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= 045807
(320 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 84.7 bits (208), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 42/104 (40%), Positives = 61/104 (58%), Gaps = 1/104 (0%)
Query: 43 SPTLLLSNMYQRPDMITPGVDPQGQALDPRKIQDHXXXXXXXX-XXXXSKYGEIESLNIC 101
S T+ L N+Y+ P + D A+ ++Q+H KYGE+E +N+C
Sbjct: 1 SQTIALLNIYRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVC 60
Query: 102 DNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFSP 145
DNL DH+VGNVYV+FR EE A A+ +LN R++ G+PI + SP
Sbjct: 61 DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSP 104
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 36.2 bits (82), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 90 SKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPI 139
SK+G+I L + D H G V FR+ E A ++ L+GR++ GR I
Sbjct: 48 SKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQI 94
>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 = 35.0 bits (79), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 90 SKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S++G+I L+I + + M G +V F+E A NALR++ G + +P+ + ++
Sbjct: 35 SQFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 87
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 34.7 bits (78), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 90 SKYGEIESLNI-CDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDF 143
++YGEI+++++ D ++ G V++ + A A+ LNG+ G+PI VD+
Sbjct: 45 AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 99
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 34.7 bits (78), Expect = 0.073, Method: Composition-based stats.
Identities = 14/33 (42%), Positives = 25/33 (75%)
Query: 110 GNVYVQFREEEHAANALRNLNGRFYAGRPIIVD 142
G + +++++E A +A+RNLNGR ++GR + VD
Sbjct: 51 GYGFCEYQDQETALSAMRNLNGREFSGRALRVD 83
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 34.7 bits (78), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 90 SKYGEIESLNI-CDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDF 143
++YGEI+++++ D ++ G V++ + A A+ LNG+ G+PI VD+
Sbjct: 29 AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 83
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 34.7 bits (78), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 90 SKYGEIESLNI-CDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDF 143
++YGEI+++++ D ++ G V++ + A A+ LNG+ G+PI VD+
Sbjct: 31 AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 85
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 34.7 bits (78), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 90 SKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S++G+I L+I + + M G +V F+E A NALR++ G + +P+ + ++
Sbjct: 34 SQFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 34.3 bits (77), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 90 SKYGEIESLNI-CDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFSPV 146
++YGEI+++++ D ++ G V++ + A A+ LNG+ G+PI VD+ V
Sbjct: 29 AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFV 86
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 34.3 bits (77), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 90 SKYGEIESLNI-CDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDF 143
++YGEI+++++ D ++ G V++ + A A+ LNG+ G+PI VD+
Sbjct: 44 AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
Length = 109
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 90 SKYGEIESLNI-CDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFSPV 146
++YGEI+++++ D ++ G V++ + A A+ LNG+ G+PI VD+ V
Sbjct: 29 AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFV 86
>pdb|2A3J|A Chain A, Structure Of Urndesign, A Complete Computational Redesign
Of Human U1a Protein
Length = 127
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 90 SKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S G+I L+I +L+D G Y+ F +E A + G + G P+++ FS
Sbjct: 55 SSQGDI--LDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFS 107
>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 = 33.1 bits (74), Expect = 0.20, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 90 SKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S++G+I L+I + + M G +V F+E A NALR++ G + +P+ + ++
Sbjct: 34 SRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 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 = 33.1 bits (74), Expect = 0.21, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 90 SKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S++G+I L+I + + M G +V F+E A NALR++ G + +P+ + ++
Sbjct: 35 SRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 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 = 33.1 bits (74), Expect = 0.22, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 90 SKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S++G+I L+I + + M G +V F+E A NALR++ G + +P+ + ++
Sbjct: 35 SRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 87
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 33.1 bits (74), Expect = 0.22, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 90 SKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S++G+I L+I + + M G +V F+E A NALR++ G + +P+ + ++
Sbjct: 34 SRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86
>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 = 33.1 bits (74), Expect = 0.22, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 90 SKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S++G+I L+I + + M G +V F+E A NALR++ G + +P+ + ++
Sbjct: 30 SRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 82
>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 = 33.1 bits (74), Expect = 0.23, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 90 SKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S++G+I L+I + + M G +V F+E A NALR++ G + +P+ + ++
Sbjct: 29 SRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 81
>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 = 33.1 bits (74), Expect = 0.23, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 90 SKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S++G+I L+I + + M G +V F+E A NALR++ G + +P+ + ++
Sbjct: 31 SRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 83
>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 = 33.1 bits (74), Expect = 0.23, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 90 SKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S++G+I L+I + + M G +V F+E A NALR++ G + +P+ + ++
Sbjct: 34 SRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 32.7 bits (73), Expect = 0.26, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 90 SKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S++G+I L+I + + M G +V F+E A NALR++ G + +P+ + ++
Sbjct: 35 SQFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 87
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 32.7 bits (73), Expect = 0.26, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 90 SKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S++G+I L+I + + M G +V F+E A NALR++ G + +P+ + ++
Sbjct: 32 SRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 84
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 32.7 bits (73), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 92 YGEIESLNIC-DNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIV 141
+G IES+ + D+ G ++ F + E A AL LNG AGRP+ V
Sbjct: 50 FGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV 100
>pdb|2PE8|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 (free
Form)
pdb|2PEH|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
pdb|2PEH|B Chain B, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
Length = 105
Score = 32.3 bits (72), Expect = 0.35, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 91 KYGEIESLNICD--NLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFSPVTD 148
KYG++ I + D ++++F E A A+ +LNGR++ GR + F +
Sbjct: 36 KYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNLDK 95
Query: 149 FR 150
FR
Sbjct: 96 FR 97
>pdb|3DXB|A Chain A, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|B Chain B, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|C Chain C, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|D Chain D, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|E Chain E, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|F Chain F, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|G Chain G, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|H Chain H, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
Length = 222
Score = 31.6 bits (70), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 22/36 (61%)
Query: 107 HMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVD 142
++ ++V+F A++ LNGR++AGR ++ +
Sbjct: 173 EIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAE 208
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp-
Interacting Repressor, Siahbp1
Length = 119
Score = 31.2 bits (69), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 22/36 (61%)
Query: 107 HMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVD 142
++ ++V+F A++ LNGR++AGR ++ +
Sbjct: 64 EIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAE 99
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 31.2 bits (69), Expect = 0.76, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 90 SKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S++G+I L+I M G +V F+E A+NALR + G + +P+ + +S
Sbjct: 32 SQFGQI--LDIVALKTLKMRGQAFVIFKEIGSASNALRTMQGFPFYDKPMQIAYS 84
>pdb|3UE2|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.23 A Resolution
pdb|3US5|A Chain A, Crystal Structure Of A Rna-Binding Domain Of A Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.38 A Resolution
Length = 118
Score = 31.2 bits (69), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 22/36 (61%)
Query: 107 HMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVD 142
++ ++V+F A++ LNGR++AGR ++ +
Sbjct: 69 EIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAE 104
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 30.8 bits (68), Expect = 0.92, Method: Composition-based stats.
Identities = 14/39 (35%), Positives = 24/39 (61%)
Query: 110 GNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFSPVTD 148
G +++FR+ E +A+A+RNLNG R + +S +D
Sbjct: 45 GYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSD 83
>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 = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 90 SKYGEIESLNIC-DNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S G I S+ +C D + +G YV F++ A AL +N G+P+ + +S
Sbjct: 37 SPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS 92
>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 = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 108 MVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
M G +V F+E + NALR L G + G+P+ + ++
Sbjct: 48 MRGQAFVIFKELGSSTNALRQLQGFPFYGKPMRIQYA 84
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 14/39 (35%), Positives = 24/39 (61%)
Query: 110 GNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFSPVTD 148
G +++FR+ E +A+A+RNLNG R + +S +D
Sbjct: 46 GYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSD 84
>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 = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 90 SKYGEIESLNIC-DNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S G I S+ +C D + +G YV F++ A AL +N G+P+ + +S
Sbjct: 32 SPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS 87
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 33/74 (44%)
Query: 91 KYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFSPVTDFR 150
K+G I + + + G ++ F A NA +++NG+ G+ I V+ + F+
Sbjct: 30 KHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQ 89
Query: 151 EATCRQYEENVCNR 164
R+ + NR
Sbjct: 90 SGGRRRPPASSRNR 103
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 90 SKYGEIESLNIC-DNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
SKYG I ++I D + G +V F + A A NG GR I VDFS
Sbjct: 34 SKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 89
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 90 SKYGEIESLNIC-DNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
SKYG I ++I D + G +V F + A A NG GR I VDFS
Sbjct: 68 SKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 123
>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 = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 90 SKYGEIESLNIC-DNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S GE+ES + D +A H +G +V + + A A+ LNG + I V ++
Sbjct: 24 SSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA 79
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 90 SKYGEIESLNIC-DNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
SKYG I ++I D + G +V F + A A NG GR I VDFS
Sbjct: 37 SKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 92
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 90 SKYGEIESLNIC-DNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S GE+ES + D +A H +G +V + + A A+ LNG + I V ++
Sbjct: 24 SSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA 79
>pdb|1OPI|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
pdb|2M0G|B Chain B, Structure, Phosphorylation And U2af65 Binding Of The
Nterminal Domain Of Splicing Factor 1 During 3 Splice
Site Recognition
Length = 104
Score = 29.6 bits (65), Expect = 2.5, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 90 SKYGEIESLNI---CDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDF 143
SKYG ++S+ I D + G ++V+F A++ L GR +A R ++ +
Sbjct: 36 SKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKY 92
>pdb|1O0P|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
Length = 104
Score = 29.6 bits (65), Expect = 2.5, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 90 SKYGEIESLNI---CDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDF 143
SKYG ++S+ I D + G ++V+F A++ L GR +A R ++ +
Sbjct: 36 SKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKY 92
>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 = 29.3 bits (64), Expect = 2.9, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 18/22 (81%)
Query: 110 GNVYVQFREEEHAANALRNLNG 131
G +++FR+ E +A+A+RNLNG
Sbjct: 47 GYAFIEFRDLESSASAVRNLNG 68
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 92 YGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
YG + S+ + N G +V+F + AA+A+R+L+GR G + V+ S
Sbjct: 97 YGPLRSVWVARNPP----GFAFVEFEDPRDAADAVRDLDGRTLCGCRVRVELS 145
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 90 SKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
SKYG + ++ G +VQ+ E HA A+ NGR AG+ + ++ +
Sbjct: 50 SKYGRVAGCSVHK-------GYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA 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 = 28.9 bits (63), Expect = 3.7, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 90 SKYGEIESLN-ICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S GE+ES I D +A H +G +V + + A A+ LNG + I V ++
Sbjct: 26 SSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA 81
>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 = 28.9 bits (63), Expect = 3.7, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 90 SKYGEIESLN-ICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S GE+ES I D +A H +G +V + + A A+ LNG + I V ++
Sbjct: 41 SSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA 96
>pdb|3S6E|A Chain A, Crystal Structure Of A Rna Binding Motif Protein 39
(Rbm39) From Mus Musculus At 0.95 A Resolution
pdb|3S6E|B Chain B, Crystal Structure Of A Rna Binding Motif Protein 39
(Rbm39) From Mus Musculus At 0.95 A Resolution
Length = 114
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 110 GNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFSPVTDF 149
GNVYV+ A A+ L+GR++AG+ I + P+ +
Sbjct: 56 GNVYVKCPSIAAAIAAVNALHGRWFAGKXITAAYVPLPTY 95
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 28.9 bits (63), Expect = 3.8, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 113 YVQFREEEHAANALRNLNGRFYAGRPIIVDFSPVTD 148
+V F E A A++ LNG+ G PI V + D
Sbjct: 55 FVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD 90
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 28.9 bits (63), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 91 KYGEIESLNI-CDNLADHMVGNVYVQFREEEHAANALRNLNG 131
+YG IES+ I CD G +V+F+ A A+ LNG
Sbjct: 65 RYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG 106
>pdb|2LQ5|A Chain A, Nmr Structure Of The Rna Binding Motif 39 (Rbm39) From Mus
Musculus
Length = 113
Score = 28.9 bits (63), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 110 GNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFSPVTDF 149
GNVYV+ A A+ L+GR++AG+ I + P+ +
Sbjct: 55 GNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTY 94
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 28.5 bits (62), Expect = 4.8, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 90 SKYGEIESLNI-CDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFSPVTD 148
S YG + L+ D+L G +V F EHA A ++G+ + GR ++ P T
Sbjct: 30 SAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGR--MLHVLPSTI 87
Query: 149 FREAT 153
+EA+
Sbjct: 88 KKEAS 92
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 28.5 bits (62), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 92 YGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
YG + S+ + N G +V+F + AA+A+R L+GR G + V+ S
Sbjct: 97 YGPLRSVWVARNPP----GFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS 145
>pdb|4FXW|A Chain A, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
pdb|4FXW|C Chain C, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
Length = 106
Score = 28.5 bits (62), Expect = 5.8, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 90 SKYGEIESLNI---CDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDF 143
SKYG ++S+ I D + G ++V+F A + L GR +A R ++ +
Sbjct: 38 SKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVVVTKY 94
>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 = 28.1 bits (61), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 92 YGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
YG+++ + I N + N VQ + A A+ +LNG G+PI + S
Sbjct: 59 YGDVQRVKILFNKKE----NALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS 107
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 28.1 bits (61), Expect = 6.7, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 90 SKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S++G+I + + +L G +V F+E A NALR+ G + +P + ++
Sbjct: 34 SRFGQILDILVSRSLKXR--GQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQYA 86
>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 = 28.1 bits (61), Expect = 6.7, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 90 SKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S++G+I + + +L G +V F+E A NALR+ G + +P + ++
Sbjct: 35 SRFGQILDILVSRSLKXR--GQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQYA 87
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 28.1 bits (61), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 92 YGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
YG+++ + I N + N VQ + A A+ +LNG G+PI + S
Sbjct: 28 YGDVQRVKILFNKKE----NALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS 76
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 28.1 bits (61), Expect = 7.1, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 90 SKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDFS 144
S++G+I + + +L G +V F+E A NALR+ G + +P + ++
Sbjct: 32 SRFGQILDILVSRSLKXR--GQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQYA 84
>pdb|3V4M|A Chain A, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
pdb|3V4M|B Chain B, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
Length = 105
Score = 28.1 bits (61), Expect = 7.4, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 90 SKYGEIESLNI---CDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIVDF 143
SKYG ++S+ I D + G ++V+F A + L GR +A R ++ +
Sbjct: 37 SKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVVVTKY 93
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 27.7 bits (60), Expect = 9.1, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 92 YGEIESLNIC-DNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPIIV 141
+G+I+++ + D+ G ++ F + E A AL LNG AGRP+ V
Sbjct: 29 FGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRV 79
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 0.137 0.429
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,846,283
Number of Sequences: 62578
Number of extensions: 212948
Number of successful extensions: 460
Number of sequences better than 100.0: 62
Number of HSP's better than 100.0 without gapping: 38
Number of HSP's successfully gapped in prelim test: 24
Number of HSP's that attempted gapping in prelim test: 419
Number of HSP's gapped (non-prelim): 64
length of query: 320
length of database: 14,973,337
effective HSP length: 99
effective length of query: 221
effective length of database: 8,778,115
effective search space: 1939963415
effective search space used: 1939963415
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)