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= psy2618
(390 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 143 bits (361), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 65/98 (66%), Positives = 77/98 (78%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS + K+DTSNH+H+FVGDLSPEI T+ +K AFAPFG+IS+ R+V+D T KSKGY
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYG 60
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPA 178
FVSF K +AENAI M GQWLG R IRTNW+TRKPPA
Sbjct: 61 FVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRKPPA 98
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 28/93 (30%), Positives = 41/93 (44%), Gaps = 14/93 (15%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
V+ G ++ E + F+PFG I D RV K+ KGY FV F K A +AI +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 263 HNTDINGHTVKCFWGKESENNSTLAQPSAPTTP 295
+ G ++ W +P AP+ P
Sbjct: 78 GGQWLGGRQIRTNWATR--------KPPAPSGP 102
>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 = 141 bits (356), Expect = 5e-34, Method: Compositional matrix adjust.
Identities = 65/98 (66%), Positives = 76/98 (77%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS + K+DTSNH+H+FVGDLSPEI T+ +K AFAPFG IS+ R+V+D T KSKGY
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPA 178
FVSF K +AENAI M GQWLG R IRTNW+TRKPPA
Sbjct: 61 FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPA 98
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 6/74 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
V+ G ++ E + F+PFG I D RV K+ KGY FV F K A +AI+ +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 263 HNTDINGHTVKCFW 276
+ G ++ W
Sbjct: 78 GGQWLGGRQIRTNW 91
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 127 bits (319), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 55/94 (58%), Positives = 73/94 (77%)
Query: 187 NSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAF 246
+ +TK + F++V NQSSP NCTVYCGG L ++L+ + FSPFG I++IRVF EKGY+F
Sbjct: 6 SGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSF 65
Query: 247 VKFTTKETATHAIESIHNTDINGHTVKCFWGKES 280
V+F+T E+A HAI S++ T I GH VKC+WGKES
Sbjct: 66 VRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES 99
Score = 48.1 bits (113), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 44/84 (52%), Gaps = 7/84 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++ G ++ + Q +++ F+PFG+I R+ KGY+FV F A +AI ++
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRV------FPEKGYSFVRFSTHESAAHAIVSV 81
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTN 181
NG + ++ W ++ P MT+
Sbjct: 82 NGTTIEGHVVKCYWG-KESPDMTS 104
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 111 bits (278), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 57/168 (33%), Positives = 91/168 (54%), Gaps = 5/168 (2%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFXXXXXXXXXXXXM 66
LYVGNLD ++TE++L F GP+ K++ + N YAF+E+ +
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 67 NKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCR 126
N + +K+NWA DT +++FVGDL+ ++ +TL+ AF F +
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDT---FNLFVGDLNVNVDDETLRNAFKDFPSYLSGH 118
Query: 127 IVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTR 174
++ D QT S+GY FVSF + +A+NA+ +M GQ L R +R NW+ +
Sbjct: 119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 73.2 bits (178), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 44/185 (23%), Positives = 87/185 (47%), Gaps = 30/185 (16%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG+L I LK+ F G I+N +I+ D K+ YAFV + + +A A+ +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNN-KNVNYAFVEYHQSHDANIALQTL 61
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKD 217
NG+ + + ++ NW+ + + SS ++ G +
Sbjct: 62 NGKQIENNIVKINWAFQSQQS-----------------------SSDDTFNLFVGDLNVN 98
Query: 218 LNEELVSKVFSPF-----GTIV-DIRVFKEKGYAFVKFTTKETATHAIESIHNTDINGHT 271
+++E + F F G ++ D++ +GY FV FT+++ A +A++S+ D+NG
Sbjct: 99 VDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRP 158
Query: 272 VKCFW 276
++ W
Sbjct: 159 LRINW 163
Score = 41.2 bits (95), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 5/83 (6%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKG-----YAFVKFTTKETATHAIESI 262
+Y G K + E+++ + F G I +I++ +K YAFV++ A A++++
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 263 HNTDINGHTVKCFWGKESENNST 285
+ I + VK W +S+ +S+
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSS 84
>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 = 111 bits (277), Expect = 8e-25, Method: Compositional matrix adjust.
Identities = 55/84 (65%), Positives = 64/84 (76%)
Query: 93 SNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAEN 152
+H+H+FVGDLSPEI T + AFAPFG IS+ R+V+D T KSKGY FVSF K +AEN
Sbjct: 4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 63
Query: 153 AITAMNGQWLGSRSIRTNWSTRKP 176
AI M GQWLG R IRTNW+TRKP
Sbjct: 64 AIQQMGGQWLGGRQIRTNWATRKP 87
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 229 PFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTDINGHTVKCFW 276
PFG I D RV K+ KGY FV F K A +AI+ + + G ++ W
Sbjct: 29 PFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW 82
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 91.7 bits (226), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 47/88 (53%), Positives = 55/88 (62%), Gaps = 1/88 (1%)
Query: 1 MCDESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE-PGNDPYAFLEFXXXXXX 59
M D+ QP TLYVGNL VTE L+ LFSQIGP K CK+I E NDPY F+EF
Sbjct: 9 MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDA 68
Query: 60 XXXXXXMNKRVFLEKEMKVNWASSPGNQ 87
MN R L KE+KVNWA++P +Q
Sbjct: 69 AAALAAMNGRKILGKEVKVNWATTPSSQ 96
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 44/76 (57%), Gaps = 2/76 (2%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG+LS ++ + + F+ G +C+++ + + + Y FV F + +A A+ AM
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAM 75
Query: 158 NGQWLGSRSIRTNWST 173
NG+ + + ++ NW+T
Sbjct: 76 NGRKILGKEVKVNWAT 91
Score = 32.7 bits (73), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 4/73 (5%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKG----YAFVKFTTKETATHAIESIH 263
T+Y G +D+ E L+ ++FS G ++ E Y FV+F A A+ +++
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 76
Query: 264 NTDINGHTVKCFW 276
I G VK W
Sbjct: 77 GRKILGKEVKVNW 89
>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 = 90.5 bits (223), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 57/185 (30%), Positives = 88/185 (47%), Gaps = 29/185 (15%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VGDL P++ L E F+P G I + R+ RD T +S GYA+V+F + A+AE A+ M
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKD 217
N + + +R WS R P +S N ++ K
Sbjct: 73 NFDVIKGKPVRIMWSQRDPS---------------------LRKSGVGN--IFIKNLDKS 109
Query: 218 LNEELVSKVFSPFGTIVDIRVFKE----KGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
++ + + FS FG I+ +V + KGY FV F T+E A AIE ++ +N K
Sbjct: 110 IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR--K 167
Query: 274 CFWGK 278
F G+
Sbjct: 168 VFVGR 172
Score = 83.2 bits (204), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 53/163 (32%), Positives = 78/163 (47%), Gaps = 8/163 (4%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE---PGNDPYAFLEFXXXXXXXXXXX 64
+LYVG+L VTE +L FS GP+ +V R+ + YA++ F
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 65 XMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISN 124
MN V K +++ W+ P S +IF+ +L I+ + L + F+ FG I +
Sbjct: 71 TMNFDVIKGKPVRIMWSQ---RDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILS 127
Query: 125 CRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSI 167
C++V D SKGY FV F + AE AI MNG L R +
Sbjct: 128 CKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 168
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 45/89 (50%), Gaps = 8/89 (8%)
Query: 200 NQSSPT--NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTT 251
N S+P+ ++Y G D+ E ++ + FSP G I+ IRV ++ GYA+V F
Sbjct: 2 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 61
Query: 252 KETATHAIESIHNTDINGHTVKCFWGKES 280
A A+++++ I G V+ W +
Sbjct: 62 PADAERALDTMNFDVIKGKPVRIMWSQRD 90
>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 = 90.5 bits (223), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 57/185 (30%), Positives = 88/185 (47%), Gaps = 29/185 (15%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VGDL P++ L E F+P G I + R+ RD T +S GYA+V+F + A+AE A+ M
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKD 217
N + + +R WS R P +S N ++ K
Sbjct: 78 NFDVIKGKPVRIMWSQRDPS---------------------LRKSGVGN--IFIKNLDKS 114
Query: 218 LNEELVSKVFSPFGTIVDIRVFKE----KGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
++ + + FS FG I+ +V + KGY FV F T+E A AIE ++ +N K
Sbjct: 115 IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR--K 172
Query: 274 CFWGK 278
F G+
Sbjct: 173 VFVGR 177
Score = 83.6 bits (205), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 53/163 (32%), Positives = 78/163 (47%), Gaps = 8/163 (4%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE---PGNDPYAFLEFXXXXXXXXXXX 64
+LYVG+L VTE +L FS GP+ +V R+ + YA++ F
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 65 XMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISN 124
MN V K +++ W+ P S +IF+ +L I+ + L + F+ FG I +
Sbjct: 76 TMNFDVIKGKPVRIMWSQ---RDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILS 132
Query: 125 CRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSI 167
C++V D SKGY FV F + AE AI MNG L R +
Sbjct: 133 CKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 173
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 8/85 (9%)
Query: 200 NQSSPT--NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTT 251
N S+P+ ++Y G D+ E ++ + FSP G I+ IRV ++ GYA+V F
Sbjct: 7 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66
Query: 252 KETATHAIESIHNTDINGHTVKCFW 276
A A+++++ I G V+ W
Sbjct: 67 PADAERALDTMNFDVIKGKPVRIMW 91
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 79.0 bits (193), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 49/154 (31%), Positives = 77/154 (50%), Gaps = 8/154 (5%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGND---PYAFLEFXXXXXXXXXXX 64
T L V L +T+ L ALF IGP+ C+++R+ YAF++F
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 65 XMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISN 124
+N K +KV++A PG + +DT +++V +L I L F +G I
Sbjct: 64 VLNGITVRNKRLKVSYAR-PGGESIKDT----NLYVTNLPRTITDDQLDTIFGKYGSIVQ 118
Query: 125 CRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMN 158
I+RD T + +G AFV + K+ EA+ AI+A+N
Sbjct: 119 KNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Score = 66.6 bits (161), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 40/175 (22%), Positives = 81/175 (46%), Gaps = 31/175 (17%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++ V L ++ + L F G I+ CRI+RD +T S GYAFV F + +++ AI
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 157 MNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGK 216
+NG + ++ ++ +++ +P S + +Y +
Sbjct: 65 LNGITVRNKRLKVSYA--RPGG-----------------------ESIKDTNLYVTNLPR 99
Query: 217 DLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESIHNT 265
+ ++ + +F +G+IV + ++K G AFV++ +E A AI +++N
Sbjct: 100 TITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNV 154
Score = 32.7 bits (73), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 22/99 (22%), Positives = 44/99 (44%), Gaps = 9/99 (9%)
Query: 205 TNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHA 258
+N + +D+ + + +F G I R+ ++ GYAFV FT++ + A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 259 IESIHNTDINGHTVKCFW---GKESENNSTLAQPSAPTT 294
I+ ++ + +K + G ES ++ L + P T
Sbjct: 62 IKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRT 100
>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 = 78.2 bits (191), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 53/202 (26%), Positives = 93/202 (46%), Gaps = 22/202 (10%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++VG + E+ T+++AFAPFG I + + D T+K KG+AFV + A+ A+
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 157 MNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGK 216
MN LG R+I+ + N D++ ++ N +Y +
Sbjct: 90 MNSVMLGGRNIKVG-------------RPSNIGQAQPIIDQLAEEARAFN-RIYVASVHQ 135
Query: 217 DLNEELVSKVFSPFGTI------VDIRVFKEKGYAFVKFTTKETATHAIESIHNTDINGH 270
DL+++ + VF FG I D K KGY F+++ +++ A+ S++ D+ G
Sbjct: 136 DLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQ 195
Query: 271 TVKCFWGKESENNSTLAQPSAP 292
++ GK L P+ P
Sbjct: 196 YLRV--GKAVTPPMPLLTPATP 215
Score = 70.5 bits (171), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 45/186 (24%), Positives = 87/186 (46%), Gaps = 16/186 (8%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKV------IREPGNDPYAFLEFXXXXXXXX 61
+ +YVG++ + E+ + F+ GP+K + ++ G +AF+E+
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKG---FAFVEYEVPEAAQL 85
Query: 62 XXXXMNKRVFLEKEMKVNWASSPG------NQPKQDTSNHYHIFVGDLSPEIETQTLKEA 115
MN + + +KV S+ G +Q ++ I+V + ++ +K
Sbjct: 86 ALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSV 145
Query: 116 FAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRK 175
F FG+I + + RDP T K KGY F+ + K +++A+++MN LG + +R +
Sbjct: 146 FEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205
Query: 176 P-PAMT 180
P P +T
Sbjct: 206 PMPLLT 211
>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 = 77.8 bits (190), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 48/184 (26%), Positives = 87/184 (47%), Gaps = 20/184 (10%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++VG + E+ T+++AFAPFG I + + D T+K KG+AFV + A+ A+
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 157 MNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGK 216
MN LG R+I+ + N D++ ++ N +Y +
Sbjct: 75 MNSVMLGGRNIKVG-------------RPSNIGQAQPIIDQLAEEARAFN-RIYVASVHQ 120
Query: 217 DLNEELVSKVFSPFGTI------VDIRVFKEKGYAFVKFTTKETATHAIESIHNTDINGH 270
DL+++ + VF FG I D K KGY F+++ +++ A+ S++ D+ G
Sbjct: 121 DLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQ 180
Query: 271 TVKC 274
++
Sbjct: 181 YLRV 184
Score = 73.6 bits (179), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 46/184 (25%), Positives = 87/184 (47%), Gaps = 16/184 (8%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKV------IREPGNDPYAFLEFXXXXXXXXXX 63
+YVG++ + E+ + F+ GP+K + ++ G +AF+E+
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKG---FAFVEYEVPEAAQLAL 72
Query: 64 XXMNKRVFLEKEMKVNWASSPG------NQPKQDTSNHYHIFVGDLSPEIETQTLKEAFA 117
MN + + +KV S+ G +Q ++ I+V + ++ +K F
Sbjct: 73 EQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFE 132
Query: 118 PFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKP- 176
FG+I +C + RDP T K KGY F+ + K +++A+++MN LG + +R + P
Sbjct: 133 AFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPM 192
Query: 177 PAMT 180
P +T
Sbjct: 193 PLLT 196
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRV------FKEKGYAFVKFTTKETATHAIE 260
C VY G +L E+ + + F+PFG I I + K KG+AFV++ E A A+E
Sbjct: 14 CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 73
Query: 261 SIHNTDINGHTVKC 274
+++ + G +K
Sbjct: 74 QMNSVMLGGRNIKV 87
>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 = 77.0 bits (188), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 50/154 (32%), Positives = 76/154 (49%), Gaps = 8/154 (5%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGND---PYAFLEFXXXXXXXXXXX 64
T L V L T+ L ALF IGP+ C++ R+ YAF++F
Sbjct: 15 TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 65 XMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISN 124
+N K +KV++A PG + +DT +++V +L I L F +G I
Sbjct: 75 VLNGITVRNKRLKVSYA-RPGGESIKDT----NLYVTNLPRTITDDQLDTIFGKYGSIVQ 129
Query: 125 CRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMN 158
I+RD T + +G AFV + K+ EA+ AI+A+N
Sbjct: 130 KNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
Score = 65.9 bits (159), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 43/186 (23%), Positives = 83/186 (44%), Gaps = 34/186 (18%)
Query: 86 NQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFV 145
N P+ +N + V L + + L F G I+ CRI RD +T S GYAFV F
Sbjct: 8 NDPRASNTN---LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFT 64
Query: 146 KKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPT 205
+ +++ AI +NG + ++ ++ +++ +P S
Sbjct: 65 SEXDSQRAIKVLNGITVRNKRLKVSYA--RPGG-----------------------ESIK 99
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAI 259
+ +Y + + ++ + +F +G+IV + ++K G AFV++ +E A AI
Sbjct: 100 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159
Query: 260 ESIHNT 265
+++N
Sbjct: 160 SALNNV 165
Score = 34.7 bits (78), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 24/108 (22%), Positives = 47/108 (43%), Gaps = 9/108 (8%)
Query: 196 DEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKF 249
D++ N +N + +D + + +F G I R+ ++ GYAFV F
Sbjct: 4 DDLMNDPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDF 63
Query: 250 TTKETATHAIESIHNTDINGHTVKCFW---GKESENNSTLAQPSAPTT 294
T++ + AI+ ++ + +K + G ES ++ L + P T
Sbjct: 64 TSEXDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRT 111
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 75.9 bits (185), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 47/156 (30%), Positives = 81/156 (51%), Gaps = 8/156 (5%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE--PGND-PYAFLEFXXXXXXXXXXX 64
T L V L ++T++ L +LFS IG V+ K+IR+ G+ Y F+ +
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 65 XMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISN 124
+N K +KV++A +P + ++++ L + + +++ F+ FG I N
Sbjct: 63 TLNGLRLQSKTIKVSYA-----RPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIIN 117
Query: 125 CRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQ 160
R++ D T S+G AF+ F K++EAE AIT+ NG
Sbjct: 118 SRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGH 153
Score = 71.2 bits (173), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 45/165 (27%), Positives = 78/165 (47%), Gaps = 36/165 (21%)
Query: 112 LKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNW 171
L+ F+ GE+ + +++RD S GY FV++V +AE AI +NG L S++I+ ++
Sbjct: 19 LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY 78
Query: 172 STRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFG 231
+ +P + EV + +Y G + + ++ V +FS FG
Sbjct: 79 A--RPSS------------------EVIK-----DANLYISGLPRTMTQKDVEDMFSRFG 113
Query: 232 TIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTDINGH 270
I++ RV + +G AF++F + A AI T NGH
Sbjct: 114 RIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI-----TSFNGH 153
Score = 33.1 bits (74), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 15/71 (21%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESIHNTDING 269
+++ ++ + +FS G + ++ ++K GY FV + T + A AI +++ +
Sbjct: 12 QNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQS 71
Query: 270 HTVKCFWGKES 280
T+K + + S
Sbjct: 72 KTIKVSYARPS 82
>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 = 75.9 bits (185), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 47/156 (30%), Positives = 81/156 (51%), Gaps = 8/156 (5%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE--PGND-PYAFLEFXXXXXXXXXXX 64
T L V L ++T++ L +LFS IG V+ K+IR+ G+ Y F+ +
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 65 XMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISN 124
+N K +KV++A +P + ++++ L + + +++ F+ FG I N
Sbjct: 63 TLNGLRLQSKTIKVSYA-----RPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIIN 117
Query: 125 CRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQ 160
R++ D T S+G AF+ F K++EAE AIT+ NG
Sbjct: 118 SRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGH 153
Score = 70.9 bits (172), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 45/165 (27%), Positives = 78/165 (47%), Gaps = 36/165 (21%)
Query: 112 LKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNW 171
L+ F+ GE+ + +++RD S GY FV++V +AE AI +NG L S++I+ ++
Sbjct: 19 LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY 78
Query: 172 STRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFG 231
+ +P + EV + +Y G + + ++ V +FS FG
Sbjct: 79 A--RPSS------------------EVIK-----DANLYISGLPRTMTQKDVEDMFSRFG 113
Query: 232 TIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTDINGH 270
I++ RV + +G AF++F + A AI T NGH
Sbjct: 114 RIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI-----TSFNGH 153
Score = 33.1 bits (74), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 15/71 (21%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESIHNTDING 269
+++ ++ + +FS G + ++ ++K GY FV + T + A AI +++ +
Sbjct: 12 QNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQS 71
Query: 270 HTVKCFWGKES 280
T+K + + S
Sbjct: 72 KTIKVSYARPS 82
>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 = 71.6 bits (174), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 52/202 (25%), Positives = 89/202 (44%), Gaps = 22/202 (10%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++VG + E+ T+++AFAPFG I + D T K KG+AFV + A+ A+
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 157 MNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGK 216
N LG R+I+ + N D++ ++ N +Y +
Sbjct: 74 XNSVXLGGRNIKVG-------------RPSNIGQAQPIIDQLAEEARAFN-RIYVASVHQ 119
Query: 217 DLNEELVSKVFSPFGTI------VDIRVFKEKGYAFVKFTTKETATHAIESIHNTDINGH 270
DL+++ + VF FG I D K KGY F+++ +++ A+ S + D+ G
Sbjct: 120 DLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQ 179
Query: 271 TVKCFWGKESENNSTLAQPSAP 292
++ GK L P+ P
Sbjct: 180 YLRV--GKAVTPPXPLLTPATP 199
Score = 66.2 bits (160), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 43/181 (23%), Positives = 82/181 (45%), Gaps = 10/181 (5%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP---GNDPYAFLEFXXXXXXXXXXXXM 66
+YVG++ + E+ + F+ GP+K + + +AF+E+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 67 NKRVFLEKEMKVNWASSPG------NQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFG 120
N + +KV S+ G +Q ++ I+V + ++ +K F FG
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 134
Query: 121 EISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKP-PAM 179
+I +C + RDP T K KGY F+ + K +++A+++ N LG + +R + P P +
Sbjct: 135 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAVTPPXPLL 194
Query: 180 T 180
T
Sbjct: 195 T 195
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIR------VFKEKGYAFVKFTTKETATHAIE 260
C VY G +L E+ + + F+PFG I I K KG+AFV++ E A A+E
Sbjct: 13 CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALE 72
Query: 261 SIHNTDINGHTVKC 274
++ + G +K
Sbjct: 73 QXNSVXLGGRNIKV 86
>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 = 70.9 bits (172), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 42/181 (23%), Positives = 86/181 (47%), Gaps = 31/181 (17%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++ V L + + + F GEI +C++VRD T +S GY FV+++ +AE AI
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 157 MNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGK 216
+NG L +++I+ +++ +P + +S + +Y G K
Sbjct: 64 LNGLRLQTKTIKVSYA--RPSS-----------------------ASIRDANLYVSGLPK 98
Query: 217 DLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTDINGH 270
+ ++ + ++FS +G I+ R+ + +G F++F + A AI+ ++ +G
Sbjct: 99 TMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA 158
Query: 271 T 271
T
Sbjct: 159 T 159
Score = 69.7 bits (169), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 44/156 (28%), Positives = 75/156 (48%), Gaps = 8/156 (5%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFXXXXXXXXXXX 64
T L V L ++T+E +LF IG ++ CK++R+ Y F+ +
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 65 XMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISN 124
+N K +KV++A +P + +++V L + + L++ F+ +G I
Sbjct: 63 TLNGLRLQTKTIKVSYA-----RPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIIT 117
Query: 125 CRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQ 160
RI+ D T S+G F+ F K+ EAE AI +NGQ
Sbjct: 118 SRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ 153
Score = 28.9 bits (63), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 20/102 (19%), Positives = 41/102 (40%), Gaps = 16/102 (15%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESIHNTDING 269
+++ +E +F G I ++ ++K GY FV + + A AI +++ +
Sbjct: 12 QNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQT 71
Query: 270 HTVKCFWGKESENNSTLAQPSAPTTPQPNSTAPQFPYIYNQQ 311
T+K + A+PS+ + N P Q+
Sbjct: 72 KTIKVSY----------ARPSSASIRDANLYVSGLPKTMTQK 103
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 70.1 bits (170), Expect = 2e-12, Method: Composition-based stats.
Identities = 36/85 (42%), Positives = 55/85 (64%), Gaps = 1/85 (1%)
Query: 92 TSNHYHIFVGDLSPEIETQTLKEAFAPFGEI-SNCRIVRDPQTLKSKGYAFVSFVKKAEA 150
+S IF+G+L PEI+ + L + F+ FG I +I+RDP T SKGYAF++F +
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 151 ENAITAMNGQWLGSRSIRTNWSTRK 175
+ AI AMNGQ+L +R I +++ +K
Sbjct: 62 DAAIEAMNGQYLCNRPITVSYAFKK 86
Score = 37.4 bits (85), Expect = 0.016, Method: Composition-based stats.
Identities = 27/91 (29%), Positives = 45/91 (49%), Gaps = 7/91 (7%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPV-KGCKVIREP--GNDP-YAFLEFXXXXXXX 60
S + +++GNLD + E+LL FS G + + K++R+P GN YAF+ F
Sbjct: 3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62
Query: 61 XXXXXMNKRVFLEKEMKVNWA---SSPGNQP 88
MN + + + V++A S G+ P
Sbjct: 63 AAIEAMNGQYLCNRPITVSYAFKKDSKGSGP 93
Score = 34.7 bits (78), Expect = 0.085, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 7/62 (11%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIV-------DIRVFKEKGYAFVKFTTKETATHAIES 261
++ G +++E+L+ FS FG I+ D KGYAF+ F + + + AIE+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 262 IH 263
++
Sbjct: 68 MN 69
>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 = 70.1 bits (170), Expect = 2e-12, Method: Composition-based stats.
Identities = 31/79 (39%), Positives = 51/79 (64%)
Query: 96 YHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
+++FVGDL+ ++ +TL+ AF F + ++ D QT S+GY FVSF + +A+NA+
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 156 AMNGQWLGSRSIRTNWSTR 174
+M GQ L R +R NW+ +
Sbjct: 62 SMQGQDLNGRPLRINWAAK 80
Score = 42.7 bits (99), Expect = 4e-04, Method: Composition-based stats.
Identities = 19/80 (23%), Positives = 43/80 (53%), Gaps = 6/80 (7%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIV------DIRVFKEKGYAFVKFTTKETATHAIESI 262
++ G ++++E + F F + + D++ +GY FV FT+++ A +A++S+
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 263 HNTDINGHTVKCFWGKESEN 282
D+NG ++ W + E+
Sbjct: 64 QGQDLNGRPLRINWAAKLEH 83
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 69.3 bits (168), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 42/156 (26%), Positives = 75/156 (48%), Gaps = 8/156 (5%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFXXXXXXXXXXX 64
T L V L ++T++ +LF IG ++ CK++R+ Y F+ +
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 65 XMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISN 124
+N K +KV++A +P + +++V L + + +++ F+ +G I
Sbjct: 65 TLNGLKLQTKTIKVSYA-----RPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIIT 119
Query: 125 CRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQ 160
RI+ D T S+G F+ F K+ EAE AI +NGQ
Sbjct: 120 SRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ 155
Score = 66.2 bits (160), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 39/173 (22%), Positives = 82/173 (47%), Gaps = 31/173 (17%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++ V L + K F G+I +C++VRD T +S GY FV++ +A+ AI
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 157 MNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGK 216
+NG L +++I+ +++ +P + +S + +Y G K
Sbjct: 66 LNGLKLQTKTIKVSYA--RPSS-----------------------ASIRDANLYVSGLPK 100
Query: 217 DLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIH 263
++++ + ++FS +G I+ R+ + +G F++F + A AI+ ++
Sbjct: 101 TMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLN 153
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 22/93 (23%), Positives = 40/93 (43%), Gaps = 19/93 (20%)
Query: 228 SPFGTIVDI---RVFKEK------GYAFVKFTTKETATHAIESIHNTDINGHTVKCFWGK 278
S FG+I DI ++ ++K GY FV ++ A AI +++ + T+K +
Sbjct: 23 SLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSY-- 80
Query: 279 ESENNSTLAQPSAPTTPQPNSTAPQFPYIYNQQ 311
A+PS+ + N P +Q+
Sbjct: 81 --------ARPSSASIRDANLYVSGLPKTMSQK 105
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 66.2 bits (160), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 42/183 (22%), Positives = 85/183 (46%), Gaps = 35/183 (19%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA- 156
+F+G LS E ++L+ F +G +++C ++RDP T +S+G+ FV++ E + A+ A
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 157 ---MNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGG 213
++G+ + + + +++P A +K ++ GG
Sbjct: 76 PHKVDGRVVEPKRAVSREDSQRPGAHLTVKK------------------------IFVGG 111
Query: 214 FGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESIHNTDI 267
+D E + F +G I I + K++G+AFV F ++ + ++T +
Sbjct: 112 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-V 170
Query: 268 NGH 270
NGH
Sbjct: 171 NGH 173
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 38/142 (26%), Positives = 58/142 (40%), Gaps = 3/142 (2%)
Query: 6 QPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFXXXXXXXXXXXX 65
Q L++G L T+E L + F Q G + C V+R+P F
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 66 MNKRVFLEKEMKVNWASSPGNQPKQDTSNHY---HIFVGDLSPEIETQTLKEAFAPFGEI 122
MN R V + + Q H IFVG + + E L++ F +G+I
Sbjct: 72 MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 131
Query: 123 SNCRIVRDPQTLKSKGYAFVSF 144
I+ D + K +G+AFV+F
Sbjct: 132 EVIEIMTDRGSGKKRGFAFVTF 153
>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 = 66.2 bits (160), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 42/183 (22%), Positives = 85/183 (46%), Gaps = 35/183 (19%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA- 156
+F+G LS E ++L+ F +G +++C ++RDP T +S+G+ FV++ E + A+ A
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 157 ---MNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGG 213
++G+ + + + +++P A +K ++ GG
Sbjct: 76 PHKVDGRVVEPKRAVSREDSQRPGAHLTVKK------------------------IFVGG 111
Query: 214 FGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESIHNTDI 267
+D E + F +G I I + K++G+AFV F ++ + ++T +
Sbjct: 112 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-V 170
Query: 268 NGH 270
NGH
Sbjct: 171 NGH 173
Score = 55.8 bits (133), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 38/142 (26%), Positives = 58/142 (40%), Gaps = 3/142 (2%)
Query: 6 QPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFXXXXXXXXXXXX 65
Q L++G L T+E L + F Q G + C V+R+P F
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 66 MNKRVFLEKEMKVNWASSPGNQPKQDTSNHY---HIFVGDLSPEIETQTLKEAFAPFGEI 122
MN R V + + Q H IFVG + + E L++ F +G+I
Sbjct: 72 MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 131
Query: 123 SNCRIVRDPQTLKSKGYAFVSF 144
I+ D + K +G+AFV+F
Sbjct: 132 EVIEIMTDRGSGKKRGFAFVTF 153
>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 = 66.2 bits (160), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 42/183 (22%), Positives = 85/183 (46%), Gaps = 35/183 (19%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA- 156
+F+G LS E ++L+ F +G +++C ++RDP T +S+G+ FV++ E + A+ A
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 74
Query: 157 ---MNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGG 213
++G+ + + + +++P A +K ++ GG
Sbjct: 75 PHKVDGRVVEPKRAVSREDSQRPGAHLTVKK------------------------IFVGG 110
Query: 214 FGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESIHNTDI 267
+D E + F +G I I + K++G+AFV F ++ + ++T +
Sbjct: 111 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-V 169
Query: 268 NGH 270
NGH
Sbjct: 170 NGH 172
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 38/142 (26%), Positives = 58/142 (40%), Gaps = 3/142 (2%)
Query: 6 QPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFXXXXXXXXXXXX 65
Q L++G L T+E L + F Q G + C V+R+P F
Sbjct: 11 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 70
Query: 66 MNKRVFLEKEMKVNWASSPGNQPKQDTSNHY---HIFVGDLSPEIETQTLKEAFAPFGEI 122
MN R V + + Q H IFVG + + E L++ F +G+I
Sbjct: 71 MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 130
Query: 123 SNCRIVRDPQTLKSKGYAFVSF 144
I+ D + K +G+AFV+F
Sbjct: 131 EVIEIMTDRGSGKKRGFAFVTF 152
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 65.9 bits (159), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 42/183 (22%), Positives = 85/183 (46%), Gaps = 35/183 (19%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA- 156
+F+G LS E ++L+ F +G +++C ++RDP T +S+G+ FV++ E + A+ A
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 157 ---MNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGG 213
++G+ + + + +++P A +K ++ GG
Sbjct: 74 PHKVDGRVVEPKRAVSREDSQRPGAHLTVKK------------------------IFVGG 109
Query: 214 FGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESIHNTDI 267
+D E + F +G I I + K++G+AFV F ++ + ++T +
Sbjct: 110 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-V 168
Query: 268 NGH 270
NGH
Sbjct: 169 NGH 171
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 38/142 (26%), Positives = 58/142 (40%), Gaps = 3/142 (2%)
Query: 6 QPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFXXXXXXXXXXXX 65
Q L++G L T+E L + F Q G + C V+R+P F
Sbjct: 10 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 69
Query: 66 MNKRVFLEKEMKVNWASSPGNQPKQDTSNHY---HIFVGDLSPEIETQTLKEAFAPFGEI 122
MN R V + + Q H IFVG + + E L++ F +G+I
Sbjct: 70 MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 129
Query: 123 SNCRIVRDPQTLKSKGYAFVSF 144
I+ D + K +G+AFV+F
Sbjct: 130 EVIEIMTDRGSGKKRGFAFVTF 151
>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 = 65.9 bits (159), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 42/183 (22%), Positives = 85/183 (46%), Gaps = 35/183 (19%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA- 156
+F+G LS E ++L+ F +G +++C ++RDP T +S+G+ FV++ E + A+ A
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 157 ---MNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGG 213
++G+ + + + +++P A +K ++ GG
Sbjct: 69 PHKVDGRVVEPKRAVSREDSQRPGAHLTVKK------------------------IFVGG 104
Query: 214 FGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESIHNTDI 267
+D E + F +G I I + K++G+AFV F ++ + ++T +
Sbjct: 105 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-V 163
Query: 268 NGH 270
NGH
Sbjct: 164 NGH 166
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 38/142 (26%), Positives = 58/142 (40%), Gaps = 3/142 (2%)
Query: 6 QPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFXXXXXXXXXXXX 65
Q L++G L T+E L + F Q G + C V+R+P F
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64
Query: 66 MNKRVFLEKEMKVNWASSPGNQPKQDTSNHY---HIFVGDLSPEIETQTLKEAFAPFGEI 122
MN R V + + Q H IFVG + + E L++ F +G+I
Sbjct: 65 MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 124
Query: 123 SNCRIVRDPQTLKSKGYAFVSF 144
I+ D + K +G+AFV+F
Sbjct: 125 EVIEIMTDRGSGKKRGFAFVTF 146
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 65.9 bits (159), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 42/183 (22%), Positives = 85/183 (46%), Gaps = 35/183 (19%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA- 156
+F+G LS E ++L+ F +G +++C ++RDP T +S+G+ FV++ E + A+ A
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 76
Query: 157 ---MNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGG 213
++G+ + + + +++P A +K ++ GG
Sbjct: 77 PHKVDGRVVEPKRAVSREDSQRPGAHLTVKK------------------------IFVGG 112
Query: 214 FGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESIHNTDI 267
+D E + F +G I I + K++G+AFV F ++ + ++T +
Sbjct: 113 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-V 171
Query: 268 NGH 270
NGH
Sbjct: 172 NGH 174
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 38/142 (26%), Positives = 58/142 (40%), Gaps = 3/142 (2%)
Query: 6 QPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFXXXXXXXXXXXX 65
Q L++G L T+E L + F Q G + C V+R+P F
Sbjct: 13 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 72
Query: 66 MNKRVFLEKEMKVNWASSPGNQPKQDTSNHY---HIFVGDLSPEIETQTLKEAFAPFGEI 122
MN R V + + Q H IFVG + + E L++ F +G+I
Sbjct: 73 MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 132
Query: 123 SNCRIVRDPQTLKSKGYAFVSF 144
I+ D + K +G+AFV+F
Sbjct: 133 EVIEIMTDRGSGKKRGFAFVTF 154
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 63.9 bits (154), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 44/159 (27%), Positives = 72/159 (45%), Gaps = 7/159 (4%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP-----YAFLEFXXXXXX 59
S ++VG + + +E+ L LF Q G V V+R+ +P F+ F
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 60 XXXXXXMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPF 119
++ L M P + K + +F+G +S + ++ F+ F
Sbjct: 61 LEAQNALHNMKVLPG-MHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSF 119
Query: 120 GEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMN 158
G+I CRI+R P L S+G AFV+F +A A+ AI AM+
Sbjct: 120 GQIEECRILRGPDGL-SRGCAFVTFTTRAMAQTAIKAMH 157
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 44/181 (24%), Positives = 76/181 (41%), Gaps = 34/181 (18%)
Query: 93 SNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRD-----PQTLKSKGYAFVSFVKK 147
S+ +FVG + + L+E F +G + ++RD PQ SKG FV+F +
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQ---SKGCCFVTFYTR 57
Query: 148 AEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNC 207
A A A++ +++ P M +N+ + +
Sbjct: 58 KAALEAQNALH-------NMKVLPGMHHPIQMKPADSEKNNAVE--------------DR 96
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFK-----EKGYAFVKFTTKETATHAIESI 262
++ G K E + +FS FG I + R+ + +G AFV FTT+ A AI+++
Sbjct: 97 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAM 156
Query: 263 H 263
H
Sbjct: 157 H 157
Score = 32.7 bits (73), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE--------KGYAFVKFTTKETATHAIE 260
++ G + +E+ + ++F +G + +I V ++ KG FV F T++ A A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 261 SIHNTDI 267
++HN +
Sbjct: 66 ALHNMKV 72
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 63.5 bits (153), Expect = 2e-10, Method: Composition-based stats.
Identities = 29/78 (37%), Positives = 52/78 (66%)
Query: 93 SNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAEN 152
S+ +FVG LS + Q+L++ F+ +G+IS +V+D +T +S+G+ FV+F +A++
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 153 AITAMNGQWLGSRSIRTN 170
A+ AMNG+ + R IR +
Sbjct: 70 AMMAMNGKSVDGRQIRVD 87
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 24/83 (28%), Positives = 45/83 (54%), Gaps = 7/83 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
++ GG D NE+ + +VFS +G I ++ V K+ +G+ FV F + A A+ ++
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 263 HNTDINGHTVKCFW-GKESENNS 284
+ ++G ++ GK S+N S
Sbjct: 75 NGKSVDGRQIRVDQAGKSSDNRS 97
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 63.2 bits (152), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 43/154 (27%), Positives = 71/154 (46%), Gaps = 7/154 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP-----YAFLEFXXXXXXXXXXX 64
++VG + + +E+ L LF Q G V V+R+ +P F+ F
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 65 XMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISN 124
++ L M P + K + +F+G +S + ++ F+ FG+I
Sbjct: 78 ALHNMKVLPG-MHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEE 136
Query: 125 CRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMN 158
CRI+R P L S+G AFV+F +A A+ AI AM+
Sbjct: 137 CRILRGPDGL-SRGCAFVTFTTRAMAQTAIKAMH 169
Score = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 49/191 (25%), Positives = 79/191 (41%), Gaps = 40/191 (20%)
Query: 86 NQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRD-----PQTLKSKGYA 140
+ P Q + +FVG + + L+E F +G + ++RD PQ SKG
Sbjct: 6 DHPDQPDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQ---SKGCC 62
Query: 141 FVSF-VKKA--EAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDE 197
FV+F +KA EA+NA+ M I+ + + +RK
Sbjct: 63 FVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRK------------- 109
Query: 198 VYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFK-----EKGYAFVKFTTK 252
++ G K E + +FS FG I + R+ + +G AFV FTT+
Sbjct: 110 -----------LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTR 158
Query: 253 ETATHAIESIH 263
A AI+++H
Sbjct: 159 AMAQTAIKAMH 169
Score = 32.7 bits (73), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE--------KGYAFVKFTTKETATHAIE 260
++ G + +E+ + ++F +G + +I V ++ KG FV F T++ A A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 261 SIHNTDI 267
++HN +
Sbjct: 78 ALHNMKV 84
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 62.4 bits (150), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 46/75 (61%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG L+ E++ + L AF PFG+I++ +I D +T K +G+AFV F +A AI M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 158 NGQWLGSRSIRTNWS 172
N L R+IR N +
Sbjct: 126 NESELFGRTIRVNLA 140
Score = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 45/72 (62%), Gaps = 6/72 (8%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRV------FKEKGYAFVKFTTKETATHAIES 261
+Y GG ++++++++ F PFG I DI++ K +G+AFV+F E A AI++
Sbjct: 65 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 124
Query: 262 IHNTDINGHTVK 273
++ +++ G T++
Sbjct: 125 MNESELFGRTIR 136
>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 = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 43/160 (26%), Positives = 71/160 (44%), Gaps = 9/160 (5%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP-----YAFLEFXXXXXX 59
S +VG + + +E+ L LF Q G V V+R+ +P F+ F
Sbjct: 1 SDAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 60 XXXXXXM-NKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAP 118
+ N +V + P + K + +F+G +S + ++ F+
Sbjct: 61 LEAQNALHNXKVLPGXHHPIQ--XKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSS 118
Query: 119 FGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMN 158
FG+I CRI+R P L S+G AFV+F +A A+ AI A +
Sbjct: 119 FGQIEECRILRGPDGL-SRGCAFVTFTTRAXAQTAIKAXH 157
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 47/184 (25%), Positives = 73/184 (39%), Gaps = 40/184 (21%)
Query: 93 SNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRD-----PQTLKSKGYAFVSF-VK 146
S+ FVG + + L+E F +G + ++RD PQ SKG FV+F +
Sbjct: 1 SDAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQ---SKGCCFVTFYTR 57
Query: 147 KA--EAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSP 204
KA EA+NA+ I+ + + +RK
Sbjct: 58 KAALEAQNALHNXKVLPGXHHPIQXKPADSEKNNAVEDRK-------------------- 97
Query: 205 TNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFK-----EKGYAFVKFTTKETATHAI 259
++ G K E + FS FG I + R+ + +G AFV FTT+ A AI
Sbjct: 98 ----LFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153
Query: 260 ESIH 263
++ H
Sbjct: 154 KAXH 157
Score = 31.6 bits (70), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 13/60 (21%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKE--------KGYAFVKFTTKETATHAIESIHNTDI 267
KDL E +F +G + +I V ++ KG FV F T++ A A ++HN +
Sbjct: 18 KDLRE-----LFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNXKV 72
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 45/192 (23%), Positives = 79/192 (41%), Gaps = 48/192 (25%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ V +L P + Q +E PFG + C +V +T +SKGY F ++KK A A + +
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 158 NGQWLGSRSIRTNWST--RKPPAMTNERKRQNSHTKTITFDEV---YNQ----------- 201
G+ LG R++ +W+ + PA+ H++ + D + +N
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALL--------HSRCLCVDRLPPGFNDVDALCRALSAV 209
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIES 261
SPT C + CG G + KG+A +++ T E A A +
Sbjct: 210 HSPTFCQLACGQDG------------------------QLKGFAVLEYETAEMAEEAQQQ 245
Query: 262 IHNTDINGHTVK 273
+ G ++
Sbjct: 246 ADGLSLGGSHLR 257
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 37/189 (19%), Positives = 67/189 (35%), Gaps = 44/189 (23%)
Query: 94 NHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENA 153
N I + L ++ Q + + + + E+ C + K KG AFV+ + +AE A
Sbjct: 21 NRRKILIRGLPGDVTNQEVHDLLSDY-ELKYCFVD------KYKGTAFVTLLNGEQAEAA 73
Query: 154 ITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGG 213
I A + L R E+ Q PT+ +
Sbjct: 74 INAFHQSRLRER-------------------------------ELSVQLQPTDALLCVAN 102
Query: 214 FGKDLNEELVSKVFSPFGT------IVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDI 267
L ++ ++ PFG+ + R + KGY F ++ K++A A + +
Sbjct: 103 LPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPL 162
Query: 268 NGHTVKCFW 276
T+ W
Sbjct: 163 GPRTLYVHW 171
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 45/192 (23%), Positives = 79/192 (41%), Gaps = 48/192 (25%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ V +L P + Q +E PFG + C +V +T +SKGY F ++KK A A + +
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 158 NGQWLGSRSIRTNWST--RKPPAMTNERKRQNSHTKTITFDEV---YNQ----------- 201
G+ LG R++ +W+ + PA+ H++ + D + +N
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALL--------HSRCLCVDRLPPGFNDVDALCRALSAV 209
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIES 261
SPT C + CG G + KG+A +++ T E A A +
Sbjct: 210 HSPTFCQLACGQDG------------------------QLKGFAVLEYETAEMAEEAQQQ 245
Query: 262 IHNTDINGHTVK 273
+ G ++
Sbjct: 246 ADGLSLGGSHLR 257
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 37/189 (19%), Positives = 67/189 (35%), Gaps = 44/189 (23%)
Query: 94 NHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENA 153
N I + L ++ Q + + + + E+ C + K KG AFV+ + +AE A
Sbjct: 21 NRRKILIRGLPGDVTNQEVHDLLSDY-ELKYCFVD------KYKGTAFVTLLNGEQAEAA 73
Query: 154 ITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGG 213
I A + L R E+ Q PT+ +
Sbjct: 74 INAFHQSRLRER-------------------------------ELSVQLQPTDALLCVAN 102
Query: 214 FGKDLNEELVSKVFSPFGTIVDI------RVFKEKGYAFVKFTTKETATHAIESIHNTDI 267
L ++ ++ PFG++ R + KGY F ++ K++A A + +
Sbjct: 103 LPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPL 162
Query: 268 NGHTVKCFW 276
T+ W
Sbjct: 163 GPRTLYVHW 171
>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 = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 45/192 (23%), Positives = 79/192 (41%), Gaps = 48/192 (25%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ V +L P + Q +E PFG + C +V +T +SKGY F ++KK A A + +
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 158 NGQWLGSRSIRTNWST--RKPPAMTNERKRQNSHTKTITFDEV---YNQ----------- 201
G+ LG R++ +W+ + PA+ H++ + D + +N
Sbjct: 156 LGKPLGPRTLYVHWTDAGQLTPALL--------HSRCLCVDRLPPGFNDVDALCRALSAV 207
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIES 261
SPT C + CG G + KG+A +++ T E A A +
Sbjct: 208 HSPTFCQLACGQDG------------------------QLKGFAVLEYETAEMAEEAQQQ 243
Query: 262 IHNTDINGHTVK 273
+ G ++
Sbjct: 244 ADGLSLGGSHLR 255
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 37/189 (19%), Positives = 67/189 (35%), Gaps = 44/189 (23%)
Query: 94 NHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENA 153
N I + L ++ Q + + + + E+ C + K KG AFV+ + +AE A
Sbjct: 19 NRRKILIRGLPGDVTNQEVHDLLSDY-ELKYCFVD------KYKGTAFVTLLNGEQAEAA 71
Query: 154 ITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGG 213
I A + L R E+ Q PT+ +
Sbjct: 72 INAFHQSRLRER-------------------------------ELSVQLQPTDALLCVAN 100
Query: 214 FGKDLNEELVSKVFSPFGTIVDI------RVFKEKGYAFVKFTTKETATHAIESIHNTDI 267
L ++ ++ PFG++ R + KGY F ++ K++A A + +
Sbjct: 101 LPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPL 160
Query: 268 NGHTVKCFW 276
T+ W
Sbjct: 161 GPRTLYVHW 169
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 60.5 bits (145), Expect = 1e-09, Method: Composition-based stats.
Identities = 30/73 (41%), Positives = 45/73 (61%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG L+ E++ + L AF PFG+I++ +I D +T K +G+AFV F +A AI M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 158 NGQWLGSRSIRTN 170
N L R+IR N
Sbjct: 68 NESELFGRTIRVN 80
Score = 52.8 bits (125), Expect = 3e-07, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 47/77 (61%), Gaps = 6/77 (7%)
Query: 203 SPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRV------FKEKGYAFVKFTTKETAT 256
S T +Y GG ++++++++ F PFG I DI++ K +G+AFV+F E A
Sbjct: 2 STTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 61
Query: 257 HAIESIHNTDINGHTVK 273
AI++++ +++ G T++
Sbjct: 62 AAIDNMNESELFGRTIR 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 = 60.5 bits (145), Expect = 1e-09, Method: Composition-based stats.
Identities = 30/73 (41%), Positives = 45/73 (61%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG L+ E++ + L AF PFG+I++ +I D +T K +G+AFV F +A AI M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 158 NGQWLGSRSIRTN 170
N L R+IR N
Sbjct: 65 NESELFGRTIRVN 77
Score = 51.2 bits (121), Expect = 9e-07, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 45/71 (63%), Gaps = 6/71 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRV------FKEKGYAFVKFTTKETATHAIESI 262
+Y GG ++++++++ F PFG I DI++ K +G+AFV+F E A AI+++
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 263 HNTDINGHTVK 273
+ +++ G T++
Sbjct: 65 NESELFGRTIR 75
>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 = 60.5 bits (145), Expect = 1e-09, Method: Composition-based stats.
Identities = 30/73 (41%), Positives = 45/73 (61%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG L+ E++ + L AF PFG+I++ +I D +T K +G+AFV F +A AI M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 158 NGQWLGSRSIRTN 170
N L R+IR N
Sbjct: 70 NESELFGRTIRVN 82
Score = 51.6 bits (122), Expect = 7e-07, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 47/77 (61%), Gaps = 6/77 (7%)
Query: 203 SPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRV------FKEKGYAFVKFTTKETAT 256
+ T +Y GG ++++++++ F PFG I DI++ K +G+AFV+F E A
Sbjct: 4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63
Query: 257 HAIESIHNTDINGHTVK 273
AI++++ +++ G T++
Sbjct: 64 AAIDNMNESELFGRTIR 80
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 60.1 bits (144), Expect = 2e-09, Method: Composition-based stats.
Identities = 30/73 (41%), Positives = 45/73 (61%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG L+ E++ + L AF PFG+I++ +I D +T K +G+AFV F +A AI M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 158 NGQWLGSRSIRTN 170
N L R+IR N
Sbjct: 75 NESELFGRTIRVN 87
Score = 51.2 bits (121), Expect = 1e-06, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 47/77 (61%), Gaps = 6/77 (7%)
Query: 203 SPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRV------FKEKGYAFVKFTTKETAT 256
+ T +Y GG ++++++++ F PFG I DI++ K +G+AFV+F E A
Sbjct: 9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 68
Query: 257 HAIESIHNTDINGHTVK 273
AI++++ +++ G T++
Sbjct: 69 AAIDNMNESELFGRTIR 85
>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 = 58.9 bits (141), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 45/178 (25%), Positives = 75/178 (42%), Gaps = 26/178 (14%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGN----------DPYAFLEFXXXXXX 59
LYVGN+ +TEE + F+ + G + + PGN +AFLEF
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGG--LTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66
Query: 60 XXXXXXMNKRVFLEKEMKV----NWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEA 115
+ +F + +K+ ++ PG + +F+G L + +KE
Sbjct: 67 TQAMA-FDGIIFQGQSLKIRRPHDYQPLPG---------AHKLFIGGLPNYLNDDQVKEL 116
Query: 116 FAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWST 173
FG + +V+D T SKGYAF +V + AI +NG LG + + ++
Sbjct: 117 LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 174
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 6/73 (8%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKET 254
Q P ++ GG LN++ V ++ + FG + + K+ KGYAF ++
Sbjct: 91 QPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINV 150
Query: 255 ATHAIESIHNTDI 267
AI ++ +
Sbjct: 151 TDQAIAGLNGMQL 163
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 58.5 bits (140), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 45/178 (25%), Positives = 75/178 (42%), Gaps = 26/178 (14%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGN----------DPYAFLEFXXXXXX 59
LYVGN+ +TEE + F+ + G + + PGN +AFLEF
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGG--LTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 60 XXXXXXMNKRVFLEKEMKV----NWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEA 115
+ +F + +K+ ++ PG + +F+G L + +KE
Sbjct: 65 TQAMA-FDGIIFQGQSLKIRRPHDYQPLPG---------AHKLFIGGLPNYLNDDQVKEL 114
Query: 116 FAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWST 173
FG + +V+D T SKGYAF +V + AI +NG LG + + ++
Sbjct: 115 LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 172
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 6/73 (8%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKET 254
Q P ++ GG LN++ V ++ + FG + + K+ KGYAF ++
Sbjct: 89 QPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINV 148
Query: 255 ATHAIESIHNTDI 267
AI ++ +
Sbjct: 149 TDQAIAGLNGMQL 161
>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 = 57.8 bits (138), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 30/93 (32%), Positives = 48/93 (51%), Gaps = 1/93 (1%)
Query: 86 NQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFV 145
+P D + V +L+ TL+ F +G + + I RD T +S+G+AFV F
Sbjct: 38 GRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFH 97
Query: 146 KKAEAENAITAMNGQWLGSRSIRTNWST-RKPP 177
K +AE+A+ AM+G L R +R + +PP
Sbjct: 98 DKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP 130
Score = 34.7 bits (78), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 33/60 (55%), Gaps = 6/60 (10%)
Query: 221 ELVSKVFSPFGTIVDI-----RVFKE-KGYAFVKFTTKETATHAIESIHNTDINGHTVKC 274
+ + +VF +G + D+ R KE +G+AFV+F K A A++++ ++G ++
Sbjct: 62 DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 121
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 57.8 bits (138), Expect = 1e-08, Method: Composition-based stats.
Identities = 31/83 (37%), Positives = 43/83 (51%), Gaps = 2/83 (2%)
Query: 85 GNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
G P S +IF+ +L I+ + L + F+ FG I +C++V D SKGY FV F
Sbjct: 1 GADPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHF 58
Query: 145 VKKAEAENAITAMNGQWLGSRSI 167
+ AE AI MNG L R +
Sbjct: 59 ETQEAAERAIEKMNGMLLNDRKV 81
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE----KGYAFVKFTTKETATHAIESIHN 264
++ K ++ + + FS FG I+ +V + KGY FV F T+E A AIE ++
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 265 TDINGHTV 272
+N V
Sbjct: 74 MLLNDRKV 81
Score = 34.3 bits (77), Expect = 0.13, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVI-REPGNDPYAFLEFXXXXXXXXXXXXMNK 68
+++ NLD S+ + L FS G + CKV+ E G+ Y F+ F MN
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 69 RVFLEKEMKV 78
+ ++++ V
Sbjct: 74 MLLNDRKVFV 83
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 57.0 bits (136), Expect = 2e-08, Method: Composition-based stats.
Identities = 31/94 (32%), Positives = 55/94 (58%), Gaps = 2/94 (2%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+G L+ E + LK F G IS +++D +T KS+G+AF++F A+A+NA M
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKDM 68
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTK 191
NG+ L ++I+ +KP + R+R + ++
Sbjct: 69 NGKSLHGKAIKVE-QAKKPSFQSGGRRRPPASSR 101
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 24/89 (26%), Positives = 39/89 (43%), Gaps = 2/89 (2%)
Query: 1 MCDESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDPYAFLEFXXXXX 58
M + P L++G L+ E++L A+F + GP+ +I R + +AF+ F
Sbjct: 1 MVEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPAD 60
Query: 59 XXXXXXXMNKRVFLEKEMKVNWASSPGNQ 87
MN + K +KV A P Q
Sbjct: 61 AKNAAKDMNGKSLHGKAIKVEQAKKPSFQ 89
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 18/70 (25%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDI-----RVFKEKGYAFVKFTTKETATHAIESIH 263
++ GG ++ NE+++ VF G I ++ R K +G+AF+ F A +A + ++
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 264 NTDINGHTVK 273
++G +K
Sbjct: 70 GKSLHGKAIK 79
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 56.6 bits (135), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 100 VGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNG 159
V +L+ TL+ F +G + + I RD T +S+G+AFV F K +AE+A+ AM+G
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 160 QWLGSRSIRTNWSTR-KPP 177
L R +R + +PP
Sbjct: 135 AVLDGRELRVQMARYGRPP 153
Score = 33.5 bits (75), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 33/60 (55%), Gaps = 6/60 (10%)
Query: 221 ELVSKVFSPFGTIVDI-----RVFKE-KGYAFVKFTTKETATHAIESIHNTDINGHTVKC 274
+ + +VF +G + D+ R KE +G+AFV+F K A A++++ ++G ++
Sbjct: 85 DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 144
>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 = 55.5 bits (132), Expect = 5e-08, Method: Composition-based stats.
Identities = 28/71 (39%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+IF+ +L I+ + L + F+ FG I +C++V D SKGY FV F + AE AI
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEK 64
Query: 157 MNGQWLGSRSI 167
MNG L R +
Sbjct: 65 MNGMLLNDRKV 75
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE----KGYAFVKFTTKETATHAIESIHN 264
++ K ++ + + FS FG I+ +V + KGY FV F T+E A AIE ++
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67
Query: 265 TDINGHTV 272
+N V
Sbjct: 68 MLLNDRKV 75
Score = 33.9 bits (76), Expect = 0.18, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVI-REPGNDPYAFLEFXXXXXXXXXXXXMNK 68
+++ NLD S+ + L FS G + CKV+ E G+ Y F+ F MN
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67
Query: 69 RVFLEKEMKV 78
+ ++++ V
Sbjct: 68 MLLNDRKVFV 77
>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 = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 45/189 (23%), Positives = 76/189 (40%), Gaps = 28/189 (14%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGN----------DPYAFLEFXXXXXX 59
LYVGN+ +TEE + F+ + G + + PGN +AFLEF
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGG--LTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 60 XXXXXXMNKRVFLEKEMKV----NWASSPGNQPKQDT-----------SNHYHIFVGDLS 104
+ +F + +K+ ++ PG + + +F+G L
Sbjct: 65 TQAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLP 123
Query: 105 PEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGS 164
+ +KE FG + +V+D T SKGYAF +V + AI +NG LG
Sbjct: 124 NYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD 183
Query: 165 RSIRTNWST 173
+ + ++
Sbjct: 184 KKLLVQRAS 192
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 32/149 (21%), Positives = 60/149 (40%), Gaps = 26/149 (17%)
Query: 132 QTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKP------PAMTNERKR 185
Q + K +AF+ F E A+ A +G +S++ R+P P M
Sbjct: 46 QINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKI----RRPHDYQPLPGM------ 94
Query: 186 QNSHTKTITFDEVYNQSSPTNC-TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE--- 241
S ++ V + P + ++ GG LN++ V ++ + FG + + K+
Sbjct: 95 --SENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSAT 152
Query: 242 ---KGYAFVKFTTKETATHAIESIHNTDI 267
KGYAF ++ AI ++ +
Sbjct: 153 GLSKGYAFCEYVDINVTDQAIAGLNGMQL 181
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 55.1 bits (131), Expect = 6e-08, Method: Composition-based stats.
Identities = 28/84 (33%), Positives = 43/84 (51%)
Query: 92 TSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAE 151
+S ++VG L I L+ F PFG+I N +++D T +SKGY F++F A
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 152 NAITAMNGQWLGSRSIRTNWSTRK 175
A+ +NG L R +R T +
Sbjct: 62 RALEQLNGFELAGRPMRVGHVTER 85
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 6/71 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
+Y G ++ E+++ +F PFG I +I + K+ KGY F+ F+ E A A+E +
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 263 HNTDINGHTVK 273
+ ++ G ++
Sbjct: 68 NGFELAGRPMR 78
Score = 28.5 bits (62), Expect = 6.9, Method: Composition-based stats.
Identities = 17/77 (22%), Positives = 34/77 (44%), Gaps = 3/77 (3%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG---NDPYAFLEFXXXXXXXX 61
S + LYVG+L ++TE++L +F G + ++++ + Y F+ F
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 62 XXXXMNKRVFLEKEMKV 78
+N + M+V
Sbjct: 63 ALEQLNGFELAGRPMRV 79
>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 = 54.7 bits (130), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 37/170 (21%), Positives = 75/170 (44%), Gaps = 33/170 (19%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+G L+ + L+E F +G +++ +I++DP T +S+G+ F+SF K + + +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKD 217
+ L + I P R Q+ K ++ GG G D
Sbjct: 66 H--ILDGKVI--------DPKRAIPRDEQDKTGK-----------------IFVGGIGPD 98
Query: 218 LNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIES 261
+ + + FS +GTI+D ++ +K G+ FV + + + ++
Sbjct: 99 VRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN 148
Score = 48.9 bits (115), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 30/138 (21%), Positives = 65/138 (47%), Gaps = 10/138 (7%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG---NDPYAFLEFXXXXXXXXXXXXM 66
+++G L+ TE+ L F + G V K++++P + + FL F +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSS-------V 58
Query: 67 NKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCR 126
++ V + + P+ + IFVG + P++ + +E F+ +G I + +
Sbjct: 59 DEVVKTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQ 118
Query: 127 IVRDPQTLKSKGYAFVSF 144
++ D T +S+G+ FV++
Sbjct: 119 LMLDKDTGQSRGFGFVTY 136
Score = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 15/67 (22%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAI 259
+C ++ GG D E+ + + F +GT+ D+++ K+ +G+ F+ F + +
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
Query: 260 ESIHNTD 266
++ H D
Sbjct: 63 KTQHILD 69
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 54.7 bits (130), Expect = 9e-08, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 44/70 (62%), Gaps = 1/70 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+G LS + + L+E F FGE+ C ++RDP T +S+G+ FV+F+ +A + + A
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK-VLAQ 61
Query: 158 NGQWLGSRSI 167
+ L S++I
Sbjct: 62 SRHELDSKTI 71
Score = 32.0 bits (71), Expect = 0.53, Method: Composition-based stats.
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP 43
+++G L T+E L F Q G VK C V+R+P
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP 36
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 54.3 bits (129), Expect = 1e-07, Method: Composition-based stats.
Identities = 33/97 (34%), Positives = 51/97 (52%), Gaps = 2/97 (2%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
+ S GN+ D + +F LS + L+E F+ +G I++ IV D Q+ +S+G+A
Sbjct: 3 SGSSGNRANPDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
FV F +A+ A NG L R IR ++S K P
Sbjct: 61 FVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRP 97
Score = 36.2 bits (82), Expect = 0.032, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 7/81 (8%)
Query: 200 NQSSPT-NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTK 252
N+++P NC + G E + +VFS +G I D+ + + +G+AFV F
Sbjct: 8 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 67
Query: 253 ETATHAIESIHNTDINGHTVK 273
+ A A E + +++G ++
Sbjct: 68 DDAKEAKERANGMELDGRRIR 88
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 54.3 bits (129), Expect = 1e-07, Method: Composition-based stats.
Identities = 28/79 (35%), Positives = 45/79 (56%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS + P + ++ I V +LS + L+E F PFG IS + +D T +SKG+A
Sbjct: 1 GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60
Query: 141 FVSFVKKAEAENAITAMNG 159
F+SF ++ +A AI ++G
Sbjct: 61 FISFHRREDAARAIAGVSG 79
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 25/90 (27%), Positives = 42/90 (46%), Gaps = 6/90 (6%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKE 253
N+ + N T+ +D E + ++F PFG+I I + K+K G+AF+ F +E
Sbjct: 9 NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 68
Query: 254 TATHAIESIHNTDINGHTVKCFWGKESENN 283
A AI + + + W K S N+
Sbjct: 69 DAARAIAGVSGFGYDHLILNVEWAKPSTNS 98
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 53.9 bits (128), Expect = 2e-07, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 44/70 (62%), Gaps = 1/70 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+G LS + + L+E F FGE+ C ++RDP T +S+G+ FV+F+ +A + + A
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 86
Query: 158 NGQWLGSRSI 167
+ L S++I
Sbjct: 87 SRHELDSKTI 96
Score = 32.0 bits (71), Expect = 0.69, Method: Composition-based stats.
Identities = 15/39 (38%), Positives = 21/39 (53%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP 43
S +++G L T+E L F Q G VK C V+R+P
Sbjct: 23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP 61
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 53.1 bits (126), Expect = 2e-07, Method: Composition-based stats.
Identities = 26/90 (28%), Positives = 47/90 (52%)
Query: 86 NQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFV 145
N ++ ++ ++VG L I L+ F PFG I + +++ D +T +SKGY F++F
Sbjct: 17 NNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFS 76
Query: 146 KKAEAENAITAMNGQWLGSRSIRTNWSTRK 175
A+ A+ +NG L R ++ T +
Sbjct: 77 DSECAKKALEQLNGFELAGRPMKVGHVTER 106
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 6/71 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESI 262
+Y G ++ E+++ +F PFG I I++ + KGY F+ F+ E A A+E +
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 263 HNTDINGHTVK 273
+ ++ G +K
Sbjct: 89 NGFELAGRPMK 99
Score = 32.0 bits (71), Expect = 0.61, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP-YAFLEFXXXXXXXXXX 63
P LYVG+L ++TE++L +F G ++ +++ E G Y F+ F
Sbjct: 26 PMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 85
Query: 64 XXMNKRVFLEKEMKV 78
+N + MKV
Sbjct: 86 EQLNGFELAGRPMKV 100
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 53.1 bits (126), Expect = 2e-07, Method: Composition-based stats.
Identities = 32/93 (34%), Positives = 49/93 (52%), Gaps = 2/93 (2%)
Query: 85 GNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
GN+ D + +F LS + L+E F+ +G I++ IV D Q+ +S+G+AFV F
Sbjct: 38 GNRANPDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 95
Query: 145 VKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
+A+ A NG L R IR ++S K P
Sbjct: 96 ENVDDAKEAKERANGMELDGRRIRVDFSITKRP 128
Score = 37.0 bits (84), Expect = 0.018, Method: Composition-based stats.
Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 198 VYNQSSPT-NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFT 250
V N+++P NC + G E + +VFS +G I D+ + + +G+AFV F
Sbjct: 37 VGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 96
Query: 251 TKETATHAIESIHNTDINGHTVK 273
+ A A E + +++G ++
Sbjct: 97 NVDDAKEAKERANGMELDGRRIR 119
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 53.1 bits (126), Expect = 3e-07, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 48/81 (59%)
Query: 76 MKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLK 135
M+ + P + K++ +F+G LS E ++L+ + +G++++C ++RDP + +
Sbjct: 8 MEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKR 67
Query: 136 SKGYAFVSFVKKAEAENAITA 156
S+G+ FV+F AE + A+ A
Sbjct: 68 SRGFGFVTFSSMAEVDAAMAA 88
Score = 30.0 bits (66), Expect = 2.2, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGN 45
++ Q L++G L TEE L + Q G + C V+R+P +
Sbjct: 23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPAS 65
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 52.4 bits (124), Expect = 4e-07, Method: Composition-based stats.
Identities = 25/79 (31%), Positives = 49/79 (62%), Gaps = 2/79 (2%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+++V +L I+ + L++AF+PFG I++ +++ + +SKG+ FV F EA A+T
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGG--RSKGFGFVCFSSPEEATKAVTE 74
Query: 157 MNGQWLGSRSIRTNWSTRK 175
MNG+ + ++ + + RK
Sbjct: 75 MNGRIVATKPLYVALAQRK 93
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/68 (36%), Positives = 37/68 (54%), Gaps = 9/68 (13%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE----KGYAFVKFTTKETATHAIESIHN 264
+Y +++E + K FSPFGTI +V E KG+ FV F++ E AT A+
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV----- 72
Query: 265 TDINGHTV 272
T++NG V
Sbjct: 73 TEMNGRIV 80
Score = 35.4 bits (80), Expect = 0.052, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 32/77 (41%), Gaps = 1/77 (1%)
Query: 6 QPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP-YAFLEFXXXXXXXXXXX 64
Q LYV NLD + +E L FS G + KV+ E G + F+ F
Sbjct: 14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVT 73
Query: 65 XMNKRVFLEKEMKVNWA 81
MN R+ K + V A
Sbjct: 74 EMNGRIVATKPLYVALA 90
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 52.4 bits (124), Expect = 4e-07, Method: Composition-based stats.
Identities = 28/75 (37%), Positives = 42/75 (56%)
Query: 103 LSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWL 162
LS + L+E F+ +G I++ IV D Q+ +S+G+AFV F +A+ A NG L
Sbjct: 20 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 79
Query: 163 GSRSIRTNWSTRKPP 177
R IR ++S K P
Sbjct: 80 DGRRIRVDFSITKRP 94
Score = 35.0 bits (79), Expect = 0.071, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAI 259
NC + G E + +VFS +G I D+ + + +G+AFV F + A A
Sbjct: 12 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 71
Query: 260 ESIHNTDINGHTVK 273
E + +++G ++
Sbjct: 72 ERANGMELDGRRIR 85
>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 = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 35/119 (29%), Positives = 53/119 (44%), Gaps = 9/119 (7%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG+LS + + E F+ G+I + D + G+ FV + +A+AENA+ +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGK 216
NG L R IRT+W R R + DE Y Q GG+GK
Sbjct: 102 NGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVR----DE-YRQDYDAG----RGGYGK 151
Score = 36.2 bits (82), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 204 PTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATH 257
+CT+Y G EE + ++FS G I I + +K G+ FV++ ++ A +
Sbjct: 37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96
Query: 258 AIESIHNTDINGHTVKCFW 276
A+ I+ T ++ ++ W
Sbjct: 97 AMRYINGTRLDDRIIRTDW 115
Score = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 11/82 (13%)
Query: 6 QPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP-------YAFLEFXXXXX 58
+ TLYVGNL TEE + LFS+ G +K K+I G D + F+E+
Sbjct: 38 KSCTLYVGNLSFYTTEEQIYELFSKSGDIK--KII--MGLDKMKKTACGFCFVEYYSRAD 93
Query: 59 XXXXXXXMNKRVFLEKEMKVNW 80
+N ++ ++ +W
Sbjct: 94 AENAMRYINGTRLDDRIIRTDW 115
>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 = 50.4 bits (119), Expect = 2e-06, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 42/69 (60%), Gaps = 1/69 (1%)
Query: 105 PEIETQ-TLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLG 163
P+ TQ L+ F+ GE+ + +++RD S GY FV++V +AE AI +NG L
Sbjct: 28 PQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQ 87
Query: 164 SRSIRTNWS 172
S++I+ +++
Sbjct: 88 SKTIKVSYA 96
Score = 32.3 bits (72), Expect = 0.51, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 6 QPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE--PGND-PYAFLEFXXXXXXXXX 62
Q T L V L + T++ L +LFS IG V+ K+IR+ G+ Y F+ +
Sbjct: 18 QGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 77
Query: 63 XXXMNKRVFLEKEMKVNWA 81
+N K +KV++A
Sbjct: 78 INTLNGLRLQSKTIKVSYA 96
Score = 31.6 bits (70), Expect = 0.84, Method: Composition-based stats.
Identities = 15/71 (21%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESIHNTDING 269
++ ++ + +FS G + ++ ++K GY FV + T + A AI +++ +
Sbjct: 29 QNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQS 88
Query: 270 HTVKCFWGKES 280
T+K + + S
Sbjct: 89 KTIKVSYARPS 99
>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 = 50.1 bits (118), Expect = 2e-06, Method: Composition-based stats.
Identities = 30/95 (31%), Positives = 48/95 (50%), Gaps = 2/95 (2%)
Query: 85 GNQP-KQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVS 143
G++P Q + + +FV + E + + + FA +GEI N + D +T KGY V
Sbjct: 12 GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 71
Query: 144 FVKKAEAENAITAMNGQWLGSRSIRTNWS-TRKPP 177
+ EA+ A+ +NGQ L + I +W R PP
Sbjct: 72 YETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPP 106
>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 = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 48/91 (52%), Gaps = 2/91 (2%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV + E + ++E F +GEI N + D +T SKGYA V + +A A A+
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 158 NGQWLGSRSIRTNWSTRKPPAMT--NERKRQ 186
NG + ++I+ +W K P +E++R+
Sbjct: 135 NGAEIMGQTIQVDWCFVKGPKRVKKSEKRRR 165
Score = 36.2 bits (82), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 6/82 (7%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTI------VDIRVFKEKGYAFVKFTTKET 254
Q S ++ ++ E+ + + F +G I +D R KGYA V++ T +
Sbjct: 67 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ 126
Query: 255 ATHAIESIHNTDINGHTVKCFW 276
A A E+++ +I G T++ W
Sbjct: 127 ALAAKEALNGAEIMGQTIQVDW 148
>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 = 49.7 bits (117), Expect = 3e-06, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 43/76 (56%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++ V L + L+ F+ GE+ + +++RD S GY FV++V +AE AI
Sbjct: 6 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 65
Query: 157 MNGQWLGSRSIRTNWS 172
+NG L S++I+ +++
Sbjct: 66 LNGLRLQSKTIKVSYA 81
Score = 32.7 bits (73), Expect = 0.38, Method: Composition-based stats.
Identities = 15/71 (21%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESIHNTDING 269
+++ ++ + +FS G + ++ ++K GY FV + T + A AI +++ +
Sbjct: 14 QNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQS 73
Query: 270 HTVKCFWGKES 280
T+K + + S
Sbjct: 74 KTIKVSYARPS 84
Score = 31.6 bits (70), Expect = 0.85, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE--PGND-PYAFLEFXXXXXXXXXXX 64
T L V L ++T++ L +LFS IG V+ K+IR+ G+ Y F+ +
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 65 XMNKRVFLEKEMKVNWA 81
+N K +KV++A
Sbjct: 65 TLNGLRLQSKTIKVSYA 81
>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 = 49.7 bits (117), Expect = 3e-06, Method: Composition-based stats.
Identities = 22/56 (39%), Positives = 32/56 (57%)
Query: 99 FVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
FVG LS + + LK+ F FGE+ +C I DP T +S+G+ F+ F A E +
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVL 70
>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 = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 41/79 (51%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++F+ L E Q L + F PFG + + ++ D QT SK + FVS+ A+ AI +
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 157 MNGQWLGSRSIRTNWSTRK 175
MNG +G + ++ K
Sbjct: 87 MNGFQIGMKRLKVQLKRSK 105
Score = 32.3 bits (72), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 7/75 (9%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKEKG------YAFVKFTTKETATHAIESIHNTDING 269
++ ++ + ++F PFG +V +VF +K + FV + +A AI+S++ I
Sbjct: 35 QEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGM 94
Query: 270 HTVKCFWGKESENNS 284
+K K S+N+S
Sbjct: 95 KRLKVQL-KRSKNDS 108
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 39/75 (52%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++F+ L E L F PFG + + ++ D QT SK + FVSF A+ AI A
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 157 MNGQWLGSRSIRTNW 171
MNG +G++ ++
Sbjct: 102 MNGFQVGTKRLKVQL 116
Score = 32.3 bits (72), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 16/76 (21%), Positives = 36/76 (47%), Gaps = 6/76 (7%)
Query: 204 PTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATH 257
P C ++ ++ + ++ F PFG ++ +VF + K + FV F ++A
Sbjct: 38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQV 97
Query: 258 AIESIHNTDINGHTVK 273
AI++++ + +K
Sbjct: 98 AIKAMNGFQVGTKRLK 113
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 49.3 bits (116), Expect = 4e-06, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 43/76 (56%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++ V L + K F G+I +C++VRD T +S GY FV++ +A+ AI
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 157 MNGQWLGSRSIRTNWS 172
+NG L +++I+ +++
Sbjct: 66 LNGLKLQTKTIKVSYA 81
Score = 29.6 bits (65), Expect = 2.7, Method: Composition-based stats.
Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 3/77 (3%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFXXXXXXXXXXX 64
T L V L ++T++ +LF IG ++ CK++R+ Y F+ +
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 65 XMNKRVFLEKEMKVNWA 81
+N K +KV++A
Sbjct: 65 TLNGLKLQTKTIKVSYA 81
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 48.9 bits (115), Expect = 4e-06, Method: Composition-based stats.
Identities = 27/83 (32%), Positives = 44/83 (53%), Gaps = 8/83 (9%)
Query: 92 TSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAE 151
+ N + IFVG++S +Q L+ F G + C +V+D YAFV K+A+A+
Sbjct: 6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAK 57
Query: 152 NAITAMNGQWLGSRSIRTNWSTR 174
AI +NG+ + + I ST+
Sbjct: 58 AAIAQLNGKEVKGKRINVELSTK 80
Score = 28.9 bits (63), Expect = 4.8, Method: Composition-based stats.
Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 11/83 (13%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFXXXXXXXXXXXXMN-- 67
++VGN+ + T + L +LF + G V C V+++ YAF+ +N
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD-----YAFVHMEKEADAKAAIAQLNGK 66
Query: 68 ----KRVFLEKEMKVNWASSPGN 86
KR+ +E K S P +
Sbjct: 67 EVKGKRINVELSTKGQKKSGPSS 89
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 48.9 bits (115), Expect = 5e-06, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 42/80 (52%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV + E + ++E F +GEI N + D +T SKGYA V + +A A A+
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 158 NGQWLGSRSIRTNWSTRKPP 177
NG + ++I+ +W K P
Sbjct: 89 NGAEIMGQTIQVDWCFVKGP 108
Score = 34.7 bits (78), Expect = 0.084, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 6/82 (7%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTI------VDIRVFKEKGYAFVKFTTKET 254
Q S ++ ++ E+ + + F +G I +D R KGYA V++ T +
Sbjct: 21 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ 80
Query: 255 ATHAIESIHNTDINGHTVKCFW 276
A A E+++ +I G T++ W
Sbjct: 81 ALAAKEALNGAEIMGQTIQVDW 102
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 48.9 bits (115), Expect = 5e-06, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 45/76 (59%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++G + + + + + + G + N +++ DPQT +SKGYAF+ F + +A+ +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 158 NGQWLGSRSIRTNWST 173
NG LGSR ++ +S+
Sbjct: 65 NGYQLGSRFLKCGYSS 80
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESI 262
VY G D EE + + S G ++++++ + KGYAF++F E++ A+ ++
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 263 HNTDINGHTVKCFWGKESE 281
+ + +KC + S+
Sbjct: 65 NGYQLGSRFLKCGYSSNSD 83
Score = 32.7 bits (73), Expect = 0.38, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 3/77 (3%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG---NDPYAFLEFXXXXXXXXXXXXM 66
+Y+G++ TEE + L S +GPV K++ +P + YAF+EF +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 67 NKRVFLEKEMKVNWASS 83
N + +K ++S+
Sbjct: 65 NGYQLGSRFLKCGYSSN 81
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 48.5 bits (114), Expect = 6e-06, Method: Composition-based stats.
Identities = 30/90 (33%), Positives = 47/90 (52%), Gaps = 2/90 (2%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
+ S GN+ D + +F LS + L+E F+ +G I++ IV D Q+ +S+G+A
Sbjct: 3 SGSSGNRANPDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTN 170
FV F +A+ A NG L R IR +
Sbjct: 61 FVYFENVDDAKEAKERANGMELDGRRIRVS 90
Score = 36.2 bits (82), Expect = 0.033, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 7/81 (8%)
Query: 200 NQSSPT-NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTK 252
N+++P NC + G E + +VFS +G I D+ + + +G+AFV F
Sbjct: 8 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 67
Query: 253 ETATHAIESIHNTDINGHTVK 273
+ A A E + +++G ++
Sbjct: 68 DDAKEAKERANGMELDGRRIR 88
>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 = 48.5 bits (114), Expect = 6e-06, Method: Composition-based stats.
Identities = 28/89 (31%), Positives = 44/89 (49%), Gaps = 1/89 (1%)
Query: 90 QDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAE 149
Q + + +FV + E + + + FA +GEI N + D +T KGY V + E
Sbjct: 2 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 61
Query: 150 AENAITAMNGQWLGSRSIRTNWS-TRKPP 177
A+ A+ +NGQ L + I +W R PP
Sbjct: 62 AQAAMEGLNGQDLMGQPISVDWCFVRGPP 90
>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 = 48.5 bits (114), Expect = 6e-06, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 45/76 (59%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++G + + + + + + G + N +++ DPQT +SKGYAF+ F + +A+ +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 158 NGQWLGSRSIRTNWST 173
NG LGSR ++ +S+
Sbjct: 66 NGYQLGSRFLKCGYSS 81
Score = 38.1 bits (87), Expect = 0.007, Method: Composition-based stats.
Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESI 262
VY G D EE + + S G ++++++ + KGYAF++F E++ A+ ++
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 263 HNTDINGHTVKCFWGKESE 281
+ + +KC + S+
Sbjct: 66 NGYQLGSRFLKCGYSSNSD 84
Score = 32.3 bits (72), Expect = 0.44, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 3/77 (3%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG---NDPYAFLEFXXXXXXXXXXXXM 66
+Y+G++ TEE + L S +GPV K++ +P + YAF+EF +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 67 NKRVFLEKEMKVNWASS 83
N + +K ++S+
Sbjct: 66 NGYQLGSRFLKCGYSSN 82
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 48.5 bits (114), Expect = 6e-06, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 47/80 (58%)
Query: 93 SNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAEN 152
+++ ++ V L ++ + L F G I+ CRI+RD +T S GYAFV F + +++
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 153 AITAMNGQWLGSRSIRTNWS 172
AI +NG + ++ ++ +++
Sbjct: 61 AIKVLNGITVRNKRLKVSYA 80
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 25/85 (29%), Positives = 38/85 (44%), Gaps = 3/85 (3%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGND---PYAFLEFXXXXXXXXXXX 64
T L V L +T+ L ALF IGP+ C+++R+ YAF++F
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 65 XMNKRVFLEKEMKVNWASSPGNQPK 89
+N K +KV++A G K
Sbjct: 64 VLNGITVRNKRLKVSYARPGGESIK 88
>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 = 7e-06, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 42/73 (57%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG++ E + LK+ F+ G + + R+V D +T K KGY F + + A +A+ +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 158 NGQWLGSRSIRTN 170
NG+ R++R +
Sbjct: 71 NGREFSGRALRVD 83
Score = 42.4 bits (98), Expect = 5e-04, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 43/82 (52%), Gaps = 3/82 (3%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP-YAFLEFXXXXXXXXXXXX 65
+++VGN+ TEE L +FS++GPV +++ RE G Y F E+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 66 MNKRVFLEKEMKVNWASSPGNQ 87
+N R F + ++V+ A+S N+
Sbjct: 70 LNGREFSGRALRVDNAASEKNK 91
Score = 38.1 bits (87), Expect = 0.010, Method: Composition-based stats.
Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 6/85 (7%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIES 261
+V+ G + EE + +FS G +V R+ K KGY F ++ +ETA A+ +
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 262 IHNTDINGHTVKCFWGKESENNSTL 286
++ + +G ++ +N L
Sbjct: 70 LNGREFSGRALRVDNAASEKNKEEL 94
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 48.1 bits (113), Expect = 8e-06, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 3/75 (4%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSK-GYAFVSFVKKAEAENAITA 156
++VG+LS + + E F+ G+I +I+ +K+ G+ FV + +A+AENA+
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIK--KIIMGLDKMKTACGFCFVEYYSRADAENAMRY 78
Query: 157 MNGQWLGSRSIRTNW 171
+NG L R IRT+W
Sbjct: 79 INGTRLDDRIIRTDW 93
Score = 36.2 bits (82), Expect = 0.036, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK-----GYAFVKFTTKETATHAIE 260
+CT+Y G EE + ++FS G I I + +K G+ FV++ ++ A +A+
Sbjct: 18 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMR 77
Query: 261 SIHNTDINGHTVKCFW 276
I+ T ++ ++ W
Sbjct: 78 YINGTRLDDRIIRTDW 93
Score = 32.0 bits (71), Expect = 0.58, Method: Composition-based stats.
Identities = 15/27 (55%), Positives = 18/27 (66%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVK 35
TLYVGNL TEE + LFS+ G +K
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIK 46
>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 = 48.1 bits (113), Expect = 8e-06, Method: Composition-based stats.
Identities = 27/88 (30%), Positives = 45/88 (51%), Gaps = 1/88 (1%)
Query: 85 GNQP-KQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVS 143
G++P Q + + +FV + E + + + FA +GEI N + D +T KGY V
Sbjct: 11 GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 70
Query: 144 FVKKAEAENAITAMNGQWLGSRSIRTNW 171
+ EA+ A+ +NGQ L + I +W
Sbjct: 71 YETYKEAQAAMEGLNGQDLMGQPISVDW 98
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 48.1 bits (113), Expect = 8e-06, Method: Composition-based stats.
Identities = 22/69 (31%), Positives = 38/69 (55%)
Query: 100 VGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNG 159
V +L+ +L+ F +G + + I R+P T +G+AFV F + +A++A AM+G
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 160 QWLGSRSIR 168
L R +R
Sbjct: 78 AELDGRELR 86
Score = 29.3 bits (64), Expect = 3.5, Method: Composition-based stats.
Identities = 13/55 (23%), Positives = 30/55 (54%), Gaps = 6/55 (10%)
Query: 225 KVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
+VF +G + D+ + +E +G+AFV+F + A A ++ +++G ++
Sbjct: 32 RVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELR 86
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 48.1 bits (113), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 34/150 (22%), Positives = 65/150 (43%), Gaps = 15/150 (10%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFXXXXXXXXXXX 64
+Q L+VGNL +TEE LF + G + R+ G + F+
Sbjct: 20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRG---FGFIRLESRTLAEIAKA 76
Query: 65 XMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISN 124
++ + + +++ +A+ + + V +LSP + + L++AF+ FG +
Sbjct: 77 ELDGTILKSRPLRIRFAT-----------HGAALTVKNLSPVVSNELLEQAFSQFGPVEK 125
Query: 125 CRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
+V D + ++ G FV F K A A+
Sbjct: 126 AVVVVDDRG-RATGKGFVEFAAKPPARKAL 154
Score = 35.4 bits (80), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 12/69 (17%), Positives = 33/69 (47%)
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNT 265
C ++ G D+ EE ++F +G ++ + +++G+ F++ ++ A A + T
Sbjct: 22 RCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGT 81
Query: 266 DINGHTVKC 274
+ ++
Sbjct: 82 ILKSRPLRI 90
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 48.1 bits (113), Expect = 9e-06, Method: Composition-based stats.
Identities = 26/84 (30%), Positives = 39/84 (46%)
Query: 196 DEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETA 255
D + + P T Y G E + +F FG I+D + + EKG F+K+ T E A
Sbjct: 17 DHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQA 76
Query: 256 THAIESIHNTDINGHTVKCFWGKE 279
I ++ N G ++ WGKE
Sbjct: 77 AVCIVALANFPFQGRNLRTGWGKE 100
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 47.8 bits (112), Expect = 9e-06, Method: Composition-based stats.
Identities = 26/66 (39%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 94 NHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENA 153
+H +FVG L+ + ++ F FG I C I+R P SKG AFV + AEA+ A
Sbjct: 14 SHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDG-NSKGCAFVKYSSHAEAQAA 72
Query: 154 ITAMNG 159
I A++G
Sbjct: 73 INALHG 78
Score = 36.2 bits (82), Expect = 0.036, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFK-----EKGYAFVKFTTKETA 255
+ P++ ++ G K +E+ V ++F FG I + + + KG AFVK+++ A
Sbjct: 10 RQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEA 69
Query: 256 THAIESIHNT 265
AI ++H +
Sbjct: 70 QAAINALHGS 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 = 47.8 bits (112), Expect = 1e-05, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 40/73 (54%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++V +L + L F+ +G++ I++D T KSKG AF+ F+ K A+N A+
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 158 NGQWLGSRSIRTN 170
N + L R I+ +
Sbjct: 79 NNKQLFGRVIKAS 91
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 203 SPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETAT 256
+P+ TVY L + ++FS +G +V + + K+K G AF+ F K++A
Sbjct: 13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
Query: 257 HAIESIHNTDINGHTVK 273
+ +I+N + G +K
Sbjct: 73 NCTRAINNKQLFGRVIK 89
>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 = 47.8 bits (112), Expect = 1e-05, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 45/76 (59%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++G + + + + + + G + N +++ DPQT +SKGYAF+ F + +A+ +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 158 NGQWLGSRSIRTNWST 173
NG LGSR ++ +S+
Sbjct: 67 NGYQLGSRFLKCGYSS 82
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 6/84 (7%)
Query: 203 SPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETAT 256
+P + VY G D EE + + S G ++++++ + KGYAF++F E++
Sbjct: 1 NPPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSA 60
Query: 257 HAIESIHNTDINGHTVKCFWGKES 280
A+ +++ + +KC + S
Sbjct: 61 SAVRNLNGYQLGSRFLKCGYSSNS 84
Score = 32.0 bits (71), Expect = 0.66, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 3/77 (3%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG---NDPYAFLEFXXXXXXXXXXXXM 66
+Y+G++ TEE + L S +GPV K++ +P + YAF+EF +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 67 NKRVFLEKEMKVNWASS 83
N + +K ++S+
Sbjct: 67 NGYQLGSRFLKCGYSSN 83
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/88 (29%), Positives = 43/88 (48%)
Query: 90 QDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAE 149
Q + + +FV + E + + + FA +GEI N + D +T KGY V + E
Sbjct: 2 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 61
Query: 150 AENAITAMNGQWLGSRSIRTNWSTRKPP 177
A+ A+ +NGQ L + I +W + P
Sbjct: 62 AQAAMEGLNGQDLMGQPISVDWCFVRGP 89
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 36/72 (50%)
Query: 96 YHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
+ +F+G L + +KE FG + +V+D T SKGYAF +V + AI
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61
Query: 156 AMNGQWLGSRSI 167
+NG LG + +
Sbjct: 62 GLNGMQLGDKKL 73
Score = 28.5 bits (62), Expect = 6.9, Method: Composition-based stats.
Identities = 15/65 (23%), Positives = 30/65 (46%), Gaps = 6/65 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
++ GG LN++ V ++ + FG + + K+ KGYAF ++ AI +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 263 HNTDI 267
+ +
Sbjct: 64 NGMQL 68
>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 = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/88 (29%), Positives = 43/88 (48%)
Query: 90 QDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAE 149
Q + + +FV + E + + + FA +GEI N + D +T KGY V + E
Sbjct: 4 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 63
Query: 150 AENAITAMNGQWLGSRSIRTNWSTRKPP 177
A+ A+ +NGQ L + I +W + P
Sbjct: 64 AQAAMEGLNGQDLMGQPISVDWCFVRGP 91
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 24/64 (37%), Positives = 34/64 (53%)
Query: 90 QDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAE 149
Q + IFVG L +L++ F FG+I ++ D QT KS+GY FV+ +A
Sbjct: 12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA 71
Query: 150 AENA 153
AE A
Sbjct: 72 AERA 75
>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 = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 41/82 (50%)
Query: 90 QDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAE 149
Q + + +FV + E + + + FA +GEI N + D +T KGY V + E
Sbjct: 2 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 61
Query: 150 AENAITAMNGQWLGSRSIRTNW 171
A+ A+ +NGQ L + I +W
Sbjct: 62 AQAAMEGLNGQDLMGQPISVDW 83
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+I+VG+L ++ +KE F+ FG++ N +++ D +T K KG+ FV +++ +E
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKL 62
Query: 157 MNGQWLGSRSIRT 169
N ++G R+IR
Sbjct: 63 DNTDFMG-RTIRV 74
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 7/72 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESI 262
+Y G E V ++FS FG + ++++ K KG+ FV+ +E+ + AI +
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIAKL 62
Query: 263 HNTDINGHTVKC 274
NTD G T++
Sbjct: 63 DNTDFMGRTIRV 74
Score = 32.3 bits (72), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 19/31 (61%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVI 40
+YVGNL S T E + LFSQ G V K+I
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLI 34
>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 = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAF 141
+ PG + +DT+ ++V +L I L F +G I I+RD T + +G AF
Sbjct: 4 ARPGGESIKDTN----LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAF 59
Query: 142 VSFVKKAEAENAITAMN 158
V + K+ EA+ AI+A+N
Sbjct: 60 VRYNKREEAQEAISALN 76
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 46.2 bits (108), Expect = 3e-05, Method: Composition-based stats.
Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG L+ + + + F PFG I C ++R P SKG AFV F EA+ AI A+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDG-SSKGCAFVKFSSHTEAQAAIHAL 76
Query: 158 NG 159
+G
Sbjct: 77 HG 78
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFK-----EKGYAFVKFTTKETATHAIESIH 263
++ G K +EE V ++F PFG I + V + KG AFVKF++ A AI ++H
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 264 NT 265
+
Sbjct: 78 GS 79
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 46.2 bits (108), Expect = 3e-05, Method: Composition-based stats.
Identities = 22/64 (34%), Positives = 37/64 (57%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+++V L + + +++ F+ +G I RI+ D T S+G F+ F K+ EAE AI
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 157 MNGQ 160
+NGQ
Sbjct: 63 LNGQ 66
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 46.2 bits (108), Expect = 3e-05, Method: Composition-based stats.
Identities = 29/75 (38%), Positives = 42/75 (56%), Gaps = 3/75 (4%)
Query: 96 YHIFVGDLSPEIETQTLKEAFAP-FGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
Y +FVGDL+P+++ L E F + ++V D QT SKGY FV F + E + A+
Sbjct: 10 YSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQKRAL 68
Query: 155 TAMNGQ-WLGSRSIR 168
T G LGS+ +R
Sbjct: 69 TECQGAVGLGSKPVR 83
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 46.2 bits (108), Expect = 3e-05, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 38/57 (66%), Gaps = 1/57 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
+F+G LS + + LK+ F+ FGE+ +C + DP T +S+G+ FV F K++E+ + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLF-KESESVDKV 57
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 45.8 bits (107), Expect = 4e-05, Method: Composition-based stats.
Identities = 24/61 (39%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG L + + +++ F PFG I C ++R P SKG AFV F AEA+ AI +
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDG-TSKGCAFVKFQTHAEAQAAINTL 73
Query: 158 N 158
+
Sbjct: 74 H 74
Score = 44.7 bits (104), Expect = 9e-05, Method: Composition-based stats.
Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 5/62 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFK-----EKGYAFVKFTTKETATHAIESIH 263
++ G GK +E V K+F PFGTI + V + KG AFVKF T A AI ++H
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
Query: 264 NT 265
++
Sbjct: 75 SS 76
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 36/63 (57%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++ V + ++ L++ F +G I + +IV D +T +S+GY FV F + A+ AI
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 157 MNG 159
+NG
Sbjct: 104 LNG 106
Score = 32.0 bits (71), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 3/82 (3%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGND-PYAFLEFXXXXXXXXXXXXM 66
L V + +V E L LF + GP++ K++ RE Y F++F +
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 67 NKRVFLEKEMKVNWASSPGNQP 88
N L K +KV A+S +P
Sbjct: 105 NGFNILNKRLKVALAASGHQRP 126
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 6/76 (7%)
Query: 218 LNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESIHNTDINGHT 271
++E + ++F +G I +++ + +GY FVKF + +A AI ++ +I
Sbjct: 54 VDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKR 113
Query: 272 VKCFWGKESENNSTLA 287
+K +A
Sbjct: 114 LKVALAASGHQRPGIA 129
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG L +TL+ F+ +GE+ +C I++D T +S+G+ FV F K + A
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF-KDPNCVGTVLAS 77
Query: 158 NGQWLGSRSI 167
L R+I
Sbjct: 78 RPHTLDGRNI 87
Score = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 22/33 (66%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE 42
L+VG LD S T+E L + FSQ G V C ++++
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKD 51
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKF 249
++ GG +E + FS +G +VD + K+K G+ FVKF
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 27/92 (29%), Positives = 51/92 (55%), Gaps = 8/92 (8%)
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAI 259
+ TVY GG + ++E L+ ++F G +V+ + K++ GY FV+F ++E A +AI
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 260 ESIHNTDINGHTVKCFWGKESENNSTLAQPSA 291
+ + + G ++ K S +N L+ PS+
Sbjct: 75 KIMDMIKLYGKPIRV--NKASAHNKNLSGPSS 104
Score = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 26/87 (29%), Positives = 44/87 (50%), Gaps = 4/87 (4%)
Query: 84 PGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVS 143
P ++ QD + ++VG L ++ L E F G + N + +D T + +GY FV
Sbjct: 8 PISERNQDAT----VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVE 63
Query: 144 FVKKAEAENAITAMNGQWLGSRSIRTN 170
F+ + +A+ AI M+ L + IR N
Sbjct: 64 FLSEEDADYAIKIMDMIKLYGKPIRVN 90
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 27/86 (31%), Positives = 41/86 (47%), Gaps = 3/86 (3%)
Query: 1 MCDESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP---GNDPYAFLEFXXXX 57
+ + +Q T+YVG LD V+E LL LF Q GPV + ++ + Y F+EF
Sbjct: 9 ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 68
Query: 58 XXXXXXXXMNKRVFLEKEMKVNWASS 83
M+ K ++VN AS+
Sbjct: 69 DADYAIKIMDMIKLYGKPIRVNKASA 94
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 26/86 (30%), Positives = 46/86 (53%), Gaps = 5/86 (5%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGE-ISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+++GDL P ++ + AFA GE + + +I+R+ T GY FV F A AE +
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 157 MNGQWL----GSRSIRTNWSTRKPPA 178
+NG+ L ++ + N++T P+
Sbjct: 72 INGKPLPGATPAKRFKLNYATYSGPS 97
Score = 29.6 bits (65), Expect = 2.9, Method: Composition-based stats.
Identities = 16/71 (22%), Positives = 35/71 (49%), Gaps = 7/71 (9%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFG-TIVDIRVFKEK------GYAFVKFTTKETATHAIE 260
+++ G ++E +S+ F+ G T++ +++ + + GY FV+F TA +
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 261 SIHNTDINGHT 271
I+ + G T
Sbjct: 71 KINGKPLPGAT 81
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 205 TNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHN 264
+N ++ F D+ E ++++F PFG + ++++ G+AFV+F E+A AIE +H
Sbjct: 30 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--GFAFVEFEEAESAAKAIEEVHG 87
Query: 265 TDINGHTVKCFWGK 278
++ + K
Sbjct: 88 KSFANQPLEVVYSK 101
Score = 33.9 bits (76), Expect = 0.15, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 10/81 (12%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV +++ L E F PFG + +I+ G+AFV F + A AI +
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEV 85
Query: 158 NGQWLGSRSIRTNWSTRKPPA 178
+G+ ++ + +S K PA
Sbjct: 86 HGKSFANQPLEVVYS--KLPA 104
Score = 29.6 bits (65), Expect = 3.0, Method: Composition-based stats.
Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 5/84 (5%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFXXXXXXXXXX 63
E T L+V + V E L +F GP+K K++ + +AF+EF
Sbjct: 28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-----NGFAFVEFEEAESAAKAI 82
Query: 64 XXMNKRVFLEKEMKVNWASSPGNQ 87
++ + F + ++V ++ P +
Sbjct: 83 EEVHGKSFANQPLEVVYSKLPAKR 106
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDI 267
T+Y +G+D+ L+ FSPFG I+D+ + + AFV + E+A A+ ++ T +
Sbjct: 17 TLYV--YGEDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQV 74
Query: 268 NGHTVKC 274
+K
Sbjct: 75 ESVQLKV 81
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/96 (26%), Positives = 49/96 (51%), Gaps = 10/96 (10%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
+ S G + N +++ D++P + L+ AF+PFG I + + DP + A
Sbjct: 3 SGSSGERRAPRKGNTLYVYGEDMTPTL----LRGAFSPFGNIIDLSM--DP----PRNCA 52
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKP 176
FV++ K A+ A+ +NG + S ++ N + ++P
Sbjct: 53 FVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP 88
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 205 TNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIE-SIH 263
T T+Y GG G + E + F FG I I V + + AF++F T++ A A E S +
Sbjct: 11 TITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFN 70
Query: 264 NTDINGHTVKCFWGK 278
+NG + WG+
Sbjct: 71 KLIVNGRRLNVKWGR 85
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 31/75 (41%), Gaps = 7/75 (9%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI-TA 156
++VG L I L+ F FGEI +V+ Q AF+ F + AE A +
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQFATRQAAEVAAEKS 68
Query: 157 MNGQWLGSRSIRTNW 171
N + R + W
Sbjct: 69 FNKLIVNGRRLNVKW 83
Score = 30.0 bits (66), Expect = 2.1, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 4/75 (5%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFXXXXXXX-XXXXXM 66
TTLYVG L ++TE L F Q G ++ V++ AF++F
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR---QQCAFIQFATRQAAEVAAEKSF 69
Query: 67 NKRVFLEKEMKVNWA 81
NK + + + V W
Sbjct: 70 NKLIVNGRRLNVKWG 84
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 30/47 (63%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
IFVG LSP+ + ++E F FGE+ + + D +T K +G+ F++F
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF 50
Score = 31.6 bits (70), Expect = 0.77, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 7/72 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTI------VDIRVFKEKGYAFVKFTTKETATHAIE-S 261
++ GG D EE + + F FG + +D + K +G+ F+ F +E +E
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 63
Query: 262 IHNTDINGHTVK 273
HN ++ +K
Sbjct: 64 YHNVGLSKCEIK 75
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 30/47 (63%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
IFVG LSP+ + ++E F FGE+ + + D +T K +G+ F++F
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF 48
Score = 31.6 bits (70), Expect = 0.79, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 7/72 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTI------VDIRVFKEKGYAFVKFTTKETATHAIE-S 261
++ GG D EE + + F FG + +D + K +G+ F+ F +E +E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 262 IHNTDINGHTVK 273
HN ++ +K
Sbjct: 62 YHNVGLSKCEIK 73
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDI 267
T+Y +G+D+ L+ FSPFG I+D+ + + AFV + E+A A+ ++ T +
Sbjct: 41 TLYV--YGEDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQV 98
Query: 268 NGHTVKC 274
+K
Sbjct: 99 ESVQLKV 105
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 45/83 (54%), Gaps = 10/83 (12%)
Query: 94 NHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENA 153
N +++ D++P + L+ AF+PFG I + + DP + AFV++ K A+ A
Sbjct: 40 NTLYVYGEDMTPTL----LRGAFSPFGNIIDLSM--DP----PRNCAFVTYEKMESADQA 89
Query: 154 ITAMNGQWLGSRSIRTNWSTRKP 176
+ +NG + S ++ N + ++P
Sbjct: 90 VAELNGTQVESVQLKVNIARKQP 112
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 43.1 bits (100), Expect = 3e-04, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 205 TNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHN 264
+N ++ F D+ E ++++F PFG + ++++ G+AFV+F E+A AIE +H
Sbjct: 3 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--GFAFVEFEEAESAAKAIEEVHG 60
Query: 265 TDINGHTVKCFWGK 278
++ + K
Sbjct: 61 KSFANQPLEVVYSK 74
Score = 33.1 bits (74), Expect = 0.24, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 8/75 (10%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV +++ L E F PFG + +I+ G+AFV F + A AI +
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEV 58
Query: 158 NGQWLGSRSIRTNWS 172
+G+ ++ + +S
Sbjct: 59 HGKSFANQPLEVVYS 73
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 218 LNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWG 277
+ EE++ K FS FG + RV K K YAF+ F ++ A A+E ++ D+ G ++ +
Sbjct: 23 VTEEILEKAFSQFGKLE--RVKKLKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA 80
Query: 278 K--ESENNSTLAQPSAPTTP 295
K + + AQ A + P
Sbjct: 81 KPPDQKRKERKAQRQAASGP 100
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 27/90 (30%), Positives = 48/90 (53%), Gaps = 11/90 (12%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV +L+ + + L++AF+ FG++ + ++D YAF+ F ++ A A+ M
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 158 NGQWLGSRSIRTNWSTRKPPAMT-NERKRQ 186
NG+ L +I ++ KPP ERK Q
Sbjct: 66 NGKDLEGENIEIVFA--KPPDQKRKERKAQ 93
Score = 35.8 bits (81), Expect = 0.039, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 5/81 (6%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFXXXXXXXXXXXXMNKR 69
L+V NL +VTEE+L FSQ G ++ K +++ YAF+ F MN +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-----YAFIHFDERDGAVKAMEEMNGK 68
Query: 70 VFLEKEMKVNWASSPGNQPKQ 90
+ +++ +A P + K+
Sbjct: 69 DLEGENIEIVFAKPPDQKRKE 89
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 5/79 (6%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG+L L+ AF+ +G + I R+P G+AFV F +AE+A+ +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRGL 57
Query: 158 NGQWLGSRSIRTNWSTRKP 176
+G+ + +R ST P
Sbjct: 58 DGKVICGSRVRVELSTGMP 76
Score = 28.9 bits (63), Expect = 5.7, Method: Composition-based stats.
Identities = 20/84 (23%), Positives = 34/84 (40%), Gaps = 1/84 (1%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK-GYAFVKFTTKETATHAIESIHNTDI 267
VY G G + + + FS +G + + + + G+AFV+F A A+ + I
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 268 NGHTVKCFWGKESENNSTLAQPSA 291
G V+ S +P A
Sbjct: 63 CGSRVRVELSTGMPRRSRFDRPPA 86
Score = 28.5 bits (62), Expect = 6.9, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEF 53
+YVGNL + L FS GP++ + R P +AF+EF
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG--FAFVEF 44
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 34/66 (51%)
Query: 91 DTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEA 150
D + +F+ +LS + E + L E FG++ R+V P T SKG AF F+ + A
Sbjct: 11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70
Query: 151 ENAITA 156
+ + A
Sbjct: 71 QKCLAA 76
Score = 29.3 bits (64), Expect = 3.7, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 6/54 (11%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETA 255
TV+ D EE + +V FG + +RV KG AF +F T+E A
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 42.4 bits (98), Expect = 5e-04, Method: Composition-based stats.
Identities = 30/95 (31%), Positives = 46/95 (48%), Gaps = 3/95 (3%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS + P + +FV LS + +TLKE+F G + RIV D +T SKG+
Sbjct: 1 GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFD--GSV-RARIVTDRETGSSKGFG 57
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRK 175
FV F + +A+ A AM + + +W+ K
Sbjct: 58 FVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPK 92
Score = 37.7 bits (86), Expect = 0.011, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 39/82 (47%), Gaps = 3/82 (3%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSP---FGTIVDIRVFKEKGYAFVKFTTKETAT 256
N S + T++ G +D EE + + F + D KG+ FV F ++E A
Sbjct: 9 NARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAK 68
Query: 257 HAIESIHNTDINGHTVKCFWGK 278
A E++ + +I+G+ V W K
Sbjct: 69 AAKEAMEDGEIDGNKVTLDWAK 90
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 49/86 (56%), Gaps = 7/86 (8%)
Query: 91 DTSNHYHIFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVK 146
+T ++ I++ +L+ +I+ LK++ F+ FG+I + + R +LK +G AFV F +
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKE 61
Query: 147 KAEAENAITAMNGQWLGSRSIRTNWS 172
+ A NA+ +M G + +R ++
Sbjct: 62 VSSATNALRSMQGFPFYDKPMRIQYA 87
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 206 NCTVYCGGFGKDLNEELVSK----VFSPFGTIVDI---RVFKEKGYAFVKFTTKETATHA 258
N T+Y + + ++ + K +FS FG I+DI R K +G AFV F +AT+A
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 68
Query: 259 IESIH 263
+ S+
Sbjct: 69 LRSMQ 73
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 39/85 (45%), Gaps = 5/85 (5%)
Query: 4 ESQPT-TLYVGNLDVSVT-EEL---LCALFSQIGPVKGCKVIREPGNDPYAFLEFXXXXX 58
E++P T+Y+ NL+ + +EL L A+FSQ G + V R AF+ F
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 59 XXXXXXXMNKRVFLEKEMKVNWASS 83
M F +K M++ +A +
Sbjct: 65 ATNALRSMQGFPFYDKPMRIQYAKT 89
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV +L ++ + LKE F+ G + I+ D KS+G V+F + EA AI+
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDG-KSRGIGTVTFEQSIEAVQAISMF 76
Query: 158 NGQWLGSRSIRTNWSTRKPP 177
NGQ L R + R P
Sbjct: 77 NGQLLFDRPMHVKMDERALP 96
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 33/150 (22%), Positives = 63/150 (42%), Gaps = 15/150 (10%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFXXXXXXXXXXX 64
+Q + L+VGNL +TEE + LF + G + ++ G + F+
Sbjct: 20 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG---FGFIRLETRTLAEIAKV 76
Query: 65 XMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISN 124
++ K+++V +A + + V +L + + L+EAF+ FG++
Sbjct: 77 ELDNMPLRGKQLRVRFACHSAS-----------LTVRNLPQYVSNELLEEAFSVFGQVER 125
Query: 125 CRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
++ D + S G V F K A A+
Sbjct: 126 AVVIVDDRGRPS-GKGIVEFSGKPAARKAL 154
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/69 (23%), Positives = 35/69 (50%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDIN 268
++ G D+ EE + K+F +G ++ + K+KG+ F++ T+ A A + N +
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLR 84
Query: 269 GHTVKCFWG 277
G ++ +
Sbjct: 85 GKQLRVRFA 93
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 35/66 (53%)
Query: 92 TSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAE 151
+S +++ L P Q L + P+G+I + + + D T K KGY FV F + A+
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61
Query: 152 NAITAM 157
A+TA+
Sbjct: 62 KAVTAL 67
Score = 28.5 bits (62), Expect = 6.9, Method: Composition-based stats.
Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESI 262
+Y G ++ + K+ P+G IV + K KGY FV F + A A+ ++
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 263 HNTDINGHTVK 273
+ + K
Sbjct: 68 KASGVQAQMAK 78
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEIS--NCRIVRDPQTLKSKG 138
A S G++P + +N I + +L+P ++ A AP+ +S N R+++D QT ++G
Sbjct: 10 ALSQGSEPSSENANDT-IILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRG 68
Query: 139 YAFVSF 144
+AF+
Sbjct: 69 FAFIQL 74
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 89 KQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKA 148
KQ + ++++ +L ++ Q L+ PFG++ + RI+RD + S+G F
Sbjct: 19 KQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTE 77
Query: 149 EAENAITAMNGQWL 162
+ E I NG+++
Sbjct: 78 KCEAVIGHFNGKFI 91
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE 42
E PT LY+ NL +S+ E+ L + G V +++R+
Sbjct: 22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD 60
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 44/180 (24%), Positives = 75/180 (41%), Gaps = 14/180 (7%)
Query: 1 MCDESQPTT---LYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDPYAFLEFXX 55
M + S+ TT L++GNL+ + + L S++ V+ R N + +++F
Sbjct: 4 MVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFES 63
Query: 56 XXXXXXXXXXMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEA 115
+VF E+K+ P + + + +LS I LKE
Sbjct: 64 AEDLEKALELTGLKVF-GNEIKL---EKPKGRDSKKVRAARTLLAKNLSFNITEDELKEV 119
Query: 116 FAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRK 175
F EI R+V Q KSKG A++ F +A+AE + G + RS+ ++ K
Sbjct: 120 FEDALEI---RLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174
Score = 35.8 bits (81), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 35/187 (18%), Positives = 79/187 (42%), Gaps = 36/187 (19%)
Query: 96 YHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
+++F+G+L+P LK A + ++ +V D +T ++ + +V F + E A+
Sbjct: 14 FNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKAL- 71
Query: 156 AMNGQWLGSRSIRTNWSTRKPPAMTNERKR--QNSHTKTITFDEVYNQSSPTNCTVYCGG 213
+ G + KP +++ R + K ++F+
Sbjct: 72 ----ELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFN----------------- 110
Query: 214 FGKDLNEELVSKVFSPFGTIVDIRVF----KEKGYAFVKFTTKETATHAIESIHNTDING 269
+ E+ + +VF ++IR+ K KG A+++F ++ A +E +I+G
Sbjct: 111 ----ITEDELKEVFED---ALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG 163
Query: 270 HTVKCFW 276
+V ++
Sbjct: 164 RSVSLYY 170
>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 = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 49/86 (56%), Gaps = 7/86 (8%)
Query: 91 DTSNHYHIFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVK 146
+T ++ I++ +L+ +I+ LK++ F+ FG+I + + R +LK +G AFV F +
Sbjct: 1 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKE 57
Query: 147 KAEAENAITAMNGQWLGSRSIRTNWS 172
+ A NA+ +M G + +R ++
Sbjct: 58 VSSATNALRSMQGFPFYDKPMRIQYA 83
Score = 36.2 bits (82), Expect = 0.033, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 206 NCTVYCGGFGKDLNEELVSK----VFSPFGTIVDI---RVFKEKGYAFVKFTTKETATHA 258
N T+Y + + ++ + K +FS FG I+DI R K +G AFV F +AT+A
Sbjct: 5 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 64
Query: 259 IESIH 263
+ S+
Sbjct: 65 LRSMQ 69
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 8/78 (10%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ VG++SP Q L+ F +G + C IV+D YAFV + +A AI +
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGL 64
Query: 158 NGQWLGSRSIRTNWSTRK 175
+ + + ST +
Sbjct: 65 DNTEFQGKRMHVQLSTSR 82
Score = 36.6 bits (83), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 5/76 (6%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFXXXXXXXXXXXXMN 67
T L+VGN+ + T + L A F + GPV C ++++ YAF+ ++
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-----YAFVHMERAEDAVEAIRGLD 65
Query: 68 KRVFLEKEMKVNWASS 83
F K M V ++S
Sbjct: 66 NTEFQGKRMHVQLSTS 81
Score = 33.5 bits (75), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 219 NEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDING 269
N+EL +K F +G +++ + K+ YAFV E A AI + NT+ G
Sbjct: 24 NQELRAK-FEEYGPVIECDIVKD--YAFVHMERAEDAVEAIRGLDNTEFQG 71
>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 = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 49/86 (56%), Gaps = 7/86 (8%)
Query: 91 DTSNHYHIFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVK 146
+T ++ I++ +L+ +I+ LK++ F+ FG+I + + R +LK +G AFV F +
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKE 60
Query: 147 KAEAENAITAMNGQWLGSRSIRTNWS 172
+ A NA+ +M G + +R ++
Sbjct: 61 VSSATNALRSMQGFPFYDKPMRIQYA 86
Score = 35.8 bits (81), Expect = 0.038, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 206 NCTVYCGGFGKDLNEELVSK----VFSPFGTIVDI---RVFKEKGYAFVKFTTKETATHA 258
N T+Y + + ++ + K +FS FG I+DI R K +G AFV F +AT+A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 67
Query: 259 IESIH 263
+ S+
Sbjct: 68 LRSMQ 72
>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 = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 49/86 (56%), Gaps = 7/86 (8%)
Query: 91 DTSNHYHIFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVK 146
+T ++ I++ +L+ +I+ LK++ F+ FG+I + + R +LK +G AFV F +
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKE 61
Query: 147 KAEAENAITAMNGQWLGSRSIRTNWS 172
+ A NA+ +M G + +R ++
Sbjct: 62 VSSATNALRSMQGFPFYDKPMRIQYA 87
Score = 35.8 bits (81), Expect = 0.038, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 206 NCTVYCGGFGKDLNEELVSK----VFSPFGTIVDI---RVFKEKGYAFVKFTTKETATHA 258
N T+Y + + ++ + K +FS FG I+DI R K +G AFV F +AT+A
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 68
Query: 259 IESIH 263
+ S+
Sbjct: 69 LRSMQ 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 = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 49/86 (56%), Gaps = 7/86 (8%)
Query: 91 DTSNHYHIFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVK 146
+T ++ I++ +L+ +I+ LK++ F+ FG+I + + R +LK +G AFV F +
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKE 60
Query: 147 KAEAENAITAMNGQWLGSRSIRTNWS 172
+ A NA+ +M G + +R ++
Sbjct: 61 VSSATNALRSMQGFPFYDKPMRIQYA 86
Score = 35.8 bits (81), Expect = 0.039, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 206 NCTVYCGGFGKDLNEELVSK----VFSPFGTIVDI---RVFKEKGYAFVKFTTKETATHA 258
N T+Y + + ++ + K +FS FG I+DI R K +G AFV F +AT+A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 67
Query: 259 IESIH 263
+ S+
Sbjct: 68 LRSMQ 72
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 49/86 (56%), Gaps = 7/86 (8%)
Query: 91 DTSNHYHIFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVK 146
+T ++ I++ +L+ +I+ LK++ F+ FG+I + + R +LK +G AFV F +
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKE 61
Query: 147 KAEAENAITAMNGQWLGSRSIRTNWS 172
+ A NA+ +M G + +R ++
Sbjct: 62 VSSATNALRSMQGFPFYDKPMRIQYA 87
Score = 35.8 bits (81), Expect = 0.037, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 206 NCTVYCGGFGKDLNEELVSK----VFSPFGTIVDI---RVFKEKGYAFVKFTTKETATHA 258
N T+Y + + ++ + K +FS FG I+DI R K +G AFV F +AT+A
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 68
Query: 259 IESIH 263
+ S+
Sbjct: 69 LRSMQ 73
Score = 30.0 bits (66), Expect = 2.5, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 39/85 (45%), Gaps = 5/85 (5%)
Query: 4 ESQPT-TLYVGNLDVSVT-EEL---LCALFSQIGPVKGCKVIREPGNDPYAFLEFXXXXX 58
E++P T+Y+ NL+ + +EL L A+FSQ G + V R AF+ F
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 64
Query: 59 XXXXXXXMNKRVFLEKEMKVNWASS 83
M F +K M++ +A +
Sbjct: 65 ATNALRSMQGFPFYDKPMRIQYAKT 89
>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 = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 49/86 (56%), Gaps = 7/86 (8%)
Query: 91 DTSNHYHIFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVK 146
+T ++ I++ +L+ +I+ LK++ F+ FG+I + + R +LK +G AFV F +
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKE 60
Query: 147 KAEAENAITAMNGQWLGSRSIRTNWS 172
+ A NA+ +M G + +R ++
Sbjct: 61 VSSATNALRSMQGFPFYDKPMRIQYA 86
Score = 35.8 bits (81), Expect = 0.040, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 206 NCTVYCGGFGKDLNEELVSK----VFSPFGTIVDI---RVFKEKGYAFVKFTTKETATHA 258
N T+Y + + ++ + K +FS FG I+DI R K +G AFV F +AT+A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 67
Query: 259 IESIH 263
+ S+
Sbjct: 68 LRSMQ 72
>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 = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 49/86 (56%), Gaps = 7/86 (8%)
Query: 91 DTSNHYHIFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVK 146
+T ++ I++ +L+ +I+ LK++ F+ FG+I + + R +LK +G AFV F +
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKE 61
Query: 147 KAEAENAITAMNGQWLGSRSIRTNWS 172
+ A NA+ +M G + +R ++
Sbjct: 62 VSSATNALRSMQGFPFYDKPMRIQYA 87
Score = 35.8 bits (81), Expect = 0.041, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 206 NCTVYCGGFGKDLNEELVSK----VFSPFGTIVDI---RVFKEKGYAFVKFTTKETATHA 258
N T+Y + + ++ + K +FS FG I+DI R K +G AFV F +AT+A
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 68
Query: 259 IESIH 263
+ S+
Sbjct: 69 LRSMQ 73
>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 = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 49/86 (56%), Gaps = 7/86 (8%)
Query: 91 DTSNHYHIFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVK 146
+T ++ I++ +L+ +I+ LK++ F+ FG+I + + R +LK +G AFV F +
Sbjct: 2 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKE 58
Query: 147 KAEAENAITAMNGQWLGSRSIRTNWS 172
+ A NA+ +M G + +R ++
Sbjct: 59 VSSATNALRSMQGFPFYDKPMRIQYA 84
Score = 35.8 bits (81), Expect = 0.042, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 206 NCTVYCGGFGKDLNEELVSK----VFSPFGTIVDI---RVFKEKGYAFVKFTTKETATHA 258
N T+Y + + ++ + K +FS FG I+DI R K +G AFV F +AT+A
Sbjct: 6 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 65
Query: 259 IESIH 263
+ S+
Sbjct: 66 LRSMQ 70
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 26/81 (32%), Positives = 40/81 (49%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV +LS + L++ F+ +G +S D T K KG+AFV+F+ A A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 158 NGQWLGSRSIRTNWSTRKPPA 178
+GQ R + ST K A
Sbjct: 71 DGQVFQGRMLHVLPSTIKKEA 91
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-KGYAFVKFTTKETATHAI 259
S P +C VY G G + N+ + + F +G + + V + G+AFV+F A A+
Sbjct: 68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAV 127
Query: 260 ESIHNTDINGHTVK 273
+ + G V+
Sbjct: 128 RDLDGRTLCGCRVR 141
Score = 36.6 bits (83), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++VG+L L+ AF +G + + + R+P G+AFV F +A +A+
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAVRD 129
Query: 157 MNGQWLGSRSIRTNWS 172
++G+ L +R S
Sbjct: 130 LDGRTLCGCRVRVELS 145
>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 = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 48/85 (56%), Gaps = 7/85 (8%)
Query: 92 TSNHYHIFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVKK 147
T ++ I++ +L+ +I+ LK++ F+ FG+I + + R +LK +G AFV F +
Sbjct: 1 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEV 57
Query: 148 AEAENAITAMNGQWLGSRSIRTNWS 172
+ A NA+ +M G + +R ++
Sbjct: 58 SSATNALRSMQGFPFYDKPMRIQYA 82
Score = 36.2 bits (82), Expect = 0.031, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 206 NCTVYCGGFGKDLNEELVSK----VFSPFGTIVDI---RVFKEKGYAFVKFTTKETATHA 258
N T+Y + + ++ + K +FS FG I+DI R K +G AFV F +AT+A
Sbjct: 4 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 63
Query: 259 IESIH 263
+ S+
Sbjct: 64 LRSMQ 68
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-KGYAFVKFTTKETATHAI 259
S P +C VY G G + N+ + + F +G + + V + G+AFV+F A A+
Sbjct: 68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAV 127
Query: 260 ESIHNTDINGHTVK 273
+ + G V+
Sbjct: 128 RELDGRTLCGCRVR 141
Score = 36.6 bits (83), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++VG+L L+ AF +G + + + R+P G+AFV F +A +A+
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAVRE 129
Query: 157 MNGQWLGSRSIRTNWS 172
++G+ L +R S
Sbjct: 130 LDGRTLCGCRVRVELS 145
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 29/114 (25%), Positives = 58/114 (50%), Gaps = 15/114 (13%)
Query: 91 DTSNHYHIFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVK 146
+T ++ I++ +L+ +I+ LK++ F+ FG+I + + R +LK +G AFV F +
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKE 60
Query: 147 KAEAENAITAMNGQWLGSRSIRTNWSTR--------KPPAMTNERKRQNSHTKT 192
+ A NA+ +M G + +R ++ K + +RKR+ K+
Sbjct: 61 VSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKS 114
Score = 35.4 bits (80), Expect = 0.057, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 206 NCTVYCGGFGKDLNEELVSK----VFSPFGTIVDI---RVFKEKGYAFVKFTTKETATHA 258
N T+Y + + ++ + K +FS FG I+DI R K +G AFV F +AT+A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 67
Query: 259 IESIH 263
+ S+
Sbjct: 68 LRSMQ 72
Score = 29.3 bits (64), Expect = 3.5, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 5/85 (5%)
Query: 4 ESQPT-TLYVGNLDVSVTEE----LLCALFSQIGPVKGCKVIREPGNDPYAFLEFXXXXX 58
E++P T+Y+ NL+ + ++ L A+FSQ G + V R AF+ F
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 59 XXXXXXXMNKRVFLEKEMKVNWASS 83
M F +K M++ +A +
Sbjct: 64 ATNALRSMQGFPFYDKPMRIQYAKT 88
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 23/93 (24%), Positives = 44/93 (47%), Gaps = 12/93 (12%)
Query: 86 NQPKQDTSNHYHIFVGDLSPE-IETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
N PK S +F+G+L+ ++ ++ F+ +G ++ C + KGYAFV +
Sbjct: 21 NDPKSINS---RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQY 69
Query: 145 VKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
+ A A+ NG+ L +++ N + P
Sbjct: 70 SNERHARAAVLGENGRVLAGQTLDINMAGEPKP 102
Score = 30.0 bits (66), Expect = 2.5, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 13/82 (15%)
Query: 198 VYNQSSPT--NCTVYCGGFGKDLNEELVSK-----VFSPFGTIVDIRVFKEKGYAFVKFT 250
V N++ P N V+ G +LN LV K +FS +G + V KGYAFV+++
Sbjct: 17 VTNKNDPKSINSRVFIG----NLNTALVKKSDVETIFSKYGRVAGCSV--HKGYAFVQYS 70
Query: 251 TKETATHAIESIHNTDINGHTV 272
+ A A+ + + G T+
Sbjct: 71 NERHARAAVLGENGRVLAGQTL 92
>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 = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/96 (22%), Positives = 44/96 (45%), Gaps = 3/96 (3%)
Query: 72 LEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDP 131
+E E+K+ W P N P +FV ++ + L+ F +G I +V
Sbjct: 82 VETELKM-W--DPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSK 138
Query: 132 QTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSI 167
++ K +GYAF+ + + + +A +G+ + R +
Sbjct: 139 RSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRV 174
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 38.1 bits (87), Expect = 0.007, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 9/70 (12%)
Query: 93 SNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKG---YAFVSFVKKAE 149
+N I+VG+L P+I T+ +++ F +G I RD +G +AFV F +
Sbjct: 20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAI------RDIDLKNRRGGPPFAFVEFEDPRD 73
Query: 150 AENAITAMNG 159
AE+A+ +G
Sbjct: 74 AEDAVYGRDG 83
Score = 36.2 bits (82), Expect = 0.032, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKG---YAFVKFTTKETATHAIESI 262
+C +Y G D+ + + VF +G I DI + +G +AFV+F A A+
Sbjct: 22 DCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGR 81
Query: 263 HNTDINGHTVK 273
D +G+ ++
Sbjct: 82 DGYDYDGYRLR 92
Score = 29.3 bits (64), Expect = 3.9, Method: Composition-based stats.
Identities = 13/44 (29%), Positives = 24/44 (54%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEF 53
+YVGNL + + + +F + G ++ + G P+AF+EF
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEF 68
>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 = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 47/82 (57%), Gaps = 7/82 (8%)
Query: 95 HYHIFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEA 150
++ I++ +L+ +I+ LK++ F+ FG+I + + R +LK +G AFV F + + A
Sbjct: 3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSA 59
Query: 151 ENAITAMNGQWLGSRSIRTNWS 172
NA+ +M G + +R ++
Sbjct: 60 TNALRSMQGFPFYDKPMRIQYA 81
Score = 36.6 bits (83), Expect = 0.026, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 206 NCTVYCGGFGKDLNEELVSK----VFSPFGTIVDI---RVFKEKGYAFVKFTTKETATHA 258
N T+Y + + ++ + K +FS FG I+DI R K +G AFV F +AT+A
Sbjct: 3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62
Query: 259 IESIH 263
+ S+
Sbjct: 63 LRSMQ 67
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 23/70 (32%), Positives = 39/70 (55%), Gaps = 4/70 (5%)
Query: 112 LKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNW 171
L++ F FG+I + I+ + + SKG+ FV+F A+A+ A ++G + R I N
Sbjct: 32 LRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN 89
Query: 172 STRKPPAMTN 181
+T + MTN
Sbjct: 90 ATAR--VMTN 97
Score = 34.3 bits (77), Expect = 0.11, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 4/55 (7%)
Query: 223 VSKVFSPFGTIVDIRV-FKE---KGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
+ ++F FG I+D+ + F E KG+ FV F A A E +H T + G ++
Sbjct: 32 LRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE 86
>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 = 37.7 bits (86), Expect = 0.012, Method: Composition-based stats.
Identities = 16/65 (24%), Positives = 34/65 (52%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDIN 268
++ G D+ EE + K+F +G ++ + K+KG+ F++ T+ A A + N +
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLR 77
Query: 269 GHTVK 273
G ++
Sbjct: 78 GKQLR 82
Score = 33.9 bits (76), Expect = 0.15, Method: Composition-based stats.
Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG+L P+I + +++ F +G+ I +D KG+ F+ + AE A +
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 71
Query: 158 NGQWLGSRSIRTNWS 172
+ L + +R ++
Sbjct: 72 DNMPLRGKQLRVRFA 86
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 37.4 bits (85), Expect = 0.013, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+FVG + ++ ++ FA +G + +I+ D +T SKGY FVSF + + + +
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVES 70
Score = 32.7 bits (73), Expect = 0.32, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDPYAFLEF 53
P T++VG +DV + E + + F++ G VK K+I R + Y F+ F
Sbjct: 10 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 58
Score = 32.3 bits (72), Expect = 0.43, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 9/71 (12%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIESI 262
TV+ GG ++E + F+ +G++ ++++ + KGY FV F +ES
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES- 70
Query: 263 HNTDINGHTVK 273
IN H K
Sbjct: 71 ---QINFHGKK 78
>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 = 37.4 bits (85), Expect = 0.013, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+FVG + ++ ++ FA +G + +I+ D +T SKGY FVSF + + + +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVES 69
Score = 32.7 bits (73), Expect = 0.32, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDPYAFLEF 53
P T++VG +DV + E + + F++ G VK K+I R + Y F+ F
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
Score = 32.3 bits (72), Expect = 0.44, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 9/71 (12%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIESI 262
TV+ GG ++E + F+ +G++ ++++ + KGY FV F +ES
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES- 69
Query: 263 HNTDINGHTVK 273
IN H K
Sbjct: 70 ---QINFHGKK 77
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 37.4 bits (85), Expect = 0.014, Method: Composition-based stats.
Identities = 22/86 (25%), Positives = 43/86 (50%), Gaps = 2/86 (2%)
Query: 90 QDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAE 149
++ S + V ++ L++ F FG+I + I+ + + SKG+ FV+F A+
Sbjct: 24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSAD 81
Query: 150 AENAITAMNGQWLGSRSIRTNWSTRK 175
A+ A ++G + R I N +T +
Sbjct: 82 ADRAREKLHGTVVEGRKIEVNNATAR 107
Score = 34.7 bits (78), Expect = 0.082, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 4/55 (7%)
Query: 223 VSKVFSPFGTIVDIRV-FKE---KGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
+ ++F FG I+D+ + F E KG+ FV F A A E +H T + G ++
Sbjct: 46 LRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE 100
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI-REPGNDPYAFLEFXXXXXXXX 61
++SQP L+V N+ + L +F Q G + ++I E G+ + F+ F
Sbjct: 25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 84
Query: 62 XXXXMNKRVFLEKEMKVNWASS 83
++ V ++++VN A++
Sbjct: 85 AREKLHGTVVEGRKIEVNNATA 106
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 37.4 bits (85), Expect = 0.015, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 27/47 (57%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
IFVG LS + +K F FG++ + ++ D T + +G+ FV+F
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48
Score = 33.1 bits (74), Expect = 0.29, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 7/72 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESI 262
++ GG + E V F FG + D + + +G+ FV F +++ E I
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60
Query: 263 HNTDINGHTVKC 274
H +IN V+C
Sbjct: 61 HFHEINNKMVEC 72
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 37.4 bits (85), Expect = 0.015, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 36/63 (57%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+G + ++ + LK F FG+I +++D T KG AF+++ ++ A A +A+
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 158 NGQ 160
+ Q
Sbjct: 76 HEQ 78
Score = 33.5 bits (75), Expect = 0.22, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 6/61 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
++ G ++L+E+ + +F FG I ++ V K+ KG AF+ + +E+A A ++
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 263 H 263
H
Sbjct: 76 H 76
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 37.0 bits (84), Expect = 0.017, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 34/63 (53%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG + ++ Q LK F FG I +++D T KG AF+++ + A A +A+
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSAL 77
Query: 158 NGQ 160
+ Q
Sbjct: 78 HEQ 80
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 37.0 bits (84), Expect = 0.019, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 40/79 (50%), Gaps = 10/79 (12%)
Query: 110 QTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRT 169
Q LKE F+ FGE+ ++ +D +T SKG+ FV F E E + M+ + + I
Sbjct: 30 QDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF---TEYETQVKVMSQRHM----IDG 82
Query: 170 NWSTRKPPAMTNERKRQNS 188
W K P N ++ Q+S
Sbjct: 83 RWCDCKLP---NSKQSQDS 98
Score = 32.3 bits (72), Expect = 0.49, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 13/81 (16%)
Query: 220 EELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
E+ + + FS FG ++ ++V K+ KG+ FV+FT ET + H I+G
Sbjct: 29 EQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHM--IDGRWCD 86
Query: 274 CFWGKESENNSTLAQPSAPTT 294
C NS +Q S P++
Sbjct: 87 C-----KLPNSKQSQDSGPSS 102
>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 = 37.0 bits (84), Expect = 0.019, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+FVG + ++ ++ FA +G + +I+ D +T SKGY FVSF + + + +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVES 69
Score = 32.3 bits (72), Expect = 0.44, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDPYAFLEF 53
P T++VG +DV + E + + F++ G VK K+I R + Y F+ F
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
Score = 32.0 bits (71), Expect = 0.64, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 9/71 (12%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIESI 262
TV+ GG ++E + F+ +G++ ++++ + KGY FV F +ES
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES- 69
Query: 263 HNTDINGHTVK 273
IN H K
Sbjct: 70 ---QINFHGKK 77
>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 = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 22/96 (22%), Positives = 44/96 (45%), Gaps = 3/96 (3%)
Query: 72 LEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDP 131
+E E+K+ W P N P +FV ++ + L+ F +G I +V
Sbjct: 82 VETELKM-W--DPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSK 138
Query: 132 QTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSI 167
++ K +GYAF+ + + + +A +G+ + R +
Sbjct: 139 RSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRV 174
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 36.6 bits (83), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 45/95 (47%), Gaps = 8/95 (8%)
Query: 89 KQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCR--------IVRDPQTLKSKGYA 140
+QD S++ IFV L + +++ + F G I + + D +T K KG A
Sbjct: 1 EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRK 175
VSF A+ AI +G+ I+ +++TR+
Sbjct: 61 TVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRR 95
Score = 28.1 bits (61), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 35/88 (39%), Gaps = 14/88 (15%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTI--------------VDIRVFKEKGYAF 246
Q + N T++ G G+++ E V+ F G I D K KG A
Sbjct: 2 QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61
Query: 247 VKFTTKETATHAIESIHNTDINGHTVKC 274
V F +A AI+ + +G+ +K
Sbjct: 62 VSFDDPPSAKAAIDWFDGKEFSGNPIKV 89
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 36.6 bits (83), Expect = 0.024, Method: Composition-based stats.
Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 2/83 (2%)
Query: 88 PKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKK 147
P Q+ ++ +FVG+L + + L E F G ++ I +D + K K + FV F
Sbjct: 10 PAQEEADRT-VFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFGFVCFKHP 67
Query: 148 AEAENAITAMNGQWLGSRSIRTN 170
AI +NG L R I +
Sbjct: 68 ESVSYAIALLNGIRLYGRPINVS 90
Score = 36.2 bits (82), Expect = 0.032, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 26/47 (55%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAF 50
E T++VGNL+ V EE+L LF Q GP+ + ++ P +F
Sbjct: 13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSF 59
Score = 28.5 bits (62), Expect = 7.5, Method: Composition-based stats.
Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIESI 262
TV+ G + EE++ ++F G + + + K+ K + FV F E+ ++AI +
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALL 77
Query: 263 HNTDINGHTV 272
+ + G +
Sbjct: 78 NGIRLYGRPI 87
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 36.6 bits (83), Expect = 0.024, Method: Composition-based stats.
Identities = 24/87 (27%), Positives = 38/87 (43%), Gaps = 8/87 (9%)
Query: 92 TSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAE 151
+S +F+G+L E Q ++ F +G++ C I+ K Y FV K AE
Sbjct: 5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAE 56
Query: 152 NAITAMNGQWLGSRSIRTNWSTRKPPA 178
+AI ++ L +I S K A
Sbjct: 57 DAIRNLHHYKLHGVNINVEASKNKSKA 83
Score = 32.3 bits (72), Expect = 0.48, Method: Composition-based stats.
Identities = 19/86 (22%), Positives = 41/86 (47%), Gaps = 7/86 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDIN 268
++ G ++ E+ + +F +G +++ + K Y FV K A AI ++H+ ++
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--YGFVHIEDKTAAEDAIRNLHHYKLH 68
Query: 269 GHTVKCFWGKESENNSTLAQPSAPTT 294
G + E+ N + A S P++
Sbjct: 69 GVNINV----EASKNKSKAS-SGPSS 89
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 14/35 (40%), Positives = 21/35 (60%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG 44
L++GNL TE+ + +LF Q G V C +I+ G
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYG 45
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 36.6 bits (83), Expect = 0.025, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F L+ I + L++ F+ G++ + RI+ D + +SKG A+V F + AI +
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GL 86
Query: 158 NGQWL 162
GQ L
Sbjct: 87 TGQRL 91
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 36.6 bits (83), Expect = 0.025, Method: Composition-based stats.
Identities = 30/89 (33%), Positives = 45/89 (50%), Gaps = 3/89 (3%)
Query: 83 SPGNQPKQ-DTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAF 141
S G+ K+ T Y +VG+L P Q +A I + R+VRD T K KG+ +
Sbjct: 2 SSGSSGKELPTEPPYTAYVGNL-PFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCY 60
Query: 142 VSFVKKAEAENAITAMNGQWLGSRSIRTN 170
V F + + A+T +G LG RS+R +
Sbjct: 61 VEFDEVDSLKEALT-YDGALLGDRSLRVD 88
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 36.6 bits (83), Expect = 0.027, Method: Composition-based stats.
Identities = 24/90 (26%), Positives = 46/90 (51%), Gaps = 10/90 (11%)
Query: 83 SPGNQPKQDT-SNHYHIFVGDLSPEIETQTLKEA-FAPFGEISNCRIVRDPQTLKSKGYA 140
S G+ K D S + +F+G+L+ + ++ EA F+ +G+I C + KG+A
Sbjct: 2 SSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFA 53
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTN 170
FV +V + A A+ +G+ + + + N
Sbjct: 54 FVQYVNERNARAAVAGEDGRMIAGQVLDIN 83
Score = 28.9 bits (63), Expect = 4.7, Method: Composition-based stats.
Identities = 18/81 (22%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 5 SQPTTLYVGNLDVSVTEEL-LCALFSQIGPVKGCKVIREPGNDPYAFLEFXXXXXXXXXX 63
S + +++GNL+ V ++ + A+FS+ G + GC V + +AF+++
Sbjct: 13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-----HKGFAFVQYVNERNARAAV 67
Query: 64 XXMNKRVFLEKEMKVNWASSP 84
+ R+ + + +N A+ P
Sbjct: 68 AGEDGRMIAGQVLDINLAAEP 88
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 36.2 bits (82), Expect = 0.029, Method: Composition-based stats.
Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 3/86 (3%)
Query: 92 TSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQ---TLKSKGYAFVSFVKKA 148
+S +F+ +L+ +TLK F+ G I +C I + L S G+ FV + K
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61
Query: 149 EAENAITAMNGQWLGSRSIRTNWSTR 174
+A+ A+ + G + + S R
Sbjct: 62 QAQKALKQLQGHTVDGHKLEVRISER 87
Score = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 14/38 (36%), Positives = 25/38 (65%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE 42
S + L++ NL+ S TEE L +FS++G +K C + ++
Sbjct: 3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKK 40
Score = 32.0 bits (71), Expect = 0.61, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 13/75 (17%)
Query: 212 GGFGKDLN----EELVSKVFSPFGTIVDIRVFKEK---------GYAFVKFTTKETATHA 258
G F K+LN EE + VFS G I + K+K G+ FV++ E A A
Sbjct: 7 GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66
Query: 259 IESIHNTDINGHTVK 273
++ + ++GH ++
Sbjct: 67 LKQLQGHTVDGHKLE 81
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 36.2 bits (82), Expect = 0.032, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 43/73 (58%), Gaps = 7/73 (9%)
Query: 91 DTSNHYHIFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVK 146
+T ++ I++ +L+ +I+ LK++ F+ FG+I + + R +LK +G AFV F +
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKXRGQAFVIFKE 60
Query: 147 KAEAENAITAMNG 159
+ A NA+ + G
Sbjct: 61 VSSATNALRSXQG 73
Score = 35.4 bits (80), Expect = 0.051, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 7/63 (11%)
Query: 206 NCTVYCGGFGKDLNEELVSK----VFSPFGTIVDI---RVFKEKGYAFVKFTTKETATHA 258
N T+Y + + ++ + K +FS FG I+DI R K +G AFV F +AT+A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNA 67
Query: 259 IES 261
+ S
Sbjct: 68 LRS 70
>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 = 36.2 bits (82), Expect = 0.032, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 43/73 (58%), Gaps = 7/73 (9%)
Query: 91 DTSNHYHIFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVK 146
+T ++ I++ +L+ +I+ LK++ F+ FG+I + + R +LK +G AFV F +
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKXRGQAFVIFKE 61
Query: 147 KAEAENAITAMNG 159
+ A NA+ + G
Sbjct: 62 VSSATNALRSXQG 74
Score = 35.4 bits (80), Expect = 0.051, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 7/63 (11%)
Query: 206 NCTVYCGGFGKDLNEELVSK----VFSPFGTIVDI---RVFKEKGYAFVKFTTKETATHA 258
N T+Y + + ++ + K +FS FG I+DI R K +G AFV F +AT+A
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNA 68
Query: 259 IES 261
+ S
Sbjct: 69 LRS 71
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 36.2 bits (82), Expect = 0.034, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 43/73 (58%), Gaps = 7/73 (9%)
Query: 91 DTSNHYHIFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVK 146
+T ++ I++ +L+ +I+ LK++ F+ FG+I + + R +LK +G AFV F +
Sbjct: 2 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKXRGQAFVIFKE 58
Query: 147 KAEAENAITAMNG 159
+ A NA+ + G
Sbjct: 59 VSSATNALRSXQG 71
Score = 35.4 bits (80), Expect = 0.056, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 7/63 (11%)
Query: 206 NCTVYCGGFGKDLNEELVSK----VFSPFGTIVDI---RVFKEKGYAFVKFTTKETATHA 258
N T+Y + + ++ + K +FS FG I+DI R K +G AFV F +AT+A
Sbjct: 6 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNA 65
Query: 259 IES 261
+ S
Sbjct: 66 LRS 68
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 35.8 bits (81), Expect = 0.043, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 8/63 (12%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV +L+ + + L+++F+ FG++ + ++D YAFV F + A A+ M
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEDRGAAVKAMDEM 69
Query: 158 NGQ 160
NG+
Sbjct: 70 NGK 72
Score = 32.3 bits (72), Expect = 0.48, Method: Composition-based stats.
Identities = 18/46 (39%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 218 LNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIH 263
+ EE++ K FS FG + RV K K YAFV F + A A++ ++
Sbjct: 27 VTEEILEKSFSEFGKLE--RVKKLKDYAFVHFEDRGAAVKAMDEMN 70
Score = 31.2 bits (69), Expect = 0.96, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFXXXXXXXXXXXXMNKR 69
L+V NL +VTEE+L FS+ G ++ K +++ YAF+ F MN +
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-----YAFVHFEDRGAAVKAMDEMNGK 72
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 35.4 bits (80), Expect = 0.052, Method: Composition-based stats.
Identities = 14/55 (25%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGE--ISNCRIVRDPQTLKSKGYAFVSFVKKAEA 150
I + +++P ++ A +P+ ++N R+++D QT +++G+AFV +A
Sbjct: 12 IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDA 66
>pdb|3U1L|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
pdb|3U1M|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
Length = 240
Score = 35.4 bits (80), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 30/68 (44%), Gaps = 9/68 (13%)
Query: 206 NCTVYCGGFGKDLN---------EELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETAT 256
N T+Y GG LN E + VFS G I IR + K FVKF + A
Sbjct: 134 NKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAE 193
Query: 257 HAIESIHN 264
A E++ N
Sbjct: 194 FAKEAMSN 201
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 35.4 bits (80), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 8/66 (12%)
Query: 219 NEELVSKVFSPFGTIVDIRVFKE-------KGYAFVKFTTKETATHAIESI-HNTDINGH 270
N+ + ++FS FG + +R+ K+ +G+ FV F TK+ A A ++ H+T + G
Sbjct: 28 NQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGR 87
Query: 271 TVKCFW 276
+ W
Sbjct: 88 RLVLEW 93
>pdb|3TP2|A Chain A, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
pdb|3TP2|B Chain B, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
Length = 229
Score = 35.0 bits (79), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 30/68 (44%), Gaps = 9/68 (13%)
Query: 206 NCTVYCGGFGKDLN---------EELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETAT 256
N T+Y GG LN E + VFS G I IR + K FVKF + A
Sbjct: 136 NKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAE 195
Query: 257 HAIESIHN 264
A E++ N
Sbjct: 196 FAKEAMSN 203
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 35.0 bits (79), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 8/73 (10%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTL--KSKGYAFVSFVKKAEAENAIT 155
+ + +LS +TL+E F ++ PQ KSKGYAF+ F +A+ A+
Sbjct: 18 LVLSNLSYSATEETLQEVF------EKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALN 71
Query: 156 AMNGQWLGSRSIR 168
+ N + + R+IR
Sbjct: 72 SCNKREIEGRAIR 84
Score = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 240 KEKGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
K KGYAF++F + E A A+ S + +I G ++
Sbjct: 51 KSKGYAFIEFASFEDAKEALNSCNKREIEGRAIR 84
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 34.7 bits (78), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 15/68 (22%), Positives = 32/68 (47%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IFVG + L+E F FG ++ ++ D + + +G+ F++F + + A+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 158 NGQWLGSR 165
+G +
Sbjct: 73 FHDIMGKK 80
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 34.7 bits (78), Expect = 0.093, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 10/81 (12%)
Query: 219 NEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWGK 278
+EE++ K F+ RV K + YAFV F+ +E A A+++++ ++G ++
Sbjct: 28 SEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV---- 83
Query: 279 ESENNSTLAQPSAPTTPQPNS 299
TLA+P + P+S
Sbjct: 84 ------TLAKPVDKDSSGPSS 98
Score = 28.1 bits (61), Expect = 8.0, Method: Composition-based stats.
Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 11/88 (12%)
Query: 83 SPGNQPKQDTSNHYHI-FVGDLSPEIETQTLKEAFAPF--GEISNCRIVRDPQTLKSKGY 139
S G+ +DT + I +V +L + +++ F G + + +RD Y
Sbjct: 2 SSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD--------Y 53
Query: 140 AFVSFVKKAEAENAITAMNGQWLGSRSI 167
AFV F + +A A+ A+NG+ L I
Sbjct: 54 AFVHFSNREDAVEAMKALNGKVLDGSPI 81
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 34.7 bits (78), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG++ Q L+ F+ G I+ I+ D + KGYA++ F ++ + A+ AM
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AM 97
Query: 158 NGQWLGSRSIR 168
+ R+I+
Sbjct: 98 DETVFRGRTIK 108
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRI-VRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+ +G L+ + + E F+ +G+I + V SKGYA+V F EAE A+
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 157 MNGQWLGSRSI 167
M+G + + I
Sbjct: 67 MDGGQIDGQEI 77
Score = 32.3 bits (72), Expect = 0.52, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 39/71 (54%), Gaps = 7/71 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTI--VDIRVFK-----EKGYAFVKFTTKETATHAIES 261
V+ G +++ ++ + ++FS +G I +D+ V + KGYA+V+F + A A++
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 262 IHNTDINGHTV 272
+ I+G +
Sbjct: 67 MDGGQIDGQEI 77
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 40/173 (23%), Positives = 72/173 (41%), Gaps = 14/173 (8%)
Query: 5 SQPTT---LYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDPYAFLEFXXXXXX 59
++PTT L+VGNL+ + + L S + V+ R + +++F
Sbjct: 2 TEPTTAFNLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDL 61
Query: 60 XXXXXXMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPF 119
+VF E+K+ ++ ++D + +L ++ LKE F
Sbjct: 62 EKALELTGLKVF-GNEIKLEKPKGKDSKKERDART---LLAKNLPYKVTQDELKEVFEDA 117
Query: 120 GEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWS 172
EI R+V + KSKG A++ F +A+AE G + RSI ++
Sbjct: 118 AEI---RLV--SKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISLYYT 165
Score = 32.7 bits (73), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 38/190 (20%), Positives = 80/190 (42%), Gaps = 42/190 (22%)
Query: 96 YHIFVGDL-----SPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEA 150
+++FVG+L +PE++T + + FA N V D + ++ + +V F +
Sbjct: 8 FNLFVGNLNFNKSAPELKT-GISDVFA-----KNDLAVVDVRIGMTRKFGYVDFESAEDL 61
Query: 151 ENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVY 210
E A+ + G N + P + +K +++ T + ++ P T
Sbjct: 62 EKALELTGLKVFG------NEIKLEKPKGKDSKKERDART-------LLAKNLPYKVT-- 106
Query: 211 CGGFGKDLNEELVSKVFSPFGTIVDIRVF----KEKGYAFVKFTTKETATHAIESIHNTD 266
++ + +VF +IR+ K KG A+++F T+ A E T+
Sbjct: 107 ---------QDELKEVFED---AAEIRLVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTE 154
Query: 267 INGHTVKCFW 276
I+G ++ ++
Sbjct: 155 IDGRSISLYY 164
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 33.9 bits (76), Expect = 0.18, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 37/78 (47%), Gaps = 5/78 (6%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ +LS I LKE F EI R+V Q KSKG A++ F +A+AE +
Sbjct: 19 LLAKNLSFNITEDELKEVFEDALEI---RLVS--QDGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 158 NGQWLGSRSIRTNWSTRK 175
G + RS+ ++ K
Sbjct: 74 QGAEIDGRSVSLYYTGEK 91
>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 = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE--------KGYAFVKFTTKETATHAIE 260
++ G + +E+ + ++F +G + +I V ++ KG FV F T++ A A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 261 SIHNTDI 267
++HN +
Sbjct: 66 ALHNMKV 72
Score = 33.1 bits (74), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 11/73 (15%)
Query: 93 SNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRD-----PQTLKSKGYAFVSF-VK 146
S+ +FVG + + L+E F +G + ++RD PQ SKG FV+F +
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQ---SKGCCFVTFYTR 57
Query: 147 KA--EAENAITAM 157
KA EA+NA+ M
Sbjct: 58 KAALEAQNALHNM 70
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 32.7 bits (73), Expect = 0.35, Method: Composition-based stats.
Identities = 18/83 (21%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 91 DTSNHYHIFVGDLSPEIETQTLKEA-FAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAE 149
D ++ I++ +++ +I+ + LK + +A F + + + +T+K +G AFV F +
Sbjct: 2 DIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGS 61
Query: 150 AENAITAMNGQWLGSRSIRTNWS 172
+ NA+ + G + +R ++
Sbjct: 62 STNALRQLQGFPFYGKPMRIQYA 84
>pdb|2PE8|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 (free
Form)
pdb|2PEH|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
pdb|2PEH|B Chain B, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
Length = 105
Score = 32.0 bits (71), Expect = 0.53, Method: Composition-based stats.
Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 2/69 (2%)
Query: 101 GDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGY-AFVSFVKKAEAENAITAMNG 159
G++ ++E +T KE +G++ C I P + F+ F + A A+ +NG
Sbjct: 20 GEVDEDLEVET-KEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNG 78
Query: 160 QWLGSRSIR 168
++ G R ++
Sbjct: 79 RYFGGRVVK 87
>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 = 32.0 bits (71), Expect = 0.64, Method: Composition-based stats.
Identities = 19/83 (22%), Positives = 39/83 (46%), Gaps = 1/83 (1%)
Query: 96 YHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
+ +F+ L + L+E G + + R+V + + K KG A+V + +++A A+
Sbjct: 18 HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYENESQASQAVM 76
Query: 156 AMNGQWLGSRSIRTNWSTRKPPA 178
M+G + I+ S P +
Sbjct: 77 KMDGMTIKENIIKVAISNSGPSS 99
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 32.0 bits (71), Expect = 0.64, Method: Composition-based stats.
Identities = 13/45 (28%), Positives = 29/45 (64%), Gaps = 2/45 (4%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIE 260
K++++E + ++FSP+G I+ I + + + F++F ++ AIE
Sbjct: 33 KNVSKEDLFRIFSPYGHIMQINI--KNAFGFIQFDNPQSVRDAIE 75
>pdb|1OT5|A Chain A, The 2.4 Angstrom Crystal Sructure Of Kex2 In Complex With
A Peptidyl- Boronic Acid Inhibitor
pdb|1OT5|B Chain B, The 2.4 Angstrom Crystal Sructure Of Kex2 In Complex With
A Peptidyl- Boronic Acid Inhibitor
Length = 477
Score = 32.0 bits (71), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 102 DLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAE-AENAITAMNGQ 160
D+ EI T + +P G ISN +VR P+ + S+G+ +F+ A EN + G
Sbjct: 391 DIDTEIRGTTTVDLISPAGIISNLGVVR-PRDVSSEGFKDWTFMSVAHWGENGV----GD 445
Query: 161 W 161
W
Sbjct: 446 W 446
>pdb|1R64|A Chain A, The 2.2 A Crystal Structure Of Kex2 Protease In Complex
With Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid
Inhibitor
pdb|1R64|B Chain B, The 2.2 A Crystal Structure Of Kex2 Protease In Complex
With Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid
Inhibitor
Length = 481
Score = 32.0 bits (71), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 102 DLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAE-AENAITAMNGQ 160
D+ EI T + +P G ISN +VR P+ + S+G+ +F+ A EN + G
Sbjct: 393 DIDTEIRGTTTVDLISPAGIISNLGVVR-PRDVSSEGFKDWTFMSVAHWGENGV----GD 447
Query: 161 W 161
W
Sbjct: 448 W 448
>pdb|2ID4|A Chain A, The 1.9 A Structure Of Kex2 In Complex With An
Ac-R-E-R-K-Chloromethyl Ketone Inhibitor.
pdb|2ID4|B Chain B, The 1.9 A Structure Of Kex2 In Complex With An
Ac-R-E-R-K-Chloromethyl Ketone Inhibitor
Length = 503
Score = 31.6 bits (70), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 102 DLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAE-AENAITAMNGQ 160
D+ EI T + +P G ISN +VR P+ + S+G+ +F+ A EN + G
Sbjct: 400 DIDTEIRGTTTVDLISPAGIISNLGVVR-PRDVSSEGFKDWTFMSVAHWGENGV----GD 454
Query: 161 W 161
W
Sbjct: 455 W 455
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 31.6 bits (70), Expect = 0.73, Method: Composition-based stats.
Identities = 13/45 (28%), Positives = 29/45 (64%), Gaps = 2/45 (4%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIE 260
K++++E + ++FSP+G I+ I + + + F++F ++ AIE
Sbjct: 33 KNVSKEDLFRIFSPYGHIMQINI--KNAFGFIQFDNPQSVRDAIE 75
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 31.6 bits (70), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 32/65 (49%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++ +LSP + + L FA F E I T + +G AF++F K A A+ +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 158 NGQWL 162
NG L
Sbjct: 88 NGYKL 92
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/93 (23%), Positives = 40/93 (43%), Gaps = 7/93 (7%)
Query: 199 YNQSSPTNCTVYCGGFGKDLNEELVSKVFSPF----GTIVDIRVF--KEKGYAFVKFTTK 252
YN P N +Y + E + +F+ F G + R+ + +G AF+ F K
Sbjct: 19 YNPGEP-NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNK 77
Query: 253 ETATHAIESIHNTDINGHTVKCFWGKESENNST 285
E A A+ ++ + G + +GK + S+
Sbjct: 78 EIAWQALHLVNGYKLYGKILVIEFGKNKKQRSS 110
>pdb|3UE2|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.23 A Resolution
pdb|3US5|A Chain A, Crystal Structure Of A Rna-Binding Domain Of A Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.38 A Resolution
Length = 118
Score = 31.6 bits (70), Expect = 0.78, Method: Composition-based stats.
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 102 DLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKG----YAFVSFVKKAEAENAITAM 157
D+ ++E + +E FG ++ I ++ Q + FV F +E AI A+
Sbjct: 33 DIDDDLEGEVTEEC-GKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL 91
Query: 158 NGQWLGSRSI 167
NG+W R +
Sbjct: 92 NGRWFAGRKV 101
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 31.6 bits (70), Expect = 0.87, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 34/69 (49%), Gaps = 6/69 (8%)
Query: 92 TSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAE 151
+S +++G+LSP + L++ F + ++ Q L GYAFV + + A
Sbjct: 5 SSGMNKLYIGNLSPAVTADDLRQLFG------DRKLPLAGQVLLKSGYAFVDYPDQNWAI 58
Query: 152 NAITAMNGQ 160
AI ++G+
Sbjct: 59 RAIETLSGK 67
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 31.2 bits (69), Expect = 0.97, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 1/76 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ V +L + ++E FA FG + + D ++ +S G A V F +KA+A A+
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQY 89
Query: 158 NGQWLGSRSIRTNWST 173
NG L R + T
Sbjct: 90 NGVPLDGRPMNIQLVT 105
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 31.2 bits (69), Expect = 0.99, Method: Composition-based stats.
Identities = 13/45 (28%), Positives = 29/45 (64%), Gaps = 2/45 (4%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIE 260
K++++E + ++FSP+G I+ I + + + F++F ++ AIE
Sbjct: 13 KNVSKEDLFRIFSPYGHIMQINI--KNAFGFIQFDNPQSVRDAIE 55
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 27/105 (25%), Positives = 46/105 (43%), Gaps = 9/105 (8%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEIS-NCR-------IVRDPQ 132
+S P +D+ N I+V L+ + L + F G + N R I D +
Sbjct: 2 SSGSSGDPDEDSDNS-AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60
Query: 133 TLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
T K KG A VS+ A+ A+ +G+ ++ + + +KPP
Sbjct: 61 TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 105
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp-
Interacting Repressor, Siahbp1
Length = 119
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 102 DLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKG----YAFVSFVKKAEAENAITAM 157
D+ ++E + +E FG ++ I ++ Q + FV F +E AI A+
Sbjct: 28 DIDDDLEGEVTEEC-GKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL 86
Query: 158 NGQWLGSRSI 167
NG+W R +
Sbjct: 87 NGRWFAGRKV 96
>pdb|3DXB|A Chain A, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|B Chain B, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|C Chain C, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|D Chain D, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|E Chain E, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|F Chain F, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|G Chain G, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|H Chain H, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
Length = 222
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 102 DLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKG----YAFVSFVKKAEAENAITAM 157
D+ ++E + +E FG ++ I ++ Q + FV F +E AI A+
Sbjct: 137 DIDDDLEGEVTEEC-GKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL 195
Query: 158 NGQWLGSRSI 167
NG+W R +
Sbjct: 196 NGRWFAGRKV 205
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 32/76 (42%), Gaps = 2/76 (2%)
Query: 92 TSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAE 151
+S IFV +L + + LK+ F G + I + KSKG V F AE
Sbjct: 5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAE 62
Query: 152 NAITAMNGQWLGSRSI 167
A MNG L R I
Sbjct: 63 RACRMMNGMKLSGREI 78
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 30.8 bits (68), Expect = 1.2, Method: Composition-based stats.
Identities = 16/71 (22%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 199 YNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHA 258
Y +++PT ++ GG G + + +++ F FG+I I K +A++++ + + A A
Sbjct: 11 YGKANPTT-RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAA 69
Query: 259 IESIHNTDING 269
+ + G
Sbjct: 70 CAKMRGFPLGG 80
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 30.8 bits (68), Expect = 1.2, Method: Composition-based stats.
Identities = 13/45 (28%), Positives = 29/45 (64%), Gaps = 2/45 (4%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIE 260
K++++E + ++FSP+G I+ I + + + F++F ++ AIE
Sbjct: 21 KNVSKEDLFRIFSPYGHIMQINI--KNAFGFIQFDNPQSVRDAIE 63
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 30.8 bits (68), Expect = 1.5, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 32/76 (42%), Gaps = 2/76 (2%)
Query: 92 TSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAE 151
+S IFV +L + + LK+ F G + I + KSKG V F AE
Sbjct: 2 SSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAE 59
Query: 152 NAITAMNGQWLGSRSI 167
A MNG L R I
Sbjct: 60 RACRMMNGMKLSGREI 75
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 30.4 bits (67), Expect = 1.6, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 10/65 (15%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKS------KGYAFVSFVKKAEAE 151
+FVG L P+I+ + +F FG + +V P +S KGYAF+ F +++ +
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPL----VVDWPHKAESKSYFPPKGYAFLLFQEESSVQ 66
Query: 152 NAITA 156
I A
Sbjct: 67 ALIDA 71
Score = 29.6 bits (65), Expect = 3.0, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 8/66 (12%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIV--------DIRVFKEKGYAFVKFTTKETATHAIE 260
V+ GG D++E+ ++ F FG +V F KGYAF+ F + + I+
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70
Query: 261 SIHNTD 266
+ D
Sbjct: 71 ACLEED 76
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 15/62 (24%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++ +L +I + + + F +G I R+ P+T +G A+V + +A+NA+ +
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAVDHL 67
Query: 158 NG 159
+G
Sbjct: 68 SG 69
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 30.4 bits (67), Expect = 1.9, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 111 TLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNG 159
+L F+ FG+I + ++ TLK +G AFV F + A NA+ M G
Sbjct: 26 SLYAIFSQFGQILDIVALK---TLKMRGQAFVIFKEIGSASNALRTMQG 71
>pdb|3BC9|A Chain A, Alpha-Amylase B In Complex With Acarbose
pdb|3BCD|A Chain A, Alpha-Amylase B In Complex With Maltotetraose And
Alpha-Cyclodextrin
pdb|3BCF|A Chain A, Alpha-Amylase B From Halothermothrix Orenii
Length = 599
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 230 FGT--IVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDI 267
+GT + D+ F +KG K+ TK +AI+++HN DI
Sbjct: 184 YGTYDLWDLGEFDQKGTVRTKYGTKGELENAIDALHNNDI 223
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 30.0 bits (66), Expect = 2.3, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 6/59 (10%)
Query: 110 QTLKEAFAPFGEISNCRIV-RDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSI 167
+ L+ + FG+I + R P G A VSF EA+ I ++G+W G R I
Sbjct: 41 EDLRVECSKFGQIRKLLLFDRHPD-----GVASVSFRDPEEADYCIQTLDGRWFGGRQI 94
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 30.0 bits (66), Expect = 2.4, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 1/68 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ V +L + ++E FA FG + + D ++ +S G A V F +KA+A A
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAXKQY 90
Query: 158 NGQWLGSR 165
NG L R
Sbjct: 91 NGVPLDGR 98
>pdb|1VJS|A Chain A, Structure Of Alpha-Amylase Precursor
Length = 483
Score = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 21/36 (58%)
Query: 233 IVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDIN 268
+ D+ F +KG K+ TK AI+S+H+ DIN
Sbjct: 61 LYDLGEFHQKGTVRTKYGTKGELQSAIKSLHSRDIN 96
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 30.0 bits (66), Expect = 2.6, Method: Composition-based stats.
Identities = 15/62 (24%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++ +L +I + + + F +G I R+ P+T +G A+V + +A+NA +
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNACDHL 71
Query: 158 NG 159
+G
Sbjct: 72 SG 73
>pdb|1BLI|A Chain A, Bacillus Licheniformis Alpha-Amylase
Length = 483
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 21/36 (58%)
Query: 233 IVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDIN 268
+ D+ F +KG K+ TK AI+S+H+ DIN
Sbjct: 61 LYDLGEFHQKGTVRTKYGTKGELQSAIKSLHSRDIN 96
>pdb|1BPL|A Chain A, Glycosyltransferase
Length = 189
Score = 29.6 bits (65), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 21/36 (58%)
Query: 233 IVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDIN 268
+ D+ F +KG K+ TK AI+S+H+ DIN
Sbjct: 61 LYDLGEFHQKGTVRTKYGTKGELQSAIKSLHSRDIN 96
>pdb|1OB0|A Chain A, Kinetic Stabilization Of Bacillus Licheniformis-Amylase
Through Introduction Of Hydrophobic Residues At The
Surface
Length = 483
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 21/36 (58%)
Query: 233 IVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDIN 268
+ D+ F +KG K+ TK AI+S+H+ DIN
Sbjct: 61 LYDLGEFHQKGTVRTKYGTKGELQSAIKSLHSRDIN 96
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 29.6 bits (65), Expect = 2.8, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 11/74 (14%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKG---YAFVSFVKKAEAENAI 154
++VG+L + LK A G + P L +G AF+ + A A+ A+
Sbjct: 22 VYVGNLPRDARVSDLKRALRELGSV--------PLRLTWQGPRRRAFLHYPDSAAAQQAV 73
Query: 155 TAMNGQWLGSRSIR 168
+ + G LG+ ++R
Sbjct: 74 SCLQGLRLGTDTLR 87
>pdb|2AD9|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd1 Complexed With Cucucu Rna
Length = 119
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETA 255
D+ E V + PFG + ++ + K K AF++ T+E A
Sbjct: 42 DVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAA 80
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 28.9 bits (63), Expect = 5.2, Method: Composition-based stats.
Identities = 15/62 (24%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++ +L +I + + + F +G I R+ P+T +G A+V + +A+NA +
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNACDHL 77
Query: 158 NG 159
+G
Sbjct: 78 SG 79
>pdb|1SJQ|A Chain A, Nmr Structure Of Rrm1 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 105
Score = 28.5 bits (62), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETA 255
D+ E V + PFG + ++ + K K AF++ T+E A
Sbjct: 27 DVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAA 65
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 28.5 bits (62), Expect = 7.2, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 6/84 (7%)
Query: 98 IFVGDLSPEI-ETQTLK--EAFAPFGEISNCRIVRDPQTLKSKG---YAFVSFVKKAEAE 151
+FV LS + + + LK E F FG+I I S+G A+V++++ +A
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 152 NAITAMNGQWLGSRSIRTNWSTRK 175
AI +N + R+++ + T K
Sbjct: 78 RAIQCVNNVVVDGRTLKASLGTTK 101
>pdb|2KH9|A Chain A, Solution Structure Of Yeast Prp24-Rrm2 Bound To A Fragment
Of U6 Rna
Length = 92
Score = 28.5 bits (62), Expect = 7.3, Method: Composition-based stats.
Identities = 14/74 (18%), Positives = 32/74 (43%), Gaps = 6/74 (8%)
Query: 205 TNCTVYCGGFGKDLNEELVSKVFSPFGTIV------DIRVFKEKGYAFVKFTTKETATHA 258
T CT++ F + + + + +R + +A++ T+KE A +
Sbjct: 2 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYC 61
Query: 259 IESIHNTDINGHTV 272
+E ++ I G+T+
Sbjct: 62 VEKLNGLKIEGYTL 75
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 28.1 bits (61), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 15/77 (19%), Positives = 33/77 (42%), Gaps = 6/77 (7%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIV------DIRVFKEKGYAFVKFTTKETA 255
S T CT++ F + + + + +R + +A++ T+KE A
Sbjct: 76 SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDA 135
Query: 256 THAIESIHNTDINGHTV 272
+ +E ++ I G+T+
Sbjct: 136 RYCVEKLNGLKIEGYTL 152
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation
Initiation Factor 4b
Length = 100
Score = 28.1 bits (61), Expect = 8.2, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGN 45
+S P T ++GNL VTEE + F + + ++ REP N
Sbjct: 16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSN 56
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 28.1 bits (61), Expect = 8.4, Method: Composition-based stats.
Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 9/82 (10%)
Query: 91 DTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEA 150
+ HY F ++ E+E E + E++ C + D G +V F ++ +A
Sbjct: 31 EMQEHYDEFFEEVFTEME-----EKYGEVEEMNVCDNLGDHLV----GNVYVKFRREEDA 81
Query: 151 ENAITAMNGQWLGSRSIRTNWS 172
E A+ +N +W + I S
Sbjct: 82 EKAVIDLNNRWFNGQPIHAELS 103
>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 = 28.1 bits (61), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 15/77 (19%), Positives = 33/77 (42%), Gaps = 6/77 (7%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIV------DIRVFKEKGYAFVKFTTKETA 255
S T CT++ F + + + + +R + +A++ T+KE A
Sbjct: 113 SHLTECTLWXTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDA 172
Query: 256 THAIESIHNTDINGHTV 272
+ +E ++ I G+T+
Sbjct: 173 RYCVEKLNGLKIEGYTL 189
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
0.316 0.130 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,687,200
Number of Sequences: 62578
Number of extensions: 399188
Number of successful extensions: 1391
Number of sequences better than 100.0: 217
Number of HSP's better than 100.0 without gapping: 166
Number of HSP's successfully gapped in prelim test: 51
Number of HSP's that attempted gapping in prelim test: 816
Number of HSP's gapped (non-prelim): 495
length of query: 390
length of database: 14,973,337
effective HSP length: 101
effective length of query: 289
effective length of database: 8,652,959
effective search space: 2500705151
effective search space used: 2500705151
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)