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= psy15187
(298 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 65.1 bits (157), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 38/109 (34%), Positives = 59/109 (54%), Gaps = 25/109 (22%)
Query: 142 PKGGNTIFVQGAGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCA 201
P+ GNT++V G ++ LR FS FG I +SM+ + FV
Sbjct: 36 PRKGNTLYVYGEDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFV----------------- 78
Query: 202 RGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVAPINDAASS 250
T++ ES+D+A+ E+NGT V+ V+LKV++AR+Q P+ DAA+
Sbjct: 79 ----TYEKMESADQAVAELNGTQVESVQLKVNIARKQ----PMLDAATG 119
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 62.4 bits (150), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 37/110 (33%), Positives = 59/110 (53%), Gaps = 25/110 (22%)
Query: 142 PKGGNTIFVQGAGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCA 201
P+ GNT++V G ++ LR FS FG I +SM+ + FV
Sbjct: 12 PRKGNTLYVYGEDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFV----------------- 54
Query: 202 RGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVAPINDAASST 251
T++ ES+D+A+ E+NGT V+ V+LKV++AR+Q P+ D+ S+
Sbjct: 55 ----TYEKMESADQAVAELNGTQVESVQLKVNIARKQ----PMLDSGPSS 96
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 51.2 bits (121), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 35/87 (40%), Positives = 45/87 (51%), Gaps = 21/87 (24%)
Query: 154 GISEEFLRQHFSIFGKICSVSMEVEKGR--GFVTFDSPESSDKAITDDCARGFVTFDSPE 211
GI +E LR+ FS FG I S + +E GR GF GFV F SPE
Sbjct: 26 GIDDERLRKAFSPFGTITSAKVMMEGGRSKGF-------------------GFVCFSSPE 66
Query: 212 SSDKAITEVNGTHVQGVKLKVSLARRQ 238
+ KA+TE+NG V L V+LA+R+
Sbjct: 67 EATKAVTEMNGRIVATKPLYVALAQRK 93
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 33/52 (63%), Gaps = 2/52 (3%)
Query: 147 TIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAI 196
T++ G +G++++ +RQ FS FG+I + + EKG FV F + ES+ AI
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAI 78
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 23/44 (52%)
Query: 193 DKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
DK GFV + P +DKAI +NG +Q +KVS AR
Sbjct: 39 DKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYAR 82
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 36.6 bits (83), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 29/101 (28%), Positives = 42/101 (41%), Gaps = 22/101 (21%)
Query: 140 EKPKGGNTIFVQGAGISEEF----LRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKA 195
E P+G N + +EF L Q F FG + S + + DK
Sbjct: 21 EGPEGANLFIYH---LPQEFGDQDLLQMFMPFGNVVSAKVFI---------------DKQ 62
Query: 196 ITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
GFV++D+P S+ AI +NG + +LKV L R
Sbjct: 63 TNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR 103
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 36.2 bits (82), Expect = 0.021, Method: Composition-based stats.
Identities = 18/44 (40%), Positives = 23/44 (52%)
Query: 193 DKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
DK GFV + P +DKAI +NG +Q +KVS AR
Sbjct: 39 DKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYAR 82
>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 = 36.2 bits (82), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 24/44 (54%)
Query: 193 DKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
DK GFV + P+ ++KAI +NG +Q +KVS AR
Sbjct: 37 DKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR 80
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 39/85 (45%), Gaps = 23/85 (27%)
Query: 155 ISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSP 210
+ E LRQ F +G I SV + E + RG+ GFV F S
Sbjct: 54 VDEVQLRQLFERYGPIESVKIVCDRETRQSRGY-------------------GFVKFQSG 94
Query: 211 ESSDKAITEVNGTHVQGVKLKVSLA 235
S+ +AI +NG ++ +LKV+LA
Sbjct: 95 SSAQQAIAGLNGFNILNKRLKVALA 119
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 36.2 bits (82), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 17/76 (22%)
Query: 160 LRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSDKAITE 219
LRQ F FGKI V + F+ E K GFVTF++ +D+A +
Sbjct: 46 LRQMFGQFGKILDVE---------IIFN--ERGSKGF------GFVTFENSADADRAREK 88
Query: 220 VNGTHVQGVKLKVSLA 235
++GT V+G K++V+ A
Sbjct: 89 LHGTVVEGRKIEVNNA 104
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 35.8 bits (81), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 21/78 (26%)
Query: 160 LRQHFSIFGKICSVSMEV-EKG-RGFVTFDSPESSDKAITDDCARGFVTFDSPESSDKAI 217
LRQ F FGKI V + E+G +GF GFVTF++ +D+A
Sbjct: 32 LRQMFGQFGKILDVEIIFNERGSKGF-------------------GFVTFENSADADRAR 72
Query: 218 TEVNGTHVQGVKLKVSLA 235
+++GT V+G K++V+ A
Sbjct: 73 EKLHGTVVEGRKIEVNNA 90
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 35.8 bits (81), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 15/79 (18%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
I+E+ LR F FG+I S+ + + DS K GF+TF E +
Sbjct: 38 ITEDMLRGIFEPFGRIESIQLMM---------DSETGRSKGY------GFITFSDSECAK 82
Query: 215 KAITEVNGTHVQGVKLKVS 233
KA+ ++NG + G +KV
Sbjct: 83 KALEQLNGFELAGRPMKVG 101
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 34.7 bits (78), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 44/94 (46%), Gaps = 25/94 (26%)
Query: 148 IFVQGAGI--SEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSDKAITDDCA 201
+FV G +E+ L Q FS +G+I V + E ++ RGF
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGF------------------ 56
Query: 202 RGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLA 235
GFVTF++ + + A+ +NG V G +++V A
Sbjct: 57 -GFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA 89
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 34.7 bits (78), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 28/99 (28%), Positives = 45/99 (45%), Gaps = 14/99 (14%)
Query: 144 GGNTIFVQGAGIS--EEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCA 201
G + +F++ S EE L+ FS G I S ++ +K + V
Sbjct: 4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLS------------MG 51
Query: 202 RGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLK 240
GFV + PE + KA+ ++ G V G KL+V ++ R K
Sbjct: 52 FGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATK 90
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 34.7 bits (78), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 30/106 (28%), Positives = 50/106 (47%), Gaps = 10/106 (9%)
Query: 146 NTIFVQGAGISEEFLRQHFSIFGKICSV-SMEVEKGRGFVTFDSPESSDKAITDDCARGF 204
+ I+VQG +++ + F K C V M G+ + + + K D
Sbjct: 16 SAIYVQG--LNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD----AT 69
Query: 205 VTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVAPINDAASS 250
V+++ P ++ A+ +G QG KLKVSLAR++ P+N SS
Sbjct: 70 VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK---PPMNSGPSS 112
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 34.7 bits (78), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 23/34 (67%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
GFV+FD+P+S+ AI +NG V +LKV L +
Sbjct: 85 GFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118
Score = 28.1 bits (61), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 13/67 (19%)
Query: 140 EKPKGGNTIFVQGAGISEEF----LRQHFSIFGKICSVSMEVEK------GRGFVTFDSP 189
E P+G N + +EF L F FG + S + ++K GFV+FD+P
Sbjct: 36 EGPEGCNLFIYH---LPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNP 92
Query: 190 ESSDKAI 196
+S+ AI
Sbjct: 93 DSAQVAI 99
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 34.3 bits (77), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 148 IFVQGA--GISEEFLRQHFSIFGKICSVSMEVEKGRG------FVTFDSPESSDKAI 196
IFV G E LR +F +GKI + + ++G G FVTFD +S DK +
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
>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 = 34.3 bits (77), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 148 IFVQGA--GISEEFLRQHFSIFGKICSVSMEVEKGRG------FVTFDSPESSDKAI 196
IFV G E LR +F +GKI + + ++G G FVTFD +S DK +
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 34.3 bits (77), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 148 IFVQGA--GISEEFLRQHFSIFGKICSVSMEVEKGRG------FVTFDSPESSDKAI 196
IFV G E LR +F +GKI + + ++G G FVTFD +S DK +
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>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 = 34.3 bits (77), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 148 IFVQGA--GISEEFLRQHFSIFGKICSVSMEVEKGRG------FVTFDSPESSDKAI 196
IFV G E LR +F +GKI + + ++G G FVTFD +S DK +
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
>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 = 34.3 bits (77), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 148 IFVQGA--GISEEFLRQHFSIFGKICSVSMEVEKGRG------FVTFDSPESSDKAI 196
IFV G E LR +F +GKI + + ++G G FVTFD +S DK +
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 34.3 bits (77), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 148 IFVQGA--GISEEFLRQHFSIFGKICSVSMEVEKGRG------FVTFDSPESSDKAI 196
IFV G E LR +F +GKI + + ++G G FVTFD +S DK +
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 33.9 bits (76), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 146 NTIFVQGA--GISEEFLRQHFSIFGKICSVSMEVE------KGRGFVTFDSPESSDKAIT 197
N IFV G E LR++F FG + V M + +G GF+TF+ +S D+A+
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
>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 = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 30/125 (24%), Positives = 52/125 (41%), Gaps = 22/125 (17%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
+ E+ +RQ F+ FG I S+ M ++DS K FV ++ PE++
Sbjct: 25 LGEDTIRQAFAPFGPIKSIDM---------SWDSVTMKHKGFA------FVEYEVPEAAQ 69
Query: 215 KAITEVNGTHVQGVKLKVSLARRQLKVAPINDAASSTTWSAIACHQSLKGNHKDKRHQVI 274
A+ ++N + G +KV + PI D + ++ + HQ +
Sbjct: 70 LALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEA-------RAFNRIYVASVHQDL 122
Query: 275 YDDDI 279
DDDI
Sbjct: 123 SDDDI 127
Score = 28.1 bits (61), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 8/66 (12%)
Query: 140 EKPKGGNTIFVQGAG--ISEEFLRQHFSIFGKICSVSMEVE------KGRGFVTFDSPES 191
E+ + N I+V +S++ ++ F FGKI S ++ + KG GF+ ++ +S
Sbjct: 105 EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQS 164
Query: 192 SDKAIT 197
S A++
Sbjct: 165 SQDAVS 170
>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 = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 30/125 (24%), Positives = 52/125 (41%), Gaps = 22/125 (17%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
+ E+ +RQ F+ FG I S+ M ++DS K FV ++ PE++
Sbjct: 40 LGEDTIRQAFAPFGPIKSIDM---------SWDSVTMKHKGFA------FVEYEVPEAAQ 84
Query: 215 KAITEVNGTHVQGVKLKVSLARRQLKVAPINDAASSTTWSAIACHQSLKGNHKDKRHQVI 274
A+ ++N + G +KV + PI D + ++ + HQ +
Sbjct: 85 LALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEA-------RAFNRIYVASVHQDL 137
Query: 275 YDDDI 279
DDDI
Sbjct: 138 SDDDI 142
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 193 DKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
DK GFV + + + +++AI +NG +Q +KVS AR
Sbjct: 37 DKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR 80
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 193 DKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
DK GFV + + + +++AI +NG +Q +KVS AR
Sbjct: 37 DKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR 80
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 32.7 bits (73), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 37/81 (45%), Gaps = 12/81 (14%)
Query: 135 RLAPNEKPKGGNTIFVQGAG--ISEEFLRQHFSIFGKICSVSMEVEK------GRGFVTF 186
R P ++ IFV G G + + + FS +G I + ++K G GFVT+
Sbjct: 77 RAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY 136
Query: 187 DSPESSDKAITDDCARGFVTF 207
DS ++ D+ C F+ F
Sbjct: 137 DSADAVDRV----CQNKFIDF 153
Score = 27.7 bits (60), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 31/57 (54%), Gaps = 8/57 (14%)
Query: 148 IFVQGAGI--SEEFLRQHFSIFGKICSVSMEVE------KGRGFVTFDSPESSDKAI 196
+F+ G +E+ LR++F +G + + + + +G GF++F+ P S D+ +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 32.3 bits (72), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 43/95 (45%), Gaps = 9/95 (9%)
Query: 146 NTIFVQGAG--ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARG 203
NTIFVQG G ++ E + +F +I + + G+ + + + K
Sbjct: 8 NTIFVQGLGENVTIESVADYFK---QIGIIKTNKKTGQPMINLYTDRETGKL----KGEA 60
Query: 204 FVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
V+FD P S+ AI +G G +KVS A R+
Sbjct: 61 TVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRR 95
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 32.0 bits (71), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 41/86 (47%), Gaps = 19/86 (22%)
Query: 144 GGNTIFVQGA--GISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDC- 200
G + ++++G G +++ L + +GKI S ++K T+ C
Sbjct: 4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDK----------------TTNKCK 47
Query: 201 ARGFVTFDSPESSDKAITEVNGTHVQ 226
GFV FDSP ++ KA+T + + VQ
Sbjct: 48 GYGFVDFDSPSAAQKAVTALKASGVQ 73
>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 = 31.6 bits (70), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 43/99 (43%), Gaps = 23/99 (23%)
Query: 138 PNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKI--CSVSMEVEKGRGFVTFDSPESSD 193
P+ + G IF++ I + L FS FG I C V + +G+
Sbjct: 91 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY---------- 140
Query: 194 KAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKV 232
GFV F++ E++++AI ++NG + K+ V
Sbjct: 141 ---------GFVHFETQEAAERAIEKMNGMLLNDRKVFV 170
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 31.6 bits (70), Expect = 0.55, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 193 DKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
DK GFV + + + +++AI +NG +Q +KVS AR
Sbjct: 54 DKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR 97
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 31.6 bits (70), Expect = 0.58, Method: Composition-based stats.
Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 15/85 (17%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
I+E+ LR F FGKI ++ + DS K GF+TF E +
Sbjct: 17 ITEDMLRGIFEPFGKIDNIVL---------MKDSDTGRSKGY------GFITFSDSECAR 61
Query: 215 KAITEVNGTHVQGVKLKVSLARRQL 239
+A+ ++NG + G ++V +L
Sbjct: 62 RALEQLNGFELAGRPMRVGHVTERL 86
>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 = 0.59, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 43/100 (43%), Gaps = 23/100 (23%)
Query: 138 PNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKI--CSVSMEVEKGRGFVTFDSPESSD 193
P+ + G IF++ I + L FS FG I C V + +G+
Sbjct: 96 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY---------- 145
Query: 194 KAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVS 233
GFV F++ E++++AI ++NG + K+ V
Sbjct: 146 ---------GFVHFETQEAAERAIEKMNGMLLNDRKVFVG 176
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 31.2 bits (69), Expect = 0.67, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 193 DKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
DK GFV + + + +++AI +NG +Q +KVS AR
Sbjct: 39 DKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR 82
>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 = 31.2 bits (69), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 20/33 (60%)
Query: 204 FVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
FV F S S +AI +NG V+ +LKVS AR
Sbjct: 60 FVDFTSEXDSQRAIKVLNGITVRNKRLKVSYAR 92
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 31.2 bits (69), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 23/82 (28%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
++EE L + FS FGK+ V K + D F+ FD + +
Sbjct: 23 VTEEILEKAFSQFGKLERV--------------------KKLKDYA---FIHFDERDGAV 59
Query: 215 KAITEVNGTHVQGVKLKVSLAR 236
KA+ E+NG ++G +++ A+
Sbjct: 60 KAMEEMNGKDLEGENIEIVFAK 81
>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 = 0.90, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 20/33 (60%)
Query: 204 FVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
FV F S S +AI +NG V+ +LKVS AR
Sbjct: 49 FVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR 81
>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 = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 29/125 (23%), Positives = 50/125 (40%), Gaps = 22/125 (17%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
+ E+ +RQ F+ FG I S+ ++DS K FV ++ PE++
Sbjct: 24 LGEDTIRQAFAPFGPIKSIDX---------SWDSVTXKHKGFA------FVEYEVPEAAQ 68
Query: 215 KAITEVNGTHVQGVKLKVSLARRQLKVAPINDAASSTTWSAIACHQSLKGNHKDKRHQVI 274
A+ + N + G +KV + PI D + ++ + HQ +
Sbjct: 69 LALEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEA-------RAFNRIYVASVHQDL 121
Query: 275 YDDDI 279
DDDI
Sbjct: 122 SDDDI 126
Score = 28.1 bits (61), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 8/66 (12%)
Query: 140 EKPKGGNTIFVQGAG--ISEEFLRQHFSIFGKICSVSMEVE------KGRGFVTFDSPES 191
E+ + N I+V +S++ ++ F FGKI S ++ + KG GF+ ++ +S
Sbjct: 104 EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQS 163
Query: 192 SDKAIT 197
S A++
Sbjct: 164 SQDAVS 169
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVS 233
GFV F PES AI +NG + G + VS
Sbjct: 60 GFVCFKHPESVSYAIALLNGIRLYGRPINVS 90
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 9/64 (14%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVE-----KGRGFVTFDSPESSDKAITDDCARG---FVT 206
+S E L + FS+FG++ + V+ G+G V F ++ KA+ D C+ G T
Sbjct: 108 VSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKAL-DRCSEGSFLLTT 166
Query: 207 FDSP 210
F P
Sbjct: 167 FPRP 170
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 30.4 bits (67), Expect = 1.1, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 30/49 (61%), Gaps = 7/49 (14%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVE-------KGRGFVTFDSPESSDKAI 196
++++ + + FS +GKI + M VE KG +V F++P+ ++KA+
Sbjct: 16 VTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 30.4 bits (67), Expect = 1.1, Method: Composition-based stats.
Identities = 16/34 (47%), Positives = 20/34 (58%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
FV F S S +AI +NG V+ +LKVS AR
Sbjct: 48 AFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR 81
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 30.0 bits (66), Expect = 1.5, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 31/51 (60%), Gaps = 2/51 (3%)
Query: 147 TIFVQGAG--ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKA 195
T++V G G I+E LR HF FG+I ++++ + F+ F + ++++ A
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVA 64
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 39/95 (41%), Gaps = 24/95 (25%)
Query: 148 IFVQGAG--ISEEFLRQHFSIFGKICSVSM---EVEKGRGFVTFDSPESSDKAITDDCAR 202
+F+ G +E+ L+ F G I V + K RGF
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFA------------------ 51
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
F+TF++P + A ++NG + G +KV A++
Sbjct: 52 -FITFENPADAKNAAKDMNGKSLHGKAIKVEQAKK 85
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 25/96 (26%), Positives = 41/96 (42%), Gaps = 23/96 (23%)
Query: 142 PKGGNTIFVQGA--GISEEFLRQHFSIFGKI--CSVSMEVEKGRGFVTFDSPESSDKAIT 197
P G IF++ I + L FS FG I C V + +G+
Sbjct: 2 PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY-------------- 47
Query: 198 DDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVS 233
GFV F++ E++++AI ++NG + K+ V
Sbjct: 48 -----GFVHFETQEAAERAIEKMNGMLLNDRKVFVG 78
>pdb|2PE8|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 (free
Form)
pdb|2PEH|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
pdb|2PEH|B Chain B, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
Length = 105
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 4/44 (9%)
Query: 184 VTFDSPESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQG 227
V F+ P + D D+ R F+ F+ ES+ KA+ ++NG + G
Sbjct: 44 VIFEIPGAPD----DEAVRIFLEFERVESAIKAVVDLNGRYFGG 83
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 6/43 (13%)
Query: 160 LRQHFSIFGKICSVSMEVE------KGRGFVTFDSPESSDKAI 196
L+ +FS FG++ +++++ +G GFV F ES DK +
Sbjct: 16 LKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM 58
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 41/92 (44%), Gaps = 9/92 (9%)
Query: 146 NTIFVQGAG--ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARG 203
NTIFVQG G ++ E + +F +I + + G+ + + + K
Sbjct: 14 NTIFVQGLGENVTIESVADYFK---QIGIIKTNKKTGQPMINLYTDRETGKL----KGEA 66
Query: 204 FVTFDSPESSDKAITEVNGTHVQGVKLKVSLA 235
V+FD P S+ AI +G G +KVS A
Sbjct: 67 TVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 17/30 (56%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKV 232
FVTF PE + KA EV+G QG L V
Sbjct: 53 AFVTFMFPEHAVKAYAEVDGQVFQGRMLHV 82
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 29.3 bits (64), Expect = 3.1, Method: Composition-based stats.
Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 23/89 (25%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKGRGFVTFDSPESSD 193
P+ + G IF++ I + L FS FG I C V + +G+
Sbjct: 4 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY---------- 53
Query: 194 KAITDDCARGFVTFDSPESSDKAITEVNG 222
GFV F++ E++++AI ++NG
Sbjct: 54 ---------GFVHFETQEAAERAIEKMNG 73
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 28.9 bits (63), Expect = 3.6, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 26/42 (61%), Gaps = 2/42 (4%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAI 196
+S+E L + FS +G I ++ ++ GF+ FD+P+S AI
Sbjct: 35 VSKEDLFRIFSPYGHIMQIN--IKNAFGFIQFDNPQSVRDAI 74
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 28.5 bits (62), Expect = 4.2, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 26/42 (61%), Gaps = 2/42 (4%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAI 196
+S+E L + FS +G I ++ ++ GF+ FD+P+S AI
Sbjct: 35 VSKEDLFRIFSPYGHIMQIN--IKNAFGFIQFDNPQSVRDAI 74
>pdb|4AV8|A Chain A, Kluyveromyces Lactis Hsv2 Complete Loop 6cd
pdb|4AV9|A Chain A, Kluyveromyces Lactis Hsv2
pdb|4EXV|A Chain A, Structure Of Kluyveromyces Lactis Hsv2p
Length = 339
Score = 28.1 bits (61), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 36/93 (38%), Gaps = 9/93 (9%)
Query: 188 SPESSDKAITDD--CARGFVTFDSPESSDKAITE-VNGTHVQ------GVKLKVSLARRQ 238
SP+ S A+ D F F+ E+ + + +N + Q KLKVS
Sbjct: 233 SPDGSKLAVVSDKWTLHVFEVFNDAENKRHVLKDWINIKYFQSEWSICNFKLKVSKGSND 292
Query: 239 LKVAPINDAASSTTWSAIACHQSLKGNHKDKRH 271
K+A I+D W + K N+ D H
Sbjct: 293 CKIAWISDTGLVIVWPNRRLADTFKLNYNDDEH 325
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 28.1 bits (61), Expect = 5.6, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 26/42 (61%), Gaps = 2/42 (4%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAI 196
+S+E L + FS +G I ++ ++ GF+ FD+P+S AI
Sbjct: 23 VSKEDLFRIFSPYGHIMQIN--IKNAFGFIQFDNPQSVRDAI 62
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 28.1 bits (61), Expect = 5.7, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 26/42 (61%), Gaps = 2/42 (4%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAI 196
+S+E L + FS +G I ++ ++ GF+ FD+P+S AI
Sbjct: 15 VSKEDLFRIFSPYGHIMQIN--IKNAFGFIQFDNPQSVRDAI 54
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 28.1 bits (61), Expect = 5.9, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
G V F+SPE +++A +NG + G ++ V + R
Sbjct: 51 GVVKFESPEVAERACRMMNGMKLSGREIDVRIDR 84
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 28.1 bits (61), Expect = 6.3, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
G V F+SPE +++A +NG + G ++ V + R
Sbjct: 48 GVVKFESPEVAERACRMMNGMKLSGREIDVRIDR 81
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 27.7 bits (60), Expect = 7.4, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 8/55 (14%)
Query: 148 IFVQGAGISE--EFLRQHFSIFGKICSVSMEVEK------GRGFVTFDSPESSDK 194
IFV G ++ E ++ +F FGK+ + +K G GFVTF+S + +K
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK 56
>pdb|2RAR|A Chain A, X-Ray Crystallographic Structures Show Conservation Of A
Trigonal- Bipyramidal Intermediate In A
Phosphoryl-Transfer Superfamily.
pdb|2RAV|A Chain A, X-Ray Crystallographic Structures Show Conservation Of A
Trigonal- Bipyramidal Intermediate In A
Phosphoryl-Transfer Superfamily
Length = 261
Score = 27.7 bits (60), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 41/90 (45%), Gaps = 3/90 (3%)
Query: 194 KAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVAPINDAASSTTW 253
KA+ D A V+F++ I + H +G+K+ ++ R + A IN+ +
Sbjct: 3 KALFFDIAGTLVSFETHRIPSSTIEALEAAHAKGLKIFIATGRPK---AIINNLSELQDR 59
Query: 254 SAIACHQSLKGNHKDKRHQVIYDDDIFGEE 283
+ I + ++ G + +VIY I EE
Sbjct: 60 NLIDGYITMNGAYCFVGEEVIYKSAIPQEE 89
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
0.312 0.129 0.366
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,916,197
Number of Sequences: 62578
Number of extensions: 366295
Number of successful extensions: 846
Number of sequences better than 100.0: 65
Number of HSP's better than 100.0 without gapping: 31
Number of HSP's successfully gapped in prelim test: 34
Number of HSP's that attempted gapping in prelim test: 755
Number of HSP's gapped (non-prelim): 92
length of query: 298
length of database: 14,973,337
effective HSP length: 98
effective length of query: 200
effective length of database: 8,840,693
effective search space: 1768138600
effective search space used: 1768138600
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 51 (24.3 bits)