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= 036905
(354 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 92.8 bits (229), Expect = 3e-19, Method: Composition-based stats.
Identities = 45/83 (54%), Positives = 60/83 (72%), Gaps = 1/83 (1%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINTL 219
NLYVKN++D +D+ L++ FS G I+S K+M G SKGFGFVCFS+P+EA +A+ +
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFSSPEEATKAVTEM 75
Query: 220 NGILFHQKPLYVAIAQTKRERTS 242
NG + KPLYVA+AQ K ER S
Sbjct: 76 NGRIVATKPLYVALAQRKEERQS 98
Score = 50.1 bits (118), Expect = 2e-06, Method: Composition-based stats.
Identities = 27/69 (39%), Positives = 42/69 (60%), Gaps = 1/69 (1%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYA 116
+ NL ID+ +L + FS FG I S+KV++ + G+SKG+GFV +S+ E A A+ ++
Sbjct: 19 YVKNLDDGIDDERLRKAFSPFGTITSAKVMM-EGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 117 ATVEGMELY 125
V LY
Sbjct: 78 RIVATKPLY 86
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 74.7 bits (182), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 59/171 (34%), Positives = 85/171 (49%), Gaps = 28/171 (16%)
Query: 64 TIDNWKLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIEKLYAATVEGM 122
T D +K +F GDI+S K+V + G+S GYGFV YS A AI T+ G+
Sbjct: 17 TQDEFK--SLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN-----TLNGL 69
Query: 123 ELYAPSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQC 182
+L +++ + S++ I D NLYV + + + E++Q FSQ
Sbjct: 70 KLQTKTIKVSYARPSSA---------------SIRDANLYVSGLPKTMSQKEMEQLFSQY 114
Query: 183 G-IISSVKIMRTNRGISKGFGFVCFSNPDEANRAINTLNGILFHQKPLYVA 232
G II+S ++ G+S+G GF+ F EA AI LNG QKPL A
Sbjct: 115 GRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNG----QKPLGAA 161
Score = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 47/77 (61%), Gaps = 1/77 (1%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTN-RGISKGFGFVCFSNPDEANRAINT 218
NL V + ++ + E K F G I S K++R G S G+GFV +S+P++A++AINT
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 219 LNGILFHQKPLYVAIAQ 235
LNG+ K + V+ A+
Sbjct: 66 LNGLKLQTKTIKVSYAR 82
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 68.6 bits (166), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 54/170 (31%), Positives = 81/170 (47%), Gaps = 26/170 (15%)
Query: 61 LASTIDNWKLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIEKLYAATV 119
L + + +F G+I+S K+V + G+S GYGFV Y + A AI T+
Sbjct: 10 LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN-----TL 64
Query: 120 EGMELYAPSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYF 179
G+ L +++ + S++ I D NLYV + + + EL+Q F
Sbjct: 65 NGLRLQTKTIKVSYARPSSA---------------SIRDANLYVSGLPKTMTQKELEQLF 109
Query: 180 SQCG-IISSVKIMRTNRGISKGFGFVCFSNPDEANRAINTLNGILFHQKP 228
SQ G II+S ++ G+S+G GF+ F EA AI LNG QKP
Sbjct: 110 SQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG----QKP 155
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTN-RGISKGFGFVCFSNPDEANRAINT 218
NL V + ++ + E + F G I S K++R G S G+GFV + +P +A +AINT
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 219 LNGILFHQKPLYVAIAQ 235
LNG+ K + V+ A+
Sbjct: 64 LNGLRLQTKTIKVSYAR 80
>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 = 67.8 bits (164), Expect = 9e-12, Method: Composition-based stats.
Identities = 38/98 (38%), Positives = 57/98 (58%), Gaps = 7/98 (7%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYA 116
F NL +IDN L+ FS FG+I S KVV ++G SKGYGFV + TQE+A AIEK+
Sbjct: 9 FIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNG 67
Query: 117 ATVEGMELYAPSLRAGRIQE------SASFNNLYVKNL 148
+ +++ ++ + +E + F N+Y+KN
Sbjct: 68 MLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNF 105
Score = 58.2 bits (139), Expect = 7e-09, Method: Composition-based stats.
Identities = 30/85 (35%), Positives = 51/85 (60%), Gaps = 1/85 (1%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINTL 219
N+++KN++ +D L FS G I S K++ G SKG+GFV F + A RAI +
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 220 NGILFHQKPLYVAIAQTKRERTSYL 244
NG+L + + ++V ++++ER + L
Sbjct: 66 NGMLLNDRKVFVGRFKSRKEREAEL 90
>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 = 65.9 bits (159), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 47/162 (29%), Positives = 81/162 (50%), Gaps = 25/162 (15%)
Query: 69 KLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAP 127
+L +FS G+++S+K++ + G S GYGFV Y T + A AI T+ G+ L +
Sbjct: 18 ELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN-----TLNGLRLQSK 72
Query: 128 SLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCG-IIS 186
+++ + S +E I D NLY+ + + + +++ FS+ G II+
Sbjct: 73 TIKVSYARPS---------------SEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIIN 117
Query: 187 SVKIMRTNRGISKGFGFVCFSNPDEANRAINTLNGILFHQKP 228
S ++ G+S+G F+ F EA AI + NG H+ P
Sbjct: 118 SRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG---HKPP 156
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 45/81 (55%), Gaps = 1/81 (1%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTN-RGISKGFGFVCFSNPDEANRAINT 218
NL V + ++ + EL+ FS G + S K++R G S G+GFV + +A RAINT
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 219 LNGILFHQKPLYVAIAQTKRE 239
LNG+ K + V+ A+ E
Sbjct: 64 LNGLRLQSKTIKVSYARPSSE 84
Score = 34.7 bits (78), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 61 LASTIDNWKLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAI 111
L T+ + +FS+FG I +S+V+V Q G S+G F+++ + A AI
Sbjct: 96 LPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 65.9 bits (159), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 47/162 (29%), Positives = 81/162 (50%), Gaps = 25/162 (15%)
Query: 69 KLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAP 127
+L +FS G+++S+K++ + G S GYGFV Y T + A AI T+ G+ L +
Sbjct: 18 ELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN-----TLNGLRLQSK 72
Query: 128 SLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCG-IIS 186
+++ + S +E I D NLY+ + + + +++ FS+ G II+
Sbjct: 73 TIKVSYARPS---------------SEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIIN 117
Query: 187 SVKIMRTNRGISKGFGFVCFSNPDEANRAINTLNGILFHQKP 228
S ++ G+S+G F+ F EA AI + NG H+ P
Sbjct: 118 SRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG---HKPP 156
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 45/81 (55%), Gaps = 1/81 (1%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTN-RGISKGFGFVCFSNPDEANRAINT 218
NL V + ++ + EL+ FS G + S K++R G S G+GFV + +A RAINT
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 219 LNGILFHQKPLYVAIAQTKRE 239
LNG+ K + V+ A+ E
Sbjct: 64 LNGLRLQSKTIKVSYARPSSE 84
Score = 34.7 bits (78), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 61 LASTIDNWKLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAI 111
L T+ + +FS+FG I +S+V+V Q G S+G F+++ + A AI
Sbjct: 96 LPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
>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 = 63.5 bits (153), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 52/199 (26%), Positives = 91/199 (45%), Gaps = 20/199 (10%)
Query: 47 SAMATPTFIPFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQE 105
SA + P + +L + L++ FS G I S +V +S GY +V +
Sbjct: 9 SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 68
Query: 106 SALNAIEKLYAATVEGMELYAPSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKN 165
A A++ + ++G + RI S +L + N+++KN
Sbjct: 69 DAERALDTMNFDVIKGKPV--------RIMWSQRDPSLRKSGVG----------NIFIKN 110
Query: 166 INDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINTLNGILFH 225
++ +D L FS G I S K++ G SKG+GFV F + A RAI +NG+L +
Sbjct: 111 LDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLN 169
Query: 226 QKPLYVAIAQTKRERTSYL 244
+ ++V ++++ER + L
Sbjct: 170 DRKVFVGRFKSRKEREAEL 188
>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 = 62.8 bits (151), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 52/205 (25%), Positives = 90/205 (43%), Gaps = 32/205 (15%)
Query: 47 SAMATPTFIPFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQE 105
SA + P + +L + L++ FS G I S +V +S GY +V +
Sbjct: 4 SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 63
Query: 106 SALNAIEKLYAATVEGMELYA------PSLRAGRIQESASFNNLYVKNLDDDVTEEILDK 159
A A++ + ++G + PSLR +
Sbjct: 64 DAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVG------------------------ 99
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINTL 219
N+++KN++ +D L FS G I S K++ G SKG+GFV F + A RAI +
Sbjct: 100 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 158
Query: 220 NGILFHQKPLYVAIAQTKRERTSYL 244
NG+L + + ++V ++++ER + L
Sbjct: 159 NGMLLNDRKVFVGRFKSRKEREAEL 183
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 62.4 bits (150), Expect = 4e-10, Method: Composition-based stats.
Identities = 33/81 (40%), Positives = 50/81 (61%), Gaps = 1/81 (1%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYA 116
F NL +IDN L+ FS FG+I S KVV ++G SKGYGFV + TQE+A AIEK+
Sbjct: 15 FIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNG 73
Query: 117 ATVEGMELYAPSLRAGRIQES 137
+ +++ ++ + +E+
Sbjct: 74 MLLNDRKVFVGRFKSRKEREA 94
Score = 57.8 bits (138), Expect = 8e-09, Method: Composition-based stats.
Identities = 29/83 (34%), Positives = 50/83 (60%), Gaps = 1/83 (1%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINTL 219
N+++KN++ +D L FS G I S K++ G SKG+GFV F + A RAI +
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 71
Query: 220 NGILFHQKPLYVAIAQTKRERTS 242
NG+L + + ++V ++++ER +
Sbjct: 72 NGMLLNDRKVFVGRFKSRKEREA 94
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 58.9 bits (141), Expect = 5e-09, Method: Composition-based stats.
Identities = 29/79 (36%), Positives = 45/79 (56%)
Query: 154 EEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEAN 213
+E D+ ++V N+ V E L + F Q G ++ V I + G K FGFVCF +P+ +
Sbjct: 12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVS 71
Query: 214 RAINTLNGILFHQKPLYVA 232
AI LNGI + +P+ V+
Sbjct: 72 YAIALLNGIRLYGRPINVS 90
Score = 33.1 bits (74), Expect = 0.21, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYA 116
F NL + + L+++F + G + + ++GK K +GFV + ES AI
Sbjct: 20 FVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAI----- 74
Query: 117 ATVEGMELYA 126
A + G+ LY
Sbjct: 75 ALLNGIRLYG 84
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 57.8 bits (138), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 47/178 (26%), Positives = 78/178 (43%), Gaps = 24/178 (13%)
Query: 61 LASTIDNWKLHQIFSKFGDIQSSKVVVS-QDGKSKGYGFVQYSTQESALNAIEKLYAATV 119
L + + +L+ +F G I + +++ + G S GY FV ++++ + AI+ L TV
Sbjct: 11 LPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITV 70
Query: 120 EGMELYAPSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYF 179
L R G E I D NLYV N+ + + +L F
Sbjct: 71 RNKRLKVSYARPG--------------------GESIKDTNLYVTNLPRTITDDQLDTIF 110
Query: 180 SQCGIISSVKIMRTN-RGISKGFGFVCFSNPDEANRAINTLNGILFH--QKPLYVAIA 234
+ G I I+R G +G FV ++ +EA AI+ LN ++ +PL V +A
Sbjct: 111 GKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
Score = 47.8 bits (112), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNR-GISKGFGFVCFSNPDEANRAINT 218
NL V + D+ + EL F G I++ +IMR + G S G+ FV F++ ++ RAI
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 219 LNGILFHQKPLYVAIAQ 235
LNGI K L V+ A+
Sbjct: 65 LNGITVRNKRLKVSYAR 81
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 36/84 (42%), Positives = 49/84 (58%), Gaps = 3/84 (3%)
Query: 159 KNLYVKNINDDVDEIELKQYFSQCGIISSVKIM--RTNRGISKGFGFVCFSNPDEANRAI 216
+NL V I VDE++L+Q F + G I SVKI+ R R S+G+GFV F + A +AI
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQ-SRGYGFVKFQSGSSAQQAI 101
Query: 217 NTLNGILFHQKPLYVAIAQTKRER 240
LNG K L VA+A + +R
Sbjct: 102 AGLNGFNILNKRLKVALAASGHQR 125
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 37/55 (67%), Gaps = 1/55 (1%)
Query: 61 LASTIDNWKLHQIFSKFGDIQSSKVVVSQDGK-SKGYGFVQYSTQESALNAIEKL 114
+ +T+D +L Q+F ++G I+S K+V ++ + S+GYGFV++ + SA AI L
Sbjct: 50 IPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
>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 = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 46/173 (26%), Positives = 76/173 (43%), Gaps = 24/173 (13%)
Query: 67 NWKLHQIFSKFGDIQSSKVVVS-QDGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELY 125
+ +L+ +F G I + ++ + G S GY FV ++++ + AI+ L TV L
Sbjct: 28 DRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKRLK 87
Query: 126 APSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGII 185
R G E I D NLYV N+ + + +L F + G I
Sbjct: 88 VSYARPG--------------------GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSI 127
Query: 186 SSVKIMRTN-RGISKGFGFVCFSNPDEANRAINTLNGILFH--QKPLYVAIAQ 235
I+R G +G FV ++ +EA AI+ LN ++ +PL V +A+
Sbjct: 128 VQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLAE 180
Score = 44.3 bits (103), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNR-GISKGFGFVCFSNPDEANRAINT 218
NL V + D + EL F G I++ +I R + G S G+ FV F++ ++ RAI
Sbjct: 16 NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
Query: 219 LNGILFHQKPLYVAIAQ 235
LNGI K L V+ A+
Sbjct: 76 LNGITVRNKRLKVSYAR 92
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 47/77 (61%), Gaps = 1/77 (1%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTN-RGISKGFGFVCFSNPDEANRAINT 218
NL V + ++ + E K F G I S K++R G S G+GFV +S+P++A++AINT
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 219 LNGILFHQKPLYVAIAQ 235
LNG+ K + V+ A+
Sbjct: 66 LNGLKLQTKTIKVSYAR 82
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 69 KLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAP 127
+ +F GDI+S K+V + G+S GYGFV YS A AI T+ G++L
Sbjct: 20 EFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN-----TLNGLKLQTK 74
Query: 128 SLRAGRIQESAS 139
+++ + S++
Sbjct: 75 TIKVSYARPSSA 86
>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 = 55.1 bits (131), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 42/156 (26%), Positives = 78/156 (50%), Gaps = 17/156 (10%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDG---KSKGYGFVQYSTQESALNAIEKLYAATVEGMELYA 126
+ Q F+ FG I+S + +S D K KG+ FV+Y E+A A+E++ + + G
Sbjct: 45 IRQAFAPFGPIKS--IDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGR---- 98
Query: 127 PSLRAGRIQESASFNNLYVKNLDDDVTEEILDKN-LYVKNINDDVDEIELKQYFSQCGII 185
+++ GR N + + D + EE N +YV +++ D+ + ++K F G I
Sbjct: 99 -NIKVGRPS-----NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKI 152
Query: 186 SSVKIMR-TNRGISKGFGFVCFSNPDEANRAINTLN 220
S + R G KG+GF+ + + A++++N
Sbjct: 153 KSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188
>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 = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 42/156 (26%), Positives = 78/156 (50%), Gaps = 17/156 (10%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDG---KSKGYGFVQYSTQESALNAIEKLYAATVEGMELYA 126
+ Q F+ FG I+S + +S D K KG+ FV+Y E+A A+E++ + + G
Sbjct: 30 IRQAFAPFGPIKS--IDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGR---- 83
Query: 127 PSLRAGRIQESASFNNLYVKNLDDDVTEEILDKN-LYVKNINDDVDEIELKQYFSQCGII 185
+++ GR N + + D + EE N +YV +++ D+ + ++K F G I
Sbjct: 84 -NIKVGRPS-----NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKI 137
Query: 186 SSVKIMR-TNRGISKGFGFVCFSNPDEANRAINTLN 220
S + R G KG+GF+ + + A++++N
Sbjct: 138 KSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 173
>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 = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 51/177 (28%), Positives = 81/177 (45%), Gaps = 33/177 (18%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQD---GKSKGYGFVQYSTQE---SALNA 110
F L+ + L F ++G + + VV +D +S+G+GFV Y+T E +A+NA
Sbjct: 17 FIGGLSFETTDESLRSHFEQWGTL--TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 111 IEKLYAATVEGMELYAPSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDV 170
V+G + P R +L V K ++V I +D
Sbjct: 75 ----RPHKVDG-RVVEPKRAVSREDSQRPGAHLTV-------------KKIFVGGIKEDT 116
Query: 171 DEIELKQYFSQCGIISSVKIMRTNRGISK--GFGFVCFSNPDEANRAI----NTLNG 221
+E L+ YF Q G I ++IM T+RG K GF FV F + D ++ + +T+NG
Sbjct: 117 EEHHLRDYFEQYGKIEVIEIM-TDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNG 172
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 159 KNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRT-NRGISKGFGFVCFSNPDEANRAIN 217
+ L++ ++ + + L+ +F Q G ++ +MR N S+GFGFV ++ +E + A+N
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 51/177 (28%), Positives = 81/177 (45%), Gaps = 33/177 (18%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQD---GKSKGYGFVQYSTQE---SALNA 110
F L+ + L F ++G + + VV +D +S+G+GFV Y+T E +A+NA
Sbjct: 17 FIGGLSFETTDESLRSHFEQWGTL--TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 111 IEKLYAATVEGMELYAPSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDV 170
V+G + P R +L V K ++V I +D
Sbjct: 75 ----RPHKVDG-RVVEPKRAVSREDSQRPGAHLTV-------------KKIFVGGIKEDT 116
Query: 171 DEIELKQYFSQCGIISSVKIMRTNRGISK--GFGFVCFSNPDEANRAI----NTLNG 221
+E L+ YF Q G I ++IM T+RG K GF FV F + D ++ + +T+NG
Sbjct: 117 EEHHLRDYFEQYGKIEVIEIM-TDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNG 172
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 159 KNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRT-NRGISKGFGFVCFSNPDEANRAIN 217
+ L++ ++ + + L+ +F Q G ++ +MR N S+GFGFV ++ +E + A+N
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 51/177 (28%), Positives = 81/177 (45%), Gaps = 33/177 (18%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQD---GKSKGYGFVQYSTQE---SALNA 110
F L+ + L F ++G + + VV +D +S+G+GFV Y+T E +A+NA
Sbjct: 15 FIGGLSFETTDESLRSHFEQWGTL--TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 111 IEKLYAATVEGMELYAPSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDV 170
V+G + P R +L V K ++V I +D
Sbjct: 73 ----RPHKVDG-RVVEPKRAVSREDSQRPGAHLTV-------------KKIFVGGIKEDT 114
Query: 171 DEIELKQYFSQCGIISSVKIMRTNRGISK--GFGFVCFSNPDEANRAI----NTLNG 221
+E L+ YF Q G I ++IM T+RG K GF FV F + D ++ + +T+NG
Sbjct: 115 EEHHLRDYFEQYGKIEVIEIM-TDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNG 170
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 159 KNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRT-NRGISKGFGFVCFSNPDEANRAIN 217
+ L++ ++ + + L+ +F Q G ++ +MR N S+GFGFV ++ +E + A+N
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
>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 = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 51/177 (28%), Positives = 81/177 (45%), Gaps = 33/177 (18%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQD---GKSKGYGFVQYSTQE---SALNA 110
F L+ + L F ++G + + VV +D +S+G+GFV Y+T E +A+NA
Sbjct: 16 FIGGLSFETTDESLRSHFEQWGTL--TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 111 IEKLYAATVEGMELYAPSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDV 170
V+G + P R +L V K ++V I +D
Sbjct: 74 ----RPHKVDG-RVVEPKRAVSREDSQRPGAHLTV-------------KKIFVGGIKEDT 115
Query: 171 DEIELKQYFSQCGIISSVKIMRTNRGISK--GFGFVCFSNPDEANRAI----NTLNG 221
+E L+ YF Q G I ++IM T+RG K GF FV F + D ++ + +T+NG
Sbjct: 116 EEHHLRDYFEQYGKIEVIEIM-TDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNG 171
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 159 KNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRT-NRGISKGFGFVCFSNPDEANRAIN 217
+ L++ ++ + + L+ +F Q G ++ +MR N S+GFGFV ++ +E + A+N
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 51/177 (28%), Positives = 81/177 (45%), Gaps = 33/177 (18%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQD---GKSKGYGFVQYSTQE---SALNA 110
F L+ + L F ++G + + VV +D +S+G+GFV Y+T E +A+NA
Sbjct: 10 FIGGLSFETTDESLRSHFEQWGTL--TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 111 IEKLYAATVEGMELYAPSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDV 170
V+G + P R +L V K ++V I +D
Sbjct: 68 ----RPHKVDG-RVVEPKRAVSREDSQRPGAHLTV-------------KKIFVGGIKEDT 109
Query: 171 DEIELKQYFSQCGIISSVKIMRTNRGISK--GFGFVCFSNPDEANRAI----NTLNG 221
+E L+ YF Q G I ++IM T+RG K GF FV F + D ++ + +T+NG
Sbjct: 110 EEHHLRDYFEQYGKIEVIEIM-TDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNG 165
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 159 KNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRT-NRGISKGFGFVCFSNPDEANRAIN 217
+ L++ ++ + + L+ +F Q G ++ +MR N S+GFGFV ++ +E + A+N
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
>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 = 53.5 bits (127), Expect = 2e-07, Method: Composition-based stats.
Identities = 28/89 (31%), Positives = 51/89 (57%), Gaps = 2/89 (2%)
Query: 155 EILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANR 214
+I+ ++V I+ +DE E++ +F++ G + VKI+ G+SKG+GFV F N + +
Sbjct: 6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQK 65
Query: 215 AINTLNGILFHQKPLYVAIAQTKRERTSY 243
+ + I FH K L + A K+ ++Y
Sbjct: 66 IVES--QINFHGKKLKLGPAIRKQNLSTY 92
Score = 36.2 bits (82), Expect = 0.031, Method: Composition-based stats.
Identities = 12/37 (32%), Positives = 24/37 (64%)
Query: 65 IDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQY 101
+D ++ F+++G ++ K++ + G SKGYGFV +
Sbjct: 21 MDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 52/178 (29%), Positives = 81/178 (45%), Gaps = 35/178 (19%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQD---GKSKGYGFVQYSTQE---SALNA 110
F L+ + L F ++G + + VV +D +S+G+GFV Y+T E +A+NA
Sbjct: 18 FIGGLSFETTDESLRSHFEQWGTL--TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 111 I-EKLYAATVEGMELYAPSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDD 169
K+ VE P R +L V K ++V I +D
Sbjct: 76 RPHKVDGRVVE------PKRAVSREDSQRPGAHLTV-------------KKIFVGGIKED 116
Query: 170 VDEIELKQYFSQCGIISSVKIMRTNRGISK--GFGFVCFSNPDEANRAI----NTLNG 221
+E L+ YF Q G I ++IM T+RG K GF FV F + D ++ + +T+NG
Sbjct: 117 TEEHHLRDYFEQYGKIEVIEIM-TDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNG 173
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 159 KNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRT-NRGISKGFGFVCFSNPDEANRAIN 217
+ L++ ++ + + L+ +F Q G ++ +MR N S+GFGFV ++ +E + A+N
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 43/76 (56%), Gaps = 5/76 (6%)
Query: 158 DKNLYVKNINDDVDEIELKQYFSQCG-IISSVKIMRTNRGISKGFGFVCFSNPDEANRAI 216
D NLYV + + + E++Q FSQ G II+S ++ G+S+G GF+ F EA AI
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 217 NTLNGILFHQKPLYVA 232
LNG QKPL A
Sbjct: 61 KGLNG----QKPLGAA 72
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIEKL 114
+ L T+ ++ Q+FS++G I +S++++ Q G S+G GF+++ + A AI+ L
Sbjct: 5 YVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 52.4 bits (124), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 48/181 (26%), Positives = 84/181 (46%), Gaps = 19/181 (10%)
Query: 55 IPFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKL 114
+ + NL I L Q F G I + K+++ ++ K+ Y FV+Y A A++ L
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 115 YAATVEGMELYAPSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIE 174
+E + A + Q+S+S DD NL+V ++N +VD+
Sbjct: 62 NGKQIENNIVKIN--WAFQSQQSSS----------DDTF------NLFVGDLNVNVDDET 103
Query: 175 LKQYFSQCGIISSVKIMR-TNRGISKGFGFVCFSNPDEANRAINTLNGILFHQKPLYVAI 233
L+ F S +M G S+G+GFV F++ D+A A++++ G + +PL +
Sbjct: 104 LRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW 163
Query: 234 A 234
A
Sbjct: 164 A 164
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 53 TFIPFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVS-QDGKSKGYGFVQYSTQESALNAI 111
TF F +L +D+ L F F S V+ Q G S+GYGFV +++Q+ A NA+
Sbjct: 87 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 146
Query: 112 EKLYAATVEGMEL 124
+ + + G L
Sbjct: 147 DSMQGQDLNGRPL 159
>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 = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTN-RGISKGFGFVCFSNPDEANRAINT 218
NL V + ++ + EL+ FS G + S K++R G S G+GFV + +A RAINT
Sbjct: 6 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 65
Query: 219 LNGILFHQKPLYVAIAQ 235
LNG+ K + V+ A+
Sbjct: 66 LNGLRLQSKTIKVSYAR 82
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 37/63 (58%), Gaps = 6/63 (9%)
Query: 69 KLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAP 127
+L +FS G+++S+K++ + G S GYGFV Y T + A AI T+ G+ L +
Sbjct: 20 ELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN-----TLNGLRLQSK 74
Query: 128 SLR 130
+++
Sbjct: 75 TIK 77
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 40/168 (23%), Positives = 73/168 (43%), Gaps = 21/168 (12%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDG---KSKGYGFVQYSTQESALNAIEK 113
F + T L ++F ++G + V+ + +SKG FV + T+++AL A
Sbjct: 19 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 78
Query: 114 LYAATV-EGMELYAPSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDE 172
L+ V GM + + +K D + + D+ L++ I+ E
Sbjct: 79 LHNMKVLPGMH-----------------HPIQMKPADSEKNNAVEDRKLFIGMISKKCTE 121
Query: 173 IELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINTLN 220
+++ FS G I +I+R G+S+G FV F+ A AI ++
Sbjct: 122 NDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 169
Score = 41.2 bits (95), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 32/50 (64%), Gaps = 1/50 (2%)
Query: 73 IFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLY-AATVEG 121
+FS FG I+ +++ DG S+G FV ++T+ A AI+ ++ A T+EG
Sbjct: 127 MFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEG 176
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 40/168 (23%), Positives = 73/168 (43%), Gaps = 21/168 (12%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDG---KSKGYGFVQYSTQESALNAIEK 113
F + T L ++F ++G + V+ + +SKG FV + T+++AL A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 114 LYAATV-EGMELYAPSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDE 172
L+ V GM + + +K D + + D+ L++ I+ E
Sbjct: 67 LHNMKVLPGMH-----------------HPIQMKPADSEKNNAVEDRKLFIGMISKKCTE 109
Query: 173 IELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINTLN 220
+++ FS G I +I+R G+S+G FV F+ A AI ++
Sbjct: 110 NDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 32/50 (64%), Gaps = 1/50 (2%)
Query: 73 IFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLY-AATVEG 121
+FS FG I+ +++ DG S+G FV ++T+ A AI+ ++ A T+EG
Sbjct: 115 MFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEG 164
>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 = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTN-RGISKGFGFVCFSNPDEANRAINT 218
NL V + + + EL+ FS G + S K++R G S G+GFV + +A RAINT
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 219 LNGILFHQKPLYVAIAQ 235
LNG+ K + V+ A+
Sbjct: 81 LNGLRLQSKTIKVSYAR 97
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 37/63 (58%), Gaps = 6/63 (9%)
Query: 69 KLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAP 127
+L +FS G+++S+K++ + G S GYGFV Y T + A AI T+ G+ L +
Sbjct: 35 ELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN-----TLNGLRLQSK 89
Query: 128 SLR 130
+++
Sbjct: 90 TIK 92
>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 = 50.8 bits (120), Expect = 1e-06, Method: Composition-based stats.
Identities = 27/84 (32%), Positives = 48/84 (57%), Gaps = 2/84 (2%)
Query: 155 EILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANR 214
+I+ ++V I+ +DE E++ +F++ G + VKI+ G+SKG+GFV F N + +
Sbjct: 6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQK 65
Query: 215 AINTLNGILFHQKPLYVAIAQTKR 238
+ + I FH K L + A K+
Sbjct: 66 IVES--QINFHGKKLKLGPAIRKQ 87
Score = 36.2 bits (82), Expect = 0.026, Method: Composition-based stats.
Identities = 12/37 (32%), Positives = 24/37 (64%)
Query: 65 IDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQY 101
+D ++ F+++G ++ K++ + G SKGYGFV +
Sbjct: 21 MDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
>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 = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 42/156 (26%), Positives = 75/156 (48%), Gaps = 17/156 (10%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDG---KSKGYGFVQYSTQESALNAIEKLYAATVEGMELYA 126
+ Q F+ FG I+S + S D K KG+ FV+Y E+A A+E+ + + G
Sbjct: 29 IRQAFAPFGPIKS--IDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGR---- 82
Query: 127 PSLRAGRIQESASFNNLYVKNLDDDVTEEILDKN-LYVKNINDDVDEIELKQYFSQCGII 185
+++ GR N + + D + EE N +YV +++ D+ + ++K F G I
Sbjct: 83 -NIKVGRPS-----NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKI 136
Query: 186 SSVKIMR-TNRGISKGFGFVCFSNPDEANRAINTLN 220
S + R G KG+GF+ + + A+++ N
Sbjct: 137 KSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN 172
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 50.8 bits (120), Expect = 1e-06, Method: Composition-based stats.
Identities = 27/84 (32%), Positives = 48/84 (57%), Gaps = 2/84 (2%)
Query: 155 EILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANR 214
+I+ ++V I+ +DE E++ +F++ G + VKI+ G+SKG+GFV F N + +
Sbjct: 7 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQK 66
Query: 215 AINTLNGILFHQKPLYVAIAQTKR 238
+ + I FH K L + A K+
Sbjct: 67 IVES--QINFHGKKLKLGPAIRKQ 88
Score = 36.2 bits (82), Expect = 0.029, Method: Composition-based stats.
Identities = 12/37 (32%), Positives = 24/37 (64%)
Query: 65 IDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQY 101
+D ++ F+++G ++ K++ + G SKGYGFV +
Sbjct: 22 MDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 58
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 50.1 bits (118), Expect = 2e-06, Method: Composition-based stats.
Identities = 31/79 (39%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 159 KNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINT 218
K L+V NI + +L+Q F Q G I V+I+ RG SKGFGFV F N +A+RA
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREK 88
Query: 219 LNGILFHQKPLYVAIAQTK 237
L+G + + + V A +
Sbjct: 89 LHGTVVEGRKIEVNNATAR 107
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATVEGMEL 124
L Q+F +FG I +++ ++ G SKG+GFV + A A EKL+ VEG ++
Sbjct: 46 LRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKI 99
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 31/79 (39%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 159 KNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINT 218
K L+V NI + +L+Q F Q G I V+I+ RG SKGFGFV F N +A+RA
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREK 74
Query: 219 LNGILFHQKPLYVAIAQTK 237
L+G + + + V A +
Sbjct: 75 LHGTVVEGRKIEVNNATAR 93
Score = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATVEGMEL 124
L Q+F +FG I +++ ++ G SKG+GFV + A A EKL+ VEG ++
Sbjct: 32 LRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKI 85
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 48.9 bits (115), Expect = 5e-06, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 40/75 (53%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINTLN 220
L++ +N + +E LK F + G IS V +++ S+GF F+ F NP +A A +N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 221 GILFHQKPLYVAIAQ 235
G H K + V A+
Sbjct: 70 GKSLHGKAIKVEQAK 84
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 6/79 (7%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYA--- 126
L +F K G I ++ + KS+G+ F+ + A NA + + ++ G +
Sbjct: 24 LKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA 83
Query: 127 --PSLRA-GRIQESASFNN 142
PS ++ GR + AS N
Sbjct: 84 KKPSFQSGGRRRPPASSRN 102
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 48.5 bits (114), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 49/84 (58%), Gaps = 2/84 (2%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGII-SSVKIMR-TNRGISKGFGFVCFSNPDEANRAINT 218
+++ N++ ++DE L FS G+I + KIMR + G SKG+ F+ F++ D ++ AI
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 219 LNGILFHQKPLYVAIAQTKRERTS 242
+NG +P+ V+ A K + S
Sbjct: 68 MNGQYLCNRPITVSYAFKKDSKGS 91
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 35/60 (58%), Gaps = 2/60 (3%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDI-QSSKVVVSQD-GKSKGYGFVQYSTQESALNAIEKL 114
F NL ID L+ FS FG I Q+ K++ D G SKGY F+ +++ +++ AIE +
Sbjct: 9 FIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAM 68
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 48.1 bits (113), Expect = 6e-06, Method: Composition-based stats.
Identities = 25/79 (31%), Positives = 42/79 (53%)
Query: 157 LDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAI 216
L ++V N++ V +LK+ FS G++ I+ G S+G G V F EA +AI
Sbjct: 14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAI 73
Query: 217 NTLNGILFHQKPLYVAIAQ 235
+ NG L +P++V + +
Sbjct: 74 SMFNGQLLFDRPMHVKMDE 92
Score = 34.3 bits (77), Expect = 0.098, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 29/55 (52%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAI 111
F NL + KL ++FS G + + ++ +DGKS+G G V + A+ AI
Sbjct: 19 FVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAI 73
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 47.8 bits (112), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 31/110 (28%), Positives = 51/110 (46%), Gaps = 13/110 (11%)
Query: 17 GTPFSLYVGDLDSTDLLRLCSALIASI-----DVHSAMATPTFIPFTV--------NLAS 63
G P +++ +RL S +A I D + P I F NL+
Sbjct: 47 GEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGAALTVKNLSP 106
Query: 64 TIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEK 113
+ N L Q FS+FG ++ + VVV G++ G GFV+++ + A A+E+
Sbjct: 107 VVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALER 156
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 40/161 (24%), Positives = 75/161 (46%), Gaps = 31/161 (19%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYA 116
F NL + I ++F ++G+ S+V +++D +G+GF++ ++ + ++
Sbjct: 26 FVGNLPTDITEEDFKRLFERYGE--PSEVFINRD---RGFGFIRLESR-----TLAEIAK 75
Query: 117 ATVEGMELYAPSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELK 176
A ++G L + LR I+ + L VKNL V+ E+L+
Sbjct: 76 AELDGTILKSRPLR---IRFATHGAALTVKNLSPVVSNELLE------------------ 114
Query: 177 QYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAIN 217
Q FSQ G + ++ +RG + G GFV F+ A +A+
Sbjct: 115 QAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALE 155
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 5/75 (6%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINTL 219
L+V N+ D+ E + K+ F + G S V I R +GFGF+ + A A L
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINR-----DRGFGFIRLESRTLAEIAKAEL 78
Query: 220 NGILFHQKPLYVAIA 234
+G + +PL + A
Sbjct: 79 DGTILKSRPLRIRFA 93
>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 = 47.8 bits (112), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 38/163 (23%), Positives = 68/163 (41%), Gaps = 19/163 (11%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDG---KSKGYGFVQYSTQESALNAIEK 113
F + T L ++F ++G + V+ + +SKG FV + T+++AL A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 114 LYAATVEGMELYAPSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEI 173
L+ V + + K D + + D+ L++ I+ E
Sbjct: 67 LHNXKVL----------------PGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTEN 110
Query: 174 ELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAI 216
+++ FS G I +I+R G+S+G FV F+ A AI
Sbjct: 111 DIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 74 FSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLY-AATVEGM 122
FS FG I+ +++ DG S+G FV ++T+ A AI+ + A T EG
Sbjct: 116 FSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIKAXHQAQTXEGC 165
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNR-GISKGFGFVCFSNPDEANRAINT 218
NL V + D+ + EL F G I++ +IMR + G S G+ FV F++ ++ RAI
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 219 LNGILFHQKPLYVAIAQ 235
LNGI K L V+ A+
Sbjct: 65 LNGITVRNKRLKVSYAR 81
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 47.8 bits (112), Expect = 1e-05, Method: Composition-based stats.
Identities = 26/68 (38%), Positives = 40/68 (58%), Gaps = 6/68 (8%)
Query: 70 LHQIFSKFGDIQSSKVVV-SQDGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAPS 128
L IF FG I+S ++++ S+ G+SKGYGF+ +S E A A+E+L G EL
Sbjct: 43 LRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL-----NGFELAGRP 97
Query: 129 LRAGRIQE 136
++ G + E
Sbjct: 98 MKVGHVTE 105
Score = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMR-TNRGISKGFGFVCFSNPDEANRAINTL 219
LYV +++ ++ E L+ F G I S+++M + G SKG+GF+ FS+ + A +A+ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 220 NGILFHQKPLYVA 232
NG +P+ V
Sbjct: 89 NGFELAGRPMKVG 101
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 47.4 bits (111), Expect = 1e-05, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMR-TNRGISKGFGFVCFSNPDEANRAINTL 219
LYV +++ ++ E L+ F G I ++ +M+ ++ G SKG+GF+ FS+ + A RA+ L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 220 NGILFHQKPLYVA 232
NG +P+ V
Sbjct: 68 NGFELAGRPMRVG 80
Score = 44.7 bits (104), Expect = 8e-05, Method: Composition-based stats.
Identities = 26/68 (38%), Positives = 36/68 (52%), Gaps = 6/68 (8%)
Query: 70 LHQIFSKFGDIQSSKVVVSQD-GKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAPS 128
L IF FG I + ++ D G+SKGYGF+ +S E A A+E+L G EL
Sbjct: 22 LRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL-----NGFELAGRP 76
Query: 129 LRAGRIQE 136
+R G + E
Sbjct: 77 MRVGHVTE 84
>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 = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 38/159 (23%), Positives = 72/159 (45%), Gaps = 26/159 (16%)
Query: 59 VNLASTIDNWKLHQIFSKFGDIQSSKVVVS-QDGKSKGYGFVQYSTQESALNAIEKLYAA 117
+N +T DN L + F K+G + K++ G+S+G+GF+ + S ++ +
Sbjct: 11 LNWDTTEDN--LREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQH-- 66
Query: 118 TVEGMELYAPSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQ 177
++G ++ P R ++ + ++V I DV E ++
Sbjct: 67 ILDG-KVIDPKRAIPRDEQDKT-------------------GKIFVGGIGPDVRPKEFEE 106
Query: 178 YFSQCGIISSVKIM-RTNRGISKGFGFVCFSNPDEANRA 215
+FSQ G I ++M + G S+GFGFV + + D +R
Sbjct: 107 FFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRV 145
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 30/105 (28%), Positives = 54/105 (51%), Gaps = 9/105 (8%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRT-NRGISKGFGFVCFSNP---DEANRA 215
+++ +N D E L++YF + G ++ +KIM+ G S+GFGF+ F P DE +
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 216 INTLNGILFHQKPLYVAIAQTKRERTSYLRIMYAKQGPGLASTNF 260
+ L+G + K AI + ++++T +I GP + F
Sbjct: 65 QHILDGKVIDPK---RAIPRDEQDKTG--KIFVGGIGPDVRPKEF 104
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 44/77 (57%), Gaps = 5/77 (6%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMR---TNRGISKGFGFVCFSNPDEANRAIN 217
L+V ++ D +E L+Q FS+ G IS V +++ T R S+GFGFV F N D+A A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQR--SRGFGFVTFENIDDAKDAMM 72
Query: 218 TLNGILFHQKPLYVAIA 234
+NG + + V A
Sbjct: 73 AMNGKSVDGRQIRVDQA 89
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 44/79 (55%), Gaps = 5/79 (6%)
Query: 49 MATPTFIPFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQD---GKSKGYGFVQYSTQE 105
MA+ F L+ + L Q+FSK+G I S+VVV +D +S+G+GFV + +
Sbjct: 8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQI--SEVVVVKDRETQRSRGFGFVTFENID 65
Query: 106 SALNAIEKLYAATVEGMEL 124
A +A+ + +V+G ++
Sbjct: 66 DAKDAMMAMNGKSVDGRQI 84
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 30/87 (34%), Positives = 44/87 (50%), Gaps = 9/87 (10%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQD-GKSKGYGFVQYSTQESALNAIEKLY 115
F N+ +L IFS+ G + S ++V ++ GK KGYGF +Y QE+AL+A+ L
Sbjct: 12 FVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLN 71
Query: 116 AATVEGMELYAPSLRAGRIQESASFNN 142
G RA R+ +AS N
Sbjct: 72 GREFSG--------RALRVDNAASEKN 90
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 45/83 (54%), Gaps = 1/83 (1%)
Query: 159 KNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNR-GISKGFGFVCFSNPDEANRAIN 217
++++V NI + E +LK FS+ G + S +++ G KG+GF + + + A A+
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 218 TLNGILFHQKPLYVAIAQTKRER 240
LNG F + L V A +++ +
Sbjct: 69 NLNGREFSGRALRVDNAASEKNK 91
>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 = 44.7 bits (104), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 28/86 (32%), Positives = 46/86 (53%), Gaps = 5/86 (5%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIM---RTNRGISKGFGFVCFSNPDEANRAI 216
NL++ ++ + + +L Q F G + S K+ +TN +SK FGFV + NP A AI
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTN--LSKCFGFVSYDNPVSAQAAI 84
Query: 217 NTLNGILFHQKPLYVAIAQTKRERTS 242
++NG K L V + ++K + S
Sbjct: 85 QSMNGFQIGMKRLKVQLKRSKNDSKS 110
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVV-SQDGKSKGYGFVQYSTQESALNAIEKL 114
F +L + L Q+F FG++ S+KV + Q SK +GFV Y SA AI+ +
Sbjct: 29 FIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 44.7 bits (104), Expect = 8e-05, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRG----ISKGFGFVCFSNPDEANRAI 216
L++KN+N E LK FS+ G I S I + +S GFGFV + P++A +A+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 217 NTLNGILFHQKPLYVAIAQ 235
L G L V I++
Sbjct: 68 KQLQGHTVDGHKLEVRISE 86
Score = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 42/87 (48%), Gaps = 10/87 (11%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGK----SKGYGFVQYSTQESALNAIE 112
F NL + L +FSK G I+S + ++ S G+GFV+Y E A A++
Sbjct: 9 FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 68
Query: 113 KLYAATVEGMELYAPSLRAGRIQESAS 139
+L TV+G +L RI E A+
Sbjct: 69 QLQGHTVDGHKLEV------RISERAT 89
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 27/93 (29%), Positives = 46/93 (49%), Gaps = 1/93 (1%)
Query: 47 SAMATPTFIPFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVS-QDGKSKGYGFVQYSTQE 105
S MAT + + LA +D+ LH F FGDI ++ + + K +G+ FV++ E
Sbjct: 6 SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 65
Query: 106 SALNAIEKLYAATVEGMELYAPSLRAGRIQESA 138
A AI+ + + + G + + RI+ES
Sbjct: 66 DAAAAIDNMNESELFGRTIRVNLAKPMRIKESG 98
Score = 31.2 bits (69), Expect = 0.87, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 1/83 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKI-MRTNRGISKGFGFVCFSNPDEANRAINTL 219
LYV + ++VD+ L F G I+ ++I + +GF FV F ++A AI+ +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 220 NGILFHQKPLYVAIAQTKRERTS 242
N + + V +A+ R + S
Sbjct: 75 NESELFGRTIRVNLAKPMRIKES 97
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 44/85 (51%), Gaps = 3/85 (3%)
Query: 154 EEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTN-RGISKGFGFVCFSNPDEA 212
E I D NLYV N+ + + +L F + G I I+R G +G FV ++ +EA
Sbjct: 9 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 68
Query: 213 NRAINTLNGILFH--QKPLYVAIAQ 235
AI+ LN ++ +PL V +A+
Sbjct: 69 QEAISALNNVIPEGGSQPLSVRLAE 93
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMR-TNRGISKGFGFVCFSNPDEANRAINT 218
NL+V ++N +VD+ L+ F S +M G S+G+GFV F++ D+A A+++
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 219 LNGILFHQKPLYVAIA 234
+ G + +PL + A
Sbjct: 63 MQGQDLNGRPLRINWA 78
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 53 TFIPFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVS-QDGKSKGYGFVQYSTQESALNAI 111
TF F +L +D+ L F F S V+ Q G S+GYGFV +++Q+ A NA+
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 112 EKLYAATVEGMEL 124
+ + + G L
Sbjct: 61 DSMQGQDLNGRPL 73
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 40/161 (24%), Positives = 71/161 (44%), Gaps = 31/161 (19%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYA 116
F NL I ++ ++F K+G ++ +V + +D KG+GF++ T+ + ++
Sbjct: 26 FVGNLPPDITEEEMRKLFEKYG--KAGEVFIHKD---KGFGFIRLETR-----TLAEIAK 75
Query: 117 ATVEGMELYAPSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELK 176
++ M L LR SAS L V+NL V+ E+L+
Sbjct: 76 VELDNMPLRGKQLRVRFACHSAS---LTVRNLPQYVSNELLE------------------ 114
Query: 177 QYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAIN 217
+ FS G + ++ +RG G G V FS A +A++
Sbjct: 115 EAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALD 155
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 31/54 (57%)
Query: 60 NLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEK 113
NL + N L + FS FG ++ + V+V G+ G G V++S + +A A+++
Sbjct: 103 NLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDR 156
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 24/61 (39%), Positives = 34/61 (55%), Gaps = 5/61 (8%)
Query: 61 LASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATVE 120
+AS + + + Q FS FG I +V KGY FV++ST ESA +AI + T+E
Sbjct: 33 IASGLTDQLMRQTFSPFGQIMEIRVF-----PEKGYSFVRFSTHESAAHAIVSVNGTTIE 87
Query: 121 G 121
G
Sbjct: 88 G 88
Score = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 7/74 (9%)
Query: 150 DDVTEEILDKN--LYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFS 207
+DV + KN +Y I + + ++Q FS G I +++ KG+ FV FS
Sbjct: 15 EDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP-----EKGYSFVRFS 69
Query: 208 NPDEANRAINTLNG 221
+ A AI ++NG
Sbjct: 70 THESAAHAIVSVNG 83
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKI-MRTNRGISKGFGFVCFSNPDEANRAINT 218
NL++ ++ + + +L F G + S K+ + +SK FGFV F NPD A AI
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 219 LNGILFHQKPLYVAIAQ 235
+NG K L V + +
Sbjct: 102 MNGFQVGTKRLKVQLKK 118
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 27/86 (31%), Positives = 42/86 (48%), Gaps = 7/86 (8%)
Query: 155 EILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANR 214
E+ + L+V+ DV E EL + F G + VKI+ GF FV F + A +
Sbjct: 28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAK 80
Query: 215 AINTLNGILFHQKPLYVAIAQTKRER 240
AI ++G F +PL V ++ +R
Sbjct: 81 AIEEVHGKSFANQPLEVVYSKLPAKR 106
Score = 33.1 bits (74), Expect = 0.22, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 36/69 (52%), Gaps = 11/69 (15%)
Query: 56 PFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLY 115
PF +++ + +L++IF FG ++ K++ G+ FV++ ESA AIE+++
Sbjct: 38 PFPLDVQES----ELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVH 86
Query: 116 AATVEGMEL 124
+ L
Sbjct: 87 GKSFANQPL 95
>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 = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/103 (25%), Positives = 49/103 (47%), Gaps = 16/103 (15%)
Query: 134 IQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRT 193
+ E+ + +Y+ NL++ + ++ L K+LY FSQ G I + + R+
Sbjct: 3 VPETRPNHTIYINNLNEKIKKDELKKSLYA--------------IFSQFGQILDILVSRS 48
Query: 194 NRGISKGFGFVCFSNPDEANRAINTLNGILFHQKPLYVAIAQT 236
+ +G FV F A A+ ++ G F+ KP+ + A+T
Sbjct: 49 LK--MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 89
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 46/91 (50%), Gaps = 8/91 (8%)
Query: 146 KNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMR-TNRGISKGFGFV 204
+ DD+ T + V N+++D E +L++ F G IS + + + G SKGF F+
Sbjct: 10 RRADDNAT-------IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFI 62
Query: 205 CFSNPDEANRAINTLNGILFHQKPLYVAIAQ 235
F ++A RAI ++G + L V A+
Sbjct: 63 SFHRREDAARAIAGVSGFGYDHLILNVEWAK 93
Score = 35.0 bits (79), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 9/81 (11%)
Query: 59 VNLASTIDNWKLHQIFSKFGDIQSSKVVVSQD---GKSKGYGFVQYSTQESALNAIEKL- 114
NL+ L ++F FG I S++ +++D G+SKG+ F+ + +E A AI +
Sbjct: 21 TNLSEDTRETDLQELFRPFGSI--SRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVS 78
Query: 115 ---YAATVEGMELYAPSLRAG 132
Y + +E PS +G
Sbjct: 79 GFGYDHLILNVEWAKPSTNSG 99
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 35/64 (54%)
Query: 158 DKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAIN 217
D+ L+V +N E ++ + F G+I ++R G SKG FV FS+ EA AI+
Sbjct: 15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIH 74
Query: 218 TLNG 221
L+G
Sbjct: 75 ALHG 78
Score = 35.0 bits (79), Expect = 0.057, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 25/46 (54%)
Query: 72 QIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAA 117
++F FG I V+ DG SKG FV++S+ A AI L+ +
Sbjct: 34 RLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGS 79
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 33/69 (47%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINTL 219
NLY+ N+ +DE EL+ G + S +I+R + G S+G GF + ++ I
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 220 NGILFHQKP 228
NG P
Sbjct: 87 NGKFIKTPP 95
Score = 32.3 bits (72), Expect = 0.37, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 26/49 (53%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQE 105
+ NL ++D +L + FG + S++++ G S+G GF + + E
Sbjct: 29 YISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTE 77
>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 = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 49/105 (46%), Gaps = 16/105 (15%)
Query: 141 NNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKG 200
+ +Y+ N++D + +E L ++LY FSQ G + + ++T + +G
Sbjct: 7 HTIYINNMNDKIKKEELKRSLYA--------------LFSQFGHVVDIVALKTMK--MRG 50
Query: 201 FGFVCFSNPDEANRAINTLNGILFHQKPLYVAIAQTKRERTSYLR 245
FV F + A+ L G F+ KP+ + A+T + S +R
Sbjct: 51 QAFVIFKELGSSTNALRQLQGFPFYGKPMRIQYAKTDSDIISKMR 95
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/103 (25%), Positives = 49/103 (47%), Gaps = 16/103 (15%)
Query: 134 IQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRT 193
+ E+ + +Y+ NL++ + ++ L K+LY FSQ G I + + R+
Sbjct: 2 VPETRPNHTIYINNLNEKIKKDELKKSLYA--------------IFSQFGQILDILVSRS 47
Query: 194 NRGISKGFGFVCFSNPDEANRAINTLNGILFHQKPLYVAIAQT 236
+ +G FV F A A+ ++ G F+ KP+ + A+T
Sbjct: 48 LK--MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 88
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 26/103 (25%), Positives = 49/103 (47%), Gaps = 16/103 (15%)
Query: 134 IQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRT 193
+ E+ + +Y+ NL++ + ++ L K+LY FSQ G I + + R+
Sbjct: 3 VPETRPNHTIYINNLNEKIKKDELKKSLYA--------------IFSQFGQILDILVSRS 48
Query: 194 NRGISKGFGFVCFSNPDEANRAINTLNGILFHQKPLYVAIAQT 236
+ +G FV F A A+ ++ G F+ KP+ + A+T
Sbjct: 49 LK--MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 89
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 41.2 bits (95), Expect = 8e-04, Method: Composition-based stats.
Identities = 26/81 (32%), Positives = 40/81 (49%), Gaps = 7/81 (8%)
Query: 155 EILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANR 214
E+ + L+V+ DV E EL + F G + VKI+ GF FV F + A +
Sbjct: 1 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAK 53
Query: 215 AINTLNGILFHQKPLYVAIAQ 235
AI ++G F +PL V ++
Sbjct: 54 AIEEVHGKSFANQPLEVVYSK 74
Score = 32.7 bits (73), Expect = 0.33, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 36/69 (52%), Gaps = 11/69 (15%)
Query: 56 PFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLY 115
PF +++ + +L++IF FG ++ K++ G+ FV++ ESA AIE+++
Sbjct: 11 PFPLDVQES----ELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVH 59
Query: 116 AATVEGMEL 124
+ L
Sbjct: 60 GKSFANQPL 68
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 18/43 (41%), Positives = 32/43 (74%), Gaps = 1/43 (2%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIE 112
+H+IFSKFG I ++ +DGK+KGY F++Y++ A++A++
Sbjct: 38 IHKIFSKFGKI-TNDFYPEEDGKTKGYIFLEYASPAHAVDAVK 79
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 47/92 (51%), Gaps = 1/92 (1%)
Query: 152 VTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTN-RGISKGFGFVCFSNPD 210
++E D +YV +++ V E L + F Q G + + + + G +G+GFV F + +
Sbjct: 9 ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 68
Query: 211 EANRAINTLNGILFHQKPLYVAIAQTKRERTS 242
+A+ AI ++ I + KP+ V A + S
Sbjct: 69 DADYAIKIMDMIKLYGKPIRVNKASAHNKNLS 100
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 18/43 (41%), Positives = 32/43 (74%), Gaps = 1/43 (2%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIE 112
+H+IFSKFG I ++ +DGK+KGY F++Y++ A++A++
Sbjct: 24 IHKIFSKFGKI-TNDFYPEEDGKTKGYIFLEYASPAHAVDAVK 65
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINTLN 220
++V+N+ D LK F++CG + I N G SKG G V F +P+ A RA +N
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVKFESPEVAERACRMMN 69
Query: 221 GILFHQKPLYVAI 233
G+ + + V I
Sbjct: 70 GMKLSGREIDVRI 82
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 26/85 (30%), Positives = 47/85 (55%), Gaps = 6/85 (7%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSV---KIMRTNRGISKGFGFVCFSNPDEANRAI 216
+L+V ++ DVD+ L ++F + + S K++ G+SKG+GFV F++ E RA+
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVK--VYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRAL 68
Query: 217 NTLNGIL-FHQKPLYVAIAQTKRER 240
G + KP+ +++A K R
Sbjct: 69 TECQGAVGLGSKPVRLSVAIPKASR 93
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 47 SAMATPTFIPFTVNLASTIDNWKLHQIFSK-FGDIQSSKVVVSQDGKSKGYGFVQYSTQE 105
S + P + F +L +D+ L++ F K + + KVV+ Q G SKGYGFV+++ +
Sbjct: 3 SGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDEL 62
Query: 106 SALNAIEKLYAA 117
A+ + A
Sbjct: 63 EQKRALTECQGA 74
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINTLN 220
++V+N+ D LK F++CG + I N G SKG G V F +P+ A RA +N
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVKFESPEVAERACRMMN 66
Query: 221 GILFHQKPLYVAI 233
G+ + + V I
Sbjct: 67 GMKLSGREIDVRI 79
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 172 EIELKQYFSQCGIISSVKIMRTNRGI-SKGFGFVCFSNPDEANRAINTLNGILFHQKPLY 230
E +L++ FS+ G I+ V I+ + S+GF FV F N D+A A NG+ + +
Sbjct: 26 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 85
Query: 231 VAIAQTKRERT 241
V + TKR T
Sbjct: 86 VDFSITKRPHT 96
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDG-KSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAPS 128
L ++FSK+G I +V Q +S+G+ FV + + A A E+ GMEL
Sbjct: 29 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER-----ANGMELDGRR 83
Query: 129 LR 130
+R
Sbjct: 84 IR 85
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 23/63 (36%), Positives = 34/63 (53%)
Query: 159 KNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINT 218
+ L+V +N E ++++ F G I I+R G SKG FV +S+ EA AIN
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINA 75
Query: 219 LNG 221
L+G
Sbjct: 76 LHG 78
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAA 117
+ ++F FG+I+ ++ DG SKG FV+YS+ A AI L+ +
Sbjct: 32 VRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALHGS 79
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 172 EIELKQYFSQCGIISSVKIMRTNRGI-SKGFGFVCFSNPDEANRAINTLNGILFHQKPLY 230
E +L++ FS+ G I+ V I+ + S+GF FV F N D+A A NG+ + +
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 88
Query: 231 VAIAQTKRERT 241
V + TKR T
Sbjct: 89 VDFSITKRPHT 99
Score = 33.5 bits (75), Expect = 0.19, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDG-KSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAPS 128
L ++FSK+G I +V Q +S+G+ FV + + A A E+ GMEL
Sbjct: 32 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER-----ANGMELDGRR 86
Query: 129 LR 130
+R
Sbjct: 87 IR 88
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 3/85 (3%)
Query: 158 DKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAIN 217
D+ L+V + + ++++ F G I ++R G SKG FV F EA AIN
Sbjct: 12 DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAIN 71
Query: 218 TLNG---ILFHQKPLYVAIAQTKRE 239
TL+ + L V A T++E
Sbjct: 72 TLHSSRTLPGASSSLVVKFADTEKE 96
Score = 36.2 bits (82), Expect = 0.027, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 26/48 (54%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAA 117
+ ++F FG I V+ DG SKG FV++ T A AI L+++
Sbjct: 29 VRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLHSS 76
>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 = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 43/84 (51%), Gaps = 6/84 (7%)
Query: 48 AMATPTFIPFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVS-QDGKSKGYGFVQYSTQES 106
+MAT + + LA +D+ LH F FGDI ++ + + K +G+ FV++ E
Sbjct: 2 SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61
Query: 107 ALNAIEKLYAATVEGMELYAPSLR 130
A AI+ + + EL+ ++R
Sbjct: 62 AAAAIDNMNES-----ELFGRTIR 80
Score = 29.6 bits (65), Expect = 2.8, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKI-MRTNRGISKGFGFVCFSNPDEANRAINTL 219
LYV + ++VD+ L F G I+ ++I + +GF FV F ++A AI+ +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 220 N 220
N
Sbjct: 70 N 70
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 59 VNLASTIDNWKLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIEKLYAA 117
NL ++ + ++ FG ++ +V S+ G+SKGYGF +Y ++SA A L
Sbjct: 101 ANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGK 160
Query: 118 TVEGMELYAPSLRAGRI 134
+ LY AG++
Sbjct: 161 PLGPRTLYVHWTDAGQL 177
Score = 31.6 bits (70), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 1/94 (1%)
Query: 139 SFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNR-GI 197
+F+ ++ + V + D L V N+ + + + ++ G + ++ + R G
Sbjct: 76 AFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQ 135
Query: 198 SKGFGFVCFSNPDEANRAINTLNGILFHQKPLYV 231
SKG+GF + D A RA + L G + LYV
Sbjct: 136 SKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 26/96 (27%), Positives = 43/96 (44%), Gaps = 9/96 (9%)
Query: 151 DVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVK---------IMRTNRGISKGF 201
D E+ + +YV+ +ND V +L +F QCG++ K + G KG
Sbjct: 8 DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 67
Query: 202 GFVCFSNPDEANRAINTLNGILFHQKPLYVAIAQTK 237
V + +P A A+ +G F L V++A+ K
Sbjct: 68 ATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 103
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 59 VNLASTIDNWKLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIEKLYAA 117
NL ++ + ++ FG ++ +V S+ G+SKGYGF +Y ++SA A L
Sbjct: 101 ANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGK 160
Query: 118 TVEGMELYAPSLRAGRI 134
+ LY AG++
Sbjct: 161 PLGPRTLYVHWTDAGQL 177
Score = 31.6 bits (70), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 1/94 (1%)
Query: 139 SFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNR-GI 197
+F+ ++ + V + D L V N+ + + + ++ G + ++ + R G
Sbjct: 76 AFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQ 135
Query: 198 SKGFGFVCFSNPDEANRAINTLNGILFHQKPLYV 231
SKG+GF + D A RA + L G + LYV
Sbjct: 136 SKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
>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 = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 59 VNLASTIDNWKLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIEKLYAA 117
NL ++ + ++ FG ++ +V S+ G+SKGYGF +Y ++SA A L
Sbjct: 99 ANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGK 158
Query: 118 TVEGMELYAPSLRAGRI 134
+ LY AG++
Sbjct: 159 PLGPRTLYVHWTDAGQL 175
Score = 31.6 bits (70), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 1/94 (1%)
Query: 139 SFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNR-GI 197
+F+ ++ + V + D L V N+ + + + ++ G + ++ + R G
Sbjct: 74 AFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQ 133
Query: 198 SKGFGFVCFSNPDEANRAINTLNGILFHQKPLYV 231
SKG+GF + D A RA + L G + LYV
Sbjct: 134 SKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 167
>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 = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 54 FIPFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIE 112
F F +L+ I + F+ FG I ++VV GKSKGYGFV + + A NAI+
Sbjct: 16 FHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 75
Query: 113 KLYAATVEGMEL 124
++ + G ++
Sbjct: 76 QMGGQWLGGRQI 87
Score = 35.4 bits (80), Expect = 0.044, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMR-TNRGISKGFGFVCFSNPDEANRAINT 218
+++V +++ ++ ++K F+ G IS ++++ G SKG+GFV F N +A AI
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 219 LNG 221
+ G
Sbjct: 77 MGG 79
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 172 EIELKQYFSQCGIISSVKIMRTNRGI-SKGFGFVCFSNPDEANRAINTLNGILFHQKPLY 230
E +L++ FS+ G I+ V I+ + S+GF FV F N D+A A NG+ + +
Sbjct: 60 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 119
Query: 231 VAIAQTKR 238
V + TKR
Sbjct: 120 VDFSITKR 127
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 8/75 (10%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDG-KSKGYGFVQYSTQESALNAIEKLY 115
F ++L +T L ++FSK+G I +V Q +S+G+ FV + + A A E+
Sbjct: 52 FGLSLYTT--ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER-- 107
Query: 116 AATVEGMELYAPSLR 130
GMEL +R
Sbjct: 108 ---ANGMELDGRRIR 119
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISS-VKIMRTNRGISKGFGFVCFSNPDEANRAIN 217
++V I + E EL++YF + G+++ V I + +GFGF+ F + ++A+N
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 4/65 (6%)
Query: 157 LDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAI 216
LD +YV N+ ++ ++ EL++ F G + SV + R GF FV F +P +A A+
Sbjct: 72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAV 127
Query: 217 NTLNG 221
L+G
Sbjct: 128 RELDG 132
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 4/65 (6%)
Query: 157 LDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAI 216
LD +YV N+ ++ ++ EL++ F G + SV + R GF FV F +P +A A+
Sbjct: 72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAV 127
Query: 217 NTLNG 221
L+G
Sbjct: 128 RDLDG 132
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 7/72 (9%)
Query: 60 NLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATV 119
NL+ + L ++F K I KV +Q+GKSKGY F+++++ E A A+ +
Sbjct: 22 NLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREI 78
Query: 120 EG----MELYAP 127
EG +EL P
Sbjct: 79 EGRAIRLELQGP 90
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 159 KNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINT 218
K L + N++ E L++ F + I K+ + G SKG+ F+ F++ ++A A+N+
Sbjct: 16 KTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNS 72
Query: 219 LN 220
N
Sbjct: 73 CN 74
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 54 FIPFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAI 111
F F +L+ I + F+ FG I ++VV GKSKGYGFV + + A NAI
Sbjct: 16 FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAI 74
Score = 35.0 bits (79), Expect = 0.059, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMR-TNRGISKGFGFVCFSNPDEANRAINT 218
+++V +++ ++ ++K F+ G IS ++++ G SKG+GFV F N +A AI
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 219 LNG 221
+ G
Sbjct: 77 MGG 79
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 6/82 (7%)
Query: 50 ATPTFIPFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVS-QDGKSKGYGFVQYSTQESAL 108
AT + + LA +D+ LH F FGDI ++ + + K +G+ FV++ E A
Sbjct: 60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 119
Query: 109 NAIEKLYAATVEGMELYAPSLR 130
AI+ + + EL+ ++R
Sbjct: 120 AAIDNMNES-----ELFGRTIR 136
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKI-MRTNRGISKGFGFVCFSNPDEANRAINTL 219
LYV + ++VD+ L F G I+ ++I + +GF FV F ++A AI+ +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 220 N 220
N
Sbjct: 126 N 126
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 38.1 bits (87), Expect = 0.007, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMR--TNRGISKGFGFVCFSNPDEANRAINT 218
+ V+NI ++ E+++ FS G + +V++ + T G +GFGFV F +A +A N
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA 77
Query: 219 L 219
L
Sbjct: 78 L 78
Score = 33.1 bits (74), Expect = 0.25, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 36/66 (54%), Gaps = 8/66 (12%)
Query: 55 IPFTVNLASTIDNWKLHQIFSKFGDIQSSKV--VVSQDGKSKGYGFVQYSTQESALNAIE 112
IPF N ++ ++FS FG++++ ++ ++ G +G+GFV + T++ A A
Sbjct: 23 IPFQAN------QREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76
Query: 113 KLYAAT 118
L +T
Sbjct: 77 ALCHST 82
>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 = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/103 (23%), Positives = 49/103 (47%), Gaps = 16/103 (15%)
Query: 134 IQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRT 193
+ E+ + +Y+ NL++ + ++ L K+L+ FS+ G I + + R+
Sbjct: 3 VPETRPNHTIYINNLNEKIKKDELKKSLHA--------------IFSRFGQILDILVSRS 48
Query: 194 NRGISKGFGFVCFSNPDEANRAINTLNGILFHQKPLYVAIAQT 236
+ +G FV F A A+ ++ G F+ KP+ + A+T
Sbjct: 49 LK--MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 89
Score = 35.4 bits (80), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAPSL 129
LH IFS+FG I ++VS+ K +G FV + SA NA+ +++G Y +
Sbjct: 30 LHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR-----SMQGFPFYDKPM 82
Query: 130 R 130
R
Sbjct: 83 R 83
>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 = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/103 (23%), Positives = 49/103 (47%), Gaps = 16/103 (15%)
Query: 134 IQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRT 193
+ E+ + +Y+ NL++ + ++ L K+L+ FS+ G I + + R+
Sbjct: 2 VPETRPNHTIYINNLNEKIKKDELKKSLHA--------------IFSRFGQILDILVSRS 47
Query: 194 NRGISKGFGFVCFSNPDEANRAINTLNGILFHQKPLYVAIAQT 236
+ +G FV F A A+ ++ G F+ KP+ + A+T
Sbjct: 48 LK--MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 88
Score = 35.4 bits (80), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAPSL 129
LH IFS+FG I ++VS+ K +G FV + SA NA+ +++G Y +
Sbjct: 29 LHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR-----SMQGFPFYDKPM 81
Query: 130 R 130
R
Sbjct: 82 R 82
>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 = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 24/103 (23%), Positives = 49/103 (47%), Gaps = 16/103 (15%)
Query: 134 IQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRT 193
+ E+ + +Y+ NL++ + ++ L K+L+ FS+ G I + + R+
Sbjct: 3 VPETRPNHTIYINNLNEKIKKDELKKSLHA--------------IFSRFGQILDILVSRS 48
Query: 194 NRGISKGFGFVCFSNPDEANRAINTLNGILFHQKPLYVAIAQT 236
+ +G FV F A A+ ++ G F+ KP+ + A+T
Sbjct: 49 LK--MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 89
Score = 35.4 bits (80), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAPSL 129
LH IFS+FG I ++VS+ K +G FV + SA NA+ +++G Y +
Sbjct: 30 LHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR-----SMQGFPFYDKPM 82
Query: 130 R 130
R
Sbjct: 83 R 83
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYA 116
F NLA+T+ L + FS+FG ++ K K K Y F+ + ++ A+ A+E++
Sbjct: 15 FVRNLANTVTEEILEKAFSQFGKLERVK-------KLKDYAFIHFDERDGAVKAMEEMNG 67
Query: 117 ATVEG 121
+EG
Sbjct: 68 KDLEG 72
Score = 34.7 bits (78), Expect = 0.082, Method: Composition-based stats.
Identities = 28/99 (28%), Positives = 48/99 (48%), Gaps = 14/99 (14%)
Query: 159 KNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINT 218
K L+V+N+ + V E L++ FSQ G + VK + K + F+ F D A +A+
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-------KDYAFIHFDERDGAVKAMEE 64
Query: 219 LNGILFHQKPLYVAIA----QTKRERTSYLRIMYAKQGP 253
+NG + + + A Q ++ER + + A GP
Sbjct: 65 MNGKDLEGENIEIVFAKPPDQKRKERKAQRQ---AASGP 100
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 1/80 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKI-MRTNRGISKGFGFVCFSNPDEANRAINTL 219
L+V+N++ E +L++ FS G +S + + + KGF FV F P+ A +A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 220 NGILFHQKPLYVAIAQTKRE 239
+G +F + L+V + K+E
Sbjct: 71 DGQVFQGRMLHVLPSTIKKE 90
>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 = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 24/103 (23%), Positives = 49/103 (47%), Gaps = 16/103 (15%)
Query: 134 IQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRT 193
+ E+ + +Y+ NL++ + ++ L K+L+ FS+ G I + + R+
Sbjct: 2 VPETRPNHTIYINNLNEKIKKDELKKSLHA--------------IFSRFGQILDILVSRS 47
Query: 194 NRGISKGFGFVCFSNPDEANRAINTLNGILFHQKPLYVAIAQT 236
+ +G FV F A A+ ++ G F+ KP+ + A+T
Sbjct: 48 LK--MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 88
Score = 35.4 bits (80), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAPSL 129
LH IFS+FG I ++VS+ K +G FV + SA NA+ +++G Y +
Sbjct: 29 LHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR-----SMQGFPFYDKPM 81
Query: 130 R 130
R
Sbjct: 82 R 82
>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 = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 24/103 (23%), Positives = 49/103 (47%), Gaps = 16/103 (15%)
Query: 134 IQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRT 193
+ E+ + +Y+ NL++ + ++ L K+L+ FS+ G I + + R+
Sbjct: 2 VPETRPNHTIYINNLNEKIKKDELKKSLHA--------------IFSRFGQILDILVSRS 47
Query: 194 NRGISKGFGFVCFSNPDEANRAINTLNGILFHQKPLYVAIAQT 236
+ +G FV F A A+ ++ G F+ KP+ + A+T
Sbjct: 48 LK--MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 88
Score = 35.4 bits (80), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAPSL 129
LH IFS+FG I ++VS+ K +G FV + SA NA+ +++G Y +
Sbjct: 29 LHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR-----SMQGFPFYDKPM 81
Query: 130 R 130
R
Sbjct: 82 R 82
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 25/86 (29%), Positives = 45/86 (52%), Gaps = 1/86 (1%)
Query: 158 DKNLYVKNINDDVDEIELKQYFSQCGIISSVKI-MRTNRGISKGFGFVCFSNPDEANRAI 216
+K LY+KN++ V E +L F++ I R G +G F+ F N + A +A+
Sbjct: 25 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84
Query: 217 NTLNGILFHQKPLYVAIAQTKRERTS 242
+ +NG + K L + + K++R+S
Sbjct: 85 HLVNGYKLYGKILVIEFGKNKKQRSS 110
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 37.7 bits (86), Expect = 0.011, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 36/63 (57%), Gaps = 2/63 (3%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVK--IMRTNRGISKGFGFVCFSNPDEANRAINT 218
+++ + +V + + + FS G I + + R + +SKG+ +V F NPDEA +A+
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 219 LNG 221
++G
Sbjct: 67 MDG 69
Score = 32.3 bits (72), Expect = 0.36, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 72 QIFSKFGDIQSSKVVVSQ--DGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAPSL 129
+IFS +G I+ + V + SKGY +V++ + A A++ + ++G E+ A ++
Sbjct: 23 EIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV 82
Query: 130 RA 131
A
Sbjct: 83 LA 84
>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 = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 48/101 (47%), Gaps = 16/101 (15%)
Query: 136 ESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNR 195
E+ + +Y+ NL++ + ++ L K+L+ FS+ G I + + R+ +
Sbjct: 2 ETRPNHTIYINNLNEKIKKDELKKSLHA--------------IFSRFGQILDILVSRSLK 47
Query: 196 GISKGFGFVCFSNPDEANRAINTLNGILFHQKPLYVAIAQT 236
+G FV F A A+ ++ G F+ KP+ + A+T
Sbjct: 48 --MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 86
Score = 35.4 bits (80), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAPSL 129
LH IFS+FG I ++VS+ K +G FV + SA NA+ +++G Y +
Sbjct: 27 LHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR-----SMQGFPFYDKPM 79
Query: 130 R 130
R
Sbjct: 80 R 80
>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 = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 48/101 (47%), Gaps = 16/101 (15%)
Query: 136 ESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNR 195
E+ + +Y+ NL++ + ++ L K+L+ FS+ G I + + R+ +
Sbjct: 1 ETRPNHTIYINNLNEKIKKDELKKSLHA--------------IFSRFGQILDILVSRSLK 46
Query: 196 GISKGFGFVCFSNPDEANRAINTLNGILFHQKPLYVAIAQT 236
+G FV F A A+ ++ G F+ KP+ + A+T
Sbjct: 47 --MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 85
Score = 35.0 bits (79), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAPSL 129
LH IFS+FG I ++VS+ K +G FV + SA NA+ +++G Y +
Sbjct: 26 LHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR-----SMQGFPFYDKPM 78
Query: 130 R 130
R
Sbjct: 79 R 79
>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 = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 5/81 (6%)
Query: 60 NLASTIDNWKLHQIFSKFGDIQSSKVVVSQD---GKSKGYGFVQYSTQESALNAIEKLYA 116
NL L ++F K+G + V + +D +S+G+ FV++ + A +A++ +
Sbjct: 54 NLTYRTSPDTLRRVFEKYGRV--GDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111
Query: 117 ATVEGMELYAPSLRAGRIQES 137
A ++G EL R GR +S
Sbjct: 112 AVLDGRELRVQMARYGRPPDS 132
Score = 35.8 bits (81), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 1/85 (1%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTN-RGISKGFGFVCFSNPDEANRAINT 218
+L V N+ L++ F + G + V I R S+GF FV F + +A A++
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 219 LNGILFHQKPLYVAIAQTKRERTSY 243
++G + + L V +A+ R S+
Sbjct: 109 MDGAVLDGRELRVQMARYGRPPDSH 133
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVS-QDGKSKGYGFVQYSTQESALNAIE 112
F L + L + F FGDI+ + V+ Q GKS+GYGFV + + +A A +
Sbjct: 21 FVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Score = 31.6 bits (70), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCG-IISSVKIMRTNRGISKGFGFVCFSNPDEANRAINT 218
++V + + L++YF G I +V I G S+G+GFV ++ A RA
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 219 LNGILFHQK 227
N I+ +K
Sbjct: 79 PNPIIDGRK 87
>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 = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 34/184 (18%), Positives = 79/184 (42%), Gaps = 14/184 (7%)
Query: 55 IPFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKL 114
IPF + + +D + + V+ Q + K + F+++ + + E
Sbjct: 12 IPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD------ETT 65
Query: 115 YAATVEGMELYAPSLRAGRIQESASFNNL------YVKNLDDDVTEEILDKNLYVKNIND 168
A +G+ SL+ R + + YV + V + K L++ + +
Sbjct: 66 QAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHK-LFIGGLPN 124
Query: 169 DVDEIELKQYFSQCGIISSVKIMR-TNRGISKGFGFVCFSNPDEANRAINTLNGILFHQK 227
+++ ++K+ + G + + +++ + G+SKG+ F + + + ++AI LNG+ K
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK 184
Query: 228 PLYV 231
L V
Sbjct: 185 KLLV 188
>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 = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 23/96 (23%), Positives = 46/96 (47%), Gaps = 16/96 (16%)
Query: 141 NNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKG 200
+ +Y+ NL++ + ++ L K+L+ FS+ G I + + R+ + +G
Sbjct: 5 HTIYINNLNEKIKKDELKKSLHA--------------IFSRFGQILDILVSRSLK--MRG 48
Query: 201 FGFVCFSNPDEANRAINTLNGILFHQKPLYVAIAQT 236
FV F A A+ ++ G F+ KP+ + A+T
Sbjct: 49 QAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 84
Score = 35.4 bits (80), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAPSL 129
LH IFS+FG I ++VS+ K +G FV + SA NA+ +++G Y +
Sbjct: 25 LHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR-----SMQGFPFYDKPM 77
Query: 130 R 130
R
Sbjct: 78 R 78
>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 = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 23/96 (23%), Positives = 46/96 (47%), Gaps = 16/96 (16%)
Query: 141 NNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKG 200
+ +Y+ NL++ + ++ L K+L+ FS+ G I + + R+ + +G
Sbjct: 4 HTIYINNLNEKIKKDELKKSLHA--------------IFSRFGQILDILVSRSLK--MRG 47
Query: 201 FGFVCFSNPDEANRAINTLNGILFHQKPLYVAIAQT 236
FV F A A+ ++ G F+ KP+ + A+T
Sbjct: 48 QAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 83
Score = 35.4 bits (80), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAPSL 129
LH IFS+FG I ++VS+ K +G FV + SA NA+ +++G Y +
Sbjct: 24 LHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR-----SMQGFPFYDKPM 76
Query: 130 R 130
R
Sbjct: 77 R 77
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 37.0 bits (84), Expect = 0.019, Method: Composition-based stats.
Identities = 23/66 (34%), Positives = 37/66 (56%), Gaps = 4/66 (6%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGK-SKGYGFVQYSTQESALNAIEKLY 115
F NL+ + L ++ +FGD++ +VV+ D + SKG F Q+ TQE+A L
Sbjct: 19 FIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKC---LA 75
Query: 116 AATVEG 121
AA++E
Sbjct: 76 AASLEA 81
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 36.6 bits (83), Expect = 0.020, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 2/57 (3%)
Query: 159 KNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRA 215
K L+VK +++D E LK+ F G + + + G SKGFGFV F++ ++A A
Sbjct: 16 KTLFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAA 70
Score = 33.5 bits (75), Expect = 0.17, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 2/75 (2%)
Query: 47 SAMATPTFIPFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQES 106
+A + P+ F L+ L + F G +++ V + G SKG+GFV ++++E
Sbjct: 9 NARSQPSKTLFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEED 66
Query: 107 ALNAIEKLYAATVEG 121
A A E + ++G
Sbjct: 67 AKAAKEAMEDGEIDG 81
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 5/71 (7%)
Query: 70 LHQIFSKFGDIQSSKVVVSQD---GKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYA 126
L ++F K+G + V + +D +S+G+ FV++ + A +A++ + A ++G EL
Sbjct: 87 LRRVFEKYGRV--GDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 144
Query: 127 PSLRAGRIQES 137
R GR +S
Sbjct: 145 QMARYGRPPDS 155
Score = 35.0 bits (79), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 175 LKQYFSQCGIISSVKIMRTN-RGISKGFGFVCFSNPDEANRAINTLNGILFHQKPLYVAI 233
L++ F + G + V I R S+GF FV F + +A A++ ++G + + L V +
Sbjct: 87 LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 146
Query: 234 AQTKR 238
A+ R
Sbjct: 147 ARYGR 151
>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 = 36.6 bits (83), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 36/152 (23%), Positives = 64/152 (42%), Gaps = 25/152 (16%)
Query: 93 SKGYGFVQYSTQESALNAIEKLYAATVEGMELYAP---SLRAGRIQESASFN--NLYVKN 147
S+ + ++ +++E A +EKL +EG L L + +SA+ + ++N
Sbjct: 158 SRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIXIRN 217
Query: 148 LDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIM--RTNRGISKGFGFVC 205
L + E+LD+NL L++ F G I + I + + F
Sbjct: 218 L----STELLDENL-------------LRESFEGFGSIEKINIPAGQKEHSFNNCCAFXV 260
Query: 206 FSNPDEANRAINTLNGILFHQKPLYVAIAQTK 237
F N D A RA+ N L + + V++A K
Sbjct: 261 FENKDSAERALQX-NRSLLGNREISVSLADKK 291
>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 = 36.6 bits (83), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 60 NLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATV 119
NL+ I +L ++F +I+ +VSQDGKSKG ++++ ++ A +E+ A +
Sbjct: 106 NLSFNITEDELKEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI 161
Query: 120 EG 121
+G
Sbjct: 162 DG 163
Score = 28.9 bits (63), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 31/57 (54%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAI 216
NL++ N+N + ELK S+ + + ++ G ++ FG+V F + ++ +A+
Sbjct: 15 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL 71
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 36.6 bits (83), Expect = 0.024, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 6/75 (8%)
Query: 60 NLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATV 119
NL+ I +L ++F +I+ +VSQDGKSKG ++++ ++ A +E+ A +
Sbjct: 23 NLSFNITEDELKEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI 78
Query: 120 EG--MELYAPSLRAG 132
+G + LY + G
Sbjct: 79 DGRSVSLYYTGEKGG 93
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 36.2 bits (82), Expect = 0.025, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 6/83 (7%)
Query: 145 VKNLDDDVTEEILDKN-----LYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNR-GIS 198
V+N DDD E ++ L+V +I+++ E E+++ F G I ++ + R G S
Sbjct: 8 VRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFS 67
Query: 199 KGFGFVCFSNPDEANRAINTLNG 221
KG+ V + +A A LNG
Sbjct: 68 KGYALVEYETHKQALAAKEALNG 90
Score = 35.0 bits (79), Expect = 0.065, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 54 FIPFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIE 112
+I F ++ ++ + F +G+I++ + + + G SKGY V+Y T + AL A E
Sbjct: 27 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 86
Query: 113 KLYAATVEGMEL 124
L A + G +
Sbjct: 87 ALNGAEIMGQTI 98
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 35.8 bits (81), Expect = 0.034, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 6/82 (7%)
Query: 50 ATPTFIPFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVS-QDGKSKGYGFVQYSTQESAL 108
+T + + LA +D+ LH F FGDI ++ + + K +G+ FV++ E A
Sbjct: 2 STTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 61
Query: 109 NAIEKLYAATVEGMELYAPSLR 130
AI+ + + EL+ ++R
Sbjct: 62 AAIDNMNES-----ELFGRTIR 78
Score = 29.6 bits (65), Expect = 2.8, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKI-MRTNRGISKGFGFVCFSNPDEANRAINTL 219
LYV + ++VD+ L F G I+ ++I + +GF FV F ++A AI+ +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 220 N 220
N
Sbjct: 68 N 68
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 35.8 bits (81), Expect = 0.036, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 61 LASTIDNWKLHQIFSKFGDIQSSKVVVS-QDGKSKGYGFVQYSTQESALNAIEKLYAATV 119
LA +D+ LH F FGDI ++ + + K +G+ FV++ E A AI+ + +
Sbjct: 10 LAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNES-- 67
Query: 120 EGMELYAPSLR 130
EL+ ++R
Sbjct: 68 ---ELFGRTIR 75
Score = 29.6 bits (65), Expect = 2.9, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKI-MRTNRGISKGFGFVCFSNPDEANRAINTL 219
LYV + ++VD+ L F G I+ ++I + +GF FV F ++A AI+ +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 220 N 220
N
Sbjct: 65 N 65
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 35.8 bits (81), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 43/87 (49%), Gaps = 10/87 (11%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKI-------MRTNR--GISKGFGFVCFSNPDE 211
++V+ + ++V + YF Q GII + K + T+R G KG V F +P
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 212 ANRAINTLNGILFHQKPLYVAIAQTKR 238
A AI+ +G F P+ V+ A T+R
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSFA-TRR 95
>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 = 35.8 bits (81), Expect = 0.041, Method: Composition-based stats.
Identities = 19/49 (38%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 77 FGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIEKLYAATVEGMEL 124
FG I ++VV GKSKGYGFV + + A NAI+++ + G ++
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78
Score = 30.0 bits (66), Expect = 1.9, Method: Composition-based stats.
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 183 GIISSVKIMR-TNRGISKGFGFVCFSNPDEANRAINTLNG 221
G IS ++++ G SKG+GFV F N +A AI + G
Sbjct: 31 GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG 70
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 35.8 bits (81), Expect = 0.042, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 42/81 (51%), Gaps = 2/81 (2%)
Query: 159 KNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTN-RGISKGFGFVCFSNPDEANRAIN 217
+++YV N++ EL+ +F CG ++ V I+ G KGF ++ FS+ E+ R
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESVRTSL 64
Query: 218 TLNGILFHQKPLYVAIAQTKR 238
L+ LF + + V +T R
Sbjct: 65 ALDESLFRGRQIKVIPKRTNR 85
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 35.4 bits (80), Expect = 0.042, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 42/81 (51%), Gaps = 2/81 (2%)
Query: 159 KNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTN-RGISKGFGFVCFSNPDEANRAIN 217
+++YV N++ EL+ +F CG ++ V I+ G KGF ++ FS+ E+ R
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESVRTSL 65
Query: 218 TLNGILFHQKPLYVAIAQTKR 238
L+ LF + + V +T R
Sbjct: 66 ALDESLFRGRQIKVIPKRTNR 86
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 35.4 bits (80), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 45/87 (51%), Gaps = 6/87 (6%)
Query: 154 EEILDKNLYVKNIN----DDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNP 209
E + ++ +Y+ N+N + + L FSQ G I + ++T + +G FV F
Sbjct: 2 EMLPNQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLK--MRGQAFVIFKEI 59
Query: 210 DEANRAINTLNGILFHQKPLYVAIAQT 236
A+ A+ T+ G F+ KP+ +A +++
Sbjct: 60 GSASNALRTMQGFPFYDKPMQIAYSKS 86
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 35.4 bits (80), Expect = 0.048, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 5/61 (8%)
Query: 159 KNLYVKNINDDVDEIELKQYFSQCGIISSVKIMR---TNRGISKGFGFVCFSNPDEANRA 215
+ L++ ++ + E L+ Y+ Q G ++ +MR + R S+GFGFV FS+ E + A
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKR--SRGFGFVTFSSMAEVDAA 85
Query: 216 I 216
+
Sbjct: 86 M 86
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 35.4 bits (80), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 24/103 (23%), Positives = 47/103 (45%), Gaps = 16/103 (15%)
Query: 134 IQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRT 193
+ E+ + +Y+ NL++ + ++ L K+L+ FS+ G I + + R+
Sbjct: 2 VPETRPNHTIYINNLNEKIKKDELKKSLHA--------------IFSRFGQILDILVSRS 47
Query: 194 NRGISKGFGFVCFSNPDEANRAINTLNGILFHQKPLYVAIAQT 236
+ +G FV F A A+ + G F+ KP + A+T
Sbjct: 48 LK--XRGQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQYAKT 88
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 10/77 (12%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAPSL 129
LH IFS+FG I ++VS+ K +G FV + SA NA+ + +G Y
Sbjct: 29 LHAIFSRFGQILD--ILVSRSLKXRGQAFVIFKEVSSATNALR-----SXQGFPFYD--- 78
Query: 130 RAGRIQESASFNNLYVK 146
+ RIQ + + +++ K
Sbjct: 79 KPXRIQYAKTDSDIIAK 95
>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 = 35.4 bits (80), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 24/103 (23%), Positives = 47/103 (45%), Gaps = 16/103 (15%)
Query: 134 IQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRT 193
+ E+ + +Y+ NL++ + ++ L K+L+ FS+ G I + + R+
Sbjct: 3 VPETRPNHTIYINNLNEKIKKDELKKSLHA--------------IFSRFGQILDILVSRS 48
Query: 194 NRGISKGFGFVCFSNPDEANRAINTLNGILFHQKPLYVAIAQT 236
+ +G FV F A A+ + G F+ KP + A+T
Sbjct: 49 LK--XRGQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQYAKT 89
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 10/77 (12%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAPSL 129
LH IFS+FG I ++VS+ K +G FV + SA NA+ + +G Y
Sbjct: 30 LHAIFSRFGQILD--ILVSRSLKXRGQAFVIFKEVSSATNALR-----SXQGFPFYD--- 79
Query: 130 RAGRIQESASFNNLYVK 146
+ RIQ + + +++ K
Sbjct: 80 KPXRIQYAKTDSDIIAK 96
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 35.4 bits (80), Expect = 0.049, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 4/85 (4%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINTLN 220
+YV N+ + EL++ FS G + +V I R GF FV F +P +A A+ L+
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLD 58
Query: 221 GILFHQKPLYVAIAQTKRERTSYLR 245
G + + V ++ R+ + R
Sbjct: 59 GKVICGSRVRVELSTGMPRRSRFDR 83
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 35.4 bits (80), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 9/83 (10%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKI-------MRTNR--GISKGFGFVCFSNPDE 211
++V+ + ++V + YF Q GII + K + T+R G KG V F +P
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 212 ANRAINTLNGILFHQKPLYVAIA 234
A AI+ +G F P+ V+ A
Sbjct: 76 AKAAIDWFDGKEFSGNPIKVSFA 98
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 35.4 bits (80), Expect = 0.054, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 9/75 (12%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMR---TNRGISKGFGFVCFSNPDEANRAI- 216
L+V ++ + L+ YFSQ G + IM+ TN+ S+GFGFV F +P+ +
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQ--SRGFGFVKFKDPNCVGTVLA 76
Query: 217 ---NTLNGILFHQKP 228
+TL+G KP
Sbjct: 77 SRPHTLDGRNIDPKP 91
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 35.0 bits (79), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 45/83 (54%), Gaps = 6/83 (7%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINTLN 220
LY+ N++ V +L+Q F + + +++ + G+ FV + + + A RAI TL+
Sbjct: 11 LYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-----LKSGYAFVDYPDQNWAIRAIETLS 65
Query: 221 G-ILFHQKPLYVAIAQTKRERTS 242
G + H K + V + +K+ R+S
Sbjct: 66 GKVELHGKIMEVDYSVSKKLRSS 88
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 35.0 bits (79), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 4/62 (6%)
Query: 60 NLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATV 119
NL + +L ++F +I+ +VS+DGKSKG ++++ T+ A E+ +
Sbjct: 100 NLPYKVTQDELKEVFEDAAEIR----LVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEI 155
Query: 120 EG 121
+G
Sbjct: 156 DG 157
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 24/97 (24%), Positives = 48/97 (49%), Gaps = 6/97 (6%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINTL 219
NL+V N+N + ELK S + + ++ G+++ FG+V F + ++ +A+ L
Sbjct: 9 NLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKALE-L 67
Query: 220 NGILFHQKPLYVAIAQ---TKRERTSYLRIMYAKQGP 253
G+ + + + +K+ER + R + AK P
Sbjct: 68 TGLKVFGNEIKLEKPKGKDSKKERDA--RTLLAKNLP 102
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 35.0 bits (79), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 160 NLYVKNI---NDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAI 216
LY++ + D D ++L Q + + I+S+ I+ KG+GFV F +P A +A+
Sbjct: 7 GLYIRGLQPGTTDQDLVKLCQPYGK--IVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
Query: 217 NTLN 220
L
Sbjct: 65 TALK 68
Score = 31.2 bits (69), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 70 LHQIFSKFGDIQSSKVVVSQD-GKSKGYGFVQYSTQESALNAIEKLYAATVE 120
L ++ +G I S+K ++ + K KGYGFV + + +A A+ L A+ V+
Sbjct: 22 LVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQ 73
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 35.0 bits (79), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 24/101 (23%), Positives = 46/101 (45%), Gaps = 16/101 (15%)
Query: 136 ESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNR 195
E+ + +Y+ NL++ + ++ L K+L+ FS+ G I + + R+ +
Sbjct: 2 ETRPNHTIYINNLNEKIKKDELKKSLHA--------------IFSRFGQILDILVSRSLK 47
Query: 196 GISKGFGFVCFSNPDEANRAINTLNGILFHQKPLYVAIAQT 236
+G FV F A A+ + G F+ KP + A+T
Sbjct: 48 --XRGQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQYAKT 86
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 10/77 (12%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAPSL 129
LH IFS+FG I ++VS+ K +G FV + SA NA+ + +G Y
Sbjct: 27 LHAIFSRFGQILD--ILVSRSLKXRGQAFVIFKEVSSATNALR-----SXQGFPFYD--- 76
Query: 130 RAGRIQESASFNNLYVK 146
+ RIQ + + +++ K
Sbjct: 77 KPXRIQYAKTDSDIIAK 93
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 34.7 bits (78), Expect = 0.073, Method: Composition-based stats.
Identities = 20/52 (38%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 172 EIELKQYFSQCGIISSVKIMRTNRGI-SKGFGFVCFSNPDEANRAINTLNGI 222
E +L++ FS+ G I+ V I+ + S+GF FV F N D+A A NG+
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGM 80
Score = 33.1 bits (74), Expect = 0.23, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDG-KSKGYGFVQYSTQESALNAIEKLYAATVEGMELYAPS 128
L ++FSK+G I +V Q +S+G+ FV + + A A E+ GMEL
Sbjct: 32 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER-----ANGMELDGRR 86
Query: 129 LR 130
+R
Sbjct: 87 IR 88
>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 = 34.7 bits (78), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 54 FIPFTVNLASTIDNWKLHQIFSKFGDIQSSKV-VVSQDGKSKGYGFVQYSTQESALNAIE 112
+I F ++ ++ + F +G+I++ + + + G SKGY V+Y T + AL A E
Sbjct: 73 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 132
Query: 113 KLYAATVEGM 122
L A + G
Sbjct: 133 ALNGAEIMGQ 142
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 6/83 (7%)
Query: 145 VKNLDDDVTEEILDKN-----LYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNR-GIS 198
V+N DDD E ++ L+V +I+++ E E+++ F G I ++ + R G S
Sbjct: 54 VRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFS 113
Query: 199 KGFGFVCFSNPDEANRAINTLNG 221
KG+ V + +A A LNG
Sbjct: 114 KGYALVEYETHKQALAAKEALNG 136
>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 = 0.085, Method: Composition-based stats.
Identities = 26/89 (29%), Positives = 44/89 (49%), Gaps = 11/89 (12%)
Query: 149 DDDVTEEILDKNLYVKNINDDVDEIELKQYFSQC--GIISSVKIMRTNRGISKGFGFVCF 206
D+D + K LYV+N+ E +++ F+ G + VK +R + FV F
Sbjct: 8 DEDTMSSV--KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD-------YAFVHF 58
Query: 207 SNPDEANRAINTLNGILFHQKPLYVAIAQ 235
SN ++A A+ LNG + P+ V +A+
Sbjct: 59 SNREDAVEAMKALNGKVLDGSPIEVTLAK 87
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDG-KSKGYGFVQYSTQESALNA 110
+ NL ++ N L++IFSK+G + ++ +D KSKG F+ + ++SA N
Sbjct: 20 YVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Score = 29.3 bits (64), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 4/61 (6%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMR-TNRGISKGFGFVCFSNPDEA---NRAI 216
+YV N+ + +L + FS+ G + V IM+ + SKG F+ F + D A RAI
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 217 N 217
N
Sbjct: 79 N 79
>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 = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/90 (23%), Positives = 47/90 (52%), Gaps = 2/90 (2%)
Query: 148 LDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTN-RGISKGFGFVCF 206
L + +EI +++YV N++ +L+ +FS CG I+ + I+ G KG+ ++ F
Sbjct: 26 LSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEF 85
Query: 207 SNPDEANRAINTLNGILFHQKPLYVAIAQT 236
+ + + A+ ++ +F + + V +T
Sbjct: 86 AERNSVDAAV-AMDETVFRGRTIKVLPKRT 114
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 35/56 (62%), Gaps = 2/56 (3%)
Query: 60 NLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKS-KGYGFVQYSTQESALNAIEKL 114
NL + + ++ ++FS+FG + + K++ ++ K KG+GFV+ +ES AI KL
Sbjct: 8 NLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAKL 62
Score = 32.0 bits (71), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 42/82 (51%), Gaps = 4/82 (4%)
Query: 159 KNLYVKNINDDVDEIELKQYFSQCGIISSVKIM--RTNRGISKGFGFVCFSNPDEANRAI 216
+N+YV N+ ++K+ FSQ G + +VK++ R + KGFGFV + + AI
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKK-PKGFGFVEMQE-ESVSEAI 59
Query: 217 NTLNGILFHQKPLYVAIAQTKR 238
L+ F + + V A K+
Sbjct: 60 AKLDNTDFMGRTIRVTEANPKK 81
>pdb|1G9L|A Chain A, Solution Structure Of The Pabc Domain Of Human Poly(A)
Binding Protein
Length = 144
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 20/26 (76%)
Query: 322 SMLAVASPDERKDILGQGLYPLVKKL 347
SMLA A P E+K +LG+ L+PL++ +
Sbjct: 56 SMLASAPPQEQKQMLGERLFPLIQAM 81
>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 = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 31/181 (17%), Positives = 74/181 (40%), Gaps = 22/181 (12%)
Query: 55 IPFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKL 114
IPF + + +D + + V+ Q + K + F+++ + + E
Sbjct: 14 IPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD------ETT 67
Query: 115 YAATVEGMELYAPSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIE 174
A +G+ SL+ R + + L++ + + +++ +
Sbjct: 68 QAMAFDGIIFQGQSLKIRRPHDYQPLPGAH---------------KLFIGGLPNYLNDDQ 112
Query: 175 LKQYFSQCGIISSVKIMR-TNRGISKGFGFVCFSNPDEANRAINTLNGILFHQKPLYVAI 233
+K+ + G + + +++ + G+SKG+ F + + + ++AI LNG+ K L V
Sbjct: 113 VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 172
Query: 234 A 234
A
Sbjct: 173 A 173
>pdb|3PTH|A Chain A, The Pabc1 Mlle Domain Bound To The Variant Pam2 Motif Of
Larp4b
Length = 82
Score = 33.1 bits (74), Expect = 0.24, Method: Composition-based stats.
Identities = 13/26 (50%), Positives = 20/26 (76%)
Query: 322 SMLAVASPDERKDILGQGLYPLVKKL 347
SMLA A P E+K +LG+ L+PL++ +
Sbjct: 9 SMLASAPPQEQKQMLGERLFPLIQAM 34
>pdb|3KUR|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|C Chain C, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|D Chain D, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|E Chain E, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|F Chain F, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|G Chain G, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|H Chain H, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
Length = 79
Score = 33.1 bits (74), Expect = 0.24, Method: Composition-based stats.
Identities = 13/26 (50%), Positives = 20/26 (76%)
Query: 322 SMLAVASPDERKDILGQGLYPLVKKL 347
SMLA A P E+K +LG+ L+PL++ +
Sbjct: 10 SMLASAPPQEQKQMLGERLFPLIQAM 35
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 33.1 bits (74), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 31/181 (17%), Positives = 74/181 (40%), Gaps = 22/181 (12%)
Query: 55 IPFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKL 114
IPF + + +D + + V+ Q + K + F+++ + + E
Sbjct: 12 IPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD------ETT 65
Query: 115 YAATVEGMELYAPSLRAGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIE 174
A +G+ SL+ R + + L++ + + +++ +
Sbjct: 66 QAMAFDGIIFQGQSLKIRRPHDYQPLPGAH---------------KLFIGGLPNYLNDDQ 110
Query: 175 LKQYFSQCGIISSVKIMR-TNRGISKGFGFVCFSNPDEANRAINTLNGILFHQKPLYVAI 233
+K+ + G + + +++ + G+SKG+ F + + + ++AI LNG+ K L V
Sbjct: 111 VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 170
Query: 234 A 234
A
Sbjct: 171 A 171
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 33.1 bits (74), Expect = 0.25, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 7/58 (12%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKL 114
F NLA+T+ L + FS+FG ++ K K K Y FV + + +A+ A++++
Sbjct: 19 FVRNLATTVTEEILEKSFSEFGKLERVK-------KLKDYAFVHFEDRGAAVKAMDEM 69
Score = 31.2 bits (69), Expect = 0.80, Method: Composition-based stats.
Identities = 26/91 (28%), Positives = 41/91 (45%), Gaps = 25/91 (27%)
Query: 131 AGRIQESASFNNLYVKNLDDDVTEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKI 190
+G + A L+V+NL VTEEIL+K+ FS+ G + VK
Sbjct: 6 SGDPEVMAKVKVLFVRNLATTVTEEILEKS------------------FSEFGKLERVKK 47
Query: 191 MRTNRGISKGFGFVCFSNPDEANRAINTLNG 221
+ K + FV F + A +A++ +NG
Sbjct: 48 L-------KDYAFVHFEDRGAAVKAMDEMNG 71
>pdb|2RQG|B Chain B, Structure Of Gspt1ERF3A-Pabc
pdb|2RQH|B Chain B, Structure Of Gspt1ERF3A-Pabc
Length = 83
Score = 33.1 bits (74), Expect = 0.25, Method: Composition-based stats.
Identities = 13/26 (50%), Positives = 20/26 (76%)
Query: 322 SMLAVASPDERKDILGQGLYPLVKKL 347
SMLA A P E+K +LG+ L+PL++ +
Sbjct: 8 SMLASAPPQEQKQMLGERLFPLIQAM 33
>pdb|2X04|A Chain A, Crystal Structure Of The Pabc-Tnrc6c Complex
pdb|2X04|B Chain B, Crystal Structure Of The Pabc-Tnrc6c Complex
Length = 80
Score = 33.1 bits (74), Expect = 0.25, Method: Composition-based stats.
Identities = 13/26 (50%), Positives = 20/26 (76%)
Query: 322 SMLAVASPDERKDILGQGLYPLVKKL 347
SMLA A P E+K +LG+ L+PL++ +
Sbjct: 9 SMLASAPPQEQKQMLGERLFPLIQAM 34
>pdb|3KUS|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KUS|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KUT|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(a)-binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KUT|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(a)-binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KTP|A Chain A, Structural Basis Of Gw182 Recognition By Poly(a)-binding
Protein
pdb|3KTR|A Chain A, Structural Basis Of Ataxin-2 Recognition By
Poly(A)-Binding
pdb|3KUI|A Chain A, Crystal Structure Of C-Terminal Domain Of Pabpc1 In
Complex Binding Region Of Erf3a
pdb|3KUJ|A Chain A, Crystal Structure Of C-Terminal Domain Of Pabpc1 In
Complex With Binding Region Of Erf3a
pdb|3PKN|A Chain A, Crystal Structure Of Mlle Domain Of Poly(A) Binding
Protein In Complex With Pam2 Motif Of La-Related Protein
4 (Larp4)
Length = 88
Score = 32.7 bits (73), Expect = 0.29, Method: Composition-based stats.
Identities = 13/26 (50%), Positives = 20/26 (76%)
Query: 322 SMLAVASPDERKDILGQGLYPLVKKL 347
SMLA A P E+K +LG+ L+PL++ +
Sbjct: 10 SMLASAPPQEQKQMLGERLFPLIQAM 35
>pdb|1JGN|A Chain A, Solution Structure Of The C-Terminal Pabc Domain Of Human
Poly(A)-Binding Protein In Complex With The Peptide From
Paip2
pdb|1JH4|A Chain A, Solution Structure Of The C-Terminal Pabc Domain Of Human
Poly(A)-Binding Protein In Complex With The Peptide From
Paip1
Length = 98
Score = 32.7 bits (73), Expect = 0.30, Method: Composition-based stats.
Identities = 13/26 (50%), Positives = 20/26 (76%)
Query: 322 SMLAVASPDERKDILGQGLYPLVKKL 347
SMLA A P E+K +LG+ L+PL++ +
Sbjct: 10 SMLASAPPQEQKQMLGERLFPLIQAM 35
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 32.7 bits (73), Expect = 0.30, Method: Composition-based stats.
Identities = 28/84 (33%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 159 KNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINT 218
+ LYV N++ DV E+ + Q FSQ G S K M T + + FV F +A A+
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCK-MITEHTSNDPYCFVEFYEHRDAAAALAA 74
Query: 219 LNGILFHQKPLYVAIAQTKRERTS 242
+NG K + V A T + S
Sbjct: 75 MNGRKILGKEVKVNWATTPSSQKS 98
>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 = 32.3 bits (72), Expect = 0.40, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 161 LYVKNINDDVDEIELKQYFSQCG-IISSVKIMRTNRGISKGFGFVCFSNPDEANRAIN-- 217
+++ ++ D + +LK YFS+ G ++ + G S+GFGFV F + ++ ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 218 --TLNGILFHQK 227
LNG + K
Sbjct: 62 EHKLNGKVIDPK 73
Score = 29.6 bits (65), Expect = 2.8, Method: Composition-based stats.
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 70 LHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQES 106
L FSKFG++ + + G+S+G+GFV + ES
Sbjct: 16 LKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESES 53
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 32.3 bits (72), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 14/65 (21%), Positives = 34/65 (52%)
Query: 60 NLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATV 119
NL + + + ++F++FG ++ + V + G+S G V + + AL A+++ +
Sbjct: 95 NLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPL 154
Query: 120 EGMEL 124
+G +
Sbjct: 155 DGRPM 159
>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 = 32.3 bits (72), Expect = 0.43, Method: Composition-based stats.
Identities = 15/76 (19%), Positives = 39/76 (51%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINTLN 220
L++ + + EL++ G + ++++ G KG +V + N +A++A+ ++
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 221 GILFHQKPLYVAIAQT 236
G+ + + VAI+ +
Sbjct: 80 GMTIKENIIKVAISNS 95
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 32.3 bits (72), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 16/77 (20%), Positives = 36/77 (46%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCFSNPDEANRAINTL 219
L V N++ V + ++++ F++ G + + G S G V F +A +A+
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 89
Query: 220 NGILFHQKPLYVAIAQT 236
NG+ +P+ + + +
Sbjct: 90 NGVPLDGRPMNIQLVTS 106
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/62 (22%), Positives = 33/62 (53%)
Query: 60 NLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATV 119
NL + + + ++F++FG ++ + V + G+S G V + + AL A+++ +
Sbjct: 35 NLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPL 94
Query: 120 EG 121
+G
Sbjct: 95 DG 96
>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 = 32.0 bits (71), Expect = 0.48, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 162 YVKNINDDVDEIELKQYFSQCGIISSVKIMRT-NRGISKGFGFVCFSNPDEANRAIN 217
+V ++ D + +LK YF++ G + I N G S+GFGF+ F + + ++
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLD 71
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 32.0 bits (71), Expect = 0.54, Method: Composition-based stats.
Identities = 17/37 (45%), Positives = 25/37 (67%), Gaps = 1/37 (2%)
Query: 172 EIELKQYFSQCGIISSVKIMRTNR-GISKGFGFVCFS 207
E +LK+YFS G + V++ + + G SKGFGFV F+
Sbjct: 29 EQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFT 65
Score = 30.4 bits (67), Expect = 1.5, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 68 WK-----LHQIFSKFGDIQSSKVVVS-QDGKSKGYGFVQYSTQESALNAIEK 113
WK L + FS FG++ +V + G SKG+GFV+++ E+ + + +
Sbjct: 25 WKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 76
>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 = 32.0 bits (71), Expect = 0.54, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 2/75 (2%)
Query: 149 DDDVTEEILDKN--LYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVCF 206
D++ E++L K+ LYV N++ E ++ + FS+ G I + + + GF FV +
Sbjct: 7 DNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEY 66
Query: 207 SNPDEANRAINTLNG 221
+ +A A+ +NG
Sbjct: 67 YSRADAENAMRYING 81
Score = 30.0 bits (66), Expect = 2.0, Method: Composition-based stats.
Identities = 15/52 (28%), Positives = 31/52 (59%)
Query: 60 NLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAI 111
NL+ +++++FSK GDI+ + + + + G+ FV+Y ++ A NA+
Sbjct: 25 NLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAM 76
>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 = 32.0 bits (71), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNR-GISKGFGFVCFSNPDEANRAINTL 219
L+V ++++ E ++ F++ G I ++ + R G KG+ V + EA A+ L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 220 NGILFHQKPLYV 231
NG +P+ V
Sbjct: 85 NGQDLMGQPISV 96
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 54 FIPFTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIE 112
+I F + +H F+++G+I++ + + + G KGY V+Y T + A A+E
Sbjct: 23 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82
Query: 113 KL 114
L
Sbjct: 83 GL 84
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 32.0 bits (71), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 69 KLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIEKLYAATVEGMEL 124
KL + F +G I+ +V S+ GK +GY F++Y + +A + ++G +
Sbjct: 118 KLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRV 174
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 31.6 bits (70), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 41/87 (47%), Gaps = 10/87 (11%)
Query: 160 NLYVKNINDDVDEIELKQYFSQCGIISS--------VKIMRTNRGISKGFGFVCFSNPDE 211
+YVKN+ V E +LK F + SS +++M+ R KG F+ N
Sbjct: 47 RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGR--MKGQAFIGLPNEKA 104
Query: 212 ANRAINTLNGILFHQKPLYVAIAQTKR 238
A +A+ NG + KP+ V A++ R
Sbjct: 105 AAKALKEANGYVLFGKPMVVQFARSAR 131
>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 = 31.2 bits (69), Expect = 0.93, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNR-GISKGFGFVCFSNPDEANRAINTL 219
L+V ++++ E ++ F++ G I ++ + R G KG+ V + EA A+ L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 220 NGILFHQKPLYV 231
NG +P+ V
Sbjct: 86 NGQDLMGQPISV 97
Score = 29.6 bits (65), Expect = 2.4, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 70 LHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIEKLYAATVEG 121
+H F+++G+I++ + + + G KGY V+Y T + A A+E L + G
Sbjct: 40 IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG 92
>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 = 31.2 bits (69), Expect = 0.93, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNR-GISKGFGFVCFSNPDEANRAINTL 219
L+V ++++ E ++ F++ G I ++ + R G KG+ V + EA A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 220 NGILFHQKPLYV 231
NG +P+ V
Sbjct: 70 NGQDLMGQPISV 81
Score = 29.6 bits (65), Expect = 2.4, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 70 LHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIEKLYAATVEG 121
+H F+++G+I++ + + + G KGY V+Y T + A A+E L + G
Sbjct: 24 IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG 76
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 31.2 bits (69), Expect = 0.93, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNR-GISKGFGFVCFSNPDEANRAINTL 219
L+V ++++ E ++ F++ G I ++ + R G KG+ V + EA A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 220 NGILFHQKPLYV 231
NG +P+ V
Sbjct: 70 NGQDLMGQPISV 81
Score = 29.6 bits (65), Expect = 2.4, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 70 LHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIEKLYAATVEG 121
+H F+++G+I++ + + + G KGY V+Y T + A A+E L + G
Sbjct: 24 IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG 76
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 31.2 bits (69), Expect = 0.93, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNR-GISKGFGFVCFSNPDEANRAINTL 219
L+V ++++ E ++ F++ G I ++ + R G KG+ V + EA A+ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 220 NGILFHQKPLYV 231
NG +P+ V
Sbjct: 72 NGQDLMGQPISV 83
Score = 29.6 bits (65), Expect = 2.4, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 70 LHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIEKLYAATVEG 121
+H F+++G+I++ + + + G KGY V+Y T + A A+E L + G
Sbjct: 26 IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG 78
>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 = 31.2 bits (69), Expect = 0.93, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNR-GISKGFGFVCFSNPDEANRAINTL 219
L+V ++++ E ++ F++ G I ++ + R G KG+ V + EA A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 220 NGILFHQKPLYV 231
NG +P+ V
Sbjct: 70 NGQDLMGQPISV 81
Score = 29.6 bits (65), Expect = 2.4, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 70 LHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIEKLYAATVEG 121
+H F+++G+I++ + + + G KGY V+Y T + A A+E L + G
Sbjct: 24 IHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG 76
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 31.2 bits (69), Expect = 0.94, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 7/49 (14%)
Query: 165 NINDDVDEIELKQYFSQCGIISSVKIM---RTNRGISKGFGFVCFSNPD 210
++N V+++ K YF Q G + +M TNR +GFGFV F + D
Sbjct: 8 SVNTTVEDV--KHYFEQFGKVDDAMLMFDKTTNR--HRGFGFVTFESED 52
>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 = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 69 KLHQIFSKFGDIQSSKVVVSQ-DGKSKGYGFVQYSTQESALNAIEKLYAATVEG 121
KL + F +G I+ +V S+ GK +GY F++Y + +A + ++G
Sbjct: 118 KLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDG 171
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMR-TNRGISKGFGFVCFSNPDEANRAINTL 219
L++ + + +++ ++K+ + G + + +++ + G+SKG+ F + + + ++AI L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 220 NGILFHQKPLYV 231
NG+ K L V
Sbjct: 64 NGMQLGDKKLLV 75
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 7/42 (16%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAI 111
+ IFSK+G + V KGY FVQYS + A A+
Sbjct: 45 VETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAV 79
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 30.4 bits (67), Expect = 1.6, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 148 LDDDV--TEEILDKNLYVKNINDDVDEIELKQYFSQCGIISSVKIMRTNRGISKGFGFVC 205
L+D V +E NL++ N+N + ELK S+ + + ++ G ++ FG+V
Sbjct: 5 LEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVD 64
Query: 206 FSNPDEANRAI 216
F + ++ +A+
Sbjct: 65 FESAEDLEKAL 75
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 16/35 (45%), Positives = 21/35 (60%), Gaps = 5/35 (14%)
Query: 175 LKQYFSQCGIISSVKIMR---TNRGISKGFGFVCF 206
L++YF Q G + +MR T R S+GFGFV F
Sbjct: 17 LREYFGQFGEVKECLVMRDPLTKR--SRGFGFVTF 49
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 16/35 (45%), Positives = 21/35 (60%), Gaps = 5/35 (14%)
Query: 175 LKQYFSQCGIISSVKIMR---TNRGISKGFGFVCF 206
L++YF Q G + +MR T R S+GFGFV F
Sbjct: 42 LREYFGQFGEVKECLVMRDPLTKR--SRGFGFVTF 74
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 14/62 (22%), Positives = 33/62 (53%)
Query: 60 NLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATV 119
NL + + + ++F++FG ++ + V + G+S G V + + AL A+++ +
Sbjct: 42 NLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPL 101
Query: 120 EG 121
+G
Sbjct: 102 DG 103
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 14/62 (22%), Positives = 33/62 (53%)
Query: 60 NLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATV 119
NL + + + ++F++FG ++ + V + G+S G V + + AL A+++ +
Sbjct: 42 NLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPL 101
Query: 120 EG 121
+G
Sbjct: 102 DG 103
>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 = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 5/58 (8%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSK---GYGFVQYSTQESALNAI 111
+ NL+ +++++FSK GDI+ K+++ D K G+ FV+Y ++ A NA+
Sbjct: 43 YVGNLSFYTTEEQIYELFSKSGDIK--KIIMGLDKMKKTACGFCFVEYYSRADAENAM 98
>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 = 29.6 bits (65), Expect = 2.3, Method: Composition-based stats.
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 10/86 (11%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYA 116
F NL I ++ ++F K+G ++ +V + +D KG+GF++ T+ A ++
Sbjct: 19 FVGNLPPDITEEEMRKLFEKYG--KAGEVFIHKD---KGFGFIRLETRTLA-----EIAK 68
Query: 117 ATVEGMELYAPSLRAGRIQESASFNN 142
++ M L LR SAS +
Sbjct: 69 VELDNMPLRGKQLRVRFACHSASLTS 94
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 29.6 bits (65), Expect = 2.3, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMRTN-RGISKGFGFVCFSNPDEANRAINTL 219
L+V I +DE +LK F + G I + +++ G+ KG F+ + D A +A + L
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSAL 77
Query: 220 N 220
+
Sbjct: 78 H 78
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 29.6 bits (65), Expect = 2.5, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 70 LHQIFSKFGDIQSSKVVVSQDGKS-KGYGFVQYSTQESALNAIEKLYAATVEGMELYAPS 128
L ++F K+G + + K+ +G+ FV++ + A +A + A ++G EL
Sbjct: 30 LRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV 89
Query: 129 LRAGR 133
R GR
Sbjct: 90 ARYGR 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 = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 14/62 (22%), Positives = 32/62 (51%)
Query: 60 NLASTIDNWKLHQIFSKFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKLYAATV 119
NL + + + ++F++FG ++ + V + G+S G V + + AL A ++ +
Sbjct: 36 NLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYNGVPL 95
Query: 120 EG 121
+G
Sbjct: 96 DG 97
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 29.3 bits (64), Expect = 3.7, Method: Composition-based stats.
Identities = 16/61 (26%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIMRTN-RGISKGFGFVCFSNPDEANRAINTL 219
L++ I ++DE +LK F + G I + +++ G+ KG F+ + + A +A + L
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 220 N 220
+
Sbjct: 76 H 76
>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 = 28.9 bits (63), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 89 QDGKSKGYGFVQYSTQESALNAIEKL 114
Q G+SKGY F+++ ES+ +A+ L
Sbjct: 41 QTGRSKGYAFIEFRDLESSASAVRNL 66
Score = 28.5 bits (62), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIM-RTNRGISKGFGFVCFSNPDEANRAINTL 219
+Y+ +I D E ++ S G + ++K+M G SKG+ F+ F + + + A+ L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 220 NG 221
NG
Sbjct: 67 NG 68
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 28.9 bits (63), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 89 QDGKSKGYGFVQYSTQESALNAIEKL 114
Q G+SKGY F+++ ES+ +A+ L
Sbjct: 39 QTGRSKGYAFIEFRDLESSASAVRNL 64
Score = 28.5 bits (62), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIM-RTNRGISKGFGFVCFSNPDEANRAINTL 219
+Y+ +I D E ++ S G + ++K+M G SKG+ F+ F + + + A+ L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 220 NG 221
NG
Sbjct: 65 NG 66
>pdb|3LP8|A Chain A, Crystal Structure Of Phosphoribosylamine-Glycine Ligase
From Ehrlichia Chaffeensis
Length = 442
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 21/39 (53%)
Query: 76 KFGDIQSSKVVVSQDGKSKGYGFVQYSTQESALNAIEKL 114
KF D +VV DG ++G G V T E A NA++ +
Sbjct: 152 KFIDKHKLPLVVKADGLAQGKGTVICHTHEEAYNAVDAM 190
>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 = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 89 QDGKSKGYGFVQYSTQESALNAIEKL 114
Q G+SKGY F+++ ES+ +A+ L
Sbjct: 40 QTGRSKGYAFIEFRDLESSASAVRNL 65
Score = 28.1 bits (61), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 161 LYVKNINDDVDEIELKQYFSQCGIISSVKIM-RTNRGISKGFGFVCFSNPDEANRAINTL 219
+Y+ +I D E ++ S G + ++K+M G SKG+ F+ F + + + A+ L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 220 NG 221
NG
Sbjct: 66 NG 67
>pdb|3AQB|B Chain B, M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate
Synthase In Complex With Magnesium
pdb|3AQB|D Chain D, M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate
Synthase In Complex With Magnesium
pdb|3AQC|B Chain B, M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate
Synthase In Complex With Magnesium And Fpp Analogue
pdb|3AQC|D Chain D, M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate
Synthase In Complex With Magnesium And Fpp Analogue
Length = 325
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 27 LDSTDLLRLCSALIASIDVHSAMATPTFI-PFTVNLASTIDNWKLHQIFSK 76
+D++D+ R +++ + D +A+ T F+ + +TI+N K HQIFSK
Sbjct: 87 IDNSDMRRGNTSVHIAFDKDTAIRTGHFLLARALQNIATINNSKFHQIFSK 137
>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 = 28.5 bits (62), Expect = 5.2, Method: Composition-based stats.
Identities = 14/60 (23%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVV-SQDGKSKGYGFVQYSTQESALNAIEKLY 115
F L+ K+ + F FG+++S ++ + ++ K +G+ F+ + +E +EK Y
Sbjct: 5 FVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKY 64
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 28.5 bits (62), Expect = 5.2, Method: Composition-based stats.
Identities = 14/60 (23%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 57 FTVNLASTIDNWKLHQIFSKFGDIQSSKVVV-SQDGKSKGYGFVQYSTQESALNAIEKLY 115
F L+ K+ + F FG+++S ++ + ++ K +G+ F+ + +E +EK Y
Sbjct: 3 FVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKY 62
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
0.318 0.134 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,768,259
Number of Sequences: 62578
Number of extensions: 385949
Number of successful extensions: 1513
Number of sequences better than 100.0: 184
Number of HSP's better than 100.0 without gapping: 103
Number of HSP's successfully gapped in prelim test: 81
Number of HSP's that attempted gapping in prelim test: 1164
Number of HSP's gapped (non-prelim): 332
length of query: 354
length of database: 14,973,337
effective HSP length: 100
effective length of query: 254
effective length of database: 8,715,537
effective search space: 2213746398
effective search space used: 2213746398
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)