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= 026902
(231 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 116 bits (291), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 52/95 (54%), Positives = 67/95 (70%)
Query: 5 DIPPNQTIYXXXXXXXXXXXXXXRSLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTA 64
DI PN TIY RSLY LFSQ+G + D+VALKT K+RGQA+V+F E+ +
Sbjct: 2 DIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGS 61
Query: 65 ASNAVRQMQNFPFYDKPMRIQYAKSKSDCVAKEDG 99
++NA+RQ+Q FPFY KPMRIQYAK+ SD ++K G
Sbjct: 62 STNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRG 96
Score = 32.0 bits (71), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 155 PNNILFIQNL----PHETTSSMLEMLFQQYPGFKEVRMIEAKP--GIAFVEFEDDVQSSM 208
PN+ ++I N+ E L LF Q+ ++ ++ G AFV F++ S+
Sbjct: 5 PNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGSSTN 64
Query: 209 AMQALQGFKITPQNPMAITFAK 230
A++ LQGF + PM I +AK
Sbjct: 65 ALRQLQGFPFYGK-PMRIQYAK 85
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 115 bits (288), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 54/97 (55%), Positives = 70/97 (72%)
Query: 5 DIPPNQTIYXXXXXXXXXXXXXXRSLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTA 64
++ PNQTIY +SLY +FSQ+G+I D+VALKT K+RGQA+V+F E+ +
Sbjct: 2 EMLPNQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIGS 61
Query: 65 ASNAVRQMQNFPFYDKPMRIQYAKSKSDCVAKEDGSF 101
ASNA+R MQ FPFYDKPM+I Y+KS SD VAK G+F
Sbjct: 62 ASNALRTMQGFPFYDKPMQIAYSKSDSDIVAKIKGTF 98
>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 = 114 bits (286), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 50/95 (52%), Positives = 68/95 (71%)
Query: 8 PNQTIYXXXXXXXXXXXXXXRSLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASN 67
PN TIY +SLY +FSQ+G+I D++ ++ K+RGQA+V+F EV++A+N
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 68 AVRQMQNFPFYDKPMRIQYAKSKSDCVAKEDGSFV 102
A+R MQ FPFYDKPMRIQYAK+ SD +AK G+FV
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 102
Score = 99.8 bits (247), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 47/77 (61%), Positives = 58/77 (75%)
Query: 155 PNNILFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSSMAMQALQ 214
PN+ILF+ NLP ET ML MLF Q+PGFKEVR++ + IAFVEF+++VQ+ A ALQ
Sbjct: 206 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQ 265
Query: 215 GFKITPQNPMAITFAKK 231
GFKIT N M I+FAKK
Sbjct: 266 GFKITQNNAMKISFAKK 282
Score = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 44/83 (53%), Gaps = 9/83 (10%)
Query: 155 PNNILFIQNLPHETTSSMLE----MLFQQYPGFKEV---RMIEAKPGIAFVEFEDDVQSS 207
PN+ ++I NL + L+ +F Q+ ++ R ++ + G AFV F++ ++
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR-GQAFVIFKEVSSAT 66
Query: 208 MAMQALQGFKITPQNPMAITFAK 230
A++++QGF PM I +AK
Sbjct: 67 NALRSMQGFPFY-DKPMRIQYAK 88
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 114 bits (286), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 50/95 (52%), Positives = 68/95 (71%)
Query: 8 PNQTIYXXXXXXXXXXXXXXRSLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASN 67
PN TIY +SLY +FSQ+G+I D++ ++ K+RGQA+V+F EV++A+N
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 68 AVRQMQNFPFYDKPMRIQYAKSKSDCVAKEDGSFV 102
A+R MQ FPFYDKPMRIQYAK+ SD +AK G+FV
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 101
Score = 30.8 bits (68), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 45/83 (54%), Gaps = 9/83 (10%)
Query: 155 PNNILFIQNLPHETTSSMLEM----LFQQYPGFKEV---RMIEAKPGIAFVEFEDDVQSS 207
PN+ ++I NL + L+ +F Q+ ++ R ++ + G AFV F++ ++
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR-GQAFVIFKEVSSAT 65
Query: 208 MAMQALQGFKITPQNPMAITFAK 230
A++++QGF + PM I +AK
Sbjct: 66 NALRSMQGFPFYDK-PMRIQYAK 87
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 111 bits (278), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 48/95 (50%), Positives = 68/95 (71%)
Query: 8 PNQTIYXXXXXXXXXXXXXXRSLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASN 67
PN TIY +SL+ +FS++G+I D++ ++ K+RGQA+V+F EV++A+N
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 68 AVRQMQNFPFYDKPMRIQYAKSKSDCVAKEDGSFV 102
A+R MQ FPFYDKPMRIQYAK+ SD +AK G+FV
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFV 101
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 44/83 (53%), Gaps = 9/83 (10%)
Query: 155 PNNILFIQNL----PHETTSSMLEMLFQQYPGFKEV---RMIEAKPGIAFVEFEDDVQSS 207
PN+ ++I NL + L +F ++ ++ R ++ + G AFV F++ ++
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR-GQAFVIFKEVSSAT 65
Query: 208 MAMQALQGFKITPQNPMAITFAK 230
A++++QGF + PM I +AK
Sbjct: 66 NALRSMQGFPFYDK-PMRIQYAK 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 = 108 bits (269), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 46/93 (49%), Positives = 66/93 (70%)
Query: 8 PNQTIYXXXXXXXXXXXXXXRSLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASN 67
PN TIY +SL+ +FS++G+I D++ ++ K+RGQA+V+F EV++A+N
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 68 AVRQMQNFPFYDKPMRIQYAKSKSDCVAKEDGS 100
A+R MQ FPFYDKPMRIQYAK+ SD +AK G+
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGT 100
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 44/83 (53%), Gaps = 9/83 (10%)
Query: 155 PNNILFIQNL----PHETTSSMLEMLFQQYPGFKEV---RMIEAKPGIAFVEFEDDVQSS 207
PN+ ++I NL + L +F ++ ++ R ++ + G AFV F++ ++
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR-GQAFVIFKEVSSAT 66
Query: 208 MAMQALQGFKITPQNPMAITFAK 230
A++++QGF + PM I +AK
Sbjct: 67 NALRSMQGFPFYDK-PMRIQYAK 88
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 107 bits (266), Expect = 7e-24, Method: Compositional matrix adjust.
Identities = 46/88 (52%), Positives = 63/88 (71%)
Query: 8 PNQTIYXXXXXXXXXXXXXXRSLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASN 67
PN TIY +SLY +FSQ+G+I D++ ++ K+RGQA+V+F EV++A+N
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 68 AVRQMQNFPFYDKPMRIQYAKSKSDCVA 95
A+R MQ FPFYDKPMRIQYAK+ SD +A
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDIIA 95
Score = 30.4 bits (67), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 45/83 (54%), Gaps = 9/83 (10%)
Query: 155 PNNILFIQNLPHETTSSMLE----MLFQQYPGFKEV---RMIEAKPGIAFVEFEDDVQSS 207
PN+ ++I NL + L+ +F Q+ ++ R ++ + G AFV F++ ++
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR-GQAFVIFKEVSSAT 66
Query: 208 MAMQALQGFKITPQNPMAITFAK 230
A++++QGF + PM I +AK
Sbjct: 67 NALRSMQGFPFYDK-PMRIQYAK 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 = 106 bits (264), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 45/89 (50%), Positives = 64/89 (71%)
Query: 8 PNQTIYXXXXXXXXXXXXXXRSLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASN 67
PN TIY +SL+ +FS++G+I D++ ++ K+RGQA+V+F EV++A+N
Sbjct: 4 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 63
Query: 68 AVRQMQNFPFYDKPMRIQYAKSKSDCVAK 96
A+R MQ FPFYDKPMRIQYAK+ SD +AK
Sbjct: 64 ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 92
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 44/83 (53%), Gaps = 9/83 (10%)
Query: 155 PNNILFIQNL----PHETTSSMLEMLFQQYPGFKEV---RMIEAKPGIAFVEFEDDVQSS 207
PN+ ++I NL + L +F ++ ++ R ++ + G AFV F++ ++
Sbjct: 4 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR-GQAFVIFKEVSSAT 62
Query: 208 MAMQALQGFKITPQNPMAITFAK 230
A++++QGF + PM I +AK
Sbjct: 63 NALRSMQGFPFYDK-PMRIQYAK 84
>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 = 106 bits (264), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 45/89 (50%), Positives = 64/89 (71%)
Query: 8 PNQTIYXXXXXXXXXXXXXXRSLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASN 67
PN TIY +SL+ +FS++G+I D++ ++ K+RGQA+V+F EV++A+N
Sbjct: 3 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 62
Query: 68 AVRQMQNFPFYDKPMRIQYAKSKSDCVAK 96
A+R MQ FPFYDKPMRIQYAK+ SD +AK
Sbjct: 63 ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 91
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 44/83 (53%), Gaps = 9/83 (10%)
Query: 155 PNNILFIQNL----PHETTSSMLEMLFQQYPGFKEV---RMIEAKPGIAFVEFEDDVQSS 207
PN+ ++I NL + L +F ++ ++ R ++ + G AFV F++ ++
Sbjct: 3 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR-GQAFVIFKEVSSAT 61
Query: 208 MAMQALQGFKITPQNPMAITFAK 230
A++++QGF + PM I +AK
Sbjct: 62 NALRSMQGFPFYDK-PMRIQYAK 83
>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 = 106 bits (264), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 45/89 (50%), Positives = 64/89 (71%)
Query: 8 PNQTIYXXXXXXXXXXXXXXRSLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASN 67
PN TIY +SL+ +FS++G+I D++ ++ K+RGQA+V+F EV++A+N
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 68 AVRQMQNFPFYDKPMRIQYAKSKSDCVAK 96
A+R MQ FPFYDKPMRIQYAK+ SD +AK
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 96
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 44/83 (53%), Gaps = 9/83 (10%)
Query: 155 PNNILFIQNL----PHETTSSMLEMLFQQYPGFKEV---RMIEAKPGIAFVEFEDDVQSS 207
PN+ ++I NL + L +F ++ ++ R ++ + G AFV F++ ++
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR-GQAFVIFKEVSSAT 66
Query: 208 MAMQALQGFKITPQNPMAITFAK 230
A++++QGF + PM I +AK
Sbjct: 67 NALRSMQGFPFYDK-PMRIQYAK 88
>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 = 105 bits (263), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 45/89 (50%), Positives = 64/89 (71%)
Query: 8 PNQTIYXXXXXXXXXXXXXXRSLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASN 67
PN TIY +SL+ +FS++G+I D++ ++ K+RGQA+V+F EV++A+N
Sbjct: 5 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 64
Query: 68 AVRQMQNFPFYDKPMRIQYAKSKSDCVAK 96
A+R MQ FPFYDKPMRIQYAK+ SD +AK
Sbjct: 65 ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 93
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 44/83 (53%), Gaps = 9/83 (10%)
Query: 155 PNNILFIQNL----PHETTSSMLEMLFQQYPGFKEV---RMIEAKPGIAFVEFEDDVQSS 207
PN+ ++I NL + L +F ++ ++ R ++ + G AFV F++ ++
Sbjct: 5 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR-GQAFVIFKEVSSAT 63
Query: 208 MAMQALQGFKITPQNPMAITFAK 230
A++++QGF + PM I +AK
Sbjct: 64 NALRSMQGFPFYDK-PMRIQYAK 85
>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 = 105 bits (263), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 45/89 (50%), Positives = 64/89 (71%)
Query: 8 PNQTIYXXXXXXXXXXXXXXRSLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASN 67
PN TIY +SL+ +FS++G+I D++ ++ K+RGQA+V+F EV++A+N
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 68 AVRQMQNFPFYDKPMRIQYAKSKSDCVAK 96
A+R MQ FPFYDKPMRIQYAK+ SD +AK
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 95
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 44/83 (53%), Gaps = 9/83 (10%)
Query: 155 PNNILFIQNL----PHETTSSMLEMLFQQYPGFKEV---RMIEAKPGIAFVEFEDDVQSS 207
PN+ ++I NL + L +F ++ ++ R ++ + G AFV F++ ++
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR-GQAFVIFKEVSSAT 65
Query: 208 MAMQALQGFKITPQNPMAITFAK 230
A++++QGF + PM I +AK
Sbjct: 66 NALRSMQGFPFYDK-PMRIQYAK 87
>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 = 105 bits (263), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 45/89 (50%), Positives = 64/89 (71%)
Query: 8 PNQTIYXXXXXXXXXXXXXXRSLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASN 67
PN TIY +SL+ +FS++G+I D++ ++ K+RGQA+V+F EV++A+N
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 68 AVRQMQNFPFYDKPMRIQYAKSKSDCVAK 96
A+R MQ FPFYDKPMRIQYAK+ SD +AK
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 95
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 44/83 (53%), Gaps = 9/83 (10%)
Query: 155 PNNILFIQNL----PHETTSSMLEMLFQQYPGFKEV---RMIEAKPGIAFVEFEDDVQSS 207
PN+ ++I NL + L +F ++ ++ R ++ + G AFV F++ ++
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR-GQAFVIFKEVSSAT 65
Query: 208 MAMQALQGFKITPQNPMAITFAK 230
A++++QGF + PM I +AK
Sbjct: 66 NALRSMQGFPFYDK-PMRIQYAK 87
>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 = 105 bits (263), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 45/89 (50%), Positives = 64/89 (71%)
Query: 8 PNQTIYXXXXXXXXXXXXXXRSLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASN 67
PN TIY +SL+ +FS++G+I D++ ++ K+RGQA+V+F EV++A+N
Sbjct: 2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61
Query: 68 AVRQMQNFPFYDKPMRIQYAKSKSDCVAK 96
A+R MQ FPFYDKPMRIQYAK+ SD +AK
Sbjct: 62 ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 90
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 44/83 (53%), Gaps = 9/83 (10%)
Query: 155 PNNILFIQNL----PHETTSSMLEMLFQQYPGFKEV---RMIEAKPGIAFVEFEDDVQSS 207
PN+ ++I NL + L +F ++ ++ R ++ + G AFV F++ ++
Sbjct: 2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR-GQAFVIFKEVSSAT 60
Query: 208 MAMQALQGFKITPQNPMAITFAK 230
A++++QGF + PM I +AK
Sbjct: 61 NALRSMQGFPFYDK-PMRIQYAK 82
>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 = 100 bits (249), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 48/77 (62%), Positives = 58/77 (75%)
Query: 155 PNNILFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSSMAMQALQ 214
PN ILF+ NLP ET ML MLF Q+PGFKEVR++ + IAFVEF ++QS+ A +ALQ
Sbjct: 7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQ 66
Query: 215 GFKITPQNPMAITFAKK 231
GFKITP + M ITFAKK
Sbjct: 67 GFKITPTHAMKITFAKK 83
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 99.8 bits (247), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 47/77 (61%), Positives = 58/77 (75%)
Query: 155 PNNILFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSSMAMQALQ 214
PN+ILF+ NLP ET ML MLF Q+PGFKEVR++ + IAFVEF+++VQ+ A ALQ
Sbjct: 12 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQ 71
Query: 215 GFKITPQNPMAITFAKK 231
GFKIT N M I+FAKK
Sbjct: 72 GFKITQNNAMKISFAKK 88
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 99.4 bits (246), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 43/89 (48%), Positives = 61/89 (68%)
Query: 8 PNQTIYXXXXXXXXXXXXXXRSLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASN 67
PN TIY +SL+ +FS++G+I D++ ++ K RGQA+V+F EV++A+N
Sbjct: 5 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATN 64
Query: 68 AVRQMQNFPFYDKPMRIQYAKSKSDCVAK 96
A+R Q FPFYDKP RIQYAK+ SD +AK
Sbjct: 65 ALRSXQGFPFYDKPXRIQYAKTDSDIIAK 93
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 99.4 bits (246), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 43/89 (48%), Positives = 61/89 (68%)
Query: 8 PNQTIYXXXXXXXXXXXXXXRSLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASN 67
PN TIY +SL+ +FS++G+I D++ ++ K RGQA+V+F EV++A+N
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATN 66
Query: 68 AVRQMQNFPFYDKPMRIQYAKSKSDCVAK 96
A+R Q FPFYDKP RIQYAK+ SD +AK
Sbjct: 67 ALRSXQGFPFYDKPXRIQYAKTDSDIIAK 95
>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 = 99.4 bits (246), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 43/89 (48%), Positives = 61/89 (68%)
Query: 8 PNQTIYXXXXXXXXXXXXXXRSLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASN 67
PN TIY +SL+ +FS++G+I D++ ++ K RGQA+V+F EV++A+N
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATN 67
Query: 68 AVRQMQNFPFYDKPMRIQYAKSKSDCVAK 96
A+R Q FPFYDKP RIQYAK+ SD +AK
Sbjct: 68 ALRSXQGFPFYDKPXRIQYAKTDSDIIAK 96
>pdb|2A3J|A Chain A, Structure Of Urndesign, A Complete Computational Redesign
Of Human U1a Protein
Length = 127
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 30 LYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQYAKS 89
LY L S G I D+V + G+A++VF+ +A V Q +PF P+ I ++++
Sbjct: 50 LYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSET 109
Query: 90 KSDCVAKEDGSF 101
VA EDGS
Sbjct: 110 PQSQVA-EDGSL 120
>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 = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 46/84 (54%), Gaps = 8/84 (9%)
Query: 139 GTAASFRNANTQETAAPNNILFIQNLPHETTSSMLEMLFQQYPGFKEVRMIE---AKP-G 194
G++ FR + + E + LFI LP T LE + + + K++R++ KP G
Sbjct: 4 GSSGVFRYSTSLE----KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKG 59
Query: 195 IAFVEFEDDVQSSMAMQALQGFKI 218
+A+VE+E++ Q+S A+ + G I
Sbjct: 60 LAYVEYENESQASQAVMKMDGMTI 83
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 147 ANTQETAAPNNILFIQNLPHETTSSMLEMLFQQYPGFKEVRM--IEAKPGIAFVEFEDDV 204
AN + N IL+I+NLP++ T+ + +F +Y +++R+ G A+V +ED
Sbjct: 3 ANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIF 62
Query: 205 QSSMAMQALQGFKIT 219
+ A L GF +
Sbjct: 63 DAKNACDHLSGFNVC 77
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 31/58 (53%)
Query: 29 SLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQY 86
+Y +F +YG I + TP+ RG A+VV+ ++ A NA + F ++ + + Y
Sbjct: 28 EMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLY 85
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 30 LYCLFSQYGRIFDVVALK---TPKLRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQY 86
L +F +G+I ++V +K T + +G ++ FS+ A A+ Q+ F +PMR+ +
Sbjct: 22 LRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGH 81
Query: 87 AKSKSD 92
+ D
Sbjct: 82 VTERLD 87
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 34/73 (46%), Gaps = 6/73 (8%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRMIE-----AKPGIAFVEFEDDVQSSMAMQAL 213
L++ +L T ML +F+ + + +++ G F+ F D + A++ L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 214 QGFKITPQNPMAI 226
GF++ + PM +
Sbjct: 68 NGFELAGR-PMRV 79
>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 = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 145 RNANTQETAAPNNILFIQNLPHETTSSMLEMLFQQYPGFKEVRM--IEAKPGIAFVEFED 202
+ AN + N IL+I+NLP++ T+ + +F +Y +++R+ G A+V +ED
Sbjct: 7 KRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYED 66
Query: 203 DVQSSMAMQALQGFKI 218
+ A L GF +
Sbjct: 67 IFDAKNACDHLSGFNV 82
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 29 SLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQY-- 86
+Y +F +YG I + TP+ RG A+VV+ ++ A NA + F ++ + + Y
Sbjct: 34 EMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN 93
Query: 87 ---AKSKSDCVAKED 98
A K D KE+
Sbjct: 94 ANRAFQKMDTKKKEE 108
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 38/66 (57%), Gaps = 2/66 (3%)
Query: 156 NNILFIQNLPHETTSSMLEMLFQQYPGFKEVRM--IEAKPGIAFVEFEDDVQSSMAMQAL 213
N IL+I+NLP++ T+ + +F +Y +++R+ G A+V +ED + A+ L
Sbjct: 8 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 214 QGFKIT 219
GF ++
Sbjct: 68 SGFNVS 73
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 5/75 (6%)
Query: 29 SLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQY-- 86
+Y +F +YG I + TP+ RG A+VV+ ++ A NAV + F ++ + + Y
Sbjct: 24 EMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN 83
Query: 87 ---AKSKSDCVAKED 98
A K D KE+
Sbjct: 84 ANRAFQKMDTKKKEE 98
>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 = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 153 AAPNNILFIQNL-PHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSSMAMQ 211
A N++L + NL P T L +LF Y + V+++ K A V+ D Q+ +AM
Sbjct: 31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMS 90
Query: 212 ALQGFKITPQNPMAITFAK 230
L G K+ + P+ IT +K
Sbjct: 91 HLNGHKLHGK-PIRITLSK 108
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSSMAMQALQGFKI 218
LFI NLP E T + LF+QY E +I+ FV ED + A++ L +K+
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIK---NYGFVHIEDKTAAEDAIRNLHHYKL 67
Query: 219 TPQN 222
N
Sbjct: 68 HGVN 71
Score = 35.0 bits (79), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 32/59 (54%), Gaps = 5/59 (8%)
Query: 33 LFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQYAKSKS 91
LF QYG++ + +K +V + TAA +A+R + ++ + + ++ +K+KS
Sbjct: 28 LFEQYGKVLECDIIKN-----YGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKS 81
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/96 (27%), Positives = 44/96 (45%), Gaps = 16/96 (16%)
Query: 140 TAASFRNANTQETAAPNNILFIQNLPHETTSSMLEMLFQQYPGFKEVRMI-----EAKPG 194
++AS R+AN L++ LP T LE LF QY R++ G
Sbjct: 82 SSASIRDAN----------LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRG 131
Query: 195 IAFVEFEDDVQSSMAMQALQGFKIT-PQNPMAITFA 229
+ F+ F+ +++ A++ L G K + P+ + FA
Sbjct: 132 VGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 2/76 (2%)
Query: 145 RNANTQETAAPNNILFIQNLPHETTSSMLEMLFQQYPGFKEVRM--IEAKPGIAFVEFED 202
+ AN + N IL I+NLP++ T+ + +F +Y +++R+ G A+V +ED
Sbjct: 7 KRANIRLPPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYED 66
Query: 203 DVQSSMAMQALQGFKI 218
+ A L GF +
Sbjct: 67 IFDAKNACDHLSGFNV 82
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 29 SLYCLFSQYGRIFDVVALKTPKLRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQY-- 86
+Y +F +YG I + TP+ RG A+VV+ ++ A NA + F ++ + + Y
Sbjct: 34 EMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN 93
Query: 87 ---AKSKSDCVAKED 98
A K D KE+
Sbjct: 94 ANRAFQKMDTKKKEE 108
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 4/83 (4%)
Query: 148 NTQETAAPNNILFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSS 207
+ QE N LF++ P + S L +F + KEV+++ G AFVEFE+ ++
Sbjct: 23 HRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN---GFAFVEFEEAESAA 79
Query: 208 MAMQALQGFKITPQNPMAITFAK 230
A++ + G Q P+ + ++K
Sbjct: 80 KAIEEVHGKSFANQ-PLEVVYSK 101
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 23/38 (60%)
Query: 51 LRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQYAK 88
L G A+V F E +A+ A+ ++ F ++P+ + Y+K
Sbjct: 64 LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSK 101
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 156 NNILFIQNL-PHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSSMAMQALQ 214
N++L + NL P T L +LF Y + V+++ K A V+ D Q+ +AM L
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62
Query: 215 GFKITPQNPMAITFAK 230
G K+ + P+ IT +K
Sbjct: 63 GHKLHGK-PIRITLSK 77
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 215
+++ NL + + LE F Y + V + PG AFVEFED ++ A++ L G
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDG 132
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 215
+++ NL + + LE F Y + V + PG AFVEFED ++ A++ L G
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDG 132
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 154 APNNILFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSSMAMQAL 213
A +LF++NL + T +LE F Q+ + V+ ++ AF+ F++ + AM+ +
Sbjct: 9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK---DYAFIHFDERDGAVKAMEEM 65
Query: 214 QGFKITPQNPMAITFAK 230
G + +N + I FAK
Sbjct: 66 NGKDLEGEN-IEIVFAK 81
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 4/86 (4%)
Query: 146 NANTQETAAPNNILFIQNLPHETTSSMLEMLFQQY-PGFKEVRMIEAKPGIAFVEFEDDV 204
++ ++T + IL+++NL T+ M+E F PG V ++ AFV F +
Sbjct: 5 SSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGA--VERVKKIRDYAFVHFSNRE 62
Query: 205 QSSMAMQALQGFKITPQNPMAITFAK 230
+ AM+AL G K+ +P+ +T AK
Sbjct: 63 DAVEAMKALNG-KVLDGSPIEVTLAK 87
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/96 (25%), Positives = 44/96 (45%), Gaps = 16/96 (16%)
Query: 140 TAASFRNANTQETAAPNNILFIQNLPHETTSSMLEMLFQQYPGFKEVRMI-----EAKPG 194
++AS R+AN L++ LP + +E LF QY R++ G
Sbjct: 84 SSASIRDAN----------LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRG 133
Query: 195 IAFVEFEDDVQSSMAMQALQGFK-ITPQNPMAITFA 229
+ F+ F+ +++ A++ L G K + P+ + FA
Sbjct: 134 VGFIRFDKRIEAEEAIKGLNGQKPLGAAEPITVKFA 169
>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 = 16/66 (24%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 30 LYCLFSQYGRIFDVVAL---KTPKLRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQY 86
L +F +GRI + + +T + +G ++ FS+ A A+ Q+ F +PM++ +
Sbjct: 43 LRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGH 102
Query: 87 AKSKSD 92
++D
Sbjct: 103 VTERTD 108
Score = 30.4 bits (67), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 6/84 (7%)
Query: 148 NTQETAAPNNILFIQNLPHETTSSMLEMLFQQYPGFKEVRMI-----EAKPGIAFVEFED 202
N Q+ +A L++ +L T ML +F+ + + ++++ G F+ F D
Sbjct: 18 NLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSD 77
Query: 203 DVQSSMAMQALQGFKITPQNPMAI 226
+ A++ L GF++ + PM +
Sbjct: 78 SECAKKALEQLNGFELAGR-PMKV 100
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 3/68 (4%)
Query: 28 RSLYCLFSQYGRIFDVVALK---TPKLRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRI 84
+SL +FS+YG+I +VV +K T + RG +V F + A +A+ M + +R+
Sbjct: 27 QSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV 86
Query: 85 QYAKSKSD 92
A SD
Sbjct: 87 DQAGKSSD 94
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 27/57 (47%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 215
+++ NL LE F Y + V + PG AFVEFED + A++ L G
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDG 59
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAK--PGIAFVEFEDDVQSSMAMQALQGF 216
+++ NLP + + +E +F +Y +++ + + P AFVEFED + A+ G+
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 84
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 4/75 (5%)
Query: 156 NNILFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 215
N LF++ P + S L +F + KEV+++ G AFVEFE+ ++ A++ + G
Sbjct: 4 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN---GFAFVEFEEAESAAKAIEEVHG 60
Query: 216 FKITPQNPMAITFAK 230
K P+ + ++K
Sbjct: 61 -KSFANQPLEVVYSK 74
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 23/38 (60%)
Query: 51 LRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQYAK 88
L G A+V F E +A+ A+ ++ F ++P+ + Y+K
Sbjct: 37 LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSK 74
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 36.2 bits (82), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 30 LYCLFSQYGRIFDVVALK---TPKLRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQY 86
LY +FS+YG++ V +K T K +G A+++F + +A N R + N + + ++
Sbjct: 33 LYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI 92
Query: 87 A 87
A
Sbjct: 93 A 93
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 36.2 bits (82), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 151 ETAAPNNILFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSSMAM 210
E A +LF++NL T +LE F ++ + V+ ++ AFV FED + AM
Sbjct: 10 EVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD---YAFVHFEDRGAAVKAM 66
Query: 211 QALQG 215
+ G
Sbjct: 67 DEMNG 71
>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 = 35.8 bits (81), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 40/95 (42%), Gaps = 7/95 (7%)
Query: 126 SSMANGTGAQSNGGTAASFRNANTQETAAPNNILFIQNLPHETTSSMLEMLFQQYPGFKE 185
S MA+ TG Q G + S+ L + NL + T+ L +F++Y +
Sbjct: 19 SHMASMTGGQQMGRGSMSY--GRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGD 76
Query: 186 V-----RMIEAKPGIAFVEFEDDVQSSMAMQALQG 215
V R + G AFV F D + AM A+ G
Sbjct: 77 VYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 35.0 bits (79), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 6/77 (7%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRMI-----EAKPGIAFVEFEDDVQSSMAMQAL 213
L++ LP + +E LF QY R++ G+ F+ F+ +++ A++ L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 214 QGFK-ITPQNPMAITFA 229
G K + P+ + FA
Sbjct: 64 NGQKPLGAAEPITVKFA 80
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 35.0 bits (79), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEV-----RMIEAKPGIAFVEFEDDVQSSMAMQAL 213
L + NL + T+ L +F++Y +V R + G AFV F D + AM A+
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 214 QG 215
G
Sbjct: 133 DG 134
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 34.7 bits (78), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 2/71 (2%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSSMAMQALQGFKI 218
LF+ NLP + T + LF++Y EV I G F+ E + +A L G I
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEV-FINRDRGFGFIRLESRTLAEIAKAELDG-TI 82
Query: 219 TPQNPMAITFA 229
P+ I FA
Sbjct: 83 LKSRPLRIRFA 93
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 34.3 bits (77), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 25/98 (25%), Positives = 47/98 (47%), Gaps = 13/98 (13%)
Query: 138 GGTAASFRNANTQETAAPNNILFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKP---- 193
G + +S NA +Q P+ LF++ L +TT E L + + G R++ +
Sbjct: 1 GSSGSSGPNARSQ----PSKTLFVKGLSEDTTE---ETLKESFDGSVRARIVTDRETGSS 53
Query: 194 -GIAFVEFEDDVQSSMAMQALQGFKITPQNPMAITFAK 230
G FV+F + + A +A++ +I N + + +AK
Sbjct: 54 KGFGFVDFNSEEDAKAAKEAMEDGEI-DGNKVTLDWAK 90
>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 = 34.3 bits (77), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 5/65 (7%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRMI----EAKP-GIAFVEFEDDVQSSMAMQAL 213
LF+ + ++TT S L F+ Y K + M+ KP G AF+E+E + A +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 214 QGFKI 218
G KI
Sbjct: 165 DGKKI 169
>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 = 33.9 bits (76), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 5/65 (7%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRMI----EAKP-GIAFVEFEDDVQSSMAMQAL 213
LF+ + ++TT S L F+ Y K + M+ KP G AF+E+E + A +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 214 QGFKI 218
G KI
Sbjct: 165 DGKKI 169
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 33.5 bits (75), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 41/83 (49%), Gaps = 8/83 (9%)
Query: 28 RSLYCLFSQYGRIFDVVALKT-----PKLRGQAWVVFSEVTA---ASNAVRQMQNFPFYD 79
+ L LF QYG ++++ L+ P+ +G +V F A A NA+ M+ P
Sbjct: 30 KDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMH 89
Query: 80 KPMRIQYAKSKSDCVAKEDGSFV 102
P++++ A S+ + ++ F+
Sbjct: 90 HPIQMKPADSEKNNAVEDRKLFI 112
Score = 28.1 bits (61), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 7/69 (10%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAK-------PGIAFVEFEDDVQSSMAMQ 211
+F+ +P + L LF+QY E+ ++ + G FV F + A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 212 ALQGFKITP 220
AL K+ P
Sbjct: 78 ALHNMKVLP 86
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/87 (21%), Positives = 41/87 (47%), Gaps = 5/87 (5%)
Query: 148 NTQETAAPNNILFIQNLPHETTSSML-EMLFQQYPGFKEVRMIEAKPGIA----FVEFED 202
+ ++ P LF+ +L + ML E + YP + +++ + G++ FV+F D
Sbjct: 1 GSSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTD 60
Query: 203 DVQSSMAMQALQGFKITPQNPMAITFA 229
+++ A+ QG P+ ++ A
Sbjct: 61 ELEQKRALTECQGAVGLGSKPVRLSVA 87
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 8/68 (11%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKP--------GIAFVEFEDDVQSSMAM 210
LFI+NL TT L+ +F + K + + K G FVE++ Q+ A+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 211 QALQGFKI 218
+ LQG +
Sbjct: 68 KQLQGHTV 75
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 41/83 (49%), Gaps = 8/83 (9%)
Query: 28 RSLYCLFSQYGRIFDVVALKT-----PKLRGQAWVVFSEVTA---ASNAVRQMQNFPFYD 79
+ L LF QYG ++++ L+ P+ +G +V F A A NA+ M+ P
Sbjct: 18 KDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMH 77
Query: 80 KPMRIQYAKSKSDCVAKEDGSFV 102
P++++ A S+ + ++ F+
Sbjct: 78 HPIQMKPADSEKNNAVEDRKLFI 100
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 7/69 (10%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAK-------PGIAFVEFEDDVQSSMAMQ 211
+F+ +P + L LF+QY E+ ++ + G FV F + A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 212 ALQGFKITP 220
AL K+ P
Sbjct: 66 ALHNMKVLP 74
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 30/60 (50%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSSMAMQALQGFKI 218
L +NLP++ T L+ +F+ + V GIA++EF+ + + + QG +I
Sbjct: 96 LLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEI 155
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
Length = 88
Score = 31.6 bits (70), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 8/71 (11%)
Query: 28 RSLYCLFSQYGRIFDVVALKT-----PKLRGQAWVVFSEVTA---ASNAVRQMQNFPFYD 79
+ L LF QYG ++++ L+ P+ +G +V F A A NA+ M+ P
Sbjct: 18 KDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMH 77
Query: 80 KPMRIQYAKSK 90
P++++ A S+
Sbjct: 78 HPIQMKPADSE 88
Score = 28.1 bits (61), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 7/69 (10%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAK-------PGIAFVEFEDDVQSSMAMQ 211
+F+ +P + L LF+QY E+ ++ + G FV F + A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 212 ALQGFKITP 220
AL K+ P
Sbjct: 66 ALHNMKVLP 74
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 31.2 bits (69), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 36/65 (55%), Gaps = 6/65 (9%)
Query: 33 LFSQYGRIFDVVALK---TPKLRGQAWVVF---SEVTAASNAVRQMQNFPFYDKPMRIQY 86
LF ++GRI+++ LK T +G A++ + A +A+ + + P ++P++++
Sbjct: 35 LFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSALHEQKTLPGMNRPIQVKP 94
Query: 87 AKSKS 91
A S+
Sbjct: 95 AASEG 99
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 31.2 bits (69), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 160 FIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSSMAMQALQGFKIT 219
+I N+PH T + L LFQ + + + K G F++++ Q+++ + AL F
Sbjct: 31 YIGNIPHFATEADLIPLFQNFGFILDFKHYPEK-GCCFIKYDTHEQAAVCIVALANFPFQ 89
Query: 220 PQN 222
+N
Sbjct: 90 GRN 92
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 31.2 bits (69), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 32/50 (64%)
Query: 40 IFDVVALKTPKLRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQYAKS 89
+FD+ +K +++GQA++ AA+ A+++ + + KPM +Q+A+S
Sbjct: 80 MFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARS 129
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 31.2 bits (69), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 4/61 (6%)
Query: 33 LFSQYGRIFDVVAL---KTPKLRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQYAKS 89
LFSQ+G++F+V + +T K +G +V E + S A+ ++ N F + +R+ A
Sbjct: 21 LFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKLDNTDFMGRTIRVTEANP 79
Query: 90 K 90
K
Sbjct: 80 K 80
>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 = 30.4 bits (67), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 1/64 (1%)
Query: 150 QETAAPNNILFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSSMA 209
++T + LF+ NLP + T + LF++Y EV I G F+ E + +A
Sbjct: 9 EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEV-FIHKDKGFGFIRLETRTLAEIA 67
Query: 210 MQAL 213
L
Sbjct: 68 KVEL 71
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 30.4 bits (67), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 158 ILFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPG----IAFVEFEDDVQSSMAMQAL 213
+L++ NL T +L+ FQ ++++ K AFVE+ +++A+Q L
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 214 QGFKITPQNPMAITFA 229
G +I N + I +A
Sbjct: 62 NGKQI-ENNIVKINWA 76
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 46 LKTPKLRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQYA 87
++T RG +V F+ A NA+ MQ +P+RI +A
Sbjct: 123 MQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 159 LFIQNLPHETTSSMLEMLFQQ--YPGFKEVRMIEAK-PGIAFVEFEDDVQSSMAMQALQG 215
+F++NLP + T ML+ F + + + +++M K G V+FE + A + + G
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNG 67
Query: 216 FKITPQ 221
K++ +
Sbjct: 68 MKLSGR 73
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 159 LFIQNLPHETTSSMLEMLFQQ--YPGFKEVRMIEAK-PGIAFVEFEDDVQSSMAMQALQG 215
+F++NLP + T ML+ F + + + +++M K G V+FE + A + + G
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNG 70
Query: 216 FKITPQ 221
K++ +
Sbjct: 71 MKLSGR 76
>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 = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 43/88 (48%), Gaps = 5/88 (5%)
Query: 136 SNGGTAASFRNANTQETAAPNNILFIQNLPHETTSSMLEMLFQQYPGFKEVRM-IEAKPG 194
S+G T S A +Q+ LFI +LP E L +F + ++ I+ +
Sbjct: 5 SSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTN 64
Query: 195 IA----FVEFEDDVQSSMAMQALQGFKI 218
++ FV +++ V + A+Q++ GF+I
Sbjct: 65 LSKCFGFVSYDNPVSAQAAIQSMNGFQI 92
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 6/83 (7%)
Query: 153 AAPNNILFIQNLPHETTSSMLEMLFQQYPGFK----EVRMIEAK-PGIAFVEFEDDVQSS 207
PN +L+++NL T L LF ++ K + RM+ + G AF+ F + +
Sbjct: 22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAW 81
Query: 208 MAMQALQGFKITPQNPMAITFAK 230
A+ + G+K+ + + I F K
Sbjct: 82 QALHLVNGYKLYGKI-LVIEFGK 103
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 24/43 (55%)
Query: 48 TPKLRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQYAKSK 90
T ++RGQA++ F A A+ + + Y K + I++ K+K
Sbjct: 63 TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNK 105
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 5/65 (7%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRM-----IEAKPGIAFVEFEDDVQSSMAMQAL 213
L + NL + T+ L +F++Y +V + +A G AFV F D + A A+
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 214 QGFKI 218
G ++
Sbjct: 76 DGAEL 80
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 9/71 (12%)
Query: 157 NILFIQNLPHETTSSMLEMLFQQYPGFKEVRMI----EAKP-GIAFVEFED----DVQSS 207
N +F+ +PH + L F+++ EV MI + +P G F+ FED D +
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 208 MAMQALQGFKI 218
M + G K+
Sbjct: 71 MHFHDIMGKKV 81
>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 = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 3/64 (4%)
Query: 30 LYCLFSQYGRIFDVVALK---TPKLRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQY 86
+ F+ +GRI D +K T K +G +V F A NA++QM + +R +
Sbjct: 32 IKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW 91
Query: 87 AKSK 90
A K
Sbjct: 92 ATRK 95
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 7/66 (10%)
Query: 156 NNILFIQNLPHETTSSMLEMLFQQYPGFKEVRMI-----EAKPGIAFVEF--EDDVQSSM 208
+FI+NL ++ L + QQ+ K VR++ E G AF +F ++ Q +
Sbjct: 15 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
Query: 209 AMQALQ 214
A +L+
Sbjct: 75 AAASLE 80
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 46 LKTPKLRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQYA 87
++T RG +V F+ A NA+ MQ +P+RI +A
Sbjct: 37 MQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 78
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKP-----GIAFVEFEDDVQSSMAMQAL 213
L + +P L LF++Y + V+++ + G FV+F+ + A+ L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 214 QGFKI 218
GF I
Sbjct: 105 NGFNI 109
>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 = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/70 (21%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 154 APNNILFIQNLPHETTSSMLEMLFQQYPGFKEVRMI-----EAKPGIAFVEFEDDVQSSM 208
P+ ++++ ++P++ T + L ++M+ G AF+EF D S+
Sbjct: 1 GPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 60
Query: 209 AMQALQGFKI 218
A++ L G+++
Sbjct: 61 AVRNLNGYQL 70
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 25/46 (54%)
Query: 47 KTPKLRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQYAKSKSD 92
+T KL+G+A V F + +A A+ F P+++ +A ++D
Sbjct: 52 ETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRAD 97
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 8/83 (9%)
Query: 28 RSLYCLFSQYGRIFDVVALKT-----PKLRGQAWVVFSEVTA---ASNAVRQMQNFPFYD 79
+ L LF QYG ++++ L+ P+ +G +V F A A NA+ + P
Sbjct: 18 KDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNXKVLPGXH 77
Query: 80 KPMRIQYAKSKSDCVAKEDGSFV 102
P++ + A S+ + ++ F+
Sbjct: 78 HPIQXKPADSEKNNAVEDRKLFI 100
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 28.9 bits (63), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 150 QETAAPNNILFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSSMA 209
++T + LF+ NLP + T + LF++Y EV I G F+ E + +A
Sbjct: 16 EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEV-FIHKDKGFGFIRLETRTLAEIA 74
>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 = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/69 (23%), Positives = 37/69 (53%), Gaps = 5/69 (7%)
Query: 155 PNNILFIQNLPHETTSS-MLEMLFQQYPGFKEVRMIEAK----PGIAFVEFEDDVQSSMA 209
P+ ++++ ++P++ T +L++ P M + + G AF+EF D S+ A
Sbjct: 3 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
Query: 210 MQALQGFKI 218
++ L G+++
Sbjct: 63 VRNLNGYQL 71
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 15/69 (21%), Positives = 35/69 (50%), Gaps = 5/69 (7%)
Query: 155 PNNILFIQNLPHETTSSMLEMLFQQYPGFKEVRMI-----EAKPGIAFVEFEDDVQSSMA 209
P+ ++++ ++P++ T + L ++M+ G AF+EF D S+ A
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 210 MQALQGFKI 218
++ L G+++
Sbjct: 61 VRNLNGYQL 69
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 32/78 (41%), Gaps = 7/78 (8%)
Query: 28 RSLYCLFSQYGRIF--DVVALKTPKLRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQ 85
+ L +FS G + D++ K K RG V F + A A+ +D+PM +
Sbjct: 30 KKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHV- 88
Query: 86 YAKSKSDCVAKEDGSFVP 103
K D A G F P
Sbjct: 89 ----KMDERALPKGDFFP 102
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 28/60 (46%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSSMAMQALQGFKI 218
L +NL T L+ +F+ + V GIA++EF+ + + ++ QG +I
Sbjct: 19 LLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI 78
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 27.7 bits (60), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 28/60 (46%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPGIAFVEFEDDVQSSMAMQALQGFKI 218
L +NL T L+ +F+ + V GIA++EF+ + + ++ QG +I
Sbjct: 102 LLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI 161
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 27.3 bits (59), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRMIEAKPG---IAFVEFEDDVQSSMAMQALQG 215
L++ NL + T ++ LF Q K +MI FVEF + ++ A+ A+ G
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNG 77
Query: 216 FKI 218
KI
Sbjct: 78 RKI 80
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 26.9 bits (58), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 5/47 (10%)
Query: 159 LFIQNLPHETTSSMLEMLFQQYPGFKEVRM----IEAKP-GIAFVEF 200
LF++NL + ++ LE LF Y E+ + KP G AFV F
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57
>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 = 26.9 bits (58), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 3/57 (5%)
Query: 37 YGRIFDVVALK---TPKLRGQAWVVFSEVTAASNAVRQMQNFPFYDKPMRIQYAKSK 90
+GRI D +K T K +G +V F A NA++QM + +R +A K
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.130 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,282,886
Number of Sequences: 62578
Number of extensions: 159754
Number of successful extensions: 510
Number of sequences better than 100.0: 87
Number of HSP's better than 100.0 without gapping: 46
Number of HSP's successfully gapped in prelim test: 41
Number of HSP's that attempted gapping in prelim test: 414
Number of HSP's gapped (non-prelim): 127
length of query: 231
length of database: 14,973,337
effective HSP length: 96
effective length of query: 135
effective length of database: 8,965,849
effective search space: 1210389615
effective search space used: 1210389615
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)