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= psy10279
(80 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 100 bits (249), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 46/57 (80%), Positives = 53/57 (92%), Gaps = 1/57 (1%)
Query: 1 MAM-SQRRANVRLPPEVNRVLYIRNLPYKITGDEMYDIFGKYGAIRQIRIGNTPDTR 56
MAM + +RAN+RLPPEVNR+LYIRNLPYKIT +EMYDIFGKYG IRQIR+GNTP+TR
Sbjct: 1 MAMQAAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR 57
>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 = 97.4 bits (241), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 45/57 (78%), Positives = 52/57 (91%), Gaps = 1/57 (1%)
Query: 1 MAM-SQRRANVRLPPEVNRVLYIRNLPYKITGDEMYDIFGKYGAIRQIRIGNTPDTR 56
MAM + +RAN+RLPPEVNR+L IRNLPYKIT +EMYDIFGKYG IRQIR+GNTP+TR
Sbjct: 1 MAMQAAKRANIRLPPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR 57
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 96.7 bits (239), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 43/50 (86%), Positives = 48/50 (96%)
Query: 7 RANVRLPPEVNRVLYIRNLPYKITGDEMYDIFGKYGAIRQIRIGNTPDTR 56
RAN+RLPPEVNR+LYIRNLPYKIT +EMYDIFGKYG IRQIR+GNTP+TR
Sbjct: 2 RANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR 51
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 92.0 bits (227), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 40/47 (85%), Positives = 45/47 (95%)
Query: 10 VRLPPEVNRVLYIRNLPYKITGDEMYDIFGKYGAIRQIRIGNTPDTR 56
+RLPPEVNR+LYIRNLPYKIT +EMYDIFGKYG IRQIR+GNTP+TR
Sbjct: 1 IRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR 47
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 10/73 (13%)
Query: 12 LPPEVNRVLYIRNLPYKITGDEMYDIFGKYGAIRQIRIGNTPDTR---------YLTKSL 62
L P + V Y+ NLP+ +T +++Y IF KYG + ++ I DTR +L K
Sbjct: 12 LAPSKSTV-YVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDS 70
Query: 63 VMKCMIFLVNMEL 75
C + N +L
Sbjct: 71 AQNCTRAINNKQL 83
>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 = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/30 (56%), Positives = 21/30 (70%)
Query: 20 LYIRNLPYKITGDEMYDIFGKYGAIRQIRI 49
LY+ NLP IT D++ IFGKYG+I Q I
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNI 45
>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 = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/30 (56%), Positives = 21/30 (70%)
Query: 20 LYIRNLPYKITGDEMYDIFGKYGAIRQIRI 49
LY+ NLP IT D++ IFGKYG+I Q I
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNI 132
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/30 (56%), Positives = 21/30 (70%)
Query: 20 LYIRNLPYKITGDEMYDIFGKYGAIRQIRI 49
LY+ NLP IT D++ IFGKYG+I Q I
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 33.1 bits (74), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 15/67 (22%), Positives = 35/67 (52%), Gaps = 11/67 (16%)
Query: 12 LPPEV--NRVLYIRNLPYKITGDEMYDIFGKYGAIRQIRIGNTPDT---------RYLTK 60
LP +V + ++IRNL + + + ++ ++G ++ +R+ PDT +++T+
Sbjct: 8 LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQ 67
Query: 61 SLVMKCM 67
KC+
Sbjct: 68 EAAQKCL 74
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 32.3 bits (72), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 18 RVLYIRNLPYKITGDEMYDIFGKYGAIR 45
R L +NLPYK+T DE+ ++F IR
Sbjct: 94 RTLLAKNLPYKVTQDELKEVFEDAAEIR 121
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 32.3 bits (72), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 15/69 (21%)
Query: 14 PEV--NRVLYIRNLPYKITGDE----MYDIFGKYGAIRQIRIGNTPDTRYLTKSLVMKCM 67
PE N +YI NL KI DE +Y IF ++G I I +++SL M+
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDI---------LVSRSLKMRGQ 53
Query: 68 IFLVNMELS 76
F++ E+S
Sbjct: 54 AFVIFKEVS 62
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 32.0 bits (71), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 22/35 (62%)
Query: 17 NRVLYIRNLPYKITGDEMYDIFGKYGAIRQIRIGN 51
N L++R P + E+ +IFG +G +++++I N
Sbjct: 4 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN 38
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 32.0 bits (71), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 15/69 (21%)
Query: 14 PEV--NRVLYIRNLPYKITGDE----MYDIFGKYGAIRQIRIGNTPDTRYLTKSLVMKCM 67
PE N +YI NL KI DE +Y IF ++G I I + ++SL M+
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---------SRSLKMRGQ 54
Query: 68 IFLVNMELS 76
F++ E+S
Sbjct: 55 AFVIFKEVS 63
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 22/35 (62%)
Query: 17 NRVLYIRNLPYKITGDEMYDIFGKYGAIRQIRIGN 51
N L++R P + E+ +IFG +G +++++I N
Sbjct: 31 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN 65
>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 = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 20 LYIRNLPYKITGDEMYDIFGKYGAIRQIRIGNTPDTRYL---TKSLVMKCMIFLVNMELS 76
L++ NLP IT +EM +F KYG ++ I ++ T++L + L NM L
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLR 77
Query: 77 DK 78
K
Sbjct: 78 GK 79
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 21/32 (65%)
Query: 20 LYIRNLPYKITGDEMYDIFGKYGAIRQIRIGN 51
+Y+ NLP I ++ D+F KYGAIR I + N
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN 56
>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 = 30.4 bits (67), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 15/69 (21%)
Query: 14 PEV--NRVLYIRNLPYKITGDE----MYDIFGKYGAIRQIRIGNTPDTRYLTKSLVMKCM 67
PE N +YI NL KI DE ++ IF ++G I I + ++SL M+
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---------SRSLKMRGQ 53
Query: 68 IFLVNMELS 76
F++ E+S
Sbjct: 54 AFVIFKEVS 62
>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 = 30.4 bits (67), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 15/69 (21%)
Query: 14 PEV--NRVLYIRNLPYKITGDE----MYDIFGKYGAIRQIRIGNTPDTRYLTKSLVMKCM 67
PE N +YI NL KI DE ++ IF ++G I I + ++SL M+
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---------SRSLKMRGQ 53
Query: 68 IFLVNMELS 76
F++ E+S
Sbjct: 54 AFVIFKEVS 62
>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 = 30.4 bits (67), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 15/69 (21%)
Query: 14 PEV--NRVLYIRNLPYKITGDE----MYDIFGKYGAIRQIRIGNTPDTRYLTKSLVMKCM 67
PE N +YI NL KI DE ++ IF ++G I I + ++SL M+
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---------SRSLKMRGQ 54
Query: 68 IFLVNMELS 76
F++ E+S
Sbjct: 55 AFVIFKEVS 63
>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 = 30.4 bits (67), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 15/69 (21%)
Query: 14 PEV--NRVLYIRNLPYKITGDE----MYDIFGKYGAIRQIRIGNTPDTRYLTKSLVMKCM 67
PE N +YI NL KI DE ++ IF ++G I I + ++SL M+
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---------SRSLKMRGQ 54
Query: 68 IFLVNMELS 76
F++ E+S
Sbjct: 55 AFVIFKEVS 63
>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 = 30.4 bits (67), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 15/69 (21%)
Query: 14 PEV--NRVLYIRNLPYKITGDE----MYDIFGKYGAIRQIRIGNTPDTRYLTKSLVMKCM 67
PE N +YI NL KI DE ++ IF ++G I I + ++SL M+
Sbjct: 1 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---------SRSLKMRGQ 51
Query: 68 IFLVNMELS 76
F++ E+S
Sbjct: 52 AFVIFKEVS 60
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 30.4 bits (67), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 24/39 (61%), Gaps = 3/39 (7%)
Query: 14 PEVNRVL---YIRNLPYKITGDEMYDIFGKYGAIRQIRI 49
P V+R L ++ N+PY+ T +++ DIF + G + R+
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRL 40
>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 = 30.4 bits (67), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 15/69 (21%)
Query: 14 PEV--NRVLYIRNLPYKITGDE----MYDIFGKYGAIRQIRIGNTPDTRYLTKSLVMKCM 67
PE N +YI NL KI DE ++ IF ++G I I + ++SL M+
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---------SRSLKMRGQ 53
Query: 68 IFLVNMELS 76
F++ E+S
Sbjct: 54 AFVIFKEVS 62
>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 = 30.4 bits (67), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 13/64 (20%)
Query: 17 NRVLYIRNLPYKITGDE----MYDIFGKYGAIRQIRIGNTPDTRYLTKSLVMKCMIFLVN 72
N +YI NL KI DE ++ IF ++G I I + ++SL M+ F++
Sbjct: 5 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---------SRSLKMRGQAFVIF 55
Query: 73 MELS 76
E+S
Sbjct: 56 KEVS 59
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 30.4 bits (67), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 22/32 (68%)
Query: 19 VLYIRNLPYKITGDEMYDIFGKYGAIRQIRIG 50
LY+ NL + T +++Y++F K G I++I +G
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMG 51
>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 = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 13/64 (20%)
Query: 17 NRVLYIRNLPYKITGDE----MYDIFGKYGAIRQIRIGNTPDTRYLTKSLVMKCMIFLVN 72
N +YI NL KI DE ++ IF ++G I I + ++SL M+ F++
Sbjct: 4 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---------SRSLKMRGQAFVIF 54
Query: 73 MELS 76
E+S
Sbjct: 55 KEVS 58
>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 = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 13/64 (20%)
Query: 17 NRVLYIRNLPYKITGDE----MYDIFGKYGAIRQIRIGNTPDTRYLTKSLVMKCMIFLVN 72
N +YI NL KI DE ++ IF ++G I I + ++SL M+ F++
Sbjct: 3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---------SRSLKMRGQAFVIF 53
Query: 73 MELS 76
E+S
Sbjct: 54 KEVS 57
>pdb|2HGN|A Chain A, Nmr Structure Of The Third Qrrm Domain Of Human Hnrnp F
pdb|2KG1|A Chain A, Structure Of The Third Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 139
Score = 30.0 bits (66), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 3/49 (6%)
Query: 16 VNRVLYIRNLPYKITGDEMYDIFGKYGAIR-QIRIGNTPDTRYLTKSLV 63
+++R LPYK T +++Y+ F +R I IG PD R ++ V
Sbjct: 45 TGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIG--PDGRVTGEADV 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 = 30.0 bits (66), Expect = 0.34, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 13/64 (20%)
Query: 17 NRVLYIRNLPYKITGDE----MYDIFGKYGAIRQIRIGNTPDTRYLTKSLVMKCMIFLVN 72
N +YI NL KI DE +Y IF ++G I I + ++SL M+ F++
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---------SRSLKMRGQAFVIF 59
Query: 73 MELS 76
E+S
Sbjct: 60 KEVS 63
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 29.6 bits (65), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 13 PPEVNRVLYIRNLPYKITGDEMYDIFGKYGAIRQIRIGNTPDTRYLTKSLVMKCMIFLVN 72
P E N+VLY++NL ++T ++ +F ++ Q + G R +T + + I N
Sbjct: 21 PGEPNKVLYLKNLSPRVTERDLVSLFARF----QEKKGPPIQFRMMTGRMRGQAFITFPN 76
Query: 73 MELS 76
E++
Sbjct: 77 KEIA 80
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 29.6 bits (65), Expect = 0.40, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 20 LYIRNLPYKITGDEMYDIFGKYGAIRQIRIGNTPD---TRYLTKSLVMKCMIFLVNMELS 76
L++ NLP IT +EM +F KYG ++ I R T++L + L NM L
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLR 84
Query: 77 DK 78
K
Sbjct: 85 GK 86
>pdb|1UKX|A Chain A, Solution Structure Of The Rwd Domain Of Mouse Gcn2
Length = 137
Score = 29.6 bits (65), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 18/29 (62%), Gaps = 4/29 (13%)
Query: 7 RANVRLPPEVNRVLYIRNLPYKITGDEMY 35
R VR PPE+N VLY P + G+E+Y
Sbjct: 38 RGRVREPPEINLVLY----PQGLAGEEVY 62
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 29.3 bits (64), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 5 QRRANVRLPPEVNRVLYIRNLPYKITGDEMYDIFGKYGAIR-QIRIGNTPDTRYLTKSLV 63
Q+R+ R P E +Y++ LP++ + D F K + I I P+ + + V
Sbjct: 13 QKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFV 72
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 29.3 bits (64), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 23/34 (67%), Gaps = 1/34 (2%)
Query: 17 NRVLYIRNL-PYKITGDEMYDIFGKYGAIRQIRI 49
N VL + NL P ++T ++ +FG YG +++++I
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKI 36
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 29.3 bits (64), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 22/32 (68%)
Query: 19 VLYIRNLPYKITGDEMYDIFGKYGAIRQIRIG 50
LY+ NL + T +++Y++F K G I++I +G
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMG 72
>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 = 29.3 bits (64), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 23/34 (67%), Gaps = 1/34 (2%)
Query: 17 NRVLYIRNL-PYKITGDEMYDIFGKYGAIRQIRI 49
N VL + NL P ++T ++ +FG YG +++++I
Sbjct: 34 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKI 67
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition
In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 28.5 bits (62), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 20 LYIRNLPYKITGDEMYDIFGKYGAIRQIRIGNTPDT 55
++I L + T D + + FGKYG + ++I P T
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPAT 41
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 28.5 bits (62), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 15/69 (21%)
Query: 14 PEV--NRVLYIRNLPYKITGDE----MYDIFGKYGAIRQIRIGNTPDTRYLTKSLVMKCM 67
PE N +YI NL KI DE ++ IF ++G I I + ++SL +
Sbjct: 1 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---------SRSLKXRGQ 51
Query: 68 IFLVNMELS 76
F++ E+S
Sbjct: 52 AFVIFKEVS 60
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 28.5 bits (62), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 15/69 (21%)
Query: 14 PEV--NRVLYIRNLPYKITGDE----MYDIFGKYGAIRQIRIGNTPDTRYLTKSLVMKCM 67
PE N +YI NL KI DE ++ IF ++G I I + ++SL +
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---------SRSLKXRGQ 53
Query: 68 IFLVNMELS 76
F++ E+S
Sbjct: 54 AFVIFKEVS 62
>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 = 28.5 bits (62), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 15/69 (21%)
Query: 14 PEV--NRVLYIRNLPYKITGDE----MYDIFGKYGAIRQIRIGNTPDTRYLTKSLVMKCM 67
PE N +YI NL KI DE ++ IF ++G I I + ++SL +
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---------SRSLKXRGQ 54
Query: 68 IFLVNMELS 76
F++ E+S
Sbjct: 55 AFVIFKEVS 63
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 20 LYIRNLPYKITGDEMYDIFGKYGAIRQIRI 49
L+I+NL + T + + +F K GAI+ I
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTI 37
>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 = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 9/30 (30%), Positives = 19/30 (63%)
Query: 20 LYIRNLPYKITGDEMYDIFGKYGAIRQIRI 49
L+I LP+ T +E+ +I +G ++ +R+
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRL 49
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af
Large Subunit
Length = 87
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 5/34 (14%)
Query: 18 RVLYIRNLPYKITGDEMYDIFGKYGAIRQIRIGN 51
R LY+ N+P+ IT + M D F Q+R+G
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNA-----QMRLGG 35
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 5/34 (14%)
Query: 18 RVLYIRNLPYKITGDEMYDIFGKYGAIRQIRIGN 51
R LY+ N+P+ IT + M D F Q+R+G
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNA-----QMRLGG 33
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 5/34 (14%)
Query: 18 RVLYIRNLPYKITGDEMYDIFGKYGAIRQIRIGN 51
R LY+ N+P+ IT + M D F Q+R+G
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNA-----QMRLGG 35
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 5/34 (14%)
Query: 18 RVLYIRNLPYKITGDEMYDIFGKYGAIRQIRIGN 51
R LY+ N+P+ IT + M D F Q+R+G
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNA-----QMRLGG 33
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 26.9 bits (58), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 5/34 (14%)
Query: 18 RVLYIRNLPYKITGDEMYDIFGKYGAIRQIRIGN 51
R LY+ N+P+ IT + M D F Q+R+G
Sbjct: 2 RRLYVGNIPFGITEEAMMDFFNA-----QMRLGG 30
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 26.6 bits (57), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 7/30 (23%), Positives = 20/30 (66%)
Query: 20 LYIRNLPYKITGDEMYDIFGKYGAIRQIRI 49
+ +RN+P++ E+ ++F +G ++ +R+
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRL 47
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 8/30 (26%), Positives = 19/30 (63%)
Query: 20 LYIRNLPYKITGDEMYDIFGKYGAIRQIRI 49
L++ N+P++ ++ +FG++G I + I
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEI 47
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1
In Complex With Ugcaugu
Length = 109
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 8/30 (26%), Positives = 19/30 (63%)
Query: 20 LYIRNLPYKITGDEMYDIFGKYGAIRQIRI 49
L++ N+P++ ++ +FG++G I + I
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEI 61
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 20 LYIRNLPYKITGDEMYDIFGKYGAIRQIRI 49
LY+ LP ++ EM +F +YG I RI
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRI 33
>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 = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 20 LYIRNLPYKITGDEMYDIFGKYGAIRQIRI 49
LY+ LP +T E+ +F +YG I RI
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRI 120
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 20 LYIRNLPYKITGDEMYDIFGKYGAIRQIRI 49
LY+ LP ++ EM +F +YG I RI
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRI 122
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 26.2 bits (56), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 14 PEVNR--VLYIRNLPYKITGDEMYDIFGKYGAIRQIRIGNTPDTR 56
P+V+ L + NL Y+ + D + +F KYG + + I P T+
Sbjct: 8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTK 52
>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 = 5.2, Method: Compositional matrix adjust.
Identities = 8/29 (27%), Positives = 18/29 (62%)
Query: 20 LYIRNLPYKITGDEMYDIFGKYGAIRQIR 48
L++RNL Y + +++ +F YG + ++
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELH 39
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 26.2 bits (56), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 20 LYIRNLPYKITGDEMYDIFGKYGAIRQIRI 49
LYI LP +T ++ D+F ++G I R+
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRV 120
>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 = 26.2 bits (56), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 20 LYIRNLPYKITGDEMYDIFGKYGAIRQIRI 49
LYI LP +T ++ D+F ++G I R+
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRV 120
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 25.8 bits (55), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 21/49 (42%)
Query: 1 MAMSQRRANVRLPPEVNRVLYIRNLPYKITGDEMYDIFGKYGAIRQIRI 49
M R R P+ N L + L T ++ ++F KYG I + I
Sbjct: 30 MGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSI 78
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 25.4 bits (54), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 20 LYIRNLPYKITGDEMYDIFGKYGAIRQIRI 49
L+I NLP + T E+ +F +YG + + I
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDI 40
>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 = 25.4 bits (54), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 12/43 (27%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 13 PPEVNRVLYIRNLPYKITGDEMYDIFGKYGAIRQIRIGNTPDT 55
PP +RV+Y+ ++PY T +++ D+ G + +++ P T
Sbjct: 2 PP--SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQT 42
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
0.325 0.141 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,152,525
Number of Sequences: 62578
Number of extensions: 68953
Number of successful extensions: 274
Number of sequences better than 100.0: 63
Number of HSP's better than 100.0 without gapping: 46
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 226
Number of HSP's gapped (non-prelim): 65
length of query: 80
length of database: 14,973,337
effective HSP length: 49
effective length of query: 31
effective length of database: 11,907,015
effective search space: 369117465
effective search space used: 369117465
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)