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= 020954
(319 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 44/81 (54%), Gaps = 4/81 (4%)
Query: 230 PCATLFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPPVAFVDFQDTVSSTAALNNL 289
P LF+ NL E L+ +F++ PGF ++++ +AFV+F + V + AA + L
Sbjct: 206 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRH-DIAFVEFDNEVQAGAARDAL 264
Query: 290 QGTILYSSPTSDGIRLEFAKS 310
QG + ++ +++ FAK
Sbjct: 265 QG---FKITQNNAMKISFAKK 282
Score = 34.7 bits (78), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 45/86 (52%), Gaps = 9/86 (10%)
Query: 230 PCATLFVANLGPTCTEQELTQ----VFSKCPGFLKLKI-QSTYGPPVAFVDFQDTVSSTA 284
P T+++ NL + EL + +FS+ L + + +S AFV F++ S+T
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 285 ALNNLQGTILYSSPTSDGIRLEFAKS 310
AL ++QG Y P +R+++AK+
Sbjct: 68 ALRSMQGFPFYDKP----MRIQYAKT 89
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 70 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN 129
LF+ LPE+ + LF +FPG++ L + AF F ++ A A AL
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD---IAFVEFDNEVQAGAARDALQ 265
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 2/67 (2%)
Query: 64 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQ--NSQPFAFAVFSDQQSA 121
S D+ LFV L +V + N F++FP Y S H+ Q +S+ + F F+ Q A
Sbjct: 83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDA 142
Query: 122 LGAMYAL 128
AM ++
Sbjct: 143 QNAMDSM 149
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 43/93 (46%), Gaps = 10/93 (10%)
Query: 224 GPKNVTPCATLFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYG-PPVAFVDFQDTVSS 282
GP C ++V NL P +++ VF K + +++ G PP AFV+F+D +
Sbjct: 16 GPAGNNDC-RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDA 74
Query: 283 TAALNNLQGTILYSSPTSDG--IRLEFAKSRMG 313
A+ G DG +R+EF +S G
Sbjct: 75 EDAVYGRDGY------DYDGYRLRVEFPRSGRG 101
Score = 36.2 bits (82), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 5/75 (6%)
Query: 71 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN- 129
++V LP D++ ++I ++F ++ L++ + PFAF F D + A A+Y +
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR-RGGPPFAFVEFEDPRDAEDAVYGRDG 83
Query: 130 ---KGSTLYIDLAKS 141
G L ++ +S
Sbjct: 84 YDYDGYRLRVEFPRS 98
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 27/90 (30%), Positives = 49/90 (54%), Gaps = 5/90 (5%)
Query: 221 APSGPKNVTP-CATLFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPPVAFVDFQDT 279
AP+ P + P LF+ NL E L+ +F++ PGF ++++ +AFV+F +
Sbjct: 2 APAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRH-DIAFVEFDNE 60
Query: 280 VSSTAALNNLQGTILYSSPTSDGIRLEFAK 309
V + AA + LQG + ++ +++ FAK
Sbjct: 61 VQAGAARDALQG---FKITQNNAMKISFAK 87
Score = 28.9 bits (63), Expect = 4.2, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 71 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 128
LF+ LPE+ + LF +FPG++ L + AF F ++ A A AL
Sbjct: 16 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD---IAFVEFDNEVQAGAARDAL 70
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 70 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQ--NSQPFAFAVFSDQQSALGAMYA 127
LFV L +V + N F++FP Y S H+ Q +S+ + F F+ Q A AM +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 128 L 128
+
Sbjct: 63 M 63
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 45/86 (52%), Gaps = 9/86 (10%)
Query: 230 PCATLFVANLGPTCTEQELTQ----VFSKCPGFLKLKI-QSTYGPPVAFVDFQDTVSSTA 284
P T+++ NL + EL + +FS+ L + + +S AFV F++ S+T
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 285 ALNNLQGTILYSSPTSDGIRLEFAKS 310
AL ++QG Y P +R+++AK+
Sbjct: 67 ALRSMQGFPFYDKP----MRIQYAKT 88
>pdb|2B0G|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
pdb|2AYM|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
Length = 83
Score = 37.0 bits (84), Expect = 0.015, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 4/80 (5%)
Query: 230 PCATLFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPPVAFVDFQDTVSSTAALNNL 289
P LF+ NL E L+ +F++ PGF ++++ +AFV+F + S AA L
Sbjct: 7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRH-DIAFVEFTTELQSNAAKEAL 65
Query: 290 QGTILYSSPTSDGIRLEFAK 309
QG + + +++ FAK
Sbjct: 66 QG---FKITPTHAMKITFAK 82
Score = 30.4 bits (67), Expect = 1.3, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 69 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 128
+ LF+ LPE+ + LF +FPG++ L N AF F+ + + A AL
Sbjct: 9 QILFLTNLPEETNEMMLSMLFNQFPGFKEVRL---VPNRHDIAFVEFTTELQSNAAKEAL 65
>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 = 35.8 bits (81), Expect = 0.036, Method: Composition-based stats.
Identities = 26/91 (28%), Positives = 43/91 (47%), Gaps = 13/91 (14%)
Query: 227 NVTPCATLFVANLGPTCTEQELTQV-------FSKCPGFLKLKIQSTYGPPVAFVDFQDT 279
++ P T+++ N+ ++EL + F + LK G AFV F++
Sbjct: 2 DIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQ--AFVIFKEL 59
Query: 280 VSSTAALNNLQGTILYSSPTSDGIRLEFAKS 310
SST AL LQG Y P +R+++AK+
Sbjct: 60 GSSTNALRQLQGFPFYGKP----MRIQYAKT 86
>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 = 35.0 bits (79), Expect = 0.058, Method: Composition-based stats.
Identities = 27/95 (28%), Positives = 48/95 (50%), Gaps = 9/95 (9%)
Query: 230 PCATLFVANLGPTCTEQELTQ----VFSKCPGFLKLKI-QSTYGPPVAFVDFQDTVSSTA 284
P T+++ NL + EL + +FS+ L + + +S AFV F++ S+T
Sbjct: 4 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 63
Query: 285 ALNNLQGTILYSSPTSDGIRLEFAKSRMGMPRKAK 319
AL ++QG Y P +R+++AK+ + K K
Sbjct: 64 ALRSMQGFPFYDKP----MRIQYAKTDSDIIAKMK 94
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 34.7 bits (78), Expect = 0.070, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 219 SSAPSG-PKNVTPCATLFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPPVAFVDFQ 277
SS SG P+ + LFV NL T TE+ L + FS+ ++K Y AFV F+
Sbjct: 2 SSGSSGDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDY----AFVHFE 57
Query: 278 DTVSSTAALNNLQG 291
D ++ A++ + G
Sbjct: 58 DRGAAVKAMDEMNG 71
>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 = 34.7 bits (78), Expect = 0.071, Method: Composition-based stats.
Identities = 27/95 (28%), Positives = 48/95 (50%), Gaps = 9/95 (9%)
Query: 230 PCATLFVANLGPTCTEQELTQ----VFSKCPGFLKLKI-QSTYGPPVAFVDFQDTVSSTA 284
P T+++ NL + EL + +FS+ L + + +S AFV F++ S+T
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 285 ALNNLQGTILYSSPTSDGIRLEFAKSRMGMPRKAK 319
AL ++QG Y P +R+++AK+ + K K
Sbjct: 68 ALRSMQGFPFYDKP----MRIQYAKTDSDIIAKMK 98
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 34.7 bits (78), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 41/94 (43%), Gaps = 24/94 (25%)
Query: 230 PCATLFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPPV------------AFVDFQ 277
P L++ NL P TE++L +F+ + Q GPP+ AF+ F
Sbjct: 24 PNKVLYLKNLSPRVTERDLVSLFA--------RFQEKKGPPIQFRMMTGRMRGQAFITFP 75
Query: 278 DTVSSTAALNNLQGTILYSSPTSDGIRLEFAKSR 311
+ + AL+ + G LY + +EF K++
Sbjct: 76 NKEIAWQALHLVNGYKLYGKI----LVIEFGKNK 105
>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 = 34.7 bits (78), Expect = 0.076, Method: Composition-based stats.
Identities = 25/86 (29%), Positives = 45/86 (52%), Gaps = 9/86 (10%)
Query: 230 PCATLFVANLGPTCTEQELTQ----VFSKCPGFLKLKI-QSTYGPPVAFVDFQDTVSSTA 284
P T+++ NL + EL + +FS+ L + + +S AFV F++ S+T
Sbjct: 2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61
Query: 285 ALNNLQGTILYSSPTSDGIRLEFAKS 310
AL ++QG Y P +R+++AK+
Sbjct: 62 ALRSMQGFPFYDKP----MRIQYAKT 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 = 34.7 bits (78), Expect = 0.077, Method: Composition-based stats.
Identities = 27/95 (28%), Positives = 48/95 (50%), Gaps = 9/95 (9%)
Query: 230 PCATLFVANLGPTCTEQELTQ----VFSKCPGFLKLKI-QSTYGPPVAFVDFQDTVSSTA 284
P T+++ NL + EL + +FS+ L + + +S AFV F++ S+T
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 285 ALNNLQGTILYSSPTSDGIRLEFAKSRMGMPRKAK 319
AL ++QG Y P +R+++AK+ + K K
Sbjct: 67 ALRSMQGFPFYDKP----MRIQYAKTDSDIIAKMK 97
>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 = 34.7 bits (78), Expect = 0.080, Method: Composition-based stats.
Identities = 27/95 (28%), Positives = 48/95 (50%), Gaps = 9/95 (9%)
Query: 230 PCATLFVANLGPTCTEQELTQ----VFSKCPGFLKLKI-QSTYGPPVAFVDFQDTVSSTA 284
P T+++ NL + EL + +FS+ L + + +S AFV F++ S+T
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 285 ALNNLQGTILYSSPTSDGIRLEFAKSRMGMPRKAK 319
AL ++QG Y P +R+++AK+ + K K
Sbjct: 67 ALRSMQGFPFYDKP----MRIQYAKTDSDIIAKMK 97
>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 = 34.7 bits (78), Expect = 0.080, Method: Composition-based stats.
Identities = 27/95 (28%), Positives = 48/95 (50%), Gaps = 9/95 (9%)
Query: 230 PCATLFVANLGPTCTEQELTQ----VFSKCPGFLKLKI-QSTYGPPVAFVDFQDTVSSTA 284
P T+++ NL + EL + +FS+ L + + +S AFV F++ S+T
Sbjct: 5 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 64
Query: 285 ALNNLQGTILYSSPTSDGIRLEFAKSRMGMPRKAK 319
AL ++QG Y P +R+++AK+ + K K
Sbjct: 65 ALRSMQGFPFYDKP----MRIQYAKTDSDIIAKMK 95
>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 = 34.7 bits (78), Expect = 0.081, Method: Composition-based stats.
Identities = 27/95 (28%), Positives = 48/95 (50%), Gaps = 9/95 (9%)
Query: 230 PCATLFVANLGPTCTEQELTQ----VFSKCPGFLKLKI-QSTYGPPVAFVDFQDTVSSTA 284
P T+++ NL + EL + +FS+ L + + +S AFV F++ S+T
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 285 ALNNLQGTILYSSPTSDGIRLEFAKSRMGMPRKAK 319
AL ++QG Y P +R+++AK+ + K K
Sbjct: 68 ALRSMQGFPFYDKP----MRIQYAKTDSDIIAKMK 98
>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 = 34.3 bits (77), Expect = 0.084, Method: Composition-based stats.
Identities = 25/86 (29%), Positives = 45/86 (52%), Gaps = 9/86 (10%)
Query: 230 PCATLFVANLGPTCTEQELTQ----VFSKCPGFLKLKI-QSTYGPPVAFVDFQDTVSSTA 284
P T+++ NL + EL + +FS+ L + + +S AFV F++ S+T
Sbjct: 3 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 62
Query: 285 ALNNLQGTILYSSPTSDGIRLEFAKS 310
AL ++QG Y P +R+++AK+
Sbjct: 63 ALRSMQGFPFYDKP----MRIQYAKT 84
>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 = 34.3 bits (77), Expect = 0.094, Method: Composition-based stats.
Identities = 25/86 (29%), Positives = 45/86 (52%), Gaps = 9/86 (10%)
Query: 230 PCATLFVANLGPTCTEQELTQ----VFSKCPGFLKLKI-QSTYGPPVAFVDFQDTVSSTA 284
P T+++ NL + EL + +FS+ L + + +S AFV F++ S+T
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 285 ALNNLQGTILYSSPTSDGIRLEFAKS 310
AL ++QG Y P +R+++AK+
Sbjct: 67 ALRSMQGFPFYDKP----MRIQYAKT 88
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 34.3 bits (77), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 6/62 (9%)
Query: 234 LFVANLGPTCTEQELTQVFS--KCPGFLKLKIQSTYGPPVAFVDFQDTVSSTAALNNLQG 291
L++ NL P T +L Q+F K P ++ ++S Y AFVD+ D + A+ L G
Sbjct: 11 LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGY----AFVDYPDQNWAIRAIETLSG 66
Query: 292 TI 293
+
Sbjct: 67 KV 68
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 26/86 (30%), Positives = 44/86 (51%), Gaps = 8/86 (9%)
Query: 234 LFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPPVAFVDFQDTVSSTAALNNLQGTI 293
++V NLG + EL + FS G L+ + P AFV+F+D + A+ L G +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYY-GPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 294 LYSSPTSDGIRLEFAKSRMGMPRKAK 319
+ S +R+E + GMPR+++
Sbjct: 62 ICGSR----VRVELS---TGMPRRSR 80
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 33.5 bits (75), Expect = 0.15, Method: Composition-based stats.
Identities = 25/86 (29%), Positives = 45/86 (52%), Gaps = 9/86 (10%)
Query: 230 PCATLFVANLGPTCTEQELTQ----VFSKCPGFLKLKI-QSTYGPPVAFVDFQDTVSSTA 284
P T+++ NL + EL + +FS+ L + + +S AFV F++ S+T
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 285 ALNNLQGTILYSSPTSDGIRLEFAKS 310
AL ++QG Y P +R+++AK+
Sbjct: 68 ALRSMQGFPFYDKP----MRIQYAKT 89
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 6/78 (7%)
Query: 69 RTLFVAGLPEDVKPREIYNLFREFPGYESSH--LRSSTQNSQPFAFAVFSDQQSALGAMY 126
R L+V GL E+V + ++ F F L T+ + FAF F + A A+
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 127 ALNK----GSTLYIDLAK 140
+N+ G T+ ++LAK
Sbjct: 73 NMNESELFGRTIRVNLAK 90
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 9/76 (11%)
Query: 234 LFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPPVAFVDF---QDTVSSTAALNN-- 288
L V N+ PTCT QEL F + ++ I Y AFV +D V + L+N
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY----AFVHMERAEDAVEAIRGLDNTE 68
Query: 289 LQGTILYSSPTSDGIR 304
QG ++ ++ +R
Sbjct: 69 FQGKRMHVQLSTSRLR 84
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 37/85 (43%), Gaps = 6/85 (7%)
Query: 224 GPKNVTPCATLFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPPVAFVDFQDTVSST 283
G K T LFV NL TE++ ++F + ++ I G F+ + +
Sbjct: 15 GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRG--FGFIRLESRTLAE 72
Query: 284 AALNNLQGTILYSSPTSDGIRLEFA 308
A L GTIL S P +R+ FA
Sbjct: 73 IAKAELDGTILKSRP----LRIRFA 93
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 32.7 bits (73), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 213 TAKFNNSSAPSGPKNVTPCATLFVANLGPTCTEQELTQVFSK 254
T N P G K T + LFV NL P TE+E+ ++F K
Sbjct: 5 TIDLKNFRKP-GEKTFTQRSRLFVGNLPPDITEEEMRKLFEK 45
>pdb|1K42|A Chain A, The Solution Structure Of The Cbm4-2 Carbohydrate Binding
Module From A Thermostable Rhodothermus Marinus
Xylanase.
pdb|1K45|A Chain A, The Solution Structure Of The Cbm4-2 Carbohydrate Binding
Module From A Thermostable Rhodothermus Marinus Xylanase
Length = 168
Score = 32.3 bits (72), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 90 REFPGYESSHLRSSTQNSQPFAFA-VFSDQQSALGA----MYALNKGSTLYID 137
+ F Y H + T QPF F SDQ++ + A YA N G+T+YID
Sbjct: 108 QSFQEYGRLHEQQITTEWQPFTFEFTVSDQETVIRAPIHFGYAANVGNTIYID 160
>pdb|2Y64|A Chain A, Xylopentaose Binding Mutated (X-2 L110f) Cbm4-2
Carbohydrate Binding Module From A Thermostable
Rhodothermus Marinus Xylanase
pdb|2Y6G|A Chain A, Cellopentaose Binding Mutated (X-2 L110f) Cbm4-2
Carbohydrate Binding Module From A Thermostable
Rhodothermus Marinus Xylanase
pdb|2Y6H|A Chain A, X-2 L110f Cbm4-2 Carbohydrate Binding Module From A
Thermostable Rhodothermus Marinus Xylanase
Length = 167
Score = 32.3 bits (72), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 90 REFPGYESSHLRSSTQNSQPFAFA-VFSDQQSALGA----MYALNKGSTLYID 137
+ F Y H + T QPF F SDQ++ + A YA N G+T+YID
Sbjct: 108 QSFDEYGRLHHQQITTEWQPFTFEFTVSDQETVIRAPIHFGYAANVGNTIYID 160
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 32.3 bits (72), Expect = 0.39, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 234 LFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPPVAFVDFQDTVSSTAALNNLQ 290
LF+ NL TEQE+ +F + L+ I YG FV +D ++ A+ NL
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYG----FVHIEDKTAAEDAIRNLH 63
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 32.0 bits (71), Expect = 0.41, Method: Composition-based stats.
Identities = 25/87 (28%), Positives = 38/87 (43%), Gaps = 8/87 (9%)
Query: 223 SGPKNVTPCATLFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPPVAFVDFQDTVSS 282
SG + LFV NL T TE+ L + FS+ ++K Y AF+ F + +
Sbjct: 3 SGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDY----AFIHFDERDGA 58
Query: 283 TAALNNLQGTILYSSPTSDGIRLEFAK 309
A+ + G L + I + FAK
Sbjct: 59 VKAMEEMNGKDL----EGENIEIVFAK 81
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 32.0 bits (71), Expect = 0.49, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 6/78 (7%)
Query: 69 RTLFVAGLPEDVKPREIYNLFREFPGYESSH--LRSSTQNSQPFAFAVFSDQQSALGAMY 126
R L+V GL E+V + ++ F F L T+ + FAF F + A A+
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 127 ALNK----GSTLYIDLAK 140
+N+ G T+ ++LAK
Sbjct: 66 NMNESELFGRTIRVNLAK 83
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 32.0 bits (71), Expect = 0.49, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 6/78 (7%)
Query: 69 RTLFVAGLPEDVKPREIYNLFREFPGYESSH--LRSSTQNSQPFAFAVFSDQQSALGAMY 126
R L+V GL E+V + ++ F F L T+ + FAF F + A A+
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 127 ALNK----GSTLYIDLAK 140
+N+ G T+ ++LAK
Sbjct: 68 NMNESELFGRTIRVNLAK 85
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 31.6 bits (70), Expect = 0.66, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 71 LFVAGLPEDVKPREIYNLFREFPG-YESSHLRSS-TQNSQPFAFAVFSDQQSALGAMYAL 128
LF+ +P ++ +++ LF EF YE + L+ T + AF + +++SAL A AL
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 129 NKGSTL 134
++ TL
Sbjct: 76 HEQKTL 81
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 31.6 bits (70), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 4/63 (6%)
Query: 233 TLFVANLGPTCTEQELTQVFSKCPGFLKLKI--QSTYGPP--VAFVDFQDTVSSTAALNN 288
++FV N+ TE++L +FS+ + ++ G P F ++QD ++ +A+ N
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 289 LQG 291
L G
Sbjct: 70 LNG 72
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 31.2 bits (69), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 6/77 (7%)
Query: 69 RTLFVAGLPEDVKPREIYNLFREFPGYESSH--LRSSTQNSQPFAFAVFSDQQSALGAMY 126
R L+V GL E+V + ++ F F L T+ + FAF F + A A+
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 127 ALNK----GSTLYIDLA 139
+N+ G T+ ++LA
Sbjct: 124 NMNESELFGRTIRVNLA 140
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 31.2 bits (69), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 63 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS--TQNSQPFAFAVFSDQQS 120
G++ V+ +FV G+ ED + + + F ++ E + + + + FAF F D S
Sbjct: 92 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 151
Query: 121 A 121
Sbjct: 152 V 152
>pdb|2Y6J|A Chain A, X-2 Engineered Mutated Cbm4-2 Carbohydrate Binding Module
From A Thermostable Rhodothermus Marinus Xylanase
pdb|2Y6K|A Chain A, Xylotetraose Bound To X-2 Engineered Mutated Cbm4-2
Carbohydrate Binding Module From A Thermostable
Rhodothermus Marinus Xylanase
pdb|2Y6L|A Chain A, Xylopentaose Binding X-2 Engineered Mutated Cbm4-2
Carbohydrate Binding Module From A Thermostable
Rhodothermus Marinus Xylanase
Length = 167
Score = 31.2 bits (69), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 95 YESSHLRSSTQNSQPFAFA-VFSDQQSALGA----MYALNKGSTLYID 137
Y H + T QPF F SDQ++ + A YA N G+T+YID
Sbjct: 113 YGRLHHQQITTEWQPFTFEFTVSDQETVIRAPIHFGYAANVGNTIYID 160
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 31.2 bits (69), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 63 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS--TQNSQPFAFAVFSDQQS 120
G++ V+ +FV G+ ED + + + F ++ E + + + + FAF F D S
Sbjct: 100 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 159
Query: 121 A 121
Sbjct: 160 V 160
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 31.2 bits (69), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 71 LFVAGLPEDVKPREIYNLFREFPGYESSHLRS--STQNSQPFAFAVFSDQQSALGAMYAL 128
L V LP+D+ RE+Y LFR + + T S +AF F+ + + A+ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 129 N 129
N
Sbjct: 66 N 66
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 31.2 bits (69), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 63 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS--TQNSQPFAFAVFSDQQS 120
G++ V+ +FV G+ ED + + + F ++ E + + + + FAF F D S
Sbjct: 99 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 158
Query: 121 A 121
Sbjct: 159 V 159
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 30.8 bits (68), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 5/83 (6%)
Query: 69 RTLFVAGLPEDVKPREIYNLFREF-PGYESSHLRSSTQNSQP---FAFAVFSDQQSALGA 124
R +FV GLP D+ EI FR F P ++ +++ P +AF +F ++ S
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68
Query: 125 MYA-LNKGSTLYIDLAKSNSRSK 146
+ A L + LY+ ++ + K
Sbjct: 69 IDACLEEDGKLYLCVSSPTIKDK 91
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 30.8 bits (68), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 30/96 (31%), Positives = 40/96 (41%), Gaps = 14/96 (14%)
Query: 218 NSSAPSGPKNVTPCATLFVANLGPTCTEQELTQVFSK----CPGFLKLKIQSTYGPPVAF 273
SS SGP+ +LFV +L P + L + F K C G + Q+ F
Sbjct: 1 GSSGSSGPEY-----SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGF 55
Query: 274 VDFQDTVSSTAALNNLQGTI-LYSSPTSDGIRLEFA 308
V F D + AL QG + L S P +RL A
Sbjct: 56 VKFTDELEQKRALTECQGAVGLGSKP----VRLSVA 87
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 30.8 bits (68), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 2/81 (2%)
Query: 229 TPCATLFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPPVAFVDFQDTVSSTAALNN 288
+P + V NL T L Q+FSK LK+ + A + + D VS+ A +
Sbjct: 31 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLS 90
Query: 289 LQGTILYSSPTSDGIRLEFAK 309
L G +Y++ + +R++F+K
Sbjct: 91 LDGQNIYNACCT--LRIDFSK 109
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 30.8 bits (68), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 63 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS--TQNSQPFAFAVFSDQQS 120
G++ V+ +FV G+ ED + + + F ++ E + + + + FAF F D S
Sbjct: 97 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 156
Query: 121 A 121
Sbjct: 157 V 157
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 30.8 bits (68), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 63 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS--TQNSQPFAFAVFSDQQS 120
G++ V+ +FV G+ ED + + + F ++ E + + + + FAF F D S
Sbjct: 99 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 158
Query: 121 A 121
Sbjct: 159 V 159
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 63 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS--TQNSQPFAFAVFSDQQS 120
G++ V+ +FV G+ ED + + + F ++ E + + + + FAF F D S
Sbjct: 98 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 157
Query: 121 A 121
Sbjct: 158 V 158
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 71 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSS--TQNSQPFAFAVFSDQQSALGAMYAL 128
L V LP+D+ RE+Y LFR + + T S +AF F+ + + A+ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 129 N 129
N
Sbjct: 66 N 66
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 30.4 bits (67), Expect = 1.2, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 234 LFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPPVAFVDFQDTVSSTAALNNLQG 291
+FV N+ CT QEL +F + ++ + Y AFV + + AA+ L G
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKDY----AFVHMEKEADAKAAIAQLNG 65
>pdb|3ZZY|A Chain A, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZY|B Chain B, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|A Chain A, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|B Chain B, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
Length = 130
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 2/81 (2%)
Query: 229 TPCATLFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPPVAFVDFQDTVSSTAALNN 288
+P + V NL T L Q+FSK LK+ + A + + D VS+ A +
Sbjct: 26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLS 85
Query: 289 LQGTILYSSPTSDGIRLEFAK 309
L G +Y++ + +R++F+K
Sbjct: 86 LDGQNIYNACCT--LRIDFSK 104
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 42/84 (50%), Gaps = 3/84 (3%)
Query: 53 GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPG-YESSHLRSS-TQNSQPF 110
GS +S +D ++ LFV +P + +++ LF EF YE + L+ T +
Sbjct: 1 GSSGSSGVPMKDHDAIK-LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGC 59
Query: 111 AFAVFSDQQSALGAMYALNKGSTL 134
AF + + SAL A AL++ TL
Sbjct: 60 AFLTYCARDSALKAQSALHEQKTL 83
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 9/78 (11%)
Query: 69 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRS--STQNSQPFAFAVFSDQQSALGAMY 126
+TLFV GL ED L F G + + + T +S+ F F F+ ++ A A
Sbjct: 16 KTLFVKGLSEDTTEE---TLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72
Query: 127 ALN----KGSTLYIDLAK 140
A+ G+ + +D AK
Sbjct: 73 AMEDGEIDGNKVTLDWAK 90
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 2/65 (3%)
Query: 66 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALG 123
D+ T+ V L ED + ++ LFR F +L +T S+ FAF F ++ A
Sbjct: 13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 72
Query: 124 AMYAL 128
A+ +
Sbjct: 73 AIAGV 77
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 32/80 (40%), Gaps = 13/80 (16%)
Query: 234 LFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPP-------VAFVDFQDTVSSTAAL 286
LF+ NL + TE+ L VFSK I FV+++ + AL
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 287 NNLQGTILYSSPTSDGIRLE 306
LQG T DG +LE
Sbjct: 68 KQLQG------HTVDGHKLE 81
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 2/81 (2%)
Query: 229 TPCATLFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPPVAFVDFQDTVSSTAALNN 288
+P + V NL T L Q+FSK LK+ + A + + D VS+ A +
Sbjct: 44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLS 103
Query: 289 LQGTILYSSPTSDGIRLEFAK 309
L G +Y++ + +R++F+K
Sbjct: 104 LDGQNIYNACCT--LRIDFSK 122
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 30.0 bits (66), Expect = 1.8, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 6/77 (7%)
Query: 69 RTLFVAGLPEDVKPREIYNLFREFPGYESSH--LRSSTQNSQPFAFAVFSDQQSALGAMY 126
R L+V GL E+V + ++ F F L T+ + FAF F + A A+
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 127 ALNK----GSTLYIDLA 139
+N+ G T+ ++LA
Sbjct: 63 NMNESELFGRTIRVNLA 79
>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 = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 4/64 (6%)
Query: 232 ATLFVANLGPTCTEQELTQVFSKCPGFL--KLKIQSTYGPP--VAFVDFQDTVSSTAALN 287
A L+V+ L T T++EL Q+FS+ + ++ + G V F+ F + + A+
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
Query: 288 NLQG 291
L G
Sbjct: 149 GLNG 152
>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 = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 21/31 (67%)
Query: 230 PCATLFVANLGPTCTEQELTQVFSKCPGFLK 260
P ATL ++N+ P+ +E++L +FS G +K
Sbjct: 150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVK 180
>pdb|3DTP|E Chain E, Tarantula Heavy Meromyosin Obtained By Flexible Docking To
Tarantula Muscle Thick Filament Cryo-Em 3d-Map
pdb|3DTP|F Chain F, Tarantula Heavy Meromyosin Obtained By Flexible Docking To
Tarantula Muscle Thick Filament Cryo-Em 3d-Map
Length = 196
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 239 LGPTCTEQELTQVFSKCPGFLKLKI-QSTYGPPVAFVDFQDTV 280
LG CTEQEL + ++ PG + + + +G +A D +D +
Sbjct: 86 LGRLCTEQELDSMVAEAPGPINFTMFLTIFGDRIAGTDEEDVI 128
>pdb|3JXS|A Chain A, Crystal Structure Of Xg34, An Evolved Xyloglucan Binding
Cbm
pdb|3JXS|B Chain B, Crystal Structure Of Xg34, An Evolved Xyloglucan Binding
Cbm
pdb|3JXS|C Chain C, Crystal Structure Of Xg34, An Evolved Xyloglucan Binding
Cbm
Length = 174
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 95 YESSHLRSSTQNSQPFAFA-VFSDQQSALGA----MYALNKGSTLYID 137
Y H + T QPF F SDQ++ + A +A N G+T+YID
Sbjct: 113 YGRLHEQQITTEWQPFTFEFTVSDQETVIRAPIHFGFAANVGNTIYID 160
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 21/31 (67%)
Query: 230 PCATLFVANLGPTCTEQELTQVFSKCPGFLK 260
P ATL ++N+ P+ +E++L +FS G +K
Sbjct: 119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVK 149
>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 = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 2/61 (3%)
Query: 71 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPF--AFAVFSDQQSALGAMYAL 128
L V LP+D RE+Y LFR + + + F AF F+ + + A+ L
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 129 N 129
N
Sbjct: 77 N 77
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 29.3 bits (64), Expect = 2.9, Method: Composition-based stats.
Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 7/66 (10%)
Query: 232 ATLFVANLGPTCTEQELTQVFSKCPGFLKLKI----QSTYGPPVAFVDFQDTVSS---TA 284
+T++V+NL + T +L ++FSK +K+ I + VAF+ F D S+ T
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 285 ALNNLQ 290
A+NN Q
Sbjct: 77 AINNKQ 82
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 34/66 (51%), Gaps = 4/66 (6%)
Query: 230 PCATLFVANLGPTCTEQELTQVFSKCPGFLKLKI----QSTYGPPVAFVDFQDTVSSTAA 285
P +++ ++ TE+++ + S + LK+ Q+ AF++F+D SS +A
Sbjct: 2 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
Query: 286 LNNLQG 291
+ NL G
Sbjct: 62 VRNLNG 67
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 233 TLFVANLGPTCTEQELTQVFSKCPGFLKL-KIQSTYGPPVAFVDFQDTVSSTAALNNLQG 291
TL ++NL + TE+ L +VF K F+K+ + Q+ AF++F + ALN+
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKAT-FIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNK 75
Query: 292 TILYSSPTSDGIRLEFAKSR 311
+ IRLE R
Sbjct: 76 REI----EGRAIRLELQGPR 91
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 28.9 bits (63), Expect = 3.6, Method: Composition-based stats.
Identities = 26/98 (26%), Positives = 40/98 (40%), Gaps = 13/98 (13%)
Query: 71 LFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALGAMYAL 128
LFV GL D + + +F ++ + TQ S+ F F F + A AM A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 129 NKGSTLYIDLAKSNSRSKRSRTDDEWTGSDKKARGPSA 166
N S ++ R D SD ++ GPS+
Sbjct: 75 NGKSV----------DGRQIRVDQAGKSSDNRS-GPSS 101
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 28.5 bits (62), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 34/66 (51%), Gaps = 4/66 (6%)
Query: 230 PCATLFVANLGPTCTEQELTQVFSKCPGFLKLKI----QSTYGPPVAFVDFQDTVSSTAA 285
P +++ ++ TE+++ + S + LK+ Q+ AF++F+D SS +A
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 286 LNNLQG 291
+ NL G
Sbjct: 61 VRNLNG 66
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 28.5 bits (62), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 34/66 (51%), Gaps = 4/66 (6%)
Query: 230 PCATLFVANLGPTCTEQELTQVFSKCPGFLKLKI----QSTYGPPVAFVDFQDTVSSTAA 285
P +++ ++ TE+++ + S + LK+ Q+ AF++F+D SS +A
Sbjct: 3 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
Query: 286 LNNLQG 291
+ NL G
Sbjct: 63 VRNLNG 68
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 28.5 bits (62), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 232 ATLFVANLGPTCTEQELTQVFSKCPGFLKLKI---QST-YGPPVAFVDFQDTVSSTAALN 287
A L+V+ L T +++E+ Q+FS+ + +I Q+T V F+ F + + A+
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 288 NLQG 291
L G
Sbjct: 62 GLNG 65
>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 = 28.5 bits (62), Expect = 5.1, Method: Composition-based stats.
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 7/67 (10%)
Query: 233 TLFVANLGPTCTEQELTQVFSKCPGFLKL-----KIQSTYGPPVAFVDFQDTVSSTAALN 287
TL+V NL TE+++ ++FSK K+ K+++ G FV++ + A+
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACG--FCFVEYYSRADAENAMR 77
Query: 288 NLQGTIL 294
+ GT L
Sbjct: 78 YINGTRL 84
>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 = 28.5 bits (62), Expect = 5.2, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 226 KNVTPCATLFVANLGPTCTEQELTQVFSK 254
K T + LFV NL P TE+E+ ++F K
Sbjct: 10 KTFTQRSRLFVGNLPPDITEEEMRKLFEK 38
>pdb|2YV5|A Chain A, Crystal Structure Of Yjeq From Aquifex Aeolicus
Length = 302
Score = 28.5 bits (62), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 80 VKPREIYNLFREFPGYESSH 99
VKPRE+ N FREF Y+ +
Sbjct: 235 VKPREVRNYFREFLRYQCKY 254
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 28.5 bits (62), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 232 ATLFVANLGPTCTEQELTQVFSKCPGFLKLKI---QST-YGPPVAFVDFQDTVSSTAALN 287
A L+V+ L T +++E+ Q+FS+ + +I Q+T V F+ F + + A+
Sbjct: 91 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150
Query: 288 NLQG 291
L G
Sbjct: 151 GLNG 154
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 27.7 bits (60), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 234 LFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPPVAFVDFQDTVSSTAALNNLQGTI 293
++V NLG + EL + F G L+ + P AFV+F+D + A+ +L G
Sbjct: 76 VYVGNLGNNGNKTELERAFGY-YGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRT 134
Query: 294 L 294
L
Sbjct: 135 L 135
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 27.7 bits (60), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 233 TLFVANLGPTCTEQELTQVFSK---CPGFLKLKIQSTYGPPVAFVDF 276
TL+V NL TE + Q+FS+ C K+ + T P FV+F
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKS-CKMITEHTSNDPYCFVEF 62
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
0.315 0.131 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,802,473
Number of Sequences: 62578
Number of extensions: 323523
Number of successful extensions: 945
Number of sequences better than 100.0: 80
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 70
Number of HSP's that attempted gapping in prelim test: 910
Number of HSP's gapped (non-prelim): 103
length of query: 319
length of database: 14,973,337
effective HSP length: 99
effective length of query: 220
effective length of database: 8,778,115
effective search space: 1931185300
effective search space used: 1931185300
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)