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= 005712
(681 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 = 59.7 bits (143), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 51/180 (28%), Positives = 86/180 (47%), Gaps = 25/180 (13%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTN--RNKGYAFVKF---------A 200
++F+G + R +++D+R++FE+ G V E+ + ++ S N ++KG FV F
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 201 NKEHAKRALTEMKNPVICGKRCGTAPSEDNDT-----LFVGNICNTWTKEAIKQKLKDYG 255
N H + L M +P+ + A SE N+ LF+G I T+ I+ +G
Sbjct: 77 NALHNMKVLPGMHHPI----QMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFG 132
Query: 256 VEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMAAYKRLQKPDVVFGHPERTVKVAFAE 315
+E ++ +GLSRG AFV F+ A A K + + + G V V FA+
Sbjct: 133 --QIEECRILRG--PDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV-VKFAD 187
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 45/180 (25%), Positives = 76/180 (42%), Gaps = 17/180 (9%)
Query: 226 PSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSD-IQHEGLSRGFAFVMFSC 284
P D +FVG + TW+++ +++ + YG V IN++ D Q+ S+G FV F
Sbjct: 11 PDLDAIKMFVGQVPRTWSEKDLRELFEQYG--AVYEINVLRDRSQNPPQSKGCCFVTFYT 68
Query: 285 HVDAMAAYKRLQKPDVVFG--HPERTVKVAFAEPLREPDPEIMAHV--KTVFLDGVPPHW 340
A+ A L V+ G HP + ++ D E V + +F+ +
Sbjct: 69 RKAALEAQNALHNMKVLPGMHHPIQ---------MKPADSEKNNAVEDRKLFIGMISKKC 119
Query: 341 KENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNS 400
EN IR +G + + R R F+ F+T A I A++ + +G S
Sbjct: 120 TENDIRVMFSSFGQIEECRILRGPDGLSR-GCAFVTFTTRAMAQTAIKAMHQAQTMEGCS 178
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 7/76 (9%)
Query: 137 ELNAIAKDRKIKKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAF 196
E N +DRK+ FIG + + T+ D+R +F G++ E R+ + ++G AF
Sbjct: 100 EKNNAVEDRKL------FIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAF 152
Query: 197 VKFANKEHAKRALTEM 212
V F + A+ A+ M
Sbjct: 153 VTFTTRAMAQTAIKAM 168
Score = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 3/84 (3%)
Query: 317 LREPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDV--IRIVLARNMSTAKRKDYGF 374
L PD + +K +F+ VP W E +R+ + YG V I ++ R+ + + K F
Sbjct: 5 LDHPDQPDLDAIK-MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCF 63
Query: 375 IDFSTHEAAVACINAINNKEFSDG 398
+ F T +AA+ NA++N + G
Sbjct: 64 VTFYTRKAALEAQNALHNMKVLPG 87
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 59.3 bits (142), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 51/180 (28%), Positives = 86/180 (47%), Gaps = 25/180 (13%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTN--RNKGYAFVKF---------A 200
++F+G + R +++D+R++FE+ G V E+ + ++ S N ++KG FV F
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 201 NKEHAKRALTEMKNPVICGKRCGTAPSEDNDT-----LFVGNICNTWTKEAIKQKLKDYG 255
N H + L M +P+ + A SE N+ LF+G I T+ I+ +G
Sbjct: 65 NALHNMKVLPGMHHPI----QMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFG 120
Query: 256 VEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMAAYKRLQKPDVVFGHPERTVKVAFAE 315
+E ++ +GLSRG AFV F+ A A K + + + G V V FA+
Sbjct: 121 --QIEECRILRG--PDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV-VKFAD 175
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 7/76 (9%)
Query: 137 ELNAIAKDRKIKKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAF 196
E N +DRK+ FIG + + T+ D+R +F G++ E R+ + ++G AF
Sbjct: 88 EKNNAVEDRKL------FIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAF 140
Query: 197 VKFANKEHAKRALTEM 212
V F + A+ A+ M
Sbjct: 141 VTFTTRAMAQTAIKAM 156
Score = 38.1 bits (87), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 331 VFLDGVPPHWKENQIRDQIKGYGDV--IRIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 388
+F+ VP W E +R+ + YG V I ++ R+ + + K F+ F T +AA+ N
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 389 AINNKEFSDG 398
A++N + G
Sbjct: 66 ALHNMKVLPG 75
>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 = 57.0 bits (136), Expect = 4e-08, Method: Composition-based stats.
Identities = 44/155 (28%), Positives = 77/155 (49%), Gaps = 13/155 (8%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALT-- 210
+ + L ++ TQE+ R +F IGE+ +L ++ T ++ GY FV + + + A++A+
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 211 -----EMKNPVICGKRCGTAPSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLV 265
+ K + R +A D + L+V + T T++ ++Q YG I LV
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIRDAN-LYVSGLPKTMTQKELEQLFSQYGRIITSRI-LV 122
Query: 266 SDIQHEGLSRGFAFVMFSCHVDAMAAYKRL--QKP 298
+ G+SRG F+ F ++A A K L QKP
Sbjct: 123 DQVT--GVSRGVGFIRFDKRIEAEEAIKGLNGQKP 155
Score = 37.0 bits (84), Expect = 0.040, Method: Composition-based stats.
Identities = 14/61 (22%), Positives = 36/61 (59%)
Query: 149 KEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRA 208
++ +++ GL + TQ+++ ++F + G +I R+ + T ++G F++F + A+ A
Sbjct: 87 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 146
Query: 209 L 209
+
Sbjct: 147 I 147
Score = 35.0 bits (79), Expect = 0.13, Method: Composition-based stats.
Identities = 38/177 (21%), Positives = 71/177 (40%), Gaps = 20/177 (11%)
Query: 233 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMAAY 292
L V + T+E + G +E+ LV D + G S G+ FV + DA A
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIG--EIESCKLVRD-KITGQSLGYGFVNYIDPKDAEKAI 61
Query: 293 KRLQKPDVVFGHPERTVKVAFAEP----LREPDPEIMAHVKTVFLDGVPPHWKENQIRDQ 348
L + +T+KV++A P +R+ + +++ G+P + ++
Sbjct: 62 NTLNGLRL----QTKTIKVSYARPSSASIRDAN---------LYVSGLPKTMTQKELEQL 108
Query: 349 IKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNSKVKLR 405
YG +I + + T + GFI F A I +N ++ S + ++
Sbjct: 109 FSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK 165
>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 = 57.0 bits (136), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 46/152 (30%), Positives = 76/152 (50%), Gaps = 16/152 (10%)
Query: 154 FIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTN--RNKGYAFVKFANKEHAKRALTE 211
F+G + R +++D+R++FE+ G V E+ + ++ S N ++KG FV F ++ A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 212 MKN-PVICGK----RCGTAPSEDNDT-----LFVGNICNTWTKEAIKQKLKDYGVEGVEN 261
+ N V+ G + A SE N+ LF+G I T+ I+ +G +E
Sbjct: 67 LHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFG--QIEE 124
Query: 262 INLVSDIQHEGLSRGFAFVMFSCHVDAMAAYK 293
++ +GLSRG AFV F+ A A K
Sbjct: 125 CRILRG--PDGLSRGCAFVTFTTRAXAQTAIK 154
Score = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 7/73 (9%)
Query: 137 ELNAIAKDRKIKKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAF 196
E N +DRK+ FIG + + T+ D+R F G++ E R+ + ++G AF
Sbjct: 88 EKNNAVEDRKL------FIGXISKKCTENDIRVXFSSFGQIEECRILRG-PDGLSRGCAF 140
Query: 197 VKFANKEHAKRAL 209
V F + A+ A+
Sbjct: 141 VTFTTRAXAQTAI 153
Score = 38.1 bits (87), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 2/69 (2%)
Query: 332 FLDGVPPHWKENQIRDQIKGYGDV--IRIVLARNMSTAKRKDYGFIDFSTHEAAVACINA 389
F+ VP W E +R+ + YG V I ++ R+ + + K F+ F T +AA+ NA
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 390 INNKEFSDG 398
++N + G
Sbjct: 67 LHNXKVLPG 75
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 56.6 bits (135), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 39/142 (27%), Positives = 68/142 (47%), Gaps = 10/142 (7%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+F+G L D T+ED +++FER GE EV + NR++G+ F++ ++ A+ A E+
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAEL 78
Query: 213 KNPVICGKRCGTAPSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEG 272
++ + + L V N+ + E ++Q +G VE +V D G
Sbjct: 79 DGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFG--PVEKAVVVVD--DRG 134
Query: 273 LSRGFAFVMFSCHVDAMAAYKR 294
+ G FV F+ A A +R
Sbjct: 135 RATGKGFVEFAAKPPARKALER 156
>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 = 56.2 bits (134), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 49/168 (29%), Positives = 81/168 (48%), Gaps = 24/168 (14%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALT- 210
++FIGGL + T E +R FE+ G + + + ++ +T R++G+ FV +A E A+
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 211 ---EMKNPVICGKRCGTAPSEDND---------TLFVGNICNTWTKEAIKQKLKDYGVEG 258
++ V+ KR ED+ +FVG I + ++ + YG
Sbjct: 74 RPHKVDGRVVEPKRA--VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG--K 129
Query: 259 VENINLVSDIQHEGLSRGFAFVMFSCH--VDAMAAYKRLQKPDVVFGH 304
+E I +++D + G RGFAFV F H VD + +QK V GH
Sbjct: 130 IEVIEIMTD-RGSGKKRGFAFVTFDDHDSVDKIV----IQKYHTVNGH 172
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 41/155 (26%), Positives = 73/155 (47%), Gaps = 15/155 (9%)
Query: 233 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSC--HVDAMA 290
LF+G + T E+++ + +G + + ++ D + SRGF FV ++ VDA A
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGT--LTDCVVMRD-PNTKRSRGFGFVTYATVEEVDA-A 70
Query: 291 AYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEIMAH--VKTVFLDGVPPHWKENQIRDQ 348
R K D P+R V RE AH VK +F+ G+ +E+ +RD
Sbjct: 71 MNARPHKVDGRVVEPKRAVS-------REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 123
Query: 349 IKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAA 383
+ YG + I + + + K++ + F+ F H++
Sbjct: 124 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 158
Score = 35.8 bits (81), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 314 AEPLREPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYG 373
+E +EP+ ++ +F+ G+ + +R + +G + V+ R+ +T + + +G
Sbjct: 3 SESPKEPE-----QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG 57
Query: 374 FIDFSTHEAAVACINA 389
F+ ++T E A +NA
Sbjct: 58 FVTYATVEEVDAAMNA 73
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 56.2 bits (134), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 49/168 (29%), Positives = 81/168 (48%), Gaps = 24/168 (14%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALT- 210
++FIGGL + T E +R FE+ G + + + ++ +T R++G+ FV +A E A+
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 211 ---EMKNPVICGKRCGTAPSEDND---------TLFVGNICNTWTKEAIKQKLKDYGVEG 258
++ V+ KR ED+ +FVG I + ++ + YG
Sbjct: 76 RPHKVDGRVVEPKRA--VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG--K 131
Query: 259 VENINLVSDIQHEGLSRGFAFVMFSCH--VDAMAAYKRLQKPDVVFGH 304
+E I +++D + G RGFAFV F H VD + +QK V GH
Sbjct: 132 IEVIEIMTD-RGSGKKRGFAFVTFDDHDSVDKIV----IQKYHTVNGH 174
Score = 48.9 bits (115), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 41/155 (26%), Positives = 73/155 (47%), Gaps = 15/155 (9%)
Query: 233 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSC--HVDAMA 290
LF+G + T E+++ + +G + + ++ D + SRGF FV ++ VDA A
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGT--LTDCVVMRD-PNTKRSRGFGFVTYATVEEVDA-A 72
Query: 291 AYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEIMAH--VKTVFLDGVPPHWKENQIRDQ 348
R K D P+R V RE AH VK +F+ G+ +E+ +RD
Sbjct: 73 MNARPHKVDGRVVEPKRAVS-------REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 125
Query: 349 IKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAA 383
+ YG + I + + + K++ + F+ F H++
Sbjct: 126 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 160
Score = 35.8 bits (81), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 314 AEPLREPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYG 373
+E +EP+ ++ +F+ G+ + +R + +G + V+ R+ +T + + +G
Sbjct: 5 SESPKEPE-----QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG 59
Query: 374 FIDFSTHEAAVACINA 389
F+ ++T E A +NA
Sbjct: 60 FVTYATVEEVDAAMNA 75
>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 = 56.2 bits (134), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 49/168 (29%), Positives = 81/168 (48%), Gaps = 24/168 (14%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALT- 210
++FIGGL + T E +R FE+ G + + + ++ +T R++G+ FV +A E A+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 211 ---EMKNPVICGKRCGTAPSEDND---------TLFVGNICNTWTKEAIKQKLKDYGVEG 258
++ V+ KR ED+ +FVG I + ++ + YG
Sbjct: 75 RPHKVDGRVVEPKRA--VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG--K 130
Query: 259 VENINLVSDIQHEGLSRGFAFVMFSCH--VDAMAAYKRLQKPDVVFGH 304
+E I +++D + G RGFAFV F H VD + +QK V GH
Sbjct: 131 IEVIEIMTD-RGSGKKRGFAFVTFDDHDSVDKIV----IQKYHTVNGH 173
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 41/155 (26%), Positives = 73/155 (47%), Gaps = 15/155 (9%)
Query: 233 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSC--HVDAMA 290
LF+G + T E+++ + +G + + ++ D + SRGF FV ++ VDA A
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGT--LTDCVVMRD-PNTKRSRGFGFVTYATVEEVDA-A 71
Query: 291 AYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEIMAH--VKTVFLDGVPPHWKENQIRDQ 348
R K D P+R V RE AH VK +F+ G+ +E+ +RD
Sbjct: 72 MNARPHKVDGRVVEPKRAVS-------REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 124
Query: 349 IKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAA 383
+ YG + I + + + K++ + F+ F H++
Sbjct: 125 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 159
Score = 35.8 bits (81), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 314 AEPLREPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYG 373
+E +EP+ ++ +F+ G+ + +R + +G + V+ R+ +T + + +G
Sbjct: 4 SESPKEPE-----QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG 58
Query: 374 FIDFSTHEAAVACINA 389
F+ ++T E A +NA
Sbjct: 59 FVTYATVEEVDAAMNA 74
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 55.8 bits (133), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 49/168 (29%), Positives = 81/168 (48%), Gaps = 24/168 (14%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALT- 210
++FIGGL + T E +R FE+ G + + + ++ +T R++G+ FV +A E A+
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 211 ---EMKNPVICGKRCGTAPSEDND---------TLFVGNICNTWTKEAIKQKLKDYGVEG 258
++ V+ KR ED+ +FVG I + ++ + YG
Sbjct: 73 RPHKVDGRVVEPKRA--VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG--K 128
Query: 259 VENINLVSDIQHEGLSRGFAFVMFSCH--VDAMAAYKRLQKPDVVFGH 304
+E I +++D + G RGFAFV F H VD + +QK V GH
Sbjct: 129 IEVIEIMTD-RGSGKKRGFAFVTFDDHDSVDKIV----IQKYHTVNGH 171
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 41/155 (26%), Positives = 73/155 (47%), Gaps = 15/155 (9%)
Query: 233 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSC--HVDAMA 290
LF+G + T E+++ + +G + + ++ D + SRGF FV ++ VDA A
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGT--LTDCVVMRD-PNTKRSRGFGFVTYATVEEVDA-A 69
Query: 291 AYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEIMAH--VKTVFLDGVPPHWKENQIRDQ 348
R K D P+R V RE AH VK +F+ G+ +E+ +RD
Sbjct: 70 MNARPHKVDGRVVEPKRAVS-------REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 122
Query: 349 IKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAA 383
+ YG + I + + + K++ + F+ F H++
Sbjct: 123 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 157
Score = 35.4 bits (80), Expect = 0.100, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 314 AEPLREPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYG 373
+E +EP+ ++ +F+ G+ + +R + +G + V+ R+ +T + + +G
Sbjct: 2 SESPKEPE-----QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG 56
Query: 374 FIDFSTHEAAVACINA 389
F+ ++T E A +NA
Sbjct: 57 FVTYATVEEVDAAMNA 72
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 55.8 bits (133), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 49/168 (29%), Positives = 81/168 (48%), Gaps = 24/168 (14%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALT- 210
++FIGGL + T E +R FE+ G + + + ++ +T R++G+ FV +A E A+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 211 ---EMKNPVICGKRCGTAPSEDND---------TLFVGNICNTWTKEAIKQKLKDYGVEG 258
++ V+ KR ED+ +FVG I + ++ + YG
Sbjct: 75 RPHKVDGRVVEPKRA--VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG--K 130
Query: 259 VENINLVSDIQHEGLSRGFAFVMFSCH--VDAMAAYKRLQKPDVVFGH 304
+E I +++D + G RGFAFV F H VD + +QK V GH
Sbjct: 131 IEVIEIMTD-RGSGKKRGFAFVTFDDHDSVDKIV----IQKYHTVNGH 173
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 41/155 (26%), Positives = 73/155 (47%), Gaps = 15/155 (9%)
Query: 233 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSC--HVDAMA 290
LF+G + T E+++ + +G + + ++ D + SRGF FV ++ VDA A
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGT--LTDCVVMRD-PNTKRSRGFGFVTYATVEEVDA-A 71
Query: 291 AYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEIMAH--VKTVFLDGVPPHWKENQIRDQ 348
R K D P+R V RE AH VK +F+ G+ +E+ +RD
Sbjct: 72 MNARPHKVDGRVVEPKRAVS-------REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 124
Query: 349 IKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAA 383
+ YG + I + + + K++ + F+ F H++
Sbjct: 125 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 159
Score = 35.4 bits (80), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 314 AEPLREPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYG 373
+E +EP+ ++ +F+ G+ + +R + +G + V+ R+ +T + + +G
Sbjct: 4 SESPKEPE-----QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG 58
Query: 374 FIDFSTHEAAVACINA 389
F+ ++T E A +NA
Sbjct: 59 FVTYATVEEVDAAMNA 74
>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 = 55.8 bits (133), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 45/175 (25%), Positives = 87/175 (49%), Gaps = 16/175 (9%)
Query: 148 KKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKR 207
K+ ++FIGGL+ D T++++R+ F + G V ++++ K+ +T R++G+ F+ F
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60
Query: 208 ALTE---MKNPVICGKRCGTAPSEDND---TLFVGNICNTWTKEAIKQKLKDYGVEGVEN 261
+ + VI KR P ++ D +FVG I + ++ +G + +
Sbjct: 61 VVKTQHILDGKVIDPKRA--IPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGT--IID 116
Query: 262 INLVSDIQHEGLSRGFAFVMFSCHVDAMAAYKRLQKPDVVFGHPERTVKVAFAEP 316
L+ D + G SRGF FV + D+ A R+ + + +R +++ AEP
Sbjct: 117 AQLMLD-KDTGQSRGFGFVTY----DSADAVDRVCQNKFI-DFKDRKIEIKRAEP 165
>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 = 55.8 bits (133), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 49/168 (29%), Positives = 81/168 (48%), Gaps = 24/168 (14%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALT- 210
++FIGGL + T E +R FE+ G + + + ++ +T R++G+ FV +A E A+
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 211 ---EMKNPVICGKRCGTAPSEDND---------TLFVGNICNTWTKEAIKQKLKDYGVEG 258
++ V+ KR ED+ +FVG I + ++ + YG
Sbjct: 68 RPHKVDGRVVEPKRA--VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG--K 123
Query: 259 VENINLVSDIQHEGLSRGFAFVMFSCH--VDAMAAYKRLQKPDVVFGH 304
+E I +++D + G RGFAFV F H VD + +QK V GH
Sbjct: 124 IEVIEIMTD-RGSGKKRGFAFVTFDDHDSVDKIV----IQKYHTVNGH 166
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 41/155 (26%), Positives = 73/155 (47%), Gaps = 15/155 (9%)
Query: 233 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSC--HVDAMA 290
LF+G + T E+++ + +G + + ++ D + SRGF FV ++ VDA A
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGT--LTDCVVMRD-PNTKRSRGFGFVTYATVEEVDA-A 64
Query: 291 AYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEIMAH--VKTVFLDGVPPHWKENQIRDQ 348
R K D P+R V RE AH VK +F+ G+ +E+ +RD
Sbjct: 65 MNARPHKVDGRVVEPKRAVS-------REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 117
Query: 349 IKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAA 383
+ YG + I + + + K++ + F+ F H++
Sbjct: 118 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 152
Score = 34.7 bits (78), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 14/63 (22%), Positives = 34/63 (53%)
Query: 327 HVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVAC 386
++ +F+ G+ + +R + +G + V+ R+ +T + + +GF+ ++T E A
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64
Query: 387 INA 389
+NA
Sbjct: 65 MNA 67
>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 = 55.5 bits (132), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 42/72 (58%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+F+G L + T ED++ F G + + R+ K+ +T ++KGY FV F NK A+ A+ +M
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 213 KNPVICGKRCGT 224
+ G++ T
Sbjct: 78 GGQWLGGRQIRT 89
Score = 29.6 bits (65), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 23/47 (48%)
Query: 331 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDF 377
VF+ + P I+ +G + + ++M+T K K YGF+ F
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 42/72 (58%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+F+G L + T ED++ F G++ + R+ K+ +T ++KGY FV F NK A+ A+ M
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 213 KNPVICGKRCGT 224
+ G++ T
Sbjct: 78 GGQWLGGRQIRT 89
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 23/47 (48%)
Query: 331 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDF 377
VF+ + P I+ +G + + ++M+T K K YGF+ F
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 64
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 44/73 (60%)
Query: 150 EHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRAL 209
E ++F+GGL D ++ + +VF + G++ EV + K+ T R++G+ FV F N + AK A+
Sbjct: 12 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71
Query: 210 TEMKNPVICGKRC 222
M + G++
Sbjct: 72 MAMNGKSVDGRQI 84
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/63 (22%), Positives = 30/63 (47%)
Query: 331 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAI 390
+F+ G+ E + YG + +V+ ++ T + + +GF+ F + A + A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 391 NNK 393
N K
Sbjct: 75 NGK 77
Score = 29.3 bits (64), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 227 SEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHV 286
+ D LFVG + +++++Q YG + + +V D + + SRGF FV F
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQ--ISEVVVVKDRETQ-RSRGFGFVTFENID 65
Query: 287 DAMAAYKRLQKPDV 300
DA A + V
Sbjct: 66 DAKDAMMAMNGKSV 79
>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 = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 41/146 (28%), Positives = 67/146 (45%), Gaps = 3/146 (2%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+++G L D T+ + + F G ++ +R+ ++ T R+ GYA+V F A+RAL M
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 213 KNPVICGKRCGTAPSEDNDTL---FVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQ 269
VI GK S+ + +L VGNI ++I K NI +
Sbjct: 78 NFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC 137
Query: 270 HEGLSRGFAFVMFSCHVDAMAAYKRL 295
E S+G+ FV F A A +++
Sbjct: 138 DENGSKGYGFVHFETQEAAERAIEKM 163
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 45/177 (25%), Positives = 78/177 (44%), Gaps = 18/177 (10%)
Query: 224 TAPSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFS 283
+APS +L+VG++ T+ + +K G + +I + D+ S G+A+V F
Sbjct: 9 SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAG--PILSIRVCRDMITR-RSLGYAYVNFQ 65
Query: 284 CHVDAMAAYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEI-MAHVKTVFLDGVPPHWKE 342
DA A + DV+ G P R + + DP + + V +F+ +
Sbjct: 66 QPADAERALDTMNF-DVIKGKPVRIM-------WSQRDPSLRKSGVGNIFIKNLDKSIDN 117
Query: 343 NQIRDQIKGYGDVI--RIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSD 397
+ D +G+++ ++V N S K YGF+ F T EAA I +N +D
Sbjct: 118 KALYDTFSAFGNILSCKVVCDENGS----KGYGFVHFETQEAAERAIEKMNGMLLND 170
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 53.1 bits (126), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 47/171 (27%), Positives = 80/171 (46%), Gaps = 13/171 (7%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+F+G L D T+E++RK+FE+ G+ EV +HK +KG+ F++ + A+ A E+
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK------DKGFGFIRLETRTLAEIAKVEL 78
Query: 213 KNPVICGKRCGTAPSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEG 272
N + GK+ + + +L V N+ + E +++ +G VE ++ D G
Sbjct: 79 DNMPLRGKQLRVRFACHSASLTVRNLPQYVSNELLEEAFSVFG--QVERAVVIVD--DRG 134
Query: 273 LSRGFAFVMFSCHVDAMAAYKRLQKPDVVFGHPERTVKVAFAEPLREPDPE 323
G V FS A A R + + R V V EP+ + D E
Sbjct: 135 RPSGKGIVEFSGKPAARKALDRCSEGSFLLTTFPRPVTV---EPMDQLDDE 182
>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 = 52.8 bits (125), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 41/146 (28%), Positives = 67/146 (45%), Gaps = 3/146 (2%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+++G L D T+ + + F G ++ +R+ ++ T R+ GYA+V F A+RAL M
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 213 KNPVICGKRCGTAPSEDNDTLF---VGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQ 269
VI GK S+ + +L VGNI ++I K NI +
Sbjct: 73 NFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC 132
Query: 270 HEGLSRGFAFVMFSCHVDAMAAYKRL 295
E S+G+ FV F A A +++
Sbjct: 133 DENGSKGYGFVHFETQEAAERAIEKM 158
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 45/177 (25%), Positives = 78/177 (44%), Gaps = 18/177 (10%)
Query: 224 TAPSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFS 283
+APS +L+VG++ T+ + +K G + +I + D+ S G+A+V F
Sbjct: 4 SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAG--PILSIRVCRDMITRR-SLGYAYVNFQ 60
Query: 284 CHVDAMAAYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEI-MAHVKTVFLDGVPPHWKE 342
DA A + DV+ G P R + + DP + + V +F+ +
Sbjct: 61 QPADAERALDTMNF-DVIKGKPVRIM-------WSQRDPSLRKSGVGNIFIKNLDKSIDN 112
Query: 343 NQIRDQIKGYGDVI--RIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSD 397
+ D +G+++ ++V N S K YGF+ F T EAA I +N +D
Sbjct: 113 KALYDTFSAFGNILSCKVVCDENGS----KGYGFVHFETQEAAERAIEKMNGMLLND 165
Score = 35.8 bits (81), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
IFI LD+ + + F G ++ ++ + N +KGY FV F +E A+RA+ +M
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 158
Query: 213 KNPVI 217
++
Sbjct: 159 NGMLL 163
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 52.0 bits (123), Expect = 1e-06, Method: Composition-based stats.
Identities = 45/165 (27%), Positives = 80/165 (48%), Gaps = 17/165 (10%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEV--IEVRLHKNFSTNRNKGYAFVKFANKEHAKRALT 210
+++G LD+ T++ +++ F+ G + I++ + KN N+N YAFV++ A AL
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN---NKNVNYAFVEYHQSHDANIALQ 59
Query: 211 EMKNPVICGK--------RCGTAPSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENI 262
+ I + + S+D LFVG++ E ++ KD+ +
Sbjct: 60 TLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDF--PSYLSG 117
Query: 263 NLVSDIQHEGLSRGFAFVMFSCHVDAMAAYKRLQKPDVVFGHPER 307
+++ D+Q G SRG+ FV F+ DA A +Q D+ G P R
Sbjct: 118 HVMWDMQ-TGSSRGYGFVSFTSQDDAQNAMDSMQGQDLN-GRPLR 160
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 51.6 bits (122), Expect = 1e-06, Method: Composition-based stats.
Identities = 21/50 (42%), Positives = 36/50 (72%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFAN 201
++F+GGLD TQE +R F + GEV++ + K+ +TN+++G+ FVKF +
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
Score = 28.9 bits (63), Expect = 9.5, Method: Composition-based stats.
Identities = 11/50 (22%), Positives = 27/50 (54%)
Query: 328 VKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDF 377
+ +F+ G+ + +R YG+V+ V+ ++ +T + + +GF+ F
Sbjct: 16 IGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 51.2 bits (121), Expect = 2e-06, Method: Composition-based stats.
Identities = 40/155 (25%), Positives = 75/155 (48%), Gaps = 13/155 (8%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALT-- 210
+ + L ++ TQ++ + +F IG++ +L ++ T ++ GY FV +++ A +A+
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 211 -----EMKNPVICGKRCGTAPSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLV 265
+ K + R +A D + L+V + T +++ ++Q YG I L
Sbjct: 67 NGLKLQTKTIKVSYARPSSASIRDAN-LYVSGLPKTMSQKEMEQLFSQYGRIITSRILL- 124
Query: 266 SDIQHEGLSRGFAFVMFSCHVDAMAAYKRL--QKP 298
Q G+SRG F+ F ++A A K L QKP
Sbjct: 125 --DQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKP 157
Score = 37.0 bits (84), Expect = 0.037, Method: Composition-based stats.
Identities = 33/140 (23%), Positives = 61/140 (43%), Gaps = 18/140 (12%)
Query: 259 VENINLVSDIQHEGLSRGFAFVMFSCHVDAMAAYKRLQKPDVVFGHPERTVKVAFAEP-- 316
+E+ LV D + G S G+ FV +S DA A L + +T+KV++A P
Sbjct: 31 IESCKLVRD-KITGQSLGYGFVNYSDPNDADKAINTLNGLKL----QTKTIKVSYARPSS 85
Query: 317 --LREPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGF 374
+R+ + +++ G+P + ++ YG +I + + +T + GF
Sbjct: 86 ASIRDAN---------LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGF 136
Query: 375 IDFSTHEAAVACINAINNKE 394
I F A I +N ++
Sbjct: 137 IRFDKRIEAEEAIKGLNGQK 156
Score = 31.6 bits (70), Expect = 1.4, Method: Composition-based stats.
Identities = 28/117 (23%), Positives = 47/117 (40%), Gaps = 23/117 (19%)
Query: 336 VPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEF 395
+P + +++ + GD+ L R+ T + YGF+++S A IN +N +
Sbjct: 12 LPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKL 71
Query: 396 SDGNSKVKLRARLSNP-----------MPKTQAVKGGMSGGFRIGHGSSRTFSRYGR 441
KV AR S+ +PKT + K + FS+YGR
Sbjct: 72 QTKTIKVSY-ARPSSASIRDANLYVSGLPKTMSQK-----------EMEQLFSQYGR 116
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 50.8 bits (120), Expect = 2e-06, Method: Composition-based stats.
Identities = 37/145 (25%), Positives = 71/145 (48%), Gaps = 9/145 (6%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+ + L ++ TQ+++R +F IGEV +L ++ + GY FV + + A+RA+ +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 213 KNPVICGKRCGTA---PSED---NDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVS 266
+ K + PS + + L++ + T T++ ++ +G + N ++
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFG--RIINSRVLV 122
Query: 267 DIQHEGLSRGFAFVMFSCHVDAMAA 291
D Q GLSRG AF+ F +A A
Sbjct: 123 D-QTTGLSRGVAFIRFDKRSEAEEA 146
Score = 49.7 bits (117), Expect = 5e-06, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 40/65 (61%)
Query: 146 KIKKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHA 205
++ K+ ++I GL R TQ+DV +F R G +I R+ + +T ++G AF++F + A
Sbjct: 84 EVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEA 143
Query: 206 KRALT 210
+ A+T
Sbjct: 144 EEAIT 148
Score = 30.8 bits (68), Expect = 2.4, Method: Composition-based stats.
Identities = 27/111 (24%), Positives = 45/111 (40%), Gaps = 11/111 (9%)
Query: 336 VPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEF 395
+P + ++++R G+V L R+ YGF+++ T + A IN +N
Sbjct: 10 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 69
Query: 396 SDGNSKVKLRARLSNPMPKTQAVKGG---MSGGFR--IGHGSSRTFSRYGR 441
KV S P ++ +K +SG R FSR+GR
Sbjct: 70 QSKTIKV------SYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGR 114
>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 = 50.8 bits (120), Expect = 3e-06, Method: Composition-based stats.
Identities = 37/145 (25%), Positives = 71/145 (48%), Gaps = 9/145 (6%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+ + L ++ TQ+++R +F IGEV +L ++ + GY FV + + A+RA+ +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 213 KNPVICGKRCGTA---PSED---NDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVS 266
+ K + PS + + L++ + T T++ ++ +G + N ++
Sbjct: 65 NGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFG--RIINSRVLV 122
Query: 267 DIQHEGLSRGFAFVMFSCHVDAMAA 291
D Q GLSRG AF+ F +A A
Sbjct: 123 D-QTTGLSRGVAFIRFDKRSEAEEA 146
Score = 49.7 bits (117), Expect = 5e-06, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 40/65 (61%)
Query: 146 KIKKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHA 205
++ K+ ++I GL R TQ+DV +F R G +I R+ + +T ++G AF++F + A
Sbjct: 84 EVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEA 143
Query: 206 KRALT 210
+ A+T
Sbjct: 144 EEAIT 148
Score = 30.8 bits (68), Expect = 2.4, Method: Composition-based stats.
Identities = 27/111 (24%), Positives = 45/111 (40%), Gaps = 11/111 (9%)
Query: 336 VPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEF 395
+P + ++++R G+V L R+ YGF+++ T + A IN +N
Sbjct: 10 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 69
Query: 396 SDGNSKVKLRARLSNPMPKTQAVKGG---MSGGFR--IGHGSSRTFSRYGR 441
KV S P ++ +K +SG R FSR+GR
Sbjct: 70 QSKTIKV------SYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGR 114
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 50.1 bits (118), Expect = 4e-06, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 43/68 (63%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+++G L + T++ +R +FE G++ + L K+ T R+KGY F+ F++ E A+RAL ++
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 213 KNPVICGK 220
+ G+
Sbjct: 68 NGFELAGR 75
Score = 36.2 bits (82), Expect = 0.055, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 29/55 (52%)
Query: 342 ENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFS 396
E+ +R + +G + IVL ++ T + K YGFI FS E A + +N E +
Sbjct: 19 EDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELA 73
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTE 211
+IF+GGL T +RK FE G++ E + + T +++GY FV A++ A+RA +
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 212 MKNPVICGKRC 222
NP+I G++
Sbjct: 79 -PNPIIDGRKA 88
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 29/53 (54%)
Query: 331 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAA 383
+F+ G+P H + +R +G+GD+ V+ + T K + YGF+ + AA
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
>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 = 49.3 bits (116), Expect = 8e-06, Method: Composition-based stats.
Identities = 40/189 (21%), Positives = 90/189 (47%), Gaps = 19/189 (10%)
Query: 233 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSD---IQHEGLSRGFAFVMFSCHVDAM 289
++VG+I ++ I+Q +G +++I++ D ++H +GFAFV + A
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFG--PIKSIDMSWDSVTMKH----KGFAFVEYEVPEAAQ 84
Query: 290 AAYKRLQK-----PDVVFGHPERTVKVAFAEPLREPDPEIMAHVKTVFLDGVPPHWKENQ 344
A +++ ++ G P + A+P+ + E +++ V ++
Sbjct: 85 LALEQMNSVMLGGRNIKVGRPS---NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDD 141
Query: 345 IRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNSKVKL 404
I+ + +G + LAR+ +T K K YGFI++ +++ ++++N F G +++
Sbjct: 142 IKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN--LFDLGGQYLRV 199
Query: 405 RARLSNPMP 413
++ PMP
Sbjct: 200 GKAVTPPMP 208
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 15/62 (24%), Positives = 39/62 (62%)
Query: 151 HEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALT 210
+ I++ + +D + +D++ VFE G++ L ++ +T ++KGY F+++ + ++ A++
Sbjct: 126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS 185
Query: 211 EM 212
M
Sbjct: 186 SM 187
Score = 38.1 bits (87), Expect = 0.019, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 40/69 (57%), Gaps = 1/69 (1%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+++G + + ++ +R+ F G + + + + T ++KG+AFV++ E A+ AL +M
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 213 KNPVICGKR 221
N V+ G R
Sbjct: 91 -NSVMLGGR 98
Score = 31.2 bits (69), Expect = 1.9, Method: Composition-based stats.
Identities = 19/89 (21%), Positives = 39/89 (43%)
Query: 325 MAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAV 384
+A + V++ + E+ IR +G + I ++ + T K K + F+++ EAA
Sbjct: 25 LAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQ 84
Query: 385 ACINAINNKEFSDGNSKVKLRARLSNPMP 413
+ +N+ N KV + + P
Sbjct: 85 LALEQMNSVMLGGRNIKVGRPSNIGQAQP 113
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 48.9 bits (115), Expect = 9e-06, Method: Composition-based stats.
Identities = 37/149 (24%), Positives = 69/149 (46%), Gaps = 9/149 (6%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+ + L +D T ++ +F IG + R+ +++ T + GYAFV F ++ ++RA+ +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 213 KNPVICGKRCGTA------PSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVS 266
+ KR + S + L+V N+ T T + + YG + N++
Sbjct: 66 NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYG--SIVQKNILR 123
Query: 267 DIQHEGLSRGFAFVMFSCHVDAMAAYKRL 295
D + G RG AFV ++ +A A L
Sbjct: 124 D-KLTGRPRGVAFVRYNKREEAQEAISAL 151
Score = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 32/134 (23%), Positives = 63/134 (47%), Gaps = 9/134 (6%)
Query: 272 GLSRGFAFVMFSCHVDAMAAYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEIMAHVKTV 331
G S G+AFV F+ +D+ A K L V + +KV++A P E + +
Sbjct: 42 GYSYGYAFVDFTSEMDSQRAIKVLNGITV----RNKRLKVSYARPGGESIKD-----TNL 92
Query: 332 FLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAIN 391
++ +P ++Q+ YG +++ + R+ T + + F+ ++ E A I+A+N
Sbjct: 93 YVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Query: 392 NKEFSDGNSKVKLR 405
N G+ + +R
Sbjct: 153 NVIPEGGSQPLSVR 166
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 48.9 bits (115), Expect = 9e-06, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 42/68 (61%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+++G L + T++ +R +FE G + ++L + T R+KGY F+ F++ E AK+AL ++
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 213 KNPVICGK 220
+ G+
Sbjct: 89 NGFELAGR 96
Score = 33.1 bits (74), Expect = 0.48, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 29/61 (47%)
Query: 342 ENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNSK 401
E+ +R + +G + I L + T + K YGFI FS E A + +N E + K
Sbjct: 40 EDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMK 99
Query: 402 V 402
V
Sbjct: 100 V 100
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 48.9 bits (115), Expect = 1e-05, Method: Composition-based stats.
Identities = 27/91 (29%), Positives = 48/91 (52%), Gaps = 5/91 (5%)
Query: 142 AKDRKIKKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFAN 201
A DR ++ +F+G + +AT+E ++ +F +G V+ RL + T + KGY F ++ +
Sbjct: 3 AVDRSLR---SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59
Query: 202 KEHAKRALTEMKNPVICGK--RCGTAPSEDN 230
+E A A+ + G+ R A SE N
Sbjct: 60 QETALSAMRNLNGREFSGRALRVDNAASEKN 90
Score = 47.0 bits (110), Expect = 3e-05, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 39/75 (52%)
Query: 322 PEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHE 381
P + +++VF+ +P E Q++D G V+ L + T K K YGF ++ E
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 382 AAVACINAINNKEFS 396
A++ + +N +EFS
Sbjct: 62 TALSAMRNLNGREFS 76
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 44/69 (63%), Gaps = 1/69 (1%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTE 211
++FIGGL+R+ ++ ++ VF + G + EV L K+ T++++G+AF+ F N AK A +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKD 67
Query: 212 MKNPVICGK 220
M + GK
Sbjct: 68 MNGKSLHGK 76
>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 = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 43/190 (22%), Positives = 92/190 (48%), Gaps = 21/190 (11%)
Query: 233 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSD---IQHEGLSRGFAFVMFSCHVDAM 289
++VG+I ++ I+Q +G +++I++ D ++H +GFAFV + A
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFG--PIKSIDMSWDSVTMKH----KGFAFVEYEVPEAAQ 69
Query: 290 AAYKRLQKPDVVFGHPERTVKVA------FAEPLREPDPEIMAHVKTVFLDGVPPHWKEN 343
A +++ V+ G R +KV A+P+ + E +++ V ++
Sbjct: 70 LALEQMN--SVMLGG--RNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDD 125
Query: 344 QIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNSKVK 403
I+ + +G + LAR+ +T K K YGFI++ +++ ++++N F G ++
Sbjct: 126 DIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN--LFDLGGQYLR 183
Query: 404 LRARLSNPMP 413
+ ++ PMP
Sbjct: 184 VGKAVTPPMP 193
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 39/62 (62%)
Query: 151 HEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALT 210
+ I++ + +D + +D++ VFE G++ L ++ +T ++KGY F+++ + ++ A++
Sbjct: 111 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 170
Query: 211 EM 212
M
Sbjct: 171 SM 172
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 143 KDRKIKKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANK 202
+ R + +++G + + ++ +R+ F G + + + + T ++KG+AFV++
Sbjct: 6 RQRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVP 65
Query: 203 EHAKRALTEMKNPVICGKR 221
E A+ AL +M N V+ G R
Sbjct: 66 EAAQLALEQM-NSVMLGGR 83
>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 = 48.1 bits (113), Expect = 2e-05, Method: Composition-based stats.
Identities = 37/149 (24%), Positives = 69/149 (46%), Gaps = 9/149 (6%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+ + L +D T ++ +F IG + R+ +++ T + GYAFV F ++ ++RA+ +
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 213 KNPVICGKRCGTA------PSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVS 266
+ KR + S + L+V N+ T T + + YG + N++
Sbjct: 77 NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYG--SIVQKNILR 134
Query: 267 DIQHEGLSRGFAFVMFSCHVDAMAAYKRL 295
D + G RG AFV ++ +A A L
Sbjct: 135 D-KLTGRPRGVAFVRYNKREEAQEAISAL 162
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 32/134 (23%), Positives = 62/134 (46%), Gaps = 9/134 (6%)
Query: 272 GLSRGFAFVMFSCHVDAMAAYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEIMAHVKTV 331
G S G+AFV F+ D+ A K L V + +KV++A P E + +
Sbjct: 53 GYSFGYAFVDFTSEXDSQRAIKVLNGITV----RNKRLKVSYARPGGESIKD-----TNL 103
Query: 332 FLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAIN 391
++ +P ++Q+ YG +++ + R+ T + + F+ ++ E A I+A+N
Sbjct: 104 YVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
Query: 392 NKEFSDGNSKVKLR 405
N G+ + +R
Sbjct: 164 NVIPEGGSQPLSVR 177
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 47.4 bits (111), Expect = 3e-05, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 45/78 (57%), Gaps = 2/78 (2%)
Query: 145 RKIKKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEH 204
R ++K ++ + GL T++D+++ F GEV+ V++ K+ T +KG+ FV+F E
Sbjct: 10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 69
Query: 205 AKRALTEMKNPVICGKRC 222
+ +++ +I G+ C
Sbjct: 70 QVKVMSQRH--MIDGRWC 85
Score = 33.5 bits (75), Expect = 0.44, Method: Composition-based stats.
Identities = 12/54 (22%), Positives = 30/54 (55%)
Query: 335 GVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 388
G+P E +++ +G+V+ + + +++ T K +GF+ F+ +E V ++
Sbjct: 22 GLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75
>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 = 47.0 bits (110), Expect = 3e-05, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 45/78 (57%), Gaps = 6/78 (7%)
Query: 144 DRKIKKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKE 203
++ + +F+G L D T+E++RK+FE+ G+ EV +HK +KG+ F++ +
Sbjct: 9 EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK------DKGFGFIRLETRT 62
Query: 204 HAKRALTEMKNPVICGKR 221
A+ A E+ N + GK+
Sbjct: 63 LAEIAKVELDNMPLRGKQ 80
>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 = 45.8 bits (107), Expect = 8e-05, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 35/59 (59%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTE 211
+FIGGL D T++D++ F + GEV++ L + T R++G+ FV F E + + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 45.8 bits (107), Expect = 8e-05, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 38/63 (60%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTE 211
++FIGGL TQE +R+ F + GEV E + ++ T R++G+ FV F ++ + L +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 212 MKN 214
++
Sbjct: 62 SRH 64
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 45.8 bits (107), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 33/57 (57%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRAL 209
IF+GGL D +E +R+ F GEV + L + TN+ +G+ F+ F +E K+ +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58
Score = 37.7 bits (86), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 5/77 (6%)
Query: 331 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAI 390
+F+ G+ P E +IR+ G+G+V I L + T KR+ + FI F E + I
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEP----VKKI 57
Query: 391 NNKEFSD-GNSKVKLRA 406
K++ + G SK +++
Sbjct: 58 MEKKYHNVGLSKCEIKV 74
>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 = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 34/58 (58%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRAL 209
+IF+GGL D +E +R+ F GEV + L + TN+ +G+ F+ F +E K+ +
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
Score = 42.7 bits (99), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 44/83 (53%), Gaps = 5/83 (6%)
Query: 328 VKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACI 387
VK +F+ G+ P E +IR+ G+G+V I L + T KR+ + FI F E +
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEP----V 56
Query: 388 NAINNKEFSD-GNSKVKLRARLS 409
I K++ + G SK +++ +S
Sbjct: 57 KKIMEKKYHNVGLSKCEIKVAMS 79
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 45.4 bits (106), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 38/63 (60%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTE 211
++FIGGL TQE +R+ F + GEV E + ++ T R++G+ FV F ++ + L +
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 212 MKN 214
++
Sbjct: 87 SRH 89
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 37/56 (66%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRA 208
IF+GGL + T EDV+ FE+ G+V + L + +TNR++G+ FV F +++ ++
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 39/75 (52%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+F+ L +++ED+ K+F G + E+ + T + KG+AFV F EHA +A E+
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 213 KNPVICGKRCGTAPS 227
V G+ PS
Sbjct: 71 DGQVFQGRMLHVLPS 85
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 36/58 (62%)
Query: 154 FIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTE 211
F+GGL D +++D++ F + GEV++ + + +T R++G+ F+ F + ++ L +
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 39/68 (57%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+++ L T D+ ++F + G+V++V + K+ T ++KG AF+ F +K+ A+ +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 213 KNPVICGK 220
N + G+
Sbjct: 79 NNKQLFGR 86
Score = 42.4 bits (98), Expect = 9e-04, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 33/66 (50%)
Query: 330 TVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINA 389
TV++ +P N + YG V+++ + ++ T K K FI F ++A C A
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 390 INNKEF 395
INNK+
Sbjct: 78 INNKQL 83
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 20/79 (25%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+++G + D T+E + + +G VI +++ + T R+KGYAF++F + E + A+ +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 213 KNPVICGK--RCGTAPSED 229
+ + +CG + + D
Sbjct: 65 NGYQLGSRFLKCGYSSNSD 83
Score = 37.4 bits (85), Expect = 0.030, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 31/63 (49%)
Query: 329 KTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 388
+ V+L +P E QI D G VI + + + T + K Y FI+F E++ + +
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 389 AIN 391
+N
Sbjct: 63 NLN 65
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 42/72 (58%)
Query: 149 KEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRA 208
++ +++GGLD ++ + ++F + G V+ + K+ T +++GY FV+F ++E A A
Sbjct: 14 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 73
Query: 209 LTEMKNPVICGK 220
+ M + GK
Sbjct: 74 IKIMDMIKLYGK 85
>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 = 42.7 bits (99), Expect = 6e-04, Method: Composition-based stats.
Identities = 20/79 (25%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+++G + D T+E + + +G VI +++ + T R+KGYAF++F + E + A+ +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 213 KNPVICGK--RCGTAPSED 229
+ + +CG + + D
Sbjct: 66 NGYQLGSRFLKCGYSSNSD 84
Score = 37.0 bits (84), Expect = 0.037, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 32/67 (47%)
Query: 329 KTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 388
+ V+L +P E QI D G VI + + + T + K Y FI+F E++ + +
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 389 AINNKEF 395
+N +
Sbjct: 64 NLNGYQL 70
>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 = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 37/59 (62%)
Query: 162 ATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEMKNPVICGK 220
+ + +R+VFE+ G V +V + ++ T ++G+AFV+F +K A+ A+ M V+ G+
Sbjct: 59 TSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGR 117
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 42/67 (62%)
Query: 143 KDRKIKKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANK 202
K R+ ++ ++FIGGL + T+E +R +E+ G++ + + ++ ++ R++G+ FV F++
Sbjct: 20 KKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSM 79
Query: 203 EHAKRAL 209
A+
Sbjct: 80 AEVDAAM 86
>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 = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 39/186 (20%), Positives = 84/186 (45%), Gaps = 13/186 (6%)
Query: 233 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMAAY 292
++VG+I ++ I+Q +G +++I+ D +GFAFV + A A
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFG--PIKSIDXSWD-SVTXKHKGFAFVEYEVPEAAQLAL 71
Query: 293 KR-----LQKPDVVFGHPERTVKVAFAEPLREPDPEIMAHVKTVFLDGVPPHWKENQIRD 347
++ L ++ G P + A+P+ + E +++ V ++ I+
Sbjct: 72 EQXNSVXLGGRNIKVGRPS---NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKS 128
Query: 348 QIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNSKVKLRAR 407
+ +G + LAR+ +T K K YGFI++ +++ +++ N F G +++
Sbjct: 129 VFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN--LFDLGGQYLRVGKA 186
Query: 408 LSNPMP 413
++ P P
Sbjct: 187 VTPPXP 192
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 14/60 (23%), Positives = 38/60 (63%)
Query: 151 HEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALT 210
+ I++ + +D + +D++ VFE G++ L ++ +T ++KGY F+++ + ++ A++
Sbjct: 110 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 169
Score = 35.8 bits (81), Expect = 0.084, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 1/82 (1%)
Query: 140 AIAKDRKIKKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKF 199
A + R + +++G + + ++ +R+ F G + + + T ++KG+AFV++
Sbjct: 2 AAQRQRALAIXCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEY 61
Query: 200 ANKEHAKRALTEMKNPVICGKR 221
E A+ AL E N V G R
Sbjct: 62 EVPEAAQLAL-EQXNSVXLGGR 82
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 37/61 (60%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
++I GL T +D+ K+ + G+++ + + +TN+ KGY FV F + A++A+T +
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 213 K 213
K
Sbjct: 68 K 68
Score = 32.7 bits (73), Expect = 0.76, Method: Composition-based stats.
Identities = 15/60 (25%), Positives = 30/60 (50%)
Query: 331 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAI 390
+++ G+ P + + + YG ++ + +T K K YGF+DF + AA + A+
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 37/66 (56%)
Query: 144 DRKIKKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKE 203
+R+ I + L D + D++++F G + + L K+ +T ++KG+AF+ F +E
Sbjct: 9 NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 68
Query: 204 HAKRAL 209
A RA+
Sbjct: 69 DAARAI 74
Score = 30.4 bits (67), Expect = 3.3, Method: Composition-based stats.
Identities = 25/96 (26%), Positives = 44/96 (45%), Gaps = 7/96 (7%)
Query: 227 SEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHV 286
++DN T+ V N+ + +++ + +G + I L D + G S+GFAF+ F
Sbjct: 12 ADDNATIRVTNLSEDTRETDLQELFRPFG--SISRIYLAKD-KTTGQSKGFAFISFHRRE 68
Query: 287 DAMAAYKRLQKPDVVFGHPERTVKVAFAEPLREPDP 322
DA A + FG+ + V +A+P P
Sbjct: 69 DAARAIAGVSG----FGYDHLILNVEWAKPSTNSGP 100
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 37/61 (60%), Gaps = 8/61 (13%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTE 211
++FIG L R+AT++++R +FE+ G+V+E + KN Y FV +K A+ A+
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRN 61
Query: 212 M 212
+
Sbjct: 62 L 62
>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 = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 39/72 (54%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+F+G L + T + F G + + R+ K+ +T ++KGY FV F NK A+ A+ +M
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 213 KNPVICGKRCGT 224
+ G++ T
Sbjct: 69 GGQWLGGRQIRT 80
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 41.6 bits (96), Expect = 0.002, Method: Composition-based stats.
Identities = 31/107 (28%), Positives = 55/107 (51%), Gaps = 5/107 (4%)
Query: 223 GTAPSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMF 282
G++ S N LF+G I +E I +++ EGV ++ + + + +RGFAFV +
Sbjct: 1 GSSGSSGNCRLFIGGIPKMKKREEILEEIAKV-TEGVLDVIVYASAADKMKNRGFAFVEY 59
Query: 283 SCHVDAMAAYKRLQKPDV-VFGHPERTVKVAFAEPLREPDPEIMAHV 328
H A A ++L + ++GH + V +AEP + D ++M V
Sbjct: 60 ESHRAAAMARRKLMPGRIQLWGH---QIAVDWAEPEIDVDEDVMETV 103
Score = 29.3 bits (64), Expect = 8.2, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 331 VFLDGVPPHWKENQIRDQI----KGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAA 383
+F+ G+P K +I ++I +G DV IV A K + + F+++ +H AA
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEGVLDV--IVYASAADKMKNRGFAFVEYESHRAA 65
>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 = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 36/60 (60%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+++G + D T+E + + +G VI +++ + T R+KGYAF++F + E + A+ +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Score = 37.0 bits (84), Expect = 0.035, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 32/67 (47%)
Query: 329 KTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 388
+ V+L +P E QI D G VI + + + T + K Y FI+F E++ + +
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 389 AINNKEF 395
+N +
Sbjct: 65 NLNGYQL 71
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 20/67 (29%), Positives = 42/67 (62%), Gaps = 3/67 (4%)
Query: 149 KEHE---IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHA 205
K+H+ +FIG + R+ ++D++ +FE G++ E+ + K+ T +KG AF+ + +E A
Sbjct: 9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA 68
Query: 206 KRALTEM 212
+A + +
Sbjct: 69 LKAQSAL 75
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 41/68 (60%), Gaps = 1/68 (1%)
Query: 145 RKIKKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEH 204
R+ ++F+G L++ +++DVR++FE G + E + + N +KG AFVK+++
Sbjct: 10 RQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGN-SKGCAFVKYSSHAE 68
Query: 205 AKRALTEM 212
A+ A+ +
Sbjct: 69 AQAAINAL 76
Score = 31.6 bits (70), Expect = 1.4, Method: Composition-based stats.
Identities = 25/90 (27%), Positives = 44/90 (48%), Gaps = 5/90 (5%)
Query: 233 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMAAY 292
LFVG + +++ +++ + +G +E ++ +G S+G AFV +S H +A AA
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFG--NIEECTILRG--PDGNSKGCAFVKYSSHAEAQAAI 73
Query: 293 KRLQKPDVVFGHPERTVKVAFAEPLREPDP 322
L + G V V FA+ +E P
Sbjct: 74 NALHGSQTMPGASSSLV-VKFADTDKESGP 102
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 35/56 (62%)
Query: 167 VRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEMKNPVICGKRC 222
+R+VFE+ G V +V + ++ T ++G+AFV+F +K A+ A+ M V+ G+
Sbjct: 87 LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 142
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 8/70 (11%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTE 211
+IF+G + T +++R +FER G VIE + K+ YAFV + AK A+ +
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQ 62
Query: 212 MKNPVICGKR 221
+ + GKR
Sbjct: 63 LNGKEVKGKR 72
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 146 KIKKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFS-TNRNKGYAFVKFANKEH 204
K + +I + + A Q ++R++F GE+ VRL K + T ++G+ FV F K+
Sbjct: 11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 205 AKRALTEM 212
AK+A +
Sbjct: 71 AKKAFNAL 78
Score = 33.1 bits (74), Expect = 0.54, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 331 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMS-TAKRKDYGFIDFSTHEAAVACINA 389
+ + +P + +IR+ +G++ + L + M+ T + +GF+DF T + A NA
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA 77
Query: 390 I 390
+
Sbjct: 78 L 78
>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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%)
Query: 319 EPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFS 378
EP P+ +F+ + +E++I+++ YG++ I L + T K Y +++
Sbjct: 63 EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE 122
Query: 379 THEAAVACINAINNKEF 395
TH+ A+A A+N E
Sbjct: 123 THKQALAAKEALNGAEI 139
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 36/68 (52%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+F+ + +A ++++++ F GE+ + L+ + T +KGYA V++ + A A +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 213 KNPVICGK 220
I G+
Sbjct: 135 NGAEIMGQ 142
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 149 KEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRA 208
++ ++F+G L + T EDVRK+FE G + E + + +KG AFVKF A+ A
Sbjct: 11 EDRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRG-PDGTSKGCAFVKFQTHAEAQAA 69
Query: 209 LTEM 212
+ +
Sbjct: 70 INTL 73
Score = 34.3 bits (77), Expect = 0.26, Method: Composition-based stats.
Identities = 26/94 (27%), Positives = 44/94 (46%), Gaps = 5/94 (5%)
Query: 229 DNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDA 288
++ LFVG + T E +++ + +G ++ ++ +G S+G AFV F H +A
Sbjct: 11 EDRKLFVGMLGKQQTDEDVRKMFEPFGT--IDECTVLRG--PDGTSKGCAFVKFQTHAEA 66
Query: 289 MAAYKRLQKPDVVFGHPERTVKVAFAEPLREPDP 322
AA L + G V V FA+ +E P
Sbjct: 67 QAAINTLHSSRTLPGASSSLV-VKFADTEKESGP 99
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 43/79 (54%), Gaps = 9/79 (11%)
Query: 149 KEHEIFIGGLDRDATQEDVRKVFERIGEVIEV-----RLHKNFSTNRNKGYAFVKFANKE 203
K ++ IG L R+ T++ + ++F G++ + R+H + S KGYA+V+F N +
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLS----KGYAYVEFENPD 58
Query: 204 HAKRALTEMKNPVICGKRC 222
A++AL M I G+
Sbjct: 59 EAEKALKHMDGGQIDGQEI 77
>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 = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 40/65 (61%), Gaps = 2/65 (3%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTN--RNKGYAFVKFANKEHAKRAL 209
++F+G + R +++D+R++FE+ G V E+ + ++ S N ++KG FV F ++ A A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 210 TEMKN 214
+ N
Sbjct: 65 NALHN 69
Score = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 331 VFLDGVPPHWKENQIRDQIKGYGDV--IRIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 388
+F+ VP W E +R+ + YG V I ++ R+ + + K F+ F T +AA+ N
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 389 AINNKEFSDG 398
A++N + G
Sbjct: 66 ALHNMKVLPG 75
Score = 36.6 bits (83), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 229 DNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSD-IQHEGLSRGFAFVMFSCHVD 287
D +FVG + TW+++ +++ + YG V IN++ D Q+ S+G FV F
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYG--AVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 59
Query: 288 AMAAYKRLQKPDVVFG--HP 305
A+ A L V+ G HP
Sbjct: 60 ALEAQNALHNMKVLPGMHHP 79
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 41/69 (59%), Gaps = 1/69 (1%)
Query: 149 KEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRA 208
++H++FI GL T+E++ ++ + G V ++RL N + KG A+V++ N+ A +A
Sbjct: 16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYENESQASQA 74
Query: 209 LTEMKNPVI 217
+ +M I
Sbjct: 75 VMKMDGMTI 83
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
I++G L AT E V+++F + G+V V+L + T + KG+ FV+ +E A+ ++
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIAKL 62
Query: 213 KNPVICGK 220
N G+
Sbjct: 63 DNTDFMGR 70
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%)
Query: 319 EPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFS 378
EP P+ +F+ + +E++I+++ YG++ I L + T K Y +++
Sbjct: 17 EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE 76
Query: 379 THEAAVACINAINNKEF 395
TH+ A+A A+N E
Sbjct: 77 THKQALAAKEALNGAEI 93
Score = 32.7 bits (73), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 36/68 (52%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+F+ + +A ++++++ F GE+ + L+ + T +KGYA V++ + A A +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 213 KNPVICGK 220
I G+
Sbjct: 89 NGAEIMGQ 96
>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 = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 151 HEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALT 210
+ +F+GG+D + ++R F R G V EV++ + T +KGY FV F N ++ +
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVE 68
Query: 211 EMKNPVICGKRCGTAPS 227
N GK+ P+
Sbjct: 69 SQIN--FHGKKLKLGPA 83
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 7/60 (11%)
Query: 320 PDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDV--IRIVLARNMSTAKRKDYGFIDF 377
P+ +IM + TVF+ G+ E +IR YG V ++I+ R T K YGF+ F
Sbjct: 3 PEGKIMPN--TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR---TGVSKGYGFVSF 57
Score = 29.3 bits (64), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 231 DTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDA 288
+T+FVG I + I+ YG V+ + +++D G+S+G+ FV F VD
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYG--SVKEVKIITD--RTGVSKGYGFVSFYNDVDV 63
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 8/73 (10%)
Query: 321 DPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTH 380
DPE+MA VK +F+ + E + +G + R+ K KDY F+ F
Sbjct: 8 DPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERV--------KKLKDYAFVHFEDR 59
Query: 381 EAAVACINAINNK 393
AAV ++ +N K
Sbjct: 60 GAAVKAMDEMNGK 72
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 36/65 (55%)
Query: 157 GLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEMKNPV 216
GL T+ D+R+VF + G + +V + + + R++G+AFV F N + AK A
Sbjct: 22 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 81
Query: 217 ICGKR 221
+ G+R
Sbjct: 82 LDGRR 86
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 29/95 (30%), Positives = 48/95 (50%), Gaps = 4/95 (4%)
Query: 223 GTAPSEDN--DTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFV 280
G+ PS +N DT+ + N+ T ++I L Y V N+ ++ D Q + L+RGFAF+
Sbjct: 14 GSEPSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQ-LNRGFAFI 72
Query: 281 MFSCHVDAMAAYKRLQKPDVVFGHPERTVKVAFAE 315
S ++A + LQ +T+ V FA+
Sbjct: 73 QLST-IEAAQLLQILQALHPPLTIDGKTINVEFAK 106
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 28/85 (32%), Positives = 40/85 (47%), Gaps = 1/85 (1%)
Query: 231 DTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMA 290
DT+ + NI ++I L Y V NI L+ D Q + +RGFAFV S +DA
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQ-NRGFAFVQLSSAMDASQ 68
Query: 291 AYKRLQKPDVVFGHPERTVKVAFAE 315
+ LQ +T+ V FA+
Sbjct: 69 LLQILQSLHPPLKIDGKTIGVDFAK 93
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 36/65 (55%)
Query: 157 GLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEMKNPV 216
GL T+ D+R+VF + G + +V + + + R++G+AFV F N + AK A
Sbjct: 22 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 81
Query: 217 ICGKR 221
+ G+R
Sbjct: 82 LDGRR 86
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 36/65 (55%)
Query: 157 GLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEMKNPV 216
GL T+ D+R+VF + G + +V + + + R++G+AFV F N + AK A
Sbjct: 53 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 112
Query: 217 ICGKR 221
+ G+R
Sbjct: 113 LDGRR 117
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 32/52 (61%)
Query: 157 GLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRA 208
GL T+ D+R+VF + G + +V + + + R++G+AFV F N + AK A
Sbjct: 19 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 70
>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 = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 151 HEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALT 210
+ +F+GG+D + ++R F R G V EV++ + T +KGY FV F N ++ +
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVE 68
Query: 211 EMKNPVICGKRCGTAPS 227
N GK+ P+
Sbjct: 69 SQIN--FHGKKLKLGPA 83
Score = 31.6 bits (70), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 7/60 (11%)
Query: 320 PDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDV--IRIVLARNMSTAKRKDYGFIDF 377
P+ +IM + TVF+ G+ E +IR YG V ++I+ R T K YGF+ F
Sbjct: 3 PEGKIMPN--TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR---TGVSKGYGFVSF 57
Score = 29.3 bits (64), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 231 DTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDA 288
+T+FVG I + I+ YG V+ + +++D G+S+G+ FV F VD
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYG--SVKEVKIITD--RTGVSKGYGFVSFYNDVDV 63
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 151 HEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALT 210
+ +F+GG+D + ++R F R G V EV++ + T +KGY FV F N ++ +
Sbjct: 11 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVE 69
Query: 211 EMKNPVICGKRCGTAPS 227
N GK+ P+
Sbjct: 70 SQIN--FHGKKLKLGPA 84
Score = 29.3 bits (64), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 330 TVFLDGVPPHWKENQIRDQIKGYGDV--IRIVLARNMSTAKRKDYGFIDF 377
TVF+ G+ E +IR YG V ++I+ R T K YGF+ F
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR---TGVSKGYGFVSF 58
Score = 28.9 bits (63), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 231 DTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDA 288
+T+FVG I + I+ YG V+ + +++D G+S+G+ FV F VD
Sbjct: 11 NTVFVGGIDVRMDETEIRSFFARYG--SVKEVKIITD--RTGVSKGYGFVSFYNDVDV 64
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+++ LD E +RK F G + ++ R+KG+ FV F++ E A +A+TEM
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 213 KNPVICGK 220
++ K
Sbjct: 76 NGRIVATK 83
>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 = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 36/68 (52%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+F+ G+ +AT+ED+ F GE+ + L+ + T KGY V++ + A+ A+ +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 213 KNPVICGK 220
+ G+
Sbjct: 86 NGQDLMGQ 93
Score = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 36/77 (46%)
Query: 319 EPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFS 378
EP P+ +F+ GV E I D+ YG++ I L + T K Y +++
Sbjct: 14 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 73
Query: 379 THEAAVACINAINNKEF 395
T++ A A + +N ++
Sbjct: 74 TYKEAQAAMEGLNGQDL 90
Score = 32.7 bits (73), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 42/87 (48%), Gaps = 4/87 (4%)
Query: 219 GKRCGTAPSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFA 278
G G S + LFV + T+E I K +YG ++NI+L D + G +G+
Sbjct: 12 GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGE--IKNIHLNLD-RRTGYLKGYT 68
Query: 279 FVMFSCHVDAMAAYKRLQKPDVVFGHP 305
V + + +A AA + L D++ G P
Sbjct: 69 LVEYETYKEAQAAMEGLNGQDLM-GQP 94
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 149 KEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRA 208
K ++ GG+ T + +R+ F G+++E+R+ KGY+FV+F+ E A A
Sbjct: 24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHA 77
Query: 209 LTEMKNPVICG 219
+ + I G
Sbjct: 78 IVSVNGTTIEG 88
Score = 31.6 bits (70), Expect = 1.6, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 6/62 (9%)
Query: 330 TVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINA 389
TV+ G+ + +R +G ++ I K Y F+ FSTHE+A I +
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEI------RVFPEKGYSFVRFSTHESAAHAIVS 80
Query: 390 IN 391
+N
Sbjct: 81 VN 82
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 151 HEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALT 210
++IF+GG+ + + ++R+ F++ G V EV + + R +G+ F+ F +++ +A+
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 211 EMKNPVICGKRCGTAPSEDNDT 232
M I GK+ +E D+
Sbjct: 71 -MHFHDIMGKKVEVKRAEPRDS 91
Score = 36.6 bits (83), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 14/58 (24%), Positives = 31/58 (53%)
Query: 331 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 388
+F+ G+P + E ++R+ K +G V +V+ + + + +GFI F ++ +N
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 38.9 bits (89), Expect = 0.010, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 37/69 (53%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+ + L +D T ++ +F IG + R+ +++ T + GYAFV F ++ ++RA+ +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 213 KNPVICGKR 221
+ KR
Sbjct: 66 NGITVRNKR 74
>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 = 38.9 bits (89), Expect = 0.010, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 34/60 (56%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+ + L ++ TQ+++R +F IGEV +L ++ + GY FV + + A+RA+ +
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Score = 29.3 bits (64), Expect = 8.4, Method: Composition-based stats.
Identities = 16/67 (23%), Positives = 29/67 (43%)
Query: 336 VPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEF 395
+P + ++++R G+V L R+ YGF+++ T + A IN +N
Sbjct: 27 LPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 86
Query: 396 SDGNSKV 402
KV
Sbjct: 87 QSKTIKV 93
>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 = 38.9 bits (89), Expect = 0.010, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 34/60 (56%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+ + L ++ TQ+++R +F IGEV +L ++ + GY FV + + A+RA+ +
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Score = 29.6 bits (65), Expect = 5.9, Method: Composition-based stats.
Identities = 16/67 (23%), Positives = 29/67 (43%)
Query: 336 VPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEF 395
+P + ++++R G+V L R+ YGF+++ T + A IN +N
Sbjct: 12 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 71
Query: 396 SDGNSKV 402
KV
Sbjct: 72 QSKTIKV 78
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 38.9 bits (89), Expect = 0.011, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEV-RLHKNFSTNRNKGYAFVKFANKEHAKRALTE 211
IFIG LD + ++ + F G +++ ++ ++ T +KGYAF+ FA+ + + A+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 212 MKNPVICGK 220
M +C +
Sbjct: 68 MNGQYLCNR 76
Score = 34.7 bits (78), Expect = 0.18, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 331 VFLDGVPPHWKENQIRDQIKGYGDVIRI-VLARNMSTAKRKDYGFIDFSTHEAAVACINA 389
+F+ + P E + D +G +++ + R+ T K Y FI+F++ +A+ A I A
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 390 INNK 393
+N +
Sbjct: 68 MNGQ 71
>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 = 38.5 bits (88), Expect = 0.011, Method: Composition-based stats.
Identities = 16/68 (23%), Positives = 38/68 (55%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+++GGL + + + F G++ ++++ ++ T +++G+AFV+F E A A+ M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 213 KNPVICGK 220
+ G+
Sbjct: 70 NESELFGR 77
Score = 31.6 bits (70), Expect = 1.4, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 26/53 (49%)
Query: 352 YGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNSKVKL 404
+GD+ I + + T K + + F++F E A A I+ +N E +V L
Sbjct: 31 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 83
>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 = 0.011, Method: Composition-based stats.
Identities = 16/68 (23%), Positives = 38/68 (55%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+++GGL + + + F G++ ++++ ++ T +++G+AFV+F E A A+ M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 213 KNPVICGK 220
+ G+
Sbjct: 75 NESELFGR 82
Score = 33.9 bits (76), Expect = 0.28, Method: Composition-based stats.
Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 233 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMAAY 292
L+VG + + + +G + +I + D + E RGFAFV F DA AA
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFG--DITDIQIPLDYETEK-HRGFAFVEFELAEDAAAAI 71
Query: 293 KRLQKPDVVFGHPERTVKVAFAEPLR 318
+ + + +FG RT++V A+P+R
Sbjct: 72 DNMNESE-LFG---RTIRVNLAKPMR 93
Score = 32.7 bits (73), Expect = 0.72, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 352 YGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNSKVKLRARLSNP 411
+GD+ I + + T K + + F++F E A A I+ +N E +R L+ P
Sbjct: 36 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRT----IRVNLAKP 91
Query: 412 M 412
M
Sbjct: 92 M 92
>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 = 38.5 bits (88), Expect = 0.013, Method: Composition-based stats.
Identities = 16/68 (23%), Positives = 38/68 (55%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+++GGL + + + F G++ ++++ ++ T +++G+AFV+F E A A+ M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 213 KNPVICGK 220
+ G+
Sbjct: 65 NESELFGR 72
Score = 31.6 bits (70), Expect = 1.6, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 26/53 (49%)
Query: 352 YGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNSKVKL 404
+GD+ I + + T K + + F++F E A A I+ +N E +V L
Sbjct: 26 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 78
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 38.5 bits (88), Expect = 0.013, Method: Composition-based stats.
Identities = 16/68 (23%), Positives = 38/68 (55%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+++GGL + + + F G++ ++++ ++ T +++G+AFV+F E A A+ M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 213 KNPVICGK 220
+ G+
Sbjct: 68 NESELFGR 75
Score = 31.6 bits (70), Expect = 1.5, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 26/53 (49%)
Query: 352 YGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNSKVKL 404
+GD+ I + + T K + + F++F E A A I+ +N E +V L
Sbjct: 29 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 81
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 38.5 bits (88), Expect = 0.014, Method: Composition-based stats.
Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 9/69 (13%)
Query: 153 IFIGGLDRDATQE-DVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTE 211
+FIG L+ ++ DV +F + G V +HK GYAFV+++N+ HA+ A+
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK--------GYAFVQYSNERHARAAVLG 81
Query: 212 MKNPVICGK 220
V+ G+
Sbjct: 82 ENGRVLAGQ 90
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 38.5 bits (88), Expect = 0.014, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 34/59 (57%)
Query: 167 VRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEMKNPVICGKRCGTA 225
+R++FER G + V++ + T +++GY FVKF + A++A+ + I KR A
Sbjct: 59 LRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA 117
Score = 36.6 bits (83), Expect = 0.053, Method: Composition-based stats.
Identities = 20/87 (22%), Positives = 42/87 (48%), Gaps = 3/87 (3%)
Query: 320 PDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFST 379
P+P+++ + + ++ +P E Q+R + YG + + + + T + + YGF+ F +
Sbjct: 37 PEPDVL---RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS 93
Query: 380 HEAAVACINAINNKEFSDGNSKVKLRA 406
+A I +N + KV L A
Sbjct: 94 GSSAQQAIAGLNGFNILNKRLKVALAA 120
>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 = 38.5 bits (88), Expect = 0.014, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 36/68 (52%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+F+ G+ +AT+ED+ F GE+ + L+ + T KGY V++ + A+ A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 213 KNPVICGK 220
+ G+
Sbjct: 70 NGQDLMGQ 77
Score = 34.3 bits (77), Expect = 0.23, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 32/65 (49%)
Query: 331 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAI 390
+F+ GV E I D+ YG++ I L + T K Y +++ T++ A A + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 391 NNKEF 395
N ++
Sbjct: 70 NGQDL 74
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 38.1 bits (87), Expect = 0.015, Method: Composition-based stats.
Identities = 25/69 (36%), Positives = 40/69 (57%), Gaps = 10/69 (14%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+ + L AT+E +++VFE+ I+V ++N ++KGYAF++FA+ E AK AL
Sbjct: 18 LVLSNLSYSATEETLQEVFEK-ATFIKVPQNQN---GKSKGYAFIEFASFEDAKEALNS- 72
Query: 213 KNPVICGKR 221
C KR
Sbjct: 73 -----CNKR 76
>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 = 38.1 bits (87), Expect = 0.015, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 36/68 (52%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+F+ G+ +AT+ED+ F GE+ + L+ + T KGY V++ + A+ A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 213 KNPVICGK 220
+ G+
Sbjct: 70 NGQDLMGQ 77
Score = 34.3 bits (77), Expect = 0.25, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 32/65 (49%)
Query: 331 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAI 390
+F+ GV E I D+ YG++ I L + T K Y +++ T++ A A + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 391 NNKEF 395
N ++
Sbjct: 70 NGQDL 74
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 38.1 bits (87), Expect = 0.015, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 36/68 (52%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+F+ G+ +AT+ED+ F GE+ + L+ + T KGY V++ + A+ A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 213 KNPVICGK 220
+ G+
Sbjct: 70 NGQDLMGQ 77
Score = 34.3 bits (77), Expect = 0.26, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 32/65 (49%)
Query: 331 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAI 390
+F+ GV E I D+ YG++ I L + T K Y +++ T++ A A + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 391 NNKEF 395
N ++
Sbjct: 70 NGQDL 74
>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 = 38.1 bits (87), Expect = 0.016, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 36/68 (52%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+F+ G+ +AT+ED+ F GE+ + L+ + T KGY V++ + A+ A+ +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 213 KNPVICGK 220
+ G+
Sbjct: 72 NGQDLMGQ 79
Score = 35.4 bits (80), Expect = 0.094, Method: Composition-based stats.
Identities = 19/76 (25%), Positives = 35/76 (46%)
Query: 320 PDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFST 379
P P+ +F+ GV E I D+ YG++ I L + T K Y +++ T
Sbjct: 1 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 60
Query: 380 HEAAVACINAINNKEF 395
++ A A + +N ++
Sbjct: 61 YKEAQAAMEGLNGQDL 76
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 38.1 bits (87), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 38/68 (55%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+++GGL + + + F G++ ++++ ++ T +++G+AFV+F E A A+ M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 213 KNPVICGK 220
+ G+
Sbjct: 126 NESELFGR 133
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/76 (21%), Positives = 34/76 (44%)
Query: 329 KTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 388
+ +++ G+ + + +GD+ I + + T K + + F++F E A A I+
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 389 AINNKEFSDGNSKVKL 404
+N E +V L
Sbjct: 124 NMNESELFGRTIRVNL 139
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 37.7 bits (86), Expect = 0.019, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 40/67 (59%), Gaps = 3/67 (4%)
Query: 149 KEHE---IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHA 205
K+H+ +F+G + R ++D++ +FE G + E+ + K+ T +KG AF+ + ++ A
Sbjct: 11 KDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSA 70
Query: 206 KRALTEM 212
+A + +
Sbjct: 71 LKAQSAL 77
>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 = 37.7 bits (86), Expect = 0.024, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 35/51 (68%), Gaps = 1/51 (1%)
Query: 158 LDRDATQEDVRKVFERIG-EVIEVRLHKNFSTNRNKGYAFVKFANKEHAKR 207
L + AT++D+R + G + EVRL +N S+ +++G+AFV+F++ + A R
Sbjct: 9 LPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATR 59
Score = 30.0 bits (66), Expect = 4.6, Method: Composition-based stats.
Identities = 19/46 (41%), Positives = 30/46 (65%), Gaps = 2/46 (4%)
Query: 243 TKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDA 288
T++ I+ +L+ +GV+ E + L+ + + G SRGFAFV FS DA
Sbjct: 14 TEDDIRGQLQSHGVQARE-VRLMRN-KSSGQSRGFAFVEFSHLQDA 57
>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 = 37.4 bits (85), Expect = 0.025, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 36/68 (52%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+F+ G+ +AT+ED+ F GE+ + L+ + T KGY V++ + A+ A+ +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 213 KNPVICGK 220
+ G+
Sbjct: 85 NGQDLMGQ 92
Score = 37.0 bits (84), Expect = 0.039, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 36/77 (46%)
Query: 319 EPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFS 378
EP P+ +F+ GV E I D+ YG++ I L + T K Y +++
Sbjct: 13 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 72
Query: 379 THEAAVACINAINNKEF 395
T++ A A + +N ++
Sbjct: 73 TYKEAQAAMEGLNGQDL 89
Score = 30.4 bits (67), Expect = 3.3, Method: Composition-based stats.
Identities = 26/87 (29%), Positives = 42/87 (48%), Gaps = 4/87 (4%)
Query: 219 GKRCGTAPSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFA 278
G G S + LFV + T+E I K +YG ++NI+L D + G +G+
Sbjct: 11 GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYG--EIKNIHLNLD-RRTGYLKGYT 67
Query: 279 FVMFSCHVDAMAAYKRLQKPDVVFGHP 305
V + + +A AA + L D++ G P
Sbjct: 68 LVEYETYKEAQAAMEGLNGQDLM-GQP 93
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 37.0 bits (84), Expect = 0.040, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+F+ GL D T+E +++ F+ + R+ + T +KG+ FV F ++E AK A M
Sbjct: 18 LFVKGLSEDTTEETLKESFD---GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 213 KNPVICGKR 221
++ I G +
Sbjct: 75 EDGEIDGNK 83
Score = 34.3 bits (77), Expect = 0.26, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 329 KTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 388
KT+F+ G+ E +++ G +R + + T K +GF+DF++ E A A
Sbjct: 16 KTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72
Query: 389 AINNKEFSDGN 399
A+ + E DGN
Sbjct: 73 AMEDGEI-DGN 82
Score = 32.7 bits (73), Expect = 0.64, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 225 APSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSC 284
A S+ + TLFV + T+E +K+ +G +V+D + G S+GF FV F+
Sbjct: 10 ARSQPSKTLFVKGLSEDTTEETLKESF-----DGSVRARIVTD-RETGSSKGFGFVDFNS 63
Query: 285 HVDAMAAYKRLQKPDV 300
DA AA + ++ ++
Sbjct: 64 EEDAKAAKEAMEDGEI 79
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 37.0 bits (84), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 35/59 (59%), Gaps = 5/59 (8%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTE 211
+F+G D T++++R+ F + G+V++V + K F + +AFV FA+ + A+ E
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQSLCGE 61
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 36.2 bits (82), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 38/69 (55%), Gaps = 9/69 (13%)
Query: 153 IFIGGLDRDATQE-DVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTE 211
+FIG L+ ++ DV +F + G+++ +HK G+AFV++ N+ +A+ A+
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAFVQYVNERNARAAVAG 69
Query: 212 MKNPVICGK 220
+I G+
Sbjct: 70 EDGRMIAGQ 78
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 36.2 bits (82), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 5/60 (8%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTE 211
++F+G D T E++++ F + GEV++V + K F + +AFV FA+ + A+ E
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFADDKVAQSLCGE 67
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 36.2 bits (82), Expect = 0.063, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 37/60 (61%), Gaps = 1/60 (1%)
Query: 150 EHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRAL 209
+ ++F+G L++ ++EDV ++F+ G + E + + +KG AFVKF++ A+ A+
Sbjct: 15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKFSSHTEAQAAI 73
Score = 33.5 bits (75), Expect = 0.43, Method: Composition-based stats.
Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 5/90 (5%)
Query: 233 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMAAY 292
LFVG + ++E + + + +GV ++ ++ +G S+G AFV FS H +A AA
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGV--IDECTVLRG--PDGSSKGCAFVKFSSHTEAQAAI 73
Query: 293 KRLQKPDVVFGHPERTVKVAFAEPLREPDP 322
L + G V V FA+ +E P
Sbjct: 74 HALHGSQTMPGASSSLV-VKFADTDKESGP 102
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 35.8 bits (81), Expect = 0.072, Method: Composition-based stats.
Identities = 21/83 (25%), Positives = 41/83 (49%), Gaps = 11/83 (13%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNK-------GYAFVKFANKEHA 205
+FI L+ T+E ++ VF ++G + + K +NK G+ FV++ E A
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISK----KKNKAGVLLSMGFGFVEYKKPEQA 63
Query: 206 KRALTEMKNPVICGKRCGTAPSE 228
++AL +++ + G + SE
Sbjct: 64 QKALKQLQGHTVDGHKLEVRISE 86
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 35.8 bits (81), Expect = 0.078, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 34/57 (59%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRAL 209
+FI L D+ +E + +V ++ G++ VR+ + T +KG AF +F +E A++ L
Sbjct: 18 VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
Score = 30.4 bits (67), Expect = 3.2, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 32/68 (47%)
Query: 322 PEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHE 381
P + KTVF+ + +E + + ++ +GD+ + + + T K F F T E
Sbjct: 9 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 68
Query: 382 AAVACINA 389
AA C+ A
Sbjct: 69 AAQKCLAA 76
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 35.8 bits (81), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
I++G +D AT E++ F G V V + + + KG+A+++F++KE + +L +
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-L 67
Query: 213 KNPVICGKRCGTAPSEDN 230
+ G++ P N
Sbjct: 68 DESLFRGRQIKVIPKRTN 85
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 35.8 bits (81), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
I++G +D AT E++ F G V V + + + KG+A+++F++KE + +L +
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-L 66
Query: 213 KNPVICGKRCGTAPSEDN 230
+ G++ P N
Sbjct: 67 DESLFRGRQIKVIPKRTN 84
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 35.8 bits (81), Expect = 0.085, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 29/51 (56%)
Query: 151 HEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFAN 201
H++FIGGL + V+++ G + L K+ +T +KGYAF ++ +
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 52
Score = 33.1 bits (74), Expect = 0.58, Method: Composition-based stats.
Identities = 14/63 (22%), Positives = 35/63 (55%), Gaps = 3/63 (4%)
Query: 331 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGF---IDFSTHEAAVACI 387
+F+ G+P + ++Q+++ + +G + L ++ +T K Y F +D + + A+A +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 388 NAI 390
N +
Sbjct: 64 NGM 66
>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 = 35.4 bits (80), Expect = 0.10, Method: Composition-based stats.
Identities = 16/68 (23%), Positives = 35/68 (51%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+F+G L+ + E +R F+ + + + T ++GY FV F +++ A+ A+ M
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 213 KNPVICGK 220
+ + G+
Sbjct: 64 QGQDLNGR 71
>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 = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 29/51 (56%)
Query: 151 HEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFAN 201
H++FIGGL + V+++ G + L K+ +T +KGYAF ++ +
Sbjct: 115 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 165
Score = 32.7 bits (73), Expect = 0.74, Method: Composition-based stats.
Identities = 14/63 (22%), Positives = 35/63 (55%), Gaps = 3/63 (4%)
Query: 331 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGF---IDFSTHEAAVACI 387
+F+ G+P + ++Q+++ + +G + L ++ +T K Y F +D + + A+A +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 388 NAI 390
N +
Sbjct: 177 NGM 179
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
IFI LD+ + + F G ++ ++ + N +KGY FV F +E A+RA+ +M
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65
Query: 213 KNPVI 217
++
Sbjct: 66 NGMLL 70
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 6/69 (8%)
Query: 331 VFLDGVPPHWKENQIRDQIKGYGDVI--RIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 388
+F+ + + D +G+++ ++V N S K YGF+ F T EAA I
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS----KGYGFVHFETQEAAERAIE 63
Query: 389 AINNKEFSD 397
+N +D
Sbjct: 64 KMNGMLLND 72
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
IFI LD+ + + F G ++ ++ + N +KGY FV F +E A+RA+ +M
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 71
Query: 213 KNPVI 217
++
Sbjct: 72 NGMLL 76
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 7/81 (8%)
Query: 320 PDPEI-MAHVKTVFLDGVPPHWKENQIRDQIKGYGDVI--RIVLARNMSTAKRKDYGFID 376
DP + + V +F+ + + D +G+++ ++V N S K YGF+
Sbjct: 2 ADPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS----KGYGFVH 57
Query: 377 FSTHEAAVACINAINNKEFSD 397
F T EAA I +N +D
Sbjct: 58 FETQEAAERAIEKMNGMLLND 78
>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 = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 23/107 (21%), Positives = 50/107 (46%), Gaps = 6/107 (5%)
Query: 324 IMAHVK--TVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHE 381
I++H+ T++ PP + + IRD ++ V + ++ + + +ID ++ E
Sbjct: 111 IVSHLTECTLWXTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKE 170
Query: 382 AAVACINAINNKEFSDGNSKVKLRARLSNPMPKTQAVKGGMSGGFRI 428
A C+ +N + +G + V ++SNP+ K++ G I
Sbjct: 171 DARYCVEKLNGLKI-EGYTLV---TKVSNPLEKSKRTDSATLEGREI 213
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 35.4 bits (80), Expect = 0.12, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 29/51 (56%)
Query: 151 HEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFAN 201
H++FIGGL + V+++ G + L K+ +T +KGYAF ++ +
Sbjct: 95 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 145
Score = 33.5 bits (75), Expect = 0.41, Method: Composition-based stats.
Identities = 17/78 (21%), Positives = 41/78 (52%), Gaps = 4/78 (5%)
Query: 317 LREP-DPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGF- 374
+R P D + + +F+ G+P + ++Q+++ + +G + L ++ +T K Y F
Sbjct: 82 IRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 141
Query: 375 --IDFSTHEAAVACINAI 390
+D + + A+A +N +
Sbjct: 142 EYVDINVTDQAIAGLNGM 159
>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 = 35.4 bits (80), Expect = 0.12, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 29/51 (56%)
Query: 151 HEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFAN 201
H++FIGGL + V+++ G + L K+ +T +KGYAF ++ +
Sbjct: 97 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 147
Score = 33.5 bits (75), Expect = 0.42, Method: Composition-based stats.
Identities = 17/78 (21%), Positives = 41/78 (52%), Gaps = 4/78 (5%)
Query: 317 LREP-DPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGF- 374
+R P D + + +F+ G+P + ++Q+++ + +G + L ++ +T K Y F
Sbjct: 84 IRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 143
Query: 375 --IDFSTHEAAVACINAI 390
+D + + A+A +N +
Sbjct: 144 EYVDINVTDQAIAGLNGM 161
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/89 (22%), Positives = 42/89 (47%), Gaps = 1/89 (1%)
Query: 142 AKDRKIKKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFAN 201
A+++K + +++G +D +T +D+ F G + + + + + KGYA+++FA
Sbjct: 28 AEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE 87
Query: 202 KEHAKRALTEMKNPVICGKRCGTAPSEDN 230
+ A+ M V G+ P N
Sbjct: 88 RNSVDAAVA-MDETVFRGRTIKVLPKRTN 115
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 33/59 (55%)
Query: 162 ATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEMKNPVICGK 220
+ + +R+VFE+ G V +V + + T +G+AFV+F ++ A+ A M + G+
Sbjct: 25 TSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGR 83
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTE 211
++++G L A + ++ + F G + V + +N G+AFV+F + A+ A+
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56
Query: 212 MKNPVICGKRC 222
+ VICG R
Sbjct: 57 LDGKVICGSRV 67
>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 = 35.0 bits (79), Expect = 0.16, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 9/63 (14%)
Query: 149 KEHEIFIGGLDRDATQEDVRKVFERIGEVIEVR----LHKNFSTNRNKGYAFVKFANKEH 204
K ++I G DAT +D+++ E G+V+ ++ LHK F KG FV F + E
Sbjct: 108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAF-----KGSIFVVFDSIES 162
Query: 205 AKR 207
AK+
Sbjct: 163 AKK 165
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 34.7 bits (78), Expect = 0.16, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 12/78 (15%)
Query: 150 EHEIFIGGLDRDATQEDVRKVFERI------GEVIEVRLHKNFSTNRNKGYAFVKFANKE 203
E+ +F+G L D + + F ++ G+V+ + T +KGY FVKF ++
Sbjct: 9 EYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ------TGVSKGYGFVKFTDEL 62
Query: 204 HAKRALTEMKNPVICGKR 221
KRALTE + V G +
Sbjct: 63 EQKRALTECQGAVGLGSK 80
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 34.7 bits (78), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 166 DVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEMKNPVICGKRC 222
D+R++F + G++++V + F+ +KG+ FV F N A RA ++ V+ G++
Sbjct: 31 DLRQMFGQFGKILDVEII--FNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKI 85
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 34.7 bits (78), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 166 DVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEMKNPVICGKRC 222
D+R++F + G++++V + F+ +KG+ FV F N A RA ++ V+ G++
Sbjct: 45 DLRQMFGQFGKILDVEII--FNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKI 99
>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 = 34.7 bits (78), Expect = 0.19, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 9/63 (14%)
Query: 149 KEHEIFIGGLDRDATQEDVRKVFERIGEVIEVR----LHKNFSTNRNKGYAFVKFANKEH 204
K ++I G DAT +D+++ E G+V+ ++ LHK F KG FV F + E
Sbjct: 110 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQXRRTLHKAF-----KGSIFVVFDSIES 164
Query: 205 AKR 207
AK+
Sbjct: 165 AKK 167
>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 = 34.7 bits (78), Expect = 0.19, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 9/63 (14%)
Query: 149 KEHEIFIGGLDRDATQEDVRKVFERIGEVIEVR----LHKNFSTNRNKGYAFVKFANKEH 204
K ++I G DAT +D+++ E G+V+ ++ LHK F KG FV F + E
Sbjct: 109 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQXRRTLHKAF-----KGSIFVVFDSIES 163
Query: 205 AKR 207
AK+
Sbjct: 164 AKK 166
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 34.7 bits (78), Expect = 0.20, Method: Composition-based stats.
Identities = 14/60 (23%), Positives = 35/60 (58%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+ + L ++ TQ++ + +F IG++ +L ++ T ++ GY FV +++ A +A+ +
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Score = 30.4 bits (67), Expect = 3.1, Method: Composition-based stats.
Identities = 16/67 (23%), Positives = 30/67 (44%)
Query: 336 VPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEF 395
+P + +++ + GD+ L R+ T + YGF+++S A IN +N +
Sbjct: 12 LPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKL 71
Query: 396 SDGNSKV 402
KV
Sbjct: 72 QTKTIKV 78
>pdb|1S79|A Chain A, Solution Structure Of The Central Rrm Of Human La Protein
Length = 103
Score = 34.3 bits (77), Expect = 0.22, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 9/63 (14%)
Query: 149 KEHEIFIGGLDRDATQEDVRKVFERIGEVIEVR----LHKNFSTNRNKGYAFVKFANKEH 204
K ++I G DAT +D+++ E G+V+ ++ LHK F KG FV F + E
Sbjct: 10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAF-----KGSIFVVFDSIES 64
Query: 205 AKR 207
AK+
Sbjct: 65 AKK 67
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 33.1 bits (74), Expect = 0.50, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 36/69 (52%), Gaps = 6/69 (8%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+++GGL T+ D+R F + GE+ + + + + AF++FA ++ A+ A +
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEI------RTITVVQRQQCAFIQFATRQAAEVAAEKS 68
Query: 213 KNPVICGKR 221
N +I R
Sbjct: 69 FNKLIVNGR 77
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 33.1 bits (74), Expect = 0.53, Method: Composition-based stats.
Identities = 18/77 (23%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 153 IFIGGLDRDATQEDVRKVFERIG--EVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALT 210
+++G T + + +V IG +V+E++ +N + ++KGYA V A++ + L
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 211 EMKNPVICGKRCGTAPS 227
+ V+ G++ P+
Sbjct: 118 LLPGKVLNGEKVDVRPA 134
>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 = 33.1 bits (74), Expect = 0.58, Method: Composition-based stats.
Identities = 17/77 (22%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 153 IFIGGLDRDATQEDVRKVFERIG--EVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALT 210
++IG L T ED+ + +G +++E++ +N + ++KG+A V ++ +K+ +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 211 EMKNPVICGKRCGTAPS 227
+ + G+ PS
Sbjct: 64 LLPKRELHGQNPVVTPS 80
>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 = 33.1 bits (74), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 15/70 (21%), Positives = 35/70 (50%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+F+ ++ D T+ +R+ FE G + + + + + + +GYAF+++ ++ A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 213 KNPVICGKRC 222
I G+R
Sbjct: 165 DGKKIDGRRV 174
Score = 32.3 bits (72), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 232 TLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMAA 291
TLFV + T+ ++++ + YG ++ I++V + G RG+AF+ + D +A
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGP--IKRIHMVYS-KRSGKPRGYAFIEYEHERDMHSA 160
Query: 292 YK 293
YK
Sbjct: 161 YK 162
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 32.7 bits (73), Expect = 0.64, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 7/72 (9%)
Query: 146 KIKKEHEIFIGGLDRDATQEDVRK----VFERIGEVIEVRLHKNFSTNRNKGYAFVKFAN 201
+ + H I+I L+ +++++K +F R G+++++ + ++ + +G AFV F
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKE 61
Query: 202 KEHAKRALTEMK 213
A AL M+
Sbjct: 62 VSSATNALRSMQ 73
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 32.7 bits (73), Expect = 0.65, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 7/72 (9%)
Query: 146 KIKKEHEIFIGGLDRDATQEDVRK----VFERIGEVIEVRLHKNFSTNRNKGYAFVKFAN 201
+ + H I+I L+ +++++K +F R G+++++ + ++ + +G AFV F
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKE 61
Query: 202 KEHAKRALTEMK 213
A AL M+
Sbjct: 62 VSSATNALRSMQ 73
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 32.7 bits (73), Expect = 0.65, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 7/72 (9%)
Query: 146 KIKKEHEIFIGGLDRDATQEDVRK----VFERIGEVIEVRLHKNFSTNRNKGYAFVKFAN 201
+ + H I+I L+ +++++K +F R G+++++ + ++ + +G AFV F
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKE 60
Query: 202 KEHAKRALTEMK 213
A AL M+
Sbjct: 61 VSSATNALRSMQ 72
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 32.7 bits (73), Expect = 0.66, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 7/72 (9%)
Query: 146 KIKKEHEIFIGGLDRDATQEDVRK----VFERIGEVIEVRLHKNFSTNRNKGYAFVKFAN 201
+ + H I+I L+ +++++K +F R G+++++ + ++ + +G AFV F
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKE 60
Query: 202 KEHAKRALTEMK 213
A AL M+
Sbjct: 61 VSSATNALRSMQ 72
>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 = 32.7 bits (73), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 15/70 (21%), Positives = 35/70 (50%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+F+ ++ D T+ +R+ FE G + + + + + + +GYAF+++ ++ A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 213 KNPVICGKRC 222
I G+R
Sbjct: 165 DGKKIDGRRV 174
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 232 TLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMAA 291
TLFV + T+ ++++ + YG ++ I++V + G RG+AF+ + D +A
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYG--PIKRIHMVYS-KRSGKPRGYAFIEYEHERDMHSA 160
Query: 292 YK 293
YK
Sbjct: 161 YK 162
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 32.7 bits (73), Expect = 0.69, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 7/72 (9%)
Query: 146 KIKKEHEIFIGGLDRDATQEDVRK----VFERIGEVIEVRLHKNFSTNRNKGYAFVKFAN 201
+ + H I+I L+ +++++K +F R G+++++ + ++ + +G AFV F
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKE 60
Query: 202 KEHAKRALTEMK 213
A AL M+
Sbjct: 61 VSSATNALRSMQ 72
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 32.7 bits (73), Expect = 0.78, Method: Composition-based stats.
Identities = 17/70 (24%), Positives = 37/70 (52%), Gaps = 7/70 (10%)
Query: 148 KKEHEIFIGGLDRDATQEDVRK----VFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKE 203
+ H I+I L+ +++++K +F R G+++++ + ++ + +G AFV F
Sbjct: 2 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKEVS 58
Query: 204 HAKRALTEMK 213
A AL M+
Sbjct: 59 SATNALRSMQ 68
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 32.3 bits (72), Expect = 0.78, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 7/72 (9%)
Query: 146 KIKKEHEIFIGGLDRDATQEDVRK----VFERIGEVIEVRLHKNFSTNRNKGYAFVKFAN 201
+ + H I+I L+ +++++K +F R G+++++ + ++ + +G AFV F
Sbjct: 1 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKE 57
Query: 202 KEHAKRALTEMK 213
A AL M+
Sbjct: 58 VSSATNALRSMQ 69
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 32.3 bits (72), Expect = 0.80, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 7/72 (9%)
Query: 146 KIKKEHEIFIGGLDRDATQEDVRK----VFERIGEVIEVRLHKNFSTNRNKGYAFVKFAN 201
+ + H I+I L+ +++++K +F R G+++++ + ++ + +G AFV F
Sbjct: 2 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKE 58
Query: 202 KEHAKRALTEMK 213
A AL M+
Sbjct: 59 VSSATNALRSMQ 70
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 32.3 bits (72), Expect = 0.82, Method: Composition-based stats.
Identities = 17/70 (24%), Positives = 37/70 (52%), Gaps = 7/70 (10%)
Query: 148 KKEHEIFIGGLDRDATQEDVRK----VFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKE 203
+ H I+I L+ +++++K +F R G+++++ + ++ + +G AFV F
Sbjct: 1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKEVS 57
Query: 204 HAKRALTEMK 213
A AL M+
Sbjct: 58 SATNALRSMQ 67
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 32.3 bits (72), Expect = 0.82, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 142 AKDRKIKKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFAN 201
K+ + + ++G L + Q D+ +F+ + + VRL ++ T++ KG+ +V+F
Sbjct: 7 GKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDE 65
Query: 202 KEHAKRALT 210
+ K ALT
Sbjct: 66 VDSLKEALT 74
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 32.3 bits (72), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 8/78 (10%)
Query: 325 MAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAV 384
MA VK +F+ + E + +G + R+ K KDY FI F + AV
Sbjct: 8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERV--------KKLKDYAFIHFDERDGAV 59
Query: 385 ACINAINNKEFSDGNSKV 402
+ +N K+ N ++
Sbjct: 60 KAMEEMNGKDLEGENIEI 77
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 32.3 bits (72), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 148 KKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKR 207
K ++ +G + T +++R FE G VIE + K+ YAFV E A
Sbjct: 8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVE 59
Query: 208 ALTEMKNPVICGKR 221
A+ + N GKR
Sbjct: 60 AIRGLDNTEFQGKR 73
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 29/69 (42%), Gaps = 8/69 (11%)
Query: 336 VPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEF 395
+ P ++R + + YG VI + KDY F+ E AV I ++N EF
Sbjct: 18 ISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLDNTEF 69
Query: 396 SDGNSKVKL 404
V+L
Sbjct: 70 QGKRMHVQL 78
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 32.3 bits (72), Expect = 0.91, Method: Composition-based stats.
Identities = 20/87 (22%), Positives = 42/87 (48%)
Query: 135 RRELNAIAKDRKIKKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGY 194
++ + A ++ + +FI L ++ +D+ ++F G V+ ++ + TN +K +
Sbjct: 10 QQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCF 69
Query: 195 AFVKFANKEHAKRALTEMKNPVICGKR 221
FV + N A+ A+ M I KR
Sbjct: 70 GFVSYDNPVSAQAAIQSMNGFQIGMKR 96
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 32.3 bits (72), Expect = 0.95, Method: Composition-based stats.
Identities = 19/91 (20%), Positives = 43/91 (47%), Gaps = 6/91 (6%)
Query: 324 IMAHVK--TVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHE 381
I++H+ T+++ PP + + IRD ++ V + ++ + + +ID ++ E
Sbjct: 74 IVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKE 133
Query: 382 AAVACINAINNKEFSDGNSKVKLRARLSNPM 412
A C+ +N + L ++SNP+
Sbjct: 134 DARYCVEKLNGLKIEG----YTLVTKVSNPL 160
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 32.3 bits (72), Expect = 0.97, Method: Composition-based stats.
Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTE 211
++++G L + + ++ + F G + V + +N G+AFV+F + A A+ E
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRE 129
Query: 212 MKNPVICGKR 221
+ +CG R
Sbjct: 130 LDGRTLCGCR 139
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 32.3 bits (72), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 14/67 (20%), Positives = 31/67 (46%)
Query: 318 REPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDF 377
RE ++ + + +PP + Q + ++ +G + R L + T + K YGF ++
Sbjct: 85 RELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEY 144
Query: 378 STHEAAV 384
++A
Sbjct: 145 MKKDSAA 151
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 32.3 bits (72), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 14/67 (20%), Positives = 31/67 (46%)
Query: 318 REPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDF 377
RE ++ + + +PP + Q + ++ +G + R L + T + K YGF ++
Sbjct: 85 RELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEY 144
Query: 378 STHEAAV 384
++A
Sbjct: 145 MKKDSAA 151
>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 = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/67 (20%), Positives = 31/67 (46%)
Query: 318 REPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDF 377
RE ++ + + +PP + Q + ++ +G + R L + T + K YGF ++
Sbjct: 83 RELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEY 142
Query: 378 STHEAAV 384
++A
Sbjct: 143 MKKDSAA 149
>pdb|2KH9|A Chain A, Solution Structure Of Yeast Prp24-Rrm2 Bound To A Fragment
Of U6 Rna
Length = 92
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 22/86 (25%), Positives = 43/86 (50%), Gaps = 10/86 (11%)
Query: 330 TVFLDGVPPHWKENQIRDQIKGYGDV---IRIVLARNMSTAKRKDYGFIDFSTHEAAVAC 386
T+++ PP + + IRD ++ V IR+ R +T++R + +ID ++ E A C
Sbjct: 5 TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRR--FAYIDVTSKEDARYC 61
Query: 387 INAINNKEFSDGNSKVKLRARLSNPM 412
+ +N + L ++SNP+
Sbjct: 62 VEKLNGLKIEG----YTLVTKVSNPL 83
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 32.0 bits (71), Expect = 1.3, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 3/62 (4%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNR--NKGYAFVKFANKEHAKRAL 209
++F+GGL D ++++ F R G ++ HK S + KGYAF+ F +E + +AL
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLF-QEESSVQAL 68
Query: 210 TE 211
+
Sbjct: 69 ID 70
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 31.2 bits (69), Expect = 1.7, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRAL 209
+++ L T+ D+ +F R E + T R +G AF+ F NKE A +AL
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 31.2 bits (69), Expect = 1.8, Method: Composition-based stats.
Identities = 17/75 (22%), Positives = 36/75 (48%)
Query: 331 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAI 390
+F+ +P + + + +G+VI + + T+ K +GF+ F ++A I A+
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 391 NNKEFSDGNSKVKLR 405
N + KV+L+
Sbjct: 103 NGFQVGTKRLKVQLK 117
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 30.8 bits (68), Expect = 2.5, Method: Composition-based stats.
Identities = 16/70 (22%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 152 EIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTE 211
++++G L + + ++ + F G + V + +N G+AFV+F + A A+ +
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRD 129
Query: 212 MKNPVICGKR 221
+ +CG R
Sbjct: 130 LDGRTLCGCR 139
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 30.4 bits (67), Expect = 3.1, Method: Composition-based stats.
Identities = 16/68 (23%), Positives = 36/68 (52%), Gaps = 7/68 (10%)
Query: 146 KIKKEHEIFIGGLDRDATQEDVRK----VFERIGEVIEVRLHKNFSTNRNKGYAFVKFAN 201
+ + H I+I L+ +++++K +F R G+++++ + ++ + +G AFV F
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KXRGQAFVIFKE 60
Query: 202 KEHAKRAL 209
A AL
Sbjct: 61 VSSATNAL 68
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 30.4 bits (67), Expect = 3.1, Method: Composition-based stats.
Identities = 16/68 (23%), Positives = 36/68 (52%), Gaps = 7/68 (10%)
Query: 146 KIKKEHEIFIGGLDRDATQEDVRK----VFERIGEVIEVRLHKNFSTNRNKGYAFVKFAN 201
+ + H I+I L+ +++++K +F R G+++++ + ++ + +G AFV F
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KXRGQAFVIFKE 61
Query: 202 KEHAKRAL 209
A AL
Sbjct: 62 VSSATNAL 69
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 30.4 bits (67), Expect = 3.2, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGE-VIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTE 211
+++G L+ + + + F +GE V+ V++ +N T GY FV+FA+ A++ L +
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 212 MKNPVICG 219
+ + G
Sbjct: 72 INGKPLPG 79
Score = 30.0 bits (66), Expect = 4.2, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 330 TVFLDGVPPHWKENQIRDQIKGYGD-VIRIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 388
++++ + P+ EN I G+ V+ + + RN T Y F++F+ A C++
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 389 AINNK 393
IN K
Sbjct: 71 KINGK 75
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 30.4 bits (67), Expect = 3.4, Method: Composition-based stats.
Identities = 16/68 (23%), Positives = 36/68 (52%), Gaps = 7/68 (10%)
Query: 146 KIKKEHEIFIGGLDRDATQEDVRK----VFERIGEVIEVRLHKNFSTNRNKGYAFVKFAN 201
+ + H I+I L+ +++++K +F R G+++++ + ++ + +G AFV F
Sbjct: 2 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KXRGQAFVIFKE 58
Query: 202 KEHAKRAL 209
A AL
Sbjct: 59 VSSATNAL 66
>pdb|2DGW|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Rna-Binding Protein 19
Length = 91
Score = 30.0 bits (66), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 151 HEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRAL 209
H + + G + T+++V + + + + +R+ +N N+ GY FV F+N+E K+AL
Sbjct: 11 HTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKT-GYIFVDFSNEEEVKQAL 67
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 29.6 bits (65), Expect = 5.3, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 5/68 (7%)
Query: 233 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMAAY 292
L+V + T +++ ++Q YG I L Q G+SRG F+ F ++A A
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILL---DQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 293 KRL--QKP 298
K L QKP
Sbjct: 61 KGLNGQKP 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 = 29.6 bits (65), Expect = 6.6, Method: Composition-based stats.
Identities = 15/75 (20%), Positives = 37/75 (49%)
Query: 331 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAI 390
+++ +P ++Q+ YG +++ + R+ T + + F+ ++ E A I+A+
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 391 NNKEFSDGNSKVKLR 405
NN G+ + +R
Sbjct: 76 NNVIPEGGSQPLSVR 90
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 29.3 bits (64), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 18/85 (21%), Positives = 39/85 (45%), Gaps = 9/85 (10%)
Query: 147 IKKEHEIFIGGLD-RDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHA 205
I + +FIG L ++ ++ED+ ++F G ++++ N + F++F N +
Sbjct: 7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQI--------NIKNAFGFIQFDNPQSV 58
Query: 206 KRALTEMKNPVICGKRCGTAPSEDN 230
+ A+ + GK+ S N
Sbjct: 59 RDAIECESQEMNFGKKLILEVSSSN 83
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 29.3 bits (64), Expect = 7.0, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 23/34 (67%)
Query: 166 DVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKF 199
D+ F +G+V +VR+ + ++ R+KG A+V+F
Sbjct: 41 DLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 74
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 29.3 bits (64), Expect = 7.5, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 6/79 (7%)
Query: 153 IFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANKEHAKRALTEM 212
+++G L RD T+ + ++F +IG ++ ++ N Y FV+F A AL M
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAM 75
Query: 213 KNPVICGKRC----GTAPS 227
I GK T PS
Sbjct: 76 NGRKILGKEVKVNWATTPS 94
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 29.3 bits (64), Expect = 7.5, Method: Composition-based stats.
Identities = 13/67 (19%), Positives = 38/67 (56%)
Query: 143 KDRKIKKEHEIFIGGLDRDATQEDVRKVFERIGEVIEVRLHKNFSTNRNKGYAFVKFANK 202
+++ +KK +++G L T+E + ++F + G++ ++ + + G+ FV++ ++
Sbjct: 32 QEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSR 91
Query: 203 EHAKRAL 209
A+ A+
Sbjct: 92 ADAENAM 98
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 28.9 bits (63), Expect = 9.1, Method: Composition-based stats.
Identities = 28/100 (28%), Positives = 47/100 (47%), Gaps = 19/100 (19%)
Query: 224 TAPSEDNDT------LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGF 277
+ S D DT L+V N+ + ++E I+++ + VE + + D +
Sbjct: 3 SGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD---------Y 53
Query: 278 AFVMFSCHVDAMAAYKRLQKPDVVFGHPERTVKVAFAEPL 317
AFV FS DA+ A K L V+ G P ++V A+P+
Sbjct: 54 AFVHFSNREDAVEAMKALNG-KVLDGSP---IEVTLAKPV 89
>pdb|2DHA|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Hypothetical Protein Flj201171
Length = 123
Score = 28.9 bits (63), Expect = 9.9, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 7/80 (8%)
Query: 147 IKKEHEIFIG--GLDRDATQEDVRKVFERIGEVI---EVRLHKNFSTNRNKGYAFVKFAN 201
+ KE+++ + GL AT E+V F + + E L + R G AFV FA
Sbjct: 18 LSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFAC 77
Query: 202 KEHAKRALTEMKNPVICGKR 221
+E+A+ AL + K+ + GKR
Sbjct: 78 EEYAQNALRKHKD--LLGKR 95
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
0.320 0.138 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,342,030
Number of Sequences: 62578
Number of extensions: 776165
Number of successful extensions: 1967
Number of sequences better than 100.0: 179
Number of HSP's better than 100.0 without gapping: 127
Number of HSP's successfully gapped in prelim test: 52
Number of HSP's that attempted gapping in prelim test: 1615
Number of HSP's gapped (non-prelim): 362
length of query: 681
length of database: 14,973,337
effective HSP length: 105
effective length of query: 576
effective length of database: 8,402,647
effective search space: 4839924672
effective search space used: 4839924672
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)