I+V NL V+ L +IF FG V K + T + Q +++ D A A ++GQ
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 108
Query: 290 IYGKHVV--IEFSRPGGHSKKF 309
IY I+FS+ + K+
Sbjct: 109 IYNACCTLRIDFSKLTSLNVKY 130
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 32.7 bits (73), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPV-KELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
I+V NL V+ L +IF FG V K + T + Q +++ D A A ++GQ
Sbjct: 36 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 95
Query: 290 IYGKHVV--IEFSR 301
IY I+FS+
Sbjct: 96 IYNACCTLRIDFSK 109
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 32.7 bits (73), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 5/66 (7%)
Query: 240 VSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKH 294
V L F FG + +++ ET + F+EF DAA A+ MN E++G+
Sbjct: 75 VDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRT 134
Query: 295 VVIEFS 300
+ + +
Sbjct: 135 IRVNLA 140
>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 = 32.3 bits (72), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 5/77 (6%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVK--ELRETPLKKHQR---FIEFYDVRDAAKALKEM 285
++V L ++ L+ +F + G V+ +L + H F+ + +DA +A+ +
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 286 NGQEIYGKHVVIEFSRP 302
NG + K + + ++RP
Sbjct: 67 NGLRLQSKTIKVSYARP 83
>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 = 32.0 bits (71), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKEL---RETPLKKHQ--RFIEFYDVRDAAKALKEM 285
I V ++ +S +K +F+AFG +K R+ KH+ FIE+ + + A+ M
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 286 NGQEIYGKHVVI 297
N ++ G+++ +
Sbjct: 173 NLFDLGGQYLRV 184
Score = 29.3 bits (64), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 41/69 (59%), Gaps = 9/69 (13%)
Query: 240 VSSSTLKEIFQAFGPVKELR---ETPLKKHQ--RFIEFYDVRDAAK-ALKEMNGQEIYGK 293
+ T+++ F FGP+K + ++ KH+ F+E Y+V +AA+ AL++MN + G+
Sbjct: 25 LGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE-YEVPEAAQLALEQMNSVMLGGR 83
Query: 294 HVVIEFSRP 302
+ I+ RP
Sbjct: 84 N--IKVGRP 90
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 32.0 bits (71), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKE---LRETPLKKHQ--RFIEFYDVRDAAKALKEM 285
I V ++ +S +K +F+AFG +K R+ KH+ FIE+ + + A+ M
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 286 NGQEIYGKHVVI 297
N ++ G+++ +
Sbjct: 188 NLFDLGGQYLRV 199
Score = 29.3 bits (64), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 41/69 (59%), Gaps = 9/69 (13%)
Query: 240 VSSSTLKEIFQAFGPVKELR---ETPLKKHQ--RFIEFYDVRDAAK-ALKEMNGQEIYGK 293
+ T+++ F FGP+K + ++ KH+ F+E Y+V +AA+ AL++MN + G+
Sbjct: 40 LGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE-YEVPEAAQLALEQMNSVMLGGR 98
Query: 294 HVVIEFSRP 302
+ I+ RP
Sbjct: 99 N--IKVGRP 105
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 32.0 bits (71), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 230 TIVVFNLD-SGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQ 288
++V NL+ V+ +L +F +G V+ ++ KK ++ D A A+ +NG
Sbjct: 5 VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGH 64
Query: 289 EIYGKHVVIEFSR 301
+++GK + I S+
Sbjct: 65 KLHGKPIRITLSK 77
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 32.0 bits (71), Expect = 0.67, Method: Composition-based stats.
Identities = 18/86 (20%), Positives = 41/86 (47%), Gaps = 5/86 (5%)
Query: 226 NNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR-----FIEFYDVRDAAK 280
+++ ++V L ++ K +F + G ++ + K + F+ + D DA K
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 281 ALKEMNGQEIYGKHVVIEFSRPGGHS 306
A+ +NG ++ K + + ++RP S
Sbjct: 62 AINTLNGLKLQTKTIKVSYARPSSAS 87
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 31.6 bits (70), Expect = 0.90, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 227 NQGTIVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKA 281
++ T+ V NL ++++ L IF +G V ++ ++T K FI F D A
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Query: 282 LKEMNGQEIYGK 293
+ +N ++++G+
Sbjct: 75 TRAINNKQLFGR 86
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 31.6 bits (70), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 8/71 (11%)
Query: 244 TLKEIFQAFGPVKELRETPLKKHQ--------RFIEFYDVRDAAKALKEMNGQEIYGKHV 295
T E FG + ++ L + + F+ + D DA KA+ +NG ++ K +
Sbjct: 17 TQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTI 76
Query: 296 VIEFSRPGGHS 306
+ ++RP S
Sbjct: 77 KVSYARPSSAS 87
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 31.2 bits (69), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 5/77 (6%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVK--ELRETPLKKHQR---FIEFYDVRDAAKALKEM 285
++V L ++ L+ +F + G V+ +L + H F+ + +DA +A+ +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 286 NGQEIYGKHVVIEFSRP 302
NG + K + + ++RP
Sbjct: 65 NGLRLQSKTIKVSYARP 81
>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 = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 5/77 (6%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVK--ELRETPLKKHQR---FIEFYDVRDAAKALKEM 285
++V L ++ L+ +F + G V+ +L + H F+ + +DA +A+ +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 286 NGQEIYGKHVVIEFSRP 302
NG + K + + ++RP
Sbjct: 65 NGLRLQSKTIKVSYARP 81
>pdb|3ZZY|A Chain A, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZY|B Chain B, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|A Chain A, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|B Chain B, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
Length = 130
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPV-KELRETPLKKHQRFIEFYDVRDAAKALKEMNGQE 289
I+V NL V+ L +IF FG V K + T + Q +++ D A A ++GQ
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 90
Query: 290 IYGK--HVVIEFSR 301
IY + I+FS+
Sbjct: 91 IYNACCTLRIDFSK 104
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 12/80 (15%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQR----------FIEFYDVRDAAK 280
+ + NL+ + TLK +F G +K T KK + F+E+ A K
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSC--TISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 281 ALKEMNGQEIYGKHVVIEFS 300
ALK++ G + G + + S
Sbjct: 66 ALKQLQGHTVDGHKLEVRIS 85
>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 = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 5/59 (8%)
Query: 247 EIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS 300
++ GPV L+ +T K FIEF D+ +A A++ +NG ++ + + +S
Sbjct: 22 DLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYS 80
>pdb|2E5I|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Heterogeneous Nuclear Ribonucleoprotein L-Like
Length = 124
Score = 30.0 bits (66), Expect = 2.2, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 43/85 (50%), Gaps = 7/85 (8%)
Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKH---QRFIEFYDVRDAA 279
P G N+ +++ ++ + + T+ ++ PV +++ + K Q +EF V A
Sbjct: 19 PSGGNK--VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQ 76
Query: 280 KALKEMNGQEIYGK--HVVIEFSRP 302
KA +NG +IY + IE++RP
Sbjct: 77 KAKAALNGADIYAGCCTLKIEYARP 101
>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 = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 5/59 (8%)
Query: 247 EIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS 300
++ GPV L+ +T K FIEF D+ +A A++ +NG ++ + + +S
Sbjct: 23 DLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYS 81
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 30.0 bits (66), Expect = 2.3, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 10/78 (12%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPV----KELR--ETPLKKHQRFIEF--YDVRDAAKAL 282
I + NLD + L + F AFG + K +R +T K FI F +D DA A+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA--AI 65
Query: 283 KEMNGQEIYGKHVVIEFS 300
+ MNGQ + + + + ++
Sbjct: 66 EAMNGQYLCNRPITVSYA 83
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 30.0 bits (66), Expect = 2.4, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 244 TLKEIFQAFGPVKEL--RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSR 301
+L IF FG + ++ +T + Q F+ F ++ A+ AL+ M G Y K + I +S+
Sbjct: 26 SLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIGSASNALRTMQGFPFYDKPMQIAYSK 85
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 5/53 (9%)
Query: 253 GPVKELR-----ETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEFS 300
GPV L+ +T K FIEF D+ +A A++ +NG ++ + + +S
Sbjct: 27 GPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYS 79
>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 = 29.6 bits (65), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKEL---RETPLKKHQ--RFIEFYDVRDAAKALKEM 285
I V ++ +S +K +F+AFG +K R+ KH+ FIE+ + + A+
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 286 NGQEIYGKHVVI 297
N ++ G+++ +
Sbjct: 172 NLFDLGGQYLRV 183
>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 = 29.3 bits (64), Expect = 3.9, Method: Composition-based stats.
Identities = 12/42 (28%), Positives = 24/42 (57%)
Query: 269 FIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFF 310
F+EF V D KA++ + G++ + VV ++ P + ++ F
Sbjct: 62 FVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDF 103
>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 = 29.3 bits (64), Expect = 4.0, Method: Composition-based stats.
Identities = 12/42 (28%), Positives = 24/42 (57%)
Query: 269 FIEFYDVRDAAKALKEMNGQEIYGKHVVIEFSRPGGHSKKFF 310
F+EF V D KA++ + G++ + VV ++ P + ++ F
Sbjct: 62 FVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDF 103
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 29.3 bits (64), Expect = 4.7, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKELRETPLKKHQRFIEFYDVRDAAKALKEMNGQEI 290
+ V NL S +++ F P R ++ + F+ F + DA +A+K +NG+ +
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYA-FVHFSNREDAVEAMKALNGKVL 76
Query: 291 YGKHVVIEFSRP 302
G + + ++P
Sbjct: 77 DGSPIEVTLAKP 88
>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 = 28.9 bits (63), Expect = 5.3, Method: Composition-based stats.
Identities = 13/56 (23%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 249 FQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF 299
F +G +K + R T K +E+ ++A A++ +NGQ++ G+ + +++
Sbjct: 43 FAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98
>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 = 28.9 bits (63), Expect = 5.3, Method: Composition-based stats.
Identities = 13/56 (23%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 249 FQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF 299
F +G +K + R T K +E+ ++A A++ +NGQ++ G+ + +++
Sbjct: 28 FAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 83
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 28.9 bits (63), Expect = 5.5, Method: Composition-based stats.
Identities = 13/56 (23%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 249 FQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF 299
F +G +K + R T K +E+ ++A A++ +NGQ++ G+ + +++
Sbjct: 28 FAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 83
>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 = 28.5 bits (62), Expect = 7.7, Method: Composition-based stats.
Identities = 13/56 (23%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 249 FQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF 299
F +G +K + R T K +E+ ++A A++ +NGQ++ G+ + +++
Sbjct: 28 FAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 83
>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 = 28.5 bits (62), Expect = 7.7, Method: Composition-based stats.
Identities = 13/56 (23%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 249 FQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF 299
F +G +K + R T K +E+ ++A A++ +NGQ++ G+ + +++
Sbjct: 30 FAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 85
>pdb|1JU8|A Chain A, Solution Structure Of Leginsulin, A Plant Hormon
Length = 37
Score = 28.5 bits (62), Expect = 7.8, Method: Composition-based stats.
Identities = 15/32 (46%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 36 GAASPPTLPPYPSNDVQVVPFG-GVGYAQYPT 66
GA SP +PP S D + VP G VG+ +PT
Sbjct: 5 GACSPFEVPPCRSRDCRCVPIGLFVGFCIHPT 36
>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 = 28.1 bits (61), Expect = 8.6, Method: Composition-based stats.
Identities = 13/56 (23%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 249 FQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEMNGQEIYGKHVVIEF 299
F +G +K + R T K +E+ ++A A++ +NGQ++ G+ + +++
Sbjct: 44 FAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 99
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 28.1 bits (61), Expect = 8.8, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 6/77 (7%)
Query: 231 IVVFNLDSGVSSSTLKEIFQAFGPVKEL-----RETPLKKHQRFIEFYDVRDAAKALKEM 285
I V NL +S +KE+F FG V + RET K F+E + ++A+ ++
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 286 NGQEIYGKHVVIEFSRP 302
+ + G+ + + + P
Sbjct: 63 DNTDFMGRTIRVTEANP 79
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 28.1 bits (61), Expect = 9.8, Method: Composition-based stats.
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 8/84 (9%)
Query: 223 PDGNNQGTIVVFNLDSGVSSSTLKEIFQAFGPVKELR-----ETPLKKHQRFIEFYDVRD 277
P+G N + +++L + + L F FG V + +T L K F+ F +
Sbjct: 38 PEGCN---LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDS 94
Query: 278 AAKALKEMNGQEIYGKHVVIEFSR 301
A A+K MNG ++ K + ++ +
Sbjct: 95 AQVAIKAMNGFQVGTKRLKVQLKK 118
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 0.136 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,525,593
Number of Sequences: 62578
Number of extensions: 457059
Number of successful extensions: 1319
Number of sequences better than 100.0: 122
Number of HSP's better than 100.0 without gapping: 56
Number of HSP's successfully gapped in prelim test: 66
Number of HSP's that attempted gapping in prelim test: 1226
Number of HSP's gapped (non-prelim): 137
length of query: 408
length of database: 14,973,337
effective HSP length: 101
effective length of query: 307
effective length of database: 8,652,959
effective search space: 2656458413
effective search space used: 2656458413
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)