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= 005692
(682 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 42/69 (60%), Gaps = 3/69 (4%)
Query: 70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALA-LNNMDVG 128
+ V N+S T ++LR LF G V+EC + K +A++ K +A AA+A LN +V
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVV--KDYAFVHMEKEADAKAAIAQLNGKEVK 69
Query: 129 GRPLNVEMA 137
G+ +NVE++
Sbjct: 70 GKRINVELS 78
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 42/71 (59%), Gaps = 3/71 (4%)
Query: 70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALNNMDVG 128
L V N+SP T ++LR F G V+EC I K +A++ + E+A A+ L+N +
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIV--KDYAFVHMERAEDAVEAIRGLDNTEFQ 70
Query: 129 GRPLNVEMAKS 139
G+ ++V+++ S
Sbjct: 71 GKRMHVQLSTS 81
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 40/74 (54%), Gaps = 5/74 (6%)
Query: 70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTITD----SKHFAYIEYSKPEEATAALA-LNN 124
L V NL + E+LR+ FS GT+ + SK F ++ +S PEEAT A+ +N
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 125 MDVGGRPLNVEMAK 138
V +PL V +A+
Sbjct: 78 RIVATKPLYVALAQ 91
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 39/78 (50%), Gaps = 10/78 (12%)
Query: 70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKH---------FAYIEYSKPEEATAAL 120
L + NL+ T E L+ +FS G + CTI+ K+ F ++EY KPE+A AL
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 121 -ALNNMDVGGRPLNVEMA 137
L V G L V ++
Sbjct: 68 KQLQGHTVDGHKLEVRIS 85
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 30/86 (34%), Positives = 50/86 (58%), Gaps = 10/86 (11%)
Query: 63 ADALKKT-LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSK------HFAYIEYSKPEE 115
+++K T L V+NL +T +QL +F G++V+ I K A++ Y+K EE
Sbjct: 8 GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE 67
Query: 116 ATAAL-ALNNM--DVGGRPLNVEMAK 138
A A+ ALNN+ + G +PL+V +A+
Sbjct: 68 AQEAISALNNVIPEGGSQPLSVRLAE 93
>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 = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 30/86 (34%), Positives = 50/86 (58%), Gaps = 10/86 (11%)
Query: 63 ADALKKT-LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKH------FAYIEYSKPEE 115
+++K T L V+NL +T +QL +F G++V+ I K A++ Y+K EE
Sbjct: 95 GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE 154
Query: 116 ATAAL-ALNNM--DVGGRPLNVEMAK 138
A A+ ALNN+ + G +PL+V +A+
Sbjct: 155 AQEAISALNNVIPEGGSQPLSVRLAE 180
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 37.4 bits (85), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKH------FAYIEYSKPEE 115
+ADA +++ V N+ T E+L F CG+V TI K FAYIE+S E
Sbjct: 2 EADA--RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES 59
Query: 116 ATAALALNNMDVGGRPLNV 134
+LAL+ GR + V
Sbjct: 60 VRTSLALDESLFRGRQIKV 78
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 37.4 bits (85), Expect = 0.031, Method: Composition-based stats.
Identities = 32/96 (33%), Positives = 49/96 (51%), Gaps = 9/96 (9%)
Query: 51 KDLSGSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSK------H 104
K L S + G L V+NL +T +QL +F G++V+ I K
Sbjct: 73 KRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRG 132
Query: 105 FAYIEYSKPEEATAAL-ALNNM--DVGGRPLNVEMA 137
A++ Y+K EEA A+ ALNN+ + G +PL+V +A
Sbjct: 133 VAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 36.6 bits (83), Expect = 0.047, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDS-----KHFAYIEYSKPEEATAALA- 121
+T+ V NL + E L +LF G + + TI K F ++ + PE + A+A
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIAL 76
Query: 122 LNNMDVGGRPLNVEMAKS 139
LN + + GRP+NV S
Sbjct: 77 LNGIRLYGRPINVSGPSS 94
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 35.8 bits (81), Expect = 0.085, Method: Composition-based stats.
Identities = 28/79 (35%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEE 115
+ADA +++ V N+ T E+L F CG+V TI K FAYIE+S E
Sbjct: 3 EADA--RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES 60
Query: 116 ATAALALNNMDVGGRPLNV 134
+LAL+ GR + V
Sbjct: 61 VRTSLALDESLFRGRQIKV 79
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 34.3 bits (77), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKH------FAYIEYSKPEEATAAL 120
K+++ V N+ T + L FS CG++ TI K +AYIE+++ AA+
Sbjct: 36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95
Query: 121 ALNNMDVGGRPLNV 134
A++ GR + V
Sbjct: 96 AMDETVFRGRTIKV 109
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 34.3 bits (77), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 43/81 (53%), Gaps = 6/81 (7%)
Query: 62 KADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD-----SKHFAYIEYSKPEEA 116
+A L T+ V+NL + ++L+++FS G VV I + S+ + + + EA
Sbjct: 10 QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEA 69
Query: 117 TAALAL-NNMDVGGRPLNVEM 136
A+++ N + RP++V+M
Sbjct: 70 VQAISMFNGQLLFDRPMHVKM 90
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 33.9 bits (76), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 5/73 (6%)
Query: 68 KTLQVSNLSPLLTVEQLRQLF---SFCGTVVECTITDSKHFAYIEYSKPEEATAAL-ALN 123
KTL +SNLS T E L+++F +F V + SK +A+IE++ E+A AL + N
Sbjct: 16 KTLVLSNLSYSATEETLQEVFEKATFI-KVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 124 NMDVGGRPLNVEM 136
++ GR + +E+
Sbjct: 75 KREIEGRAIRLEL 87
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 33.9 bits (76), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 6/69 (8%)
Query: 70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALN 123
L + LS T E LR F GT+ +C + S+ F ++ Y+ EE AA+
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 76
Query: 124 NMDVGGRPL 132
V GR +
Sbjct: 77 PHKVDGRVV 85
>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 = 33.9 bits (76), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 34/63 (53%), Gaps = 3/63 (4%)
Query: 69 TLQVSNLSPLLTVEQLRQLFSFCGTVVEC--TITDSKHFAYIEYSKPEEATAALA-LNNM 125
TL +SN+ P ++ E L+ LFS G VV+ + A I+ EEA AL L+N
Sbjct: 153 TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNH 212
Query: 126 DVG 128
D+G
Sbjct: 213 DLG 215
>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 = 33.9 bits (76), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 6/69 (8%)
Query: 70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALN 123
L + LS T E LR F GT+ +C + S+ F ++ Y+ EE AA+
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 74
Query: 124 NMDVGGRPL 132
V GR +
Sbjct: 75 PHKVDGRVV 83
>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 = 33.5 bits (75), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 6/69 (8%)
Query: 70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALN 123
L + LS T E LR F GT+ +C + S+ F ++ Y+ EE AA+
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 124 NMDVGGRPL 132
V GR +
Sbjct: 76 PHKVDGRVV 84
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 33.5 bits (75), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNMDVGG 129
L + NL T +++R LF G V+EC I + F +IE K A L++ + G
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIE-DKTAAEDAIRNLHHYKLHG 69
Query: 130 RPLNVEMAK 138
+NVE +K
Sbjct: 70 VNINVEASK 78
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 33.5 bits (75), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 34/63 (53%), Gaps = 3/63 (4%)
Query: 69 TLQVSNLSPLLTVEQLRQLFSFCGTVVEC--TITDSKHFAYIEYSKPEEATAALA-LNNM 125
TL +SN+ P ++ E L+ LFS G VV+ + A I+ EEA AL L+N
Sbjct: 122 TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNH 181
Query: 126 DVG 128
D+G
Sbjct: 182 DLG 184
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 33.5 bits (75), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 7/77 (9%)
Query: 69 TLQVSNLSPLLTVEQLRQLFSFCGTVVEC------TITDSKHFAYIEYSKPEEATAALA- 121
T++V+NLS L++LF G++ T SK FA+I + + E+A A+A
Sbjct: 17 TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 76
Query: 122 LNNMDVGGRPLNVEMAK 138
++ LNVE AK
Sbjct: 77 VSGFGYDHLILNVEWAK 93
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 33.1 bits (74), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 6/69 (8%)
Query: 70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALN 123
L + LS T E LR F GT+ +C + S+ F ++ Y+ EE AA+
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 124 NMDVGGRPL 132
V GR +
Sbjct: 76 PHKVDGRVV 84
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 33.1 bits (74), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 6/69 (8%)
Query: 70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALN 123
L + LS T E LR F GT+ +C + S+ F ++ Y+ EE AA+
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 124 NMDVGGRPL 132
V GR +
Sbjct: 74 PHKVDGRVV 82
>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 = 32.7 bits (73), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 6/69 (8%)
Query: 70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAALALN 123
L + LS T E LR F GT+ +C + S+ F ++ Y+ EE AA+
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 124 NMDVGGRPL 132
V GR +
Sbjct: 69 PHKVDGRVV 77
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 32.7 bits (73), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 5/42 (11%)
Query: 84 LRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL 120
+R+LF G + ECTI +SK A+++YS EA AA+
Sbjct: 32 VRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAI 73
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 32.3 bits (72), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 38/79 (48%), Gaps = 7/79 (8%)
Query: 68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEATAAL- 120
+++ V N+ T EQL+ +FS G VV + K + + EY E A +A+
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 121 ALNNMDVGGRPLNVEMAKS 139
LN + GR L V+ A S
Sbjct: 69 NLNGREFSGRALRVDNAAS 87
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 7/83 (8%)
Query: 70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIE-YSKPEEATAALAL 122
+ V +LSP +T E ++ F+ G + + + SK + ++ Y+K + A + +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 123 NNMDVGGRPLNVEMAKSFPQKPS 145
+GGR + A P PS
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAPS 100
>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 = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 69 TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAALAL 122
+L V +L P +T L + FS G ++ + S +AY+ + +P +A AL
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 123 NNMDV-GGRPLNV 134
N DV G+P+ +
Sbjct: 77 MNFDVIKGKPVRI 89
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 31.6 bits (70), Expect = 1.7, Method: Composition-based stats.
Identities = 28/84 (33%), Positives = 40/84 (47%), Gaps = 4/84 (4%)
Query: 61 GKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAAL 120
GKA+ + L V L P ++ L + F G++ FAYI+Y + A AA
Sbjct: 12 GKANPTTR-LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAAC 70
Query: 121 A-LNNMDVGG--RPLNVEMAKSFP 141
A + +GG R L V+ AKS P
Sbjct: 71 AKMRGFPLGGPDRRLRVDFAKSGP 94
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 31.2 bits (69), Expect = 1.9, Method: Composition-based stats.
Identities = 27/104 (25%), Positives = 49/104 (47%), Gaps = 17/104 (16%)
Query: 55 GSPDKAGKADALKKTLQ----------VSNLSPLLTVEQLRQLFSFCGTVVECTI----T 100
G P G+A + L V+++ L+ + ++ +F G + CT+ T
Sbjct: 87 GRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPT 146
Query: 101 DSKH--FAYIEYSKPEEATAALALNNM-DVGGRPLNVEMAKSFP 141
KH + +IEY K + + A++ N+ D+GG+ L V A + P
Sbjct: 147 TGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAVTPP 190
>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 = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 69 TLQVSNLSPLLTVEQLRQLFSFCGTVVECTITD------SKHFAYIEYSKPEEATAALAL 122
+L V +L P +T L + FS G ++ + S +AY+ + +P +A AL
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 123 NNMDV-GGRPLNV 134
N DV G+P+ +
Sbjct: 72 MNFDVIKGKPVRI 84
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 30.8 bits (68), Expect = 2.3, Method: Composition-based stats.
Identities = 27/78 (34%), Positives = 38/78 (48%), Gaps = 7/78 (8%)
Query: 67 KKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT------DSKHFAYIEYSKPEEA-TAA 119
K T+ VSNL LT L ++FS G VV+ TI SK A+I + + A
Sbjct: 16 KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCT 75
Query: 120 LALNNMDVGGRPLNVEMA 137
A+NN + GR + +A
Sbjct: 76 RAINNKQLFGRVIKASIA 93
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 30.4 bits (67), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 5/56 (8%)
Query: 70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-----DSKHFAYIEYSKPEEATAAL 120
L V L T E +R++F GT+ ECT+ SK A++++ EA AA+
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAI 70
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 70 LQVSNLSPLLTVEQLRQLFSFCGTVVECTITDSKHFAYIEYSKPEEATAALALNNM 125
L + NLSP +T + LRQLF + + +A+++Y P++ A A+ +
Sbjct: 11 LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDY--PDQNWAIRAIETL 64
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 30.4 bits (67), Expect = 3.6, Method: Composition-based stats.
Identities = 27/87 (31%), Positives = 45/87 (51%), Gaps = 7/87 (8%)
Query: 55 GSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-DS-----KHFAYI 108
GS + A A+ + V ++ L + +RQ F+ G + ++ DS K FA++
Sbjct: 16 GSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFV 75
Query: 109 EYSKPEEATAAL-ALNNMDVGGRPLNV 134
EY PE A AL +N++ +GGR + V
Sbjct: 76 EYEVPEAAQLALEQMNSVMLGGRNIKV 102
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 30.0 bits (66), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 44/91 (48%), Gaps = 8/91 (8%)
Query: 55 GSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI----TDSKH--FAYI 108
GS +G A K+ L V L+ + + L F G + + I KH FA++
Sbjct: 1 GSSGSSGMATT-KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 59
Query: 109 EYSKPEEATAAL-ALNNMDVGGRPLNVEMAK 138
E+ E+A AA+ +N ++ GR + V +AK
Sbjct: 60 EFELAEDAAAAIDNMNESELFGRTIRVNLAK 90
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 30.0 bits (66), Expect = 5.0, Method: Composition-based stats.
Identities = 26/87 (29%), Positives = 46/87 (52%), Gaps = 7/87 (8%)
Query: 55 GSPDKAGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTIT-DS-----KHFAYI 108
G+ + +A A+ + V ++ L + +RQ F+ G + ++ DS K FA++
Sbjct: 1 GAMAQRQRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFV 60
Query: 109 EYSKPEEATAAL-ALNNMDVGGRPLNV 134
EY PE A AL +N++ +GGR + V
Sbjct: 61 EYEVPEAAQLALEQMNSVMLGGRNIKV 87
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 29.6 bits (65), Expect = 5.1, Method: Composition-based stats.
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 8/82 (9%)
Query: 68 KTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI------TDSKHFAYIEYSKPEEATAALA 121
+ + V NL T EQ+++LFS G V + K F ++E + + A
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61
Query: 122 LNNMDVGGRPLNVEMAKSFPQK 143
L+N D GR + V A P+K
Sbjct: 62 LDNTDFMGRTIRVTEAN--PKK 81
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 29.3 bits (64), Expect = 7.5, Method: Composition-based stats.
Identities = 24/71 (33%), Positives = 42/71 (59%), Gaps = 5/71 (7%)
Query: 60 AGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVE-CTITDSKHF-AYIEYSKPEEAT 117
AG++ L+ + V NL +T++ L Q+FS GTV++ T T + F A ++Y+ P A
Sbjct: 41 AGQSPVLR--IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQ 98
Query: 118 -AALALNNMDV 127
A L+L+ ++
Sbjct: 99 HAKLSLDGQNI 109
>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 = 29.3 bits (64), Expect = 7.9, Method: Composition-based stats.
Identities = 24/71 (33%), Positives = 42/71 (59%), Gaps = 5/71 (7%)
Query: 60 AGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVE-CTITDSKHF-AYIEYSKPEEAT 117
AG++ L+ + V NL +T++ L Q+FS GTV++ T T + F A ++Y+ P A
Sbjct: 23 AGQSPVLR--IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQ 80
Query: 118 -AALALNNMDV 127
A L+L+ ++
Sbjct: 81 HAKLSLDGQNI 91
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 29.3 bits (64), Expect = 8.1, Method: Composition-based stats.
Identities = 24/71 (33%), Positives = 42/71 (59%), Gaps = 5/71 (7%)
Query: 60 AGKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVE-CTITDSKHF-AYIEYSKPEEAT 117
AG++ L+ + V NL +T++ L Q+FS GTV++ T T + F A ++Y+ P A
Sbjct: 28 AGQSPVLR--IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQ 85
Query: 118 -AALALNNMDV 127
A L+L+ ++
Sbjct: 86 HAKLSLDGQNI 96
>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 = 28.9 bits (63), Expect = 8.7, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 40/85 (47%), Gaps = 7/85 (8%)
Query: 61 GKADALKKTLQVSNLSPLLTVEQLRQLFSFCGTVVECTI----TDSKH--FAYIEYSKPE 114
G K+ L V L+ + + L F G + + I KH FA++E+ E
Sbjct: 1 GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 115 EATAAL-ALNNMDVGGRPLNVEMAK 138
+A AA+ +N ++ GR + V +AK
Sbjct: 61 DAAAAIDNMNESELFGRTIRVNLAK 85
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
0.307 0.124 0.342
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,866,290
Number of Sequences: 62578
Number of extensions: 376448
Number of successful extensions: 543
Number of sequences better than 100.0: 46
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 42
Number of HSP's that attempted gapping in prelim test: 529
Number of HSP's gapped (non-prelim): 47
length of query: 682
length of database: 14,973,337
effective HSP length: 105
effective length of query: 577
effective length of database: 8,402,647
effective search space: 4848327319
effective search space used: 4848327319
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 55 (25.8 bits)