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= 025982
(245 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 204 bits (518), Expect = 5e-53, Method: Compositional matrix adjust.
Identities = 118/278 (42%), Positives = 152/278 (54%), Gaps = 43/278 (15%)
Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
E PN+TIYINNLNEK+K D+LK+SL+A+F QFG IL+IL ++LK +GQA+++FK+V+S
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPXXXXXXXXXXXXXXXDQHDAN 130
AT A+ MQGFPFYDKPMRIQYAKT SDIIAK GTFV
Sbjct: 65 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKA 124
Query: 131 QAGMGLNPXXXXXXXXT---PPLSQIPY-------------------------------- 155
G G P PP++Q P
Sbjct: 125 VQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGA 184
Query: 156 -------PGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP 208
PG P + PPN+ILF+ N+P +T + L M F+QFPGFKEVR+V +
Sbjct: 185 MPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRH 244
Query: 209 GIAFVEYGDEMQATVAMQSLQSLKIGQQQLL-ITYAKK 245
IAFVE+ +E+QA A +LQ KI Q + I++AKK
Sbjct: 245 DIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 282
>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 = 149 bits (376), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 68/98 (69%), Positives = 84/98 (85%)
Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
E PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL ++LK +GQA+++FK+V+S
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFV 108
AT A+ MQGFPFYDKPMRIQYAKT SDIIAK GTFV
Sbjct: 64 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 101
Score = 30.4 bits (67), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 8/88 (9%)
Query: 163 IPEAPAPPNNILFVQN----VPHDTTPMALQMFFSQFPGFKEVRMVEA--KPGIAFVEYG 216
+PE PN+ +++ N + D +L FS+F ++ + + G AFV +
Sbjct: 2 VPETR--PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFK 59
Query: 217 DEMQATVAMQSLQSLKIGQQQLLITYAK 244
+ AT A++S+Q + + I YAK
Sbjct: 60 EVSSATNALRSMQGFPFYDKPMRIQYAK 87
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 149 bits (375), Expect = 2e-36, Method: Compositional matrix adjust.
Identities = 68/98 (69%), Positives = 84/98 (85%)
Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
E PN+TIYINNLNEK+K D+LK+SL+A+F QFG IL+IL ++LK +GQA+++FK+V+S
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFV 108
AT A+ MQGFPFYDKPMRIQYAKT SDIIAK GTFV
Sbjct: 64 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 101
Score = 31.2 bits (69), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 44/89 (49%), Gaps = 10/89 (11%)
Query: 163 IPEAPAPPNNILFVQN----VPHDTTPMALQMFFSQFPGFKEV---RMVEAKPGIAFVEY 215
+PE PN+ +++ N + D +L FSQF ++ R ++ + G AFV +
Sbjct: 2 VPETR--PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR-GQAFVIF 58
Query: 216 GDEMQATVAMQSLQSLKIGQQQLLITYAK 244
+ AT A++S+Q + + I YAK
Sbjct: 59 KEVSSATNALRSMQGFPFYDKPMRIQYAK 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 = 145 bits (366), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 66/96 (68%), Positives = 82/96 (85%)
Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
E PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL ++LK +GQA+++FK+V+S
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGT 106
AT A+ MQGFPFYDKPMRIQYAKT SDIIAK GT
Sbjct: 65 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGT 100
Score = 30.4 bits (67), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 8/88 (9%)
Query: 163 IPEAPAPPNNILFVQN----VPHDTTPMALQMFFSQFPGFKEVRMVEA--KPGIAFVEYG 216
+PE PN+ +++ N + D +L FS+F ++ + + G AFV +
Sbjct: 3 VPETR--PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFK 60
Query: 217 DEMQATVAMQSLQSLKIGQQQLLITYAK 244
+ AT A++S+Q + + I YAK
Sbjct: 61 EVSSATNALRSMQGFPFYDKPMRIQYAK 88
>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 = 142 bits (357), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 64/92 (69%), Positives = 80/92 (86%)
Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
E PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL ++LK +GQA+++FK+V+S
Sbjct: 1 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 60
Query: 71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
AT A+ MQGFPFYDKPMRIQYAKT SDIIAK
Sbjct: 61 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 92
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 170 PNNILFVQN----VPHDTTPMALQMFFSQFPGFKEVRMVEA--KPGIAFVEYGDEMQATV 223
PN+ +++ N + D +L FS+F ++ + + G AFV + + AT
Sbjct: 4 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 63
Query: 224 AMQSLQSLKIGQQQLLITYAK 244
A++S+Q + + I YAK
Sbjct: 64 ALRSMQGFPFYDKPMRIQYAK 84
>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 = 141 bits (356), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 64/92 (69%), Positives = 80/92 (86%)
Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
E PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL ++LK +GQA+++FK+V+S
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
AT A+ MQGFPFYDKPMRIQYAKT SDIIAK
Sbjct: 65 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 96
Score = 30.4 bits (67), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 8/88 (9%)
Query: 163 IPEAPAPPNNILFVQN----VPHDTTPMALQMFFSQFPGFKEVRMVEA--KPGIAFVEYG 216
+PE PN+ +++ N + D +L FS+F ++ + + G AFV +
Sbjct: 3 VPETR--PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFK 60
Query: 217 DEMQATVAMQSLQSLKIGQQQLLITYAK 244
+ AT A++S+Q + + I YAK
Sbjct: 61 EVSSATNALRSMQGFPFYDKPMRIQYAK 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 = 141 bits (356), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 64/92 (69%), Positives = 80/92 (86%)
Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
E PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL ++LK +GQA+++FK+V+S
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
AT A+ MQGFPFYDKPMRIQYAKT SDIIAK
Sbjct: 64 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 95
Score = 30.8 bits (68), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 8/88 (9%)
Query: 163 IPEAPAPPNNILFVQN----VPHDTTPMALQMFFSQFPGFKEVRMVEA--KPGIAFVEYG 216
+PE PN+ +++ N + D +L FS+F ++ + + G AFV +
Sbjct: 2 VPETR--PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFK 59
Query: 217 DEMQATVAMQSLQSLKIGQQQLLITYAK 244
+ AT A++S+Q + + I YAK
Sbjct: 60 EVSSATNALRSMQGFPFYDKPMRIQYAK 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 = 141 bits (356), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 64/92 (69%), Positives = 80/92 (86%)
Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
E PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL ++LK +GQA+++FK+V+S
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
AT A+ MQGFPFYDKPMRIQYAKT SDIIAK
Sbjct: 64 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 95
Score = 30.4 bits (67), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 8/88 (9%)
Query: 163 IPEAPAPPNNILFVQN----VPHDTTPMALQMFFSQFPGFKEVRMVEA--KPGIAFVEYG 216
+PE PN+ +++ N + D +L FS+F ++ + + G AFV +
Sbjct: 2 VPETR--PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFK 59
Query: 217 DEMQATVAMQSLQSLKIGQQQLLITYAK 244
+ AT A++S+Q + + I YAK
Sbjct: 60 EVSSATNALRSMQGFPFYDKPMRIQYAK 87
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 141 bits (355), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 64/92 (69%), Positives = 80/92 (86%)
Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
E PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL ++LK +GQA+++FK+V+S
Sbjct: 2 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 61
Query: 71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
AT A+ MQGFPFYDKPMRIQYAKT SDIIAK
Sbjct: 62 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 93
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 170 PNNILFVQN----VPHDTTPMALQMFFSQFPGFKEVRMVEA--KPGIAFVEYGDEMQATV 223
PN+ +++ N + D +L FS+F ++ + + G AFV + + AT
Sbjct: 5 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 64
Query: 224 AMQSLQSLKIGQQQLLITYAK 244
A++S+Q + + I YAK
Sbjct: 65 ALRSMQGFPFYDKPMRIQYAK 85
>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 = 140 bits (352), Expect = 9e-34, Method: Compositional matrix adjust.
Identities = 63/89 (70%), Positives = 79/89 (88%)
Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL ++LK +GQA+++FK+V+SAT
Sbjct: 3 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 62
Query: 74 AVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
A+ MQGFPFYDKPMRIQYAKT SDIIAK
Sbjct: 63 ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 91
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 170 PNNILFVQN----VPHDTTPMALQMFFSQFPGFKEVRMVEA--KPGIAFVEYGDEMQATV 223
PN+ +++ N + D +L FS+F ++ + + G AFV + + AT
Sbjct: 3 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 62
Query: 224 AMQSLQSLKIGQQQLLITYAK 244
A++S+Q + + I YAK
Sbjct: 63 ALRSMQGFPFYDKPMRIQYAK 83
>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 = 140 bits (352), Expect = 9e-34, Method: Compositional matrix adjust.
Identities = 63/89 (70%), Positives = 79/89 (88%)
Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL ++LK +GQA+++FK+V+SAT
Sbjct: 2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61
Query: 74 AVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
A+ MQGFPFYDKPMRIQYAKT SDIIAK
Sbjct: 62 ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 90
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 170 PNNILFVQN----VPHDTTPMALQMFFSQFPGFKEVRMVEA--KPGIAFVEYGDEMQATV 223
PN+ +++ N + D +L FS+F ++ + + G AFV + + AT
Sbjct: 2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61
Query: 224 AMQSLQSLKIGQQQLLITYAK 244
A++S+Q + + I YAK
Sbjct: 62 ALRSMQGFPFYDKPMRIQYAK 82
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 139 bits (349), Expect = 2e-33, Method: Compositional matrix adjust.
Identities = 63/91 (69%), Positives = 79/91 (86%)
Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
E PN+TIYINNLNEK+K D+LK+SL+A+F QFG IL+IL ++LK +GQA+++FK+V+S
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIA 101
AT A+ MQGFPFYDKPMRIQYAKT SDIIA
Sbjct: 65 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIA 95
Score = 30.8 bits (68), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 42/88 (47%), Gaps = 8/88 (9%)
Query: 163 IPEAPAPPNNILFVQN----VPHDTTPMALQMFFSQFPGFKEVRMVEA--KPGIAFVEYG 216
+PE PN+ +++ N + D +L FSQF ++ + + G AFV +
Sbjct: 3 VPETR--PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 60
Query: 217 DEMQATVAMQSLQSLKIGQQQLLITYAK 244
+ AT A++S+Q + + I YAK
Sbjct: 61 EVSSATNALRSMQGFPFYDKPMRIQYAK 88
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 136 bits (342), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 62/92 (67%), Positives = 78/92 (84%)
Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
E PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL ++LK +GQA+++FK+V+S
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSS 63
Query: 71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
AT A+ QGFPFYDKP RIQYAKT SDIIAK
Sbjct: 64 ATNALRSXQGFPFYDKPXRIQYAKTDSDIIAK 95
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 8/88 (9%)
Query: 163 IPEAPAPPNNILFVQN----VPHDTTPMALQMFFSQFPGFKEVRMVEA--KPGIAFVEYG 216
+PE PN+ +++ N + D +L FS+F ++ + + G AFV +
Sbjct: 2 VPETR--PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFK 59
Query: 217 DEMQATVAMQSLQSLKIGQQQLLITYAK 244
+ AT A++S Q + I YAK
Sbjct: 60 EVSSATNALRSXQGFPFYDKPXRIQYAK 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 = 136 bits (342), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 62/92 (67%), Positives = 78/92 (84%)
Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
E PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL ++LK +GQA+++FK+V+S
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSS 64
Query: 71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
AT A+ QGFPFYDKP RIQYAKT SDIIAK
Sbjct: 65 ATNALRSXQGFPFYDKPXRIQYAKTDSDIIAK 96
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 8/88 (9%)
Query: 163 IPEAPAPPNNILFVQN----VPHDTTPMALQMFFSQFPGFKEVRMVEA--KPGIAFVEYG 216
+PE PN+ +++ N + D +L FS+F ++ + + G AFV +
Sbjct: 3 VPETR--PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFK 60
Query: 217 DEMQATVAMQSLQSLKIGQQQLLITYAK 244
+ AT A++S Q + I YAK
Sbjct: 61 EVSSATNALRSXQGFPFYDKPXRIQYAK 88
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 136 bits (342), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 62/92 (67%), Positives = 78/92 (84%)
Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
E PN+TIYINNLNEK+K D+LK+SLHA+F +FG IL+IL ++LK +GQA+++FK+V+S
Sbjct: 2 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSS 61
Query: 71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAK 102
AT A+ QGFPFYDKP RIQYAKT SDIIAK
Sbjct: 62 ATNALRSXQGFPFYDKPXRIQYAKTDSDIIAK 93
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 6/81 (7%)
Query: 170 PNNILFVQN----VPHDTTPMALQMFFSQFPGFKEVRMVEA--KPGIAFVEYGDEMQATV 223
PN+ +++ N + D +L FS+F ++ + + G AFV + + AT
Sbjct: 5 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATN 64
Query: 224 AMQSLQSLKIGQQQLLITYAK 244
A++S Q + I YAK
Sbjct: 65 ALRSXQGFPFYDKPXRIQYAK 85
>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 = 130 bits (328), Expect = 5e-31, Method: Compositional matrix adjust.
Identities = 56/95 (58%), Positives = 82/95 (86%)
Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
+I PN+TIYINN+N+K+K ++LK+SL+A+F QFG +++I+A KT+K +GQA+++FK++ S
Sbjct: 2 DIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGS 61
Query: 71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADG 105
+T A+ ++QGFPFY KPMRIQYAKT SDII+K G
Sbjct: 62 STNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRG 96
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 122 bits (306), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 61/97 (62%), Positives = 82/97 (84%)
Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVAS 70
E+ PN TIYINNLNEK+K ++LK+SL+A+F QFG IL+I+A KTLK +GQA+++FK++ S
Sbjct: 2 EMLPNQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIGS 61
Query: 71 ATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTF 107
A+ A+ MQGFPFYDKPM+I Y+K+ SDI+AK GTF
Sbjct: 62 ASNALRTMQGFPFYDKPMQIAYSKSDSDIVAKIKGTF 98
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 83.6 bits (205), Expect = 9e-17, Method: Compositional matrix adjust.
Identities = 41/83 (49%), Positives = 57/83 (68%), Gaps = 1/83 (1%)
Query: 164 PEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATV 223
P + PPN+ILF+ N+P +T + L M F+QFPGFKEVR+V + IAFVE+ +E+QA
Sbjct: 6 PLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGA 65
Query: 224 AMQSLQSLKIGQQQLL-ITYAKK 245
A +LQ KI Q + I++AKK
Sbjct: 66 ARDALQGFKITQNNAMKISFAKK 88
>pdb|2B0G|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
pdb|2AYM|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
Length = 83
Score = 81.3 bits (199), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 40/78 (51%), Positives = 53/78 (67%), Gaps = 1/78 (1%)
Query: 169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSL 228
PPN ILF+ N+P +T M L M F+QFPGFKEVR+V + IAFVE+ E+Q+ A ++L
Sbjct: 6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEAL 65
Query: 229 QSLKIG-QQQLLITYAKK 245
Q KI + IT+AKK
Sbjct: 66 QGFKITPTHAMKITFAKK 83
>pdb|2A3J|A Chain A, Structure Of Urndesign, A Complete Computational Redesign
Of Human U1a Protein
Length = 127
Score = 57.8 bits (138), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 32/105 (30%), Positives = 59/105 (56%), Gaps = 1/105 (0%)
Query: 3 PEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAW 62
P++ + P+ + I N+N +V ++L+ L+A+ G IL+I+ + + G+A+
Sbjct: 17 PDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAY 76
Query: 63 LVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTF 107
+VF SA A VE QG+PF P+ I +++T +A+ DG+
Sbjct: 77 IVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAE-DGSL 120
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 46/89 (51%), Gaps = 7/89 (7%)
Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVA 69
S ++ +Y+ +L+ + D L+ +F+ FG I I+ K T + KG ++ F D
Sbjct: 3 SGSSGLYVGSLHFNITEDMLR----GIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSE 58
Query: 70 SATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
A A+E++ GF +PMR+ + + D
Sbjct: 59 CARRALEQLNGFELAGRPMRVGHVTERLD 87
>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 = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 46/89 (51%), Gaps = 7/89 (7%)
Query: 9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVF 65
G+ + +Y+ L E+V + LHA F FG I +I L ++T KH+G A++ F
Sbjct: 1 GSMATTKRVLYVGGLAEEVD----DKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 56
Query: 66 KDVASATAAVEKMQGFPFYDKPMRIQYAK 94
+ A AA++ M + + +R+ AK
Sbjct: 57 ELAEDAAAAIDNMNESELFGRTIRVNLAK 85
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 7/85 (8%)
Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVFKDVA 69
+ +Y+ L E+V + LHA F FG I +I L ++T KH+G A++ F+
Sbjct: 10 TTKRVLYVGGLAEEVD----DKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 65
Query: 70 SATAAVEKMQGFPFYDKPMRIQYAK 94
A AA++ M + + +R+ AK
Sbjct: 66 DAAAAIDNMNESELFGRTIRVNLAK 90
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 7/85 (8%)
Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVFKDVA 69
+ +Y+ L E+V + LHA F FG I +I L ++T KH+G A++ F+
Sbjct: 3 TTKRVLYVGGLAEEVD----DKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 58
Query: 70 SATAAVEKMQGFPFYDKPMRIQYAK 94
A AA++ M + + +R+ AK
Sbjct: 59 DAAAAIDNMNESELFGRTIRVNLAK 83
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 44/84 (52%), Gaps = 7/84 (8%)
Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVFKDVASATAA 74
+Y+ +L+ + D L+ +F+ FG I I + +T + KG ++ F D A A
Sbjct: 29 LYVGSLHFNITEDMLR----GIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA 84
Query: 75 VEKMQGFPFYDKPMRIQYAKTKSD 98
+E++ GF +PM++ + ++D
Sbjct: 85 LEQLNGFELAGRPMKVGHVTERTD 108
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 43.9 bits (102), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 31/97 (31%), Positives = 46/97 (47%), Gaps = 15/97 (15%)
Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE-----------ILAFKTLKHKGQA 61
S NNTI++ L E V I +S+ FKQ G I +T K KG+A
Sbjct: 5 SDNNTIFVQGLGENVTI----ESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60
Query: 62 WLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSD 98
+ F D SA AA++ G F P+++ +A ++D
Sbjct: 61 TVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRAD 97
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 31/98 (31%), Positives = 47/98 (47%), Gaps = 15/98 (15%)
Query: 10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTI----------LEI-LAFKTLKHK 58
+E S N+ IY+ LN+ V +D L FKQ G + + I L +T K K
Sbjct: 10 DEDSDNSAIYVQGLNDSVTLDDLAD----FFKQCGVVKMNKRTGQPMIHIYLDKETGKPK 65
Query: 59 GQAWLVFKDVASATAAVEKMQGFPFYDKPMRIQYAKTK 96
G A + ++D +A AAVE G F +++ A+ K
Sbjct: 66 GDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 103
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 7/84 (8%)
Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVFKDVA 69
+ +Y+ L E+V + LHA F FG I +I L ++T KH+G A++ F+
Sbjct: 61 TTKRVLYVGGLAEEVD----DKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 116
Query: 70 SATAAVEKMQGFPFYDKPMRIQYA 93
A AA++ M + + +R+ A
Sbjct: 117 DAAAAIDNMNESELFGRTIRVNLA 140
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 44/93 (47%), Gaps = 8/93 (8%)
Query: 157 GGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIA 211
G + S P A + P+ LFV+ + DTT L+ F G R+V + G
Sbjct: 1 GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFG 57
Query: 212 FVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
FV++ E A A ++++ +I ++ + +AK
Sbjct: 58 FVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK 90
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 43/82 (52%), Gaps = 6/82 (7%)
Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK--TLKHKGQAWLVFKDVASATAAV 75
++I LN + LK AVF + G I E+L K T K +G A++ F++ A A A
Sbjct: 10 LFIGGLNRETNEKMLK----AVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAA 65
Query: 76 EKMQGFPFYDKPMRIQYAKTKS 97
+ M G + K ++++ AK S
Sbjct: 66 KDMNGKSLHGKAIKVEQAKKPS 87
>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 = 41.2 bits (95), Expect = 5e-04, Method: Composition-based stats.
Identities = 25/79 (31%), Positives = 42/79 (53%), Gaps = 7/79 (8%)
Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEI---LAFKTLKHKGQAWLVFKDVASATAA 74
+Y+ L E+V + LHA F FG I +I L ++T KH+G A++ F+ A AA
Sbjct: 5 LYVGGLAEEVD----DKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 75 VEKMQGFPFYDKPMRIQYA 93
++ M + + +R+ A
Sbjct: 61 IDNMNESELFGRTIRVNLA 79
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 30/87 (34%), Positives = 45/87 (51%), Gaps = 7/87 (8%)
Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
SP I + NL V +D LH +F +FGT+L+I+ F T ++ QA L + D SA
Sbjct: 31 SPVLRIIVENLFYPVTLD----VLHQIFSKFGTVLKIITF-TKNNQFQALLQYADPVSAQ 85
Query: 73 AAVEKMQGFPFYDK--PMRIQYAKTKS 97
A + G Y+ +RI ++K S
Sbjct: 86 HAKLSLDGQNIYNACCTLRIDFSKLTS 112
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 30/87 (34%), Positives = 45/87 (51%), Gaps = 7/87 (8%)
Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
SP I + NL V +D LH +F +FGT+L+I+ F T ++ QA L + D SA
Sbjct: 44 SPVLRIIVENLFYPVTLD----VLHQIFSKFGTVLKIITF-TKNNQFQALLQYADPVSAQ 98
Query: 73 AAVEKMQGFPFYDK--PMRIQYAKTKS 97
A + G Y+ +RI ++K S
Sbjct: 99 HAKLSLDGQNIYNACCTLRIDFSKLTS 125
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 44/90 (48%), Gaps = 15/90 (16%)
Query: 15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTI----------LEILAFK-TLKHKGQAWL 63
NNTI++ L E V I +S+ FKQ G I + + + T K KG+A +
Sbjct: 13 NNTIFVQGLGENVTI----ESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 68
Query: 64 VFKDVASATAAVEKMQGFPFYDKPMRIQYA 93
F D SA AA++ G F P+++ +A
Sbjct: 69 SFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 30/87 (34%), Positives = 45/87 (51%), Gaps = 7/87 (8%)
Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASAT 72
SP I + NL V +D LH +F +FGT+L+I+ F T ++ QA L + D SA
Sbjct: 26 SPVLRIIVENLFYPVTLD----VLHQIFSKFGTVLKIITF-TKNNQFQALLQYADPVSAQ 80
Query: 73 AAVEKMQGFPFYDK--PMRIQYAKTKS 97
A + G Y+ +RI ++K S
Sbjct: 81 HAKLSLDGQNIYNACCTLRIDFSKLTS 107
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 8/88 (9%)
Query: 13 SPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAF----KTLKHKGQAWLVFKDV 68
S ++ I+I NL+ ++ ++ L+ F FG IL+ T KG A++ F
Sbjct: 3 SGSSGIFIGNLDPEID----EKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASF 58
Query: 69 ASATAAVEKMQGFPFYDKPMRIQYAKTK 96
++ AA+E M G ++P+ + YA K
Sbjct: 59 DASDAAIEAMNGQYLCNRPITVSYAFKK 86
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 47/91 (51%), Gaps = 15/91 (16%)
Query: 10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKH-KGQ--AWLVFK 66
+ +P +++ L + L + F +FG+I +T+ H KG A++ ++
Sbjct: 12 GKANPTTRLWVGGLGPNTSLAALARE----FDRFGSI------RTIDHVKGDSFAYIQYE 61
Query: 67 DVASATAAVEKMQGFPFY--DKPMRIQYAKT 95
+ +A AA KM+GFP D+ +R+ +AK+
Sbjct: 62 SLDAAQAACAKMRGFPLGGPDRRLRVDFAKS 92
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 2/78 (2%)
Query: 167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRM--VEAKPGIAFVEYGDEMQATVA 224
P N IL+++N+P+ T + F ++ +++R+ G A+V Y D A A
Sbjct: 4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 63
Query: 225 MQSLQSLKIGQQQLLITY 242
+ L + + L++ Y
Sbjct: 64 VDHLSGFNVSNRYLVVLY 81
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 2/87 (2%)
Query: 158 GAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRM--VEAKPGIAFVEY 215
AK P N IL+++N+P+ T + F ++ +++R+ G A+V Y
Sbjct: 5 AAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVY 64
Query: 216 GDEMQATVAMQSLQSLKIGQQQLLITY 242
D A A L + + L++ Y
Sbjct: 65 EDIFDAKNACDHLSGFNVCNRYLVVLY 91
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 2/78 (2%)
Query: 167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA--KPGIAFVEYGDEMQATVA 224
P N IL+++N+P+ T + F ++ +++R+ G A+V Y D A A
Sbjct: 8 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 67
Query: 225 MQSLQSLKIGQQQLLITY 242
L + + L++ Y
Sbjct: 68 CDHLSGFNVCNRYLVVLY 85
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 45/97 (46%), Gaps = 11/97 (11%)
Query: 15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTIL--EILAFKTLKHKGQAWLVFKDVASAT 72
+T+++ NL+ KV +LK+ VF G ++ +IL K K +G + F+ A
Sbjct: 15 GSTVFVANLDYKVGWKKLKE----VFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAV 70
Query: 73 AAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVP 109
A+ G +D+PM + K D A G F P
Sbjct: 71 QAISMFNGQLLFDRPMHV-----KMDERALPKGDFFP 102
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 15 NNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKDVASA 71
N TI + NL+E D + L +F+ FG+I I K T + KG A++ F A
Sbjct: 15 NATIRVTNLSE----DTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDA 70
Query: 72 TAAVEKMQGFPFYDKPMRIQYAK 94
A+ + GF + + +++AK
Sbjct: 71 ARAIAGVSGFGYDHLILNVEWAK 93
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 37.0 bits (84), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 5/72 (6%)
Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSL 228
LFV V +DTT L+ F + K + MV +K G AF+EY E A +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 229 QSLKIGQQQLLI 240
KI +++L+
Sbjct: 165 DGKKIDGRRVLV 176
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV----EAKP-GIAFVEYGDEMQATVAMQS 227
LFV V +DTT L+ F + K + MV KP G AF+EY E A +
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 228 LQSLKIGQQQLLI 240
KI +++L+
Sbjct: 164 ADGKKIDGRRVLV 176
>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 = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 2/87 (2%)
Query: 158 GAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRM--VEAKPGIAFVEY 215
AK P N IL ++N+P+ T + F ++ +++R+ G A+V Y
Sbjct: 5 AAKRANIRLPPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVY 64
Query: 216 GDEMQATVAMQSLQSLKIGQQQLLITY 242
D A A L + + L++ Y
Sbjct: 65 EDIFDAKNACDHLSGFNVCNRYLVVLY 91
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 36.2 bits (82), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 5/82 (6%)
Query: 18 IYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAFKTLKHKGQAWLVFKDVASATAAVE 76
+Y+ NL++ + ++L+++ F FGTI + + + KG ++ F AT AV
Sbjct: 18 LYVKNLDDGIDDERLRKA----FSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVT 73
Query: 77 KMQGFPFYDKPMRIQYAKTKSD 98
+M G KP+ + A+ K +
Sbjct: 74 EMNGRIVATKPLYVALAQRKEE 95
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQS 230
N LFV+ P D L F F KEV+++ G AFVE+ + A A++ +
Sbjct: 31 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN---GFAFVEFEEAESAAKAIEEVHG 87
Query: 231 LKIGQQQLLITYAK 244
Q L + Y+K
Sbjct: 88 KSFANQPLEVVYSK 101
Score = 34.7 bits (78), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 38/66 (57%), Gaps = 5/66 (7%)
Query: 29 IDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM 88
+D + L+ +F FG + E+ K L G A++ F++ SA A+E++ G F ++P+
Sbjct: 41 LDVQESELNEIFGPFGPMKEV---KILN--GFAFVEFEEAESAAKAIEEVHGKSFANQPL 95
Query: 89 RIQYAK 94
+ Y+K
Sbjct: 96 EVVYSK 101
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 35.8 bits (81), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQS 230
N LFV+ P D L F F KEV+++ G AFVE+ + A A++ +
Sbjct: 4 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN---GFAFVEFEEAESAAKAIEEVHG 60
Query: 231 LKIGQQQLLITYAK 244
Q L + Y+K
Sbjct: 61 KSFANQPLEVVYSK 74
Score = 34.7 bits (78), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 38/66 (57%), Gaps = 5/66 (7%)
Query: 29 IDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPM 88
+D + L+ +F FG + E+ K L G A++ F++ SA A+E++ G F ++P+
Sbjct: 14 LDVQESELNEIFGPFGPMKEV---KILN--GFAFVEFEEAESAAKAIEEVHGKSFANQPL 68
Query: 89 RIQYAK 94
+ Y+K
Sbjct: 69 EVVYSK 74
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 35.8 bits (81), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 46/87 (52%), Gaps = 6/87 (6%)
Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGT-----ILEILAFKTLKHKGQAWLVFKDV 68
PN IY+ NL + V+ LK + + F + + +I K + KGQA++ +
Sbjct: 44 PNCRIYVKNLAKHVQEKDLKY-IFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNE 102
Query: 69 ASATAAVEKMQGFPFYDKPMRIQYAKT 95
+A A+++ G+ + KPM +Q+A++
Sbjct: 103 KAAAKALKEANGYVLFGKPMVVQFARS 129
>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 = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 4/80 (5%)
Query: 158 GAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVE---AKP-GIAFV 213
G+ V + + + LF+ +P T L+ K++R+V KP G+A+V
Sbjct: 4 GSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYV 63
Query: 214 EYGDEMQATVAMQSLQSLKI 233
EY +E QA+ A+ + + I
Sbjct: 64 EYENESQASQAVMKMDGMTI 83
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 35.4 bits (80), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 5/75 (6%)
Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMV----EAKP-GIAFVEYGDEMQATVAMQSL 228
+FV N+P++ T L+ FS+ R+V KP G F EY D+ A AM++L
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 229 QSLKIGQQQLLITYA 243
+ + L + A
Sbjct: 71 NGREFSGRALRVDNA 85
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 35.4 bits (80), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 1/83 (1%)
Query: 14 PNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATA 73
PN +Y+ NL+ +V L SL A F++ T + +GQA++ F + A
Sbjct: 24 PNKVLYLKNLSPRVTERDL-VSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 82
Query: 74 AVEKMQGFPFYDKPMRIQYAKTK 96
A+ + G+ Y K + I++ K K
Sbjct: 83 ALHLVNGYKLYGKILVIEFGKNK 105
>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 = 35.0 bits (79), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 19/87 (21%), Positives = 45/87 (51%), Gaps = 7/87 (8%)
Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKD 67
++ ++ ++NL + D L++ VF+++G + ++ + T + +G A++ F D
Sbjct: 43 DVEGMTSLKVDNLTYRTSPDTLRR----VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 98
Query: 68 VASATAAVEKMQGFPFYDKPMRIQYAK 94
A A++ M G + +R+Q A+
Sbjct: 99 KRDAEDAMDAMDGAVLDGRELRVQMAR 125
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 35.0 bits (79), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 5/79 (6%)
Query: 171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAM 225
N L V +P D T L F R++ G AFV++ EM + A+
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 226 QSLQSLKIGQQQLLITYAK 244
+ L + + ++L ++YA+
Sbjct: 63 KVLNGITVRNKRLKVSYAR 81
Score = 30.4 bits (67), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 33/68 (48%), Gaps = 3/68 (4%)
Query: 30 DQLKQSLHAVFKQFG---TILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK 86
D + L+A+F+ G T + +KT G A++ F + A++ + G +K
Sbjct: 14 DMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNK 73
Query: 87 PMRIQYAK 94
+++ YA+
Sbjct: 74 RLKVSYAR 81
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 5/63 (7%)
Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSL 228
L+V N+P T L F ++ + ++ K G+AFV Y +A A+ +L
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 229 QSL 231
++
Sbjct: 152 NNV 154
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 35.0 bits (79), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 5/79 (6%)
Query: 171 NNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVE-----AKPGIAFVEYGDEMQATVAM 225
N L V +P D T L F R++ G AFV++ EM + A+
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 226 QSLQSLKIGQQQLLITYAK 244
+ L + + ++L ++YA+
Sbjct: 63 KVLNGITVRNKRLKVSYAR 81
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 33/68 (48%), Gaps = 3/68 (4%)
Query: 30 DQLKQSLHAVFKQFG---TILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK 86
D + L+A+F+ G T + +KT G A++ F + A++ + G +K
Sbjct: 14 DMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNK 73
Query: 87 PMRIQYAK 94
+++ YA+
Sbjct: 74 RLKVSYAR 81
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 34.3 bits (77), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLK 232
+LFV+N+ + T L+ FSQF + V+ ++ AF+ + + A AM+ +
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVKKLK---DYAFIHFDERDGAVKAMEEMNGKD 69
Query: 233 IGQQQLLITYAK 244
+ + + I +AK
Sbjct: 70 LEGENIEIVFAK 81
>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 = 34.3 bits (77), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 34/83 (40%), Gaps = 5/83 (6%)
Query: 167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQA 221
P N L V +P D T L F R+ G AFV++ E +
Sbjct: 10 PRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDS 69
Query: 222 TVAMQSLQSLKIGQQQLLITYAK 244
A++ L + + ++L ++YA+
Sbjct: 70 QRAIKVLNGITVRNKRLKVSYAR 92
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 7/79 (8%)
Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSL 228
L+V N+P T L F ++ + ++ K G+AFV Y +A A+ +L
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 162
Query: 229 QSL--KIGQQQLLITYAKK 245
++ + G Q L + A++
Sbjct: 163 NNVIPEGGSQPLSVRLAEE 181
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 3/68 (4%)
Query: 30 DQLKQSLHAVFKQFG---TILEILAFKTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDK 86
D + L+A+F+ G T +KT G A++ F + A++ + G +K
Sbjct: 25 DXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNK 84
Query: 87 PMRIQYAK 94
+++ YA+
Sbjct: 85 RLKVSYAR 92
>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 = 33.9 bits (76), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 5/83 (6%)
Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAFKTLKHKGQAWLVFKDVASATAAV 75
I+I NL++ + ++L+ F FG IL + KG ++ F+ +A A+
Sbjct: 105 NIFIKNLDKSID----NKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAI 160
Query: 76 EKMQGFPFYDKPMRIQYAKTKSD 98
EKM G D+ + + K++ +
Sbjct: 161 EKMNGMLLNDRKVFVGRFKSRKE 183
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 33.5 bits (75), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 5/76 (6%)
Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSL 228
L V +P + T + F + ++V K G FV Y D A A+ +L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 229 QSLKIGQQQLLITYAK 244
LK+ + + ++YA+
Sbjct: 67 NGLKLQTKTIKVSYAR 82
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 5/83 (6%)
Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAFKTLKHKGQAWLVFKDVASATAAV 75
I+I NL++ + ++L+ F FG IL + KG ++ F+ +A A+
Sbjct: 100 NIFIKNLDKSID----NKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAI 155
Query: 76 EKMQGFPFYDKPMRIQYAKTKSD 98
EKM G D+ + + K++ +
Sbjct: 156 EKMNGMLLNDRKVFVGRFKSRKE 178
>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 = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 53/246 (21%), Positives = 96/246 (39%), Gaps = 50/246 (20%)
Query: 3 PEVANQGNEISPNNTIYINNLN-EKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQA 61
P +A GN + + ++NLN E+V QSL +F +G + + K L +K +
Sbjct: 27 PGLAGAGNSV-----LLVSNLNPERVT----PQSLFILFGVYGDVQRV---KILFNKKEN 74
Query: 62 WLV-FKDVASATAAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPXXXXXXXXXXX 120
LV D A A+ + G + KP+RI +K ++ + +
Sbjct: 75 ALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPRE----------------- 117
Query: 121 XXXXDQHDANQAGMGLNPXXXXXXXXTPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVP 180
Q GL PL + PG + PP+ L + N+P
Sbjct: 118 ---------GQEDQGL-----TKDYGNSPLHRFKKPGSKNF---QNIFPPSATLHLSNIP 160
Query: 181 HDTTPMALQMFFSQFPG-FKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQ-QQL 238
+ L++ FS G K + + +A ++ G +A A+ L + +G+ L
Sbjct: 161 PSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHL 220
Query: 239 LITYAK 244
++++K
Sbjct: 221 RVSFSK 226
>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 = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 5/83 (6%)
Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAFKTLKHKGQAWLVFKDVASATAAV 75
I+I NL++ + ++L+ F FG IL + KG ++ F+ +A A+
Sbjct: 7 NIFIKNLDKSID----NKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAI 62
Query: 76 EKMQGFPFYDKPMRIQYAKTKSD 98
EKM G D+ + + K++ +
Sbjct: 63 EKMNGMLLNDRKVFVGRFKSRKE 85
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 5/83 (6%)
Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEI-LAFKTLKHKGQAWLVFKDVASATAAV 75
I+I NL++ + ++L+ F FG IL + KG ++ F+ +A A+
Sbjct: 13 NIFIKNLDKSID----NKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAI 68
Query: 76 EKMQGFPFYDKPMRIQYAKTKSD 98
EKM G D+ + + K++ +
Sbjct: 69 EKMNGMLLNDRKVFVGRFKSRKE 91
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 44/92 (47%), Gaps = 7/92 (7%)
Query: 6 ANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAW 62
+ G ++ T+ ++NL + D L++ VF+++G + ++ + T +G A+
Sbjct: 4 GSSGPDVDGMITLKVDNLTYRTSPDSLRR----VFEKYGRVGDVYIPREPHTKAPRGFAF 59
Query: 63 LVFKDVASATAAVEKMQGFPFYDKPMRIQYAK 94
+ F D A A M G + +R+Q A+
Sbjct: 60 VRFHDRRDAQDAEAAMDGAELDGRELRVQVAR 91
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 50/234 (21%), Positives = 92/234 (39%), Gaps = 45/234 (19%)
Query: 15 NNTIYINNLN-EKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLV-FKDVASAT 72
N+ + ++NLN E+V QSL +F +G + + K L +K + LV D A
Sbjct: 3 NSVLLVSNLNPERVT----PQSLFILFGVYGDVQRV---KILFNKKENALVQMADGNQAQ 55
Query: 73 AAVEKMQGFPFYDKPMRIQYAKTKSDIIAKADGTFVPXXXXXXXXXXXXXXXDQHDANQA 132
A+ + G + KP+RI +K ++ + + Q
Sbjct: 56 LAMSHLNGHKLHGKPIRITLSKHQNVQLPRE--------------------------GQE 89
Query: 133 GMGLNPXXXXXXXXTPPLSQIPYPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFF 192
GL PL + PG + PP+ L + N+P + L++ F
Sbjct: 90 DQGL-----TKDYGNSPLHRFKKPGSKNF---QNIFPPSATLHLSNIPPSVSEEDLKVLF 141
Query: 193 SQFPG-FKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKIGQ-QQLLITYAK 244
S G K + + +A ++ G +A A+ L + +G+ L ++++K
Sbjct: 142 SSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK 195
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 32.7 bits (73), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 5/76 (6%)
Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSL 228
L V +P + T + F + ++V K G FV Y D A A+ +L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 229 QSLKIGQQQLLITYAK 244
LK+ + + ++YA+
Sbjct: 67 NGLKLQTKTIKVSYAR 82
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 38/82 (46%), Gaps = 8/82 (9%)
Query: 16 NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAV 75
N +YI NL+ V D L+Q FG LA + L G A++ + D A A+
Sbjct: 9 NKLYIGNLSPAVTADDLRQ-------LFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAI 61
Query: 76 EKMQG-FPFYDKPMRIQYAKTK 96
E + G + K M + Y+ +K
Sbjct: 62 ETLSGKVELHGKIMEVDYSVSK 83
>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 = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 7/80 (8%)
Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVASATA 73
+++ +LN V +D ++L FK F + L + +T +G ++ F A
Sbjct: 3 NLFVGDLN--VNVD--DETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 58
Query: 74 AVEKMQGFPFYDKPMRIQYA 93
A++ MQG +P+RI +A
Sbjct: 59 AMDSMQGQDLNGRPLRINWA 78
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/87 (21%), Positives = 45/87 (51%), Gaps = 7/87 (8%)
Query: 11 EISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFKD 67
++ ++ ++NL + D L++ VF+++G + ++ + T + +G A++ F D
Sbjct: 66 DVEGMTSLKVDNLTYRTSPDTLRR----VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 121
Query: 68 VASATAAVEKMQGFPFYDKPMRIQYAK 94
A A++ M G + +R+Q A+
Sbjct: 122 KRDAEDAMDAMDGAVLDGRELRVQMAR 148
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 2/79 (2%)
Query: 168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGI-AFVEYGDEMQATVAMQ 226
AP ++V N+P D L+ + G +R+ P AF+ Y D A A+
Sbjct: 16 APLAADVYVGNLPRDARVSDLKRALREL-GSVPLRLTWQGPRRRAFLHYPDSAAAQQAVS 74
Query: 227 SLQSLKIGQQQLLITYAKK 245
LQ L++G L + A++
Sbjct: 75 CLQGLRLGTDTLRVALARQ 93
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 32.3 bits (72), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 5/82 (6%)
Query: 168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQAT 222
P L V +P + T L+ FS + +++ K G FV Y A
Sbjct: 1 GPGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAE 60
Query: 223 VAMQSLQSLKIGQQQLLITYAK 244
A+ +L L++ + + ++YA+
Sbjct: 61 RAINTLNGLRLQSKTIKVSYAR 82
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 32.3 bits (72), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 33/73 (45%)
Query: 168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQS 227
P + ++V N+ ++ L+ F + + V + PG AFVE+ D A A++
Sbjct: 70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRD 129
Query: 228 LQSLKIGQQQLLI 240
L + ++ +
Sbjct: 130 LDGRTLCGCRVRV 142
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 32.0 bits (71), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 8/80 (10%)
Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP--------GIAFVEYGDEMQATVAM 225
LF++N+ TT L+ FS+ K + + K G FVEY QA A+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 226 QSLQSLKIGQQQLLITYAKK 245
+ LQ + +L + +++
Sbjct: 68 KQLQGHTVDGHKLEVRISER 87
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 32.0 bits (71), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 42/87 (48%), Gaps = 7/87 (8%)
Query: 10 NEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFK---TLKHKGQAWLVFK 66
+E + + T+Y+ L+EKV + L +F Q G ++ K T +H+G ++ F
Sbjct: 10 SERNQDATVYVGGLDEKVS----EPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFL 65
Query: 67 DVASATAAVEKMQGFPFYDKPMRIQYA 93
A A++ M Y KP+R+ A
Sbjct: 66 SEEDADYAIKIMDMIKLYGKPIRVNKA 92
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 33/73 (45%)
Query: 168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQS 227
P + ++V N+ ++ L+ F + + V + PG AFVE+ D A A++
Sbjct: 70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRE 129
Query: 228 LQSLKIGQQQLLI 240
L + ++ +
Sbjct: 130 LDGRTLCGCRVRV 142
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 5/83 (6%)
Query: 168 APPNNILFVQNVPHDTTPMALQMFFSQFPGFKEV-----RMVEAKPGIAFVEYGDEMQAT 222
A LFV + DT +L+ FS++ EV R + G FV + + A
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 223 VAMQSLQSLKIGQQQLLITYAKK 245
AM ++ + +Q+ + A K
Sbjct: 69 DAMMAMNGKSVDGRQIRVDQAGK 91
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 31.6 bits (70), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 7/80 (8%)
Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILE---ILAFKTLKHKGQAWLVFKDVASATA 73
+++ +LN V +D ++L FK F + L + +T +G ++ F A
Sbjct: 89 NLFVGDLN--VNVD--DETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 144
Query: 74 AVEKMQGFPFYDKPMRIQYA 93
A++ MQG +P+RI +A
Sbjct: 145 AMDSMQGQDLNGRPLRINWA 164
Score = 26.9 bits (58), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 4/75 (5%)
Query: 173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPG----IAFVEYGDEMQATVAMQSL 228
+L+V N+ T L+ +F ++++ K AFVEY A +A+Q+L
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 229 QSLKIGQQQLLITYA 243
+I + I +A
Sbjct: 62 NGKQIENNIVKINWA 76
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 31.6 bits (70), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 5/76 (6%)
Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQSL 228
L V +P + T L+ FS + +++ K G FV Y A A+ +L
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 229 QSLKIGQQQLLITYAK 244
L++ + + ++YA+
Sbjct: 82 NGLRLQSKTIKVSYAR 97
>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 = 31.6 bits (70), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 34 QSLHAVFKQFGTILEILAF---KTLKHKGQAWLVFKDVASATAAVEKMQGFPFYDKPMRI 90
Q L +F FG ++ F +T K ++ + + SA AA++ M GF K +++
Sbjct: 40 QDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV 99
Query: 91 QYAKTKSD 98
Q ++K+D
Sbjct: 100 QLKRSKND 107
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 31.2 bits (69), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 21/93 (22%), Positives = 45/93 (48%), Gaps = 6/93 (6%)
Query: 9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILAFKTLKHKGQAWLVFK 66
G + + ++NL+ V + +F +FGT+ + + ++ + G A + F+
Sbjct: 82 GEGVETGAKLLVSNLDFGVS----DADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFE 137
Query: 67 DVASATAAVEKMQGFPFYDKPMRIQYAKTKSDI 99
A A A+++ +G P +PM IQ ++ D+
Sbjct: 138 RRADALKAMKQYKGVPLDGRPMDIQLVASQIDL 170
>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 = 0.61, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 5/76 (6%)
Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQSL 228
L V +P + T L+ FS + +++ K G FV Y A A+ +L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 229 QSLKIGQQQLLITYAK 244
L++ + + ++YA+
Sbjct: 65 NGLRLQSKTIKVSYAR 80
>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 = 31.2 bits (69), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 17/81 (20%), Positives = 39/81 (48%), Gaps = 5/81 (6%)
Query: 169 PPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV-----EAKPGIAFVEYGDEMQATV 223
PP+ ++++ ++P+D T + S ++M+ G AF+E+ D +
Sbjct: 2 PPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 61
Query: 224 AMQSLQSLKIGQQQLLITYAK 244
A+++L ++G + L Y+
Sbjct: 62 AVRNLNGYQLGSRFLKCGYSS 82
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 30.8 bits (68), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 5/76 (6%)
Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQSL 228
L V +P + T L+ FS + +++ K G FV Y A A+ +L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 229 QSLKIGQQQLLITYAK 244
L++ + + ++YA+
Sbjct: 65 NGLRLQSKTIKVSYAR 80
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 30.8 bits (68), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 7/80 (8%)
Query: 17 TIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAWLVFKDVASATAAVE 76
T YI N+ + L +F+ FG IL+ FK KG ++ + A +
Sbjct: 29 TAYIGNIPHFAT----EADLIPLFQNFGFILD---FKHYPEKGCCFIKYDTHEQAAVCIV 81
Query: 77 KMQGFPFYDKPMRIQYAKTK 96
+ FPF + +R + K +
Sbjct: 82 ALANFPFQGRNLRTGWGKER 101
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 30.8 bits (68), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKI 233
LFV N+P D T ++ F ++ EV + G F+ A +A L ++ +
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEV-FIHKDKGFGFIRLETRTLAEIAKVELDNMPL 76
Query: 234 GQQQLLITYA 243
+QL + +A
Sbjct: 77 RGKQLRVRFA 86
>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 = 30.8 bits (68), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 25/105 (23%), Positives = 47/105 (44%), Gaps = 12/105 (11%)
Query: 148 PPLSQIP---YPGGAKSVIPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV 204
P +S+ P PG +V+P++ + LF+ +P+ ++ + F K +V
Sbjct: 92 PGMSENPSVYVPGVVSTVVPDSA----HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLV 147
Query: 205 EAKP-----GIAFVEYGDEMQATVAMQSLQSLKIGQQQLLITYAK 244
+ G AF EY D A+ L +++G ++LL+ A
Sbjct: 148 KDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 192
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 30.8 bits (68), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 21/93 (22%), Positives = 45/93 (48%), Gaps = 6/93 (6%)
Query: 9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILAFKTLKHKGQAWLVFK 66
G + + ++NL+ V + +F +FGT+ + + ++ + G A + F+
Sbjct: 29 GEGVETGAKLLVSNLDFGVS----DADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFE 84
Query: 67 DVASATAAVEKMQGFPFYDKPMRIQYAKTKSDI 99
A A A+++ +G P +PM IQ ++ D+
Sbjct: 85 RRADALKAMKQYKGVPLDGRPMDIQLVASQIDL 117
>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 = 0.87, Method: Compositional matrix adjust.
Identities = 21/93 (22%), Positives = 45/93 (48%), Gaps = 6/93 (6%)
Query: 9 GNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILE--ILAFKTLKHKGQAWLVFK 66
G + + ++NL+ V + +F +FGT+ + + ++ + G A + F+
Sbjct: 29 GEGVETGAKLLVSNLDFGVS----DADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFE 84
Query: 67 DVASATAAVEKMQGFPFYDKPMRIQYAKTKSDI 99
A A A+++ +G P +PM IQ ++ D+
Sbjct: 85 RRADALKAMKQYKGVPLDGRPMDIQLVASQIDL 117
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 30.4 bits (67), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKI 233
LFV N+P D T ++ F ++ EV + G F+ A +A L ++ +
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEV-FIHKDKGFGFIRLETRTLAEIAKVELDNMPL 83
Query: 234 GQQQLLITYA 243
+QL + +A
Sbjct: 84 RGKQLRVRFA 93
>pdb|2VOD|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VOD|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VON|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VON|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VOO|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOO|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOP|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auuuu
Length = 193
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 6/76 (7%)
Query: 3 PEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKH--KGQ 60
PEV ++ N ++YI +D +K+ L G +L I +TL KG
Sbjct: 97 PEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDK----GQVLNIQMRRTLHKAFKGS 152
Query: 61 AWLVFKDVASATAAVE 76
++VF + SA VE
Sbjct: 153 IFVVFDSIESAKKFVE 168
>pdb|1YTY|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1YTY|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 194
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 6/76 (7%)
Query: 3 PEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKH--KGQ 60
PEV ++ N ++YI +D +K+ L G +L I +TL KG
Sbjct: 98 PEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDK----GQVLNIQXRRTLHKAFKGS 153
Query: 61 AWLVFKDVASATAAVE 76
++VF + SA VE
Sbjct: 154 IFVVFDSIESAKKFVE 169
>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 = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 5/76 (6%)
Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQATVAMQSL 228
L V +P + T + F + ++V K G FV Y D A A+ +L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 229 QSLKIGQQQLLITYAK 244
L++ + + ++YA+
Sbjct: 65 NGLRLQTKTIKVSYAR 80
>pdb|1ZH5|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1ZH5|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 195
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 6/76 (7%)
Query: 3 PEVANQGNEISPNNTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKH--KGQ 60
PEV ++ N ++YI +D +K+ L G +L I +TL KG
Sbjct: 99 PEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDK----GQVLNIQXRRTLHKAFKGS 154
Query: 61 AWLVFKDVASATAAVE 76
++VF + SA VE
Sbjct: 155 IFVVFDSIESAKKFVE 170
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/92 (23%), Positives = 46/92 (50%), Gaps = 13/92 (14%)
Query: 163 IPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIA----FVEYGDE 218
+PE PN + FV + ++ FF+++ KEV+++ + G++ FV + ++
Sbjct: 2 LPEGKIMPNTV-FVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYND 60
Query: 219 MQATVAMQSL-----QSLKIG---QQQLLITY 242
+ ++S + LK+G ++Q L TY
Sbjct: 61 VDVQKIVESQINFHGKKLKLGPAIRKQNLSTY 92
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 172 NILFVQNVPHDTTPMALQMFFSQFPGFKEVRMV----EAKP-GIAFVEYGDEMQATVAM 225
N +FV +PH+ L+ +F +F EV M+ + +P G F+ + DE A+
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKI 233
LF+ N+P + T ++ F Q+ E +++ FV D+ A A+++L K+
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIK---NYGFVHIEDKTAAEDAIRNLHHYKL 67
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/69 (21%), Positives = 35/69 (50%), Gaps = 5/69 (7%)
Query: 163 IPEAPAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIA----FVEYGDE 218
+PE PN + FV + ++ FF+++ KEV+++ + G++ FV + ++
Sbjct: 2 LPEGKIMPNTV-FVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYND 60
Query: 219 MQATVAMQS 227
+ ++S
Sbjct: 61 VDVQKIVES 69
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 7/79 (8%)
Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAK-----PGIAFVEYGDEMQATVAMQSL 228
L+V N+P T L F ++ + ++ K G+AFV Y +A A+ +L
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 229 QSL--KIGQQQLLITYAKK 245
++ + G Q L + A++
Sbjct: 76 NNVIPEGGSQPLSVRLAEE 94
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 173 ILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSL 228
+LFV+N+ T L+ FS+F + V+ ++ AFV + D A AM +
Sbjct: 17 VLFVRNLATTVTEEILEKSFSEFGKLERVKKLK---DYAFVHFEDRGAAVKAMDEM 69
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 30/67 (44%)
Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQATVAMQSLQSLKI 233
++V N+ L+ FS + + V + PG AFVE+ D A A++ L I
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 234 GQQQLLI 240
++ +
Sbjct: 63 CGSRVRV 69
>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 = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 5/82 (6%)
Query: 167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKP-----GIAFVEYGDEMQA 221
P P + LF+ +P+ ++ + F K +V+ G AF EY D
Sbjct: 92 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 151
Query: 222 TVAMQSLQSLKIGQQQLLITYA 243
A+ L +++G ++LL+ A
Sbjct: 152 DQAIAGLNGMQLGDKKLLVQRA 173
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 5/82 (6%)
Query: 167 PAPPNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVE-----AKPGIAFVEYGDEMQA 221
P P + LF+ +P+ ++ + F K +V+ G AF EY D
Sbjct: 90 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 149
Query: 222 TVAMQSLQSLKIGQQQLLITYA 243
A+ L +++G ++LL+ A
Sbjct: 150 DQAIAGLNGMQLGDKKLLVQRA 171
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 32/72 (44%), Gaps = 6/72 (8%)
Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEA---KPGIAFVEYGDEMQATVAMQSLQS 230
L +N+P+ T L+ F E+R+V GIA++E+ E A + Q
Sbjct: 96 LLAKNLPYKVTQDELKEVFEDAA---EIRLVSKDGKSKGIAYIEFKTEADAEKTFEEKQG 152
Query: 231 LKIGQQQLLITY 242
+I + + + Y
Sbjct: 153 TEIDGRSISLYY 164
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 36/84 (42%), Gaps = 4/84 (4%)
Query: 163 IPEAPAP-PNNILFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPGIAFVEYGDEMQA 221
PE AP N L+V D TP L+ FS F ++ M + AFV Y A
Sbjct: 30 FPERRAPRKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDLSMDPPR-NCAFVTYEKMESA 86
Query: 222 TVAMQSLQSLKIGQQQLLITYAKK 245
A+ L ++ QL + A+K
Sbjct: 87 DQAVAELNGTQVESVQLKVNIARK 110
>pdb|1ORJ|A Chain A, Flagellar Export Chaperone
pdb|1ORJ|B Chain B, Flagellar Export Chaperone
pdb|1ORJ|C Chain C, Flagellar Export Chaperone
pdb|1ORJ|D Chain D, Flagellar Export Chaperone
Length = 130
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 29/56 (51%), Gaps = 13/56 (23%)
Query: 8 QGNEISPN-NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAW 62
+G EI+ N +TIY LN VK+D+ K+ L ILEI LK +AW
Sbjct: 74 KGKEIAKNLDTIYTIILNTLVKVDKTKEELQK-------ILEI-----LKDLREAW 117
>pdb|1ORY|A Chain A, Flagellar Export Chaperone In Complex With Its Cognate
Binding Partner
Length = 130
Score = 28.1 bits (61), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 29/56 (51%), Gaps = 13/56 (23%)
Query: 8 QGNEISPN-NTIYINNLNEKVKIDQLKQSLHAVFKQFGTILEILAFKTLKHKGQAW 62
+G EI+ N +TIY LN VK+D+ K+ L ILEI LK +AW
Sbjct: 74 KGKEIAKNLDTIYTIILNTLVKVDKTKEELQK-------ILEI-----LKDLREAW 117
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 27.7 bits (60), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 3/73 (4%)
Query: 174 LFVQNVPHDTTPMALQMFFSQFPGFKEVRMVEAKPG---IAFVEYGDEMQATVAMQSLQS 230
L+V N+ D T + + FSQ K +M+ FVE+ + A A+ ++
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNG 77
Query: 231 LKIGQQQLLITYA 243
KI +++ + +A
Sbjct: 78 RKILGKEVKVNWA 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
0.317 0.133 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,608,592
Number of Sequences: 62578
Number of extensions: 238707
Number of successful extensions: 630
Number of sequences better than 100.0: 112
Number of HSP's better than 100.0 without gapping: 50
Number of HSP's successfully gapped in prelim test: 62
Number of HSP's that attempted gapping in prelim test: 532
Number of HSP's gapped (non-prelim): 149
length of query: 245
length of database: 14,973,337
effective HSP length: 96
effective length of query: 149
effective length of database: 8,965,849
effective search space: 1335911501
effective search space used: 1335911501
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)