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= 033648
(114 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 87.0 bits (214), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 47/101 (46%), Positives = 60/101 (59%), Gaps = 4/101 (3%)
Query: 7 EEILSLPMFKNYTAGNPASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQE 66
EEI +PMF +Y G P VLY+KNL+ SLF K I M
Sbjct: 8 EEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLV----SLFARFQEKKGPPIQFRMMT 63
Query: 67 GRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 107
GRMRGQAF+TFP+ E+A +AL+LVNGY GK ++I+FG+N
Sbjct: 64 GRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN 104
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 75.9 bits (185), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 43/113 (38%), Positives = 66/113 (58%), Gaps = 4/113 (3%)
Query: 2 GKLPPEEILSLPMFKNYTAGNPASVLYIKNLAKXXXXXXXXXXXGSLFG-SIDAAKSGLI 60
G++ EE+ +L +F++Y G P +Y+KNLAK G S + +
Sbjct: 23 GRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFD 82
Query: 61 VKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAAKP 113
++LM+EGRM+GQAF+ P+ + A +AL NGYV GKPM++QF R +A+P
Sbjct: 83 IRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFAR---SARP 132
>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 = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 23 PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
P +YI NL + ++F ++ G I+ ++ + +MRGQAFV F V
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKMRGQAFVIFKEV 61
Query: 81 ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
A AL + G+ F KPM IQ+ + +
Sbjct: 62 SSATNALRSMQGFPFYDKPMRIQYAKTDS 90
>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 = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 23 PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
P +YI NL + ++F ++ G I+ ++ + +MRGQAFV F V
Sbjct: 5 PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKMRGQAFVIFKEV 59
Query: 81 ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
A AL + G+ F KPM IQ+ + +
Sbjct: 60 SSATNALRSMQGFPFYDKPMRIQYAKTDS 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 = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 23 PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
P +YI NL + ++F ++ G I+ ++ + +MRGQAFV F V
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKMRGQAFVIFKEV 61
Query: 81 ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
A AL + G+ F KPM IQ+ + +
Sbjct: 62 SSATNALRSMQGFPFYDKPMRIQYAKTDS 90
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 23 PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
P +YI NL + ++F ++ G I+ ++ + +MRGQAFV F V
Sbjct: 3 PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKMRGQAFVIFKEV 57
Query: 81 ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
A AL + G+ F KPM IQ+ + +
Sbjct: 58 SSATNALRSMQGFPFYDKPMRIQYAKTDS 86
>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 = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 23 PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
P +YI NL + ++F ++ G I+ ++ + +MRGQAFV F V
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKMRGQAFVIFKEV 62
Query: 81 ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
A AL + G+ F KPM IQ+ + +
Sbjct: 63 SSATNALRSMQGFPFYDKPMRIQYAKTDS 91
>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 = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 23 PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
P +YI NL + ++F ++ G I+ ++ + +MRGQAFV F V
Sbjct: 4 PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKMRGQAFVIFKEV 58
Query: 81 ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
A AL + G+ F KPM IQ+ + +
Sbjct: 59 SSATNALRSMQGFPFYDKPMRIQYAKTDS 87
>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 = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 23 PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
P +YI NL + ++F ++ G I+ ++ + +MRGQAFV F V
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKMRGQAFVIFKEV 62
Query: 81 ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
A AL + G+ F KPM IQ+ + +
Sbjct: 63 SSATNALRSMQGFPFYDKPMRIQYAKTDS 91
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 23 PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
P +YI NL + ++F ++ G I+ ++ + +MRGQAFV F V
Sbjct: 2 PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKMRGQAFVIFKEV 56
Query: 81 ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
A AL + G+ F KPM IQ+ + +
Sbjct: 57 SSATNALRSMQGFPFYDKPMRIQYAKTDS 85
>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 = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 23 PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
P +YI NL + ++F ++ G I+ ++ + +MRGQAFV F V
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKMRGQAFVIFKEV 61
Query: 81 ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
A AL + G+ F KPM IQ+ + +
Sbjct: 62 SSATNALRSMQGFPFYDKPMRIQYAKTDS 90
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 3/54 (5%)
Query: 49 FGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII 102
FG ID +++K GR +G F+TF E A RAL +NG+ G+PM +
Sbjct: 29 FGKIDNI---VLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRV 79
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 39/87 (44%), Gaps = 3/87 (3%)
Query: 23 PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
P +YI NL + ++F L+ + + +MRGQAFV F V
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL---KMRGQAFVIFKEVSS 63
Query: 83 AHRALNLVNGYVFKGKPMIIQFGRNPA 109
A AL + G+ F KPM IQ+ + +
Sbjct: 64 ATNALRSMQGFPFYDKPMRIQYAKTDS 90
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 39/87 (44%), Gaps = 3/87 (3%)
Query: 23 PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
P +YI NL + ++F L+ + + +MRGQAFV F V
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL---KMRGQAFVIFKEVSS 64
Query: 83 AHRALNLVNGYVFKGKPMIIQFGRNPA 109
A AL + G+ F KPM IQ+ + +
Sbjct: 65 ATNALRSMQGFPFYDKPMRIQYAKTDS 91
>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 = 42.7 bits (99), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 38/85 (44%), Gaps = 3/85 (3%)
Query: 23 PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
P +YI NL + ++F L+ + + +MRGQAFV F V
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL---KMRGQAFVIFKEVSS 64
Query: 83 AHRALNLVNGYVFKGKPMIIQFGRN 107
A AL + G+ F KPM IQ+ +
Sbjct: 65 ATNALRSMQGFPFYDKPMRIQYAKT 89
>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 = 42.4 bits (98), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 39/87 (44%), Gaps = 3/87 (3%)
Query: 23 PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
P +YI N+ +LF + +K M +MRGQAFV F +
Sbjct: 5 PNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTM---KMRGQAFVIFKELGS 61
Query: 83 AHRALNLVNGYVFKGKPMIIQFGRNPA 109
+ AL + G+ F GKPM IQ+ + +
Sbjct: 62 STNALRQLQGFPFYGKPMRIQYAKTDS 88
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 6/76 (7%)
Query: 27 LYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
LY+KNL S FG+I +AK +M+ GR +G FV F S E A +A
Sbjct: 18 LYVKNLDDGIDDERLRKAF-SPFGTITSAKV-----MMEGGRSKGFGFVCFSSPEEATKA 71
Query: 87 LNLVNGYVFKGKPMII 102
+ +NG + KP+ +
Sbjct: 72 VTEMNGRIVATKPLYV 87
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 9/57 (15%)
Query: 49 FGSIDAAKSGLIVKLMQE---GRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII 102
FG I++ ++LM + GR +G F+TF E A +AL +NG+ G+PM +
Sbjct: 50 FGRIES------IQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV 100
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 37.7 bits (86), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 40/89 (44%), Gaps = 7/89 (7%)
Query: 23 PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
P +YI NL + ++F ++ G I+ ++ + + RGQAFV F V
Sbjct: 5 PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKXRGQAFVIFKEV 59
Query: 81 ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
A AL G+ F KP IQ+ + +
Sbjct: 60 SSATNALRSXQGFPFYDKPXRIQYAKTDS 88
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 40/89 (44%), Gaps = 7/89 (7%)
Query: 23 PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
P +YI NL + ++F ++ G I+ ++ + + RGQAFV F V
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKXRGQAFVIFKEV 61
Query: 81 ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
A AL G+ F KP IQ+ + +
Sbjct: 62 SSATNALRSXQGFPFYDKPXRIQYAKTDS 90
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 40/89 (44%), Gaps = 7/89 (7%)
Query: 23 PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLM--QEGRMRGQAFVTFPSV 80
P +YI NL + ++F ++ G I+ ++ + + RGQAFV F V
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLHAIF-----SRFGQILDILVSRSLKXRGQAFVIFKEV 62
Query: 81 ELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
A AL G+ F KP IQ+ + +
Sbjct: 63 SSATNALRSXQGFPFYDKPXRIQYAKTDS 91
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 3/87 (3%)
Query: 23 PASVLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVEL 82
P +YI NL + ++F + +K + +MRGQAFV F +
Sbjct: 5 PNQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTL---KMRGQAFVIFKEIGS 61
Query: 83 AHRALNLVNGYVFKGKPMIIQFGRNPA 109
A AL + G+ F KPM I + ++ +
Sbjct: 62 ASNALRTMQGFPFYDKPMQIAYSKSDS 88
>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 = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 27/48 (56%)
Query: 57 SGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
SG ++ MQ G RG FV+F S + A A++ + G G+P+ I +
Sbjct: 30 SGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW 77
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 27/48 (56%)
Query: 57 SGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
SG ++ MQ G RG FV+F S + A A++ + G G+P+ I +
Sbjct: 116 SGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW 163
>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 = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 31/60 (51%)
Query: 47 SLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 106
SLF SI +S +++ G G FV + + + A RA+N +NG + K + + + R
Sbjct: 38 SLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR 97
>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 = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 31/60 (51%)
Query: 47 SLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 106
SLF SI +S +++ G G FV + + + A RA+N +NG + K + + + R
Sbjct: 23 SLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR 82
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 47 SLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 106
SLFGSI +S +V+ G+ G FV + A +A+N +NG + K + + + R
Sbjct: 23 SLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYAR 82
Query: 107 NPAAA 111
P++A
Sbjct: 83 -PSSA 86
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 31/60 (51%)
Query: 47 SLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 106
SLF SI +S +++ G G FV + + + A RA+N +NG + K + + + R
Sbjct: 21 SLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR 80
>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 = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 31/60 (51%)
Query: 47 SLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 106
SLF SI +S +++ G G FV + + + A RA+N +NG + K + + + R
Sbjct: 21 SLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR 80
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 34/65 (52%)
Query: 47 SLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 106
SLFGSI +S +V+ G+ G FV + A +A+N +NG + K + + + R
Sbjct: 23 SLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYAR 82
Query: 107 NPAAA 111
+A+
Sbjct: 83 PSSAS 87
>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 = 35.4 bits (80), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 35/65 (53%)
Query: 47 SLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 106
SLFGSI +S +V+ G+ G FV + + A +A+N +NG + K + + + R
Sbjct: 21 SLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR 80
Query: 107 NPAAA 111
+A+
Sbjct: 81 PSSAS 85
>pdb|2A3J|A Chain A, Structure Of Urndesign, A Complete Computational Redesign
Of Human U1a Protein
Length = 127
Score = 34.7 bits (78), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 58 GLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAA 110
++V L + G+A++ F + E A + GY F+G P++I F P +
Sbjct: 62 DIVVDLSDDNS--GKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQS 112
>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 = 33.1 bits (74), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 60 IVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFG-RNPAAAK 112
+ + M R G A+V F A RAL+ +N V KGKP+ I + R+P+ K
Sbjct: 47 VCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRK 100
Score = 29.6 bits (65), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 6/76 (7%)
Query: 27 LYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
++IKNL K S FG+I + K + E +G FV F + E A RA
Sbjct: 106 IFIKNLDKSIDNKALYDTF-SAFGNILSCKV-----VCDENGSKGYGFVHFETQEAAERA 159
Query: 87 LNLVNGYVFKGKPMII 102
+ +NG + + + +
Sbjct: 160 IEKMNGMLLNDRKVFV 175
>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 = 33.1 bits (74), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 60 IVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFG-RNPAAAK 112
+ + M R G A+V F A RAL+ +N V KGKP+ I + R+P+ K
Sbjct: 42 VCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRK 95
Score = 29.6 bits (65), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 6/76 (7%)
Query: 27 LYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
++IKNL K S FG+I + K + E +G FV F + E A RA
Sbjct: 101 IFIKNLDKSIDNKALYDTF-SAFGNILSCKV-----VCDENGSKGYGFVHFETQEAAERA 154
Query: 87 LNLVNGYVFKGKPMII 102
+ +NG + + + +
Sbjct: 155 IEKMNGMLLNDRKVFV 170
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 32.7 bits (73), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%)
Query: 47 SLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 106
+LF +I + I++ + G G AFV F S + RA+ ++NG + K + + + R
Sbjct: 22 ALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR 81
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 32.7 bits (73), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%)
Query: 47 SLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 106
+LF +I + I++ + G G AFV F S + RA+ ++NG + K + + + R
Sbjct: 22 ALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR 81
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 27 LYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
LY+ NL + G +GSI K+ L KL GR RG AFV + E A A
Sbjct: 92 LYVTNLPRTITDDQLDTIFGK-YGSI-VQKNILRDKLT--GRPRGVAFVRYNKREEAQEA 147
Query: 87 LNLVNGYVFKG 97
++ +N + +G
Sbjct: 148 ISALNNVIPEG 158
>pdb|1WG1|A Chain A, Solution Structure Of Rna Binding Domain In
Bab13405(Homolog Exc-7)
Length = 88
Score = 32.3 bits (72), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 68 RMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
R + AFVT + E A A+ + + Y F+GK +I+Q
Sbjct: 38 RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQL 74
>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 = 32.3 bits (72), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 30/60 (50%)
Query: 47 SLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 106
+LF +I + I + + G G AFV F S + RA+ ++NG + K + + + R
Sbjct: 33 ALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKRLKVSYAR 92
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 39/80 (48%), Gaps = 6/80 (7%)
Query: 27 LYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
LY+ NL + G +GSI K+ L KL GR RG AFV + E A A
Sbjct: 103 LYVTNLPRTITDDQLDTIFGK-YGSI-VQKNILRDKLT--GRPRGVAFVRYNKREEAQEA 158
Query: 87 LNLVNGYVFKG--KPMIIQF 104
++ +N + +G +P+ ++
Sbjct: 159 ISALNNVIPEGGSQPLSVRL 178
>pdb|2HGM|A Chain A, Nmr Structure Of The Second Qrrm Domain Of Human Hnrnp F
pdb|2KG0|A Chain A, Structure Of The Second Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 126
Score = 32.0 bits (71), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 25/40 (62%)
Query: 48 LFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRAL 87
F ++ +G+ + + EG++ G+AFV F S ELA +AL
Sbjct: 62 FFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKAL 101
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 31.6 bits (70), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 65 QEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
Q G+ +G AF+ F S E A ALN N +G+ + ++
Sbjct: 48 QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL 87
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 22/45 (48%)
Query: 60 IVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
IV Q R RG AFV F +V+ A A NG G+ + + F
Sbjct: 47 IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 91
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 22/45 (48%)
Query: 60 IVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
IV Q R RG AFV F +V+ A A NG G+ + + F
Sbjct: 44 IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 88
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 25/45 (55%)
Query: 59 LIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ 103
++VK + R RG FVTF +++ A A+ +NG G+ + +
Sbjct: 43 VVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD 87
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 30.8 bits (68), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 22/45 (48%)
Query: 60 IVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
IV Q R RG AFV F +V+ A A NG G+ + + F
Sbjct: 78 IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 122
>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 = 30.4 bits (67), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 65 QEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
+ G+++G+A V+F A A++ +G F G P+ + F
Sbjct: 58 ETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97
>pdb|1WG5|A Chain A, Solution Structure Of The First Rrm Domain In
Heterogeneous Nuclear Ribonucleoprotein H
Length = 104
Score = 30.4 bits (67), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 24/40 (60%)
Query: 48 LFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRAL 87
F ++ +G+ + + +GR G+AFV F S E+A +AL
Sbjct: 35 FFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL 74
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 30.0 bits (66), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 65 QEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
+ G+++G+A V+F A A++ +G F G P+ + F
Sbjct: 52 ETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 91
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 29.6 bits (65), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 68 RMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 106
++R AFV F + E A A+ +NG V G P+ + +
Sbjct: 49 KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK 87
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 29.6 bits (65), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 5/58 (8%)
Query: 62 KLMQE---GRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ--FGRNPAAAKPS 114
K+M++ G +G AF+ F S + + A+ +NG +P+ + F ++ + PS
Sbjct: 37 KIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGSGPS 94
>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 = 29.6 bits (65), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 6/76 (7%)
Query: 27 LYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
++IKNL K S FG+I + K + E +G FV F + E A RA
Sbjct: 8 IFIKNLDKSIDNKALYDTF-SAFGNILSCKV-----VCDENGSKGYGFVHFETQEAAERA 61
Query: 87 LNLVNGYVFKGKPMII 102
+ +NG + + + +
Sbjct: 62 IEKMNGMLLNDRKVFV 77
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 29.6 bits (65), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 6/76 (7%)
Query: 27 LYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
++IKNL K S FG+I + K + E +G FV F + E A RA
Sbjct: 14 IFIKNLDKSIDNKALYDTF-SAFGNILSCKV-----VCDENGSKGYGFVHFETQEAAERA 67
Query: 87 LNLVNGYVFKGKPMII 102
+ +NG + + + +
Sbjct: 68 IEKMNGMLLNDRKVFV 83
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 29.3 bits (64), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 21/43 (48%)
Query: 60 IVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII 102
IV Q R RG AFV F +V+ A A NG G+ + +
Sbjct: 47 IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 28.9 bits (63), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 23/41 (56%)
Query: 69 MRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
+ G AFV F E A +A+ V+G F +P+ + + + PA
Sbjct: 64 LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPA 104
>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 = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 65 QEGRMRGQAFVTFPSVELAHRALNLVNGY 93
Q GR +G AF+ F +E + A+ +NGY
Sbjct: 40 QTGRSKGYAFIEFRDLESSASAVRNLNGY 68
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 65 QEGRMRGQAFVTFPSVELAHRALNLVNGY 93
Q GR +G AF+ F +E + A+ +NGY
Sbjct: 39 QTGRSKGYAFIEFRDLESSASAVRNLNGY 67
>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 = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 49 FGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFG-RN 107
FG I A+ +VK M G+ +G FV+F + A A+ + G G+ + + R
Sbjct: 39 FGRISDAR---VVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 95
Query: 108 PAAAKPS 114
P A K +
Sbjct: 96 PPAPKST 102
>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 = 1.1, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 65 QEGRMRGQAFVTFPSVELAHRALNLVNGY 93
Q GR +G AF+ F +E + A+ +NGY
Sbjct: 41 QTGRSKGYAFIEFRDLESSASAVRNLNGY 69
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 23/43 (53%)
Query: 68 RMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAA 110
R RG F+ S LA A ++G + K +P+ I+F + AA
Sbjct: 56 RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGAA 98
>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 = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 39/80 (48%), Gaps = 6/80 (7%)
Query: 27 LYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRA 86
LY+ NL + G +GSI K+ L KL GR RG AFV + E A A
Sbjct: 16 LYVTNLPRTITDDQLDTIFGK-YGSI-VQKNILRDKLT--GRPRGVAFVRYNKREEAQEA 71
Query: 87 LNLVNGYVFKG--KPMIIQF 104
++ +N + +G +P+ ++
Sbjct: 72 ISALNNVIPEGGSQPLSVRL 91
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 7/65 (10%)
Query: 49 FGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNP 108
FG I A+ +VK M G+ +G FV+F + A A+ + G G+ Q N
Sbjct: 30 FGRISDAR---VVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGR----QIRTNW 82
Query: 109 AAAKP 113
A KP
Sbjct: 83 ATRKP 87
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 69 MRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 106
+ G AFV F E A +A+ V+G F +P+ + + +
Sbjct: 37 LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSK 74
>pdb|2OSR|A Chain A, Nmr Structure Of Rrm-2 Of Yeast Npl3 Protein
Length = 87
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 19/38 (50%)
Query: 71 GQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNP 108
G + FPS E+ AL +N F+G + ++ NP
Sbjct: 46 GTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNP 83
>pdb|2JVR|A Chain A, Segmental Isotope Labeling Of Npl3p
Length = 111
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 19/38 (50%)
Query: 71 GQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNP 108
G + FPS E+ AL +N F+G + ++ NP
Sbjct: 68 GTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNP 105
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 25/56 (44%), Gaps = 4/56 (7%)
Query: 49 FGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 104
FG++ A V + GR G A V F A +A+ NG G+PM IQ
Sbjct: 52 FGTLKKA----AVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 103
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 3/66 (4%)
Query: 49 FGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNP 108
FGSI + K G+ +G AF++F E A RA+ V+G+ + + +++ +
Sbjct: 39 FGSISRI---YLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS 95
Query: 109 AAAKPS 114
+ PS
Sbjct: 96 TNSGPS 101
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 12/83 (14%)
Query: 26 VLYIKNLAKXXXXXXXXXXXGSLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHR 85
VL+++NLA S FG ++ K +++ AF+ F + A +
Sbjct: 13 VLFVRNLANTVTEEILEKAF-SQFGKLERVK-----------KLKDYAFIHFDERDGAVK 60
Query: 86 ALNLVNGYVFKGKPMIIQFGRNP 108
A+ +NG +G+ + I F + P
Sbjct: 61 AMEEMNGKDLEGENIEIVFAKPP 83
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 5/68 (7%)
Query: 49 FGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFG--R 106
FG I A+ +VK M G+ +G FV+F + A A+ + G G+ + + +
Sbjct: 39 FGKISDAR---VVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRK 95
Query: 107 NPAAAKPS 114
PA + PS
Sbjct: 96 PPAPSGPS 103
>pdb|2DHA|A Chain A, Solution Structure Of The Second Rna Recognition Motif
In Hypothetical Protein Flj201171
Length = 123
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 17/36 (47%)
Query: 52 IDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRAL 87
I K G++ +GR G AFV F E A AL
Sbjct: 50 ITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 68 RMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 109
+ RG AF+TF + A A +NG GK + ++ + P+
Sbjct: 46 KSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPS 87
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 26.2 bits (56), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 70 RGQAFVTFPSVELAHRALNLVNGYVFKGK 98
+G AFVTF E A +A V+G VF+G+
Sbjct: 50 KGFAFVTFMFPEHAVKAYAEVDGQVFQGR 78
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 26.2 bits (56), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 23/39 (58%)
Query: 65 QEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQ 103
++G+ RG VTF A +A+++ NG + +PM ++
Sbjct: 51 KDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK 89
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 25.4 bits (54), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 3/66 (4%)
Query: 47 SLFGSIDAAKSGLIVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 106
+F + S +V + G+ +G F + E A A+ +NG F G+ + +
Sbjct: 27 DIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVD--- 83
Query: 107 NPAAAK 112
N A+ K
Sbjct: 84 NAASEK 89
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
0.320 0.137 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,967,631
Number of Sequences: 62578
Number of extensions: 84545
Number of successful extensions: 273
Number of sequences better than 100.0: 75
Number of HSP's better than 100.0 without gapping: 69
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 196
Number of HSP's gapped (non-prelim): 81
length of query: 114
length of database: 14,973,337
effective HSP length: 77
effective length of query: 37
effective length of database: 10,154,831
effective search space: 375728747
effective search space used: 375728747
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: 45 (21.9 bits)