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= psy4057
(246 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 150 bits (380), Expect = 5e-37, Method: Compositional matrix adjust.
Identities = 69/91 (75%), Positives = 83/91 (91%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LKKSLYAIFSQFGQI+DI+ ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 20 IKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 79
Query: 79 PMRIQYSKTDSDVISKIKGTFMERPKKVRKQ 109
PMRIQY+KTDSD+I+K+KGTF+ER +K K+
Sbjct: 80 PMRIQYAKTDSDIIAKMKGTFVERDRKREKR 110
Score = 27.3 bits (59), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 9/89 (10%)
Query: 164 GVPEQPPNQILFLTNLPE--ETSEMMLSM--LFNQFPGFKEV---RLVPNRHDIAFVEFE 216
VPE PN +++ NL E + E+ S+ +F+QF ++ R + R AFV F+
Sbjct: 1 AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQ-AFVIFK 59
Query: 217 NEMQSAAAKLALHGFKITPTHAMKISFAK 245
+ A ++ GF M+I +AK
Sbjct: 60 EVSSATNALRSMQGFPFY-DKPMRIQYAK 87
>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 = 150 bits (378), Expect = 7e-37, Method: Compositional matrix adjust.
Identities = 69/91 (75%), Positives = 83/91 (91%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LKKSLYAIFSQFGQI+DI+ ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 21 IKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 80
Query: 79 PMRIQYSKTDSDVISKIKGTFMERPKKVRKQ 109
PMRIQY+KTDSD+I+K+KGTF+ER +K K+
Sbjct: 81 PMRIQYAKTDSDIIAKMKGTFVERDRKREKR 111
Score = 138 bits (347), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 65/80 (81%), Positives = 72/80 (90%)
Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKL 226
E PPN ILFLTNLPEET+E+MLSMLFNQFPGFKEVRLVP RHDIAFVEF+NE+Q+ AA+
Sbjct: 203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARD 262
Query: 227 ALHGFKITPTHAMKISFAKK 246
AL GFKIT +AMKISFAKK
Sbjct: 263 ALQGFKITQNNAMKISFAKK 282
>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 = 150 bits (378), Expect = 8e-37, Method: Compositional matrix adjust.
Identities = 72/80 (90%), Positives = 75/80 (93%)
Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKL 226
EQPPNQILFLTNLPEET+EMMLSMLFNQFPGFKEVRLVPNRHDIAFVEF E+QS AAK
Sbjct: 4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKE 63
Query: 227 ALHGFKITPTHAMKISFAKK 246
AL GFKITPTHAMKI+FAKK
Sbjct: 64 ALQGFKITPTHAMKITFAKK 83
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 147 bits (372), Expect = 4e-36, Method: Compositional matrix adjust.
Identities = 68/79 (86%), Positives = 76/79 (96%)
Query: 27 SLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK 86
SLYAIFSQFGQI+DIVALKTLKMRGQAFVIFKEI SA+NALR+MQGFPFYDKPM+I YSK
Sbjct: 26 SLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIGSASNALRTMQGFPFYDKPMQIAYSK 85
Query: 87 TDSDVISKIKGTFMERPKK 105
+DSD+++KIKGTF ERPKK
Sbjct: 86 SDSDIVAKIKGTFKERPKK 104
>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 = 139 bits (350), Expect = 2e-33, Method: Compositional matrix adjust.
Identities = 63/82 (76%), Positives = 77/82 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LKKSL+AIFS+FGQI+DI+ ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 20 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 79
Query: 79 PMRIQYSKTDSDVISKIKGTFM 100
PMRIQY+KTDSD+I+K+KGTF+
Sbjct: 80 PMRIQYAKTDSDIIAKMKGTFV 101
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 137 bits (344), Expect = 8e-33, Method: Compositional matrix adjust.
Identities = 65/80 (81%), Positives = 72/80 (90%)
Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKL 226
E PPN ILFLTNLPEET+E+MLSMLFNQFPGFKEVRLVP RHDIAFVEF+NE+Q+ AA+
Sbjct: 9 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARD 68
Query: 227 ALHGFKITPTHAMKISFAKK 246
AL GFKIT +AMKISFAKK
Sbjct: 69 ALQGFKITQNNAMKISFAKK 88
>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 = 136 bits (343), Expect = 9e-33, Method: Compositional matrix adjust.
Identities = 62/80 (77%), Positives = 75/80 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LKKSL+AIFS+FGQI+DI+ ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 21 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 80
Query: 79 PMRIQYSKTDSDVISKIKGT 98
PMRIQY+KTDSD+I+K+KGT
Sbjct: 81 PMRIQYAKTDSDIIAKMKGT 100
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 133 bits (334), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 59/79 (74%), Positives = 72/79 (91%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LK+SLYA+FSQFG ++DIVALKT+KMRGQAFVIFKE+ S+TNALR +QGFPFY K
Sbjct: 18 IKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGSSTNALRQLQGFPFYGK 77
Query: 79 PMRIQYSKTDSDVISKIKG 97
PMRIQY+KTDSD+ISK++G
Sbjct: 78 PMRIQYAKTDSDIISKMRG 96
>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 = 132 bits (332), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 60/78 (76%), Positives = 73/78 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LKKSL+AIFS+FGQI+DI+ ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 17 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 76
Query: 79 PMRIQYSKTDSDVISKIK 96
PMRIQY+KTDSD+I+K+K
Sbjct: 77 PMRIQYAKTDSDIIAKMK 94
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 132 bits (332), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 60/75 (80%), Positives = 70/75 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LKKSLYAIFSQFGQI+DI+ ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 21 IKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 80
Query: 79 PMRIQYSKTDSDVIS 93
PMRIQY+KTDSD+I+
Sbjct: 81 PMRIQYAKTDSDIIA 95
Score = 27.7 bits (60), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 9/89 (10%)
Query: 164 GVPEQPPNQILFLTNLPEET--SEMMLSM--LFNQFPGFKEV---RLVPNRHDIAFVEFE 216
VPE PN +++ NL E+ E+ S+ +F+QF ++ R + R AFV F+
Sbjct: 2 AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQ-AFVIFK 60
Query: 217 NEMQSAAAKLALHGFKITPTHAMKISFAK 245
+ A ++ GF M+I +AK
Sbjct: 61 EVSSATNALRSMQGFPFY-DKPMRIQYAK 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 = 132 bits (331), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 60/78 (76%), Positives = 73/78 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LKKSL+AIFS+FGQI+DI+ ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 20 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 79
Query: 79 PMRIQYSKTDSDVISKIK 96
PMRIQY+KTDSD+I+K+K
Sbjct: 80 PMRIQYAKTDSDIIAKMK 97
>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 = 132 bits (331), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 60/78 (76%), Positives = 73/78 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LKKSL+AIFS+FGQI+DI+ ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 21 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 80
Query: 79 PMRIQYSKTDSDVISKIK 96
PMRIQY+KTDSD+I+K+K
Sbjct: 81 PMRIQYAKTDSDIIAKMK 98
>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 = 132 bits (331), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 60/78 (76%), Positives = 73/78 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LKKSL+AIFS+FGQI+DI+ ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 18 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 77
Query: 79 PMRIQYSKTDSDVISKIK 96
PMRIQY+KTDSD+I+K+K
Sbjct: 78 PMRIQYAKTDSDIIAKMK 95
>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 = 130 bits (327), Expect = 7e-31, Method: Compositional matrix adjust.
Identities = 59/77 (76%), Positives = 72/77 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LKKSL+AIFS+FGQI+DI+ ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 20 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 79
Query: 79 PMRIQYSKTDSDVISKI 95
PMRIQY+KTDSD+I+K+
Sbjct: 80 PMRIQYAKTDSDIIAKM 96
>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 = 130 bits (326), Expect = 8e-31, Method: Compositional matrix adjust.
Identities = 59/76 (77%), Positives = 71/76 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LKKSL+AIFS+FGQI+DI+ ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 16 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 75
Query: 79 PMRIQYSKTDSDVISK 94
PMRIQY+KTDSD+I+K
Sbjct: 76 PMRIQYAKTDSDIIAK 91
>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 = 130 bits (326), Expect = 9e-31, Method: Compositional matrix adjust.
Identities = 59/76 (77%), Positives = 71/76 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LKKSL+AIFS+FGQI+DI+ ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 15 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 74
Query: 79 PMRIQYSKTDSDVISK 94
PMRIQY+KTDSD+I+K
Sbjct: 75 PMRIQYAKTDSDIIAK 90
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 124 bits (311), Expect = 5e-29, Method: Compositional matrix adjust.
Identities = 57/78 (73%), Positives = 69/78 (88%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LKKSL+AIFS+FGQI+DI+ ++LK RGQAFVIFKE++SATNALRS QGFPFYDK
Sbjct: 20 IKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDK 79
Query: 79 PMRIQYSKTDSDVISKIK 96
P RIQY+KTDSD+I+K K
Sbjct: 80 PXRIQYAKTDSDIIAKXK 97
>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 = 124 bits (311), Expect = 5e-29, Method: Compositional matrix adjust.
Identities = 57/78 (73%), Positives = 69/78 (88%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LKKSL+AIFS+FGQI+DI+ ++LK RGQAFVIFKE++SATNALRS QGFPFYDK
Sbjct: 21 IKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDK 80
Query: 79 PMRIQYSKTDSDVISKIK 96
P RIQY+KTDSD+I+K K
Sbjct: 81 PXRIQYAKTDSDIIAKXK 98
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 123 bits (308), Expect = 1e-28, Method: Compositional matrix adjust.
Identities = 56/76 (73%), Positives = 68/76 (89%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LKKSL+AIFS+FGQI+DI+ ++LK RGQAFVIFKE++SATNALRS QGFPFYDK
Sbjct: 18 IKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDK 77
Query: 79 PMRIQYSKTDSDVISK 94
P RIQY+KTDSD+I+K
Sbjct: 78 PXRIQYAKTDSDIIAK 93
>pdb|2A3J|A Chain A, Structure Of Urndesign, A Complete Computational Redesign
Of Human U1a Protein
Length = 127
Score = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 45/85 (52%), Gaps = 4/85 (4%)
Query: 7 HICVTNFVYVTHIS----STDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIAS 62
H + V +T+I+ L+ LYA+ S G I+DIV + G+A+++F S
Sbjct: 25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQES 84
Query: 63 ATNALRSMQGFPFYDKPMRIQYSKT 87
A + + QG+PF P+ I +S+T
Sbjct: 85 AQAFVEAFQGYPFQGNPLVITFSET 109
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 45/80 (56%), Gaps = 3/80 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
++V +S ++SL +FS++GQI ++V +K T + RG FV F+ I A +A+ +M
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 71 QGFPFYDKPMRIQYSKTDSD 90
G + +R+ + SD
Sbjct: 75 NGKSVDGRQIRVDQAGKSSD 94
Score = 32.7 bits (73), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFENEMQSAAAKLAL 228
LF+ L +T+E L +F+++ EV +V +R FV FEN + A +A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 229 HGFKITPTHAMKISFAKK 246
+G K +++ A K
Sbjct: 75 NG-KSVDGRQIRVDQAGK 91
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK--TLKMRGQAFVIFKEIASATNALRSMQ 71
+++ ++ +K L A+F + G I +++ +K T K RG AF+ F+ A A NA + M
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 72 GFPFYDKPMRIQYSKTDS 89
G + K ++++ +K S
Sbjct: 70 GKSLHGKAIKVEQAKKPS 87
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 40/79 (50%), Gaps = 9/79 (11%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFEN--EMQSAAAKL- 226
LF+ L ET+E ML +F + EV L+ +R AF+ FEN + ++AA +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 227 --ALHGFKITPTHAMKISF 243
+LHG I A K SF
Sbjct: 70 GKSLHGKAIKVEQAKKPSF 88
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+YV + + L IF FG+I +IV +K T + +G F+ F + A AL +
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 71 QGFPFYDKPMRIQY 84
GF +PMR+ +
Sbjct: 68 NGFELAGRPMRVGH 81
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 35/64 (54%)
Query: 10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
V +Y+ ++ + +Y IF ++G I I T + RG A+V++++I A NA+
Sbjct: 7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDH 66
Query: 70 MQGF 73
+ GF
Sbjct: 67 LSGF 70
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 18/79 (22%), Positives = 41/79 (51%), Gaps = 4/79 (5%)
Query: 169 PP--NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRL--VPNRHDIAFVEFENEMQSAAA 224
PP N+IL++ NLP + + + +F ++ +++R+ P A+V +E+ + A
Sbjct: 4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 63
Query: 225 KLALHGFKITPTHAMKISF 243
L GF ++ + + + +
Sbjct: 64 VDHLSGFNVSNRYLVVLYY 82
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 39/75 (52%)
Query: 10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
V +Y+ ++ + +Y IF ++G I I T + RG A+V++++I A NA
Sbjct: 17 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDH 76
Query: 70 MQGFPFYDKPMRIQY 84
+ GF ++ + + Y
Sbjct: 77 LSGFNVCNRYLVVLY 91
Score = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 169 PP--NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRL--VPNRHDIAFVEFENEMQSAAA 224
PP N+IL++ NLP + + + +F ++ +++R+ P A+V +E+ + A
Sbjct: 14 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 73
Query: 225 KLALHGFKIT 234
L GF +
Sbjct: 74 CDHLSGFNVC 83
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 39/75 (52%)
Query: 10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
V +Y+ ++ + +Y IF ++G I I T + RG A+V++++I A NA
Sbjct: 11 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDH 70
Query: 70 MQGFPFYDKPMRIQY 84
+ GF ++ + + Y
Sbjct: 71 LSGFNVCNRYLVVLY 85
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/79 (22%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 169 PP--NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRL--VPNRHDIAFVEFENEMQSAAA 224
PP N+IL++ NLP + + + +F ++ +++R+ P A+V +E+ + A
Sbjct: 8 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 67
Query: 225 KLALHGFKITPTHAMKISF 243
L GF + + + + +
Sbjct: 68 CDHLSGFNVCNRYLVVLYY 86
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
Length = 125
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 33/59 (55%)
Query: 26 KSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY 84
+ +Y IF ++G I I T + RG A+V++++I A NA + GF ++ + + Y
Sbjct: 33 EEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLY 91
Score = 30.8 bits (68), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 169 PP--NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRL--VPNRHDIAFVEFENEMQSAAA 224
PP N+IL + NLP + + + +F ++ +++R+ P A+V +E+ + A
Sbjct: 14 PPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 73
Query: 225 KLALHGFKIT 234
L GF +
Sbjct: 74 CDHLSGFNVC 83
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 41/71 (57%), Gaps = 3/71 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
VYV+++ + LY IFS++G+++ + +K T K +G AF++F + SA N R++
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 71 QGFPFYDKPMR 81
+ + ++
Sbjct: 79 NNKQLFGRVIK 89
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLALH 229
LF++ LP ++ L + K++RLV NR +A+VE+ENE Q++ A + +
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 230 GFKI 233
G I
Sbjct: 80 GMTI 83
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 3/80 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSM 70
+YV + + L IF FG+I I + +T + +G F+ F + A AL +
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 71 QGFPFYDKPMRIQYSKTDSD 90
GF +PM++ + +D
Sbjct: 89 NGFELAGRPMKVGHVTERTD 108
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 5/80 (6%)
Query: 161 ATAGVPEQPPN-QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLV----PNRHDIAFVEF 215
++G QPP+ + LF+ L ++ SE + LF F +E ++ N AFV++
Sbjct: 4 GSSGCLRQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKY 63
Query: 216 ENEMQSAAAKLALHGFKITP 235
+ ++ AA ALHG + P
Sbjct: 64 SSHAEAQAAINALHGSQTMP 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 = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPG-FKEVRLVPNRHDIAFVEFENEMQSAAAKLA 227
PP+ L L+N+P SE L +LF+ G K + +A ++ + ++ A +
Sbjct: 149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALID 208
Query: 228 LHGFKITPTHAMKISFAK 245
LH + H +++SF+K
Sbjct: 209 LHNHDLGENHHLRVSFSK 226
Score = 30.8 bits (68), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 171 NQILFLTNL-PEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALH 229
N +L ++NL PE + L +LF + + V+++ N+ + A V+ + Q+ A L+
Sbjct: 34 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 93
Query: 230 GFKI 233
G K+
Sbjct: 94 GHKL 97
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPG-FKEVRLVPNRHDIAFVEFENEMQSAAAKLA 227
PP+ L L+N+P SE L +LF+ G K + +A ++ + ++ A +
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALID 177
Query: 228 LHGFKITPTHAMKISFAK 245
LH + H +++SF+K
Sbjct: 178 LHNHDLGENHHLRVSFSK 195
Score = 30.4 bits (67), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 171 NQILFLTNL-PEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALH 229
N +L ++NL PE + L +LF + + V+++ N+ + A V+ + Q+ A L+
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62
Query: 230 GFKI 233
G K+
Sbjct: 63 GHKL 66
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 6/65 (9%)
Query: 23 DLKKS-LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR 81
D+++S L IF FG + ++ L G AFV F+E SA A+ + G F ++P+
Sbjct: 15 DVQESELNEIFGPFGPMKEVKIL-----NGFAFVEFEEAESAAKAIEEVHGKSFANQPLE 69
Query: 82 IQYSK 86
+ YSK
Sbjct: 70 VVYSK 74
Score = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG 230
N LF+ P + E L+ +F F KEV+++ + AFVEFE +A A +HG
Sbjct: 4 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHG 60
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 6/65 (9%)
Query: 23 DLKKS-LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR 81
D+++S L IF FG + ++ L G AFV F+E SA A+ + G F ++P+
Sbjct: 42 DVQESELNEIFGPFGPMKEVKILN-----GFAFVEFEEAESAAKAIEEVHGKSFANQPLE 96
Query: 82 IQYSK 86
+ YSK
Sbjct: 97 VVYSK 101
Score = 32.3 bits (72), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG 230
N LF+ P + E L+ +F F KEV+++ + AFVEFE +A A +HG
Sbjct: 31 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHG 87
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 3/76 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI---VALKTLKMRGQAFVIFKEIASATNALRSM 70
+YV ++ K L+A F FG I DI + +T K RG AFV F+ A A+ +M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 71 QGFPFYDKPMRIQYSK 86
+ + +R+ +K
Sbjct: 68 NESELFGRTIRVNLAK 83
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFENEMQSAAAKLA 227
ILF+T++ EE E + F + K + L +R A VE+E Q+ AAK A
Sbjct: 74 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133
Query: 228 LHGFKI 233
L+G +I
Sbjct: 134 LNGAEI 139
>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 = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 3/76 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI---VALKTLKMRGQAFVIFKEIASATNALRSM 70
+YV ++ K L+A F FG I DI + +T K RG AFV F+ A A+ +M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 71 QGFPFYDKPMRIQYSK 86
+ + +R+ +K
Sbjct: 70 NESELFGRTIRVNLAK 85
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 36.6 bits (83), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 36 GQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS 85
G +M ++T RG FV F A NA+ SMQG +P+RI ++
Sbjct: 31 GHVM--WDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 78
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 38/75 (50%), Gaps = 4/75 (5%)
Query: 172 QILFLTNLPEETSEMMLSMLFNQF-PGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG 230
+IL++ NL TSE M+ FN PG V V D AFV F N + A AL+G
Sbjct: 16 KILYVRNLMLSTSEEMIEKEFNNIKPGA--VERVKKIRDYAFVHFSNREDAVEAMKALNG 73
Query: 231 FKITPTHAMKISFAK 245
K+ ++++ AK
Sbjct: 74 -KVLDGSPIEVTLAK 87
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 36.2 bits (82), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 36 GQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS 85
G +M ++T RG FV F A NA+ SMQG +P+RI ++
Sbjct: 117 GHVM--WDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 36.2 bits (82), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 3/76 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI---VALKTLKMRGQAFVIFKEIASATNALRSM 70
+YV ++ K L+A F FG I DI + +T K RG AFV F+ A A+ +M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 71 QGFPFYDKPMRIQYSK 86
+ + +R+ +K
Sbjct: 75 NESELFGRTIRVNLAK 90
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 36.2 bits (82), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFENEMQSAAAKLA 227
ILF+T++ EE E + F + K + L +R A VE+E Q+ AAK A
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 228 LHGFKI 233
L+G +I
Sbjct: 88 LNGAEI 93
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 6/69 (8%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
LF+ NLP E +E + LF Q+ E ++ N FV E++ + A LH +K+
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKN---YGFVHIEDKTAAEDAIRNLHHYKL 67
Query: 234 TPTHAMKIS 242
H + I+
Sbjct: 68 ---HGVNIN 73
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 36.2 bits (82), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 3/77 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
+Y+ ++S ++ L ++F++F + + T +MRGQAF+ F A AL +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 71 QGFPFYDKPMRIQYSKT 87
G+ Y K + I++ K
Sbjct: 88 NGYKLYGKILVIEFGKN 104
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 5/69 (7%)
Query: 170 PNQILFLTNLPEETSEMMLSMLFNQFPGFK----EVRLVPNR-HDIAFVEFENEMQSAAA 224
PN++L+L NL +E L LF +F K + R++ R AF+ F N+ + A
Sbjct: 24 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQA 83
Query: 225 KLALHGFKI 233
++G+K+
Sbjct: 84 LHLVNGYKL 92
>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 = 35.8 bits (81), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 3/78 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMR---GQAFVIFKEIASATNALRSM 70
+YV + + LY FS G I+ I + + R G A+V F++ A A AL +M
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 71 QGFPFYDKPMRIQYSKTD 88
KP+RI +S+ D
Sbjct: 73 NFDVIKGKPVRIMWSQRD 90
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQG 72
+++ ++ + K+LY FS FG I+ V +G FV F+ +A A+ M G
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 160
Query: 73 FPFYDK 78
D+
Sbjct: 161 MLLNDR 166
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 42/86 (48%), Gaps = 6/86 (6%)
Query: 6 AHICVTNFVYVTHISSTDLKK--SLYAIFSQFGQ--IMDIVALKTLKMRGQAFVIFKEIA 61
I V N H+ DLK Y FS Q + DI +K +M+GQAF+
Sbjct: 46 CRIYVKNLA--KHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEK 103
Query: 62 SATNALRSMQGFPFYDKPMRIQYSKT 87
+A AL+ G+ + KPM +Q++++
Sbjct: 104 AAAKALKEANGYVLFGKPMVVQFARS 129
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 3/78 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMR---GQAFVIFKEIASATNALRSM 70
+YV + + LY FS G I+ I + + R G A+V F++ A A AL +M
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 71 QGFPFYDKPMRIQYSKTD 88
KP+RI +S+ D
Sbjct: 78 NFDVIKGKPVRIMWSQRD 95
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQG 72
+++ ++ + K+LY FS FG I+ V +G FV F+ +A A+ M G
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 165
Query: 73 FPFYDK 78
D+
Sbjct: 166 MLLNDR 171
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 9/81 (11%)
Query: 170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFENEMQSAAA 224
P++ LF+ L E+T+E L F+ G R+V +R FV+F +E + AA
Sbjct: 14 PSKTLFVKGLSEDTTEETLKESFD---GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAA 70
Query: 225 KLALHGFKITPTHAMKISFAK 245
K A+ +I + + + +AK
Sbjct: 71 KEAMEDGEI-DGNKVTLDWAK 90
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 35.4 bits (80), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 3/80 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
VY I+S + + FS FGQIM+I + +G +FV F SA +A+ S+ G
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEI---RVFPEKGYSFVRFSTHESAAHAIVSVNGT 84
Query: 74 PFYDKPMRIQYSKTDSDVIS 93
++ + K D+ S
Sbjct: 85 TIEGHVVKCYWGKESPDMTS 104
Score = 31.2 bits (69), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 37/78 (47%), Gaps = 2/78 (2%)
Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL 228
P N ++ + ++ ++ F+ F E+R+ P + +FV F +A A +++
Sbjct: 23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK-GYSFVRFSTHESAAHAIVSV 81
Query: 229 HGFKITPTHAMKISFAKK 246
+G I H +K + K+
Sbjct: 82 NGTTI-EGHVVKCYWGKE 98
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 35.4 bits (80), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 47/81 (58%), Gaps = 4/81 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSM 70
VY+ I ++ + + S G ++++ + +T + +G AF+ F+++ S+ +A+R++
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 71 QGFPFYDKPMRIQYSKTDSDV 91
G+ + ++ YS ++SD+
Sbjct: 65 NGYQLGSRFLKCGYS-SNSDI 84
>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 = 35.4 bits (80), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 47/81 (58%), Gaps = 4/81 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSM 70
VY+ I ++ + + S G ++++ + +T + +G AF+ F+++ S+ +A+R++
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 71 QGFPFYDKPMRIQYSKTDSDV 91
G+ + ++ YS ++SD+
Sbjct: 66 NGYQLGSRFLKCGYS-SNSDI 85
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 35.0 bits (79), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIV-ALKTLKMR-GQAFVIFKEIASATNALRSMQ 71
+YV ++S ++ +Y +FS+ G I I+ L +K G FV + A A NA+R +
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYIN 80
Query: 72 GFPFYDKPMRIQYS 85
G D+ +R +
Sbjct: 81 GTRLDDRIIRTDWD 94
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 35.0 bits (79), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI---VALKTLKMRGQAFVIFKEIASATNALRSM 70
+YV ++ K L+A F FG I DI + +T K RG AFV F+ A A+ +M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 71 QGFPFYDKPMRIQ 83
+ + +R+
Sbjct: 126 NESELFGRTIRVN 138
>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 = 34.7 bits (78), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 9/85 (10%)
Query: 5 LAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIA 61
+ + V N Y T S D +L +F ++G++ D+ + T + RG AFV F +
Sbjct: 47 MTSLKVDNLTYRT---SPD---TLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKR 100
Query: 62 SATNALRSMQGFPFYDKPMRIQYSK 86
A +A+ +M G + +R+Q ++
Sbjct: 101 DAEDAMDAMDGAVLDGRELRVQMAR 125
>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 = 34.7 bits (78), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 16/77 (20%), Positives = 42/77 (54%), Gaps = 3/77 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSM 70
VY+ I ++ + + S G ++++ + +T + +G AF+ F+++ S+ +A+R++
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 71 QGFPFYDKPMRIQYSKT 87
G+ + ++ YS
Sbjct: 67 NGYQLGSRFLKCGYSSN 83
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 5/71 (7%)
Query: 168 QPPNQILFLTNLP-EETSEMMLSMLFNQFPGFK-EVRLVPN---RHDIAFVEFENEMQSA 222
PP+++++L ++P ++T E +L + N P ++ P AF+EF + SA
Sbjct: 1 NPPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSA 60
Query: 223 AAKLALHGFKI 233
+A L+G+++
Sbjct: 61 SAVRNLNGYQL 71
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 34.3 bits (77), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
++V + + +++L + FSQ+G+++D V +K T + RG FV FK+ L S
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 34.3 bits (77), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 9/85 (10%)
Query: 5 LAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIA 61
+ + V N Y T S D +L +F ++G++ D+ + T + RG AFV F +
Sbjct: 70 MTSLKVDNLTYRT---SPD---TLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKR 123
Query: 62 SATNALRSMQGFPFYDKPMRIQYSK 86
A +A+ +M G + +R+Q ++
Sbjct: 124 DAEDAMDAMDGAVLDGRELRVQMAR 148
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In
Cytotoxic Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 33.5 bits (75), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 3/75 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
V+V +S + + A F+ FG+I D +K T K +G FV F A NA++ M
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 71 QGFPFYDKPMRIQYS 85
G + +R ++
Sbjct: 78 GGQWLGGRQIRTNWA 92
>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 = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 43/77 (55%), Gaps = 5/77 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
+Y++ + T +K + +FS+FG+I++ +V T RG AF+ F + + A A+ S
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 71 QGF--PFYDKPMRIQYS 85
G P +P+ ++++
Sbjct: 151 NGHKPPGSSEPITVKFA 167
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 15 YVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNAL 67
+V +S KK L F++FG+++D T + RG F++FK+ AS L
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVL 70
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 41/87 (47%), Gaps = 12/87 (13%)
Query: 8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASAT 64
+ V N Y T S D SL +F ++G++ D+ + T RG AFV F + A
Sbjct: 16 LKVDNLTYRT---SPD---SLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQ 69
Query: 65 NALRSMQGFPFYDKPMRIQ---YSKTD 88
+A +M G + +R+Q Y + D
Sbjct: 70 DAEAAMDGAELDGRELRVQVARYGRRD 96
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQG 72
+++ ++ + K+LY FS FG I+ V +G FV F+ +A A+ M G
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 73 FPFYDKPM 80
D+ +
Sbjct: 74 MLLNDRKV 81
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 4 ILAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIV-ALKTLKMR--GQAFVIFKEI 60
+L C +YV ++S ++ +Y +FS+ G I I+ L +K G FV +
Sbjct: 35 LLKKSCT---LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSR 91
Query: 61 ASATNALRSMQGFPFYDKPMRIQYS 85
A A NA+R + G D+ +R +
Sbjct: 92 ADAENAMRYINGTRLDDRIIRTDWD 116
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 29/96 (30%), Positives = 45/96 (46%), Gaps = 9/96 (9%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIM--DIVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
V+V ++ K L +FS G ++ DI+ K K RG V F++ A A+
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFN 77
Query: 72 GFPFYDKPMRIQYSKTDSDVISKIKGTFM--ERPKK 105
G +D+PM + K D + KG F ERP++
Sbjct: 78 GQLLFDRPMHV---KMDERALP--KGDFFPPERPQQ 108
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human
Pabpc1 At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human
Pabpc1 A Ph 9.0
Length = 115
Score = 32.7 bits (73), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQG 72
+++ ++ + K+LY FS FG I+ V +G FV F+ +A A+ M G
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67
Query: 73 FPFYDKPM 80
D+ +
Sbjct: 68 MLLNDRKV 75
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 32.7 bits (73), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
+Y++ + T +K + +FS+FG+I++ +V T RG AF+ F + + A A+ S
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 71 QGF--PFYDKPMRIQYS 85
G P +P+ + ++
Sbjct: 151 NGHKPPGSSEPITVXFA 167
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 32.7 bits (73), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
++V +IS T + L A F ++G +++ +K AFV + A A+R +
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY-----AFVHMERAEDAVEAIRGLDNT 67
Query: 74 PFYDKPMRIQYSKT 87
F K M +Q S +
Sbjct: 68 EFQGKRMHVQLSTS 81
>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 = 32.7 bits (73), Expect = 0.19, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI---VALKTLKMRGQAFVIFKEIASATNALRSM 70
+YV ++ K L+A F FG I DI + +T K RG AFV F+ A A+ +M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 71 QGFPFYDKPMRIQYS 85
+ + +R+ +
Sbjct: 65 NESELFGRTIRVNLA 79
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFENEMQSAAAK 225
N L + LP++ ++ L LF R++ + + AFV+F +EM S A
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 226 LALHGFKITPTHAMKISFAK 245
L+G + +K+S+A+
Sbjct: 63 KVLNGITVR-NKRLKVSYAR 81
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFENEMQSAAAK 225
N L + LP++ ++ L LF R++ + + AFV+F +EM S A
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 226 LALHGFKITPTHAMKISFAK 245
L+G + +K+S+A+
Sbjct: 63 KVLNGITVR-NKRLKVSYAR 81
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
++V ++++T ++ L FSQFG++ + LK AF+ F E A A+ M G
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKDY-----AFIHFDERDGAVKAMEEMNGK 68
Query: 74 PFYDKPMRIQYSK 86
+ + I ++K
Sbjct: 69 DLEGENIEIVFAK 81
Score = 30.4 bits (67), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGF 231
++LF+ NL +E +L F+QF + V+ + D AF+ F+ + A ++G
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNG- 67
Query: 232 KITPTHAMKISFAK 245
K ++I FAK
Sbjct: 68 KDLEGENIEIVFAK 81
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 25 KKSLYAIFSQFGQIMDIVAL----KTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPM 80
+K LY FS FG I+ + T +G AF+ F ++ A+ +M G ++P+
Sbjct: 19 EKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPI 78
Query: 81 RIQYS-KTDS 89
+ Y+ K DS
Sbjct: 79 TVSYAFKKDS 88
>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 = 31.6 bits (70), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
+YV+ + T +K L +FSQ+G+I+ +V T RG F+ F + A A++ +
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 71 QG 72
G
Sbjct: 151 NG 152
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 17/77 (22%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLAL 228
L+++ LP+ ++ L LF+Q+ R++ ++ + F+ F+ +++ A L
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 229 HGFKIT-PTHAMKISFA 244
+G K + T + + FA
Sbjct: 151 NGQKPSGATEPITVKFA 167
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 31.6 bits (70), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 8/80 (10%)
Query: 6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVAL--KTLKMRGQAFVIFKEIASA 63
A + V+N + +S D+++ +F++FG + ++ + G A V F+ A A
Sbjct: 89 AKLLVSNLDF--GVSDADIQE----LFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADA 142
Query: 64 TNALRSMQGFPFYDKPMRIQ 83
A++ +G P +PM IQ
Sbjct: 143 LKAMKQYKGVPLDGRPMDIQ 162
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 31.2 bits (69), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 3/76 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+ VT++S + L +F FG I I K T + +G AF+ F A A+ +
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 71 QGFPFYDKPMRIQYSK 86
GF + + ++++K
Sbjct: 78 SGFGYDHLILNVEWAK 93
Score = 31.2 bits (69), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 28/66 (42%), Gaps = 5/66 (7%)
Query: 171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAK 225
N + +TNL E+T E L LF F + L ++ AF+ F +A A
Sbjct: 15 NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
Query: 226 LALHGF 231
+ GF
Sbjct: 75 AGVSGF 80
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 31.2 bits (69), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 24 LKKSLYAIFSQFGQIM-DIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
LK ++ IFS+FG+I D + K +G F+ + A A +A+++ G+
Sbjct: 34 LKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGY 84
>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 = 30.8 bits (68), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 28 LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK--PMRIQYS 85
L+ IFS+FG ++ I+ T + QA + + + SA +A S+ G Y+ +RI +S
Sbjct: 45 LHQIFSKFGTVLKIITF-TKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS 103
Query: 86 KTDS 89
K S
Sbjct: 104 KLTS 107
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 30.8 bits (68), Expect = 0.71, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 5/58 (8%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK----TLKMRGQAFVIFKEIASATNAL 67
+++ +S KK L FS+FG+++D LK T + RG FV+FKE S +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVD-CTLKLDPITGRSRGFGFVLFKESESVDKVM 58
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 30.8 bits (68), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 28 LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK--PMRIQYS 85
L+ IFS+FG ++ I+ T + QA + + + SA +A S+ G Y+ +RI +S
Sbjct: 50 LHQIFSKFGTVLKIITF-TKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS 108
Query: 86 KTDS 89
K S
Sbjct: 109 KLTS 112
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 30.4 bits (67), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 28 LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK--PMRIQYS 85
L+ IFS+FG ++ I+ T + QA + + + SA +A S+ G Y+ +RI +S
Sbjct: 63 LHQIFSKFGTVLKIITF-TKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS 121
Query: 86 KTDS 89
K S
Sbjct: 122 KLTS 125
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 30.4 bits (67), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMR--GQAFVIFKEIASA 63
A + V+N + +S D+++ +F++FG + R G A V F+ A A
Sbjct: 36 AKLLVSNLDF--GVSDADIQE----LFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADA 89
Query: 64 TNALRSMQGFPFYDKPMRIQ 83
A++ +G P +PM IQ
Sbjct: 90 LKAMKQYKGVPLDGRPMDIQ 109
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 30.4 bits (67), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD---IAFVEFENEMQSAAAKLALHG 230
L ++N+P + L +F QF +V ++ N FV FEN + A+ LHG
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 77
Score = 30.4 bits (67), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 27 SLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQG 72
L +F QFG+I+D+ + +G FV F+ A A A + G
Sbjct: 31 DLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 77
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1
In Complex With Ugcaugu
Length = 109
Score = 30.4 bits (67), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 27 SLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQG 72
L +F QFG+I+D+ + +G FV F+ A A A + G
Sbjct: 45 DLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 91
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD---IAFVEFENEMQSAAAKLALHG 230
L ++N+P + L +F QF +V ++ N FV FEN + A+ LHG
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 91
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 161 ATAGVPE-QPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEM 219
++G PE ++LF+ NL +E +L F++F + V+ + D AFV FE+
Sbjct: 4 GSSGDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKL---KDYAFVHFEDRG 60
Query: 220 QSAAAKLALHG 230
+ A ++G
Sbjct: 61 AAVKAMDEMNG 71
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 38/69 (55%), Gaps = 8/69 (11%)
Query: 4 ILAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASA 63
++A + V ++V ++++T ++ L FS+FG++ + LK AFV F++ +A
Sbjct: 11 VMAKVKV---LFVRNLATTVTEEILEKSFSEFGKLERVKKLKDY-----AFVHFEDRGAA 62
Query: 64 TNALRSMQG 72
A+ M G
Sbjct: 63 VKAMDEMNG 71
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 8/80 (10%)
Query: 6 AHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVAL--KTLKMRGQAFVIFKEIASA 63
A + V+N + +S D+++ +F++FG + ++ + G A V F+ A A
Sbjct: 36 AKLLVSNLDF--GVSDADIQE----LFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADA 89
Query: 64 TNALRSMQGFPFYDKPMRIQ 83
A++ +G P +PM IQ
Sbjct: 90 LKAMKQYKGVPLDGRPMDIQ 109
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
+YV+ + T +K + +FSQ+G+I+ ++ T RG F+ F + A A++ +
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 71 QG 72
G
Sbjct: 64 NG 65
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 27 SLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFY--DKPMRIQY 84
SL A+ +F + I + +K A++ ++ + +A A M+GFP D+ +R+ +
Sbjct: 30 SLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF 89
Query: 85 SKT 87
+K+
Sbjct: 90 AKS 92
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
+YV+ + T +K + +FSQ+G+I+ ++ T RG F+ F + A A++ +
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 71 QG 72
G
Sbjct: 153 NG 154
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 5/78 (6%)
Query: 161 ATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEF 215
A E P LF+ +LP+E + L +F F ++ ++ FV +
Sbjct: 15 AAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 74
Query: 216 ENEMQSAAAKLALHGFKI 233
+N + + AA +++GF+I
Sbjct: 75 DNPVSAQAAIQSMNGFQI 92
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 8/78 (10%)
Query: 8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMR--GQAFVIFKEIASATN 65
+ V+N + +S D+++ +F++FG + R G A V F+ A A
Sbjct: 31 LLVSNLDF--GVSDADIQE----LFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALK 84
Query: 66 ALRSMQGFPFYDKPMRIQ 83
A++ G P +PM IQ
Sbjct: 85 AMKQYNGVPLDGRPMNIQ 102
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 2/71 (2%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
LF+ NLP + +E LF ++ EV + +R F+ E+ + AK L G I
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR-GFGFIRLESRTLAEIAKAELDG-TI 82
Query: 234 TPTHAMKISFA 244
+ ++I FA
Sbjct: 83 LKSRPLRIRFA 93
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 28.9 bits (63), Expect = 2.6, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 24 LKKSLYAIFSQFGQIM-DIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
LK ++ IFS+FG+I D + K +G F+ + A A +A+++ G+
Sbjct: 20 LKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGY 70
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQS 221
E P LF+ +LP+E ++ L+ F F ++ ++ FV F+N +
Sbjct: 36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95
Query: 222 AAAKLALHGFKITPTHAMKISFAK 245
A A++GF++ T +K+ K
Sbjct: 96 QVAIKAMNGFQVG-TKRLKVQLKK 118
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 28.1 bits (61), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 1/70 (1%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQG 72
+YV ++ + L FS FG I V ++ + +G FV F AT A+ M G
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 73 FPFYDKPMRI 82
KP+ +
Sbjct: 78 RIVATKPLYV 87
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 3/73 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
VYV + + L+ +F Q G +++ K T + +G FV F A A++ M
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 71 QGFPFYDKPMRIQ 83
Y KP+R+
Sbjct: 78 DMIKLYGKPIRVN 90
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 28.1 bits (61), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLV----PNRHDIAFVEFENEMQSAAAKL 226
++ LF+ L ++ SE + LF F E ++ + AFV+F + ++ AA
Sbjct: 15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIH 74
Query: 227 ALHGFKITP--THAMKISFA 244
ALHG + P + ++ + FA
Sbjct: 75 ALHGSQTMPGASSSLVVKFA 94
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 27.7 bits (60), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSM 70
+YV ++ + + + +FSQFG++ ++ + +T K +G FV +E S + A+ +
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 71 QGFPFYDKPMRI 82
F + +R+
Sbjct: 63 DNTDFMGRTIRV 74
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 27.7 bits (60), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 3/54 (5%)
Query: 35 FGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS 85
FG+I D +K T K +G FV F A NA++ M G + +R ++
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 83
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 4/76 (5%)
Query: 172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVP---NRHDIAFVEFENEMQSAAAKLAL 228
+ L++ NL + +E+++ LF+Q K +++ + FVEF +AAA A+
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAM 75
Query: 229 HGFKITPTHAMKISFA 244
+G KI +K+++A
Sbjct: 76 NGRKIL-GKEVKVNWA 90
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
0.323 0.135 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,306,592
Number of Sequences: 62578
Number of extensions: 166754
Number of successful extensions: 515
Number of sequences better than 100.0: 100
Number of HSP's better than 100.0 without gapping: 44
Number of HSP's successfully gapped in prelim test: 56
Number of HSP's that attempted gapping in prelim test: 416
Number of HSP's gapped (non-prelim): 145
length of query: 246
length of database: 14,973,337
effective HSP length: 96
effective length of query: 150
effective length of database: 8,965,849
effective search space: 1344877350
effective search space used: 1344877350
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)