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= 013047
(450 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 43/190 (22%), Positives = 92/190 (48%), Gaps = 21/190 (11%)
Query: 33 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSD---IQHEGLSRGFAFVMFSCHVDAM 89
++VG+I ++ I+Q +G +++I++ D ++H +GFAFV + A
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGP--IKSIDMSWDSVTMKH----KGFAFVEYEVPEAAQ 84
Query: 90 AAYKRLQKPDVVFGHPERTVKVA------FAEPLREPDPEIMAHVKTVFLDGVPPHWKEN 143
A +++ V+ G R +KV A+P+ + E +++ V ++
Sbjct: 85 LALEQMN--SVMLGG--RNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDD 140
Query: 144 QIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNSKVK 203
I+ + +G + LAR+ +T K K YGFI++ +++ ++++N F G ++
Sbjct: 141 DIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN--LFDLGGQYLR 198
Query: 204 LRARLSNPMP 213
+ ++ PMP
Sbjct: 199 VGKAVTPPMP 208
Score = 32.7 bits (73), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 19/89 (21%), Positives = 39/89 (43%)
Query: 125 MAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAV 184
+A + V++ + E+ IR +G + I ++ + T K K + F+++ EAA
Sbjct: 25 LAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQ 84
Query: 185 ACINAINNKEFSDGNSKVKLRARLSNPMP 213
+ +N+ N KV + + P
Sbjct: 85 LALEQMNSVMLGGRNIKVGRPSNIGQAQP 113
>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 = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 43/190 (22%), Positives = 92/190 (48%), Gaps = 21/190 (11%)
Query: 33 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSD---IQHEGLSRGFAFVMFSCHVDAM 89
++VG+I ++ I+Q +G +++I++ D ++H +GFAFV + A
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFG--PIKSIDMSWDSVTMKH----KGFAFVEYEVPEAAQ 69
Query: 90 AAYKRLQKPDVVFGHPERTVKVA------FAEPLREPDPEIMAHVKTVFLDGVPPHWKEN 143
A +++ V+ G R +KV A+P+ + E +++ V ++
Sbjct: 70 LALEQMN--SVMLGG--RNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDD 125
Query: 144 QIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNSKVK 203
I+ + +G + LAR+ +T K K YGFI++ +++ ++++N F G ++
Sbjct: 126 DIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN--LFDLGGQYLR 183
Query: 204 LRARLSNPMP 213
+ ++ PMP
Sbjct: 184 VGKAVTPPMP 193
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 41/155 (26%), Positives = 73/155 (47%), Gaps = 15/155 (9%)
Query: 33 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSC--HVDAMA 90
LF+G + T E+++ + +G + + ++ D + SRGF FV ++ VDA A
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGT--LTDCVVMRD-PNTKRSRGFGFVTYATVEEVDA-A 72
Query: 91 AYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEIMAH--VKTVFLDGVPPHWKENQIRDQ 148
R K D P+R V RE AH VK +F+ G+ +E+ +RD
Sbjct: 73 MNARPHKVDGRVVEPKRAVS-------REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 125
Query: 149 IKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAA 183
+ YG + I + + + K++ + F+ F H++
Sbjct: 126 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 160
Score = 35.4 bits (80), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 114 AEPLREPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYG 173
+E +EP+ ++ +F+ G+ + +R + +G + V+ R+ +T + + +G
Sbjct: 5 SESPKEPE-----QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG 59
Query: 174 FIDFSTHEAAVACINA 189
F+ ++T E A +NA
Sbjct: 60 FVTYATVEEVDAAMNA 75
>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 = 48.1 bits (113), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 41/155 (26%), Positives = 73/155 (47%), Gaps = 15/155 (9%)
Query: 33 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSC--HVDAMA 90
LF+G + T E+++ + +G + + ++ D + SRGF FV ++ VDA A
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGT--LTDCVVMRD-PNTKRSRGFGFVTYATVEEVDA-A 70
Query: 91 AYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEIMAH--VKTVFLDGVPPHWKENQIRDQ 148
R K D P+R V RE AH VK +F+ G+ +E+ +RD
Sbjct: 71 MNARPHKVDGRVVEPKRAVS-------REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 123
Query: 149 IKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAA 183
+ YG + I + + + K++ + F+ F H++
Sbjct: 124 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 158
Score = 35.4 bits (80), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 114 AEPLREPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYG 173
+E +EP+ ++ +F+ G+ + +R + +G + V+ R+ +T + + +G
Sbjct: 3 SESPKEPE-----QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG 57
Query: 174 FIDFSTHEAAVACINA 189
F+ ++T E A +NA
Sbjct: 58 FVTYATVEEVDAAMNA 73
>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 = 48.1 bits (113), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 41/155 (26%), Positives = 73/155 (47%), Gaps = 15/155 (9%)
Query: 33 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSC--HVDAMA 90
LF+G + T E+++ + +G + + ++ D + SRGF FV ++ VDA A
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGT--LTDCVVMRD-PNTKRSRGFGFVTYATVEEVDA-A 71
Query: 91 AYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEIMAH--VKTVFLDGVPPHWKENQIRDQ 148
R K D P+R V RE AH VK +F+ G+ +E+ +RD
Sbjct: 72 MNARPHKVDGRVVEPKRAVS-------REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 124
Query: 149 IKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAA 183
+ YG + I + + + K++ + F+ F H++
Sbjct: 125 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 159
Score = 35.4 bits (80), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 114 AEPLREPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYG 173
+E +EP+ ++ +F+ G+ + +R + +G + V+ R+ +T + + +G
Sbjct: 4 SESPKEPE-----QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG 58
Query: 174 FIDFSTHEAAVACINA 189
F+ ++T E A +NA
Sbjct: 59 FVTYATVEEVDAAMNA 74
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 45/180 (25%), Positives = 76/180 (42%), Gaps = 17/180 (9%)
Query: 26 PSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSD-IQHEGLSRGFAFVMFSC 84
P D +FVG + TW+++ +++ + YG V IN++ D Q+ S+G FV F
Sbjct: 11 PDLDAIKMFVGQVPRTWSEKDLRELFEQYG--AVYEINVLRDRSQNPPQSKGCCFVTFYT 68
Query: 85 HVDAMAAYKRLQKPDVVFG--HPERTVKVAFAEPLREPDPEIMAHV--KTVFLDGVPPHW 140
A+ A L V+ G HP + ++ D E V + +F+ +
Sbjct: 69 RKAALEAQNALHNMKVLPGMHHPIQ---------MKPADSEKNNAVEDRKLFIGMISKKC 119
Query: 141 KENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNS 200
EN IR +G + + R R F+ F+T A I A++ + +G S
Sbjct: 120 TENDIRVMFSSFGQIEECRILRGPDGLSR-GCAFVTFTTRAMAQTAIKAMHQAQTMEGCS 178
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 3/84 (3%)
Query: 117 LREPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDV--IRIVLARNMSTAKRKDYGF 174
L PD + +K +F+ VP W E +R+ + YG V I ++ R+ + + K F
Sbjct: 5 LDHPDQPDLDAIK-MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCF 63
Query: 175 IDFSTHEAAVACINAINNKEFSDG 198
+ F T +AA+ NA++N + G
Sbjct: 64 VTFYTRKAALEAQNALHNMKVLPG 87
Score = 33.1 bits (74), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 29/96 (30%), Positives = 43/96 (44%), Gaps = 10/96 (10%)
Query: 25 APSEDNDT-----LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAF 79
A SE N+ LF+G I T+ I+ +G +E ++ +GLSRG AF
Sbjct: 97 ADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFG--QIEECRILRG--PDGLSRGCAF 152
Query: 80 VMFSCHVDAMAAYKRLQKPDVVFGHPERTVKVAFAE 115
V F+ A A K + + + G V V FA+
Sbjct: 153 VTFTTRAMAQTAIKAMHQAQTMEGCSSPMV-VKFAD 187
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
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: 33 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSC--HVDAMA 90
LF+G + T E+++ + +G + + ++ D + SRGF FV ++ VDA A
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGT--LTDCVVMRD-PNTKRSRGFGFVTYATVEEVDA-A 71
Query: 91 AYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEIMAH--VKTVFLDGVPPHWKENQIRDQ 148
R K D P+R V RE AH VK +F+ G+ +E+ +RD
Sbjct: 72 MNARPHKVDGRVVEPKRAVS-------REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 124
Query: 149 IKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAA 183
+ YG + I + + + K++ + F+ F H++
Sbjct: 125 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 159
Score = 35.4 bits (80), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 114 AEPLREPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYG 173
+E +EP+ ++ +F+ G+ + +R + +G + V+ R+ +T + + +G
Sbjct: 4 SESPKEPE-----QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG 58
Query: 174 FIDFSTHEAAVACINA 189
F+ ++T E A +NA
Sbjct: 59 FVTYATVEEVDAAMNA 74
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 48.1 bits (113), Expect = 1e-05, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 39/75 (52%)
Query: 122 PEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHE 181
P + +++VF+ +P E Q++D G V+ L + T K K YGF ++ E
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 182 AAVACINAINNKEFS 196
A++ + +N +EFS
Sbjct: 62 TALSAMRNLNGREFS 76
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 41/155 (26%), Positives = 73/155 (47%), Gaps = 15/155 (9%)
Query: 33 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSC--HVDAMA 90
LF+G + T E+++ + +G + + ++ D + SRGF FV ++ VDA A
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGT--LTDCVVMRD-PNTKRSRGFGFVTYATVEEVDA-A 69
Query: 91 AYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEIMAH--VKTVFLDGVPPHWKENQIRDQ 148
R K D P+R V RE AH VK +F+ G+ +E+ +RD
Sbjct: 70 MNARPHKVDGRVVEPKRAVS-------REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 122
Query: 149 IKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAA 183
+ YG + I + + + K++ + F+ F H++
Sbjct: 123 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 157
Score = 35.0 bits (79), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 114 AEPLREPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYG 173
+E +EP+ ++ +F+ G+ + +R + +G + V+ R+ +T + + +G
Sbjct: 2 SESPKEPE-----QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG 56
Query: 174 FIDFSTHEAAVACINA 189
F+ ++T E A +NA
Sbjct: 57 FVTYATVEEVDAAMNA 72
>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 = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 41/155 (26%), Positives = 73/155 (47%), Gaps = 15/155 (9%)
Query: 33 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSC--HVDAMA 90
LF+G + T E+++ + +G + + ++ D + SRGF FV ++ VDA A
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGT--LTDCVVMRD-PNTKRSRGFGFVTYATVEEVDA-A 64
Query: 91 AYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEIMAH--VKTVFLDGVPPHWKENQIRDQ 148
R K D P+R V RE AH VK +F+ G+ +E+ +RD
Sbjct: 65 MNARPHKVDGRVVEPKRAVS-------REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDY 117
Query: 149 IKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAA 183
+ YG + I + + + K++ + F+ F H++
Sbjct: 118 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 152
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 14/63 (22%), Positives = 34/63 (53%)
Query: 127 HVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVAC 186
++ +F+ G+ + +R + +G + V+ R+ +T + + +GF+ ++T E A
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64
Query: 187 INA 189
+NA
Sbjct: 65 MNA 67
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 44/177 (24%), Positives = 75/177 (42%), Gaps = 17/177 (9%)
Query: 29 DNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSD-IQHEGLSRGFAFVMFSCHVD 87
D +FVG + TW+++ +++ + YG V IN++ D Q+ S+G FV F
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYG--AVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 59
Query: 88 AMAAYKRLQKPDVVFG--HPERTVKVAFAEPLREPDPEIMAHV--KTVFLDGVPPHWKEN 143
A+ A L V+ G HP + ++ D E V + +F+ + EN
Sbjct: 60 ALEAQNALHNMKVLPGMHHPIQ---------MKPADSEKNNAVEDRKLFIGMISKKCTEN 110
Query: 144 QIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNS 200
IR +G + + R R F+ F+T A I A++ + +G S
Sbjct: 111 DIRVMFSSFGQIEECRILRGPDGLSR-GCAFVTFTTRAMAQTAIKAMHQAQTMEGCS 166
Score = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 29/96 (30%), Positives = 43/96 (44%), Gaps = 10/96 (10%)
Query: 25 APSEDNDT-----LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAF 79
A SE N+ LF+G I T+ I+ +G +E ++ +GLSRG AF
Sbjct: 85 ADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFG--QIEECRILRG--PDGLSRGCAF 140
Query: 80 VMFSCHVDAMAAYKRLQKPDVVFGHPERTVKVAFAE 115
V F+ A A K + + + G V V FA+
Sbjct: 141 VTFTTRAMAQTAIKAMHQAQTMEGCSSPMV-VKFAD 175
>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 = 45.1 bits (105), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 45/177 (25%), Positives = 78/177 (44%), Gaps = 18/177 (10%)
Query: 24 TAPSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFS 83
+APS +L+VG++ T+ + +K G + +I + D+ S G+A+V F
Sbjct: 9 SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAG--PILSIRVCRDMITR-RSLGYAYVNFQ 65
Query: 84 CHVDAMAAYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEI-MAHVKTVFLDGVPPHWKE 142
DA A + DV+ G P R + + DP + + V +F+ +
Sbjct: 66 QPADAERALDTMNF-DVIKGKPVRIM-------WSQRDPSLRKSGVGNIFIKNLDKSIDN 117
Query: 143 NQIRDQIKGYGDVI--RIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSD 197
+ D +G+++ ++V N S K YGF+ F T EAA I +N +D
Sbjct: 118 KALYDTFSAFGNILSCKVVCDENGS----KGYGFVHFETQEAAERAIEKMNGMLLND 170
>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 = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 43/172 (25%), Positives = 71/172 (41%), Gaps = 17/172 (9%)
Query: 34 FVGNICNTWTKEAIKQKLKDYGVEGVENINLVSD-IQHEGLSRGFAFVMFSCHVDAMAAY 92
FVG + TW+++ +++ + YG V IN++ D Q+ S+G FV F A+ A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYG--AVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 93 KRLQKPDVVFG--HPERTVKVAFAEPLREPDPEIMAHV--KTVFLDGVPPHWKENQIRDQ 148
L V+ G HP + + D E V + +F+ + EN IR
Sbjct: 65 NALHNXKVLPGXHHPIQX---------KPADSEKNNAVEDRKLFIGXISKKCTENDIRVX 115
Query: 149 IKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNS 200
+G + + R R F+ F+T A I A + + +G S
Sbjct: 116 FSSFGQIEECRILRGPDGLSR-GCAFVTFTTRAXAQTAIKAXHQAQTXEGCS 166
Score = 32.7 bits (73), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 9/74 (12%)
Query: 25 APSEDNDT-----LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAF 79
A SE N+ LF+G I T+ I+ +G +E ++ +GLSRG AF
Sbjct: 85 ADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFG--QIEECRILRG--PDGLSRGCAF 140
Query: 80 VMFSCHVDAMAAYK 93
V F+ A A K
Sbjct: 141 VTFTTRAXAQTAIK 154
>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 = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 45/177 (25%), Positives = 78/177 (44%), Gaps = 18/177 (10%)
Query: 24 TAPSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFS 83
+APS +L+VG++ T+ + +K G + +I + D+ S G+A+V F
Sbjct: 4 SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAG--PILSIRVCRDMITRR-SLGYAYVNFQ 60
Query: 84 CHVDAMAAYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEI-MAHVKTVFLDGVPPHWKE 142
DA A + DV+ G P R + + DP + + V +F+ +
Sbjct: 61 QPADAERALDTMNF-DVIKGKPVRIM-------WSQRDPSLRKSGVGNIFIKNLDKSIDN 112
Query: 143 NQIRDQIKGYGDVI--RIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSD 197
+ D +G+++ ++V N S K YGF+ F T EAA I +N +D
Sbjct: 113 KALYDTFSAFGNILSCKVVCDENGS----KGYGFVHFETQEAAERAIEKMNGMLLND 165
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 32/134 (23%), Positives = 63/134 (47%), Gaps = 9/134 (6%)
Query: 72 GLSRGFAFVMFSCHVDAMAAYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEIMAHVKTV 131
G S G+AFV F+ +D+ A K L V + +KV++A P E + +
Sbjct: 42 GYSYGYAFVDFTSEMDSQRAIKVLNGITV----RNKRLKVSYARPGGESIKD-----TNL 92
Query: 132 FLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAIN 191
++ +P ++Q+ YG +++ + R+ T + + F+ ++ E A I+A+N
Sbjct: 93 YVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Query: 192 NKEFSDGNSKVKLR 205
N G+ + +R
Sbjct: 153 NVIPEGGSQPLSVR 166
>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 = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 39/186 (20%), Positives = 84/186 (45%), Gaps = 13/186 (6%)
Query: 33 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMAAY 92
++VG+I ++ I+Q +G +++I+ D +GFAFV + A A
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFG--PIKSIDXSWD-SVTXKHKGFAFVEYEVPEAAQLAL 71
Query: 93 KR-----LQKPDVVFGHPERTVKVAFAEPLREPDPEIMAHVKTVFLDGVPPHWKENQIRD 147
++ L ++ G P + A+P+ + E +++ V ++ I+
Sbjct: 72 EQXNSVXLGGRNIKVGRPS---NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKS 128
Query: 148 QIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNSKVKLRAR 207
+ +G + LAR+ +T K K YGFI++ +++ +++ N F G +++
Sbjct: 129 VFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN--LFDLGGQYLRVGKA 186
Query: 208 LSNPMP 213
++ P P
Sbjct: 187 VTPPXP 192
>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 = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 32/134 (23%), Positives = 62/134 (46%), Gaps = 9/134 (6%)
Query: 72 GLSRGFAFVMFSCHVDAMAAYKRLQKPDVVFGHPERTVKVAFAEPLREPDPEIMAHVKTV 131
G S G+AFV F+ D+ A K L V + +KV++A P E + +
Sbjct: 53 GYSFGYAFVDFTSEXDSQRAIKVLNGITV----RNKRLKVSYARPGGESIKD-----TNL 103
Query: 132 FLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAIN 191
++ +P ++Q+ YG +++ + R+ T + + F+ ++ E A I+A+N
Sbjct: 104 YVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
Query: 192 NKEFSDGNSKVKLR 205
N G+ + +R
Sbjct: 164 NVIPEGGSQPLSVR 177
>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 = 42.4 bits (98), Expect = 5e-04, Method: Composition-based stats.
Identities = 26/83 (31%), Positives = 44/83 (53%), Gaps = 5/83 (6%)
Query: 128 VKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACI 187
VK +F+ G+ P E +IR+ G+G+V I L + T KR+ + FI F E +
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEP----V 56
Query: 188 NAINNKEFSD-GNSKVKLRARLS 209
I K++ + G SK +++ +S
Sbjct: 57 KKIMEKKYHNVGLSKCEIKVAMS 79
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 42.4 bits (98), Expect = 6e-04, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 33/66 (50%)
Query: 130 TVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINA 189
TV++ +P N + YG V+++ + ++ T K K FI F ++A C A
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 190 INNKEF 195
INNK+
Sbjct: 78 INNKQL 83
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 42.4 bits (98), Expect = 6e-04, Method: Composition-based stats.
Identities = 31/107 (28%), Positives = 55/107 (51%), Gaps = 5/107 (4%)
Query: 23 GTAPSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMF 82
G++ S N LF+G I +E I +++ EGV ++ + + + +RGFAFV +
Sbjct: 1 GSSGSSGNCRLFIGGIPKMKKREEILEEIAKV-TEGVLDVIVYASAADKMKNRGFAFVEY 59
Query: 83 SCHVDAMAAYKRLQKPDV-VFGHPERTVKVAFAEPLREPDPEIMAHV 128
H A A ++L + ++GH + V +AEP + D ++M V
Sbjct: 60 ESHRAAAMARRKLMPGRIQLWGH---QIAVDWAEPEIDVDEDVMETV 103
Score = 29.6 bits (65), Expect = 3.3, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 131 VFLDGVPPHWKENQIRDQI----KGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAA 183
+F+ G+P K +I ++I +G DV IV A K + + F+++ +H AA
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEGVLDV--IVYASAADKMKNRGFAFVEYESHRAA 65
>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 = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%)
Query: 119 EPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFS 178
EP P+ +F+ + +E++I+++ YG++ I L + T K Y +++
Sbjct: 63 EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE 122
Query: 179 THEAAVACINAINNKEF 195
TH+ A+A A+N E
Sbjct: 123 THKQALAAKEALNGAEI 139
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 39/76 (51%)
Query: 119 EPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFS 178
EP P+ +F+ + +E++I+++ YG++ I L + T K Y +++
Sbjct: 17 EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE 76
Query: 179 THEAAVACINAINNKE 194
TH+ A+A A+N E
Sbjct: 77 THKQALAAKEALNGAE 92
>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 = 0.003, Method: Composition-based stats.
Identities = 29/95 (30%), Positives = 48/95 (50%), Gaps = 4/95 (4%)
Query: 23 GTAPSEDN--DTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFV 80
G+ PS +N DT+ + N+ T ++I L Y V N+ ++ D Q + L+RGFAF+
Sbjct: 14 GSEPSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQ-LNRGFAFI 72
Query: 81 MFSCHVDAMAAYKRLQKPDVVFGHPERTVKVAFAE 115
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 = 0.003, Method: Composition-based stats.
Identities = 28/85 (32%), Positives = 40/85 (47%), Gaps = 1/85 (1%)
Query: 31 DTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMA 90
DT+ + NI ++I L Y V NI L+ D Q + +RGFAFV S +DA
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQ-NRGFAFVQLSSAMDASQ 68
Query: 91 AYKRLQKPDVVFGHPERTVKVAFAE 115
+ LQ +T+ V FA+
Sbjct: 69 LLQILQSLHPPLKIDGKTIGVDFAK 93
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 8/73 (10%)
Query: 121 DPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTH 180
DPE+MA VK +F+ + E + +G + R+ K KDY F+ F
Sbjct: 8 DPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERV--------KKLKDYAFVHFEDR 59
Query: 181 EAAVACINAINNK 193
AAV ++ +N K
Sbjct: 60 GAAVKAMDEMNGK 72
>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 = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDV--IRIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 188
+F+ VP W E +R+ + YG V I ++ R+ + + K F+ F T +AA+ N
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 189 AINNKEFSDG 198
A++N + G
Sbjct: 66 ALHNMKVLPG 75
Score = 36.6 bits (83), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 29 DNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSD-IQHEGLSRGFAFVMFSCHVD 87
D +FVG + TW+++ +++ + YG V IN++ D Q+ S+G FV F
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYG--AVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 59
Query: 88 AMAAYKRLQKPDVVFG--HP 105
A+ A L V+ G HP
Sbjct: 60 ALEAQNALHNMKVLPGMHHP 79
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 38.5 bits (88), Expect = 0.008, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 29/53 (54%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAA 183
+F+ G+P H + +R +G+GD+ V+ + T K + YGF+ + AA
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 38.1 bits (87), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%)
Query: 139 HWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFS 196
+ E+ +R + +G + IVL ++ T + K YGFI FS E A + +N E +
Sbjct: 16 NITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELA 73
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 38.1 bits (87), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 33/138 (23%), Positives = 59/138 (42%), Gaps = 14/138 (10%)
Query: 59 VENINLVSDIQHEGLSRGFAFVMFSCHVDAMAAYKRLQKPDVVFGHPERTVKVAFAEPLR 118
+E+ LV D + G S G+ FV +S DA A L +T+KV++A P
Sbjct: 31 IESCKLVRD-KITGQSLGYGFVNYSDPNDADKAINTLNG----LKLQTKTIKVSYARPSS 85
Query: 119 EPDPEIMAHVK--TVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFID 176
A ++ +++ G+P + ++ YG +I + + +T + GFI
Sbjct: 86 -------ASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIR 138
Query: 177 FSTHEAAVACINAINNKE 194
F A I +N ++
Sbjct: 139 FDKRIEAEEAIKGLNGQK 156
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 39/84 (46%), Gaps = 9/84 (10%)
Query: 33 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMAAY 92
L+V + T +++ ++Q YG I L Q G+SRG F+ F ++A A
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLD---QATGVSRGVGFIRFDKRIEAEEAI 149
Query: 93 KRL--QKPDVVFGHPERTVKVAFA 114
K L QKP G E + V FA
Sbjct: 150 KGLNGQKP---LGAAE-PITVKFA 169
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 34/78 (43%)
Query: 125 MAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAV 184
M + ++ +P + +++ + GD+ L R+ T + YGF+++S A
Sbjct: 1 MDSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDAD 60
Query: 185 ACINAINNKEFSDGNSKV 202
IN +N + KV
Sbjct: 61 KAINTLNGLKLQTKTIKV 78
>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 = 37.7 bits (86), Expect = 0.013, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 36/77 (46%)
Query: 119 EPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFS 178
EP P+ +F+ GV E I D+ YG++ I L + T K Y +++
Sbjct: 13 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 72
Query: 179 THEAAVACINAINNKEF 195
T++ A A + +N ++
Sbjct: 73 TYKEAQAAMEGLNGQDL 89
Score = 31.6 bits (70), Expect = 0.96, Method: Composition-based stats.
Identities = 26/87 (29%), Positives = 42/87 (48%), Gaps = 4/87 (4%)
Query: 19 GKRCGTAPSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFA 78
G G S + LFV + T+E I K +YG ++NI+L D + G +G+
Sbjct: 11 GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYG--EIKNIHLNLD-RRTGYLKGYT 67
Query: 79 FVMFSCHVDAMAAYKRLQKPDVVFGHP 105
V + + +A AA + L D++ G P
Sbjct: 68 LVEYETYKEAQAAMEGLNGQDLM-GQP 93
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 37.4 bits (85), Expect = 0.016, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 28/51 (54%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHE 181
+F+ G+ P E +IR+ G+G+V I L + T KR+ + FI F E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 52
>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 = 37.4 bits (85), Expect = 0.017, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 36/77 (46%)
Query: 119 EPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFS 178
EP P+ +F+ GV E I D+ YG++ I L + T K Y +++
Sbjct: 14 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 73
Query: 179 THEAAVACINAINNKEF 195
T++ A A + +N ++
Sbjct: 74 TYKEAQAAMEGLNGQDL 90
Score = 31.2 bits (69), Expect = 1.4, Method: Composition-based stats.
Identities = 26/87 (29%), Positives = 42/87 (48%), Gaps = 4/87 (4%)
Query: 19 GKRCGTAPSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFA 78
G G S + LFV + T+E I K +YG ++NI+L D + G +G+
Sbjct: 12 GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYG--EIKNIHLNLD-RRTGYLKGYT 68
Query: 79 FVMFSCHVDAMAAYKRLQKPDVVFGHP 105
V + + +A AA + L D++ G P
Sbjct: 69 LVEYETYKEAQAAMEGLNGQDLM-GQP 94
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 37.4 bits (85), Expect = 0.019, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 31/63 (49%)
Query: 129 KTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 188
+ V+L +P E QI D G VI + + + T + K Y FI+F E++ + +
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 189 AIN 191
+N
Sbjct: 63 NLN 65
>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 = 37.0 bits (84), Expect = 0.025, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 32/67 (47%)
Query: 129 KTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 188
+ V+L +P E QI D G VI + + + T + K Y FI+F E++ + +
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 189 AINNKEF 195
+N +
Sbjct: 64 NLNGYQL 70
>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 = 36.6 bits (83), Expect = 0.026, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 32/67 (47%)
Query: 129 KTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 188
+ V+L +P E QI D G VI + + + T + K Y FI+F E++ + +
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 189 AINNKEF 195
+N +
Sbjct: 65 NLNGYQL 71
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 36.6 bits (83), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 14/58 (24%), Positives = 31/58 (53%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 188
+F+ G+P + E ++R+ K +G V +V+ + + + +GFI F ++ +N
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 35.8 bits (81), Expect = 0.045, Method: Composition-based stats.
Identities = 20/87 (22%), Positives = 42/87 (48%), Gaps = 3/87 (3%)
Query: 120 PDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFST 179
P+P+++ + + ++ +P E Q+R + YG + + + + T + + YGF+ F +
Sbjct: 37 PEPDVL---RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS 93
Query: 180 HEAAVACINAINNKEFSDGNSKVKLRA 206
+A I +N + KV L A
Sbjct: 94 GSSAQQAIAGLNGFNILNKRLKVALAA 120
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 35.8 bits (81), Expect = 0.046, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 129 KTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 188
KT+F+ G+ E +++ G +R + + T K +GF+DF++ E A A
Sbjct: 16 KTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72
Query: 189 AINNKEFSDGNSKVKL 204
A+ + E DGN KV L
Sbjct: 73 AMEDGEI-DGN-KVTL 86
Score = 34.7 bits (78), Expect = 0.12, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 25 APSEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSC 84
A S+ + TLFV + T+E +K+ +G +V+D + G S+GF FV F+
Sbjct: 10 ARSQPSKTLFVKGLSEDTTEETLKESF-----DGSVRARIVTD-RETGSSKGFGFVDFNS 63
Query: 85 HVDAMAAYKRLQKPDV 100
DA AA + ++ ++
Sbjct: 64 EEDAKAAKEAMEDGEI 79
>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 = 35.8 bits (81), Expect = 0.050, Method: Composition-based stats.
Identities = 19/76 (25%), Positives = 35/76 (46%)
Query: 120 PDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFST 179
P P+ +F+ GV E I D+ YG++ I L + T K Y +++ T
Sbjct: 1 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 60
Query: 180 HEAAVACINAINNKEF 195
++ A A + +N ++
Sbjct: 61 YKEAQAAMEGLNGQDL 76
>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 = 35.4 bits (80), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 33/151 (21%), Positives = 63/151 (41%), Gaps = 18/151 (11%)
Query: 59 VENINLVSDIQHEGLSRGFAFVMFSCHVDAMAAYKRLQKPDVVFGHPERTVKVAFAEP-- 116
+E+ LV D + G S G+ FV + DA A L + +T+KV++A P
Sbjct: 29 IESCKLVRD-KITGQSLGYGFVNYIDPKDAEKAINTLNGLRL----QTKTIKVSYARPSS 83
Query: 117 --LREPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGF 174
+R+ + +++ G+P + ++ YG +I + + T + GF
Sbjct: 84 ASIRDAN---------LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGF 134
Query: 175 IDFSTHEAAVACINAINNKEFSDGNSKVKLR 205
I F A I +N ++ S + ++
Sbjct: 135 IRFDKRIEAEEAIKGLNGQKPSGATEPITVK 165
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 35.0 bits (79), Expect = 0.095, Method: Composition-based stats.
Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 33 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMAAY 92
L+VG + + + +G + +I + D + E RGFAFV F DA AA
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFG--DITDIQIPLDYETEK-HRGFAFVEFELAEDAAAAI 71
Query: 93 KRLQKPDVVFGHPERTVKVAFAEPLR 118
+ + + +FG RT++V A+P+R
Sbjct: 72 DNMNESE-LFG---RTIRVNLAKPMR 93
Score = 33.1 bits (74), Expect = 0.31, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 152 YGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNSKVKLRARLSNP 211
+GD+ I + + T K + + F++F E A A I+ +N E +R L+ P
Sbjct: 36 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRT----IRVNLAKP 91
Query: 212 M 212
M
Sbjct: 92 M 92
>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 = 34.7 bits (78), Expect = 0.098, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 32/65 (49%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAI 190
+F+ GV E I D+ YG++ I L + T K Y +++ T++ A A + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 191 NNKEF 195
N ++
Sbjct: 70 NGQDL 74
>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 = 34.7 bits (78), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 23/107 (21%), Positives = 50/107 (46%), Gaps = 6/107 (5%)
Query: 124 IMAHVK--TVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHE 181
I++H+ T++ PP + + IRD ++ V + ++ + + +ID ++ E
Sbjct: 111 IVSHLTECTLWXTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKE 170
Query: 182 AAVACINAINNKEFSDGNSKVKLRARLSNPMPKTQAVKGGMSGGFRI 228
A C+ +N + +G + V ++SNP+ K++ G I
Sbjct: 171 DARYCVEKLNGLKI-EGYTLV---TKVSNPLEKSKRTDSATLEGREI 213
>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 = 34.7 bits (78), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 14/63 (22%), Positives = 35/63 (55%), Gaps = 3/63 (4%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGF---IDFSTHEAAVACI 187
+F+ G+P + ++Q+++ + +G + L ++ +T K Y F +D + + A+A +
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 188 NAI 190
N +
Sbjct: 159 NGM 161
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 34.7 bits (78), Expect = 0.10, Method: Composition-based stats.
Identities = 26/94 (27%), Positives = 44/94 (46%), Gaps = 5/94 (5%)
Query: 29 DNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDA 88
++ LFVG + T E +++ + +G ++ ++ +G S+G AFV F H +A
Sbjct: 11 EDRKLFVGMLGKQQTDEDVRKMFEPFGT--IDECTVLRG--PDGTSKGCAFVKFQTHAEA 66
Query: 89 MAAYKRLQKPDVVFGHPERTVKVAFAEPLREPDP 122
AA L + G V V FA+ +E P
Sbjct: 67 QAAINTLHSSRTLPGASSSLV-VKFADTEKESGP 99
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 14/63 (22%), Positives = 35/63 (55%), Gaps = 3/63 (4%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGF---IDFSTHEAAVACI 187
+F+ G+P + ++Q+++ + +G + L ++ +T K Y F +D + + A+A +
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 188 NAI 190
N +
Sbjct: 157 NGM 159
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 34.7 bits (78), Expect = 0.12, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRI-VLARNMSTAKRKDYGFIDFSTHEAAVACINA 189
+F+ + P E + D +G +++ + R+ T K Y FI+F++ +A+ A I A
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 190 INNK 193
+N +
Sbjct: 68 MNGQ 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 = 34.7 bits (78), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 14/63 (22%), Positives = 35/63 (55%), Gaps = 3/63 (4%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGF---IDFSTHEAAVACI 187
+F+ G+P + ++Q+++ + +G + L ++ +T K Y F +D + + A+A +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 188 NAI 190
N +
Sbjct: 177 NGM 179
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 34.7 bits (78), Expect = 0.13, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 32/65 (49%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAI 190
+F+ GV E I D+ YG++ I L + T K Y +++ T++ A A + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 191 NNKEF 195
N ++
Sbjct: 70 NGQDL 74
>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 = 34.3 bits (77), Expect = 0.13, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 32/65 (49%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAI 190
+F+ GV E I D+ YG++ I L + T K Y +++ T++ A A + +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 191 NNKEF 195
N ++
Sbjct: 70 NGQDL 74
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 33.9 bits (76), Expect = 0.22, Method: Composition-based stats.
Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 5/90 (5%)
Query: 33 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMAAY 92
LFVG + ++E + + + +GV ++ ++ +G S+G AFV FS H +A AA
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGV--IDECTVLRG--PDGSSKGCAFVKFSSHTEAQAAI 73
Query: 93 KRLQKPDVVFGHPERTVKVAFAEPLREPDP 122
L + G V V FA+ +E P
Sbjct: 74 HALHGSQTMPGASSSLV-VKFADTDKESGP 102
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 33.5 bits (75), Expect = 0.23, Method: Composition-based stats.
Identities = 12/54 (22%), Positives = 30/54 (55%)
Query: 135 GVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 188
G+P E +++ +G+V+ + + +++ T K +GF+ F+ +E V ++
Sbjct: 22 GLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 33.5 bits (75), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 43/85 (50%), Gaps = 8/85 (9%)
Query: 25 APSEDNDTLFVGNICNTWTKEAIKQKLKDYG--VEGVENINLVSDIQHEGLSRGFAFVMF 82
+ S+D LFVG++ E ++ KD+ + G +++ D+Q G SRG+ FV F
Sbjct: 82 SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSG----HVMWDMQ-TGSSRGYGFVSF 136
Query: 83 SCHVDAMAAYKRLQKPDVVFGHPER 107
+ DA A +Q D+ G P R
Sbjct: 137 TSQDDAQNAMDSMQGQDLN-GRPLR 160
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 33.5 bits (75), Expect = 0.27, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 29/61 (47%)
Query: 142 ENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNSK 201
E+ +R + +G + I L + T + K YGFI FS E A + +N E + K
Sbjct: 40 EDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMK 99
Query: 202 V 202
V
Sbjct: 100 V 100
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 33.1 bits (74), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 20/91 (21%), Positives = 46/91 (50%), Gaps = 6/91 (6%)
Query: 124 IMAHVK--TVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHE 181
I++H+ T+++ PP + + IRD ++ V + ++ + + +ID ++ E
Sbjct: 74 IVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKE 133
Query: 182 AAVACINAINNKEFSDGNSKVKLRARLSNPM 212
A C+ +N + +G + L ++SNP+
Sbjct: 134 DARYCVEKLNGLKI-EGYT---LVTKVSNPL 160
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 33.1 bits (74), Expect = 0.34, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMS-TAKRKDYGFIDFSTHEAAVACINA 189
+ + +P + +IR+ +G++ + L + M+ T + +GF+DF T + A NA
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA 77
Query: 190 I 190
+
Sbjct: 78 L 78
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 33.1 bits (74), Expect = 0.36, Method: Composition-based stats.
Identities = 14/63 (22%), Positives = 35/63 (55%), Gaps = 3/63 (4%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGF---IDFSTHEAAVACI 187
+F+ G+P + ++Q+++ + +G + L ++ +T K Y F +D + + A+A +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 188 NAI 190
N +
Sbjct: 64 NGM 66
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 32.7 bits (73), Expect = 0.41, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 26/53 (49%)
Query: 152 YGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNSKVKL 204
+GD+ I + + T K + + F++F E A A I+ +N E +V L
Sbjct: 87 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 139
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 32.7 bits (73), Expect = 0.47, Method: Composition-based stats.
Identities = 15/60 (25%), Positives = 30/60 (50%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAI 190
+++ G+ P + + + YG ++ + +T K K YGF+DF + AA + A+
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
>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 = 32.7 bits (73), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 32 TLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMAA 91
TLFV + T+ ++++ + YG ++ I++V + G RG+AF+ + D +A
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGP--IKRIHMVYS-KRSGKPRGYAFIEYEHERDMHSA 160
Query: 92 YK 93
YK
Sbjct: 161 YK 162
Score = 28.1 bits (61), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 28/50 (56%)
Query: 129 KTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFS 178
KT+F+ V E+++R + + YG + RI + + + K + Y FI++
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYE 152
>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 = 32.3 bits (72), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 14/67 (20%), Positives = 31/67 (46%)
Query: 118 REPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDF 177
RE ++ + + +PP + Q + ++ +G + R L + T + K YGF ++
Sbjct: 83 RELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEY 142
Query: 178 STHEAAV 184
++A
Sbjct: 143 MKKDSAA 149
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 32.3 bits (72), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 14/67 (20%), Positives = 31/67 (46%)
Query: 118 REPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDF 177
RE ++ + + +PP + Q + ++ +G + R L + T + K YGF ++
Sbjct: 85 RELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEY 144
Query: 178 STHEAAV 184
++A
Sbjct: 145 MKKDSAA 151
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 32.3 bits (72), Expect = 0.50, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 26/53 (49%)
Query: 152 YGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNSKVKL 204
+GD+ I + + T K + + F++F E A A I+ +N E +V L
Sbjct: 31 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 83
Score = 29.3 bits (64), Expect = 4.3, Method: Composition-based stats.
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 7/83 (8%)
Query: 33 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMAAY 92
L+VG + + + +G + +I + D + E RGFAFV F DA AA
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFG--DITDIQIPLDYETEK-HRGFAFVEFELAEDAAAAI 66
Query: 93 KRLQKPDVVFGHPERTVKVAFAE 115
+ + + +FG RT++V A+
Sbjct: 67 DNMNESE-LFG---RTIRVNLAK 85
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 32.3 bits (72), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 14/67 (20%), Positives = 31/67 (46%)
Query: 118 REPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDF 177
RE ++ + + +PP + Q + ++ +G + R L + T + K YGF ++
Sbjct: 85 RELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEY 144
Query: 178 STHEAAV 184
++A
Sbjct: 145 MKKDSAA 151
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 32.3 bits (72), Expect = 0.55, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 26/53 (49%)
Query: 152 YGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNSKVKL 204
+GD+ I + + T K + + F++F E A A I+ +N E +V L
Sbjct: 29 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 81
Score = 29.3 bits (64), Expect = 5.1, Method: Composition-based stats.
Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 7/89 (7%)
Query: 27 SEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHV 86
S L+VG + + + +G + +I + D + E RGFAFV F
Sbjct: 2 STTKRVLYVGGLAEEVDDKVLHAAFIPFG--DITDIQIPLDYETEK-HRGFAFVEFELAE 58
Query: 87 DAMAAYKRLQKPDVVFGHPERTVKVAFAE 115
DA AA + + + +FG RT++V A+
Sbjct: 59 DAAAAIDNMNESE-LFG---RTIRVNLAK 83
>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 = 0.56, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 29/69 (42%), Gaps = 8/69 (11%)
Query: 136 VPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEF 195
+ P ++R + + YG VI + KDY F+ E AV I ++N EF
Sbjct: 18 ISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLDNTEF 69
Query: 196 SDGNSKVKL 204
V+L
Sbjct: 70 QGKRMHVQL 78
>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 = 32.3 bits (72), Expect = 0.59, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 26/53 (49%)
Query: 152 YGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEFSDGNSKVKL 204
+GD+ I + + T K + + F++F E A A I+ +N E +V L
Sbjct: 26 FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 78
>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 = 32.0 bits (71), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 32 TLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMAA 91
TLFV + T+ ++++ + YG ++ I++V + G RG+AF+ + D +A
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYG--PIKRIHMVYS-KRSGKPRGYAFIEYEHERDMHSA 160
Query: 92 YK 93
YK
Sbjct: 161 YK 162
Score = 28.5 bits (62), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 28/50 (56%)
Query: 129 KTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFS 178
KT+F+ V E+++R + + YG + RI + + + K + Y FI++
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYE 152
>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 = 0.65, Method: Composition-based stats.
Identities = 22/86 (25%), Positives = 43/86 (50%), Gaps = 10/86 (11%)
Query: 130 TVFLDGVPPHWKENQIRDQIKGYGDV---IRIVLARNMSTAKRKDYGFIDFSTHEAAVAC 186
T+++ PP + + IRD ++ V IR+ R +T++R + +ID ++ E A C
Sbjct: 5 TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRR--FAYIDVTSKEDARYC 61
Query: 187 INAINNKEFSDGNSKVKLRARLSNPM 212
+ +N + L ++SNP+
Sbjct: 62 VEKLNGLKIEG----YTLVTKVSNPL 83
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 31.6 bits (70), Expect = 0.83, Method: Composition-based stats.
Identities = 25/90 (27%), Positives = 44/90 (48%), Gaps = 5/90 (5%)
Query: 33 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMAAY 92
LFVG + +++ +++ + +G +E ++ +G S+G AFV +S H +A AA
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFG--NIEECTILRG--PDGNSKGCAFVKYSSHAEAQAAI 73
Query: 93 KRLQKPDVVFGHPERTVKVAFAEPLREPDP 122
L + G V V FA+ +E P
Sbjct: 74 NALHGSQTMPGASSSLV-VKFADTDKESGP 102
Score = 28.5 bits (62), Expect = 7.9, Method: Composition-based stats.
Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 6/84 (7%)
Query: 117 LREPDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFID 176
LR+P + +F+ + E+ +R + +G++ + R K F+
Sbjct: 9 LRQPPSH-----RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRG-PDGNSKGCAFVK 62
Query: 177 FSTHEAAVACINAINNKEFSDGNS 200
+S+H A A INA++ + G S
Sbjct: 63 YSSHAEAQAAINALHGSQTMPGAS 86
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 31.6 bits (70), Expect = 0.85, Method: Composition-based stats.
Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 8/78 (10%)
Query: 125 MAHVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAV 184
MA VK +F+ + E + +G + R+ K KDY FI F + AV
Sbjct: 8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERV--------KKLKDYAFIHFDERDGAV 59
Query: 185 ACINAINNKEFSDGNSKV 202
+ +N K+ N ++
Sbjct: 60 KAMEEMNGKDLEGENIEI 77
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 31.6 bits (70), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 23/47 (48%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDF 177
VF+ + P I+ +G + + ++M+T K K YGF+ F
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 64
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 29/106 (27%), Positives = 50/106 (47%), Gaps = 6/106 (5%)
Query: 122 PEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDV--IRIVLARNMSTAKRKDYGFIDFST 179
P + KTVF+ + +E + + ++ +GD+ +R+VL + T K F F T
Sbjct: 9 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVL--HPDTEHSKGCAFAQFMT 66
Query: 180 HEAAVACINAINNKEFSDGNSKVKLRA-RLSNPMPKTQAVKGGMSG 224
EAA C+ A + E G K+ R ++ + + +A G SG
Sbjct: 67 QEAAQKCL-AAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSSG 111
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 17/75 (22%), Positives = 36/75 (48%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAI 190
+F+ +P + + + +G+VI + + T+ K +GF+ F ++A I A+
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 191 NNKEFSDGNSKVKLR 205
N + KV+L+
Sbjct: 103 NGFQVGTKRLKVQLK 117
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 31.2 bits (69), Expect = 1.2, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 6/62 (9%)
Query: 130 TVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINA 189
TV+ G+ + +R +G ++ I K Y F+ FSTHE+A I +
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEI------RVFPEKGYSFVRFSTHESAAHAIVS 80
Query: 190 IN 191
+N
Sbjct: 81 VN 82
>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 = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 7/60 (11%)
Query: 120 PDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDV--IRIVLARNMSTAKRKDYGFIDF 177
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 = 4.5, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 31 DTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDA 88
+T+FVG I + I+ YG V+ + +++D G+S+G+ FV F VD
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYG--SVKEVKIITD--RTGVSKGYGFVSFYNDVDV 63
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 27/116 (23%), Positives = 48/116 (41%), Gaps = 11/116 (9%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAI 190
+ ++ +P + ++++R G+V L R+ YGF+++ T + A IN +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 191 NNKEFSDGNSKVKLRARLSNPMPKTQAVKGG---MSGGFR--IGHGSSRTFSRYGR 241
N KV S P ++ +K +SG R FSR+GR
Sbjct: 65 NGLRLQSKTIKV------SYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGR 114
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 30.8 bits (68), Expect = 1.5, Method: Composition-based stats.
Identities = 16/67 (23%), Positives = 30/67 (44%)
Query: 136 VPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEF 195
+P + +++ + GD+ L R+ T + YGF+++S A IN +N +
Sbjct: 12 LPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKL 71
Query: 196 SDGNSKV 202
KV
Sbjct: 72 QTKTIKV 78
>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 = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 7/60 (11%)
Query: 120 PDPEIMAHVKTVFLDGVPPHWKENQIRDQIKGYGDV--IRIVLARNMSTAKRKDYGFIDF 177
P+ +IM + TVF+ G+ E +IR YG V ++I+ R T K YGF+ F
Sbjct: 3 PEGKIMPN--TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR---TGVSKGYGFVSF 57
Score = 29.6 bits (65), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 31 DTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDA 88
+T+FVG I + I+ YG V+ + +++D G+S+G+ FV F VD
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYG--SVKEVKIITD--RTGVSKGYGFVSFYNDVDV 63
>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 = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 27/116 (23%), Positives = 48/116 (41%), Gaps = 11/116 (9%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAI 190
+ ++ +P + ++++R G+V L R+ YGF+++ T + A IN +
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 191 NNKEFSDGNSKVKLRARLSNPMPKTQAVKGG---MSGGFR--IGHGSSRTFSRYGR 241
N KV S P ++ +K +SG R FSR+GR
Sbjct: 65 NGLRLQSKTIKV------SYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGR 114
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 30.4 bits (67), Expect = 2.0, Method: Composition-based stats.
Identities = 14/63 (22%), Positives = 30/63 (47%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAI 190
+F+ G+ E + YG + +V+ ++ T + + +GF+ F + A + A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 191 NNK 193
N K
Sbjct: 75 NGK 77
Score = 28.1 bits (61), Expect = 9.9, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 27 SEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHV 86
+ D LFVG + +++++Q YG + + +V D + + SRGF FV F
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYG--QISEVVVVKDRETQ-RSRGFGFVTFENID 65
Query: 87 DAMAA 91
DA A
Sbjct: 66 DAKDA 70
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 30.4 bits (67), Expect = 2.1, Method: Composition-based stats.
Identities = 25/96 (26%), Positives = 44/96 (45%), Gaps = 7/96 (7%)
Query: 27 SEDNDTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHV 86
++DN T+ V N+ + +++ + +G + I L D + G S+GFAF+ F
Sbjct: 12 ADDNATIRVTNLSEDTRETDLQELFRPFG--SISRIYLAKD-KTTGQSKGFAFISFHRRE 68
Query: 87 DAMAAYKRLQKPDVVFGHPERTVKVAFAEPLREPDP 122
DA A + FG+ + V +A+P P
Sbjct: 69 DAARAIAGVSG----FGYDHLILNVEWAKPSTNSGP 100
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 30.4 bits (67), Expect = 2.1, Method: Composition-based stats.
Identities = 28/100 (28%), Positives = 47/100 (47%), Gaps = 19/100 (19%)
Query: 24 TAPSEDNDT------LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGF 77
+ S D DT L+V N+ + ++E I+++ + VE + + D +
Sbjct: 3 SGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD---------Y 53
Query: 78 AFVMFSCHVDAMAAYKRLQKPDVVFGHPERTVKVAFAEPL 117
AFV FS DA+ A K L V+ G P ++V A+P+
Sbjct: 54 AFVHFSNREDAVEAMKALNG-KVLDGSP---IEVTLAKPV 89
Score = 30.0 bits (66), Expect = 2.6, Method: Composition-based stats.
Identities = 26/96 (27%), Positives = 42/96 (43%), Gaps = 14/96 (14%)
Query: 121 DPEIMAHVKTVFLDGVPPHWKENQIRDQIKGY--GDVIRIVLARNMSTAKRKDYGFIDFS 178
D + M+ VK +++ + E I + G V R+ K +DY F+ FS
Sbjct: 8 DEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV--------KKIRDYAFVHFS 59
Query: 179 THEAAVACINAINNKEFSDGNSKVKLRARLSNPMPK 214
E AV + A+N K DG+ + L+ P+ K
Sbjct: 60 NREDAVEAMKALNGKVL-DGSP---IEVTLAKPVDK 91
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 30.4 bits (67), Expect = 2.3, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 7/80 (8%)
Query: 121 DPEIM-AHVKTVFLDGVPPHWKENQIRDQIKGYGDVI--RIVLARNMSTAKRKDYGFIDF 177
DP + + V +F+ + + D +G+++ ++V N S K YGF+ F
Sbjct: 3 DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS----KGYGFVHF 58
Query: 178 STHEAAVACINAINNKEFSD 197
T EAA I +N +D
Sbjct: 59 ETQEAAERAIEKMNGMLLND 78
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 11/51 (21%), Positives = 27/51 (52%)
Query: 127 HVKTVFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDF 177
+ +F+ G+ + +R YG+V+ V+ ++ +T + + +GF+ F
Sbjct: 15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 30.4 bits (67), Expect = 2.4, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 5/68 (7%)
Query: 33 LFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDAMAAY 92
L+V + T +++ ++Q YG I L Q G+SRG F+ F ++A A
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILL---DQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 93 KRL--QKP 98
K L QKP
Sbjct: 61 KGLNGQKP 68
>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 = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 23/47 (48%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDF 177
VF+ + P I+ +G + + ++M+T K K YGF+ F
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 30.0 bits (66), Expect = 2.5, Method: Composition-based stats.
Identities = 19/46 (41%), Positives = 30/46 (65%), Gaps = 2/46 (4%)
Query: 43 TKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDA 88
T++ I+ +L+ +GV+ E + L+ + + G SRGFAFV FS DA
Sbjct: 14 TEDDIRGQLQSHGVQARE-VRLMRN-KSSGQSRGFAFVEFSHLQDA 57
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 30.0 bits (66), Expect = 3.0, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 130 TVFLDGVPPHWKENQIRDQIKGYGD-VIRIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 188
++++ + P+ EN I G+ V+ + + RN T Y F++F+ A C++
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 189 AINNK 193
IN K
Sbjct: 71 KINGK 75
>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 = 29.6 bits (65), Expect = 3.3, Method: Composition-based stats.
Identities = 16/67 (23%), Positives = 29/67 (43%)
Query: 136 VPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEF 195
+P + ++++R G+V L R+ YGF+++ T + A IN +N
Sbjct: 12 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 71
Query: 196 SDGNSKV 202
KV
Sbjct: 72 QSKTIKV 78
>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 = 3.5, Method: Composition-based stats.
Identities = 15/75 (20%), Positives = 37/75 (49%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAI 190
+++ +P ++Q+ YG +++ + R+ T + + F+ ++ E A I+A+
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 191 NNKEFSDGNSKVKLR 205
NN G+ + +R
Sbjct: 76 NNVIPEGGSQPLSVR 90
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 29.6 bits (65), Expect = 3.6, Method: Composition-based stats.
Identities = 13/45 (28%), Positives = 24/45 (53%)
Query: 167 AKRKDYGFIDFSTHEAAVACINAINNKEFSDGNSKVKLRARLSNP 211
K K Y FI+F++ E A +N+ N +E +++L+ +P
Sbjct: 50 GKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSP 94
>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 = 29.6 bits (65), Expect = 4.0, Method: Composition-based stats.
Identities = 16/67 (23%), Positives = 29/67 (43%)
Query: 136 VPPHWKENQIRDQIKGYGDVIRIVLARNMSTAKRKDYGFIDFSTHEAAVACINAINNKEF 195
+P + ++++R G+V L R+ YGF+++ T + A IN +N
Sbjct: 27 LPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 86
Query: 196 SDGNSKV 202
KV
Sbjct: 87 QSKTIKV 93
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 29.3 bits (64), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 31 DTLFVGNICNTWTKEAIKQKLKDYGVEGVENINLVSDIQHEGLSRGFAFVMFSCHVDA 88
+T+FVG I + I+ YG V+ + +++D G+S+G+ FV F VD
Sbjct: 11 NTVFVGGIDVRMDETEIRSFFARYG--SVKEVKIITD--RTGVSKGYGFVSFYNDVDV 64
Score = 29.3 bits (64), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 130 TVFLDGVPPHWKENQIRDQIKGYGDV--IRIVLARNMSTAKRKDYGFIDF 177
TVF+ G+ E +IR YG V ++I+ R T K YGF+ F
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR---TGVSKGYGFVSF 58
>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 = 29.3 bits (64), Expect = 5.2, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 6/69 (8%)
Query: 131 VFLDGVPPHWKENQIRDQIKGYGDVI--RIVLARNMSTAKRKDYGFIDFSTHEAAVACIN 188
+F+ + + D +G+++ ++V N S K YGF+ F T EAA I
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS----KGYGFVHFETQEAAERAIE 63
Query: 189 AINNKEFSD 197
+N +D
Sbjct: 64 KMNGMLLND 72
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
0.323 0.140 0.447
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,883,534
Number of Sequences: 62578
Number of extensions: 581981
Number of successful extensions: 1249
Number of sequences better than 100.0: 100
Number of HSP's better than 100.0 without gapping: 69
Number of HSP's successfully gapped in prelim test: 31
Number of HSP's that attempted gapping in prelim test: 1123
Number of HSP's gapped (non-prelim): 148
length of query: 450
length of database: 14,973,337
effective HSP length: 102
effective length of query: 348
effective length of database: 8,590,381
effective search space: 2989452588
effective search space used: 2989452588
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)