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= 004041
(777 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 72.0 bits (175), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 47/173 (27%), Positives = 88/173 (50%), Gaps = 8/173 (4%)
Query: 272 PSQDSDTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVED-SNNEGMNRGFAFLEFSS 330
P D+ +F+G + +TW+++ L+E + YG V ++ ++ D S N ++G F+ F +
Sbjct: 11 PDLDAIKMFVGQVPRTWSEKDLRELFEQYGA--VYEINVLRDRSQNPPQSKGCCFVTFYT 68
Query: 331 RSDAMDAFKRLQKRDVLFGVDRPAKVSFADSFIDPGDEIMAQVKTVFVDGLPASWDEDRV 390
R A++A L VL G+ P ++ ADS + E + +F+ + E+ +
Sbjct: 69 RKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVED----RKLFIGMISKKCTENDI 124
Query: 391 RELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSINNAELGEG 443
R + ++G+I + + R P + FVTF T A T K+++ A+ EG
Sbjct: 125 RVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEG 176
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 46/165 (27%), Positives = 75/165 (45%), Gaps = 34/165 (20%)
Query: 217 FSQVGEVTEVRLM----MNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTP 272
F Q G V E+ ++ NP ++KG F+ F T R+A E +N + N K V P
Sbjct: 36 FEQYGAVYEINVLRDRSQNP--PQSKGCCFVTFYT----RKAALEAQNALHNMK---VLP 86
Query: 273 SQ---------DSDT--------LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSN 315
DS+ LF+G I K T+ ++ +G +E+ ++
Sbjct: 87 GMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFG--QIEECRILRGP- 143
Query: 316 NEGMNRGFAFLEFSSRSDAMDAFKRLQKRDVLFGVDRPAKVSFAD 360
+G++RG AF+ F++R+ A A K + + + G P V FAD
Sbjct: 144 -DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD 187
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 70.1 bits (170), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 46/170 (27%), Positives = 87/170 (51%), Gaps = 8/170 (4%)
Query: 275 DSDTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVED-SNNEGMNRGFAFLEFSSRSD 333
D+ +F+G + +TW+++ L+E + YG V ++ ++ D S N ++G F+ F +R
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGA--VYEINVLRDRSQNPPQSKGCCFVTFYTRKA 59
Query: 334 AMDAFKRLQKRDVLFGVDRPAKVSFADSFIDPGDEIMAQVKTVFVDGLPASWDEDRVREL 393
A++A L VL G+ P ++ ADS + E + +F+ + E+ +R +
Sbjct: 60 ALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVED----RKLFIGMISKKCTENDIRVM 115
Query: 394 LKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSINNAELGEG 443
++G+I + + R P + FVTF T A T K+++ A+ EG
Sbjct: 116 FSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEG 164
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 46/165 (27%), Positives = 75/165 (45%), Gaps = 34/165 (20%)
Query: 217 FSQVGEVTEVRLM----MNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTP 272
F Q G V E+ ++ NP ++KG F+ F T R+A E +N + N K V P
Sbjct: 24 FEQYGAVYEINVLRDRSQNP--PQSKGCCFVTFYT----RKAALEAQNALHNMK---VLP 74
Query: 273 SQ---------DSDT--------LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSN 315
DS+ LF+G I K T+ ++ +G +E+ ++
Sbjct: 75 GMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFG--QIEECRILRGP- 131
Query: 316 NEGMNRGFAFLEFSSRSDAMDAFKRLQKRDVLFGVDRPAKVSFAD 360
+G++RG AF+ F++R+ A A K + + + G P V FAD
Sbjct: 132 -DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD 175
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 65.9 bits (159), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 43/150 (28%), Positives = 76/150 (50%), Gaps = 6/150 (4%)
Query: 279 LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAF 338
LF+G + T E+L+ + +G + D ++ D N + +RGF F+ +++ + +DA
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWG--TLTDCVVMRDPNTK-RSRGFGFVTYAT-VEEVDAA 72
Query: 339 KRLQKRDVLFGVDRPAKVSFADSFIDPGDEIMAQVKTVFVDGLPASWDEDRVRELLKNYG 398
+ V V P + + PG + VK +FV G+ +E +R+ + YG
Sbjct: 73 MNARPHKVDGRVVEPKRAVSREDSQRPGAHLT--VKKIFVGGIKEDTEEHHLRDYFEQYG 130
Query: 399 EITKIELARNMPSAKRKDFGFVTFDTHDAA 428
+I IE+ + S K++ F FVTFD HD+
Sbjct: 131 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 160
Score = 50.1 bits (118), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 35/125 (28%), Positives = 64/125 (51%), Gaps = 18/125 (14%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVT----ELKNPVINGKQCGVTP 272
F Q G +T+ +M +P TK+++GF F+ +ATVE+ A+ ++ V+ K+
Sbjct: 35 FEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA--VS 92
Query: 273 SQDSD---------TLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGF 323
+DS +F+G I + + L++ + YG +E + ++ D + G RGF
Sbjct: 93 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG--KIEVIEIMTDRGS-GKKRGF 149
Query: 324 AFLEF 328
AF+ F
Sbjct: 150 AFVTF 154
Score = 34.3 bits (77), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 30/53 (56%)
Query: 372 QVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDT 424
Q++ +F+ GL ++ +R + +G +T + R+ + + + FGFVT+ T
Sbjct: 13 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT 65
>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 = 65.5 bits (158), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 43/150 (28%), Positives = 76/150 (50%), Gaps = 6/150 (4%)
Query: 279 LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAF 338
LF+G + T E+L+ + +G + D ++ D N + +RGF F+ +++ + +DA
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWG--TLTDCVVMRDPNTK-RSRGFGFVTYAT-VEEVDAA 70
Query: 339 KRLQKRDVLFGVDRPAKVSFADSFIDPGDEIMAQVKTVFVDGLPASWDEDRVRELLKNYG 398
+ V V P + + PG + VK +FV G+ +E +R+ + YG
Sbjct: 71 MNARPHKVDGRVVEPKRAVSREDSQRPGAHLT--VKKIFVGGIKEDTEEHHLRDYFEQYG 128
Query: 399 EITKIELARNMPSAKRKDFGFVTFDTHDAA 428
+I IE+ + S K++ F FVTFD HD+
Sbjct: 129 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 158
Score = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 35/125 (28%), Positives = 64/125 (51%), Gaps = 18/125 (14%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVT----ELKNPVINGKQCGVTP 272
F Q G +T+ +M +P TK+++GF F+ +ATVE+ A+ ++ V+ K+
Sbjct: 33 FEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA--VS 90
Query: 273 SQDSD---------TLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGF 323
+DS +F+G I + + L++ + YG +E + ++ D + G RGF
Sbjct: 91 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG--KIEVIEIMTDRGS-GKKRGF 147
Query: 324 AFLEF 328
AF+ F
Sbjct: 148 AFVTF 152
Score = 34.3 bits (77), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 30/53 (56%)
Query: 372 QVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDT 424
Q++ +F+ GL ++ +R + +G +T + R+ + + + FGFVT+ T
Sbjct: 11 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT 63
>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 = 65.5 bits (158), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 43/150 (28%), Positives = 76/150 (50%), Gaps = 6/150 (4%)
Query: 279 LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAF 338
LF+G + T E+L+ + +G + D ++ D N + +RGF F+ +++ + +DA
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWG--TLTDCVVMRDPNTK-RSRGFGFVTYAT-VEEVDAA 71
Query: 339 KRLQKRDVLFGVDRPAKVSFADSFIDPGDEIMAQVKTVFVDGLPASWDEDRVRELLKNYG 398
+ V V P + + PG + VK +FV G+ +E +R+ + YG
Sbjct: 72 MNARPHKVDGRVVEPKRAVSREDSQRPGAHLT--VKKIFVGGIKEDTEEHHLRDYFEQYG 129
Query: 399 EITKIELARNMPSAKRKDFGFVTFDTHDAA 428
+I IE+ + S K++ F FVTFD HD+
Sbjct: 130 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 159
Score = 49.7 bits (117), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 35/125 (28%), Positives = 64/125 (51%), Gaps = 18/125 (14%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVT----ELKNPVINGKQCGVTP 272
F Q G +T+ +M +P TK+++GF F+ +ATVE+ A+ ++ V+ K+
Sbjct: 34 FEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA--VS 91
Query: 273 SQDSD---------TLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGF 323
+DS +F+G I + + L++ + YG +E + ++ D + G RGF
Sbjct: 92 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG--KIEVIEIMTDRGS-GKKRGF 148
Query: 324 AFLEF 328
AF+ F
Sbjct: 149 AFVTF 153
Score = 34.3 bits (77), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 30/53 (56%)
Query: 372 QVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDT 424
Q++ +F+ GL ++ +R + +G +T + R+ + + + FGFVT+ T
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT 64
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 64.7 bits (156), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 43/150 (28%), Positives = 76/150 (50%), Gaps = 6/150 (4%)
Query: 279 LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAF 338
LF+G + T E+L+ + +G + D ++ D N + +RGF F+ +++ + +DA
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWG--TLTDCVVMRDPNTK-RSRGFGFVTYAT-VEEVDAA 69
Query: 339 KRLQKRDVLFGVDRPAKVSFADSFIDPGDEIMAQVKTVFVDGLPASWDEDRVRELLKNYG 398
+ V V P + + PG + VK +FV G+ +E +R+ + YG
Sbjct: 70 MNARPHKVDGRVVEPKRAVSREDSQRPGAHLT--VKKIFVGGIKEDTEEHHLRDYFEQYG 127
Query: 399 EITKIELARNMPSAKRKDFGFVTFDTHDAA 428
+I IE+ + S K++ F FVTFD HD+
Sbjct: 128 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 157
Score = 49.3 bits (116), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 35/125 (28%), Positives = 64/125 (51%), Gaps = 18/125 (14%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVT----ELKNPVINGKQCGVTP 272
F Q G +T+ +M +P TK+++GF F+ +ATVE+ A+ ++ V+ K+
Sbjct: 32 FEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA--VS 89
Query: 273 SQDSD---------TLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGF 323
+DS +F+G I + + L++ + YG +E + ++ D + G RGF
Sbjct: 90 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG--KIEVIEIMTDRGS-GKKRGF 146
Query: 324 AFLEF 328
AF+ F
Sbjct: 147 AFVTF 151
Score = 33.9 bits (76), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 30/53 (56%)
Query: 372 QVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDT 424
Q++ +F+ GL ++ +R + +G +T + R+ + + + FGFVT+ T
Sbjct: 10 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT 62
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 64.7 bits (156), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 43/150 (28%), Positives = 76/150 (50%), Gaps = 6/150 (4%)
Query: 279 LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAF 338
LF+G + T E+L+ + +G + D ++ D N + +RGF F+ +++ + +DA
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWG--TLTDCVVMRDPNTK-RSRGFGFVTYAT-VEEVDAA 71
Query: 339 KRLQKRDVLFGVDRPAKVSFADSFIDPGDEIMAQVKTVFVDGLPASWDEDRVRELLKNYG 398
+ V V P + + PG + VK +FV G+ +E +R+ + YG
Sbjct: 72 MNARPHKVDGRVVEPKRAVSREDSQRPGAHLT--VKKIFVGGIKEDTEEHHLRDYFEQYG 129
Query: 399 EITKIELARNMPSAKRKDFGFVTFDTHDAA 428
+I IE+ + S K++ F FVTFD HD+
Sbjct: 130 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 159
Score = 49.3 bits (116), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 35/125 (28%), Positives = 64/125 (51%), Gaps = 18/125 (14%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVT----ELKNPVINGKQCGVTP 272
F Q G +T+ +M +P TK+++GF F+ +ATVE+ A+ ++ V+ K+
Sbjct: 34 FEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA--VS 91
Query: 273 SQDSD---------TLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGF 323
+DS +F+G I + + L++ + YG +E + ++ D + G RGF
Sbjct: 92 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG--KIEVIEIMTDRGS-GKKRGF 148
Query: 324 AFLEF 328
AF+ F
Sbjct: 149 AFVTF 153
Score = 33.9 bits (76), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 30/53 (56%)
Query: 372 QVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDT 424
Q++ +F+ GL ++ +R + +G +T + R+ + + + FGFVT+ T
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT 64
>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 = 63.9 bits (154), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 43/150 (28%), Positives = 76/150 (50%), Gaps = 6/150 (4%)
Query: 279 LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAF 338
LF+G + T E+L+ + +G + D ++ D N + +RGF F+ +++ + +DA
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWG--TLTDCVVMRDPNTK-RSRGFGFVTYAT-VEEVDAA 64
Query: 339 KRLQKRDVLFGVDRPAKVSFADSFIDPGDEIMAQVKTVFVDGLPASWDEDRVRELLKNYG 398
+ V V P + + PG + VK +FV G+ +E +R+ + YG
Sbjct: 65 MNARPHKVDGRVVEPKRAVSREDSQRPGAHLT--VKKIFVGGIKEDTEEHHLRDYFEQYG 122
Query: 399 EITKIELARNMPSAKRKDFGFVTFDTHDAA 428
+I IE+ + S K++ F FVTFD HD+
Sbjct: 123 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 152
Score = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 35/125 (28%), Positives = 64/125 (51%), Gaps = 18/125 (14%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVT----ELKNPVINGKQCGVTP 272
F Q G +T+ +M +P TK+++GF F+ +ATVE+ A+ ++ V+ K+
Sbjct: 27 FEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA--VS 84
Query: 273 SQDSD---------TLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGF 323
+DS +F+G I + + L++ + YG +E + ++ D + G RGF
Sbjct: 85 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG--KIEVIEIMTDRGS-GKKRGF 141
Query: 324 AFLEF 328
AF+ F
Sbjct: 142 AFVTF 146
Score = 33.9 bits (76), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 30/53 (56%)
Query: 372 QVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDT 424
Q++ +F+ GL ++ +R + +G +T + R+ + + + FGFVT+ T
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT 57
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 62.4 bits (150), Expect = 1e-09, Method: Composition-based stats.
Identities = 46/170 (27%), Positives = 82/170 (48%), Gaps = 8/170 (4%)
Query: 275 DSDTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVED-SNNEGMNRGFAFLEFSSRSD 333
D+ F+G + +TW+++ L+E + YG V ++ ++ D S N ++G F+ F +R
Sbjct: 2 DAIKXFVGQVPRTWSEKDLRELFEQYGA--VYEINVLRDRSQNPPQSKGCCFVTFYTRKA 59
Query: 334 AMDAFKRLQKRDVLFGVDRPAKVSFADSFIDPGDEIMAQVKTVFVDGLPASWDEDRVREL 393
A++A L VL G P + ADS + E + +F+ + E+ +R
Sbjct: 60 ALEAQNALHNXKVLPGXHHPIQXKPADSEKNNAVE----DRKLFIGXISKKCTENDIRVX 115
Query: 394 LKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSINNAELGEG 443
++G+I + + R P + FVTF T A T K+ + A+ EG
Sbjct: 116 FSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAXAQTAIKAXHQAQTXEG 164
Score = 45.4 bits (106), Expect = 1e-04, Method: Composition-based stats.
Identities = 44/158 (27%), Positives = 72/158 (45%), Gaps = 20/158 (12%)
Query: 217 FSQVGEVTEVRLM----MNPQTKKNKGFAFLRFATVEQARQAVTELKN-PVINGKQCGV- 270
F Q G V E+ ++ NP ++KG F+ F T + A +A L N V+ G +
Sbjct: 24 FEQYGAVYEINVLRDRSQNP--PQSKGCCFVTFYTRKAALEAQNALHNXKVLPGXHHPIQ 81
Query: 271 TPSQDSDT--------LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRG 322
DS+ LF+G I K T+ ++ +G +E+ ++ +G++RG
Sbjct: 82 XKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFG--QIEECRILRGP--DGLSRG 137
Query: 323 FAFLEFSSRSDAMDAFKRLQKRDVLFGVDRPAKVSFAD 360
AF+ F++R+ A A K + G P V FAD
Sbjct: 138 CAFVTFTTRAXAQTAIKAXHQAQTXEGCSSPXVVKFAD 175
>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 = 51.6 bits (122), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 37/168 (22%), Positives = 79/168 (47%), Gaps = 10/168 (5%)
Query: 279 LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAF 338
+++G+I ++ +++ +G ++ + + DS ++GFAF+E+ A A
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFG--PIKSIDMSWDSVTM-KHKGFAFVEYEVPEAAQLAL 87
Query: 339 KRLQKRDVLFG-----VDRPAKVSFADSFIDPGDEIMAQVKTVFVDGLPASWDEDRVREL 393
+ Q V+ G V RP+ + A ID E ++V + +D ++ +
Sbjct: 88 E--QMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSV 145
Query: 394 LKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSINNAELG 441
+ +G+I LAR+ + K K +GF+ ++ ++ S+N +LG
Sbjct: 146 FEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLG 193
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 28/147 (19%), Positives = 66/147 (44%), Gaps = 20/147 (13%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGV------ 270
F+ G + + + + T K+KGFAF+ + E A+ A+ ++ + ++ G+ V
Sbjct: 49 FAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI 108
Query: 271 ---TPSQDS--------DTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGM 319
P D + +++ ++ + + + +K + +G ++ TL D G
Sbjct: 109 GQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG--KIKSATLARDPTT-GK 165
Query: 320 NRGFAFLEFSSRSDAMDAFKRLQKRDV 346
++G+ F+E+ + DA + D+
Sbjct: 166 HKGYGFIEYEKAQSSQDAVSSMNLFDL 192
>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 = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 37/168 (22%), Positives = 79/168 (47%), Gaps = 10/168 (5%)
Query: 279 LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAF 338
+++G+I ++ +++ +G ++ + + DS ++GFAF+E+ A A
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFG--PIKSIDMSWDSVTMK-HKGFAFVEYEVPEAAQLAL 72
Query: 339 KRLQKRDVLFG-----VDRPAKVSFADSFIDPGDEIMAQVKTVFVDGLPASWDEDRVREL 393
+ Q V+ G V RP+ + A ID E ++V + +D ++ +
Sbjct: 73 E--QMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSV 130
Query: 394 LKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSINNAELG 441
+ +G+I LAR+ + K K +GF+ ++ ++ S+N +LG
Sbjct: 131 FEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLG 178
Score = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 28/147 (19%), Positives = 66/147 (44%), Gaps = 20/147 (13%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGV------ 270
F+ G + + + + T K+KGFAF+ + E A+ A+ ++ + ++ G+ V
Sbjct: 34 FAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI 93
Query: 271 ---TPSQDS--------DTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGM 319
P D + +++ ++ + + + +K + +G ++ TL D G
Sbjct: 94 GQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG--KIKSCTLARDPTT-GK 150
Query: 320 NRGFAFLEFSSRSDAMDAFKRLQKRDV 346
++G+ F+E+ + DA + D+
Sbjct: 151 HKGYGFIEYEKAQSSQDAVSSMNLFDL 177
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 50.1 bits (118), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 50/88 (56%), Gaps = 3/88 (3%)
Query: 275 DSDTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVED-SNNEGMNRGFAFLEFSSRSD 333
D+ +F+G + +TW+++ L+E + YG V ++ ++ D S N ++G F+ F +R
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGA--VYEINVLRDRSQNPPQSKGCCFVTFYTRKA 59
Query: 334 AMDAFKRLQKRDVLFGVDRPAKVSFADS 361
A++A L VL G+ P ++ ADS
Sbjct: 60 ALEAQNALHNMKVLPGMHHPIQMKPADS 87
Score = 42.7 bits (99), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 2/70 (2%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSA--KRKDFGFVTFDTHDAAVTCAK 433
+FV +P +W E +REL + YG + +I + R+ + K FVTF T AA+
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 434 SINNAELGEG 443
+++N ++ G
Sbjct: 66 ALHNMKVLPG 75
>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 = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 36/124 (29%), Positives = 66/124 (53%), Gaps = 8/124 (6%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRF---ATVEQARQAVTELKNPVINGKQCGVTPS 273
F + G VT++++M +P T +++GF FL F ++V++ + L VI+ K+
Sbjct: 24 FGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPRDE 83
Query: 274 QD-SDTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRS 332
QD + +F+G I + +E +G + D L+ D + G +RGF F+ + S +
Sbjct: 84 QDKTGKIFVGGIGPDVRPKEFEEFFSQWG--TIIDAQLMLDKDT-GQSRGFGFVTYDS-A 139
Query: 333 DAMD 336
DA+D
Sbjct: 140 DAVD 143
Score = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 43/159 (27%), Positives = 67/159 (42%), Gaps = 21/159 (13%)
Query: 274 QDSDTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSD 333
++S +F+G + T++ L+E YG V DL +++D G +RGF FL F S
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYG--TVTDLKIMKDPAT-GRSRGFGFLSFEKPSS 57
Query: 334 AMDAFKRLQKRDVLFGVDRPAKVSFADSFIDPGDEI----MAQVKTVFVDGLPASWDEDR 389
+ K D KV IDP I + +FV G+
Sbjct: 58 VDEVVKTQHILD--------GKV------IDPKRAIPRDEQDKTGKIFVGGIGPDVRPKE 103
Query: 390 VRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAA 428
E +G I +L + + + + FGFVT+D+ DA
Sbjct: 104 FEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAV 142
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 31/128 (24%), Positives = 64/128 (50%), Gaps = 9/128 (7%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPSQDS 276
FS +GEV +L+ + + G+ F+ + T + A +A+ L + K V+ ++ S
Sbjct: 23 FSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS 82
Query: 277 D------TLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSS 330
L++ + +T T++ +++ +G + LV+ + G++RG AF+ F
Sbjct: 83 SEVIKDANLYISGLPRTMTQKDVEDMFSRFG-RIINSRVLVDQTT--GLSRGVAFIRFDK 139
Query: 331 RSDAMDAF 338
RS+A +A
Sbjct: 140 RSEAEEAI 147
Score = 34.3 bits (77), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 31/65 (47%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSI 435
+ V+ LP + +D +R L + GE+ +L R+ + +GFV + T A ++
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 436 NNAEL 440
N L
Sbjct: 65 NGLRL 69
Score = 31.6 bits (70), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTEL 258
FS+ G + R++++ T ++G AF+RF +A +A+T
Sbjct: 109 FSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
>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 = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 31/128 (24%), Positives = 64/128 (50%), Gaps = 9/128 (7%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPSQDS 276
FS +GEV +L+ + + G+ F+ + T + A +A+ L + K V+ ++ S
Sbjct: 23 FSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS 82
Query: 277 D------TLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSS 330
L++ + +T T++ +++ +G + LV+ + G++RG AF+ F
Sbjct: 83 SEVIKDANLYISGLPRTMTQKDVEDMFSRFG-RIINSRVLVDQTT--GLSRGVAFIRFDK 139
Query: 331 RSDAMDAF 338
RS+A +A
Sbjct: 140 RSEAEEAI 147
Score = 34.3 bits (77), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 31/65 (47%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSI 435
+ V+ LP + +D +R L + GE+ +L R+ + +GFV + T A ++
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 436 NNAEL 440
N L
Sbjct: 65 NGLRL 69
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTEL 258
FS+ G + R++++ T ++G AF+RF +A +A+T
Sbjct: 109 FSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
>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 = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 32/127 (25%), Positives = 58/127 (45%), Gaps = 7/127 (5%)
Query: 320 NRGFAFLEFSSRSDAMDAFKRLQKRDVLFG-----VDRPAKVSFADSFIDPGDEIMAQVK 374
++GFAF+E+ A A + Q V G V RP+ + A ID E
Sbjct: 53 HKGFAFVEYEVPEAAQLALE--QXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFN 110
Query: 375 TVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKS 434
++V + +D ++ + + +G+I LAR+ + K K +GF+ ++ ++ S
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 170
Query: 435 INNAELG 441
N +LG
Sbjct: 171 XNLFDLG 177
Score = 35.8 bits (81), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 27/138 (19%), Positives = 60/138 (43%), Gaps = 20/138 (14%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGV------ 270
F+ G + + + T K+KGFAF+ + E A+ A+ + + + G+ V
Sbjct: 33 FAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKVGRPSNI 92
Query: 271 ---TPSQDS--------DTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGM 319
P D + +++ ++ + + + +K + +G ++ TL D G
Sbjct: 93 GQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG--KIKSCTLARDPTT-GK 149
Query: 320 NRGFAFLEFSSRSDAMDA 337
++G+ F+E+ + DA
Sbjct: 150 HKGYGFIEYEKAQSSQDA 167
Score = 29.3 bits (64), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVT 256
F G++ L +P T K+KG+ F+ + + ++ AV+
Sbjct: 130 FEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 169
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 38/163 (23%), Positives = 79/163 (48%), Gaps = 12/163 (7%)
Query: 279 LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAF 338
L++GN+ K T++ LK+ + G + ++ ++ D NN+ +N +AF+E+ DA A
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGG--PIANIKIMIDKNNKNVN--YAFVEYHQSHDANIAL 58
Query: 339 KRLQKRDVLFGVDRPAKVSFA-DSFIDPGDEIMAQVKTVFVDGLPASWDEDRVRELLKNY 397
+ L + + + K+++A S D+ +FV L + D++ +R K++
Sbjct: 59 QTLNGKQIENNI---VKINWAFQSQQSSSDDTF----NLFVGDLNVNVDDETLRNAFKDF 111
Query: 398 GEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSINNAEL 440
+ +M + + +GFV+F + D A S+ +L
Sbjct: 112 PSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDL 154
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 47.0 bits (110), Expect = 4e-05, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 36/66 (54%)
Query: 375 TVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKS 434
TV+V LP S + + + YG++ K+ + ++ + K K F+ F D+A C ++
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 435 INNAEL 440
INN +L
Sbjct: 78 INNKQL 83
Score = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 29/50 (58%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGK 266
FS+ G+V +V +M + T+K+KG AF+ F + A+ + N + G+
Sbjct: 37 FSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGR 86
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 35/148 (23%), Positives = 68/148 (45%), Gaps = 24/148 (16%)
Query: 302 VDNVEDLTLVEDSNNEGMNR---------GFAFLEFSSRSDAMDAFKRLQKRDVLFGVDR 352
+DN E+ + ED + +G+ R G F S+ +A+ +++R++ D
Sbjct: 7 IDNAEEFEVDEDGD-QGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNED------- 58
Query: 353 PAKVSFADSFIDPGDEIMAQVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSA 412
D ++PG + + +FV + ED ++E +YGEI I L + +
Sbjct: 59 -------DDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTG 111
Query: 413 KRKDFGFVTFDTHDAAVTCAKSINNAEL 440
K + V ++TH A+ +++N AE+
Sbjct: 112 FSKGYALVEYETHKQALAAKEALNGAEI 139
Score = 31.6 bits (70), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 27/54 (50%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGV 270
F GE+ + L ++ +T +KG+A + + T +QA A L I G+ V
Sbjct: 93 FCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 146
Score = 29.6 bits (65), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 26/122 (21%), Positives = 59/122 (48%), Gaps = 5/122 (4%)
Query: 226 VRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPSQDSDTLFLGNIC 285
VRL + +K +GF + +A + ++N + + G S + LF+ +I
Sbjct: 24 VRLKEKAKHRKGRGFG--SDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIH 81
Query: 286 KTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAFKRLQKRD 345
+ ++ ++EK YG ++++ L D G ++G+A +E+ + A+ A + L +
Sbjct: 82 EEAQEDEIQEKFCDYG--EIKNIHLNLDRRT-GFSKGYALVEYETHKQALAAKEALNGAE 138
Query: 346 VL 347
++
Sbjct: 139 IM 140
>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 = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 32/134 (23%), Positives = 64/134 (47%), Gaps = 13/134 (9%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPSQDS 276
FS G + +R+ + T+++ G+A++ F A +A+ + VI GK + SQ
Sbjct: 36 FSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRD 95
Query: 277 DTL--------FLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEF 328
+L F+ N+ K+ +AL + +G N+ +V D N ++G+ F+ F
Sbjct: 96 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG--NILSCKVVCDENG---SKGYGFVHF 150
Query: 329 SSRSDAMDAFKRLQ 342
++ A A +++
Sbjct: 151 ETQEAAERAIEKMN 164
Score = 36.2 bits (82), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 39/172 (22%), Positives = 76/172 (44%), Gaps = 11/172 (6%)
Query: 271 TPSQDSDTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSS 330
PS +L++G++ T+ L EK G + + + D + G+A++ F
Sbjct: 10 APSYPMASLYVGDLHPDVTEAMLYEKFSPAG--PILSIRVCRDMITR-RSLGYAYVNFQQ 66
Query: 331 RSDAMDAFKRLQKRDVLFGVDRPAKVSFADSFIDPGDEIMAQVKTVFVDGLPASWDEDRV 390
+DA A + DV+ G +P ++ ++ DP + V +F+ L S D +
Sbjct: 67 PADAERALDTMN-FDVIKG--KPVRIMWSQR--DPSLR-KSGVGNIFIKNLDKSIDNKAL 120
Query: 391 RELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSINNAELGE 442
+ +G I ++ + +K +GFV F+T +AA + +N L +
Sbjct: 121 YDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAIEKMNGMLLND 170
>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 = 45.8 bits (107), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 32/124 (25%), Positives = 61/124 (49%), Gaps = 14/124 (11%)
Query: 318 GMNRGFAFLEFSSRSDAMDAFKRLQKRDVLFGV---DRPAKVSFADSFIDPGDEIMAQVK 374
G + G+AF++F+S D+ A K VL G+ ++ KVS+A PG E +
Sbjct: 53 GYSFGYAFVDFTSEXDSQRAIK------VLNGITVRNKRLKVSYAR----PGGESIKDTN 102
Query: 375 TVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKS 434
++V LP + +D++ + YG I + + R+ + + + FV ++ + A +
Sbjct: 103 -LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 161
Query: 435 INNA 438
+NN
Sbjct: 162 LNNV 165
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 28/46 (60%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPV 262
F + G + + ++ + T + +G AF+R+ E+A++A++ L N +
Sbjct: 121 FGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 166
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 31/121 (25%), Positives = 59/121 (48%), Gaps = 8/121 (6%)
Query: 318 GMNRGFAFLEFSSRSDAMDAFKRLQKRDVLFGVDRPAKVSFADSFIDPGDEIMAQVKTVF 377
G + G+AF++F+S D+ A K L V ++ KVS+A PG E + ++
Sbjct: 42 GYSYGYAFVDFTSEMDSQRAIKVLNGITVR---NKRLKVSYAR----PGGESIKDTN-LY 93
Query: 378 VDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSINN 437
V LP + +D++ + YG I + + R+ + + + FV ++ + A ++NN
Sbjct: 94 VTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNN 153
Query: 438 A 438
Sbjct: 154 V 154
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 34/132 (25%), Positives = 65/132 (49%), Gaps = 9/132 (6%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVT---PS 273
F +G + R+M + +T + G+AF+ F + +++A+ L + K+ V+ P
Sbjct: 24 FRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPG 83
Query: 274 QDS--DT-LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSS 330
+S DT L++ N+ +T T + L YG ++ ++ D G RG AF+ ++
Sbjct: 84 GESIKDTNLYVTNLPRTITDDQLDTIFGKYG--SIVQKNILRDKLT-GRPRGVAFVRYNK 140
Query: 331 RSDAMDAFKRLQ 342
R +A +A L
Sbjct: 141 REEAQEAISALN 152
Score = 31.6 bits (70), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 28/46 (60%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPV 262
F + G + + ++ + T + +G AF+R+ E+A++A++ L N +
Sbjct: 110 FGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 52/93 (55%), Gaps = 5/93 (5%)
Query: 271 TPSQDSDT--LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEF 328
P +D D LF+G I + ++ LK + +G + +LT+++D G+++G AFL +
Sbjct: 8 VPMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFG--RIYELTVLKDRLT-GLHKGCAFLTY 64
Query: 329 SSRSDAMDAFKRLQKRDVLFGVDRPAKVSFADS 361
+R A+ A L ++ L G++RP +V A S
Sbjct: 65 CARDSALKAQSALHEQKTLPGMNRPIQVKPAAS 97
Score = 34.3 bits (77), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 15/71 (21%), Positives = 36/71 (50%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSI 435
+FV +P DE ++ L + +G I ++ + ++ + K F+T+ D+A+ ++
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSAL 77
Query: 436 NNAELGEGDNK 446
+ + G N+
Sbjct: 78 HEQKTLPGMNR 88
>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 = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 32/134 (23%), Positives = 64/134 (47%), Gaps = 13/134 (9%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPSQDS 276
FS G + +R+ + T+++ G+A++ F A +A+ + VI GK + SQ
Sbjct: 31 FSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRD 90
Query: 277 DTL--------FLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEF 328
+L F+ N+ K+ +AL + +G N+ +V D N ++G+ F+ F
Sbjct: 91 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG--NILSCKVVCDENG---SKGYGFVHF 145
Query: 329 SSRSDAMDAFKRLQ 342
++ A A +++
Sbjct: 146 ETQEAAERAIEKMN 159
Score = 34.3 bits (77), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 39/172 (22%), Positives = 76/172 (44%), Gaps = 11/172 (6%)
Query: 271 TPSQDSDTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSS 330
PS +L++G++ T+ L EK G + + + D + G+A++ F
Sbjct: 5 APSYPMASLYVGDLHPDVTEAMLYEKFSPAG--PILSIRVCRDMITR-RSLGYAYVNFQQ 61
Query: 331 RSDAMDAFKRLQKRDVLFGVDRPAKVSFADSFIDPGDEIMAQVKTVFVDGLPASWDEDRV 390
+DA A + DV+ G +P ++ ++ DP + V +F+ L S D +
Sbjct: 62 PADAERALDTMN-FDVIKG--KPVRIMWSQR--DPSLR-KSGVGNIFIKNLDKSIDNKAL 115
Query: 391 RELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSINNAELGE 442
+ +G I ++ + +K +GFV F+T +AA + +N L +
Sbjct: 116 YDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAIEKMNGMLLND 165
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 49/87 (56%), Gaps = 3/87 (3%)
Query: 274 QDSDTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSD 333
D+ LF+G I + ++ LK + +G + +LT+++D GM++G AFL + R
Sbjct: 11 HDAIKLFIGQIPRNLDEKDLKPLFEEFG--KIYELTVLKDRFT-GMHKGCAFLTYCERES 67
Query: 334 AMDAFKRLQKRDVLFGVDRPAKVSFAD 360
A+ A L ++ L G++RP +V AD
Sbjct: 68 ALKAQSALHEQKTLPGMNRPIQVKPAD 94
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 32/140 (22%), Positives = 57/140 (40%), Gaps = 19/140 (13%)
Query: 302 VDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAFK-----RLQKRDVLFGVDRPAKV 356
+ ++E LV D G + G+ F+ +S +DA A +LQ + + RP+
Sbjct: 28 IGDIESCKLVRDKIT-GQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPSSA 86
Query: 357 SFADSFIDPGDEIMAQVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKD 416
S D+ ++V GLP + + + +L YG I + + + +
Sbjct: 87 SIRDA-------------NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRG 133
Query: 417 FGFVTFDTHDAAVTCAKSIN 436
GF+ FD A K +N
Sbjct: 134 VGFIRFDKRIEAEEAIKGLN 153
Score = 29.6 bits (65), Expect = 6.1, Method: Composition-based stats.
Identities = 18/87 (20%), Positives = 38/87 (43%), Gaps = 4/87 (4%)
Query: 370 MAQVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAV 429
M + V+ LP + +D + L + G+I +L R+ + + +GFV + + A
Sbjct: 1 MDSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 430 TCAKSINNAELGEGDNKAKVRARLSRP 456
++N +L ++ +RP
Sbjct: 61 KAINTLNGLKL----QTKTIKVSYARP 83
Score = 29.6 bits (65), Expect = 6.2, Method: Composition-based stats.
Identities = 13/42 (30%), Positives = 24/42 (57%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTEL 258
FSQ G + R++++ T ++G F+RF +A +A+ L
Sbjct: 111 FSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 44/149 (29%), Positives = 64/149 (42%), Gaps = 11/149 (7%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPSQDS 276
F + G+ EV + K+KGF F+R T A A EL N + GKQ V + S
Sbjct: 43 FEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS 96
Query: 277 DTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMD 336
+L + N+ + + E L+E +G VE ++ D + G G +EFS + A
Sbjct: 97 ASLTVRNLPQYVSNELLEEAFSVFG--QVERAVVIVD--DRGRPSGKGIVEFSGKPAARK 152
Query: 337 AFKRLQKRDVLFGV-DRPAKVSFADSFID 364
A R + L RP V D D
Sbjct: 153 ALDRCSEGSFLLTTFPRPVTVEPMDQLDD 181
Score = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 6/80 (7%)
Query: 361 SFIDPGDEIMAQVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFV 420
+F PG++ Q +FV LP E+ +R+L + YG+ ++ + ++ K FGF+
Sbjct: 10 NFRKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFI 63
Query: 421 TFDTHDAAVTCAKSINNAEL 440
+T A ++N L
Sbjct: 64 RLETRTLAEIAKVELDNMPL 83
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 43.5 bits (101), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 45/87 (51%), Gaps = 9/87 (10%)
Query: 366 GDEIMAQVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTH 425
G MA+VK +FV L + E+ + + +G++ +++ K KD+ F+ FD
Sbjct: 4 GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDER 55
Query: 426 DAAVTCAKSINNAELGEGDNKAKVRAR 452
D AV + +N +L EG+N V A+
Sbjct: 56 DGAVKAMEEMNGKDL-EGENIEIVFAK 81
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 43.1 bits (100), Expect = 6e-04, Method: Composition-based stats.
Identities = 20/50 (40%), Positives = 30/50 (60%)
Query: 373 VKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTF 422
VK +FV GL E+++RE +GE+ IEL + + KR+ F F+TF
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF 50
Score = 29.3 bits (64), Expect = 8.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQ 253
F GEV + L M+ +T K +GF F+ F E ++
Sbjct: 22 FGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK 58
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 42.7 bits (99), Expect = 8e-04, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 41/81 (50%)
Query: 360 DSFIDPGDEIMAQVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGF 419
D ++PG + + +FV + ED ++E +YGEI I L + + K +
Sbjct: 13 DDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYAL 72
Query: 420 VTFDTHDAAVTCAKSINNAEL 440
V ++TH A+ +++N AE+
Sbjct: 73 VEYETHKQALAAKEALNGAEI 93
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 35/60 (58%), Gaps = 2/60 (3%)
Query: 218 SQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGK--QCGVTPSQD 275
S VG V +++M +PQT ++KG+AF+ F +E + AV L + + +CG + + D
Sbjct: 24 SNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSD 83
>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 = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 32/140 (22%), Positives = 54/140 (38%), Gaps = 19/140 (13%)
Query: 302 VDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAFK-----RLQKRDVLFGVDRPAKV 356
+ +E LV D G + G+ F+ + DA A RLQ + + RP+
Sbjct: 26 IGEIESCKLVRDKIT-GQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSA 84
Query: 357 SFADSFIDPGDEIMAQVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKD 416
S D+ ++V GLP + + + +L YG I + + + +
Sbjct: 85 SIRDA-------------NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRG 131
Query: 417 FGFVTFDTHDAAVTCAKSIN 436
GF+ FD A K +N
Sbjct: 132 VGFIRFDKRIEAEEAIKGLN 151
Score = 29.3 bits (64), Expect = 8.3, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTF-DTHDA 427
+ V+ LP + ++ R L + GEI +L R+ + + +GFV + D DA
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDA 57
>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 = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 35/60 (58%), Gaps = 2/60 (3%)
Query: 218 SQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGK--QCGVTPSQD 275
S VG V +++M +PQT ++KG+AF+ F +E + AV L + + +CG + + D
Sbjct: 25 SNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSD 84
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 31/57 (54%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPS 273
FS G ++E+ ++ TKK KGFAF+ F E A +A E+ V G+ V PS
Sbjct: 29 FSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS 85
>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 = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 31/52 (59%), Gaps = 5/52 (9%)
Query: 218 SQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCG 269
S VG V +++M +PQT ++KG+AF+ F +E + AV L NG Q G
Sbjct: 26 SNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL-----NGYQLG 72
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 35/61 (57%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSI 435
+FV GL +E + ++ YG+I+++ + ++ + + + FGFVTF+ D A ++
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 436 N 436
N
Sbjct: 75 N 75
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 36/54 (66%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGV 270
FS+ G+++EV ++ + +T++++GF F+ F ++ A+ A+ + ++G+Q V
Sbjct: 33 FSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV 86
Score = 34.3 bits (77), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 3/74 (4%)
Query: 273 SQDSDTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRS 332
+ D LF+G + +++L++ YG + ++ +V+D + +RGF F+ F +
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYG--QISEVVVVKDRETQ-RSRGFGFVTFENID 65
Query: 333 DAMDAFKRLQKRDV 346
DA DA + + V
Sbjct: 66 DAKDAMMAMNGKSV 79
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 28/102 (27%), Positives = 51/102 (50%), Gaps = 10/102 (9%)
Query: 233 QTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPSQD------SDTLFLGNICK 286
Q ++K FAFL F +V++ QA+ + G+ + D + LF+G +
Sbjct: 46 QINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPN 104
Query: 287 TWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEF 328
+ +KE L +G ++ LV+DS G+++G+AF E+
Sbjct: 105 YLNDDQVKELLTSFG--PLKAFNLVKDSAT-GLSKGYAFCEY 143
Score = 39.7 bits (91), Expect = 0.007, Method: Composition-based stats.
Identities = 40/170 (23%), Positives = 74/170 (43%), Gaps = 19/170 (11%)
Query: 279 LFLGNICKTWTKEALKE----KLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDA 334
L++GNI T+EA+ + +++ G+ ++ N+ N FAFLEF S +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN--FAFLEFRSVDET 64
Query: 335 MDA--FKRLQKRDVLFGVDRPAKVSFADSFIDPGDEIMAQVKTVFVDGLPASWDEDRVRE 392
A F + + + RP D PG +F+ GLP ++D+V+E
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPH-----DYQPLPG------AHKLFIGGLPNYLNDDQVKE 113
Query: 393 LLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSINNAELGE 442
LL ++G + L ++ + K + F + + +N +LG+
Sbjct: 114 LLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD 163
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 28/102 (27%), Positives = 51/102 (50%), Gaps = 10/102 (9%)
Query: 233 QTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPSQD------SDTLFLGNICK 286
Q ++K FAFL F +V++ QA+ + G+ + D + LF+G +
Sbjct: 48 QINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPN 106
Query: 287 TWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEF 328
+ +KE L +G ++ LV+DS G+++G+AF E+
Sbjct: 107 YLNDDQVKELLTSFG--PLKAFNLVKDSAT-GLSKGYAFCEY 145
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 41/177 (23%), Positives = 76/177 (42%), Gaps = 19/177 (10%)
Query: 272 PSQDSDTLFLGNICKTWTKEALKE----KLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLE 327
P + L++GNI T+EA+ + +++ G+ ++ N+ N FAFLE
Sbjct: 2 PLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN--FAFLE 59
Query: 328 FSSRSDAMDA--FKRLQKRDVLFGVDRPAKVSFADSFIDPGDEIMAQVKTVFVDGLPASW 385
F S + A F + + + RP D PG +F+ GLP
Sbjct: 60 FRSVDETTQAMAFDGIIFQGQSLKIRRPH-----DYQPLPG------AHKLFIGGLPNYL 108
Query: 386 DEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSINNAELGE 442
++D+V+ELL ++G + L ++ + K + F + + +N +LG+
Sbjct: 109 NDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD 165
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 29/48 (60%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFD 423
+FV G+P + E +RE K +G +T++ + + + + FGF+TF+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE 60
Score = 29.6 bits (65), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 23/40 (57%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVT 256
F + G VTEV ++ + + ++ +GF F+ F + QAV
Sbjct: 31 FKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 32/106 (30%), Positives = 55/106 (51%), Gaps = 4/106 (3%)
Query: 269 GVTPSQDSDTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEF 328
G + S + LF+G I K +E + E++ + V D+ + + ++ NRGFAF+E+
Sbjct: 1 GSSGSSGNCRLFIGGIPKMKKREEILEEIAKV-TEGVLDVIVYASAADKMKNRGFAFVEY 59
Query: 329 SS-RSDAMDAFKRLQKRDVLFGVDRPAKVSFADSFIDPGDEIMAQV 373
S R+ AM K + R L+G V +A+ ID +++M V
Sbjct: 60 ESHRAAAMARRKLMPGRIQLWG--HQIAVDWAEPEIDVDEDVMETV 103
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 40.0 bits (92), Expect = 0.005, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 28/47 (59%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTF 422
+FV GL E+++RE +GE+ IEL + + KR+ F F+TF
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF 48
Score = 29.3 bits (64), Expect = 8.3, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQ 253
F GEV + L M+ +T K +GF F+ F E ++
Sbjct: 20 FGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK 56
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 39.7 bits (91), Expect = 0.007, Method: Composition-based stats.
Identities = 27/86 (31%), Positives = 41/86 (47%), Gaps = 2/86 (2%)
Query: 277 DTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMD 336
DT+ L NI +++ L Y V ++ L++D + NRGFAF++ SS DA
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQ-QNRGFAFVQLSSAMDASQ 68
Query: 337 AFKRLQKRDVLFGVD-RPAKVSFADS 361
+ LQ +D + V FA S
Sbjct: 69 LLQILQSLHPPLKIDGKTIGVDFAKS 94
Score = 36.6 bits (83), Expect = 0.058, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 34/52 (65%), Gaps = 4/52 (7%)
Query: 223 VTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKN---PV-INGKQCGV 270
V +RL+ + QT++N+GFAF++ ++ A Q + L++ P+ I+GK GV
Sbjct: 38 VNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGV 89
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 35/65 (53%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSI 435
++V L + ED +R + + +G+I I L ++ + + K +GF+TF + A + +
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 436 NNAEL 440
N EL
Sbjct: 68 NGFEL 72
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 39.3 bits (90), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 35/58 (60%), Gaps = 2/58 (3%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPSQ 274
FS G +T ++MM + ++KGF F+ F++ E+A +AVTE+ ++ K V +Q
Sbjct: 36 FSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQ 91
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 54/223 (24%), Positives = 97/223 (43%), Gaps = 28/223 (12%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPSQDS 276
F G + V + KKN FA + FA + A A+T+ V G+ +
Sbjct: 62 FKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALAAITKTHKVV--GQNEIIVSHLTE 117
Query: 277 DTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMD 336
TL+ N ++T+ +++ L+ NV L++ S +R FA+++ +S+ DA
Sbjct: 118 CTLWXTNFPPSYTQRNIRDLLQDI---NVVALSIRLPSLRFNTSRRFAYIDVTSKEDARY 174
Query: 337 AFKRLQKRDV-----LFGVDRPA-KVSFADSFIDPGDEIMAQVKTVFVDGLPASWDEDRV 390
++L + + V P K DS G EI ++ + + L DE+ +
Sbjct: 175 CVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREI--XIRNLSTELL----DENLL 228
Query: 391 RELLKNYGEITKIELARNMPSAKRKD-----FGFVTFDTHDAA 428
RE + +G I KI N+P+ +++ F F+ D+A
Sbjct: 229 RESFEGFGSIEKI----NIPAGQKEHSFNNCCAFXVFENKDSA 267
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 38.9 bits (89), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/64 (23%), Positives = 36/64 (56%)
Query: 373 VKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCA 432
++ + V+ +P + DE ++R+L + YG I +++ + + + + +GFV F + +A
Sbjct: 42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
Query: 433 KSIN 436
+N
Sbjct: 102 AGLN 105
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 11/43 (25%), Positives = 28/43 (65%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELK 259
F + G + V+++ + +T++++G+ F++F + A+QA+ L
Sbjct: 63 FERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLN 105
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 29/54 (53%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAV 429
+ V GLP E ++E +GE+ +++ +++ + K FGFV F ++ V
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV 71
Score = 34.3 bits (77), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 30/52 (57%), Gaps = 2/52 (3%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQC 268
FS GEV V++ + +T +KGF F+RF E + +++ +I+G+ C
Sbjct: 36 FSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWC 85
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 45/83 (54%), Gaps = 4/83 (4%)
Query: 279 LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAF 338
LF+G + K +++ ++ + +G N+E+ T++ +G ++G AF+++SS ++A A
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFG--NIEECTILRGP--DGNSKGCAFVKYSSHAEAQAAI 73
Query: 339 KRLQKRDVLFGVDRPAKVSFADS 361
L + G V FAD+
Sbjct: 74 NALHGSQTMPGASSSLVVKFADT 96
Score = 32.3 bits (72), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 1/76 (1%)
Query: 374 KTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAK 433
+ +FV L ED VR L + +G I + + R P K FV + +H A
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRG-PDGNSKGCAFVKYSSHAEAQAAIN 74
Query: 434 SINNAELGEGDNKAKV 449
+++ ++ G + + V
Sbjct: 75 ALHGSQTMPGASSSLV 90
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 38.5 bits (88), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 45/94 (47%), Gaps = 5/94 (5%)
Query: 366 GDEIMAQVKTV-FVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDT 424
G MA K V +V GL D+ + +G+IT I++ + + K + F FV F+
Sbjct: 4 GSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 63
Query: 425 HDAAVTCAKSINNAELGEGDNKAKVRARLSRPLQ 458
+ A ++N +EL +R L++P++
Sbjct: 64 AEDAAAAIDNMNESEL----FGRTIRVNLAKPMR 93
Score = 36.2 bits (82), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 34/58 (58%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPSQ 274
F G++T++++ ++ +T+K++GFAF+ F E A A+ + + G+ V ++
Sbjct: 33 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 90
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 38.5 bits (88), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 3/63 (4%)
Query: 372 QVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTH---DAA 428
Q + +F+ GL E+ +R + +G++T + R+ S + + FGFVTF + DAA
Sbjct: 26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 85
Query: 429 VTC 431
+
Sbjct: 86 MAA 88
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 38.5 bits (88), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 8/69 (11%)
Query: 368 EIMAQVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDA 427
E+MA+VK +FV L + E+ + + +G++ +++ K KD+ FV F+ A
Sbjct: 10 EVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVK--------KLKDYAFVHFEDRGA 61
Query: 428 AVTCAKSIN 436
AV +N
Sbjct: 62 AVKAMDEMN 70
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 38.1 bits (87), Expect = 0.018, Method: Composition-based stats.
Identities = 41/179 (22%), Positives = 77/179 (43%), Gaps = 17/179 (9%)
Query: 279 LFLGNICKTWTKEALKE----KLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDA 334
L++GNI T+EA+ + +++ G+ ++ N+ N FAFLEF S +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN--FAFLEFRSVDET 64
Query: 335 MDA--FKRLQKRDVLFGVDRP------AKVSFADSFIDPG---DEIMAQVKTVFVDGLPA 383
A F + + + RP +S S PG + +F+ GLP
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124
Query: 384 SWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSINNAELGE 442
++D+V+ELL ++G + L ++ + K + F + + +N +LG+
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD 183
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 37.7 bits (86), Expect = 0.024, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 9/73 (12%)
Query: 275 DSDTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVE-DSNNEGMNRGFAFLEFSSRSD 333
+S TL L N+ + T+E L+E E T ++ N G ++G+AF+EF+S D
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVF--------EKATFIKVPQNQNGKSKGYAFIEFASFED 65
Query: 334 AMDAFKRLQKRDV 346
A +A KR++
Sbjct: 66 AKEALNSCNKREI 78
Score = 29.6 bits (65), Expect = 6.3, Method: Composition-based stats.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 233 QTKKNKGFAFLRFATVEQARQAVTELKNPVINGK 266
Q K+KG+AF+ FA+ E A++A+ I G+
Sbjct: 48 QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGR 81
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 37.7 bits (86), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 279 LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAF 338
L++GN+ T E L E + GV+++ ++ E+ N G ++GFA + S + +
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRAN-GQSKGFALVGVGSEASSKKLM 129
Query: 339 KRLQKRDV 346
L KR++
Sbjct: 130 DLLPKREL 137
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 37.4 bits (85), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 11/80 (13%)
Query: 361 SFIDPGDEIMAQVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFV 420
SF+ PG++ Q +FV LP E+ + L + YGE +++ + R+ + FGF+
Sbjct: 10 SFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFI 63
Query: 421 TFDTHDAAVTCAKSINNAEL 440
++ A I AEL
Sbjct: 64 RLESRTLA-----EIAKAEL 78
Score = 37.4 bits (85), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 35/149 (23%), Positives = 62/149 (41%), Gaps = 11/149 (7%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPSQDS 276
F + GE +EV + +++GF F+R + A A EL ++ + + +
Sbjct: 43 FERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHG 96
Query: 277 DTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMD 336
L + N+ + E L++ +G VE +V D +G F+EF+++ A
Sbjct: 97 AALTVKNLSPVVSNELLEQAFSQFG--PVEKAVVVVDDRGRATGKG--FVEFAAKPPARK 152
Query: 337 AFKRLQKRDVLFGVD-RPAKVSFADSFID 364
A +R L RP V + F D
Sbjct: 153 ALERCGDGAFLLTTTPRPVIVEPMEQFDD 181
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 37.0 bits (84), Expect = 0.039, Method: Composition-based stats.
Identities = 16/67 (23%), Positives = 34/67 (50%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSI 435
+F+ GLP ++D+V+ELL ++G + L ++ + K + F + + +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 436 NNAELGE 442
N +LG+
Sbjct: 64 NGMQLGD 70
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 37.0 bits (84), Expect = 0.041, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 31/50 (62%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGK 266
F G + ++LMM+ +T ++KG+ F+ F+ E A++A+ +L + G+
Sbjct: 47 FEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGR 96
Score = 36.6 bits (83), Expect = 0.055, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 34/66 (51%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSI 435
++V L + ED +R + + +G I I+L + + + K +GF+TF + A + +
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 436 NNAELG 441
N EL
Sbjct: 89 NGFELA 94
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 37.0 bits (84), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 35/55 (63%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVT 271
FS+ G + +V ++ + Q+++++GFAF+ F V+ A++A ++G++ V+
Sbjct: 36 FSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS 90
Score = 33.1 bits (74), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 28/63 (44%)
Query: 378 VDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSINN 437
V GL E +RE+ YG I + + + S + + F FV F+ D A + N
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 438 AEL 440
EL
Sbjct: 80 MEL 82
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 36.6 bits (83), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 17/80 (21%), Positives = 34/80 (42%)
Query: 189 QERRKRKEFEVFXXXXXXXXXXXXXXXXFSQVGEVTEVRLMMNPQTKKNKGFAFLRFATV 248
Q++ F VF F+ G++++ R++ + T K+KG+ F+ F
Sbjct: 8 QKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNK 67
Query: 249 EQARQAVTELKNPVINGKQC 268
A A+ + + G+Q
Sbjct: 68 LDAENAIVHMGGQWLGGRQI 87
Score = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTF 422
VFV L + ++ +G+I+ + ++M + K K +GFV+F
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 64
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 36.6 bits (83), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPSQDS 276
FSQ G+V V+L+ + +TKK KGF F+ E +A+ +L N G+ VT +
Sbjct: 22 FSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKLDNTDFMGRTIRVTEANPK 80
Query: 277 DTL 279
+L
Sbjct: 81 KSL 83
Score = 34.7 bits (78), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 34/69 (49%)
Query: 373 VKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCA 432
++ ++V L S ++V+EL +G++ ++L + + K K FGFV + A
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIA 60
Query: 433 KSINNAELG 441
K N +G
Sbjct: 61 KLDNTDFMG 69
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 36.6 bits (83), Expect = 0.055, Method: Composition-based stats.
Identities = 14/50 (28%), Positives = 31/50 (62%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGK 266
F G++T++++ ++ +T+K++GFAF+ F E A A+ + + G+
Sbjct: 84 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGR 133
Score = 36.2 bits (82), Expect = 0.068, Method: Composition-based stats.
Identities = 17/67 (25%), Positives = 34/67 (50%)
Query: 374 KTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAK 433
+ ++V GL D+ + +G+IT I++ + + K + F FV F+ + A
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 434 SINNAEL 440
++N +EL
Sbjct: 124 NMNESEL 130
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 36.6 bits (83), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 43/83 (51%), Gaps = 4/83 (4%)
Query: 279 LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAF 338
LF+G + K T E +++ + +G +++ T++ +G ++G AF++F + ++A A
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFG--TIDECTVLR--GPDGTSKGCAFVKFQTHAEAQAAI 70
Query: 339 KRLQKRDVLFGVDRPAKVSFADS 361
L L G V FAD+
Sbjct: 71 NTLHSSRTLPGASSSLVVKFADT 93
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 36.6 bits (83), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 44/83 (53%), Gaps = 4/83 (4%)
Query: 279 LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAF 338
LF+G + K ++E + + +GV +++ T++ +G ++G AF++FSS ++A A
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGV--IDECTVLR--GPDGSSKGCAFVKFSSHTEAQAAI 73
Query: 339 KRLQKRDVLFGVDRPAKVSFADS 361
L + G V FAD+
Sbjct: 74 HALHGSQTMPGASSSLVVKFADT 96
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 36.2 bits (82), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 34/54 (62%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGV 270
FS+ G + +V ++ + Q+++++GFAF+ F V+ A++A ++G++ V
Sbjct: 36 FSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
Score = 33.1 bits (74), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 28/63 (44%)
Query: 378 VDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSINN 437
V GL E +RE+ YG I + + + S + + F FV F+ D A + N
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 438 AEL 440
EL
Sbjct: 80 MEL 82
>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 = 36.2 bits (82), Expect = 0.077, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 370 MAQVKTV-FVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAA 428
MA K V +V GL D+ + +G+IT I++ + + K + F FV F+ + A
Sbjct: 3 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 62
Query: 429 VTCAKSINNAEL 440
++N +EL
Sbjct: 63 AAAIDNMNESEL 74
Score = 35.8 bits (81), Expect = 0.099, Method: Composition-based stats.
Identities = 14/50 (28%), Positives = 31/50 (62%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGK 266
F G++T++++ ++ +T+K++GFAF+ F E A A+ + + G+
Sbjct: 28 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGR 77
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 36.2 bits (82), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 31/54 (57%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGV 270
F + G V +V + + TK+++GFAF+RF A A+ + V++G++ V
Sbjct: 68 FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 121
Score = 30.0 bits (66), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 19/84 (22%), Positives = 39/84 (46%), Gaps = 1/84 (1%)
Query: 373 VKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCA 432
+ ++ VD L D +R + + YG + + + R+ + + + F FV F A
Sbjct: 47 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106
Query: 433 KSINNAELGEGDNKAKVRARLSRP 456
+++ A L + + ++ AR RP
Sbjct: 107 DAMDGAVLDGRELRVQM-ARYGRP 129
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 36.2 bits (82), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 34/54 (62%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGV 270
FS+ G + +V ++ + Q+++++GFAF+ F V+ A++A ++G++ V
Sbjct: 33 FSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 86
Score = 33.1 bits (74), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 28/63 (44%)
Query: 378 VDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSINN 437
V GL E +RE+ YG I + + + S + + F FV F+ D A + N
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 438 AEL 440
EL
Sbjct: 77 MEL 79
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 35.8 bits (81), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 49/211 (23%), Positives = 87/211 (41%), Gaps = 18/211 (8%)
Query: 236 KNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPSQDSDTLFLGNICKTWTKEALKE 295
K KG AF+ EQA A+ + ++ V L + N+ + T++ +E
Sbjct: 53 KYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEE 112
Query: 296 KLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAFKRLQKRDVL---FGVDR 352
++ +G ++E LV S G ++G+ F E+ + A A K D+L G R
Sbjct: 113 LVRPFG--SLERCFLVY-SERTGQSKGYGFAEYMKKDSAARA-----KSDLLGKPLG-PR 163
Query: 353 PAKVSFADSF-IDPGDEIMAQVKTVFVDGLPASW-DEDRVRELLKNYGEITKIELARNMP 410
V + D+ + P + + + VD LP + D D + L T +LA
Sbjct: 164 TLYVHWTDAGQLTPA---LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ- 219
Query: 411 SAKRKDFGFVTFDTHDAAVTCAKSINNAELG 441
+ K F + ++T + A + + LG
Sbjct: 220 DGQLKGFAVLEYETAEMAEEAQQQADGLSLG 250
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 35.8 bits (81), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 49/211 (23%), Positives = 87/211 (41%), Gaps = 18/211 (8%)
Query: 236 KNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPSQDSDTLFLGNICKTWTKEALKE 295
K KG AF+ EQA A+ + ++ V L + N+ + T++ +E
Sbjct: 55 KYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEE 114
Query: 296 KLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAFKRLQKRDVL---FGVDR 352
++ +G ++E LV S G ++G+ F E+ + A A K D+L G R
Sbjct: 115 LVRPFG--SLERCFLVY-SERTGQSKGYGFAEYMKKDSAARA-----KSDLLGKPLG-PR 165
Query: 353 PAKVSFADSF-IDPGDEIMAQVKTVFVDGLPASW-DEDRVRELLKNYGEITKIELARNMP 410
V + D+ + P + + + VD LP + D D + L T +LA
Sbjct: 166 TLYVHWTDAGQLTPA---LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ- 221
Query: 411 SAKRKDFGFVTFDTHDAAVTCAKSINNAELG 441
+ K F + ++T + A + + LG
Sbjct: 222 DGQLKGFAVLEYETAEMAEEAQQQADGLSLG 252
>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 = 35.8 bits (81), Expect = 0.10, Method: Composition-based stats.
Identities = 14/50 (28%), Positives = 31/50 (62%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGK 266
F G++T++++ ++ +T+K++GFAF+ F E A A+ + + G+
Sbjct: 23 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGR 72
Score = 35.4 bits (80), Expect = 0.12, Method: Composition-based stats.
Identities = 17/67 (25%), Positives = 34/67 (50%)
Query: 374 KTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAK 433
+ ++V GL D+ + +G+IT I++ + + K + F FV F+ + A
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 434 SINNAEL 440
++N +EL
Sbjct: 63 NMNESEL 69
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 34/54 (62%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGV 270
FS+ G + +V ++ + Q+++++GFAF+ F V+ A++A ++G++ V
Sbjct: 67 FSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 120
Score = 33.5 bits (75), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 28/63 (44%)
Query: 378 VDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSINN 437
V GL E +RE+ YG I + + + S + + F FV F+ D A + N
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 438 AEL 440
EL
Sbjct: 111 MEL 113
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 14/50 (28%), Positives = 31/50 (62%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGK 266
F G++T++++ ++ +T+K++GFAF+ F E A A+ + + G+
Sbjct: 26 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGR 75
Score = 35.4 bits (80), Expect = 0.13, Method: Composition-based stats.
Identities = 17/67 (25%), Positives = 34/67 (50%)
Query: 374 KTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAK 433
+ ++V GL D+ + +G+IT I++ + + K + F FV F+ + A
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 434 SINNAEL 440
++N +EL
Sbjct: 66 NMNESEL 72
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 36/56 (64%), Gaps = 3/56 (5%)
Query: 224 TEVRLMMNPQTKKNKGFAFLRFATVEQAR--QAVTELKNPV-INGKQCGVTPSQDS 276
+ VR++ + QT+ N+GFAF++ +T+E A+ Q + L P+ I+GK V ++ S
Sbjct: 53 SNVRVIKDKQTQLNRGFAFIQLSTIEAAQLLQILQALHPPLTIDGKTINVEFAKGS 108
Score = 33.1 bits (74), Expect = 0.54, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 37/64 (57%), Gaps = 3/64 (4%)
Query: 269 GVTPSQDS--DTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFL 326
G PS ++ DT+ L N+ T +++ L Y V + ++ +++D + +NRGFAF+
Sbjct: 14 GSEPSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQ-LNRGFAFI 72
Query: 327 EFSS 330
+ S+
Sbjct: 73 QLST 76
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 49/211 (23%), Positives = 87/211 (41%), Gaps = 18/211 (8%)
Query: 236 KNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPSQDSDTLFLGNICKTWTKEALKE 295
K KG AF+ EQA A+ + ++ V L + N+ + T++ +E
Sbjct: 55 KYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEE 114
Query: 296 KLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAFKRLQKRDVL---FGVDR 352
++ +G ++E LV S G ++G+ F E+ + A A K D+L G R
Sbjct: 115 LVRPFG--SLERCFLVY-SERTGQSKGYGFAEYMKKDSAARA-----KSDLLGKPLG-PR 165
Query: 353 PAKVSFADSF-IDPGDEIMAQVKTVFVDGLPASW-DEDRVRELLKNYGEITKIELARNMP 410
V + D+ + P + + + VD LP + D D + L T +LA
Sbjct: 166 TLYVHWTDAGQLTPA---LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ- 221
Query: 411 SAKRKDFGFVTFDTHDAAVTCAKSINNAELG 441
+ K F + ++T + A + + LG
Sbjct: 222 DGQLKGFAVLEYETAEMAEEAQQQADGLSLG 252
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic
Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 35.4 bits (80), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/80 (21%), Positives = 34/80 (42%)
Query: 189 QERRKRKEFEVFXXXXXXXXXXXXXXXXFSQVGEVTEVRLMMNPQTKKNKGFAFLRFATV 248
Q++ F VF F+ G +++ R++ + T K+KG+ F+ F
Sbjct: 8 QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNK 67
Query: 249 EQARQAVTELKNPVINGKQC 268
A A+ ++ + G+Q
Sbjct: 68 WDAENAIQQMGGQWLGGRQI 87
Score = 30.4 bits (67), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 29/66 (43%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSI 435
VFV L + ++ +G I+ + ++M + K K +GFV+F A + +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 436 NNAELG 441
LG
Sbjct: 78 GGQWLG 83
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 35.0 bits (79), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSI 435
+F+ GL +E ++ + +G I+++ L ++ S K + F F+TF+ A AK +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS-KSRGFAFITFENPADAKNAAKDM 68
Query: 436 NNAEL 440
N L
Sbjct: 69 NGKSL 73
Score = 34.7 bits (78), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGV 270
F + G ++EV L++ +T K++GFAF+ F A+ A ++ ++GK V
Sbjct: 28 FGKHGPISEV-LLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKV 80
Score = 33.9 bits (76), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 39/68 (57%), Gaps = 4/68 (5%)
Query: 279 LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAF 338
LF+G + + ++ LK +G + ++ L++D ++ +RGFAF+ F + +DA +A
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGP--ISEVLLIKDRTSK--SRGFAFITFENPADAKNAA 65
Query: 339 KRLQKRDV 346
K + + +
Sbjct: 66 KDMNGKSL 73
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 35.0 bits (79), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 28/54 (51%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGV 270
F + G V +V + P TK +GFAF+RF A+ A + ++G++ V
Sbjct: 34 FEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRV 87
Score = 30.4 bits (67), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 278 TLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDA 337
TL + N+ + ++L+ + YG V D+ + + + + RGFAF+ F R DA DA
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYG--RVGDVYIPREPHTKA-PRGFAFVRFHDRRDAQDA 71
Score = 30.0 bits (66), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 29/66 (43%)
Query: 375 TVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKS 434
T+ VD L D +R + + YG + + + R + + F FV F A +
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 435 INNAEL 440
++ AEL
Sbjct: 75 MDGAEL 80
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 35.0 bits (79), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 31/54 (57%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGV 270
F + G V +V + + TK+++GFAF+RF A A+ + V++G++ V
Sbjct: 91 FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 144
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 35.0 bits (79), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 27/51 (52%)
Query: 372 QVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTF 422
++ +FV GL S ++ +R YGE+ + ++ + + + FGFV F
Sbjct: 15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
Score = 32.7 bits (73), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 11/66 (16%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRF------ATVEQARQAVTELKNPVINGKQC-- 268
FSQ GEV + +M + T +++GF F++F TV +R + +N I+ K C
Sbjct: 37 FSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRN--IDPKPCTP 94
Query: 269 -GVTPS 273
G+ PS
Sbjct: 95 RGMQPS 100
>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 = 35.0 bits (79), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGK 266
FS+ GEV + L ++P T +++GF F+ F E + V + K +NGK
Sbjct: 20 FSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDK-VMDQKEHKLNGK 68
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 35.0 bits (79), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRF 245
F Q GEV E +M +P TK+++GF F+ F
Sbjct: 46 FGQFGEVKECLVMRDPLTKRSRGFGFVTF 74
Score = 34.7 bits (78), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 27/47 (57%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTF 422
+F+ GL ++ +RE +GE+ + + R+ + + + FGFVTF
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 34.7 bits (78), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 8/80 (10%)
Query: 278 TLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDA 337
TLF+ + T+ L+ + + YG ++ + +V S G RG+AF+E+ D A
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGP--IKRIHMVY-SKRSGKPRGYAFIEYEHERDMHSA 160
Query: 338 F-----KRLQKRDVLFGVDR 352
+ K++ R VL V+R
Sbjct: 161 YKHADGKKIDGRRVLVDVER 180
Score = 29.3 bits (64), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 7/71 (9%)
Query: 364 DPGDEIMAQ---VKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFV 420
DP ++ AQ KT+FV + E ++R + YG I +I + + S K + + F+
Sbjct: 90 DPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFI 149
Query: 421 TF----DTHDA 427
+ D H A
Sbjct: 150 EYEHERDMHSA 160
>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex
pdb|3P5T|M Chain M, Cfim25-Cfim68 Complex
pdb|3P5T|N Chain N, Cfim25-Cfim68 Complex
pdb|3P5T|O Chain O, Cfim25-Cfim68 Complex
pdb|3P5T|P Chain P, Cfim25-Cfim68 Complex
pdb|3P5T|Q Chain Q, Cfim25-Cfim68 Complex
pdb|3P6Y|C Chain C, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|D Chain D, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|G Chain G, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|H Chain H, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|K Chain K, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|L Chain L, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|O Chain O, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|P Chain P, Cf Im25-Cf Im68-Uguaa Complex
Length = 90
Score = 34.3 bits (77), Expect = 0.24, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 279 LFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAF 338
L++GN+ T E L E + GV+++ ++ E+ N G ++GFA + S + +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRAN-GQSKGFALVGVGSEASSKKLM 62
Query: 339 KRLQKRDV 346
L KR++
Sbjct: 63 DLLPKREL 70
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 34.3 bits (77), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRF 245
F Q GEV E +M +P TK+++GF F+ F
Sbjct: 21 FGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
Score = 33.5 bits (75), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 27/47 (57%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTF 422
+F+ GL ++ +RE +GE+ + + R+ + + + FGFVTF
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 34.3 bits (77), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 26/39 (66%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAV 255
Q G++ VR++++P T+ +KG AF +F T E A++ +
Sbjct: 36 LQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
Score = 33.5 bits (75), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 30/58 (51%)
Query: 374 KTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTC 431
KTVF+ L +E+ + E+L+ +G++ + + + + K F F T +AA C
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKC 73
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 33.9 bits (76), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 375 TVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTF 422
TVFV G+ DE +R YG + ++++ + K +GFV+F
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVS-KGYGFVSF 58
>pdb|3S8S|A Chain A, Crystal Structure Of The Rrm Domain Of Human Setd1a
Length = 110
Score = 33.9 bits (76), Expect = 0.38, Method: Composition-based stats.
Identities = 14/40 (35%), Positives = 26/40 (65%)
Query: 219 QVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTEL 258
+ GEV EV ++++P+T+K+ G A + F + A++ V L
Sbjct: 29 KYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNL 68
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 33.9 bits (76), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 375 TVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTF 422
TVFV G+ DE +R YG + ++++ + K +GFV+F
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVS-KGYGFVSF 57
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 33.5 bits (75), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 8/80 (10%)
Query: 278 TLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDA 337
TLF+ + T+ L+ + + YG ++ + +V S G RG+AF+E+ D A
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYG--PIKRIHMVY-SKRSGKPRGYAFIEYEHERDMHSA 160
Query: 338 F-----KRLQKRDVLFGVDR 352
+ K++ R VL V+R
Sbjct: 161 YKHADGKKIDGRRVLVDVER 180
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 33.5 bits (75), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 35/77 (45%)
Query: 364 DPGDEIMAQVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFD 423
+PG + + +FV G+ E+ + + YGEI I L + + K + V ++
Sbjct: 14 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 73
Query: 424 THDAAVTCAKSINNAEL 440
T+ A + +N +L
Sbjct: 74 TYKEAQAAMEGLNGQDL 90
Score = 30.0 bits (66), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 29/54 (53%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGV 270
F++ GE+ + L ++ +T KG+ + + T ++A+ A+ L + G+ V
Sbjct: 44 FAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 97
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 33.5 bits (75), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 375 TVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTF 422
TVFV G+ DE +R YG + ++++ + + K +GFV+F
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 33.5 bits (75), Expect = 0.47, Method: Composition-based stats.
Identities = 14/51 (27%), Positives = 28/51 (54%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHD 426
+FV GL + + V+ + +G++ L + + + + FGFVTF++ D
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52
Score = 32.7 bits (73), Expect = 0.76, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGK 266
F Q G+V + LM + T +++GF F+ F + E + V E+ IN K
Sbjct: 20 FEQFGKVDDAMLMFDKTTNRHRGFGFVTFES-EDIVEKVCEIHFHEINNK 68
>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 = 33.5 bits (75), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 361 SFIDPGDEIMAQVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFV 420
S+ PG E + ++V LP + +D++ + YG I + + R+ + + + FV
Sbjct: 2 SYARPGGESIKDTN-LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFV 60
Query: 421 TFDTHDAAVTCAKSINNA 438
++ + A ++NN
Sbjct: 61 RYNKREEAQEAISALNNV 78
Score = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 29/49 (59%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVING 265
F + G + + ++ + T + +G AF+R+ E+A++A++ L N + G
Sbjct: 34 FGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEG 82
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 33.1 bits (74), Expect = 0.58, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 35/65 (53%), Gaps = 2/65 (3%)
Query: 374 KTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAK 433
+TVFV L A E+ + EL G +TK+ + ++ K K FGFV F H +V+ A
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCF-KHPESVSYAI 74
Query: 434 SINNA 438
++ N
Sbjct: 75 ALLNG 79
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 33.1 bits (74), Expect = 0.63, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 6/49 (12%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVING 265
FS G++ E+R+ KG++F+RF+T E A A+ + I G
Sbjct: 46 FSPFGQIMEIRVF------PEKGYSFVRFSTHESAAHAIVSVNGTTIEG 88
Score = 30.4 bits (67), Expect = 3.5, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 6/66 (9%)
Query: 375 TVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKS 434
TV+ G+ + + +R+ +G+I +I R P K + FV F TH++A S
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEI---RVFP---EKGYSFVRFSTHESAAHAIVS 80
Query: 435 INNAEL 440
+N +
Sbjct: 81 VNGTTI 86
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 33.1 bits (74), Expect = 0.63, Method: Composition-based stats.
Identities = 25/98 (25%), Positives = 45/98 (45%), Gaps = 4/98 (4%)
Query: 264 NGKQCGVTPSQDSDTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGF 323
+G V Q + + + NI + ++E +G ++ + L + G +RGF
Sbjct: 3 SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFG--ELKTVRLPKKMTGTGAHRGF 60
Query: 324 AFLEFSSRSDAMDAFKRLQKRDVLFGVDRPAKVSFADS 361
F++F ++ DA AF L L+G R + +ADS
Sbjct: 61 GFVDFITKQDAKKAFNALCHSTHLYG--RRLVLEWADS 96
Score = 32.7 bits (73), Expect = 0.78, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMP-SAKRKDFGFVTFDTHDAA 428
+ V +P ++ +REL +GE+ + L + M + + FGFV F T A
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 71
>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 = 33.1 bits (74), Expect = 0.65, Method: Composition-based stats.
Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 4/85 (4%)
Query: 372 QVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTC 431
Q + V+ LP + +D +R L + GE+ +L R+ + +GFV + T A
Sbjct: 18 QGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 77
Query: 432 AKSINNAELGEGDNKAKVRARLSRP 456
++N L ++ +RP
Sbjct: 78 INTLNGLRL----QSKTIKVSYARP 98
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 33.1 bits (74), Expect = 0.66, Method: Composition-based stats.
Identities = 17/75 (22%), Positives = 38/75 (50%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSI 435
+F+ LP + + + +G + ++ + ++ K FGFV+FD D+A K++
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 436 NNAELGEGDNKAKVR 450
N ++G K +++
Sbjct: 103 NGFQVGTKRLKVQLK 117
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 33.1 bits (74), Expect = 0.67, Method: Composition-based stats.
Identities = 28/107 (26%), Positives = 53/107 (49%), Gaps = 5/107 (4%)
Query: 235 KKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPSQDSDTLFLGNICKTWTKEALK 294
KKN FA + FA + A A+T+ V G+ + TL++ N ++T+ ++
Sbjct: 41 KKNFRFARIEFARYDGALAAITKTHKVV--GQNEIIVSHLTECTLWMTNFPPSYTQRNIR 98
Query: 295 EKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAFKRL 341
+ L+ NV L++ S +R FA+++ +S+ DA ++L
Sbjct: 99 DLLQDI---NVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 142
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 33.1 bits (74), Expect = 0.67, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 4/76 (5%)
Query: 273 SQDSDTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEG--MNRGFAFLEFSS 330
S S LF+ N+ + T+E LK G ++ T+ + N G ++ GF F+E+
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGA--IKSCTISKKKNKAGVLLSMGFGFVEYKK 59
Query: 331 RSDAMDAFKRLQKRDV 346
A A K+LQ V
Sbjct: 60 PEQAQKALKQLQGHTV 75
Score = 29.3 bits (64), Expect = 8.3, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 11/65 (16%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNK-------GFAFLRFATVEQARQAVTELKNPVINGKQCG 269
FS+VG + + KKNK GF F+ + EQA++A+ +L+ ++G +
Sbjct: 26 FSKVGAIKSCTI----SKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLE 81
Query: 270 VTPSQ 274
V S+
Sbjct: 82 VRISE 86
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 32.7 bits (73), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 28/53 (52%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAA 428
+FV GLP + +R+ + +G+I + + + + K + +GFVT AA
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Score = 32.7 bits (73), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGV 270
F G++ E ++ + QT K++G+ F+ A A +A + NP+I+G++ V
Sbjct: 38 FEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD-PNPIIDGRKANV 90
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 26/39 (66%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAV 255
FS VG+V +VR++ + ++++KG A++ F ++ A+
Sbjct: 46 FSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 84
>pdb|1S79|A Chain A, Solution Structure Of The Central Rrm Of Human La Protein
Length = 103
Score = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 374 KTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAA 428
++V++ G P D ++E L++ G++ I++ R + A + FV FD+ ++A
Sbjct: 12 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSI-FVVFDSIESA 65
>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 = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 4/81 (4%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSI 435
+ V+ LP + +D +R L + GE+ +L R+ + +GFV + T A ++
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 436 NNAELGEGDNKAKVRARLSRP 456
N L ++ +RP
Sbjct: 67 NGLRL----QSKTIKVSYARP 83
>pdb|2VOD|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VOD|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VON|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VON|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VOO|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOO|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOP|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auuuu
Length = 193
Score = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 374 KTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAA 428
++V++ G P D ++E L++ G++ I++ R + A + FV FD+ ++A
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSI-FVVFDSIESA 163
>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 = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 367 DEIMAQVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHD 426
++ Q +FV LP E+ +R+L + YG+ ++ + ++ K FGF+ +T
Sbjct: 9 EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRT 62
Query: 427 AAVTCAKSINNAEL 440
A ++N L
Sbjct: 63 LAEIAKVELDNMPL 76
Score = 30.4 bits (67), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 30/63 (47%), Gaps = 6/63 (9%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPSQDS 276
F + G+ EV + K+KGF F+R T A A EL N + GKQ V + S
Sbjct: 36 FEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS 89
Query: 277 DTL 279
+L
Sbjct: 90 ASL 92
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 273 SQDSDTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRS 332
SQ S TLF+ + + T+E LKE D +V D G ++GF F++F+S
Sbjct: 12 SQPSKTLFVKGLSEDTTEETLKESF-----DGSVRARIVTDRET-GSSKGFGFVDFNSEE 65
Query: 333 DAMDAFKRLQKRDV 346
DA A + ++ ++
Sbjct: 66 DAKAAKEAMEDGEI 79
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 27/54 (50%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGV 270
FS+VG V RL+ + +T K KG+ F + E A A+ L +G+ V
Sbjct: 29 FSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRV 82
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 31.6 bits (70), Expect = 1.5, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 27/61 (44%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSI 435
++V GLP + + + +L YG I + + + + GF+ FD A K +
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 436 N 436
N
Sbjct: 64 N 64
Score = 29.3 bits (64), Expect = 7.9, Method: Composition-based stats.
Identities = 13/42 (30%), Positives = 24/42 (57%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTEL 258
FSQ G + R++++ T ++G F+RF +A +A+ L
Sbjct: 22 FSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 31.6 bits (70), Expect = 1.7, Method: Composition-based stats.
Identities = 18/77 (23%), Positives = 35/77 (45%)
Query: 364 DPGDEIMAQVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFD 423
+PG + + +FV G+ E+ + + YGEI I L + + K + V ++
Sbjct: 13 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 72
Query: 424 THDAAVTCAKSINNAEL 440
T+ A + +N +L
Sbjct: 73 TYKEAQAAMEGLNGQDL 89
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 31.6 bits (70), Expect = 1.7, Method: Composition-based stats.
Identities = 28/126 (22%), Positives = 56/126 (44%), Gaps = 17/126 (13%)
Query: 229 MMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVTPSQDSD--------TLF 280
+++ +T N+ F ++ F + E +A+ EL + G + + + D TL
Sbjct: 45 VVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKVRAARTLL 103
Query: 281 LGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDAFKR 340
N+ T++ LKE ED + + +G ++G A++EF S +DA +
Sbjct: 104 AKNLSFNITEDELKEVF--------EDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEE 155
Query: 341 LQKRDV 346
Q ++
Sbjct: 156 KQGAEI 161
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 31.6 bits (70), Expect = 1.9, Method: Composition-based stats.
Identities = 18/76 (23%), Positives = 34/76 (44%)
Query: 365 PGDEIMAQVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDT 424
PG + + +FV G+ E+ + + YGEI I L + + K + V ++T
Sbjct: 1 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 60
Query: 425 HDAAVTCAKSINNAEL 440
+ A + +N +L
Sbjct: 61 YKEAQAAMEGLNGQDL 76
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 30/132 (22%), Positives = 58/132 (43%), Gaps = 23/132 (17%)
Query: 223 VTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGV--------TPSQ 274
V +VR+ M + F ++ F + E +A+ EL + G + + +
Sbjct: 39 VVDVRIGMTRK------FGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGKDSKKER 91
Query: 275 DSDTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDA 334
D+ TL N+ T++ LKE ED + + +G ++G A++EF + +DA
Sbjct: 92 DARTLLAKNLPYKVTQDELKEVF--------EDAAEIRLVSKDGKSKGIAYIEFKTEADA 143
Query: 335 MDAFKRLQKRDV 346
F+ Q ++
Sbjct: 144 EKTFEEKQGTEI 155
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/48 (25%), Positives = 26/48 (54%)
Query: 221 GEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQC 268
G +++ R++ + T K+KG+ F+ F A A+ ++ + G+Q
Sbjct: 31 GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 30.8 bits (68), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGV 270
F Q G++ +V ++ N + +KGF F+ F A +A +L V+ G++ V
Sbjct: 36 FGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV 87
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 30.8 bits (68), Expect = 2.9, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 376 VFVDGL-PASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAA 428
+++ GL P + D+D V+ L + YG+I + + + K K +GFV FD+ AA
Sbjct: 8 LYIRGLQPGTTDQDLVK-LCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Score = 30.0 bits (66), Expect = 4.9, Method: Composition-based stats.
Identities = 13/39 (33%), Positives = 24/39 (61%)
Query: 221 GEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELK 259
G++ + +++ T K KG+ F+ F + A++AVT LK
Sbjct: 30 GKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALK 68
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
Length = 109
Score = 30.8 bits (68), Expect = 3.0, Method: Composition-based stats.
Identities = 16/65 (24%), Positives = 30/65 (46%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSI 435
+FV G+ E+ + + YGEI I L + + K + V ++T+ A + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 436 NNAEL 440
N +L
Sbjct: 70 NGQDL 74
>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 = 30.8 bits (68), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 27/42 (64%), Gaps = 3/42 (7%)
Query: 318 GMNRGFAFLEFSSRSDAMDAFKRLQKRDVLFGVDRPAKVSFA 359
G +RG+ F+ F+S+ DA +A +Q +D+ RP ++++A
Sbjct: 40 GSSRGYGFVSFTSQDDAQNAMDSMQGQDL---NGRPLRINWA 78
Score = 30.0 bits (66), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 31/66 (46%)
Query: 375 TVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKS 434
+FV L + D++ +R K++ + +M + + +GFV+F + D A S
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 435 INNAEL 440
+ +L
Sbjct: 63 MQGQDL 68
>pdb|1ZH5|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1ZH5|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 195
Score = 30.8 bits (68), Expect = 3.3, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 374 KTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAA 428
++V++ G P D ++E L++ G++ I+ R + A + FV FD+ ++A
Sbjct: 112 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQXRRTLHKAFKGSI-FVVFDSIESA 165
>pdb|1YTY|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1YTY|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 194
Score = 30.8 bits (68), Expect = 3.3, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 374 KTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAA 428
++V++ G P D ++E L++ G++ I+ R + A + FV FD+ ++A
Sbjct: 111 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQXRRTLHKAFKGSI-FVVFDSIESA 164
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 30.4 bits (67), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVTELKNPVINGKQCGVT 271
F Q G++ +V ++ N + +KGF F+ F A +A +L V+ G++ V
Sbjct: 50 FGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN 102
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 30.4 bits (67), Expect = 4.0, Method: Composition-based stats.
Identities = 16/65 (24%), Positives = 30/65 (46%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSI 435
+FV G+ E+ + + YGEI I L + + K + V ++T+ A + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 436 NNAEL 440
N +L
Sbjct: 70 NGQDL 74
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 30.4 bits (67), Expect = 4.2, Method: Composition-based stats.
Identities = 12/30 (40%), Positives = 21/30 (70%)
Query: 222 EVTEVRLMMNPQTKKNKGFAFLRFATVEQA 251
+ EVRLM N + +++GFAF+ F+ ++ A
Sbjct: 28 QAREVRLMRNKSSGQSRGFAFVEFSHLQDA 57
Score = 30.0 bits (66), Expect = 4.6, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 276 SDTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDA 334
S+ + L + + T++ ++ +L+ +GV E + S+ G +RGFAF+EFS DA
Sbjct: 1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSS--GQSRGFAFVEFSHLQDA 57
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 30.0 bits (66), Expect = 4.9, Method: Composition-based stats.
Identities = 18/87 (20%), Positives = 38/87 (43%), Gaps = 4/87 (4%)
Query: 370 MAQVKTVFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAV 429
M + V+ LP + +D + L + G+I +L R+ + + +GFV + + A
Sbjct: 1 MDSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 430 TCAKSINNAELGEGDNKAKVRARLSRP 456
++N +L ++ +RP
Sbjct: 61 KAINTLNGLKL----QTKTIKVSYARP 83
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 30.0 bits (66), Expect = 5.2, Method: Composition-based stats.
Identities = 16/65 (24%), Positives = 30/65 (46%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSI 435
+FV G+ E+ + + YGEI I L + + K + V ++T+ A + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 436 NNAEL 440
N +L
Sbjct: 70 NGQDL 74
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 30.0 bits (66), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 223 VTEVRLMMNPQTKKNKGFAFLRFATVEQARQAVT 256
+ VRL+ + T K KGF ++ F V+ ++A+T
Sbjct: 41 IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 74
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 30.0 bits (66), Expect = 5.8, Method: Composition-based stats.
Identities = 15/65 (23%), Positives = 33/65 (50%), Gaps = 8/65 (12%)
Query: 376 VFVDGLPASWDEDRVRELLKNYGEITKIELARNMPSAKRKDFGFVTFDTHDAAVTCAKSI 435
+F+ LP E +R L + YG++ + ++ +N +GFV + AA +++
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRNL 62
Query: 436 NNAEL 440
++ +L
Sbjct: 63 HHYKL 67
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 30.0 bits (66), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 12/82 (14%)
Query: 278 TLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAMDA 337
L++ N+ + ++E ++++ + VE + + D +AF+ FS+R DA++A
Sbjct: 17 ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD---------YAFVHFSNREDAVEA 67
Query: 338 FKRLQKRDVLFGVDRPAKVSFA 359
K L + VL G P +V+ A
Sbjct: 68 MKALNGK-VLDG--SPIEVTLA 86
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 29.6 bits (65), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 217 FSQVGEVTEVRLMMNPQTKKNKGFAFLRFATVEQARQAV 255
F G ++ + L + T ++KGFAF+ F E A +A+
Sbjct: 36 FRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 29.3 bits (64), Expect = 7.8, Method: Composition-based stats.
Identities = 13/43 (30%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 217 FSQVGEVTEV-RLMMNPQTKKNKGFAFLRFATVEQARQAVTEL 258
FS G + + ++M +P T +KG+AF+ FA+ + + A+ +
Sbjct: 26 FSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAM 68
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 29.3 bits (64), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 11/66 (16%)
Query: 276 SDTLFLGNICKTWTKEALKEKLKHYGVDNVEDLTLVEDSNNEGMNRGFAFLEFSSRSDAM 335
S L +GNI T T + L+ K + YG V + +V+D +AF+ DA+
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYG--PVIECDIVKD---------YAFVHMERAEDAV 58
Query: 336 DAFKRL 341
+A + L
Sbjct: 59 EAIRGL 64
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.314 0.134 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,155,595
Number of Sequences: 62578
Number of extensions: 647086
Number of successful extensions: 1442
Number of sequences better than 100.0: 145
Number of HSP's better than 100.0 without gapping: 104
Number of HSP's successfully gapped in prelim test: 41
Number of HSP's that attempted gapping in prelim test: 1161
Number of HSP's gapped (non-prelim): 303
length of query: 777
length of database: 14,973,337
effective HSP length: 106
effective length of query: 671
effective length of database: 8,340,069
effective search space: 5596186299
effective search space used: 5596186299
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 bits)