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= psy12549
(336 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 214 bits (546), Expect = 4e-56, Method: Compositional matrix adjust.
Identities = 105/141 (74%), Positives = 118/141 (83%), Gaps = 3/141 (2%)
Query: 63 GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
G V QP D ERALDTMNFD +KG+P+RIMWSQRDPSLRKSGVGN+FIKNLDKSI
Sbjct: 53 GYAYVNFQQP--ADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSI 110
Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
DNKA+YDTFSAFG+ILSCKV DE G SKGYGFVHFET+EAA ++IEK+NGMLLN + VF
Sbjct: 111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 169
Query: 183 VGKFIPRKEREKELGEKAKLF 203
VG+F RKERE ELG +AK F
Sbjct: 170 VGRFKSRKEREAELGARAKEF 190
Score = 91.7 bits (226), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 54/191 (28%), Positives = 105/191 (54%), Gaps = 7/191 (3%)
Query: 102 DPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFET 160
+PS + ++++ +L + +Y+ FS G ILS +V +D S GY +V+F+
Sbjct: 2 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 61
Query: 161 EEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKL 220
A ++++ +N ++ K V I +R+ L + N++IKN + +++ L
Sbjct: 62 PADAERALDTMNFDVIKGKPVR----IMWSQRDPSLRKSG--VGNIFIKNLDKSIDNKAL 115
Query: 221 KEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK 280
+ F +G I S +V+ ++ S+G+GFV +E+ E AE+A++ NG ++ + ++VGR +
Sbjct: 116 YDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 175
Query: 281 KAERTQELKRR 291
+ ER EL R
Sbjct: 176 RKEREAELGAR 186
Score = 59.3 bits (142), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 40/136 (29%), Positives = 64/136 (47%), Gaps = 20/136 (14%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
++Y+ + D + L E F P G I S RV + +S G+ +V ++ P AE+A+
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGV-NLYVKNLDDSIDDE 320
N + GK + + +Q+ R GV N+++KNLD SID++
Sbjct: 71 TMNFDVIKGKPVRIMWSQRDPSL-----------------RKSGVGNIFIKNLDKSIDNK 113
Query: 321 RLRKEFTPFGTITSAK 336
L F+ FG I S K
Sbjct: 114 ALYDTFSAFGNILSCK 129
>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 = 214 bits (545), Expect = 5e-56, Method: Compositional matrix adjust.
Identities = 105/141 (74%), Positives = 118/141 (83%), Gaps = 3/141 (2%)
Query: 63 GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
G V QP D ERALDTMNFD +KG+P+RIMWSQRDPSLRKSGVGN+FIKNLDKSI
Sbjct: 58 GYAYVNFQQP--ADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSI 115
Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
DNKA+YDTFSAFG+ILSCKV DE G SKGYGFVHFET+EAA ++IEK+NGMLLN + VF
Sbjct: 116 DNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 174
Query: 183 VGKFIPRKEREKELGEKAKLF 203
VG+F RKERE ELG +AK F
Sbjct: 175 VGRFKSRKEREAELGARAKEF 195
Score = 91.7 bits (226), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 54/191 (28%), Positives = 105/191 (54%), Gaps = 7/191 (3%)
Query: 102 DPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFET 160
+PS + ++++ +L + +Y+ FS G ILS +V +D S GY +V+F+
Sbjct: 7 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66
Query: 161 EEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKL 220
A ++++ +N ++ K V I +R+ L + N++IKN + +++ L
Sbjct: 67 PADAERALDTMNFDVIKGKPVR----IMWSQRDPSLRKSG--VGNIFIKNLDKSIDNKAL 120
Query: 221 KEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK 280
+ F +G I S +V+ ++ S+G+GFV +E+ E AE+A++ NG ++ + ++VGR +
Sbjct: 121 YDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 180
Query: 281 KAERTQELKRR 291
+ ER EL R
Sbjct: 181 RKEREAELGAR 191
Score = 58.9 bits (141), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 40/137 (29%), Positives = 64/137 (46%), Gaps = 20/137 (14%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV 260
++Y+ + D + L E F P G I S RV + +S G+ +V ++ P AE+A+
Sbjct: 15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74
Query: 261 QAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGV-NLYVKNLDDSIDD 319
N + GK + + +Q+ R GV N+++KNLD SID+
Sbjct: 75 DTMNFDVIKGKPVRIMWSQRDPSL-----------------RKSGVGNIFIKNLDKSIDN 117
Query: 320 ERLRKEFTPFGTITSAK 336
+ L F+ FG I S K
Sbjct: 118 KALYDTFSAFGNILSCK 134
>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 = 165 bits (417), Expect = 4e-41, Method: Compositional matrix adjust.
Identities = 81/104 (77%), Positives = 91/104 (87%), Gaps = 1/104 (0%)
Query: 109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSI 168
G GN+FIKNLDKSIDNKA+YDTFSAFG+ILSCKV DE G SKGYGFVHFET+EAA ++I
Sbjct: 4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAI 62
Query: 169 EKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFG 212
EK+NGMLLN + VFVG+F RKERE ELG +AK FTNVYIKNFG
Sbjct: 63 EKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFG 106
Score = 66.6 bits (161), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 34/109 (31%), Positives = 63/109 (57%), Gaps = 10/109 (9%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
N++IKN + +++ L + F +G I S +V+ ++ S+G+GFV +E+ E AE+A++ N
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 66
Query: 265 GKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNL 313
G ++ + ++VGR + + ER EL R + N+Y+KN
Sbjct: 67 GMLLNDRKVFVGRFKSRKEREAELGARAKEF----------TNVYIKNF 105
Score = 36.2 bits (82), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 21/30 (70%)
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
N+++KNLD SID++ L F+ FG I S K
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCK 36
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 154 bits (389), Expect = 7e-38, Method: Compositional matrix adjust.
Identities = 75/94 (79%), Positives = 84/94 (89%), Gaps = 1/94 (1%)
Query: 102 DPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETE 161
DPSLRKSGVGN+FIKNLDKSIDNKA+YDTFSAFG+ILSCKV DE G SKGYGFVHFET+
Sbjct: 3 DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQ 61
Query: 162 EAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKE 195
EAA ++IEK+NGMLLN + VFVG+F RKERE E
Sbjct: 62 EAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 95
Score = 63.5 bits (153), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 54/83 (65%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
N++IKN + +++ L + F +G I S +V+ ++ S+G+GFV +E+ E AE+A++ N
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 72
Query: 265 GKEVDGKILYVGRAQKKAERTQE 287
G ++ + ++VGR + + ER E
Sbjct: 73 GMLLNDRKVFVGRFKSRKEREAE 95
Score = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 24/36 (66%), Gaps = 1/36 (2%)
Query: 302 RYQGV-NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
R GV N+++KNLD SID++ L F+ FG I S K
Sbjct: 7 RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCK 42
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 89.7 bits (221), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 42/80 (52%), Positives = 56/80 (70%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
N+Y+KN + +DE+L++ F P+GTITS +VM G+S+GFGFV + SPE A KAV N
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 265 GKEVDGKILYVGRAQKKAER 284
G+ V K LYV AQ+K ER
Sbjct: 77 GRIVATKPLYVALAQRKEER 96
Score = 72.0 bits (175), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 32/39 (82%), Positives = 35/39 (89%)
Query: 298 ERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+R+ RYQ VNLYVKNLDD IDDERLRK F+PFGTITSAK
Sbjct: 8 DRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAK 46
Score = 67.0 bits (162), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 34/84 (40%), Positives = 55/84 (65%), Gaps = 1/84 (1%)
Query: 110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE 169
V N+++KNLD ID++ + FS FG+I S KV E G SKG+GFV F + E A K++
Sbjct: 15 VVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM-EGGRSKGFGFVCFSSPEEATKAVT 73
Query: 170 KVNGMLLNSKIVFVGKFIPRKERE 193
++NG ++ +K ++V ++ER+
Sbjct: 74 EMNGRIVATKPLYVALAQRKEERQ 97
>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 = 85.1 bits (209), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 48/172 (27%), Positives = 95/172 (55%), Gaps = 6/172 (3%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKV 171
V++ ++ + + F+ FG I S ++ D KG+ FV +E EAA ++E++
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 172 NGMLLNSKIVFVGKFIPRKEREK---ELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYG 228
N ++L + + VG+ + + +L E+A+ F +Y+ + +D +D+ +K +FE +G
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 135
Query: 229 TITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA 278
I S + + GK +G+GF+ YE + ++ AV + N ++ G+ L VG+A
Sbjct: 136 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 187
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 42/154 (27%), Positives = 72/154 (46%), Gaps = 27/154 (17%)
Query: 191 EREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDG---KSRGFGF 247
+R++ L + VY+ + + ++ +++ F P+G I S M+ D K +GF F
Sbjct: 5 QRQRALA----IMCRVYVGSIYYELGEDTIRQAFAPFGPIKSID-MSWDSVTMKHKGFAF 59
Query: 248 VAYESPEFAEKAVQAWNGKEVDGKILYVGR------AQKKAERTQELKRRFEMLKIERLN 301
V YE PE A+ A++ N + G+ + VGR AQ ++ E R F N
Sbjct: 60 VEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF--------N 111
Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSA 335
R +YV ++ + D+ ++ F FG I S
Sbjct: 112 R-----IYVASVHQDLSDDDIKSVFEAFGKIKSC 140
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 38/152 (25%), Positives = 70/152 (46%), Gaps = 15/152 (9%)
Query: 46 TVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRI----MWSQR 101
++ WDS H+ G V+ P + AL+ MN L GR I++ Q
Sbjct: 42 SIDMSWDSVTMKHK---GFAFVEYEVPEA--AQLALEQMNSVMLGGRNIKVGRPSNIGQA 96
Query: 102 DPSLRK-----SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGF 155
P + + +++ ++ + + + + F AFG I SC +A+D G KGYGF
Sbjct: 97 QPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGF 156
Query: 156 VHFETEEAANKSIEKVNGMLLNSKIVFVGKFI 187
+ +E +++ ++ +N L + + VGK +
Sbjct: 157 IEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 188
>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 = 84.7 bits (208), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 48/172 (27%), Positives = 95/172 (55%), Gaps = 6/172 (3%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKV 171
V++ ++ + + F+ FG I S ++ D KG+ FV +E EAA ++E++
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 172 NGMLLNSKIVFVGKFIPRKEREK---ELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYG 228
N ++L + + VG+ + + +L E+A+ F +Y+ + +D +D+ +K +FE +G
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 150
Query: 229 TITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA 278
I S + + GK +G+GF+ YE + ++ AV + N ++ G+ L VG+A
Sbjct: 151 KIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
Score = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 41/143 (28%), Positives = 69/143 (48%), Gaps = 23/143 (16%)
Query: 202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDG---KSRGFGFVAYESPEFAEK 258
+ + VY+ + + ++ +++ F P+G I S M+ D K +GF FV YE PE A+
Sbjct: 27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSID-MSWDSVTMKHKGFAFVEYEVPEAAQL 85
Query: 259 AVQAWNGKEVDGKILYVGR------AQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKN 312
A++ N + G+ + VGR AQ ++ E R F NR +YV +
Sbjct: 86 ALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF--------NR-----IYVAS 132
Query: 313 LDDSIDDERLRKEFTPFGTITSA 335
+ + D+ ++ F FG I SA
Sbjct: 133 VHQDLSDDDIKSVFEAFGKIKSA 155
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 37/152 (24%), Positives = 69/152 (45%), Gaps = 15/152 (9%)
Query: 46 TVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIM----WSQR 101
++ WDS H+ G V+ P + AL+ MN L GR I++ Q
Sbjct: 57 SIDMSWDSVTMKHK---GFAFVEYEVPEA--AQLALEQMNSVMLGGRNIKVGRPSNIGQA 111
Query: 102 DPSLRK-----SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGF 155
P + + +++ ++ + + + + F AFG I S +A+D G KGYGF
Sbjct: 112 QPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGF 171
Query: 156 VHFETEEAANKSIEKVNGMLLNSKIVFVGKFI 187
+ +E +++ ++ +N L + + VGK +
Sbjct: 172 IEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 203
>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 = 82.0 bits (201), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 48/172 (27%), Positives = 92/172 (53%), Gaps = 6/172 (3%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKV 171
V++ ++ + + F+ FG I S + D KG+ FV +E EAA ++E+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 172 NGMLLNSKIVFVGKFIPRKEREK---ELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYG 228
N + L + + VG+ + + +L E+A+ F +Y+ + +D +D+ +K +FE +G
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 134
Query: 229 TITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA 278
I S + + GK +G+GF+ YE + ++ AV + N ++ G+ L VG+A
Sbjct: 135 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKA 186
Score = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 41/153 (26%), Positives = 68/153 (44%), Gaps = 25/153 (16%)
Query: 191 EREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFV 248
+R++ L +++ GED +++ F P+G I S + K +GF FV
Sbjct: 4 QRQRALAIXCRVYVGSIYYELGED----TIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFV 59
Query: 249 AYESPEFAEKAVQAWNGKEVDGKILYVGR------AQKKAERTQELKRRFEMLKIERLNR 302
YE PE A+ A++ N + G+ + VGR AQ ++ E R F NR
Sbjct: 60 EYEVPEAAQLALEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF--------NR 111
Query: 303 YQGVNLYVKNLDDSIDDERLRKEFTPFGTITSA 335
+YV ++ + D+ ++ F FG I S
Sbjct: 112 -----IYVASVHQDLSDDDIKSVFEAFGKIKSC 139
Score = 47.8 bits (112), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 37/152 (24%), Positives = 68/152 (44%), Gaps = 15/152 (9%)
Query: 46 TVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRI----MWSQR 101
++ WDS H+ G V+ P + AL+ N L GR I++ Q
Sbjct: 41 SIDXSWDSVTXKHK---GFAFVEYEVPEA--AQLALEQXNSVXLGGRNIKVGRPSNIGQA 95
Query: 102 DPSLRK-----SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGF 155
P + + +++ ++ + + + + F AFG I SC +A+D G KGYGF
Sbjct: 96 QPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGF 155
Query: 156 VHFETEEAANKSIEKVNGMLLNSKIVFVGKFI 187
+ +E +++ ++ N L + + VGK +
Sbjct: 156 IEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAV 187
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 79.7 bits (195), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 46/156 (29%), Positives = 82/156 (52%), Gaps = 11/156 (7%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
N+ + L + + ++ +Y F A G I +C++ +D + G S GY FV F +E + ++I+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTI 230
+NG+ + +K + V P E K+ TN+Y+ N D++L +F YG+I
Sbjct: 65 LNGITVRNKRLKVSYARPGGESIKD--------TNLYVTNLPRTITDDQLDTIFGKYGSI 116
Query: 231 TSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAWN 264
++ + G+ RG FV Y E A++A+ A N
Sbjct: 117 VQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Score = 54.3 bits (129), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 37/131 (28%), Positives = 60/131 (45%), Gaps = 20/131 (15%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
TN+ + +D D +L +F G I + R+M + G S G+ FV + S +++A++
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
NG V K L V A+ E ++ NLYV NL +I D++
Sbjct: 64 VLNGITVRNKRLKVSYARPGGESIKD------------------TNLYVTNLPRTITDDQ 105
Query: 322 LRKEFTPFGTI 332
L F +G+I
Sbjct: 106 LDTIFGKYGSI 116
>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 = 78.2 bits (191), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 46/156 (29%), Positives = 81/156 (51%), Gaps = 11/156 (7%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
N+ + L + ++ +Y F A G I +C++ +D + G S GY FV F +E + ++I+
Sbjct: 16 NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTI 230
+NG+ + +K + V P E K+ TN+Y+ N D++L +F YG+I
Sbjct: 76 LNGITVRNKRLKVSYARPGGESIKD--------TNLYVTNLPRTITDDQLDTIFGKYGSI 127
Query: 231 TSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAWN 264
++ + G+ RG FV Y E A++A+ A N
Sbjct: 128 VQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 36/131 (27%), Positives = 59/131 (45%), Gaps = 20/131 (15%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
TN+ + +D D +L +F G I + R+ + G S G+ FV + S +++A++
Sbjct: 15 TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
NG V K L V A+ E ++ NLYV NL +I D++
Sbjct: 75 VLNGITVRNKRLKVSYARPGGESIKD------------------TNLYVTNLPRTITDDQ 116
Query: 322 LRKEFTPFGTI 332
L F +G+I
Sbjct: 117 LDTIFGKYGSI 127
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 77.0 bits (188), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 48/165 (29%), Positives = 85/165 (51%), Gaps = 11/165 (6%)
Query: 109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKS 167
G N+ + L +++ + FS+ G + S K+ +D+ G+S GYGFV++ T + A ++
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 168 IEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPY 227
I +NG+ L SK + V P E K+ N+YI + +++MF +
Sbjct: 61 INTLNGLRLQSKTIKVSYARPSSEVIKD--------ANLYISGLPRTMTQKDVEDMFSRF 112
Query: 228 GTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG 270
G I + RV+ G SRG F+ ++ AE+A+ ++NG + G
Sbjct: 113 GRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPG 157
Score = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 35/117 (29%), Positives = 62/117 (52%), Gaps = 7/117 (5%)
Query: 58 HQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKN 117
H LG G + + D ERA++T+N L+ + I++ +++ PS N++I
Sbjct: 42 HSLGYGFVNYVTAK----DAERAINTLNGLRLQSKTIKVSYAR--PSSEVIKDANLYISG 95
Query: 118 LDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNG 173
L +++ K + D FS FG I++ +V D+ G S+G F+ F+ A ++I NG
Sbjct: 96 LPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 30/135 (22%), Positives = 63/135 (46%), Gaps = 20/135 (14%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
TN+ + ++ ++L+ +F G + S +++ + G S G+GFV Y + + AE+A+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
NG + K + V A+ +E ++ NLY+ L ++ +
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSEVIKD------------------ANLYISGLPRTMTQKD 104
Query: 322 LRKEFTPFGTITSAK 336
+ F+ FG I +++
Sbjct: 105 VEDMFSRFGRIINSR 119
>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 = 77.0 bits (188), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 48/165 (29%), Positives = 85/165 (51%), Gaps = 11/165 (6%)
Query: 109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKS 167
G N+ + L +++ + FS+ G + S K+ +D+ G+S GYGFV++ T + A ++
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 168 IEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPY 227
I +NG+ L SK + V P E K+ N+YI + +++MF +
Sbjct: 61 INTLNGLRLQSKTIKVSYARPSSEVIKD--------ANLYISGLPRTMTQKDVEDMFSRF 112
Query: 228 GTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG 270
G I + RV+ G SRG F+ ++ AE+A+ ++NG + G
Sbjct: 113 GRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPG 157
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 35/117 (29%), Positives = 62/117 (52%), Gaps = 7/117 (5%)
Query: 58 HQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKN 117
H LG G + + D ERA++T+N L+ + I++ +++ PS N++I
Sbjct: 42 HSLGYGFVNYVTAK----DAERAINTLNGLRLQSKTIKVSYAR--PSSEVIKDANLYISG 95
Query: 118 LDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNG 173
L +++ K + D FS FG I++ +V D+ G S+G F+ F+ A ++I NG
Sbjct: 96 LPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 48.1 bits (113), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 30/135 (22%), Positives = 63/135 (46%), Gaps = 20/135 (14%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
TN+ + ++ ++L+ +F G + S +++ + G S G+GFV Y + + AE+A+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
NG + K + V A+ +E ++ NLY+ L ++ +
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSEVIKD------------------ANLYISGLPRTMTQKD 104
Query: 322 LRKEFTPFGTITSAK 336
+ F+ FG I +++
Sbjct: 105 VEDMFSRFGRIINSR 119
>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 = 77.0 bits (188), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 45/162 (27%), Positives = 85/162 (52%), Gaps = 11/162 (6%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEK 170
N+ + L +++ + F + G I SCK+ +D+ G S GYGFV++ + A K+I
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTI 230
+NG+ L +K + V P ++ N+Y+ + ++L+++F YG I
Sbjct: 64 LNGLRLQTKTIKVSYARPSSASIRD--------ANLYVSGLPKTMTQKELEQLFSQYGRI 115
Query: 231 TSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDG 270
+ R++ + G SRG GF+ ++ AE+A++ NG++ G
Sbjct: 116 ITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSG 157
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/99 (28%), Positives = 58/99 (58%), Gaps = 3/99 (3%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
D E+A++T+N L+ + I++ +++ PS N+++ L K++ K + FS +G
Sbjct: 56 DAEKAINTLNGLRLQTKTIKVSYAR--PSSASIRDANLYVSGLPKTMTQKELEQLFSQYG 113
Query: 136 SILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNG 173
I++ ++ D+ G S+G GF+ F+ A ++I+ +NG
Sbjct: 114 RIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 152
Score = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 33/135 (24%), Positives = 63/135 (46%), Gaps = 20/135 (14%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
TN+ + ++ E+ + +F G I S +++ + G+S G+GFV Y P+ AEKA+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
NG + K + V A+ + ++ NLYV L ++ +
Sbjct: 63 TLNGLRLQTKTIKVSYARPSSASIRD------------------ANLYVSGLPKTMTQKE 104
Query: 322 LRKEFTPFGTITSAK 336
L + F+ +G I +++
Sbjct: 105 LEQLFSQYGRIITSR 119
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 75.1 bits (183), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 44/162 (27%), Positives = 84/162 (51%), Gaps = 11/162 (6%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEK 170
N+ + L +++ F + G I SCK+ +D+ G S GYGFV++ A+K+I
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTI 230
+NG+ L +K + V P ++ N+Y+ + + ++++++F YG I
Sbjct: 66 LNGLKLQTKTIKVSYARPSSASIRD--------ANLYVSGLPKTMSQKEMEQLFSQYGRI 117
Query: 231 TSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG 270
+ R++ G SRG GF+ ++ AE+A++ NG++ G
Sbjct: 118 ITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLG 159
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 31/135 (22%), Positives = 63/135 (46%), Gaps = 20/135 (14%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
TN+ + ++ ++ K +F G I S +++ + G+S G+GFV Y P A+KA+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
NG ++ K + V A+ + ++ NLYV L ++ +
Sbjct: 65 TLNGLKLQTKTIKVSYARPSSASIRD------------------ANLYVSGLPKTMSQKE 106
Query: 322 LRKEFTPFGTITSAK 336
+ + F+ +G I +++
Sbjct: 107 MEQLFSQYGRIITSR 121
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 70.9 bits (172), Expect = 9e-13, Method: Compositional matrix adjust.
Identities = 37/78 (47%), Positives = 54/78 (69%), Gaps = 2/78 (2%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSIL-SCKVAQD-EQGNSKGYGFVHFETEEAAN 165
SG +FI NLD ID K +YDTFSAFG IL + K+ +D + GNSKGY F++F + +A++
Sbjct: 3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62
Query: 166 KSIEKVNGMLLNSKIVFV 183
+IE +NG L ++ + V
Sbjct: 63 AAIEAMNGQYLCNRPITV 80
Score = 36.2 bits (82), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 20/84 (23%), Positives = 47/84 (55%), Gaps = 3/84 (3%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTI-TSYRVMNND--GKSRGFGFVAYESPEFAEKAV 260
+ ++I N + +++ L + F +G I + ++M + G S+G+ F+ + S + ++ A+
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 261 QAWNGKEVDGKILYVGRAQKKAER 284
+A NG+ + + + V A KK +
Sbjct: 66 EAMNGQYLCNRPITVSYAFKKDSK 89
>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 = 70.9 bits (172), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 42/148 (28%), Positives = 79/148 (53%), Gaps = 15/148 (10%)
Query: 117 NLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGML 175
N D + DN Y F +G++ K+ +D G S+G+GF+ FE + ++ ++ + +
Sbjct: 12 NWDTTEDNLREY--FGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQH--I 67
Query: 176 LNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRV 235
L+ K++ + IPR E++K +++ G D ++ +E F +GTI ++
Sbjct: 68 LDGKVIDPKRAIPRDEQDKT--------GKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQL 119
Query: 236 M--NNDGKSRGFGFVAYESPEFAEKAVQ 261
M + G+SRGFGFV Y+S + ++ Q
Sbjct: 120 MLDKDTGQSRGFGFVTYDSADAVDRVCQ 147
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 48/83 (57%), Gaps = 4/83 (4%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
++I D ++ L+E F YGT+T ++M + G+SRGFGF+++E P ++ V+
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Query: 262 AWNGKEVDGKILYVGRAQKKAER 284
+ +DGK++ RA + E+
Sbjct: 64 TQH--ILDGKVIDPKRAIPRDEQ 84
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 103 PSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETE 161
P + G +F+ + + K + FS +G+I+ ++ D + G S+G+GFV +++
Sbjct: 80 PRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSA 139
Query: 162 EAANKSIE 169
+A ++ +
Sbjct: 140 DAVDRVCQ 147
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 69.3 bits (168), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 43/170 (25%), Positives = 87/170 (51%), Gaps = 8/170 (4%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+++ NLDK+I + F G I + K+ D+ + Y FV + AN +++ +N
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 173 GMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITS 232
G + + IV + ++ + F N+++ + + +DE L+ F+ + + S
Sbjct: 63 GKQIENNIVKINWAFQSQQSSSD-----DTF-NLFVGDLNVNVDDETLRNAFKDFPSYLS 116
Query: 233 YRVMNN--DGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK 280
VM + G SRG+GFV++ S + A+ A+ + G++++G+ L + A K
Sbjct: 117 GHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 57.8 bits (138), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 31/105 (29%), Positives = 58/105 (55%), Gaps = 1/105 (0%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
D AL T+N ++ ++I W+ + N+F+ +L+ ++D++ + + F F
Sbjct: 53 DANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFP 112
Query: 136 SILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVNGMLLNSK 179
S LS V D Q G+S+GYGFV F +++ A +++ + G LN +
Sbjct: 113 SYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGR 157
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 32/131 (24%), Positives = 62/131 (47%), Gaps = 17/131 (12%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQAWN 264
+Y+ N + ++ LK+ F+ G I + ++M + + K+ + FV Y A A+Q N
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 265 GKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRK 324
GK+++ I+ + A + + + + NL+V +L+ ++DDE LR
Sbjct: 63 GKQIENNIVKINWAFQSQQSSSD----------------DTFNLFVGDLNVNVDDETLRN 106
Query: 325 EFTPFGTITSA 335
F F + S
Sbjct: 107 AFKDFPSYLSG 117
Score = 31.2 bits (69), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQR 101
D + A+D+M L GRP+RI W+ +
Sbjct: 141 DAQNAMDSMQGQDLNGRPLRINWAAK 166
>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 = 57.8 bits (138), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 52/194 (26%), Positives = 92/194 (47%), Gaps = 23/194 (11%)
Query: 99 SQRDP-SLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFV 156
S ++P LRK +G + + D+S+ + F +G++ C V +D S+G+GFV
Sbjct: 6 SPKEPEQLRKLFIGGLSFETTDESLRSH-----FEQWGTLTDCVVMRDPNTKRSRGFGFV 60
Query: 157 HFETEE----AANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFG 212
+ T E A N KV+G ++ K + + R++ ++ +++
Sbjct: 61 TYATVEEVDAAMNARPHKVDGRVVEPK-----RAVSREDSQRPGAHLT--VKKIFVGGIK 113
Query: 213 EDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV-QAWNGKEVD 269
ED + L++ FE YG I +M + GK RGF FV ++ + +K V Q ++ V+
Sbjct: 114 EDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVN 171
Query: 270 GKILYVGRAQKKAE 283
G V +A K E
Sbjct: 172 GHNCEVRKALSKQE 185
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 43/148 (29%), Positives = 71/148 (47%), Gaps = 19/148 (12%)
Query: 187 IPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRG 244
+ + E KE + KLF I + DE L+ FE +GT+T VM N +SRG
Sbjct: 1 MSKSESPKEPEQLRKLF----IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG 56
Query: 245 FGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQ 304
FGFV Y + E + A+ A K VDG+++ RA + ++ +R L +++
Sbjct: 57 FGFVTYATVEEVDAAMNARPHK-VDGRVVEPKRAVSR----EDSQRPGAHLTVKK----- 106
Query: 305 GVNLYVKNLDDSIDDERLRKEFTPFGTI 332
++V + + ++ LR F +G I
Sbjct: 107 ---IFVGGIKEDTEEHHLRDYFEQYGKI 131
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 45/170 (26%), Positives = 81/170 (47%), Gaps = 20/170 (11%)
Query: 99 SQRDP-SLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFV 156
S ++P LRK +G + + D+S+ + F +G++ C V +D S+G+GFV
Sbjct: 6 SPKEPEQLRKLFIGGLSFETTDESLRSH-----FEQWGTLTDCVVMRDPNTKRSRGFGFV 60
Query: 157 HFETEE----AANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFG 212
+ T E A N KV+G ++ K + + R++ ++ +++
Sbjct: 61 TYATVEEVDAAMNARPHKVDGRVVEPK-----RAVSREDSQRPGAHLT--VKKIFVGGIK 113
Query: 213 EDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV 260
ED + L++ FE YG I +M + GK RGF FV ++ + +K V
Sbjct: 114 EDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 43/148 (29%), Positives = 71/148 (47%), Gaps = 19/148 (12%)
Query: 187 IPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRG 244
+ + E KE + KLF I + DE L+ FE +GT+T VM N +SRG
Sbjct: 1 MSKSESPKEPEQLRKLF----IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG 56
Query: 245 FGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQ 304
FGFV Y + E + A+ A K VDG+++ K+A ++ +R L +++
Sbjct: 57 FGFVTYATVEEVDAAMNARPHK-VDGRVV----EPKRAVSREDSQRPGAHLTVKK----- 106
Query: 305 GVNLYVKNLDDSIDDERLRKEFTPFGTI 332
++V + + ++ LR F +G I
Sbjct: 107 ---IFVGGIKEDTEEHHLRDYFEQYGKI 131
>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 = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 55/195 (28%), Positives = 89/195 (45%), Gaps = 25/195 (12%)
Query: 99 SQRDP-SLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFV 156
S ++P LRK +G + + D+S+ + F +G++ C V +D S+G+GFV
Sbjct: 5 SPKEPEQLRKLFIGGLSFETTDESLRSH-----FEQWGTLTDCVVMRDPNTKRSRGFGFV 59
Query: 157 HFETEE----AANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKL-FTNVYIKNF 211
+ T E A N KV+G ++ K RE A L +++
Sbjct: 60 TYATVEEVDAAMNARPHKVDGRVVEPKRAV--------SREDSQRPGAHLTVKKIFVGGI 111
Query: 212 GEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV-QAWNGKEV 268
ED + L++ FE YG I +M + GK RGF FV ++ + +K V Q ++ V
Sbjct: 112 KEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TV 169
Query: 269 DGKILYVGRAQKKAE 283
+G V +A K E
Sbjct: 170 NGHNCEVRKALSKQE 184
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 43/146 (29%), Positives = 70/146 (47%), Gaps = 19/146 (13%)
Query: 189 RKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFG 246
+ E KE + KLF I + DE L+ FE +GT+T VM N +SRGFG
Sbjct: 2 KSESPKEPEQLRKLF----IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG 57
Query: 247 FVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGV 306
FV Y + E + A+ A K VDG+++ RA + ++ +R L +++
Sbjct: 58 FVTYATVEEVDAAMNARPHK-VDGRVVEPKRAVSR----EDSQRPGAHLTVKK------- 105
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTI 332
++V + + ++ LR F +G I
Sbjct: 106 -IFVGGIKEDTEEHHLRDYFEQYGKI 130
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 45/170 (26%), Positives = 81/170 (47%), Gaps = 20/170 (11%)
Query: 99 SQRDP-SLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFV 156
S ++P LRK +G + + D+S+ + F +G++ C V +D S+G+GFV
Sbjct: 4 SPKEPEQLRKLFIGGLSFETTDESLRSH-----FEQWGTLTDCVVMRDPNTKRSRGFGFV 58
Query: 157 HFETEE----AANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFG 212
+ T E A N KV+G ++ K + + R++ ++ +++
Sbjct: 59 TYATVEEVDAAMNARPHKVDGRVVEPK-----RAVSREDSQRPGAHLT--VKKIFVGGIK 111
Query: 213 EDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV 260
ED + L++ FE YG I +M + GK RGF FV ++ + +K V
Sbjct: 112 EDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 43/146 (29%), Positives = 70/146 (47%), Gaps = 19/146 (13%)
Query: 189 RKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFG 246
+ E KE + KLF I + DE L+ FE +GT+T VM N +SRGFG
Sbjct: 1 KSESPKEPEQLRKLF----IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG 56
Query: 247 FVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGV 306
FV Y + E + A+ A K VDG+++ K+A ++ +R L +++
Sbjct: 57 FVTYATVEEVDAAMNARPHK-VDGRVV----EPKRAVSREDSQRPGAHLTVKK------- 104
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTI 332
++V + + ++ LR F +G I
Sbjct: 105 -IFVGGIKEDTEEHHLRDYFEQYGKI 129
>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 = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 47/179 (26%), Positives = 84/179 (46%), Gaps = 17/179 (9%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEE----AANKS 167
+FI L ++++ F +G++ C V +D S+G+GFV + T E A N
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 168 IEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPY 227
KV+G ++ K + + R++ ++ +++ ED + L++ FE Y
Sbjct: 69 PHKVDGRVVEPK-----RAVSREDSQRPGAHLT--VKKIFVGGIKEDTEEHHLRDYFEQY 121
Query: 228 GTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV-QAWNGKEVDGKILYVGRAQKKAE 283
G I +M + GK RGF FV ++ + +K V Q ++ V+G V +A K E
Sbjct: 122 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVNGHNCEVRKALSKQE 178
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 37/129 (28%), Positives = 64/129 (49%), Gaps = 15/129 (11%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAW 263
++I + DE L+ FE +GT+T VM N +SRGFGFV Y + E + A+ A
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 264 NGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLR 323
K VDG+++ RA + ++ +R L +++ ++V + + ++ LR
Sbjct: 69 PHK-VDGRVVEPKRAVSR----EDSQRPGAHLTVKK--------IFVGGIKEDTEEHHLR 115
Query: 324 KEFTPFGTI 332
F +G I
Sbjct: 116 DYFEQYGKI 124
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 54/195 (27%), Positives = 94/195 (48%), Gaps = 25/195 (12%)
Query: 99 SQRDP-SLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFV 156
S ++P LRK +G + + D+S+ + F +G++ C V +D S+G+GFV
Sbjct: 7 SPKEPEQLRKLFIGGLSFETTDESLRSH-----FEQWGTLTDCVVMRDPNTKRSRGFGFV 61
Query: 157 HFETEE----AANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKL-FTNVYIKNF 211
+ T E A N KV+G ++ K + + R++ ++ A L +++
Sbjct: 62 TYATVEEVDAAMNARPHKVDGRVVEPK-----RAVSREDSQRP---GAHLTVKKIFVGGI 113
Query: 212 GEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV-QAWNGKEV 268
ED + L++ FE YG I +M + GK RGF FV ++ + +K V Q ++ V
Sbjct: 114 KEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TV 171
Query: 269 DGKILYVGRAQKKAE 283
+G V +A K E
Sbjct: 172 NGHNCEVRKALSKQE 186
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 43/146 (29%), Positives = 70/146 (47%), Gaps = 19/146 (13%)
Query: 189 RKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFG 246
+ E KE + KLF I + DE L+ FE +GT+T VM N +SRGFG
Sbjct: 4 KSESPKEPEQLRKLF----IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG 59
Query: 247 FVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGV 306
FV Y + E + A+ A K VDG+++ RA + ++ +R L +++
Sbjct: 60 FVTYATVEEVDAAMNARPHK-VDGRVVEPKRAVSR----EDSQRPGAHLTVKK------- 107
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTI 332
++V + + ++ LR F +G I
Sbjct: 108 -IFVGGIKEDTEEHHLRDYFEQYGKI 132
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 54.3 bits (129), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 50/80 (62%), Gaps = 2/80 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAW 263
+Y+ + + ++ L+ +FEP+G I S ++M + G+S+G+GF+ + E A+KA++
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 264 NGKEVDGKILYVGRAQKKAE 283
NG E+ G+ + VG ++ +
Sbjct: 89 NGFELAGRPMKVGHVTERTD 108
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 45/85 (52%), Gaps = 1/85 (1%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANK 166
+G +++ +L +I + F FG I S ++ D E G SKGYGF+ F E A K
Sbjct: 24 AGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKK 83
Query: 167 SIEKVNGMLLNSKIVFVGKFIPRKE 191
++E++NG L + + VG R +
Sbjct: 84 ALEQLNGFELAGRPMKVGHVTERTD 108
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 50/80 (62%), Gaps = 2/80 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
+++ D N++ L+++F YG I+ V+ + +SRGFGFV +E+ + A+ A+ A
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 264 NGKEVDGKILYVGRAQKKAE 283
NGK VDG+ + V +A K ++
Sbjct: 75 NGKSVDGRQIRVDQAGKSSD 94
Score = 36.2 bits (82), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIE 169
G +F+ L + +++ FS +G I V +D E S+G+GFV FE + A ++
Sbjct: 13 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72
Query: 170 KVNGMLLNSKIVFV 183
+NG ++ + + V
Sbjct: 73 AMNGKSVDGRQIRV 86
>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 = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 45/74 (60%), Gaps = 2/74 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
N++I + ++F D+ L +MF P+G + S +V S+ FGFV+Y++P A+ A+Q
Sbjct: 26 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85
Query: 262 AWNGKEVDGKILYV 275
+ NG ++ K L V
Sbjct: 86 SMNGFQIGMKRLKV 99
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 41/69 (59%), Gaps = 1/69 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEK 170
N+FI +L + ++ + F FG+++S KV D+Q N SK +GFV ++ +A +I+
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 171 VNGMLLNSK 179
+NG + K
Sbjct: 87 MNGFQIGMK 95
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 304 QGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+G NL++ +L D+ L + F PFG + SAK
Sbjct: 24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAK 56
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 42/171 (24%), Positives = 74/171 (43%), Gaps = 18/171 (10%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
+ + NL S+ + + FGS+ C + E+ G SKGYGF + +++A ++ +
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 172 NGMLLNSKIVFV-----GKFIPRKEREKELGEKAKLFTNVYIKNFGEDFND-EKLKEMFE 225
G L + ++V G+ P + L + FND + L
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALLHSRCL----------CVDRLPPGFNDVDALCRALS 207
Query: 226 PYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYV 275
+ T ++ DG+ +GF + YE+ E AE+A Q +G + G L V
Sbjct: 208 AVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 258
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 36/166 (21%), Positives = 70/166 (42%), Gaps = 24/166 (14%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+ I+ L + N+ ++D S + + C V + KG FV E A +I
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDY-ELKYCFVDK-----YKGTAFVTLLNGEQAEAAI---- 74
Query: 173 GMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVY-IKNFGEDFNDEKLKEMFEPYGTIT 231
F + RE+EL + + + + N ++ +E+ P+G++
Sbjct: 75 -----------NAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLE 123
Query: 232 SYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYV 275
++ ++ G+S+G+GF Y + A +A GK + + LYV
Sbjct: 124 RCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
Score = 35.8 bits (81), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 26/104 (25%), Positives = 46/104 (44%), Gaps = 6/104 (5%)
Query: 89 LKGRPIRIMWS---QRDPSLRKSGVGNVFIKNLDKSI-DNKAMYDTFSAFGSILSCKVAQ 144
L R + + W+ Q P+L S + + L D A+ SA S C++A
Sbjct: 162 LGPRTLYVHWTDAGQLTPALLHSRC--LCVDRLPPGFNDVDALCRALSAVHSPTFCQLAC 219
Query: 145 DEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP 188
+ G KG+ + +ET E A ++ ++ +G+ L + V P
Sbjct: 220 GQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAP 263
>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 = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 42/171 (24%), Positives = 74/171 (43%), Gaps = 18/171 (10%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
+ + NL S+ + + FGS+ C + E+ G SKGYGF + +++A ++ +
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 172 NGMLLNSKIVFV-----GKFIPRKEREKELGEKAKLFTNVYIKNFGEDFND-EKLKEMFE 225
G L + ++V G+ P + L + FND + L
Sbjct: 156 LGKPLGPRTLYVHWTDAGQLTPALLHSRCL----------CVDRLPPGFNDVDALCRALS 205
Query: 226 PYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYV 275
+ T ++ DG+ +GF + YE+ E AE+A Q +G + G L V
Sbjct: 206 AVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 256
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 36/166 (21%), Positives = 70/166 (42%), Gaps = 24/166 (14%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+ I+ L + N+ ++D S + + C V + KG FV E A +I
Sbjct: 23 ILIRGLPGDVTNQEVHDLLSDY-ELKYCFVDK-----YKGTAFVTLLNGEQAEAAI---- 72
Query: 173 GMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVY-IKNFGEDFNDEKLKEMFEPYGTIT 231
F + RE+EL + + + + N ++ +E+ P+G++
Sbjct: 73 -----------NAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLE 121
Query: 232 SYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYV 275
++ ++ G+S+G+GF Y + A +A GK + + LYV
Sbjct: 122 RCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 167
Score = 35.8 bits (81), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 26/104 (25%), Positives = 46/104 (44%), Gaps = 6/104 (5%)
Query: 89 LKGRPIRIMWS---QRDPSLRKSGVGNVFIKNLDKSI-DNKAMYDTFSAFGSILSCKVAQ 144
L R + + W+ Q P+L S + + L D A+ SA S C++A
Sbjct: 160 LGPRTLYVHWTDAGQLTPALLHSRC--LCVDRLPPGFNDVDALCRALSAVHSPTFCQLAC 217
Query: 145 DEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP 188
+ G KG+ + +ET E A ++ ++ +G+ L + V P
Sbjct: 218 GQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAP 261
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 42/171 (24%), Positives = 74/171 (43%), Gaps = 18/171 (10%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
+ + NL S+ + + FGS+ C + E+ G SKGYGF + +++A ++ +
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 172 NGMLLNSKIVFV-----GKFIPRKEREKELGEKAKLFTNVYIKNFGEDFND-EKLKEMFE 225
G L + ++V G+ P + L + FND + L
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALLHSRCL----------CVDRLPPGFNDVDALCRALS 207
Query: 226 PYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYV 275
+ T ++ DG+ +GF + YE+ E AE+A Q +G + G L V
Sbjct: 208 AVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 258
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 36/166 (21%), Positives = 70/166 (42%), Gaps = 24/166 (14%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+ I+ L + N+ ++D S + + C V + KG FV E A +I
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDY-ELKYCFVDK-----YKGTAFVTLLNGEQAEAAINA-- 76
Query: 173 GMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVY-IKNFGEDFNDEKLKEMFEPYGTIT 231
F + RE+EL + + + + N ++ +E+ P+G++
Sbjct: 77 -------------FHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLE 123
Query: 232 SYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYV 275
++ ++ G+S+G+GF Y + A +A GK + + LYV
Sbjct: 124 RCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
Score = 35.8 bits (81), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 26/104 (25%), Positives = 46/104 (44%), Gaps = 6/104 (5%)
Query: 89 LKGRPIRIMWS---QRDPSLRKSGVGNVFIKNLDKSI-DNKAMYDTFSAFGSILSCKVAQ 144
L R + + W+ Q P+L S + + L D A+ SA S C++A
Sbjct: 162 LGPRTLYVHWTDAGQLTPALLHSRC--LCVDRLPPGFNDVDALCRALSAVHSPTFCQLAC 219
Query: 145 DEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP 188
+ G KG+ + +ET E A ++ ++ +G+ L + V P
Sbjct: 220 GQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAP 263
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 39/64 (60%), Gaps = 1/64 (1%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQA 262
TN+YI N ++++L+ M +P+G + S R++ ++ G SRG GF ES E E +
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 85
Query: 263 WNGK 266
+NGK
Sbjct: 86 FNGK 89
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 35/67 (52%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
N++I NL S+D + + + FG ++S ++ +D G S+G GF E+ E I
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 172 NGMLLNS 178
NG + +
Sbjct: 87 NGKFIKT 93
Score = 32.0 bits (71), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 306 VNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
NLY+ NL S+D++ L PFG + S +
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTR 56
>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 = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 46/171 (26%), Positives = 85/171 (49%), Gaps = 19/171 (11%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILS---CKVAQDEQGNSKGYGFVHFETEEAANKSI 168
N+FI NL+ NK++ + A + + V G ++ +G+V FE+ E K++
Sbjct: 15 NLFIGNLNP---NKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL 71
Query: 169 EKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYG 228
E + ++I K K R+ +K + + KN + +++LKE+FE
Sbjct: 72 ELTGLKVFGNEI----KLEKPKGRD---SKKVRAARTLLAKNLSFNITEDELKEVFEDAL 124
Query: 229 TITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK---ILYVG 276
I R+++ DGKS+G ++ ++S AEK ++ G E+DG+ + Y G
Sbjct: 125 EI---RLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG 172
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 2/74 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
N++I + ++F D L F P+G + S +V S+ FGFV++++P+ A+ A++
Sbjct: 41 CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK 100
Query: 262 AWNGKEVDGKILYV 275
A NG +V K L V
Sbjct: 101 AMNGFQVGTKRLKV 114
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 43/69 (62%), Gaps = 1/69 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEK 170
N+FI +L + + + TF FG+++S KV D+Q + SK +GFV F+ ++A +I+
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 171 VNGMLLNSK 179
+NG + +K
Sbjct: 102 MNGFQVGTK 110
Score = 32.3 bits (72), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 304 QGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
+G NL++ +L D L F PFG + SAK
Sbjct: 39 EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAK 71
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 45/89 (50%), Gaps = 9/89 (10%)
Query: 89 LKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQG 148
LK RP+RI ++ +L +KNL + N+ + FS FG + V D++G
Sbjct: 83 LKSRPLRIRFATHGAALT--------VKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRG 134
Query: 149 NSKGYGFVHFETEEAANKSIEKV-NGMLL 176
+ G GFV F + A K++E+ +G L
Sbjct: 135 RATGKGFVEFAAKPPARKALERCGDGAFL 163
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 44/143 (30%), Positives = 63/143 (44%), Gaps = 32/143 (22%)
Query: 193 EKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYES 252
EK ++ +LF + N D +E K +FE YG + +N D RGFGF+ ES
Sbjct: 16 EKTYTQRCRLF----VGNLPTDITEEDFKRLFERYGEPSEV-FINRD---RGFGFIRLES 67
Query: 253 PEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKN 312
AE A E+DG IL +++ L+ RF G L VKN
Sbjct: 68 RTLAEIA-----KAELDGTIL----------KSRPLRIRFAT---------HGAALTVKN 103
Query: 313 LDDSIDDERLRKEFTPFGTITSA 335
L + +E L + F+ FG + A
Sbjct: 104 LSPVVSNELLEQAFSQFGPVEKA 126
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 33/150 (22%), Positives = 68/150 (45%), Gaps = 20/150 (13%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+F+ NL I + F +G + +D +G+GF+ E+ A + +++
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELD 79
Query: 173 GMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITS 232
G +L S+ + + +F A + +KN ++E L++ F +G +
Sbjct: 80 GTILKSRPLRI-RF-------------ATHGAALTVKNLSPVVSNELLEQAFSQFGPVEK 125
Query: 233 YRVMNND-GKSRGFGFVAYESPEFAEKAVQ 261
V+ +D G++ G GFV + + A KA++
Sbjct: 126 AVVVVDDRGRATGKGFVEFAAKPPARKALE 155
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 50/87 (57%), Gaps = 3/87 (3%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQA 262
+V++ N + +E+LK++F G + S+R++ GK +G+GF Y+ E A A++
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 263 WNGKEVDGKILYVGRAQKKAERTQELK 289
NG+E G+ L V A + + +ELK
Sbjct: 70 LNGREFSGRALRVDNAASEKNK-EELK 95
Score = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 31/105 (29%), Positives = 51/105 (48%), Gaps = 8/105 (7%)
Query: 102 DPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFET 160
D SLR +VF+ N+ + + D FS G ++S ++ D E G KGYGF ++
Sbjct: 5 DRSLR-----SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59
Query: 161 EEAANKSIEKVNGMLLNSKIVFVGKFIPRKERE--KELGEKAKLF 203
+E A ++ +NG + + + V K +E K LG A +
Sbjct: 60 QETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAPVI 104
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 41/72 (56%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
++++N DF + LK+ F G + + +GKS+G G V +ESPE AE+A +
Sbjct: 9 CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMM 68
Query: 264 NGKEVDGKILYV 275
NG ++ G+ + V
Sbjct: 69 NGMKLSGREIDV 80
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
SG +F++NL K + D F+ G +L + E G SKG G V FE+ E A ++
Sbjct: 6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM-ENGKSKGCGVVKFESPEVAERA 64
Query: 168 IEKVNGMLLNSKIVFV 183
+NGM L+ + + V
Sbjct: 65 CRMMNGMKLSGREIDV 80
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 42/72 (58%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
+ ++++N DF + LK+ F G + + +GKS+G G V +ESPE AE+A +
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMM 65
Query: 264 NGKEVDGKILYV 275
NG ++ G+ + V
Sbjct: 66 NGMKLSGREIDV 77
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
SG +F++NL K + D F+ G +L + E G SKG G V FE+ E A ++
Sbjct: 3 SGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM-ENGKSKGCGVVKFESPEVAERA 61
Query: 168 IEKVNGMLLNSKIVFV 183
+NGM L+ + + V
Sbjct: 62 CRMMNGMKLSGREIDV 77
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 49/82 (59%), Gaps = 2/82 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
+ +Y+ + + ++ L+ +FEP+G I + +M + G+S+G+GF+ + E A +A++
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 262 AWNGKEVDGKILYVGRAQKKAE 283
NG E+ G+ + VG ++ +
Sbjct: 66 QLNGFELAGRPMRVGHVTERLD 87
Score = 46.2 bits (108), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/83 (31%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANK 166
SG +++ +L +I + F FG I + + +D + G SKGYGF+ F E A +
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 167 SIEKVNGMLLNSKIVFVGKFIPR 189
++E++NG L + + VG R
Sbjct: 63 ALEQLNGFELAGRPMRVGHVTER 85
>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 = 49.7 bits (117), Expect = 3e-06, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 44/69 (63%), Gaps = 1/69 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
N+F+ +L+ ++D++ + + F F S LS V D Q G+S+GYGFV F +++ A +++
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 171 VNGMLLNSK 179
+ G LN +
Sbjct: 63 MQGQDLNGR 71
Score = 45.4 bits (106), Expect = 4e-05, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 46/78 (58%), Gaps = 2/78 (2%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQA 262
N+++ + + +DE L+ F+ + + S VM G SRG+GFV++ S + A+ A+ +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 263 WNGKEVDGKILYVGRAQK 280
G++++G+ L + A K
Sbjct: 63 MQGQDLNGRPLRINWAAK 80
Score = 30.4 bits (67), Expect = 1.4, Method: Composition-based stats.
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQR 101
D + A+D+M L GRP+RI W+ +
Sbjct: 55 DAQNAMDSMQGQDLNGRPLRINWAAK 80
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGK-----SRGFGFVAYESPEFAEK 258
+ ++IKN +E LK +F G I S + K S GFGFV Y+ PE A+K
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 259 AVQAWNGKEVDGKILYV 275
A++ G VDG L V
Sbjct: 66 ALKQLQGHTVDGHKLEV 82
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 4/74 (5%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN----SKGYGFVHFETEEA 163
SG +FIKNL+ S + + FS G+I SC +++ + S G+GFV ++ E
Sbjct: 3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62
Query: 164 ANKSIEKVNGMLLN 177
A K+++++ G ++
Sbjct: 63 AQKALKQLQGHTVD 76
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQAWN 264
++I + N++ LK +F +G I+ ++ + KSRGF F+ +E+P A+ A + N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 265 GKEVDGKILYVGRAQKKA 282
GK + GK + V +A+K +
Sbjct: 70 GKSLHGKAIKVEQAKKPS 87
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 35/73 (47%)
Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK 170
G +FI L++ + K + F G I + +D S+G+ F+ FE A + +
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKD 67
Query: 171 VNGMLLNSKIVFV 183
+NG L+ K + V
Sbjct: 68 MNGKSLHGKAIKV 80
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 47.8 bits (112), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 43/181 (23%), Positives = 81/181 (44%), Gaps = 31/181 (17%)
Query: 113 VFIKNLDKSIDNKAMYDTFSA---FG--------SILSCKVAQDEQGNSKGYGFVHFETE 161
+++ N+ I +AM D F+A G +L+ ++ QD K + F+ F
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEF--- 58
Query: 162 EAANKSIEKVNGMLLNSKIVFVGKF--IPRKEREKELGEKAKLFTNVYIKNFGEDFNDEK 219
+S+++ + I+F G+ I R + L KLF I ND++
Sbjct: 59 ----RSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLF----IGGLPNYLNDDQ 110
Query: 220 LKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR 277
+KE+ +G + ++ ++ + G S+G+ F Y ++A+ NG ++ K L V R
Sbjct: 111 VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 170
Query: 278 A 278
A
Sbjct: 171 A 171
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 26/104 (25%), Positives = 49/104 (47%), Gaps = 5/104 (4%)
Query: 83 TMNFDAL--KGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSC 140
M FD + +G+ ++I L G +FI L +++ + + ++FG + +
Sbjct: 67 AMAFDGIIFQGQSLKIRRPHDYQPL--PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAF 124
Query: 141 KVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
+ +D G SKGY F + +++I +NGM L K + V
Sbjct: 125 NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 168
>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 = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 43/181 (23%), Positives = 81/181 (44%), Gaps = 31/181 (17%)
Query: 113 VFIKNLDKSIDNKAMYDTFSA---FG--------SILSCKVAQDEQGNSKGYGFVHFETE 161
+++ N+ I +AM D F+A G +L+ ++ QD K + F+ F
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEF--- 60
Query: 162 EAANKSIEKVNGMLLNSKIVFVGKF--IPRKEREKELGEKAKLFTNVYIKNFGEDFNDEK 219
+S+++ + I+F G+ I R + L KLF I ND++
Sbjct: 61 ----RSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLF----IGGLPNYLNDDQ 112
Query: 220 LKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR 277
+KE+ +G + ++ ++ + G S+G+ F Y ++A+ NG ++ K L V R
Sbjct: 113 VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 172
Query: 278 A 278
A
Sbjct: 173 A 173
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 26/104 (25%), Positives = 49/104 (47%), Gaps = 5/104 (4%)
Query: 83 TMNFDAL--KGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSC 140
M FD + +G+ ++I L G +FI L +++ + + ++FG + +
Sbjct: 69 AMAFDGIIFQGQSLKIRRPHDYQPL--PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAF 126
Query: 141 KVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
+ +D G SKGY F + +++I +NGM L K + V
Sbjct: 127 NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 170
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 43/77 (55%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
+++ N F D L++MF +G I ++ N+ S+GFGFV +E+ A++A + +G
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 91
Query: 266 KEVDGKILYVGRAQKKA 282
V+G+ + V A +
Sbjct: 92 TVVEGRKIEVNNATARV 108
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANK 166
KS + + N+ + + F FG IL ++ +E+G SKG+GFV FE A++
Sbjct: 26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADR 84
Query: 167 SIEKVNGMLLNSKIVFV 183
+ EK++G ++ + + V
Sbjct: 85 AREKLHGTVVEGRKIEV 101
>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 = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKS 167
G N+ + L +++ + FS+ G + S K+ +D+ G+S GYGFV++ T + A ++
Sbjct: 3 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
Query: 168 IEKVNGMLLNSKIVFVGKFIP 188
I +NG+ L SK + V P
Sbjct: 63 INTLNGLRLQSKTIKVSYARP 83
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
TN+ + ++ ++L+ +F G + S +++ + G S G+GFV Y + + AE+A+
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 262 AWNGKEVDGKILYVGRAQ 279
NG + K + V A+
Sbjct: 65 TLNGLRLQSKTIKVSYAR 82
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 43/76 (56%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
+++ N F D L++MF +G I ++ N+ S+GFGFV +E+ A++A + +G
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 77
Query: 266 KEVDGKILYVGRAQKK 281
V+G+ + V A +
Sbjct: 78 TVVEGRKIEVNNATAR 93
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 115 IKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGM 174
+ N+ + + F FG IL ++ +E+G SKG+GFV FE A+++ EK++G
Sbjct: 20 VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGT 78
Query: 175 LLNSK 179
++ +
Sbjct: 79 VVEGR 83
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 42/69 (60%), Gaps = 1/69 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
N+ + L + + ++ +Y F A G I +C++ +D + G S GY FV F +E + ++I+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 171 VNGMLLNSK 179
+NG+ + +K
Sbjct: 65 LNGITVRNK 73
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 2/82 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
TN+ + +D D +L +F G I + R+M + G S G+ FV + S +++A++
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 262 AWNGKEVDGKILYVGRAQKKAE 283
NG V K L V A+ E
Sbjct: 64 VLNGITVRNKRLKVSYARPGGE 85
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 47/98 (47%), Gaps = 10/98 (10%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
VF+ NLD + K + + FS G ++ + +D+ G S+G G V FE A ++I
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 172 NGMLLNSKIVFV---------GKFIPRKEREKELGEKA 200
NG LL + + V G F P ER ++ G +
Sbjct: 77 NGQLLFDRPMHVKMDERALPKGDFFP-PERPQQSGPSS 113
Score = 41.2 bits (95), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 198 EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFA 256
+ +L + V++ N +KLKE+F G + ++ + DGKSRG G V +E A
Sbjct: 10 QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEA 69
Query: 257 EKAVQAWNGKEVDGKILYV 275
+A+ +NG+ + + ++V
Sbjct: 70 VQAISMFNGQLLFDRPMHV 88
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 46/187 (24%), Positives = 83/187 (44%), Gaps = 35/187 (18%)
Query: 96 IMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGF 155
+ +++ P L K+G+ +VF KN V G ++ +G+
Sbjct: 15 LNFNKSAPEL-KTGISDVFAKN---------------------DLAVVDVRIGMTRKFGY 52
Query: 156 VHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDF 215
V FE+ E K++E L VF + K + K+ +K + + KN
Sbjct: 53 VDFESAEDLEKALE------LTGLKVFGNEIKLEKPKGKD-SKKERDARTLLAKNLPYKV 105
Query: 216 NDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK---I 272
++LKE+FE I R+++ DGKS+G ++ +++ AEK + G E+DG+ +
Sbjct: 106 TQDELKEVFEDAAEI---RLVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISL 162
Query: 273 LYVGRAQ 279
Y G +
Sbjct: 163 YYTGEPK 169
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 25/106 (23%), Positives = 47/106 (44%), Gaps = 5/106 (4%)
Query: 76 DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
D E+AL+ G I++ + S ++ + KNL + + + F
Sbjct: 60 DLEKALELTGLKVF-GNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAA 118
Query: 136 SILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIV 181
I V++D G SKG ++ F+TE A K+ E+ G ++ + +
Sbjct: 119 EIRL--VSKD--GKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSI 160
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEK 170
N+ + L +++ F + G I SCK+ +D+ G S GYGFV++ A+K+I
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 171 VNGMLLNSKIVFVGKFIP 188
+NG+ L +K + V P
Sbjct: 66 LNGLKLQTKTIKVSYARP 83
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 43/81 (53%), Gaps = 2/81 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
TN+ + ++ ++ K +F G I S +++ + G+S G+GFV Y P A+KA+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 262 AWNGKEVDGKILYVGRAQKKA 282
NG ++ K + V A+ +
Sbjct: 65 TLNGLKLQTKTIKVSYARPSS 85
>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 = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 45/79 (56%), Gaps = 2/79 (2%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQA 262
+V++ + + E +K F P+G I+ RV+ + GKS+G+GFV++ + AE A+Q
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 263 WNGKEVDGKILYVGRAQKK 281
G+ + G+ + A +K
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
+VF+ +L I + + F+ FG I +V +D G SKGYGFV F + A +I++
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 171 VNGMLLNSKIV 181
+ G L + +
Sbjct: 77 MGGQWLGGRQI 87
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 16/34 (47%)
Query: 75 LDTERALDTMNFDALKGRPIRIMWSQRDPSLRKS 108
D E A+ M L GR IR W+ R P KS
Sbjct: 68 WDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKS 101
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 46/83 (55%), Gaps = 2/83 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTIT--SYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
++++N ++E L+++F YG ++ Y + + K +GF FV + PE A KA
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 264 NGKEVDGKILYVGRAQKKAERTQ 286
+G+ G++L+V + K E +Q
Sbjct: 71 DGQVFQGRMLHVLPSTIKKEASQ 93
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKV 171
+F++NL + + + FSA+G + D KG+ FV F E A K+ +V
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 172 NGMLLNSKIVFV 183
+G + +++ V
Sbjct: 71 DGQVFQGRMLHV 82
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
T ++++ F D + +L E+F P+G + +++N GF FV +E E A KA++
Sbjct: 32 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN------GFAFVEFEEAESAAKAIEEV 85
Query: 264 NGKEVDGKILYVGRAQKKAER 284
+GK + L V ++ A+R
Sbjct: 86 HGKSFANQPLEVVYSKLPAKR 106
Score = 35.4 bits (80), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 7/61 (11%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+F++ + + + F FG + K+ G+ FV FE E+A K+IE+V+
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEVH 86
Query: 173 G 173
G
Sbjct: 87 G 87
>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 = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEK 170
N+ + L ++ + FS+ G + S K+ +D+ G+S GYGFV++ T + A ++I
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 171 VNGMLLNSKIVFVGKFIP 188
+NG+ L SK + V P
Sbjct: 81 LNGLRLQSKTIKVSYARP 98
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
TN+ + ++ ++L+ +F G + S +++ + G S G+GFV Y + + AE+A+
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 262 AWNGKEVDGKILYVGRAQ 279
NG + K + V A+
Sbjct: 80 TLNGLRLQSKTIKVSYAR 97
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 47/92 (51%), Gaps = 11/92 (11%)
Query: 81 LDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSC 140
LD M L+G+ +R+ ++ SL ++NL + + N+ + + FS FG +
Sbjct: 78 LDNM---PLRGKQLRVRFACHSASLT--------VRNLPQYVSNELLEEAFSVFGQVERA 126
Query: 141 KVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
V D++G G G V F + AA K++++ +
Sbjct: 127 VVIVDDRGRPSGKGIVEFSGKPAARKALDRCS 158
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/147 (25%), Positives = 62/147 (42%), Gaps = 32/147 (21%)
Query: 189 RKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFV 248
RK EK ++++LF + N D +E+++++FE YG + K +GFGF+
Sbjct: 12 RKPGEKTFTQRSRLF----VGNLPPDITEEEMRKLFEKYGKAGEVFI----HKDKGFGFI 63
Query: 249 AYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNL 308
E+ AE A + + GK L V A A +L
Sbjct: 64 RLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA------------------------SL 99
Query: 309 YVKNLDDSIDDERLRKEFTPFGTITSA 335
V+NL + +E L + F+ FG + A
Sbjct: 100 TVRNLPQYVSNELLEEAFSVFGQVERA 126
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 36/149 (24%), Positives = 65/149 (43%), Gaps = 20/149 (13%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+F+ NL I + M F +G + +D KG+GF+ ET A + +++
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELD 79
Query: 173 GMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITS 232
M L K + V +F A ++ ++N + ++E L+E F +G +
Sbjct: 80 NMPLRGKQLRV-RF-------------ACHSASLTVRNLPQYVSNELLEEAFSVFGQVER 125
Query: 233 YRVMNND-GKSRGFGFVAYESPEFAEKAV 260
V+ +D G+ G G V + A KA+
Sbjct: 126 AVVIVDDRGRPSGKGIVEFSGKPAARKAL 154
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 44.7 bits (104), Expect = 8e-05, Method: Composition-based stats.
Identities = 28/85 (32%), Positives = 45/85 (52%), Gaps = 2/85 (2%)
Query: 112 NVFIKNLDKSIDNKAMYDTF-SAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK 170
++F+ +L +D+ +Y+ F + S KV D+ G SKGYGFV F E +++ +
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 171 VNGML-LNSKIVFVGKFIPRKEREK 194
G + L SK V + IP+ R K
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASRVK 95
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 44.7 bits (104), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 49/92 (53%), Gaps = 2/92 (2%)
Query: 195 ELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYES 252
++ + + N+ + ++ +L+++FE YG I S +++ + +SRG+GFV ++S
Sbjct: 34 QMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS 93
Query: 253 PEFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
A++A+ NG + K L V A +R
Sbjct: 94 GSSAQQAIAGLNGFNILNKRLKVALAASGHQR 125
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
N+ + + ++D + F +G I S K+ D E S+GYGFV F++ +A ++I
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 171 VNGM-LLNSKI 180
+NG +LN ++
Sbjct: 104 LNGFNILNKRL 114
>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 = 44.3 bits (103), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
TN+Y+ N D++L +F YG+I ++ + G+ RG FV Y E A++A+
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 262 AWN 264
A N
Sbjct: 74 ALN 76
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
+ +YI+ D+ L ++ +PYG I S + + K +G+GFV ++SP A+KAV
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 262 AWNGKEVDGKI 272
A V ++
Sbjct: 66 ALKASGVQAQM 76
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS-KGYGFVHFETEEAANK 166
SG ++I+ L ++ + +G I+S K D+ N KGYGFV F++ AA K
Sbjct: 3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62
Query: 167 SI 168
++
Sbjct: 63 AV 64
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
N+++ L K++ K M FS +G I++ ++ D+ G S+G GF+ F+ A ++I+
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 171 VNG 173
+NG
Sbjct: 63 LNG 65
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 40/69 (57%), Gaps = 2/69 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
N+Y+ + + ++++++F YG I + R++ G SRG GF+ ++ AE+A++
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 262 AWNGKEVDG 270
NG++ G
Sbjct: 62 GLNGQKPLG 70
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 45/77 (58%), Gaps = 3/77 (3%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-GKSRGFGFVAYESPEFAEKAVQAWN 264
+++K ED +E LKE F+ G++ + V + + G S+GFGFV + S E A+ A +A
Sbjct: 18 LFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME 75
Query: 265 GKEVDGKILYVGRAQKK 281
E+DG + + A+ K
Sbjct: 76 DGEIDGNKVTLDWAKPK 92
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 3/81 (3%)
Query: 103 PSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEE 162
P+ R +F+K L + + + ++F GS+ + V E G+SKG+GFV F +EE
Sbjct: 8 PNARSQPSKTLFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEE 65
Query: 163 AANKSIEKV-NGMLLNSKIVF 182
A + E + +G + +K+
Sbjct: 66 DAKAAKEAMEDGEIDGNKVTL 86
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 199 KAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEK 258
K + + KN + +++LKE+FE I R+++ DGKS+G ++ ++S AEK
Sbjct: 12 KVRAARTLLAKNLSFNITEDELKEVFEDALEI---RLVSQDGKSKGIAYIEFKSEADAEK 68
Query: 259 AVQAWNGKEVDGK---ILYVG 276
++ G E+DG+ + Y G
Sbjct: 69 NLEEKQGAEIDGRSVSLYYTG 89
>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 = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIE-- 169
+FI L K + D FS FG ++ C + D G S+G+GFV F+ E+ +K ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 170 --KVNGMLLNSK 179
K+NG +++ K
Sbjct: 62 EHKLNGKVIDPK 73
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTI--TSYRVMNNDGKSRGFGFVAYESPEFAEKAV--- 260
++I D + LK+ F +G + + ++ G+SRGFGFV ++ E +K +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 261 -QAWNGKEVDGK 271
NGK +D K
Sbjct: 62 EHKLNGKVIDPK 73
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 32/100 (32%), Positives = 50/100 (50%), Gaps = 11/100 (11%)
Query: 187 IPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDG--KSRG 244
+ RK+REKE F ++I + +E L+ +E +G +T VM + +SRG
Sbjct: 17 LERKKREKEQ------FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRG 70
Query: 245 FGFVAYESPEFAE-KAVQAWNGKEVDGKILYVGRAQKKAE 283
FGFV + S AE A A +DG+++ RA + E
Sbjct: 71 FGFVTFSS--MAEVDAAMAARPHSIDGRVVEPKRAVAREE 108
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 39/71 (54%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
VF+ NL+ + + +Y+ F G + + +D +G K +GFV F+ E+ + +I +N
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 173 GMLLNSKIVFV 183
G+ L + + V
Sbjct: 79 GIRLYGRPINV 89
Score = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQAWN 264
V++ N +E L E+F G +T + + +GK + FGFV ++ PE A+ N
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 265 GKEVDGKILYV 275
G + G+ + V
Sbjct: 79 GIRLYGRPINV 89
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQA 262
+V++ + + E +K F P+G I+ RV+ + GKS+G+GFV++ + AE A+
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 263 WNGKEVDGKILYVGRAQKK 281
G+ + G+ + A +K
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
+VF+ +L I + + F+ FG I +V +D G SKGYGFV F + A +I
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 171 VNGMLLNSKIV 181
+ G L + +
Sbjct: 77 MGGQWLGGRQI 87
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 6/72 (8%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
T ++++ F D + +L E+F P+G + +++N GF FV +E E A KA++
Sbjct: 5 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN------GFAFVEFEEAESAAKAIEEV 58
Query: 264 NGKEVDGKILYV 275
+GK + L V
Sbjct: 59 HGKSFANQPLEV 70
Score = 34.7 bits (78), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 7/61 (11%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+F++ + + + F FG + K+ G+ FV FE E+A K+IE+V+
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEVH 59
Query: 173 G 173
G
Sbjct: 60 G 60
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 24/65 (36%), Positives = 37/65 (56%), Gaps = 5/65 (7%)
Query: 197 GEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEF 255
GE KLF + G+ DE +++MFEP+GTI V+ DG S+G FV +++
Sbjct: 10 GEDRKLFVGM----LGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAE 65
Query: 256 AEKAV 260
A+ A+
Sbjct: 66 AQAAI 70
Score = 36.6 bits (83), Expect = 0.023, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 30/60 (50%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+F+ L K ++ + F FG+I C V + G SKG FV F+T A +I ++
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 44/84 (52%), Gaps = 4/84 (4%)
Query: 196 LGEKAKLFTNVYIKNFGEDF--NDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYE 251
LG +A N + FG + L+E+F YG I ++ +SRGF FV +E
Sbjct: 3 LGSRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 62
Query: 252 SPEFAEKAVQAWNGKEVDGKILYV 275
+ + A++A + NG E+DG+ + V
Sbjct: 63 NVDDAKEAKERANGMELDGRRIRV 86
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 125 KAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
+ + + FS +G I + D+Q S+G+ FV+FE + A ++ E+ NGM L+ + + V
Sbjct: 27 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 86
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 4/86 (4%)
Query: 194 KELGEKAKLFTNVYIKNFGEDF--NDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVA 249
+ +G +A N + FG + L+E+F YG I ++ +SRGF FV
Sbjct: 35 RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 94
Query: 250 YESPEFAEKAVQAWNGKEVDGKILYV 275
+E+ + A++A + NG E+DG+ + V
Sbjct: 95 FENVDDAKEAKERANGMELDGRRIRV 120
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 125 KAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
+ + + FS +G I + D+Q S+G+ FV+FE + A ++ E+ NGM L+ + + V
Sbjct: 61 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 120
>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: Composition-based stats.
Identities = 23/76 (30%), Positives = 42/76 (55%), Gaps = 2/76 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAW 263
+ + N ED + L+E+F P+G+I+ + + G+S+GF F+++ E A +A+
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 264 NGKEVDGKILYVGRAQ 279
+G D IL V A+
Sbjct: 78 SGFGYDHLILNVEWAK 93
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 103 PSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETE 161
P+ R + + NL + + + F FGSI +A+D+ G SKG+ F+ F
Sbjct: 8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67
Query: 162 EAANKSIEKVNG 173
E A ++I V+G
Sbjct: 68 EDAARAIAGVSG 79
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 5/69 (7%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
V+ + + ++ M TFS FG I+ +V + KGY FV F T E+A +I VN
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVN 82
Query: 173 GMLLNSKIV 181
G + +V
Sbjct: 83 GTTIEGHVV 91
Score = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
VY D+ +++ F P+G I RV +G+ FV + + E A A+ + NG
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVF----PEKGYSFVRFSTHESAAHAIVSVNG 83
Query: 266 KEVDGKIL 273
++G ++
Sbjct: 84 TTIEGHVV 91
>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 = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 30/58 (51%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE 169
VF+ +D +D + F+ +GS+ K+ D G SKGYGFV F + K +E
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 20/87 (22%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 196 LGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPE 254
L E + V++ ++ +++ F YG++ +++ + G S+G+GFV++ +
Sbjct: 2 LPEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDV 61
Query: 255 FAEKAVQAWNGKEVDGKILYVGRAQKK 281
+K V++ GK L +G A +K
Sbjct: 62 DVQKIVESQ--INFHGKKLKLGPAIRK 86
>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 = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 30/58 (51%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE 169
VF+ +D +D + F+ +GS+ K+ D G SKGYGFV F + K +E
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68
Score = 28.9 bits (63), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 20/87 (22%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 196 LGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPE 254
L E + V++ ++ +++ F YG++ +++ + G S+G+GFV++ +
Sbjct: 2 LPEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDV 61
Query: 255 FAEKAVQAWNGKEVDGKILYVGRAQKK 281
+K V++ GK L +G A +K
Sbjct: 62 DVQKIVESQ--INFHGKKLKLGPAIRK 86
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 30/58 (51%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE 169
VF+ +D +D + F+ +GS+ K+ D G SKGYGFV F + K +E
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 69
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 20/87 (22%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 196 LGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPE 254
LG + V++ ++ +++ F YG++ +++ + G S+G+GFV++ +
Sbjct: 3 LGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDV 62
Query: 255 FAEKAVQAWNGKEVDGKILYVGRAQKK 281
+K V++ GK L +G A +K
Sbjct: 63 DVQKIVESQ--INFHGKKLKLGPAIRK 87
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
+Y+ E+ +D+ L F P+G IT ++ + K RGF FV +E E A A+
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 264 NGKEVDGKILYVGRA 278
N E+ G+ + V A
Sbjct: 126 NESELFGRTIRVNLA 140
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
+++ L + +D+K ++ F FG I ++ D E +G+ FV FE E A +I+ +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 172 N 172
N
Sbjct: 126 N 126
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTIT 333
LYV L + +DD+ L F PFG IT
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDIT 91
>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 = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 2/75 (2%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAV 260
F +++ D + KL+ FE YG I ++ GK RG+ F+ YE A
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 261 QAWNGKEVDGKILYV 275
+ +GK++DG+ + V
Sbjct: 162 KHADGKKIDGRRVLV 176
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 2/76 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
+Y+ E+ +D+ L F P+G IT ++ + K RGF FV +E E A A+
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 264 NGKEVDGKILYVGRAQ 279
N E+ G+ + V A+
Sbjct: 75 NESELFGRTIRVNLAK 90
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 1/82 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
+++ L + +D+K ++ F FG I ++ D E +G+ FV FE E A +I+ +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 172 NGMLLNSKIVFVGKFIPRKERE 193
N L + + V P + +E
Sbjct: 75 NESELFGRTIRVNLAKPMRIKE 96
Score = 31.2 bits (69), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTIT 333
LYV L + +DD+ L F PFG IT
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDIT 40
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 41.2 bits (95), Expect = 9e-04, Method: Composition-based stats.
Identities = 20/67 (29%), Positives = 37/67 (55%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+ + NLD + + + + F+ FG++ V D G S G VHFE + A K++++ N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 173 GMLLNSK 179
G+ L+ +
Sbjct: 91 GVPLDGR 97
Score = 33.5 bits (75), Expect = 0.19, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 208 IKNFGEDFNDEKLKEMFEPYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQAWNGK 266
+ N +D ++E+F +GT+ V + G+S G V +E A KA++ +NG
Sbjct: 33 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGV 92
Query: 267 EVDGK 271
+DG+
Sbjct: 93 PLDGR 97
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 10/74 (13%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+F++NL ++ + + FS FG + K +D Y F+HF+ + A K++E++N
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 66
Query: 173 GMLL---NSKIVFV 183
G L N +IVF
Sbjct: 67 GKDLEGENIEIVFA 80
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 4/83 (4%)
Query: 197 GEKAKLFTNVYIKNFGEDF--NDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYES 252
G +A N + FG + L+E+F YG I ++ +SRGF FV +E+
Sbjct: 7 GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66
Query: 253 PEFAEKAVQAWNGKEVDGKILYV 275
+ A++A + NG E+DG+ + V
Sbjct: 67 VDDAKEAKERANGMELDGRRIRV 89
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 125 KAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
+ + + FS +G I + D+Q S+G+ FV+FE + A ++ E+ NGM L+ + + V
Sbjct: 30 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
>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 = 21/74 (28%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKV 171
V++ LD+ + +++ F G +++ + +D G +GYGFV F +EE A+ +I+ +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 172 NGMLLNSKIVFVGK 185
+ + L K + V K
Sbjct: 78 DMIKLYGKPIRVNK 91
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 40/202 (19%), Positives = 87/202 (43%), Gaps = 43/202 (21%)
Query: 113 VFIKNLDKSIDNKAMYDTFSA---FG--------SILSCKVAQDEQGNSKGYGFVHFETE 161
+++ N+ I +AM D F+A G +L+ ++ QD K + F+ F
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEF--- 58
Query: 162 EAANKSIEKVNGMLLNSKIVFVGKFIP-RKEREKE----LGEKAKLFT------------ 204
+S+++ + I+F G+ + R+ + + + E ++
Sbjct: 59 ----RSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSA 114
Query: 205 -NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
++I ND+++KE+ +G + ++ ++ + G S+G+ F Y ++A+
Sbjct: 115 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 174
Query: 262 AWNGKEVDGKILYVGRAQKKAE 283
NG ++ K L V RA A+
Sbjct: 175 GLNGMQLGDKKLLVQRASVGAK 196
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 100 QRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFE 159
++ PS RK +F+ L+K + F AFG+I C + + GNSKG FV +
Sbjct: 10 RQPPSHRK-----LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYS 64
Query: 160 TEEAANKSIEKVNG 173
+ A +I ++G
Sbjct: 65 SHAEAQAAINALHG 78
Score = 36.2 bits (82), Expect = 0.025, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 5/68 (7%)
Query: 201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKA 259
KLF + K ED ++ +FE +G I ++ DG S+G FV Y S A+ A
Sbjct: 17 KLFVGMLNKQQSED----DVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAA 72
Query: 260 VQAWNGKE 267
+ A +G +
Sbjct: 73 INALHGSQ 80
>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 = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 2/76 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
+Y+ E+ +D+ L F P+G IT ++ + K RGF FV +E E A A+
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 264 NGKEVDGKILYVGRAQ 279
N E+ G+ + V A+
Sbjct: 70 NESELFGRTIRVNLAK 85
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
+++ L + +D+K ++ F FG I ++ D E +G+ FV FE E A +I+ +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 172 N 172
N
Sbjct: 70 N 70
Score = 29.6 bits (65), Expect = 2.6, Method: Composition-based stats.
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTIT 333
LYV L + +DD+ L F PFG IT
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDIT 35
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 38/82 (46%), Gaps = 8/82 (9%)
Query: 198 EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAE 257
+ L VY+ N G + N +L+ F YG + S V N GF FV +E P A
Sbjct: 68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN---PPGFAFVEFEDPRDAA 124
Query: 258 KAVQAWNGKEVDGKILYVGRAQ 279
AV +E+DG+ L R +
Sbjct: 125 DAV-----RELDGRTLCGCRVR 141
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 2/76 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
+Y+ E+ +D+ L F P+G IT ++ + K RGF FV +E E A A+
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 264 NGKEVDGKILYVGRAQ 279
N E+ G+ + V A+
Sbjct: 68 NESELFGRTIRVNLAK 83
Score = 37.4 bits (85), Expect = 0.011, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
+++ L + +D+K ++ F FG I ++ D E +G+ FV FE E A +I+ +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 172 N 172
N
Sbjct: 68 N 68
Score = 29.6 bits (65), Expect = 2.7, Method: Composition-based stats.
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTIT 333
LYV L + +DD+ L F PFG IT
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDIT 33
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 4/83 (4%)
Query: 197 GEKAKLFTNVYIKNFGEDF--NDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYES 252
G +A N + FG + L+E+F YG I ++ +SRGF FV +E+
Sbjct: 7 GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66
Query: 253 PEFAEKAVQAWNGKEVDGKILYV 275
+ A++A + NG E+DG+ + V
Sbjct: 67 VDDAKEAKERANGMELDGRRIRV 89
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 125 KAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
+ + + FS +G I + D+Q S+G+ FV+FE + A ++ E+ NGM L+ + + V
Sbjct: 30 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
>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 = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
+Y+ E+ +D+ L F P+G IT ++ + K RGF FV +E E A A+
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 264 NGKEVDGKILYVGRA 278
N E+ G+ + V A
Sbjct: 65 NESELFGRTIRVNLA 79
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
+++ L + +D+K ++ F FG I ++ D E +G+ FV FE E A +I+ +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 172 N 172
N
Sbjct: 65 N 65
Score = 29.6 bits (65), Expect = 2.5, Method: Composition-based stats.
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 308 LYVKNLDDSIDDERLRKEFTPFGTIT 333
LYV L + +DD+ L F PFG IT
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDIT 30
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 2/79 (2%)
Query: 199 KAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFA 256
+ F +++ D + KL+ FE YG I ++ GK RG+ F+ YE
Sbjct: 98 QGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDM 157
Query: 257 EKAVQAWNGKEVDGKILYV 275
A + +GK++DG+ + V
Sbjct: 158 HSAYKHADGKKIDGRRVLV 176
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 198 EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAE 257
+ L VY+ N G + N +L+ F YG + S V N GF FV +E P A
Sbjct: 68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN---PPGFAFVEFEDPRDAA 124
Query: 258 KAVQAWNGKEVDG 270
AV+ +G+ + G
Sbjct: 125 DAVRDLDGRTLCG 137
>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 = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 20/67 (29%), Positives = 36/67 (53%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+ + NLD + + + + F+ FG++ V D G S G VHFE + A K+ ++ N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 173 GMLLNSK 179
G+ L+ +
Sbjct: 92 GVPLDGR 98
Score = 32.3 bits (72), Expect = 0.36, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 208 IKNFGEDFNDEKLKEMFEPYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQAWNGK 266
+ N +D ++E+F +GT+ V + G+S G V +E A KA + +NG
Sbjct: 34 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYNGV 93
Query: 267 EVDGK 271
+DG+
Sbjct: 94 PLDGR 98
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 42/85 (49%), Gaps = 6/85 (7%)
Query: 198 EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEF 255
+K FT +++ D L++ FE +G I V+ + GKSRG+GFV
Sbjct: 12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA 71
Query: 256 AEKAVQAWN----GKEVDGKILYVG 276
AE+A + N G++ + + Y+G
Sbjct: 72 AERACKDPNPIIDGRKANVNLAYLG 96
Score = 35.4 bits (80), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 42/99 (42%), Gaps = 6/99 (6%)
Query: 100 QRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHF 158
Q+D + K +F+ L + ++ F FG I V D Q G S+GYGFV
Sbjct: 12 QKDTTFTK-----IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTM 66
Query: 159 ETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELG 197
AA ++ + N ++ K ++ K R + G
Sbjct: 67 ADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTG 105
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 8/75 (10%)
Query: 99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHF 158
S DP + + V +F++NL ++ + + +FS FG + K +D Y FVHF
Sbjct: 5 SSGDPEVM-AKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHF 56
Query: 159 ETEEAANKSIEKVNG 173
E AA K+++++NG
Sbjct: 57 EDRGAAVKAMDEMNG 71
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 37/71 (52%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+ + NLD + + + + F+ FG++ V D G S G VHFE A K++++
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 173 GMLLNSKIVFV 183
G+ L+ + + +
Sbjct: 151 GVPLDGRPMDI 161
Score = 32.7 bits (73), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 197 GEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRV-MNNDGKSRGFGFVAYESPEF 255
GE + + + N +D ++E+F +GT+ V + G+S G V +E
Sbjct: 82 GEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRAD 141
Query: 256 AEKAVQAWNGKEVDGKILYV 275
A KA++ + G +DG+ + +
Sbjct: 142 ALKAMKQYKGVPLDGRPMDI 161
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 211 FGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG 270
+GED L+ F P+G I + R FV YE E A++AV NG +V+
Sbjct: 21 YGEDMTPTLLRGAFSPFGNIIDLSM----DPPRNCAFVTYEKMESADQAVAELNGTQVES 76
Query: 271 KILYVGRAQKK 281
L V A+K+
Sbjct: 77 VQLKVNIARKQ 87
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 211 FGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG 270
+GED L+ F P+G I + R FV YE E A++AV NG +V+
Sbjct: 45 YGEDMTPTLLRGAFSPFGNIIDLSM----DPPRNCAFVTYEKMESADQAVAELNGTQVES 100
Query: 271 KILYVGRAQKK 281
L V A+K+
Sbjct: 101 VQLKVNIARKQ 111
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRV---MNNDGKSRGFGFVAYESPEFAEKAV 260
T V+I + + + E+F YG I + + S+G+ +V +E+P+ AEKA+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 261 QAWNGKEVDGK 271
+ +G ++DG+
Sbjct: 65 KHMDGGQIDGQ 75
Score = 33.1 bits (74), Expect = 0.24, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSI--LSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK 170
V I L +++ + + FS +G I + V + SKGY +V FE + A K+++
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 171 VNG 173
++G
Sbjct: 67 MDG 69
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 20/80 (25%), Positives = 41/80 (51%), Gaps = 2/80 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAW 263
++I ND+++KE+ +G + ++ ++ + G S+G+ F Y ++A+
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 264 NGKEVDGKILYVGRAQKKAE 283
NG ++ K L V RA A+
Sbjct: 64 NGMQLGDKKLLVQRASVGAK 83
Score = 34.3 bits (77), Expect = 0.100, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKV 171
+FI L +++ + + ++FG + + + +D G SKGY F + +++I +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 172 NGMLLNSKIVFVGK 185
NGM L K + V +
Sbjct: 64 NGMQLGDKKLLVQR 77
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 46/83 (55%), Gaps = 2/83 (2%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
N+++ NL S ++ + + FS FG + + K+ D E KG+GFV + EE+ +++I K
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 171 VNGMLLNSKIVFVGKFIPRKERE 193
++ + + V + P+K E
Sbjct: 62 LDNTDFMGRTIRVTEANPKKSLE 84
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQA 262
N+Y+ N E++KE+F +G + + +++ + K +GFGFV + +E A+
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIAK 61
Query: 263 WNGKEVDGKILYVGRAQKK 281
+ + G+ + V A K
Sbjct: 62 LDNTDFMGRTIRVTEANPK 80
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
VY+ N G +L+ F YG + + + N GF FV +E P AE AV+ +G
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN---PPGFAFVEFEDPRDAEDAVRGLDG 59
Query: 266 KEVDG 270
K + G
Sbjct: 60 KVICG 64
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 23/70 (32%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
+Y+ N D + ++++F YG I + N G F FV +E P AE AV +G
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPP-FAFVEFEDPRDAEDAVYGRDG 83
Query: 266 KEVDGKILYV 275
+ DG L V
Sbjct: 84 YDYDGYRLRV 93
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 35/67 (52%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+ + NLD + + + + F+ FG++ V D G S G VHFE A K++++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 173 GMLLNSK 179
G+ L+ +
Sbjct: 98 GVPLDGR 104
Score = 32.3 bits (72), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 197 GEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRV-MNNDGKSRGFGFVAYESPEF 255
GE + + + N +D ++E+F +GT+ V + G+S G V +E
Sbjct: 29 GEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRAD 88
Query: 256 AEKAVQAWNGKEVDGKILYV 275
A KA++ + G +DG+ + +
Sbjct: 89 ALKAMKQYKGVPLDGRPMDI 108
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 35/67 (52%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+ + NLD + + + + F+ FG++ V D G S G VHFE A K++++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 173 GMLLNSK 179
G+ L+ +
Sbjct: 98 GVPLDGR 104
Score = 32.3 bits (72), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 197 GEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRV-MNNDGKSRGFGFVAYESPEF 255
GE + + + N +D ++E+F +GT+ V + G+S G V +E
Sbjct: 29 GEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRAD 88
Query: 256 AEKAVQAWNGKEVDGKILYV 275
A KA++ + G +DG+ + +
Sbjct: 89 ALKAMKQYKGVPLDGRPMDI 108
>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 = 38.1 bits (87), Expect = 0.007, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 35/58 (60%), Gaps = 2/58 (3%)
Query: 226 PYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK 281
P+G I+ RV+ + GKS+G+GFV++ + AE A+Q G+ + G+ + A +K
Sbjct: 29 PFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86
Score = 35.0 bits (79), Expect = 0.057, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
+VF+ +L I A+ F+ FG I +V +D G SKGYGFV F + A +I++
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 171 VNGMLLNSK 179
+ G L +
Sbjct: 68 MGGQWLGGR 76
>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 = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 5/75 (6%)
Query: 110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSI 168
G F+ L K + D F+ FG ++ C + D G S+G+GF+ F+ + K +
Sbjct: 11 AGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVL 70
Query: 169 E----KVNGMLLNSK 179
+ +++G +++ K
Sbjct: 71 DQKEHRLDGRVIDPK 85
Score = 31.2 bits (69), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 207 YIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWN 264
++ D + + LK+ F +G + + N G+SRGFGF+ ++ EK +
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 265 GKEVDGKIL 273
+ +DG+++
Sbjct: 75 HR-LDGRVI 82
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 37.7 bits (86), Expect = 0.008, Method: Composition-based stats.
Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 3/67 (4%)
Query: 199 KAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRV---MNNDGKSRGFGFVAYESPEF 255
K + + + ++N N +++E+F +G + + R+ M G RGFGFV + + +
Sbjct: 11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 256 AEKAVQA 262
A+KA A
Sbjct: 71 AKKAFNA 77
Score = 33.5 bits (75), Expect = 0.18, Method: Composition-based stats.
Identities = 15/64 (23%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS--KGYGFVHFETEEA 163
+K + ++N+ + + + + FS FG + + ++ + G +G+GFV F T++
Sbjct: 11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 164 ANKS 167
A K+
Sbjct: 71 AKKA 74
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
+ + N +E L+E+FE T +V N +GKS+G+ F+ + S E A++A+ + N
Sbjct: 18 LVLSNLSYSATEETLQEVFE---KATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 265 GKEVDGKIL 273
+E++G+ +
Sbjct: 75 KREIEGRAI 83
Score = 32.3 bits (72), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+ + NL S + + + F I KV Q++ G SKGY F+ F + E A +++ N
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 12/75 (16%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
SG+ +FI NL + + + F +G +L C + K YGFVH E + AA +
Sbjct: 6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDA 58
Query: 168 IE-----KVNGMLLN 177
I K++G+ +N
Sbjct: 59 IRNLHHYKLHGVNIN 73
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/80 (21%), Positives = 41/80 (51%), Gaps = 6/80 (7%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
++I N + +++++ +FE YG + ++ N +GFV E AE A++ +
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKN------YGFVHIEDKTAAEDAIRNLHH 64
Query: 266 KEVDGKILYVGRAQKKAERT 285
++ G + V ++ K++ +
Sbjct: 65 YKLHGVNINVEASKNKSKAS 84
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 7/71 (9%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+F+ N+ + ++ + F G ++ C V +D Y FVH E E A +I ++N
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQLN 64
Query: 173 GMLLNSKIVFV 183
G + K + V
Sbjct: 65 GKEVKGKRINV 75
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 44/93 (47%), Gaps = 8/93 (8%)
Query: 193 EKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYES 252
EK ++++LF + N D +E+++++FE YG + K +GFGF+ E+
Sbjct: 9 EKTFTQRSRLF----VGNLPPDITEEEMRKLFEKYGKAGEVFIH----KDKGFGFIRLET 60
Query: 253 PEFAEKAVQAWNGKEVDGKILYVGRAQKKAERT 285
AE A + + GK L V A A T
Sbjct: 61 RTLAEIAKVELDNMPLRGKQLRVRFACHSASLT 93
Score = 29.6 bits (65), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 5/67 (7%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+F+ NL I + M F +G + +D KG+GF+ ET A + +++
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELD 72
Query: 173 GMLLNSK 179
M L K
Sbjct: 73 NMPLRGK 79
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
V++ ++ + + D S G +++ K+ D Q G SKGY F+ F E++ ++ +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 172 NGMLLNSKIVFVG 184
NG L S+ + G
Sbjct: 65 NGYQLGSRFLKCG 77
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAW 263
VY+ + D +E++ ++ G + + ++M G+S+G+ F+ + E + AV+
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 264 NGKEVDGKILYVG 276
NG ++ + L G
Sbjct: 65 NGYQLGSRFLKCG 77
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV 260
T++ + N + + L+ +FE YG + + + +SRGF FV + AE A+
Sbjct: 47 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106
Query: 261 QAWNGKEVDGKILYV 275
A +G +DG+ L V
Sbjct: 107 DAMDGAVLDGRELRV 121
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 8/65 (12%)
Query: 113 VFIKNLDKSIDNKAMYDT-FSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
VFI NL+ ++ K+ +T FS +G + C V KGY FV + E A ++
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGE 82
Query: 172 NGMLL 176
NG +L
Sbjct: 83 NGRVL 87
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 7/67 (10%)
Query: 220 LKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA- 278
++ +F YG + V +G+ FV Y + A AV NG+ + G+ L + A
Sbjct: 45 VETIFSKYGRVAGCSVH------KGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAG 98
Query: 279 QKKAERT 285
+ K +R+
Sbjct: 99 EPKPDRS 105
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 37.0 bits (84), Expect = 0.017, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 30/61 (49%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+F+ L+K + + F FG I C V + G+SKG FV F + A +I ++
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 173 G 173
G
Sbjct: 78 G 78
Score = 35.4 bits (80), Expect = 0.042, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 5/68 (7%)
Query: 201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKA 259
KLF + K E E + +F+P+G I V+ DG S+G FV + S A+ A
Sbjct: 17 KLFVGMLNKQQSE----EDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAA 72
Query: 260 VQAWNGKE 267
+ A +G +
Sbjct: 73 IHALHGSQ 80
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
V++ ++ + + D S G +++ K+ D Q G SKGY F+ F E++ ++ +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 172 NGMLLNSKIVFVG 184
NG L S+ + G
Sbjct: 66 NGYQLGSRFLKCG 78
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 47/99 (47%), Gaps = 23/99 (23%)
Query: 178 SKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN 237
S++V++G IP + E+++ L +NV G N LK MF+P
Sbjct: 3 SRVVYLGS-IPYDQTEEQI---LDLCSNV-----GPVIN---LKMMFDP----------- 39
Query: 238 NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVG 276
G+S+G+ F+ + E + AV+ NG ++ + L G
Sbjct: 40 QTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCG 78
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 2/79 (2%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV 260
T++ + N + + L+ +FE YG + + + +SRGF FV + AE A+
Sbjct: 70 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 129
Query: 261 QAWNGKEVDGKILYVGRAQ 279
A +G +DG+ L V A+
Sbjct: 130 DAMDGAVLDGRELRVQMAR 148
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 36.6 bits (83), Expect = 0.018, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
V++ ++ + + D S G +++ K+ D Q G SKGY F+ F E++ ++ +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 172 NGMLLNSKIVFVG 184
NG L S+ + G
Sbjct: 67 NGYQLGSRFLKCG 79
Score = 33.1 bits (74), Expect = 0.21, Method: Composition-based stats.
Identities = 17/73 (23%), Positives = 39/73 (53%), Gaps = 2/73 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
VY+ + D +E++ ++ G + + ++M + G+S+G+ F+ + E + AV+
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 264 NGKEVDGKILYVG 276
NG ++ + L G
Sbjct: 67 NGYQLGSRFLKCG 79
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 36.6 bits (83), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 30/60 (50%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+FI + K + FS+FG I C++ + G S+G FV F T A +I+ ++
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM----NNDGKSRGFGFVAYESPEFAEKAVQ 261
+++ ++++ L+E+FE YG + V+ N +S+G FV + + + A +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 262 AWNGKEV 268
A + +V
Sbjct: 66 ALHNMKV 72
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 36.6 bits (83), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 30/60 (50%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+FI + K + FS+FG I C++ + G S+G FV F T A +I+ ++
Sbjct: 110 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 169
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM----NNDGKSRGFGFVAYESPEFAEKAVQ 261
+++ ++++ L+E+FE YG + V+ N +S+G FV + + + A +A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 262 AWNGKEV 268
A + +V
Sbjct: 78 ALHNMKV 84
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 36.6 bits (83), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 4/56 (7%)
Query: 218 EKLK----EMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVD 269
EKLK ++F +G IT+ DGK++G+ F+ Y SP A AV+ +G ++D
Sbjct: 32 EKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 87
Score = 28.5 bits (62), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 126 AMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
++ FS FG I + +E G +KGY F+ + + A +++ +G L+ + F
Sbjct: 37 VIHKIFSKFGKI-TNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 92
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 4/56 (7%)
Query: 218 EKLK----EMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVD 269
EKLK ++F +G IT+ DGK++G+ F+ Y SP A AV+ +G ++D
Sbjct: 18 EKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 73
Score = 28.1 bits (61), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 126 AMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
++ FS FG I + +E G +KGY F+ + + A +++ +G L+ + F
Sbjct: 23 VIHKIFSKFGKI-TNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 78
>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 = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE 169
+FI + K + FS+FG I C++ + G S+G FV F T A +I+
Sbjct: 98 LFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIK 154
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 26/135 (19%), Positives = 55/135 (40%), Gaps = 20/135 (14%)
Query: 207 YIKNFGEDFNDEKLKEMFEPYGTITSYRVM----NNDGKSRGFGFVAYESPEFAEKAVQA 262
++ ++++ L+E+FE YG + V+ N +S+G FV + + + A +A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 263 W-NGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
N K + G + +E+ ++ R L++ + +
Sbjct: 67 LHNXKVLPGXHHPIQXKPADSEKNNAVEDR---------------KLFIGXISKKCTEND 111
Query: 322 LRKEFTPFGTITSAK 336
+R F+ FG I +
Sbjct: 112 IRVXFSSFGQIEECR 126
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 36.2 bits (82), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 28/93 (30%), Positives = 46/93 (49%), Gaps = 2/93 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
+YI+N E++ ++F YG I RV N ++RG +V YE A+ AV +G
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRV-GNTPETRGTAYVVYEDIFDAKNAVDHLSG 69
Query: 266 KEVDGKILYVGRAQ-KKAERTQELKRRFEMLKI 297
V + L V +A + + K++ E LK+
Sbjct: 70 FNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKL 102
Score = 34.3 bits (77), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
++I+NL I + MYD F +G I +V + ++G +V +E A +++ ++
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNAVDHLS 68
Query: 173 GMLLNSKIVFV 183
G ++++ + V
Sbjct: 69 GFNVSNRYLVV 79
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 35.8 bits (81), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 42/73 (57%), Gaps = 4/73 (5%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAVQA 262
+++ + E+ +++++E F YG I + +N D G S+G+ V YE+ + A A +A
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIH-LNLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 263 WNGKEVDGKILYV 275
NG E+ G+ + V
Sbjct: 88 LNGAEIMGQTIQV 100
Score = 32.0 bits (71), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 2/84 (2%)
Query: 102 DPSLRKSGVGNV-FIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFE 159
+P ++S G + F+ ++ + + + F +G I + + D + G SKGY V +E
Sbjct: 17 EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE 76
Query: 160 TEEAANKSIEKVNGMLLNSKIVFV 183
T + A + E +NG + + + V
Sbjct: 77 THKQALAAKEALNGAEIMGQTIQV 100
>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 = 35.8 bits (81), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 42/73 (57%), Gaps = 4/73 (5%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAVQA 262
+++ + E+ +++++E F YG I + +N D G S+G+ V YE+ + A A +A
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIH-LNLDRRTGFSKGYALVEYETHKQALAAKEA 133
Query: 263 WNGKEVDGKILYV 275
NG E+ G+ + V
Sbjct: 134 LNGAEIMGQTIQV 146
Score = 31.6 bits (70), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
+F+ ++ + + + F +G I + + D + G SKGY V +ET + A + E +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 172 NGMLLNSKIVFV 183
NG + + + V
Sbjct: 135 NGAEIMGQTIQV 146
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 35.8 bits (81), Expect = 0.038, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDG--KSRGFGFVAYESPEFAEKAVQ 261
+ VY+ N + L +F YG + +M + KS+G F+ + + A+ +
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 262 AWNGKEVDGKIL 273
A N K++ G+++
Sbjct: 77 AINNKQLFGRVI 88
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 35.0 bits (79), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 3/63 (4%)
Query: 218 EKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYV 275
E +K FE +G + +M + RGFGFV +ES + EK + + E++ K++
Sbjct: 14 EDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI-HFHEINNKMVEC 72
Query: 276 GRA 278
+A
Sbjct: 73 KKA 75
>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 = 35.0 bits (79), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 44/84 (52%), Gaps = 2/84 (2%)
Query: 102 DPSLRKSGVGNV-FIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFE 159
+P ++S G + F+ + + + ++D F+ +G I + + D + G KGY V +E
Sbjct: 13 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 72
Query: 160 TEEAANKSIEKVNGMLLNSKIVFV 183
T + A ++E +NG L + + V
Sbjct: 73 TYKEAQAAMEGLNGQDLMGQPISV 96
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAVQA 262
+++ E+ +E + + F YG I + +N D G +G+ V YE+ + A+ A++
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIH-LNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83
Query: 263 WNGKEVDGKILYV 275
NG+++ G+ + V
Sbjct: 84 LNGQDLMGQPISV 96
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 35.0 bits (79), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 26/43 (60%)
Query: 240 GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKA 282
GK +G V+YE P A+ AV+ ++GK+ G L V A+KK
Sbjct: 62 GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP 104
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 34.7 bits (78), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
+F+ + + + ++D F+ +G I + + D + G KGY V +ET + A ++E +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 172 NGMLLNSKIVFV 183
NG L + + V
Sbjct: 70 NGQDLMGQPISV 81
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAVQA 262
+++ E+ +E + + F YG I + +N D G +G+ V YE+ + A+ A++
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIH-LNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 263 WNGKEVDGKILYV 275
NG+++ G+ + V
Sbjct: 69 LNGQDLMGQPISV 81
>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 = 34.7 bits (78), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
+F+ + + + ++D F+ +G I + + D + G KGY V +ET + A ++E +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 172 NGMLLNSKIVFV 183
NG L + + V
Sbjct: 72 NGQDLMGQPISV 83
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAVQA 262
+++ E+ +E + + F YG I + +N D G +G+ V YE+ + A+ A++
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIH-LNLDRRTGYLKGYTLVEYETYKEAQAAMEG 70
Query: 263 WNGKEVDGKILYV 275
NG+++ G+ + V
Sbjct: 71 LNGQDLMGQPISV 83
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 34.7 bits (78), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
+F+ + + + ++D F+ +G I + + D + G KGY V +ET + A ++E +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 172 NGMLLNSKIVFV 183
NG L + + V
Sbjct: 70 NGQDLMGQPISV 81
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAVQA 262
+++ E+ +E + + F YG I + +N D G +G+ V YE+ + A+ A++
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIH-LNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 263 WNGKEVDGKILYV 275
NG+++ G+ + V
Sbjct: 69 LNGQDLMGQPISV 81
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 34.3 bits (77), Expect = 0.096, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 6/82 (7%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV--- 260
++I E L+E F +G + VM + +SRGFGFV + +K +
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87
Query: 261 -QAWNGKEVDGKILYVGRAQKK 281
+ K +D K+ + RAQ K
Sbjct: 88 RHELDSKTIDPKVAFPRRAQPK 109
Score = 32.3 bits (72), Expect = 0.34, Method: Composition-based stats.
Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 10/87 (11%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANK----S 167
+FI L + + + F FG + C V +D S+G+GFV F + +K S
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87
Query: 168 IEKVNGMLLNSKIVFVGKFIPRKEREK 194
+++ ++ K+ F PR+ + K
Sbjct: 88 RHELDSKTIDPKVAF-----PRRAQPK 109
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 29/98 (29%), Positives = 46/98 (46%), Gaps = 12/98 (12%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
+YI+N E++ ++F YG I RV N ++RG +V YE A+ A +G
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRV-GNTPETRGTAYVVYEDIFDAKNACDHLSG 79
Query: 266 KEVDGKILYV-----GRA------QKKAERTQELKRRF 292
V + L V RA +KK E+ + LK ++
Sbjct: 80 FNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKY 117
Score = 32.0 bits (71), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
++I+NL I + MYD F +G I +V + ++G +V +E A + + ++
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNACDHLS 78
Query: 173 GMLLNSKIVFV 183
G + ++ + V
Sbjct: 79 GFNVCNRYLVV 89
>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 = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
+F+ + + + ++D F+ +G I + + D + G KGY V +ET + A ++E +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 172 NGMLLNSKIVFV 183
NG L + + V
Sbjct: 70 NGQDLMGQPISV 81
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAVQA 262
+++ E+ +E + + F YG I + +N D G +G+ V YE+ + A+ A++
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIH-LNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 263 WNGKEVDGKILYV 275
NG+++ G+ + V
Sbjct: 69 LNGQDLMGQPISV 81
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 33.9 bits (76), Expect = 0.13, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVA-QDEQGNSKGYGFVHFETEEAANKSI 168
VFI+NL + +A+ + FG + +V + +SKG F F T+EAA K +
Sbjct: 18 VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 46/88 (52%), Gaps = 9/88 (10%)
Query: 201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDG---KSRGFGFVAYESPEFAE 257
K+F N GE +L+E F+ +G +T VM D + RGFGF+ +E + +
Sbjct: 12 KIFVGGIPHNCGET----ELREYFKKFGVVTEV-VMIYDAEKQRPRGFGFITFEDEQSVD 66
Query: 258 KAVQAWNGKEVDGKILYVGRAQKKAERT 285
+AV + ++ GK + V RA+ + ++
Sbjct: 67 QAVN-MHFHDIMGKKVEVKRAEPRDSKS 93
Score = 28.9 bits (63), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 12/57 (21%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSI 168
+F+ + + + + F FG + + D E+ +G+GF+ FE E++ ++++
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>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 = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 31/129 (24%), Positives = 56/129 (43%), Gaps = 7/129 (5%)
Query: 138 LSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELG 197
LS ++ S+ + ++ ++E A +EK+NG+ + V K E+ K
Sbjct: 146 LSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEG-YTLVTKVSNPLEKSKRTD 204
Query: 198 EKAKLFTNVYIKNFGEDFNDEK-LKEMFEPYGTITSYRVMNNDGKSRGF----GFVAYES 252
+ I+N + DE L+E FE +G+I + K F F +E+
Sbjct: 205 SATLEGREIXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQ-KEHSFNNCCAFXVFEN 263
Query: 253 PEFAEKAVQ 261
+ AE+A+Q
Sbjct: 264 KDSAERALQ 272
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
+YI+N E++ ++F YG I RV N ++RG +V YE A+ A +G
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRV-GNTPETRGTAYVVYEDIFDAKNACDHLSG 73
Query: 266 KEVDGKILYV 275
V + L V
Sbjct: 74 FNVCNRYLVV 83
Score = 30.4 bits (67), Expect = 1.4, Method: Composition-based stats.
Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
++I+NL I + MYD F +G I +V + ++G +V +E A + + ++
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNACDHLS 72
Query: 173 G 173
G
Sbjct: 73 G 73
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 131 FSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK---VNGMLLNSKI 180
FS FG +L +V +D + G+SKG+GFV F E K + + ++G + K+
Sbjct: 36 FSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKL 89
>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 = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS-KGYGFVHFETEEAANKSI 168
V +F+ L + + + F FG + S ++ D + N +G+ F+ F+ EE K +
Sbjct: 1 VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
Query: 169 EK 170
EK
Sbjct: 61 EK 62
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
+++ D +EK++E F +G + S + N K RGF F+ ++ E +K ++
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 33.1 bits (74), Expect = 0.21, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
+F+ + + + ++D F+ +G I + + D + G KGY V +ET + A ++E +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 172 NG 173
NG
Sbjct: 86 NG 87
Score = 31.2 bits (69), Expect = 0.80, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAVQA 262
+++ E+ +E + + F YG I + +N D G +G+ V YE+ + A+ A++
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIH-LNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84
Query: 263 WNGKEVDGKILYV 275
NG+++ G+ + V
Sbjct: 85 LNGQDLMGQPISV 97
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 32.7 bits (73), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS-KGYGFVHFETEEAANKSIEK 170
+F+ L + + + F FG + S ++ D + N +G+ F+ F+ EE K +EK
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
+++ D +EK++E F +G + S + N K RGF F+ ++ E +K ++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 32.7 bits (73), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 7/71 (9%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+ + N+ + N+ + F +G ++ C + +D Y FVH E E A ++I ++
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGLD 65
Query: 173 GMLLNSKIVFV 183
K + V
Sbjct: 66 NTEFQGKRMHV 76
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 32.7 bits (73), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 11/65 (16%)
Query: 199 KAKLFT-NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAE 257
K++LF N+ +KN + E L +F PYG I + N FGF+ +++P+
Sbjct: 2 KSRLFIGNLPLKNVSK----EDLFRIFSPYGHIMQINIKN------AFGFIQFDNPQSVR 51
Query: 258 KAVQA 262
A++
Sbjct: 52 DAIEC 56
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 32.3 bits (72), Expect = 0.36, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 218 EKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYV 275
+ L+ +FE YG + + + RGF FV + A+ A A +G E+DG+ L V
Sbjct: 28 DSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRV 87
Query: 276 GRAQ 279
A+
Sbjct: 88 QVAR 91
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 32.0 bits (71), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 11/64 (17%)
Query: 199 KAKLFT-NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAE 257
K++LF N+ +KN + E L +F PYG I + N FGF+ +++P+
Sbjct: 22 KSRLFIGNLPLKNVSK----EDLFRIFSPYGHIMQINIKN------AFGFIQFDNPQSVR 71
Query: 258 KAVQ 261
A++
Sbjct: 72 DAIE 75
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 32.0 bits (71), Expect = 0.50, Method: Composition-based stats.
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 218 EKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESP 253
E L+ F YG + +M + +SRGFGFV ++ P
Sbjct: 31 ETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP 68
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 31.6 bits (70), Expect = 0.58, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 11/64 (17%)
Query: 199 KAKLFT-NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAE 257
K++LF N+ +KN + E L +F PYG I + N FGF+ +++P+
Sbjct: 10 KSRLFIGNLPLKNVSK----EDLFRIFSPYGHIMQINIKN------AFGFIQFDNPQSVR 59
Query: 258 KAVQ 261
A++
Sbjct: 60 DAIE 63
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 31.6 bits (70), Expect = 0.69, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 11/64 (17%)
Query: 199 KAKLFT-NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAE 257
K++LF N+ +KN + E L +F PYG I + N FGF+ +++P+
Sbjct: 22 KSRLFIGNLPLKNVSK----EDLFRIFSPYGHIMQINIKN------AFGFIQFDNPQSVR 71
Query: 258 KAVQ 261
A++
Sbjct: 72 DAIE 75
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 31.2 bits (69), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 28/96 (29%), Positives = 44/96 (45%), Gaps = 12/96 (12%)
Query: 208 IKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKE 267
I+N E++ ++F YG I RV N ++RG +V YE A+ A +G
Sbjct: 23 IRNLPYKITAEEMYDIFGKYGPIRQIRV-GNTPETRGTAYVVYEDIFDAKNACDHLSGFN 81
Query: 268 VDGKILYV-----GRA------QKKAERTQELKRRF 292
V + L V RA +KK E+ + LK ++
Sbjct: 82 VCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKY 117
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
+ I+NL I + MYD F +G I +V + ++G +V +E A + + ++
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNACDHLS 78
Query: 173 GMLLNSKIVFV 183
G + ++ + V
Sbjct: 79 GFNVCNRYLVV 89
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANK----S 167
+FI L + + + F FG + C V +D S+G+GFV F + +K S
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 168 IEKVNGMLLNSKIVF 182
+++ ++ K+ F
Sbjct: 63 RHELDSKTIDPKVAF 77
Score = 29.6 bits (65), Expect = 2.5, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 3/70 (4%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
++I E L+E F +G + VM + +SRGFGFV + +K V A
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK-VLAQ 61
Query: 264 NGKEVDGKIL 273
+ E+D K +
Sbjct: 62 SRHELDSKTI 71
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFG-SILSCKVAQDE-QGNSKGYGFVHFETEEAANKSI 168
++++ +L+ +D + F+ G +++S K+ ++ G GY FV F A K +
Sbjct: 10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL 69
Query: 169 EKVNG 173
K+NG
Sbjct: 70 HKING 74
>pdb|3SDS|A Chain A, Crystal Structure Of A Mitochondrial Ornithine
Carbamoyltransferase From Coccidioides Immitis
pdb|3SDS|B Chain B, Crystal Structure Of A Mitochondrial Ornithine
Carbamoyltransferase From Coccidioides Immitis
pdb|3SDS|C Chain C, Crystal Structure Of A Mitochondrial Ornithine
Carbamoyltransferase From Coccidioides Immitis
Length = 353
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 9/66 (13%)
Query: 88 ALKGRPIRIMWSQRDPSLRKSGVGNV--------FIKNLDKSID-NKAMYDTFSAFGSIL 138
AL G+ + +M+S+R R S G V F+ D + N+++YDT S++
Sbjct: 63 ALSGKTVAMMFSKRSTRTRVSTEGAVVKMGGHPMFLGKDDIQLGVNESLYDTSVVISSMV 122
Query: 139 SCKVAQ 144
SC VA+
Sbjct: 123 SCIVAR 128
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 7/75 (9%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAF----GSILSCKVAQDEQGNSKGYGFVHFETEEAANKSI 168
+++KNL + + + F+ F G + ++ G +G F+ F +E A +++
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMT---GRMRGQAFITFPNKEIAWQAL 84
Query: 169 EKVNGMLLNSKIVFV 183
VNG L KI+ +
Sbjct: 85 HLVNGYKLYGKILVI 99
>pdb|1S79|A Chain A, Solution Structure Of The Central Rrm Of Human La Protein
Length = 103
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 29/87 (33%), Positives = 44/87 (50%), Gaps = 5/87 (5%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKS-RGFGFVAYESPEFAEKAVQA- 262
+VYIK F D + +KE E G + + ++ K+ +G FV ++S E A+K V+
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 72
Query: 263 -WNGKEVDGKILYVGR--AQKKAERTQ 286
KE D IL+ A+K ER Q
Sbjct: 73 GQKYKETDLLILFKDDYFAKKNEERKQ 99
>pdb|2VOD|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VOD|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VON|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VON|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VOO|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOO|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOP|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auuuu
Length = 193
Score = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKS-RGFGFVAYESPEFAEKAVQA- 262
+VYIK F D + +KE E G + + ++ K+ +G FV ++S E A+K V+
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 170
Query: 263 -WNGKEVDGKILY 274
KE D IL+
Sbjct: 171 GQKYKETDLLILF 183
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 28.9 bits (63), Expect = 4.2, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKS 167
+FI + +++D K + F FG I V +D G KG F+ + E+A K+
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 28.9 bits (63), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 4/74 (5%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
+Y++N ++E +++ F RV K R + FV + + E A +A++A NG
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVK----KIRDYAFVHFSNREDAVEAMKALNG 73
Query: 266 KEVDGKILYVGRAQ 279
K +DG + V A+
Sbjct: 74 KVLDGSPIEVTLAK 87
>pdb|2R3A|A Chain A, Methyltransferase Domain Of Human Suppressor Of
Variegation 3-9 Homolog 2
Length = 300
Score = 28.9 bits (63), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 4/62 (6%)
Query: 70 GQPYMLDTERALDTMNFDALK-GRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMY 128
G Y+ D + D DA + G + DP+L+ V NVFI NLD + A++
Sbjct: 191 GITYLFDLDYESDEFTVDAARYGNVSHFVNHSCDPNLQ---VFNVFIDNLDTRLPRIALF 247
Query: 129 DT 130
T
Sbjct: 248 ST 249
>pdb|3QXY|A Chain A, Human Setd6 In Complex With Rela Lys310
pdb|3QXY|B Chain B, Human Setd6 In Complex With Rela Lys310
pdb|3RC0|A Chain A, Human Setd6 In Complex With Rela Lys310 Peptide
pdb|3RC0|B Chain B, Human Setd6 In Complex With Rela Lys310 Peptide
Length = 449
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 23/53 (43%)
Query: 138 LSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRK 190
LS KVA QG GYG V E+ +A LL+ +G + R+
Sbjct: 36 LSPKVAVSRQGTVAGYGMVARESVQAGELLFVVPRAALLSQHTCSIGGLLERE 88
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM----NNDGKSRGFGFVAYESPEFAEKAVQ 261
+++ ++++ L+E+FE YG + V+ N +S+G FV + + + A +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 262 AWNGKEV 268
A + +V
Sbjct: 66 ALHNMKV 72
>pdb|1ZH5|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1ZH5|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 195
Score = 28.1 bits (61), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 3/73 (4%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKS-RGFGFVAYESPEFAEKAVQA- 262
+VYIK F D + +KE E G + + + K+ +G FV ++S E A+K V+
Sbjct: 113 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQXRRTLHKAFKGSIFVVFDSIESAKKFVETP 172
Query: 263 -WNGKEVDGKILY 274
KE D IL+
Sbjct: 173 GQKYKETDLLILF 185
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 28.1 bits (61), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 2/67 (2%)
Query: 220 LKEMFEPYGTITS--YRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR 277
L +F G + + + + GK++GF FV S A+K +++++GK +D K
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLY 88
Query: 278 AQKKAER 284
K ER
Sbjct: 89 TMKDVER 95
>pdb|1YTY|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1YTY|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 194
Score = 28.1 bits (61), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 3/73 (4%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKS-RGFGFVAYESPEFAEKAVQA- 262
+VYIK F D + +KE E G + + + K+ +G FV ++S E A+K V+
Sbjct: 112 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQXRRTLHKAFKGSIFVVFDSIESAKKFVETP 171
Query: 263 -WNGKEVDGKILY 274
KE D IL+
Sbjct: 172 GQKYKETDLLILF 184
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 27.7 bits (60), Expect = 8.8, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 218 EKLKEMFEPYGTITS--YRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK 271
+ L +F G + + + + GK++GF FV S A+K +++++GK +D K
Sbjct: 27 KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK 82
>pdb|2VFP|A Chain A, Low Temperature Structure Of P22 Tailspike Protein
Fragment (109-666), Mutant V349l
Length = 559
Score = 27.7 bits (60), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 227 YGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
YG+++S + + NN G R G + + S E V+ W G
Sbjct: 221 YGSVSSAQFLRNNGGFERDGGLIGFTSYRAGESGVKTWQG 260
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.134 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,961,651
Number of Sequences: 62578
Number of extensions: 429395
Number of successful extensions: 1626
Number of sequences better than 100.0: 189
Number of HSP's better than 100.0 without gapping: 116
Number of HSP's successfully gapped in prelim test: 73
Number of HSP's that attempted gapping in prelim test: 1149
Number of HSP's gapped (non-prelim): 399
length of query: 336
length of database: 14,973,337
effective HSP length: 99
effective length of query: 237
effective length of database: 8,778,115
effective search space: 2080413255
effective search space used: 2080413255
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)