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= 020632
(323 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 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
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 224 GPKNVTPCATLFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYG-PPVAFVDFQ 277
GP C ++V NL P +++ VF K + +++ G PP AFV+F+
Sbjct: 16 GPAGNNDC-RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFE 69
>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 = 36.2 bits (82), Expect = 0.028, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 71 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQ--NSQPFAFAVFSDQQSALGAMYAL 128
LFV L +V + N F++FP Y S H+ Q +S+ + F F+ Q A AM ++
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 33.1 bits (74), Expect = 0.21, 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|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 32.3 bits (72), Expect = 0.39, 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|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 32.3 bits (72), Expect = 0.40, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 41/72 (56%), Gaps = 3/72 (4%)
Query: 65 YDEVRTLFVAGLPEDVKPREIYNLFREFPG-YESSHLRSS-TQNSQPFAFAVFSDQQSAL 122
+D ++ LF+ +P ++ +++ LF EF YE + L+ T + AF + +++SAL
Sbjct: 11 HDAIK-LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESAL 69
Query: 123 GAMYALNKGSTL 134
A AL++ TL
Sbjct: 70 KAQSALHEQKTL 81
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 32.0 bits (71), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 8/44 (18%)
Query: 230 PCATLFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPPVAF 273
P L++ NL P TE++L +F+ + Q GPP+ F
Sbjct: 24 PNKVLYLKNLSPRVTERDLVSLFA--------RFQEKKGPPIQF 59
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 32.0 bits (71), Expect = 0.48, 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 = 0.48, 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|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 = 31.6 bits (70), Expect = 0.55, 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 = 31.6 bits (70), Expect = 0.62, 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|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 = 31.2 bits (69), Expect = 0.73, 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
Score = 28.1 bits (61), Expect = 6.4, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 230 PCATLFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPPVAFVDF 276
P LF+ NL E L+ +F++ PGF ++++ +AFV+F
Sbjct: 7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRH-DIAFVEF 52
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 31.2 bits (69), Expect = 0.82, 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: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 127 ALNK----GSTLYIDLAK 140
+N+ G T+ ++LAK
Sbjct: 73 NMNESELFGRTIRVNLAK 90
>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 = 30.8 bits (68), Expect = 0.94, 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|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 30.8 bits (68), Expect = 1.1, 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|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 30.8 bits (68), Expect = 1.1, 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|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 30.8 bits (68), Expect = 1.2, 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|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 30.4 bits (67), Expect = 1.3, 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|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 = 30.4 bits (67), Expect = 1.3, 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 = 30.4 bits (67), Expect = 1.3, 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|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 = 30.4 bits (67), Expect = 1.3, 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|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 30.4 bits (67), Expect = 1.4, 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|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 = 30.0 bits (66), Expect = 1.6, 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|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 30.0 bits (66), Expect = 1.6, 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|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|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 30.0 bits (66), Expect = 1.7, 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|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|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 29.6 bits (65), Expect = 2.1, Method: Composition-based stats.
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|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 9/78 (11%)
Query: 69 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS--TQNSQPFAFAVFSDQQSALGAMY 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|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 29.6 bits (65), Expect = 2.4, 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|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 29.6 bits (65), Expect = 2.4, 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|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 3/59 (5%)
Query: 71 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN 129
LF+ LPE+ + LF +FPG++ L + AF F ++ A A AL
Sbjct: 210 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD---IAFVEFDNEVQAGAARDALQ 265
>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 = 29.3 bits (64), Expect = 3.2, 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|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 29.3 bits (64), Expect = 3.5, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 219 SSAPSG-PKNVTPCATLFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPPVAFVDFQ 277
SS SG P+ + LFV NL T TE+ L + FS+ ++K Y AFV F+
Sbjct: 2 SSGSSGDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDY----AFVHFE 57
>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 = 28.9 bits (63), Expect = 3.6, 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|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 234 LFVANLGPTCTEQELTQVFSKCPGFLKLKIQSTYGPPVAFVDFQ 277
L V N+ PTCT QEL F + ++ I Y AFV +
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY----AFVHME 52
>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 = 28.5 bits (62), Expect = 4.6, 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|2YV5|A Chain A, Crystal Structure Of Yjeq From Aquifex Aeolicus
Length = 302
Score = 27.7 bits (60), Expect = 8.6, 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|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 27.7 bits (60), Expect = 8.7, Method: Composition-based stats.
Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 70 TLFVAGLPEDVKPREIYNLFREFPGYESSHLR--SSTQNSQPFAFAVFSDQQSALGAMYA 127
T++V+ LP + ++Y +F ++ + T+ S+ AF +F D+ SA A
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 128 LN 129
+N
Sbjct: 78 IN 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
0.318 0.133 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,299,430
Number of Sequences: 62578
Number of extensions: 343144
Number of successful extensions: 893
Number of sequences better than 100.0: 44
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 35
Number of HSP's that attempted gapping in prelim test: 874
Number of HSP's gapped (non-prelim): 55
length of query: 323
length of database: 14,973,337
effective HSP length: 99
effective length of query: 224
effective length of database: 8,778,115
effective search space: 1966297760
effective search space used: 1966297760
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)