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= 039336
(167 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 80.5 bits (197), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 48/128 (37%), Positives = 71/128 (55%), Gaps = 3/128 (2%)
Query: 36 PNKEDSDVKP--FATPEELEMGKLPPEEILSLPMFKNYAAGNPASVLYIKNLAKDVIPXX 93
P DSD P + ELE G++ EE+ +L +F++Y G P +Y+KNLAK V
Sbjct: 2 PLGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKD 61
Query: 94 XXXXXXXXXX-XXDAAKCGLTVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKP 152
+ + ++LM+EGRM+GQAF+ P+ + A +AL NGYV GKP
Sbjct: 62 LKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP 121
Query: 153 MIIQFGRN 160
M++QF R+
Sbjct: 122 MVVQFARS 129
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 80.1 bits (196), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 45/102 (44%), Positives = 60/102 (58%), Gaps = 6/102 (5%)
Query: 60 EEILSLPMFKNYAAGNPASVLYIKNLAKDVIPXXXXXXXXXXXXXXDAAKCGLTVKL-MQ 118
EEI +PMF +Y G P VLY+KNL+ V K G ++ M
Sbjct: 8 EEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQ-----EKKGPPIQFRMM 62
Query: 119 EGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 160
GRMRGQAF+TFP+ E+A +AL+LVNGY GK ++I+FG+N
Sbjct: 63 TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN 104
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/42 (45%), Positives = 25/42 (59%)
Query: 121 RMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 162
+MRGQAFV F V A AL + G+ F KPM IQ+ + +
Sbjct: 49 KMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS 90
>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 = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 29/51 (56%)
Query: 112 LTVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 162
L + + + +MRGQAFV F V A AL + G+ F KPM IQ+ + +
Sbjct: 40 LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS 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 = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 29/51 (56%)
Query: 112 LTVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 162
L + + + +MRGQAFV F V A AL + G+ F KPM IQ+ + +
Sbjct: 38 LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS 88
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 29/51 (56%)
Query: 112 LTVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 162
L + + + +MRGQAFV F V A AL + G+ F KPM IQ+ + +
Sbjct: 41 LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS 91
>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 = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 29/51 (56%)
Query: 112 LTVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 162
L + + + +MRGQAFV F V A AL + G+ F KPM IQ+ + +
Sbjct: 40 LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS 90
>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 = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 29/51 (56%)
Query: 112 LTVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 162
L + + + +MRGQAFV F V A AL + G+ F KPM IQ+ + +
Sbjct: 41 LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS 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 = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 29/51 (56%)
Query: 112 LTVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 162
L + + + +MRGQAFV F V A AL + G+ F KPM IQ+ + +
Sbjct: 37 LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS 87
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 29/51 (56%)
Query: 112 LTVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 162
L + + + +MRGQAFV F V A AL + G+ F KPM IQ+ + +
Sbjct: 41 LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS 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 = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 29/51 (56%)
Query: 112 LTVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 162
L + + + +MRGQAFV F V A AL + G+ F KPM IQ+ + +
Sbjct: 35 LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS 85
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 29/51 (56%)
Query: 112 LTVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 162
L + + + +MRGQAFV F V A AL + G+ F KPM IQ+ + +
Sbjct: 36 LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS 86
>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 = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 24/40 (60%)
Query: 121 RMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 160
+MRGQAFV F V A AL + G+ F KPM IQ+ +
Sbjct: 50 KMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 89
>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 = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 29/51 (56%)
Query: 112 LTVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 162
L + + + +MRGQAFV F V A AL + G+ F KPM IQ+ + +
Sbjct: 40 LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS 90
>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 = 39.7 bits (91), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 26/42 (61%)
Query: 121 RMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 162
+MRGQAFV F + + AL + G+ F GKPM IQ+ + +
Sbjct: 47 KMRGQAFVIFKELGSSTNALRQLQGFPFYGKPMRIQYAKTDS 88
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 27/45 (60%), Gaps = 3/45 (6%)
Query: 114 VKLMQE---GRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII 155
+ LM++ GR +G F+TF E A RAL +NG+ G+PM +
Sbjct: 35 IVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRV 79
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 27/44 (61%), Gaps = 3/44 (6%)
Query: 113 TVKLMQE---GRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPM 153
+++LM + GR +G F+TF E A +AL +NG+ G+PM
Sbjct: 55 SIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM 98
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 25/42 (59%)
Query: 121 RMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 162
+MRGQAFV F + A AL + G+ F KPM I + ++ +
Sbjct: 47 KMRGQAFVIFKEIGSASNALRTMQGFPFYDKPMQIAYSKSDS 88
>pdb|2A3J|A Chain A, Structure Of Urndesign, A Complete Computational Redesign
Of Human U1a Protein
Length = 127
Score = 35.0 bits (79), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 123 RGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNP 161
G+A++ F + E A + GY F+G P++I F P
Sbjct: 72 SGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETP 110
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 35.0 bits (79), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 26/51 (50%)
Query: 112 LTVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 162
L + + + + RGQAFV F V A AL G+ F KP IQ+ + +
Sbjct: 40 LDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQYAKTDS 90
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 35.0 bits (79), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 26/51 (50%)
Query: 112 LTVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 162
L + + + + RGQAFV F V A AL G+ F KP IQ+ + +
Sbjct: 38 LDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQYAKTDS 88
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 35.0 bits (79), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%)
Query: 110 CGLTVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 157
G + MQ G RG FV+F S + A A++ + G G+P+ I +
Sbjct: 116 SGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW 163
>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 = 35.0 bits (79), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 26/51 (50%)
Query: 112 LTVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 162
L + + + + RGQAFV F V A AL G+ F KP IQ+ + +
Sbjct: 41 LDILVSRSLKXRGQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQYAKTDS 91
>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 = 34.3 bits (77), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%)
Query: 110 CGLTVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 157
G + MQ G RG FV+F S + A A++ + G G+P+ I +
Sbjct: 30 SGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW 77
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 33.5 bits (75), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 6/76 (7%)
Query: 80 LYIKNLAKDVIPXXXXXXXXXXXXXXDAAKCGLTVKLMQEGRMRGQAFVTFPSVELAHRA 139
LY+KNL D I +AK +M+ GR +G FV F S E A +A
Sbjct: 18 LYVKNL-DDGIDDERLRKAFSPFGTITSAKV-----MMEGGRSKGFGFVCFSSPEEATKA 71
Query: 140 LNLVNGYVFKGKPMII 155
+ +NG + KP+ +
Sbjct: 72 VTEMNGRIVATKPLYV 87
>pdb|1WG1|A Chain A, Solution Structure Of Rna Binding Domain In
Bab13405(Homolog Exc-7)
Length = 88
Score = 32.3 bits (72), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 121 RMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 157
R + AFVT + E A A+ + + Y F+GK +I+Q
Sbjct: 38 RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQL 74
>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 = 31.2 bits (69), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 22/31 (70%)
Query: 111 GLTVKLMQEGRMRGQAFVTFPSVELAHRALN 141
G+T+ + EG++ G+AFV F S ELA +AL
Sbjct: 72 GITLPVDPEGKITGEAFVQFASQELAEKALG 102
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 30.8 bits (68), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 118 QEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 157
Q G+ +G AF+ F S E A ALN N +G+ + ++
Sbjct: 48 QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL 87
>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 = 30.4 bits (67), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 121 RMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFG-RNPAAAK 165
R G A+V F A RAL+ +N V KGKP+ I + R+P+ K
Sbjct: 55 RSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRK 100
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 30.4 bits (67), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 113 TVKLMQE---GRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 159
T ++M++ G G AFV F S + RA+ ++NG + K + + + R
Sbjct: 32 TCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR 81
>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 = 30.4 bits (67), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 121 RMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFG-RNPAAAK 165
R G A+V F A RAL+ +N V KGKP+ I + R+P+ K
Sbjct: 50 RSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRK 95
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 30.0 bits (66), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 113 TVKLMQE---GRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 159
T ++M++ G G AFV F S + RA+ ++NG + K + + + R
Sbjct: 32 TCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR 81
>pdb|1WG5|A Chain A, Solution Structure Of The First Rrm Domain In
Heterogeneous Nuclear Ribonucleoprotein H
Length = 104
Score = 30.0 bits (66), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 21/30 (70%)
Query: 111 GLTVKLMQEGRMRGQAFVTFPSVELAHRAL 140
G+T+ + +GR G+AFV F S E+A +AL
Sbjct: 45 GMTLPVDFQGRSTGEAFVQFASQEIAEKAL 74
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 29.6 bits (65), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 112 LTVKLM---QEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 160
+ +K+M Q GR +G AF+ F +E + A+ +NGY + + + N
Sbjct: 32 INLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN 83
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 29.6 bits (65), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 112 LTVKLM---QEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 160
+ +K+M Q GR +G AF+ F +E + A+ +NGY + + + N
Sbjct: 30 INLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN 81
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 29.6 bits (65), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 112 LTVKLM---QEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRN 160
+ +K+M Q GR +G AF+ F +E + A+ +NGY + + + N
Sbjct: 31 INLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN 82
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 29.6 bits (65), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 113 TVKLMQE---GRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 157
T K+M++ G +G AF+ F S + + A+ +NG +P+ + +
Sbjct: 35 TPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY 82
>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 = 29.3 bits (64), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 113 TVKLMQE---GRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 159
+ KL+++ G G FV + + + A RA+N +NG + K + + + R
Sbjct: 48 SAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR 97
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 29.3 bits (64), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 23/43 (53%)
Query: 121 RMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAA 163
R RG F+ S LA A ++G + K +P+ I+F + AA
Sbjct: 56 RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGAA 98
>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 = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 124 GQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 159
G AFV F S + RA+ ++NG + K + + + R
Sbjct: 57 GYAFVDFTSEXDSQRAIKVLNGITVRNKRLKVSYAR 92
>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 = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 113 TVKLMQE---GRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 159
+ KL+++ G G FV + + + A RA+N +NG + K + + + R
Sbjct: 31 SAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR 80
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 113 TVKLMQE---GRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 159
+ KL+++ G G FV + + + A RA+N +NG + K + + + R
Sbjct: 31 SAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR 80
>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 = 1.2, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 113 TVKLMQE---GRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 159
+ KL+++ G G FV + + + A RA+N +NG + K + + + R
Sbjct: 33 SAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR 82
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 24/45 (53%)
Query: 118 QEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 162
+ G+++G+A V+F A A++ +G F G P+ + F A
Sbjct: 52 ETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRA 96
>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 = 1.6, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 121 RMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 159
++R AFV F + E A A+ +NG V G P+ + +
Sbjct: 49 KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK 87
>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 = 28.5 bits (62), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 118 QEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 157
+ G+++G+A V+F A A++ +G F G P+ + F
Sbjct: 58 ETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 28.5 bits (62), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 118 QEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 157
Q R RG AFV F +V+ A A NG G+ + + F
Sbjct: 52 QSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 91
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 118 QEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 157
Q R RG AFV F +V+ A A NG G+ + + F
Sbjct: 49 QSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 88
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 24/44 (54%)
Query: 112 LTVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMII 155
+ VK + R RG FVTF +++ A A+ +NG G+ + +
Sbjct: 43 VVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV 86
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 27.7 bits (60), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 23/41 (56%)
Query: 122 MRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPA 162
+ G AFV F E A +A+ V+G F +P+ + + + PA
Sbjct: 64 LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPA 104
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 27.3 bits (59), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 106 DAAKCGLTVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAA 164
D C L V+ G+ G FV + A +A+N +NG + K + + + R P++A
Sbjct: 30 DIESCKL-VRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYAR-PSSA 86
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 26.9 bits (58), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 118 QEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQF 157
Q R RG AFV F +V+ A A NG G+ + + F
Sbjct: 83 QSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 122
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 26.6 bits (57), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 123 RGQAFVTFPSVELAHRALNLVNGYVFKGKPMII 155
+G AFVTF E A +A V+G VF+G+ + +
Sbjct: 50 KGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHV 82
>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 = 7.4, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 106 DAAKCGLTVKLMQEGRMRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGRNPAAA 164
D C L V+ G+ G FV + A +A+N +NG + K + + + R +A+
Sbjct: 30 DIESCKL-VRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPSSAS 87
>pdb|1XOM|A Chain A, Catalytic Domain Of Human Phosphodiesterase 4d In
Complex With Cilomilast
pdb|1XOM|B Chain B, Catalytic Domain Of Human Phosphodiesterase 4d In
Complex With Cilomilast
pdb|1XON|A Chain A, Catalytic Domain Of Human Phosphodiesterase 4d In
Complex With Piclamilast
pdb|1XON|B Chain B, Catalytic Domain Of Human Phosphodiesterase 4d In
Complex With Piclamilast
pdb|1XOQ|A Chain A, Catalytic Domain Of Human Phosphodiesterase 4d In
Complex With Roflumilast
pdb|1XOQ|B Chain B, Catalytic Domain Of Human Phosphodiesterase 4d In
Complex With Roflumilast
pdb|1XOR|A Chain A, Catalytic Domain Of Human Phosphodiesterase 4d In
Complex With Zardaverine
pdb|1XOR|B Chain B, Catalytic Domain Of Human Phosphodiesterase 4d In
Complex With Zardaverine
pdb|1Y2B|A Chain A, Catalytic Domain Of Human Phosphodiesterase 4d In
Complex With 3,5- Dimethyl-1h-Pyrazole-4-Carboxylic
Acid Ethyl Ester
pdb|1Y2B|B Chain B, Catalytic Domain Of Human Phosphodiesterase 4d In
Complex With 3,5- Dimethyl-1h-Pyrazole-4-Carboxylic
Acid Ethyl Ester
pdb|1Y2C|A Chain A, Catalytic Domain Of Human Phosphodiesterase 4d In
Complex With 3,5-
Dimethyl-1-Phenyl-1h-Pyrazole-4-Carboxylic Acid Ethyl
Ester
pdb|1Y2C|B Chain B, Catalytic Domain Of Human Phosphodiesterase 4d In
Complex With 3,5-
Dimethyl-1-Phenyl-1h-Pyrazole-4-Carboxylic Acid Ethyl
Ester
pdb|1Y2D|A Chain A, Catalytic Domain Of Human Phosphodiesterase 4d In
Complex With 1-(4-
Methoxy-Phenyl)-3,5-Dimethyl-1h-Pyrazole-4-Carboxylic
Acid Ethyl Ester
pdb|1Y2D|B Chain B, Catalytic Domain Of Human Phosphodiesterase 4d In
Complex With 1-(4-
Methoxy-Phenyl)-3,5-Dimethyl-1h-Pyrazole-4-Carboxylic
Acid Ethyl Ester
pdb|1Y2E|A Chain A, Catalytic Domain Of Human Phosphodiesterase 4d In
Complex With 1-(4-
Amino-Phenyl)-3,5-Dimethyl-1h-Pyrazole-4-Carboxylic
Acid Ethyl Ester
pdb|1Y2E|B Chain B, Catalytic Domain Of Human Phosphodiesterase 4d In
Complex With 1-(4-
Amino-Phenyl)-3,5-Dimethyl-1h-Pyrazole-4-Carboxylic
Acid Ethyl Ester
pdb|1Y2K|A Chain A, Catalytic Domain Of Human Phosphodiesterase 4d In
Complex With 3,5-
Dimethyl-1-(3-Nitro-Phenyl)-1h-Pyrazole-4-Carboxylic
Acid Ethyl Ester
pdb|1Y2K|B Chain B, Catalytic Domain Of Human Phosphodiesterase 4d In
Complex With 3,5-
Dimethyl-1-(3-Nitro-Phenyl)-1h-Pyrazole-4-Carboxylic
Acid Ethyl Ester
pdb|3IAK|A Chain A, Crystal Structure Of Human Phosphodiesterase 4d (Pde4d)
With Papaverine.
pdb|3K4S|A Chain A, The Structure Of The Catalytic Domain Of Human Pde4d
With 4-
(3-Butoxy-4-Methoxyphenyl)methyl-2-Imidazolidone
Length = 349
Score = 26.2 bits (56), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 15 ITPKASQTEDKDDSVAKELEEPNK 38
+ P+ S +++D +AKELE+ NK
Sbjct: 14 LVPRGSHMTEQEDVLAKELEDVNK 37
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 26.2 bits (56), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 122 MRGQAFVTFPSVELAHRALNLVNGYVFKGKPMIIQFGR 159
+ G AFV F E A +A+ V+G F +P+ + + +
Sbjct: 37 LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSK 74
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
0.314 0.133 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,608,211
Number of Sequences: 62578
Number of extensions: 163518
Number of successful extensions: 438
Number of sequences better than 100.0: 65
Number of HSP's better than 100.0 without gapping: 64
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 368
Number of HSP's gapped (non-prelim): 69
length of query: 167
length of database: 14,973,337
effective HSP length: 92
effective length of query: 75
effective length of database: 9,216,161
effective search space: 691212075
effective search space used: 691212075
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)