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= psy2983
(370 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 150 bits (379), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 71/92 (77%), Positives = 83/92 (90%), Gaps = 1/92 (1%)
Query: 105 NLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH 164
NLQ +G+ GPMRLY+GSLHFNITEDMLRGIFEPFG+I++IQLM+D +TGRSKGYGFITF
Sbjct: 18 NLQ-KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFS 76
Query: 165 SADDAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
++ AKKA EQLNGFELAGRPMKVG VT+R +
Sbjct: 77 DSECAKKALEQLNGFELAGRPMKVGHVTERTD 108
Score = 34.7 bits (78), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 33 LEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIV 89
L F G++ ++L+ ++T R KG +I F D E A+ LNG +L G P+ V
Sbjct: 43 LRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV 100
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 144 bits (362), Expect = 1e-34, Method: Compositional matrix adjust.
Identities = 67/92 (72%), Positives = 82/92 (89%)
Query: 7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
D+LSPEERDART+FCMQL+ RIR RDLE+FFS+VGKVRDVR+I+ +RR KGIAY+EF
Sbjct: 16 DNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFC 75
Query: 67 DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNR 98
+ +SVPLA+GL GQ+LLG+PIIVQ +QAEKNR
Sbjct: 76 EIQSVPLAIGLTGQRLLGVPIIVQASQAEKNR 107
Score = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 1/72 (1%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
++ L I L F GK+ +++++ D ++ RSKG ++ F A L
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GL 86
Query: 177 NGFELAGRPMKV 188
G L G P+ V
Sbjct: 87 TGQRLLGVPIIV 98
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 139 bits (350), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 69/95 (72%), Positives = 79/95 (83%), Gaps = 1/95 (1%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
G+ G LY+GSLHFNITEDMLRGIFEPFGKIDNI LM D DTGRSKGYGFITF ++ A
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
++A EQLNGFELAGRPM+VG VT+R + G GPS+
Sbjct: 61 RRALEQLNGFELAGRPMRVGHVTERLDG-GSGPSS 94
Score = 33.5 bits (75), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
++ L I L F GK+ ++ L+ + T R KG +I F D E A+ L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 78 NGQKLLGIPIIV 89
NG +L G P+ V
Sbjct: 68 NGFELAGRPMRV 79
>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 = 87.4 bits (215), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 52/172 (30%), Positives = 89/172 (51%), Gaps = 31/172 (18%)
Query: 33 LEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLG-------- 84
+ + F+ G ++ + + + T + KG A++E++ PE+ LA+ +LG
Sbjct: 30 IRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGR 89
Query: 85 -------IPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEP 137
PII Q AE+ RA N R+Y+ S+H ++++D ++ +FE
Sbjct: 90 PSNIGQAQPIIDQ--LAEEARAFN--------------RIYVASVHQDLSDDDIKSVFEA 133
Query: 138 FGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
FGKI + L DP TG+ KGYGFI + A ++ A +N F+L G+ ++VG
Sbjct: 134 FGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVG 185
Score = 65.5 bits (158), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 46/74 (62%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
R+Y+GS+++ + ED +R F PFG I +I + D T + KG+ F+ + + A+ A EQ
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 176 LNGFELAGRPMKVG 189
+N L GR +KVG
Sbjct: 75 MNSVMLGGRNIKVG 88
Score = 35.8 bits (81), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 31/64 (48%)
Query: 7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
D L+ E R I+ + Q + D++ F + GK++ L T + KG +IE++
Sbjct: 101 DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYE 160
Query: 67 DPES 70
+S
Sbjct: 161 KAQS 164
>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 = 87.0 bits (214), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 52/172 (30%), Positives = 89/172 (51%), Gaps = 31/172 (18%)
Query: 33 LEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLG-------- 84
+ + F+ G ++ + + + T + KG A++E++ PE+ LA+ +LG
Sbjct: 45 IRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGR 104
Query: 85 -------IPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEP 137
PII Q AE+ RA N R+Y+ S+H ++++D ++ +FE
Sbjct: 105 PSNIGQAQPIIDQ--LAEEARAFN--------------RIYVASVHQDLSDDDIKSVFEA 148
Query: 138 FGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
FGKI + L DP TG+ KGYGFI + A ++ A +N F+L G+ ++VG
Sbjct: 149 FGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVG 200
Score = 64.7 bits (156), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 46/74 (62%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
R+Y+GS+++ + ED +R F PFG I +I + D T + KG+ F+ + + A+ A EQ
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 176 LNGFELAGRPMKVG 189
+N L GR +KVG
Sbjct: 90 MNSVMLGGRNIKVG 103
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 31/64 (48%)
Query: 7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
D L+ E R I+ + Q + D++ F + GK++ L T + KG +IE++
Sbjct: 116 DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYE 175
Query: 67 DPES 70
+S
Sbjct: 176 KAQS 179
>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 = 84.0 bits (206), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 51/170 (30%), Positives = 89/170 (52%), Gaps = 27/170 (15%)
Query: 33 LEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM------GLNGQKL-LGI 85
+ + F+ G ++ + + T + KG A++E++ PE+ LA+ L G+ + +G
Sbjct: 29 IRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKVGR 88
Query: 86 PIIVQPTQ------AEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFG 139
P + Q AE+ RA N R+Y+ S+H ++++D ++ +FE FG
Sbjct: 89 PSNIGQAQPIIDQLAEEARAFN--------------RIYVASVHQDLSDDDIKSVFEAFG 134
Query: 140 KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
KI + L DP TG+ KGYGFI + A ++ A N F+L G+ ++VG
Sbjct: 135 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVG 184
Score = 63.9 bits (154), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 44/74 (59%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
R+Y+GS+++ + ED +R F PFG I +I D T + KG+ F+ + + A+ A EQ
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 176 LNGFELAGRPMKVG 189
N L GR +KVG
Sbjct: 74 XNSVXLGGRNIKVG 87
Score = 35.8 bits (81), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 31/64 (48%)
Query: 7 DDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
D L+ E R I+ + Q + D++ F + GK++ L T + KG +IE++
Sbjct: 100 DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYE 159
Query: 67 DPES 70
+S
Sbjct: 160 KAQS 163
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 78.2 bits (191), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 46/174 (26%), Positives = 91/174 (52%), Gaps = 15/174 (8%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM- 75
R ++ L + I L+++F G + +++ I +K + A++E+ +A+
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIK-IMIDKNNKNVNYAFVEYHQSHDANIALQ 59
Query: 76 GLNGQKLLG-IPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGI 134
LNG+++ I I Q++++ + +T L++G L+ N+ ++ LR
Sbjct: 60 TLNGKQIENNIVKINWAFQSQQSSSDDTF------------NLFVGDLNVNVDDETLRNA 107
Query: 135 FEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
F+ F + +M D TG S+GYGF++F S DDA+ A + + G +L GRP+++
Sbjct: 108 FKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 161
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 35/126 (27%), Positives = 63/126 (50%), Gaps = 10/126 (7%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
LY+G+L ITED+L+ F+ G I NI++M+D + ++ Y F+ +H + DA A + L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNN-KNVNYAFVEYHQSHDANIALQTL 61
Query: 177 NGFELAGRPMKVGTVTDRNES---------VGGGPSNLDTDEMERAGVDLGATGRLQLMF 227
NG ++ +K+ +S VG N+D + + A D + +M+
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 121
Query: 228 KLAEGT 233
+ G+
Sbjct: 122 DMQTGS 127
>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 = 70.1 bits (170), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 50/165 (30%), Positives = 81/165 (49%), Gaps = 14/165 (8%)
Query: 33 LEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP 91
L E FS G + +R+ TRR G AY+ F+ P A+ +N + G P+ +
Sbjct: 27 LYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW 86
Query: 92 TQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPD 151
+Q + P+L+ G G ++I +L +I L F FG I + +++ D +
Sbjct: 87 SQRD--------PSLRKSGVGN---IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN 135
Query: 152 TGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
SKGYGF+ F + + A++A E++NG L R + VG R E
Sbjct: 136 G--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE 178
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 48/84 (57%), Gaps = 1/84 (1%)
Query: 106 LQPRGTGGPM-RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH 164
+ P PM LY+G LH ++TE ML F P G I +I++ D T RS GY ++ F
Sbjct: 1 MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQ 60
Query: 165 SADDAKKAQEQLNGFELAGRPMKV 188
DA++A + +N + G+P+++
Sbjct: 61 QPADAERALDTMNFDVIKGKPVRI 84
>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 = 69.3 bits (168), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 50/165 (30%), Positives = 81/165 (49%), Gaps = 14/165 (8%)
Query: 33 LEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKLLGIPIIVQP 91
L E FS G + +R+ TRR G AY+ F+ P A+ +N + G P+ +
Sbjct: 32 LYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW 91
Query: 92 TQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPD 151
+Q + P+L+ G G ++I +L +I L F FG I + +++ D +
Sbjct: 92 SQRD--------PSLRKSGVGN---IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN 140
Query: 152 TGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
SKGYGF+ F + + A++A E++NG L R + VG R E
Sbjct: 141 G--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE 183
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 31/87 (35%), Positives = 50/87 (57%), Gaps = 1/87 (1%)
Query: 103 LPNLQPRGTGGPM-RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFI 161
L ++ P PM LY+G LH ++TE ML F P G I +I++ D T RS GY ++
Sbjct: 3 LGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 62
Query: 162 TFHSADDAKKAQEQLNGFELAGRPMKV 188
F DA++A + +N + G+P+++
Sbjct: 63 NFQQPADAERALDTMNFDVIKGKPVRI 89
>pdb|2LQ5|A Chain A, Nmr Structure Of The Rna Binding Motif 39 (Rbm39) From Mus
Musculus
Length = 113
Score = 67.8 bits (164), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 28/39 (71%), Positives = 32/39 (82%)
Query: 267 PIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
P+ATQCF L+NMF+P TE WD EI+DDVIEECNKHG
Sbjct: 3 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHG 41
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 67.8 bits (164), Expect = 9e-12, Method: Composition-based stats.
Identities = 40/96 (41%), Positives = 54/96 (56%), Gaps = 2/96 (2%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKI-DNIQLMVDPDTGRSKGYGFITFHSADD 168
G+ G ++IG+L I E +L F FG I ++M DPDTG SKGY FI F S D
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 169 AKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
+ A E +NG L RP+ V + + +S G GPS+
Sbjct: 61 SDAAIEAMNGQYLCNRPITV-SYAFKKDSKGSGPSS 95
>pdb|3S6E|A Chain A, Crystal Structure Of A Rna Binding Motif Protein 39
(Rbm39) From Mus Musculus At 0.95 A Resolution
pdb|3S6E|B Chain B, Crystal Structure Of A Rna Binding Motif Protein 39
(Rbm39) From Mus Musculus At 0.95 A Resolution
Length = 114
Score = 67.4 bits (163), Expect = 1e-11, Method: Composition-based stats.
Identities = 27/39 (69%), Positives = 31/39 (79%)
Query: 267 PIATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHG 305
P+ATQCF L+N F+P TE WD EI+DDVIEECNKHG
Sbjct: 4 PLATQCFQLSNXFNPQTEEEVGWDTEIKDDVIEECNKHG 42
>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 = 66.6 bits (161), Expect = 2e-11, Method: Composition-based stats.
Identities = 32/86 (37%), Positives = 52/86 (60%), Gaps = 1/86 (1%)
Query: 113 GPMRL-YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
GP R+ Y+GS+ ++ TE+ + + G + N+++M DP TGRSKGY FI F + +
Sbjct: 1 GPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 60
Query: 172 AQEQLNGFELAGRPMKVGTVTDRNES 197
A LNG++L R +K G ++ + S
Sbjct: 61 AVRNLNGYQLGSRFLKCGYSSNSDIS 86
Score = 33.9 bits (76), Expect = 0.15, Method: Composition-based stats.
Identities = 20/46 (43%), Positives = 31/46 (67%), Gaps = 1/46 (2%)
Query: 38 SSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKL 82
S+VG V +++++ +T R KG A+IEF+D ES A+ LNG +L
Sbjct: 25 SNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 70
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 66.2 bits (160), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 47/73 (64%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L++G L F+ E L +F +G+I + ++ D +T RS+G+GF+TF + DDAK A
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 176 LNGFELAGRPMKV 188
+NG + GR ++V
Sbjct: 74 MNGKSVDGRQIRV 86
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 47/88 (53%), Gaps = 2/88 (2%)
Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
D +F LS + LE+ FS G++ +V ++ +T+R +G ++ F++ + A
Sbjct: 11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 75 -MGLNGQKLLGIPIIV-QPTQAEKNRAG 100
M +NG+ + G I V Q ++ NR+G
Sbjct: 71 MMAMNGKSVDGRQIRVDQAGKSSDNRSG 98
>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 = 65.5 bits (158), Expect = 4e-11, Method: Composition-based stats.
Identities = 28/72 (38%), Positives = 47/72 (65%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L++G L+ N+ ++ LR F+ F + +M D TG S+GYGF++F S DDA+ A + +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 177 NGFELAGRPMKV 188
G +L GRP+++
Sbjct: 64 QGQDLNGRPLRI 75
>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 = 65.1 bits (157), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 47/77 (61%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
+Y+GS+ ++ TE+ + + G + N+++M DP TGRSKGY FI F + + A L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 177 NGFELAGRPMKVGTVTD 193
NG++L R +K G ++
Sbjct: 67 NGYQLGSRFLKCGYSSN 83
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 31/46 (67%), Gaps = 1/46 (2%)
Query: 38 SSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKL 82
S+VG V +++++ +T R KG A+IEF+D ES A+ LNG +L
Sbjct: 26 SNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 71
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 64.7 bits (156), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 44/163 (26%), Positives = 75/163 (46%), Gaps = 8/163 (4%)
Query: 10 SPEE-RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP 68
SP+E R +F LS L F G + D ++ T+R +G ++ +
Sbjct: 5 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 64
Query: 69 ESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITE 128
E V AM K+ G +V+P RA + + +P ++++G + + E
Sbjct: 65 EEVDAAMNARPHKVDGR--VVEP-----KRAVSREDSQRPGAHLTVKKIFVGGIKEDTEE 117
Query: 129 DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
LR FE +GKI+ I++M D +G+ +G+ F+TF D K
Sbjct: 118 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 160
Score = 54.7 bits (130), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 8/73 (10%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L+IG L F T++ LR FE +G + + +M DP+T RS+G+GF+T+ + ++ A
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 70
Query: 176 LNGFELAGRPMKV 188
+ RP KV
Sbjct: 71 -----MNARPHKV 78
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 64.7 bits (156), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 45/167 (26%), Positives = 76/167 (45%), Gaps = 8/167 (4%)
Query: 6 SDDLSPEE-RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIE 64
S SP+E R +F LS L F G + D ++ T+R +G ++
Sbjct: 3 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 62
Query: 65 FKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHF 124
+ E V AM K+ G +V+P RA + + +P ++++G +
Sbjct: 63 YATVEEVDAAMNARPHKVDGR--VVEP-----KRAVSREDSQRPGAHLTVKKIFVGGIKE 115
Query: 125 NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
+ E LR FE +GKI+ I++M D +G+ +G+ F+TF D K
Sbjct: 116 DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 162
Score = 54.7 bits (130), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 8/73 (10%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L+IG L F T++ LR FE +G + + +M DP+T RS+G+GF+T+ + ++ A
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 72
Query: 176 LNGFELAGRPMKV 188
+ RP KV
Sbjct: 73 -----MNARPHKV 80
>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 = 64.7 bits (156), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 44/163 (26%), Positives = 75/163 (46%), Gaps = 8/163 (4%)
Query: 10 SPEE-RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP 68
SP+E R +F LS L F G + D ++ T+R +G ++ +
Sbjct: 6 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 65
Query: 69 ESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITE 128
E V AM K+ G +V+P RA + + +P ++++G + + E
Sbjct: 66 EEVDAAMNARPHKVDGR--VVEP-----KRAVSREDSQRPGAHLTVKKIFVGGIKEDTEE 118
Query: 129 DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
LR FE +GKI+ I++M D +G+ +G+ F+TF D K
Sbjct: 119 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 161
Score = 54.7 bits (130), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 8/73 (10%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L+IG L F T++ LR FE +G + + +M DP+T RS+G+GF+T+ + ++ A
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 71
Query: 176 LNGFELAGRPMKV 188
+ RP KV
Sbjct: 72 -----MNARPHKV 79
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 64.7 bits (156), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 44/163 (26%), Positives = 75/163 (46%), Gaps = 8/163 (4%)
Query: 10 SPEE-RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP 68
SP+E R +F LS L F G + D ++ T+R +G ++ +
Sbjct: 6 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 65
Query: 69 ESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITE 128
E V AM K+ G +V+P RA + + +P ++++G + + E
Sbjct: 66 EEVDAAMNARPHKVDGR--VVEP-----KRAVSREDSQRPGAHLTVKKIFVGGIKEDTEE 118
Query: 129 DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
LR FE +GKI+ I++M D +G+ +G+ F+TF D K
Sbjct: 119 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 161
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 8/73 (10%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L+IG L F T++ LR FE +G + + +M DP+T RS+G+GF+T+ + ++ A
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 71
Query: 176 LNGFELAGRPMKV 188
+ RP KV
Sbjct: 72 -----MNARPHKV 79
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 64.7 bits (156), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 44/163 (26%), Positives = 75/163 (46%), Gaps = 8/163 (4%)
Query: 10 SPEE-RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP 68
SP+E R +F LS L F G + D ++ T+R +G ++ +
Sbjct: 4 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 63
Query: 69 ESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITE 128
E V AM K+ G +V+P RA + + +P ++++G + + E
Sbjct: 64 EEVDAAMNARPHKVDGR--VVEP-----KRAVSREDSQRPGAHLTVKKIFVGGIKEDTEE 116
Query: 129 DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
LR FE +GKI+ I++M D +G+ +G+ F+TF D K
Sbjct: 117 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 159
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 8/73 (10%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L+IG L F T++ LR FE +G + + +M DP+T RS+G+GF+T+ + ++ A
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 69
Query: 176 LNGFELAGRPMKV 188
+ RP KV
Sbjct: 70 -----MNARPHKV 77
>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 = 64.7 bits (156), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 31/95 (32%), Positives = 56/95 (58%)
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
G++ + Q + T +++G L IT + ++ F PFG+I + +++ D TG+SKGYG
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR 194
F++F + DA+ A +Q+ G L GR ++ T +
Sbjct: 61 FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 95
Score = 36.2 bits (82), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 32/66 (48%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLN 78
+F LS I T D++ F+ G++ D R++ T + KG ++ F + A+
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 79 GQKLLG 84
G + LG
Sbjct: 78 GGQWLG 83
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 64.3 bits (155), Expect = 1e-10, Method: Composition-based stats.
Identities = 31/85 (36%), Positives = 51/85 (60%), Gaps = 1/85 (1%)
Query: 114 PMRL-YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
P R+ Y+GS+ ++ TE+ + + G + N+++M DP TGRSKGY FI F + + A
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 173 QEQLNGFELAGRPMKVGTVTDRNES 197
LNG++L R +K G ++ + S
Sbjct: 61 VRNLNGYQLGSRFLKCGYSSNSDIS 85
Score = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 20/46 (43%), Positives = 31/46 (67%), Gaps = 1/46 (2%)
Query: 38 SSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKL 82
S+VG V +++++ +T R KG A+IEF+D ES A+ LNG +L
Sbjct: 24 SNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 69
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 64.3 bits (155), Expect = 1e-10, Method: Composition-based stats.
Identities = 35/105 (33%), Positives = 59/105 (56%), Gaps = 1/105 (0%)
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
G++ + Q + T +++G L IT + ++ F PFGKI + +++ D TG+SKGYG
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYG 60
Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
F++F++ DA+ A + G L GR ++ T R GPS+
Sbjct: 61 FVSFYNKLDAENAIVHMGGQWLGGRQIRTNWAT-RKPPAPSGPSS 104
Score = 35.0 bits (79), Expect = 0.076, Method: Composition-based stats.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 5/69 (7%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK---DPESVPLAM 75
+F LS I T D++ F+ GK+ D R++ T + KG ++ F D E+ + M
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 76 GLNGQKLLG 84
G GQ L G
Sbjct: 78 G--GQWLGG 84
>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 = 64.3 bits (155), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 41/155 (26%), Positives = 71/155 (45%), Gaps = 7/155 (4%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
R +F LS L F G + D ++ T+R +G ++ + E V AM
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 77 LNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFE 136
K+ G +V+P RA + + +P ++++G + + E LR FE
Sbjct: 67 ARPHKVDGR--VVEP-----KRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 119
Query: 137 PFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
+GKI+ I++M D +G+ +G+ F+TF D K
Sbjct: 120 QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 154
Score = 54.3 bits (129), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 8/73 (10%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L+IG L F T++ LR FE +G + + +M DP+T RS+G+GF+T+ + ++ A
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 64
Query: 176 LNGFELAGRPMKV 188
+ RP KV
Sbjct: 65 -----MNARPHKV 72
>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 = 63.5 bits (153), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 40/136 (29%), Positives = 71/136 (52%), Gaps = 14/136 (10%)
Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQP 91
+L E+F G V D++++ T R +G ++ F+ P SV + Q +L +I P
Sbjct: 19 NLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV--VKTQHILDGKVI-DP 75
Query: 92 TQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPD 151
+A +P + TG ++++G + ++ F +G I + QLM+D D
Sbjct: 76 KRA--------IPRDEQDKTG---KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKD 124
Query: 152 TGRSKGYGFITFHSAD 167
TG+S+G+GF+T+ SAD
Sbjct: 125 TGQSRGFGFVTYDSAD 140
Score = 59.7 bits (143), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 27/66 (40%), Positives = 45/66 (68%), Gaps = 3/66 (4%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH---SADDAKKA 172
+++IG L+++ TED LR F +G + ++++M DP TGRS+G+GF++F S D+ K
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 173 QEQLNG 178
Q L+G
Sbjct: 65 QHILDG 70
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 63.2 bits (152), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 35/103 (33%), Positives = 55/103 (53%), Gaps = 7/103 (6%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L + L N+T+D + +F G I++ +L+ D TG+S GYGF+ + +DA KA L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 177 NGFELAGRPMKV-------GTVTDRNESVGGGPSNLDTDEMER 212
NG +L + +KV ++ D N V G P + EME+
Sbjct: 67 NGLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQ 109
Score = 54.7 bits (130), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 43/169 (25%), Positives = 77/169 (45%), Gaps = 21/169 (12%)
Query: 15 DART-IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
D++T + L Q + + + F S+G + +L+ T + G ++ + DP
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 74 AMG-LNGQKLLGIPIIV---QPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITED 129
A+ LNG KL I V +P+ A A LY+ L +++
Sbjct: 62 AINTLNGLKLQTKTIKVSYARPSSASIRDA----------------NLYVSGLPKTMSQK 105
Query: 130 MLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNG 178
+ +F +G+I ++++D TG S+G GFI F +A++A + LNG
Sbjct: 106 EMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNG 154
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/93 (30%), Positives = 49/93 (52%), Gaps = 4/93 (4%)
Query: 1 MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
++ +Y+ S RDA ++ L + + +++E+ FS G++ R++ T +G+
Sbjct: 76 IKVSYARPSSASIRDA-NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGV 134
Query: 61 AYIEF-KDPESVPLAMGLNGQKLLGI--PIIVQ 90
+I F K E+ GLNGQK LG PI V+
Sbjct: 135 GFIRFDKRIEAEEAIKGLNGQKPLGAAEPITVK 167
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 62.0 bits (149), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 34/90 (37%), Positives = 55/90 (61%), Gaps = 3/90 (3%)
Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
+ LY+ +L I ++ LR F PFG I + ++M++ GRSKG+GF+ F S ++A KA
Sbjct: 16 VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVT 73
Query: 175 QLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
++NG +A +P+ V + R E GPS+
Sbjct: 74 EMNGRIVATKPLYV-ALAQRKEERQSGPSS 102
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 62.0 bits (149), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 33/106 (31%), Positives = 55/106 (51%), Gaps = 7/106 (6%)
Query: 113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
G L + L N+T+D LR +F G++++ +L+ D G S GYGF+ + +A DA++A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 173 QEQLNGFELAGRPMKVG-------TVTDRNESVGGGPSNLDTDEME 211
LNG L + +KV + D N + G P + ++E
Sbjct: 61 INTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVE 106
Score = 52.4 bits (124), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 43/158 (27%), Positives = 69/158 (43%), Gaps = 18/158 (11%)
Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL 82
L Q + +L FSS+G+V +LI G ++ + + A+ LNG +L
Sbjct: 10 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 69
Query: 83 LGIPIIVQPTQ--AEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGK 140
I V + +E + N LYI L +T+ + +F FG+
Sbjct: 70 QSKTIKVSYARPSSEVIKDAN---------------LYISGLPRTMTQKDVEDMFSRFGR 114
Query: 141 IDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNG 178
I N +++VD TG S+G FI F +A++A NG
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 32.7 bits (73), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 1 MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
++ +Y+ S +DA ++ L + + +D+E+ FS G++ + R++ T +G+
Sbjct: 74 IKVSYARPSSEVIKDA-NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGV 132
Query: 61 AYIEF-KDPESVPLAMGLNGQK 81
A+I F K E+ NG K
Sbjct: 133 AFIRFDKRSEAEEAITSFNGHK 154
>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 = 62.0 bits (149), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 33/106 (31%), Positives = 55/106 (51%), Gaps = 7/106 (6%)
Query: 113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
G L + L N+T+D LR +F G++++ +L+ D G S GYGF+ + +A DA++A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 173 QEQLNGFELAGRPMKVG-------TVTDRNESVGGGPSNLDTDEME 211
LNG L + +KV + D N + G P + ++E
Sbjct: 61 INTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVE 106
Score = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 43/158 (27%), Positives = 69/158 (43%), Gaps = 18/158 (11%)
Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL 82
L Q + +L FSS+G+V +LI G ++ + + A+ LNG +L
Sbjct: 10 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 69
Query: 83 LGIPIIVQPTQ--AEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGK 140
I V + +E + N LYI L +T+ + +F FG+
Sbjct: 70 QSKTIKVSYARPSSEVIKDAN---------------LYISGLPRTMTQKDVEDMFSRFGR 114
Query: 141 IDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNG 178
I N +++VD TG S+G FI F +A++A NG
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 32.7 bits (73), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 1 MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
++ +Y+ S +DA ++ L + + +D+E+ FS G++ + R++ T +G+
Sbjct: 74 IKVSYARPSSEVIKDA-NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGV 132
Query: 61 AYIEF-KDPESVPLAMGLNGQK 81
A+I F K E+ NG K
Sbjct: 133 AFIRFDKRSEAEEAITSFNGHK 154
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 45/72 (62%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L + L TE LR +F +G I ++ ++ D + RS+G+ F+ F + DDAK+A+E+
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 177 NGFELAGRPMKV 188
NG EL GR ++V
Sbjct: 78 NGMELDGRRIRV 89
Score = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL 82
LS RDL E FS G + DV ++ ++RR +G A++ F++ + A NG +L
Sbjct: 23 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 82
Query: 83 LGIPIIV 89
G I V
Sbjct: 83 DGRRIRV 89
>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 = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 34/103 (33%), Positives = 55/103 (53%), Gaps = 7/103 (6%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L + L N+T++ R +F G+I++ +L+ D TG+S GYGF+ + DA+KA L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 177 NGFELAGRPMKV-------GTVTDRNESVGGGPSNLDTDEMER 212
NG L + +KV ++ D N V G P + E+E+
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQ 107
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 44/164 (26%), Positives = 76/164 (46%), Gaps = 20/164 (12%)
Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL 82
L Q + + F S+G++ +L+ T + G ++ + DP+ A+ LNG +L
Sbjct: 10 LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRL 69
Query: 83 LGIPIIV---QPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFG 139
I V +P+ A A LY+ L +T+ L +F +G
Sbjct: 70 QTKTIKVSYARPSSASIRDAN----------------LYVSGLPKTMTQKELEQLFSQYG 113
Query: 140 KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAG 183
+I +++VD TG S+G GFI F +A++A + LNG + +G
Sbjct: 114 RIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSG 157
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 28/93 (30%), Positives = 48/93 (51%), Gaps = 4/93 (4%)
Query: 1 MRPAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGI 60
++ +Y+ S RDA ++ L + + ++LE+ FS G++ R++ T +G+
Sbjct: 74 IKVSYARPSSASIRDA-NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGV 132
Query: 61 AYIEF-KDPESVPLAMGLNGQKLLGI--PIIVQ 90
+I F K E+ GLNGQK G PI V+
Sbjct: 133 GFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK 165
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 45/72 (62%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L + L TE LR +F +G I ++ ++ D + RS+G+ F+ F + DDAK+A+E+
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 177 NGFELAGRPMKV 188
NG EL GR ++V
Sbjct: 78 NGMELDGRRIRV 89
Score = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL 82
LS RDL E FS G + DV ++ ++RR +G A++ F++ + A NG +L
Sbjct: 23 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 82
Query: 83 LGIPIIV 89
G I V
Sbjct: 83 DGRRIRV 89
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 45/72 (62%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L + L TE LR +F +G I ++ ++ D + RS+G+ F+ F + DDAK+A+E+
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 177 NGFELAGRPMKV 188
NG EL GR ++V
Sbjct: 75 NGMELDGRRIRV 86
Score = 36.2 bits (82), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL 82
LS RDL E FS G + DV ++ ++RR +G A++ F++ + A NG +L
Sbjct: 20 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 79
Query: 83 LGIPIIV 89
G I V
Sbjct: 80 DGRRIRV 86
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 45/72 (62%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L + L TE LR +F +G I ++ ++ D + RS+G+ F+ F + DDAK+A+E+
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 177 NGFELAGRPMKV 188
NG EL GR ++V
Sbjct: 109 NGMELDGRRIRV 120
Score = 36.6 bits (83), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL 82
LS RDL E FS G + DV ++ ++RR +G A++ F++ + A NG +L
Sbjct: 54 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 113
Query: 83 LGIPIIV 89
G I V
Sbjct: 114 DGRRIRV 120
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 53/183 (28%), Positives = 88/183 (48%), Gaps = 22/183 (12%)
Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTR--RFKGIAYIEFKDPESVP 72
DA +F Q+ + +DL E F G V ++ ++ + KG ++ F ++
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 73 LAM-GLNGQKLL-GI--PIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITE 128
A L+ K+L G+ PI ++P +EKN A ++ R +L+IG + TE
Sbjct: 62 EAQNALHNMKVLPGMHHPIQMKPADSEKNNA------VEDR------KLFIGMISKKCTE 109
Query: 129 DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS---ADDAKKAQEQLNGFELAGRP 185
+ +R +F FG+I+ +++ PD G S+G F+TF + A A KA Q E P
Sbjct: 110 NDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSP 168
Query: 186 MKV 188
M V
Sbjct: 169 MVV 171
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 53/183 (28%), Positives = 88/183 (48%), Gaps = 22/183 (12%)
Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLIT--CNKTRRFKGIAYIEFKDPESVP 72
DA +F Q+ + +DL E F G V ++ ++ + KG ++ F ++
Sbjct: 14 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 73
Query: 73 LAM-GLNGQKLL-GI--PIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITE 128
A L+ K+L G+ PI ++P +EKN A ++ R +L+IG + TE
Sbjct: 74 EAQNALHNMKVLPGMHHPIQMKPADSEKNNA------VEDR------KLFIGMISKKCTE 121
Query: 129 DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS---ADDAKKAQEQLNGFELAGRP 185
+ +R +F FG+I+ +++ PD G S+G F+TF + A A KA Q E P
Sbjct: 122 NDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSP 180
Query: 186 MKV 188
M V
Sbjct: 181 MVV 183
>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 = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 47/147 (31%), Positives = 72/147 (48%), Gaps = 28/147 (19%)
Query: 43 VRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQ---AEKNRA 99
V DVR T R+F Y++F+ E + A+ L G K+ G I ++ + ++K RA
Sbjct: 45 VVDVRTGT---NRKF---GYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRA 98
Query: 100 GNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYG 159
TL +L FNITED L+ +FE D +++ + G+SKG
Sbjct: 99 ARTL--------------LAKNLSFNITEDELKEVFE-----DALEIRLVSQDGKSKGIA 139
Query: 160 FITFHSADDAKKAQEQLNGFELAGRPM 186
+I F S DA+K E+ G E+ GR +
Sbjct: 140 YIEFKSEADAEKNLEEKQGAEIDGRSV 166
>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 = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 30/78 (38%), Positives = 47/78 (60%), Gaps = 2/78 (2%)
Query: 113 GPMR--LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAK 170
GP R L + L N+T+D LR +F G++++ +L+ D G S GYGF+ + +A DA+
Sbjct: 1 GPGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAE 60
Query: 171 KAQEQLNGFELAGRPMKV 188
+A LNG L + +KV
Sbjct: 61 RAINTLNGLRLQSKTIKV 78
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 59.7 bits (143), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 44/73 (60%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
LY+G L + + +L F PFG I +IQ+ +D +T + +G+ F+ F A+DA A + +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 177 NGFELAGRPMKVG 189
N EL GR ++V
Sbjct: 126 NESELFGRTIRVN 138
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 59.7 bits (143), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 45/75 (60%), Gaps = 1/75 (1%)
Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
P +L+IG L+ E ML+ +F G I + L+ D T +S+G+ FITF + DAK A
Sbjct: 7 PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAA 65
Query: 174 EQLNGFELAGRPMKV 188
+ +NG L G+ +KV
Sbjct: 66 KDMNGKSLHGKAIKV 80
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 59.7 bits (143), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 34/95 (35%), Positives = 52/95 (54%), Gaps = 14/95 (14%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L+IG L F TE+ LR +E +GK+ + +M DP + RS+G+GF+TF S + A
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA--- 85
Query: 176 LNGFELAGRPMKV-GTVTDRNESV-----GGGPSN 204
+A RP + G V + +V G GPS+
Sbjct: 86 -----MAARPHSIDGRVVEPKRAVAREESGSGPSS 115
>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 = 59.3 bits (142), Expect = 4e-09, Method: Composition-based stats.
Identities = 27/72 (37%), Positives = 44/72 (61%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
LY+G L + + +L F PFG I +IQ+ +D +T + +G+ F+ F A+DA A + +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 177 NGFELAGRPMKV 188
N EL GR ++V
Sbjct: 65 NESELFGRTIRV 76
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 58.9 bits (141), Expect = 4e-09, Method: Composition-based stats.
Identities = 27/72 (37%), Positives = 44/72 (61%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
LY+G L + + +L F PFG I +IQ+ +D +T + +G+ F+ F A+DA A + +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 177 NGFELAGRPMKV 188
N EL GR ++V
Sbjct: 70 NESELFGRTIRV 81
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 58.9 bits (141), Expect = 5e-09, Method: Composition-based stats.
Identities = 27/72 (37%), Positives = 44/72 (61%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
LY+G L + + +L F PFG I +IQ+ +D +T + +G+ F+ F A+DA A + +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 177 NGFELAGRPMKV 188
N EL GR ++V
Sbjct: 68 NESELFGRTIRV 79
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 58.5 bits (140), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 33/96 (34%), Positives = 57/96 (59%), Gaps = 9/96 (9%)
Query: 106 LQPRGT-------GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGY 158
L PRG+ P RL++ ++ F + LR +F FGKI +++++ + SKG+
Sbjct: 14 LVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGF 71
Query: 159 GFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDR 194
GF+TF ++ DA +A+E+L+G + GR ++V T R
Sbjct: 72 GFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 58.5 bits (140), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 52/81 (64%), Gaps = 2/81 (2%)
Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
P RL++ ++ F + LR +F FGKI +++++ + SKG+GF+TF ++ DA +A+
Sbjct: 15 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAR 72
Query: 174 EQLNGFELAGRPMKVGTVTDR 194
E+L+G + GR ++V T R
Sbjct: 73 EKLHGTVVEGRKIEVNNATAR 93
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 58.2 bits (139), Expect = 8e-09, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 44/72 (61%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
+++G++ + TE+ L+ IF G + + +L+ D +TG+ KGYGF + + A A L
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 177 NGFELAGRPMKV 188
NG E +GR ++V
Sbjct: 71 NGREFSGRALRV 82
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 57.4 bits (137), Expect = 1e-08, Method: Composition-based stats.
Identities = 27/72 (37%), Positives = 44/72 (61%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
LY+G L + + +L F PFG I +IQ+ +D +T + +G+ F+ F A+DA A + +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 177 NGFELAGRPMKV 188
N EL GR ++V
Sbjct: 75 NESELFGRTIRV 86
>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 = 57.4 bits (137), Expect = 1e-08, Method: Composition-based stats.
Identities = 31/84 (36%), Positives = 48/84 (57%), Gaps = 4/84 (4%)
Query: 105 NLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH 164
NL +GT L + L N T+D LR +F G++++ +L+ D G S GYGF+ +
Sbjct: 14 NLYFQGTN----LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYV 69
Query: 165 SADDAKKAQEQLNGFELAGRPMKV 188
+A DA++A LNG L + +KV
Sbjct: 70 TAKDAERAINTLNGLRLQSKTIKV 93
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 48/83 (57%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L + + + E LR +FE +G I++++++ D +T +S+GYGF+ F S A++A L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 177 NGFELAGRPMKVGTVTDRNESVG 199
NGF + + +KV ++ G
Sbjct: 105 NGFNILNKRLKVALAASGHQRPG 127
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 49/84 (58%), Gaps = 5/84 (5%)
Query: 110 GTGGP-----MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH 164
G+ GP + L + +L + + D LR +FE +G++ ++ + +P T +G+ F+ FH
Sbjct: 4 GSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFH 63
Query: 165 SADDAKKAQEQLNGFELAGRPMKV 188
DA+ A+ ++G EL GR ++V
Sbjct: 64 DRRDAQDAEAAMDGAELDGRELRV 87
>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 = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 46/82 (56%), Gaps = 6/82 (7%)
Query: 113 GPMR------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
GP R L++ S+H ED ++ F +G+I NI L +D TG SKGY + + +
Sbjct: 65 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 124
Query: 167 DDAKKAQEQLNGFELAGRPMKV 188
A A+E LNG E+ G+ ++V
Sbjct: 125 KQALAAKEALNGAEIMGQTIQV 146
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 56.2 bits (134), Expect = 3e-08, Method: Composition-based stats.
Identities = 30/82 (36%), Positives = 46/82 (56%), Gaps = 6/82 (7%)
Query: 113 GPMR------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
GP R L++ S+H ED ++ F +G+I NI L +D TG SKGY + + +
Sbjct: 19 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 78
Query: 167 DDAKKAQEQLNGFELAGRPMKV 188
A A+E LNG E+ G+ ++V
Sbjct: 79 KQALAAKEALNGAEIMGQTIQV 100
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 55.8 bits (133), Expect = 4e-08, Method: Composition-based stats.
Identities = 24/58 (41%), Positives = 36/58 (62%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
+++G L N T + ++ FE FGK+D+ LM D T R +G+GF+TF S D +K E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 55.1 bits (131), Expect = 5e-08, Method: Composition-based stats.
Identities = 28/82 (34%), Positives = 46/82 (56%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L + L N+T+D + +F G I++ +L+ D TG+S GYGF+ + +DA KA L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 177 NGFELAGRPMKVGTVTDRNESV 198
NG +L + +KV + S+
Sbjct: 67 NGLKLQTKTIKVSYARPSSASI 88
Score = 30.0 bits (66), Expect = 2.2, Method: Composition-based stats.
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG-LNGQKL 82
L Q + + + F S+G + +L+ T + G ++ + DP A+ LNG KL
Sbjct: 12 LPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKL 71
>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 = 55.1 bits (131), Expect = 7e-08, Method: Composition-based stats.
Identities = 26/72 (36%), Positives = 42/72 (58%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L++ +H TE+ + F +G+I NI L +D TG KGY + + + +A+ A E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 177 NGFELAGRPMKV 188
NG +L G+P+ V
Sbjct: 70 NGQDLMGQPISV 81
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
+F + + D+ + F+ G+++++ L +T KG +E++ + AM GL
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 78 NGQKLLGIPIIV 89
NGQ L+G PI V
Sbjct: 70 NGQDLMGQPISV 81
>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 = 55.1 bits (131), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 45/82 (54%), Gaps = 6/82 (7%)
Query: 113 GPMR------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
GP R L++ +H TE+ + F +G+I NI L +D TG KGY + + +
Sbjct: 15 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 74
Query: 167 DDAKKAQEQLNGFELAGRPMKV 188
+A+ A E LNG +L G+P+ V
Sbjct: 75 KEAQAAMEGLNGQDLMGQPISV 96
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
+F + + D+ + F+ G+++++ L +T KG +E++ + AM GL
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 78 NGQKLLGIPIIV 89
NGQ L+G PI V
Sbjct: 85 NGQDLMGQPISV 96
>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 = 54.7 bits (130), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 51/183 (27%), Positives = 82/183 (44%), Gaps = 22/183 (12%)
Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLIT--CNKTRRFKGIAYIEFKDPESVP 72
DA F Q+ + +DL E F G V ++ ++ + KG ++ F ++
Sbjct: 2 DAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 73 LAM-GLNGQKLL---GIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITE 128
A L+ K+L PI +P +EKN A ++ R +L+IG + TE
Sbjct: 62 EAQNALHNXKVLPGXHHPIQXKPADSEKNNA------VEDR------KLFIGXISKKCTE 109
Query: 129 DMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS---ADDAKKAQEQLNGFELAGRP 185
+ +R F FG+I+ +++ PD G S+G F+TF + A A KA Q E P
Sbjct: 110 NDIRVXFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAXAQTAIKAXHQAQTXEGCSSP 168
Query: 186 MKV 188
V
Sbjct: 169 XVV 171
>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 = 54.7 bits (130), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 45/82 (54%), Gaps = 6/82 (7%)
Query: 113 GPMR------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
GP R L++ +H TE+ + F +G+I NI L +D TG KGY + + +
Sbjct: 2 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 61
Query: 167 DDAKKAQEQLNGFELAGRPMKV 188
+A+ A E LNG +L G+P+ V
Sbjct: 62 KEAQAAMEGLNGQDLMGQPISV 83
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
+F + + D+ + F+ G+++++ L +T KG +E++ + AM GL
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 78 NGQKLLGIPIIV 89
NGQ L+G PI V
Sbjct: 72 NGQDLMGQPISV 83
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 54.7 bits (130), Expect = 8e-08, Method: Composition-based stats.
Identities = 29/82 (35%), Positives = 45/82 (54%), Gaps = 6/82 (7%)
Query: 113 GPMR------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSA 166
GP R L++ +H TE+ + F +G+I NI L +D TG KGY + + +
Sbjct: 16 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 75
Query: 167 DDAKKAQEQLNGFELAGRPMKV 188
+A+ A E LNG +L G+P+ V
Sbjct: 76 KEAQAAMEGLNGQDLMGQPISV 97
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
+F + + D+ + F+ G+++++ L +T KG +E++ + AM GL
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 78 NGQKLLGIPIIV 89
NGQ L+G PI V
Sbjct: 86 NGQDLMGQPISV 97
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 54.7 bits (130), Expect = 8e-08, Method: Composition-based stats.
Identities = 26/71 (36%), Positives = 41/71 (57%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
+Y+ +L F++T + L IF +GK+ + +M D DT +SKG FI F D A+ +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 177 NGFELAGRPMK 187
N +L GR +K
Sbjct: 79 NNKQLFGRVIK 89
Score = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVP-LAMG 76
T++ L + DL FS GKV V ++ TR+ KG+A+I F D +S
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 77 LNGQKLLG 84
+N ++L G
Sbjct: 78 INNKQLFG 85
>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 = 54.7 bits (130), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 42/72 (58%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L++ +H TE+ + F +G+I NI L +D TG KGY + + + +A+ A E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 177 NGFELAGRPMKV 188
NG +L G+P+ V
Sbjct: 70 NGQDLMGQPISV 81
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
+F + + D+ + F+ G+++++ L +T KG +E++ + AM GL
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 78 NGQKLLGIPIIV 89
NGQ L+G PI V
Sbjct: 70 NGQDLMGQPISV 81
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 54.3 bits (129), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 42/72 (58%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L++ +H TE+ + F +G+I NI L +D TG KGY + + + +A+ A E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 177 NGFELAGRPMKV 188
NG +L G+P+ V
Sbjct: 70 NGQDLMGQPISV 81
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
+F + + D+ + F+ G+++++ L +T KG +E++ + AM GL
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 78 NGQKLLGIPIIV 89
NGQ L+G PI V
Sbjct: 70 NGQDLMGQPISV 81
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 44/76 (57%)
Query: 113 GPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
G L + +L + + D LR +FE +G++ ++ + D T S+G+ F+ FH DA+ A
Sbjct: 69 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 128
Query: 173 QEQLNGFELAGRPMKV 188
+ ++G L GR ++V
Sbjct: 129 MDAMDGAVLDGRELRV 144
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 1/68 (1%)
Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKL 82
L+ R L F G+V DV + T+ +G A++ F D AM ++G L
Sbjct: 78 LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL 137
Query: 83 LGIPIIVQ 90
G + VQ
Sbjct: 138 DGRELRVQ 145
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 49/84 (58%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
+Y+G L ++E +L +F G + N + D TG+ +GYGF+ F S +DA A + +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 177 NGFELAGRPMKVGTVTDRNESVGG 200
+ +L G+P++V + N+++ G
Sbjct: 78 DMIKLYGKPIRVNKASAHNKNLSG 101
Score = 32.0 bits (71), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 43/94 (45%), Gaps = 3/94 (3%)
Query: 9 LSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDP 68
+S +DA T++ L +++ L E F G V + + T + +G ++EF
Sbjct: 9 ISERNQDA-TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 67
Query: 69 ESVPLAMG-LNGQKLLGIPIIVQPTQAE-KNRAG 100
E A+ ++ KL G PI V A KN +G
Sbjct: 68 EDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSG 101
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 43/77 (55%), Gaps = 7/77 (9%)
Query: 110 GTGGPMR-------LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFIT 162
G+ GP R + + +L + E L+ +F PFG I I L D TG+SKG+ FI+
Sbjct: 4 GSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFIS 63
Query: 163 FHSADDAKKAQEQLNGF 179
FH +DA +A ++GF
Sbjct: 64 FHRREDAARAIAGVSGF 80
Score = 35.4 bits (80), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
D TI LS+ R DL+E F G + + L T + KG A+I F E A
Sbjct: 14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73
Query: 75 M-GLNG 79
+ G++G
Sbjct: 74 IAGVSG 79
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 43/72 (59%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L + +L + + D LR +FE +G++ ++ + D T S+G+ F+ FH DA+ A + +
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 177 NGFELAGRPMKV 188
+G L GR ++V
Sbjct: 110 DGAVLDGRELRV 121
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 1/68 (1%)
Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKL 82
L+ R L F G+V DV + T+ +G A++ F D AM ++G L
Sbjct: 55 LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL 114
Query: 83 LGIPIIVQ 90
G + VQ
Sbjct: 115 DGRELRVQ 122
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 52.4 bits (124), Expect = 4e-07, Method: Composition-based stats.
Identities = 29/98 (29%), Positives = 53/98 (54%), Gaps = 4/98 (4%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTG---RSKGYGFITFHSA 166
G+ G L+I +L+F+ TE+ L+G+F G I + + + S G+GF+ +
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 167 DDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
+ A+KA +QL G + G ++V +++R GPS+
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEV-RISERATKPASGPSS 97
>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 = 52.0 bits (123), Expect = 5e-07, Method: Composition-based stats.
Identities = 24/66 (36%), Positives = 40/66 (60%), Gaps = 4/66 (6%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ- 175
++IG L ++ T+ L+ F FG++ + L +DP TGRS+G+GF+ F ++ K +Q
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 176 ---LNG 178
LNG
Sbjct: 62 EHKLNG 67
Score = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLN 78
+F LS +DL+++FS G+V D L T R +G ++ FK+ ESV M
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 79 GQKLLGIPIIVQPTQA 94
KL G ++ P +A
Sbjct: 62 EHKLNG--KVIDPKRA 75
>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 = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 48/186 (25%), Positives = 81/186 (43%), Gaps = 15/186 (8%)
Query: 6 SDDLSPEERDART-IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIE 64
SDDL + R + T + L Q R+L F ++G + R+ KT G A+++
Sbjct: 3 SDDLMNDPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVD 62
Query: 65 FKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHF 124
F A+ + L GI + + + R G + LY+ +L
Sbjct: 63 FTSEXDSQRAIKV----LNGITVRNKRLKVSYARPGGE--------SIKDTNLYVTNLPR 110
Query: 125 NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF--ELA 182
IT+D L IF +G I ++ D TGR +G F+ ++ ++A++A LN E
Sbjct: 111 TITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGG 170
Query: 183 GRPMKV 188
+P+ V
Sbjct: 171 SQPLSV 176
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 49/102 (48%), Gaps = 7/102 (6%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L + L + T+ L +F G I+ ++ D TG S GY F+ F S D+++A + L
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 177 NGFELAGRPMKVG-------TVTDRNESVGGGPSNLDTDEME 211
NG + + +KV ++ D N V P + D+++
Sbjct: 77 NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLD 118
>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 = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 48/83 (57%)
Query: 112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
G +++G L IT + F PFG+I + +++ D TG+SKGYGF++F + DA+
Sbjct: 4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 63
Query: 172 AQEQLNGFELAGRPMKVGTVTDR 194
A +Q+ G L GR ++ T +
Sbjct: 64 AIQQMGGQWLGGRQIRTNWATRK 86
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 51.6 bits (122), Expect = 6e-07, Method: Composition-based stats.
Identities = 26/89 (29%), Positives = 48/89 (53%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
RL++ +L + +E+ L +F +G + + +D T + KG+ F+TF + A KA +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 176 LNGFELAGRPMKVGTVTDRNESVGGGPSN 204
++G GR + V T + E+ GPS+
Sbjct: 70 VDGQVFQGRMLHVLPSTIKKEASQSGPSS 98
Score = 34.7 bits (78), Expect = 0.086, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE-SVPLAMGL 77
+F LS DLE+ FS+ G + ++ + T++ KG A++ F PE +V +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 78 NGQKLLGIPIIVQPTQAEK 96
+GQ G + V P+ +K
Sbjct: 71 DGQVFQGRMLHVLPSTIKK 89
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 51.2 bits (121), Expect = 9e-07, Method: Composition-based stats.
Identities = 31/93 (33%), Positives = 50/93 (53%), Gaps = 5/93 (5%)
Query: 104 PNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITF 163
P+L+ G G ++I +L +I L F FG I + +++ D + SKGYGF+ F
Sbjct: 4 PSLRKSGVGN---IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHF 58
Query: 164 HSADDAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
+ + A++A E++NG L R + VG R E
Sbjct: 59 ETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE 91
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 41/144 (28%), Positives = 69/144 (47%), Gaps = 22/144 (15%)
Query: 43 VRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNT 102
V DVR+ TR+F Y++F+ E + A+ L G K+ G I + EK + ++
Sbjct: 39 VVDVRI---GMTRKF---GYVDFESAEDLEKALELTGLKVFGNEI-----KLEKPKGKDS 87
Query: 103 LPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFIT 162
R L +L + +T+D L+ +FE D ++ + G+SKG +I
Sbjct: 88 KKERDAR------TLLAKNLPYKVTQDELKEVFE-----DAAEIRLVSKDGKSKGIAYIE 136
Query: 163 FHSADDAKKAQEQLNGFELAGRPM 186
F + DA+K E+ G E+ GR +
Sbjct: 137 FKTEADAEKTFEEKQGTEIDGRSI 160
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 33/57 (57%), Gaps = 5/57 (8%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
S +ERDART+ L ++ +L+E F ++R V +K + KGIAYIEFK
Sbjct: 87 SKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLV-----SKDGKSKGIAYIEFK 138
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 50.8 bits (120), Expect = 1e-06, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 47/79 (59%), Gaps = 1/79 (1%)
Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDP-DTGRSKGYGFITFHSADDAKKA 172
P +++IG L N+T+D + IF +GKI I + V+ SKGY ++ F + D+A+KA
Sbjct: 4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKA 63
Query: 173 QEQLNGFELAGRPMKVGTV 191
+ ++G ++ G+ + V
Sbjct: 64 LKHMDGGQIDGQEITATAV 82
Score = 28.5 bits (62), Expect = 7.1, Method: Composition-based stats.
Identities = 14/54 (25%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 23 QLSQRIRTRDLEEFFSSVGKVRDVRL-ITCNKTRRFKGIAYIEFKDPESVPLAM 75
+L++ + + E FS+ GK++ + + + KG AY+EF++P+ A+
Sbjct: 11 RLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
>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: Composition-based stats.
Identities = 31/95 (32%), Positives = 53/95 (55%), Gaps = 7/95 (7%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
G+ G ++++ +L F+ T ML+ F G + + + + G+SKG G + F S + A
Sbjct: 4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVA 61
Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
++A +NG +L+GR + V DRN S GPS+
Sbjct: 62 ERACRMMNGMKLSGREIDVR--IDRNAS---GPSS 91
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 45/72 (62%), Gaps = 1/72 (1%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
+Y+G+L ++ T + ++ +F FGK+ N++L+ D +T + KG+GF+ + +A +L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 177 NGFELAGRPMKV 188
+ + GR ++V
Sbjct: 63 DNTDFMGRTIRV 74
Score = 37.7 bits (86), Expect = 0.011, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 43/82 (52%), Gaps = 2/82 (2%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMG 76
R I+ L + ++E FS GKV +V+LI +T++ KG ++E ++ ESV A+
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIA 60
Query: 77 -LNGQKLLGIPIIVQPTQAEKN 97
L+ +G I V +K+
Sbjct: 61 KLDNTDFMGRTIRVTEANPKKS 82
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 49.7 bits (117), Expect = 3e-06, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 45/82 (54%), Gaps = 3/82 (3%)
Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
P G P +++G + + E +R F +G + ++++ D TG SKGYGF++F++
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDV 61
Query: 168 DAKKAQEQLNGFELAGRPMKVG 189
D +K E F G+ +K+G
Sbjct: 62 DVQKIVESQINFH--GKKLKLG 81
Score = 30.4 bits (67), Expect = 1.6, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
T+F + R+ ++ FF+ G V++V++IT ++T KG ++ F
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIIT-DRTGVSKGYGFVSF 57
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 42/167 (25%), Positives = 74/167 (44%), Gaps = 14/167 (8%)
Query: 24 LSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLL 83
L Q + R+L F ++G + R++ KT G A+++F A+ + L
Sbjct: 11 LPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV----LN 66
Query: 84 GIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDN 143
GI + + + R G + LY+ +L IT+D L IF +G I
Sbjct: 67 GITVRNKRLKVSYARPGGE--------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQ 118
Query: 144 IQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGF--ELAGRPMKV 188
++ D TGR +G F+ ++ ++A++A LN E +P+ V
Sbjct: 119 KNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 165
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 51/102 (50%), Gaps = 7/102 (6%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L + L ++T+ L +F G I+ ++M D TG S GY F+ F S D+++A + L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 177 NGFELAGRPMKVG-------TVTDRNESVGGGPSNLDTDEME 211
NG + + +KV ++ D N V P + D+++
Sbjct: 66 NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLD 107
>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 = 49.3 bits (116), Expect = 3e-06, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 45/82 (54%), Gaps = 3/82 (3%)
Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
P G P +++G + + E +R F +G + ++++ D TG SKGYGF++F++
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDV 61
Query: 168 DAKKAQEQLNGFELAGRPMKVG 189
D +K E F G+ +K+G
Sbjct: 62 DVQKIVESQINFH--GKKLKLG 81
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
T+F + R+ ++ FF+ G V++V++IT ++T KG ++ F
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIIT-DRTGVSKGYGFVSF 57
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 49.3 bits (116), Expect = 3e-06, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 42/72 (58%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L+I L T+ L F PFG + + ++ +D T SK +GF++F + D A+ A + +
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 177 NGFELAGRPMKV 188
NGF++ + +KV
Sbjct: 103 NGFQVGTKRLKV 114
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 38/62 (61%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
++++G L ++ T+ LR FE FG I+ ++ D TG+S+GYGF+T A++A +
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 176 LN 177
N
Sbjct: 79 PN 80
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 49.3 bits (116), Expect = 3e-06, Method: Composition-based stats.
Identities = 30/89 (33%), Positives = 48/89 (53%), Gaps = 5/89 (5%)
Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
P G+G ++I +L +I L F FG I + +++ D + SKGYGF+ F + +
Sbjct: 2 PLGSGN---IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQE 56
Query: 168 DAKKAQEQLNGFELAGRPMKVGTVTDRNE 196
A++A E++NG L R + VG R E
Sbjct: 57 AAERAIEKMNGMLLNDRKVFVGRFKSRKE 85
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 48.9 bits (115), Expect = 5e-06, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 37/60 (61%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+ ++G L ++ ++ L+ F FG++ + + DP+TGRS+G+GFI F A +K +Q
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 2/85 (2%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPE 69
S E DA F LS +DL+++F+ G+V D + T R +G +I FKD
Sbjct: 5 SKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAA 64
Query: 70 SVPLAMGLNGQKLLGIPIIVQPTQA 94
SV + +L G ++ P +A
Sbjct: 65 SVEKVLDQKEHRLDG--RVIDPKKA 87
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 48.9 bits (115), Expect = 5e-06, Method: Composition-based stats.
Identities = 26/84 (30%), Positives = 47/84 (55%), Gaps = 5/84 (5%)
Query: 108 PRGTGG--PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHS 165
P G+G P +++G + + E +R F +G + ++++ D TG SKGYGF++F++
Sbjct: 2 PLGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYN 60
Query: 166 ADDAKKAQEQLNGFELAGRPMKVG 189
D +K E F G+ +K+G
Sbjct: 61 DVDVQKIVESQINFH--GKKLKLG 82
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 18 TIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
T+F + R+ ++ FF+ G V++V++IT ++T KG ++ F
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIIT-DRTGVSKGYGFVSF 58
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 105 NLQPRGT---GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFI 161
L PRG+ +++IG L + T++ LR F FG++ +M DP T RS+G+GF+
Sbjct: 13 GLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV 72
Query: 162 TFHSADDAKKAQEQ 175
TF K Q
Sbjct: 73 TFMDQAGVDKVLAQ 86
Score = 29.3 bits (64), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 26/53 (49%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
+F LS + L E+F G+V++ ++ T+R +G ++ F D V
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGV 80
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 48.5 bits (114), Expect = 5e-06, Method: Composition-based stats.
Identities = 27/93 (29%), Positives = 49/93 (52%), Gaps = 6/93 (6%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA---- 172
++I +L F+ E+ L + + FG + +++++ PDT SKG F F + + A+K
Sbjct: 18 VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 77
Query: 173 --QEQLNGFELAGRPMKVGTVTDRNESVGGGPS 203
+ + G +L GR +KV R+E+ G S
Sbjct: 78 SLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSS 110
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 52/90 (57%), Gaps = 10/90 (11%)
Query: 99 AGNTLPNL--QPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSK 156
+G++ PN QP T L++ L + TE+ L+ F+ G + +++ D +TG SK
Sbjct: 3 SGSSGPNARSQPSKT-----LFVKGLSEDTTEETLKESFD--GSV-RARIVTDRETGSSK 54
Query: 157 GYGFITFHSADDAKKAQEQLNGFELAGRPM 186
G+GF+ F+S +DAK A+E + E+ G +
Sbjct: 55 GFGFVDFNSEEDAKAAKEAMEDGEIDGNKV 84
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 16 ARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA 74
++T+F LS+ L+E F G VR R++T +T KG +++F E A
Sbjct: 15 SKTLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFNSEEDAKAA 70
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 48.5 bits (114), Expect = 6e-06, Method: Composition-based stats.
Identities = 31/95 (32%), Positives = 52/95 (54%), Gaps = 7/95 (7%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
G+ G +++ +L F+ T ML+ F G + + + + G+SKG G + F S + A
Sbjct: 1 GSSGSSGIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVA 58
Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
++A +NG +L+GR + V DRN S GPS+
Sbjct: 59 ERACRMMNGMKLSGREIDVR--IDRNAS---GPSS 88
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 48.5 bits (114), Expect = 7e-06, Method: Composition-based stats.
Identities = 26/68 (38%), Positives = 40/68 (58%), Gaps = 5/68 (7%)
Query: 121 SLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFE 180
+L FNITED L+ +FE D +++ + G+SKG +I F S DA+K E+ G E
Sbjct: 23 NLSFNITEDELKEVFE-----DALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAE 77
Query: 181 LAGRPMKV 188
+ GR + +
Sbjct: 78 IDGRSVSL 85
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 5/57 (8%)
Query: 10 SPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
S + R ART+ LS I +L+E F ++R V ++ + KGIAYIEFK
Sbjct: 10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFK 61
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 48.1 bits (113), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 35/131 (26%), Positives = 57/131 (43%), Gaps = 13/131 (9%)
Query: 58 KGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRL 117
K A++EF+ + AM +G II Q + R + P G +L
Sbjct: 51 KNFAFLEFRSVDETTQAMAFDG-------IIFQGQSLKIRRPHDYQP------LPGAHKL 97
Query: 118 YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN 177
+IG L + +D ++ + FG + L+ D TG SKGY F + + +A LN
Sbjct: 98 FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 157
Query: 178 GFELAGRPMKV 188
G +L + + V
Sbjct: 158 GMQLGDKKLLV 168
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 31/133 (23%), Positives = 56/133 (42%), Gaps = 13/133 (9%)
Query: 112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNI-QLMVDP----DTGRSKGYGFITFHSA 166
G RLY+G++ F ITE+ + F ++ + Q +P + K + F+ F S
Sbjct: 2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61
Query: 167 DDAKKAQEQLNGFELAGRPMKVGTVTD-------RNESVGGGPSNLDTDEMERAGVDLGA 219
D+ +A +G G+ +K+ D +GG P+ L+ D+++ G
Sbjct: 62 DETTQAMA-FDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGP 120
Query: 220 TGRLQLMFKLAEG 232
L+ A G
Sbjct: 121 LKAFNLVKDSATG 133
>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 = 48.1 bits (113), Expect = 8e-06, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 48/77 (62%), Gaps = 2/77 (2%)
Query: 128 EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMK 187
+D+L+ +F PFG + + ++ +D T SK +GF+++ + A+ A + +NGF++ + +K
Sbjct: 40 QDLLQ-MFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK 98
Query: 188 VGTVTDRNESVGGGPSN 204
V +N+S GPS+
Sbjct: 99 VQLKRSKNDS-KSGPSS 114
>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 = 48.1 bits (113), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 35/131 (26%), Positives = 57/131 (43%), Gaps = 13/131 (9%)
Query: 58 KGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRL 117
K A++EF+ + AM +G II Q + R + P G +L
Sbjct: 53 KNFAFLEFRSVDETTQAMAFDG-------IIFQGQSLKIRRPHDYQP------LPGAHKL 99
Query: 118 YIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLN 177
+IG L + +D ++ + FG + L+ D TG SKGY F + + +A LN
Sbjct: 100 FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 159
Query: 178 GFELAGRPMKV 188
G +L + + V
Sbjct: 160 GMQLGDKKLLV 170
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 31/133 (23%), Positives = 56/133 (42%), Gaps = 13/133 (9%)
Query: 112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNI-QLMVDP----DTGRSKGYGFITFHSA 166
G RLY+G++ F ITE+ + F ++ + Q +P + K + F+ F S
Sbjct: 4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 63
Query: 167 DDAKKAQEQLNGFELAGRPMKVGTVTD-------RNESVGGGPSNLDTDEMERAGVDLGA 219
D+ +A +G G+ +K+ D +GG P+ L+ D+++ G
Sbjct: 64 DETTQAMA-FDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGP 122
Query: 220 TGRLQLMFKLAEG 232
L+ A G
Sbjct: 123 LKAFNLVKDSATG 135
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 47.8 bits (112), Expect = 9e-06, Method: Composition-based stats.
Identities = 20/48 (41%), Positives = 32/48 (66%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITF 163
+++IG L + T++ LR F FG++ +M DP T RS+G+GF+TF
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
Score = 28.5 bits (62), Expect = 5.7, Method: Composition-based stats.
Identities = 14/53 (26%), Positives = 26/53 (49%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
+F LS + L E+F G+V++ ++ T+R +G ++ F D V
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGV 55
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 47.4 bits (111), Expect = 1e-05, Method: Composition-based stats.
Identities = 26/82 (31%), Positives = 43/82 (52%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L + L ++T+ L +F G I+ ++M D TG S GY F+ F S D+++A + L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 177 NGFELAGRPMKVGTVTDRNESV 198
NG + + +KV ES+
Sbjct: 66 NGITVRNKRLKVSYARPGGESI 87
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 47.4 bits (111), Expect = 1e-05, Method: Composition-based stats.
Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L + +L F +++ ++ +F FG + + D +GRS G + F DA KA +Q
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 88
Query: 176 LNGFELAGRPMKVGTVT 192
NG L GRPM + VT
Sbjct: 89 YNGVPLDGRPMNIQLVT 105
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 38/63 (60%)
Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
++L+IG + N+ E L+ +FE FGKI + ++ D TG KG F+T+ + A KAQ
Sbjct: 14 IKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQS 73
Query: 175 QLN 177
L+
Sbjct: 74 ALH 76
Score = 34.7 bits (78), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 43/85 (50%), Gaps = 4/85 (4%)
Query: 12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
++ DA +F Q+ + + +DL+ F GK+ ++ ++ T KG A++ + + ES
Sbjct: 9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA 68
Query: 72 PLAM-GLNGQKLL---GIPIIVQPT 92
A L+ QK L PI V+P
Sbjct: 69 LKAQSALHEQKTLPGMNRPIQVKPA 93
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 42/178 (23%), Positives = 71/178 (39%), Gaps = 31/178 (17%)
Query: 14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
R+ R I L + +++ + S D L C ++KG A++ + E
Sbjct: 20 RNRRKILIRGLPGDVTNQEVHDLLS------DYELKYCF-VDKYKGTAFVTLLNGEQAEA 72
Query: 74 AMGLNGQKLL---GIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDM 130
A+ Q L + + +QPT A L + +L ++T+
Sbjct: 73 AINAFHQSRLRERELSVQLQPTDA---------------------LLCVANLPPSLTQQQ 111
Query: 131 LRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
+ PFG ++ L+ TG+SKGYGF + D A +A+ L G L R + V
Sbjct: 112 FEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 43/182 (23%), Positives = 74/182 (40%), Gaps = 10/182 (5%)
Query: 8 DLSPEERDARTIFCM-QLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
+LS + + + C+ L + + EE G + L+ +T + KG + E+
Sbjct: 86 ELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYM 145
Query: 67 DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
+S A LLG P+ + AG P L RL G FN
Sbjct: 146 KKDSAARAKS----DLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPG---FND 198
Query: 127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
+ + R + QL D G+ KG+ + + +A+ A++AQ+Q +G L G +
Sbjct: 199 VDALCRAL-SAVHSPTFCQLACGQD-GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHL 256
Query: 187 KV 188
+V
Sbjct: 257 RV 258
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 42/178 (23%), Positives = 71/178 (39%), Gaps = 31/178 (17%)
Query: 14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
R+ R I L + +++ + S D L C ++KG A++ + E
Sbjct: 20 RNRRKILIRGLPGDVTNQEVHDLLS------DYELKYCF-VDKYKGTAFVTLLNGEQAEA 72
Query: 74 AMGLNGQKLL---GIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDM 130
A+ Q L + + +QPT A L + +L ++T+
Sbjct: 73 AINAFHQSRLRERELSVQLQPTDA---------------------LLCVANLPPSLTQQQ 111
Query: 131 LRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
+ PFG ++ L+ TG+SKGYGF + D A +A+ L G L R + V
Sbjct: 112 FEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 43/182 (23%), Positives = 74/182 (40%), Gaps = 10/182 (5%)
Query: 8 DLSPEERDARTIFCM-QLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
+LS + + + C+ L + + EE G + L+ +T + KG + E+
Sbjct: 86 ELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYM 145
Query: 67 DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
+S A LLG P+ + AG P L RL G FN
Sbjct: 146 KKDSAARAKS----DLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPG---FND 198
Query: 127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
+ + R + QL D G+ KG+ + + +A+ A++AQ+Q +G L G +
Sbjct: 199 VDALCRAL-SAVHSPTFCQLACGQD-GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHL 256
Query: 187 KV 188
+V
Sbjct: 257 RV 258
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 24/63 (38%), Positives = 36/63 (57%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
G+ G LYI L T+ L + +P+GKI + + ++D T + KGYGF+ F S A
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 170 KKA 172
+KA
Sbjct: 61 QKA 63
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 42/178 (23%), Positives = 71/178 (39%), Gaps = 31/178 (17%)
Query: 14 RDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPL 73
R+ R I L + +++ + S D L C ++KG A++ + E
Sbjct: 18 RNRRKILIRGLPGDVTNQEVHDLLS------DYELKYCF-VDKYKGTAFVTLLNGEQAEA 70
Query: 74 AMGLNGQKLL---GIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDM 130
A+ Q L + + +QPT A L + +L ++T+
Sbjct: 71 AINAFHQSRLRERELSVQLQPTDA---------------------LLCVANLPPSLTQQQ 109
Query: 131 LRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
+ PFG ++ L+ TG+SKGYGF + D A +A+ L G L R + V
Sbjct: 110 FEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 167
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 43/182 (23%), Positives = 74/182 (40%), Gaps = 10/182 (5%)
Query: 8 DLSPEERDARTIFCM-QLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
+LS + + + C+ L + + EE G + L+ +T + KG + E+
Sbjct: 84 ELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYM 143
Query: 67 DPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTLPNLQPRGTGGPMRLYIGSLHFNI 126
+S A LLG P+ + AG P L RL G FN
Sbjct: 144 KKDSAARAKS----DLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPG---FND 196
Query: 127 TEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPM 186
+ + R + QL D G+ KG+ + + +A+ A++AQ+Q +G L G +
Sbjct: 197 VDALCRAL-SAVHSPTFCQLACGQD-GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHL 254
Query: 187 KV 188
+V
Sbjct: 255 RV 256
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L++G L+ +ED +R +FE FG I+ ++ PD G SKG F+ + S +A+ A
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPD-GNSKGCAFVKYSSHAEAQAAINA 75
Query: 176 LNG 178
L+G
Sbjct: 76 LHG 78
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L++G L T++ +R +FEPFG ID ++ PD G SKG F+ F + +A+ A
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPD-GTSKGCAFVKFQTHAEAQAAINT 72
Query: 176 LN 177
L+
Sbjct: 73 LH 74
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 38/63 (60%)
Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
++L++G + + E L+ +FE FG+I + ++ D TG KG F+T+ + D A KAQ
Sbjct: 16 IKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQS 75
Query: 175 QLN 177
L+
Sbjct: 76 ALH 78
Score = 32.3 bits (72), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 46/88 (52%), Gaps = 4/88 (4%)
Query: 12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
++ DA +F Q+ + + +DL+ F G++ ++ ++ T KG A++ + +S
Sbjct: 11 KDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSA 70
Query: 72 PLAM-GLNGQKLL-GI--PIIVQPTQAE 95
A L+ QK L G+ PI V+P +E
Sbjct: 71 LKAQSALHEQKTLPGMNRPIQVKPAASE 98
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 50/89 (56%), Gaps = 7/89 (7%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
RL++G+L +ITE+ +R +FE +GK + + D KG+GFI + A+ A+ +
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 176 LNGFELAGRPMKVGTVTDRNESVGGGPSN 204
L+ L G+ ++V + S+ GPS+
Sbjct: 71 LDNMPLRGKQLRV-RFACHSASLTSGPSS 98
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 44/77 (57%), Gaps = 6/77 (7%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
RL++G+L +ITE+ + +FE +G+ + + R +G+GFI S A+ A+ +
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 77
Query: 176 LNGFELAGRPMKVGTVT 192
L+G L RP+++ T
Sbjct: 78 LDGTILKSRPLRIRFAT 94
Score = 36.2 bits (82), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
L + +L ++ ++L F FG ++ ++VD D GR+ G GF+ F + A+KA E+
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALER 156
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 45.1 bits (105), Expect = 7e-05, Method: Composition-based stats.
Identities = 32/90 (35%), Positives = 48/90 (53%), Gaps = 9/90 (10%)
Query: 117 LYIGSLHFNITEDMLRGIFEP--FGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
L + +L ++ TE+ L+ +FE F K+ Q G+SKGY FI F S +DAK+A
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFIKVPQNQ------NGKSKGYAFIEFASFEDAKEALN 71
Query: 175 QLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
N E+ GR +++ R S GPS+
Sbjct: 72 SCNKREIEGRAIRLELQGPRG-SPNSGPSS 100
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 45.1 bits (105), Expect = 7e-05, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 37/60 (61%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
++++G L + E+ +R F FG++++I+L +D T + +G+ FITF + KK E+
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
Score = 35.8 bits (81), Expect = 0.035, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 28/59 (47%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM 75
+ IF LS + E+F G+V + L NKT + +G +I FK+ E V M
Sbjct: 2 KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 45.1 bits (105), Expect = 7e-05, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 8/73 (10%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
RL++ ++ E L IF PFG + ++++ G+ F+ F A+ A KA E+
Sbjct: 6 RLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEE 57
Query: 176 LNGFELAGRPMKV 188
++G A +P++V
Sbjct: 58 VHGKSFANQPLEV 70
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 44.7 bits (104), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 30/88 (34%), Positives = 41/88 (46%), Gaps = 2/88 (2%)
Query: 13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVP 72
E DAR+I+ + +LE F G V V ++ + KG AYIEF D ESV
Sbjct: 2 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 61
Query: 73 LAMGLNGQKLLGIPIIVQPTQAEKNRAG 100
++ L+ G I V P + NR G
Sbjct: 62 TSLALDESLFRGRQIKVIPKRT--NRPG 87
Score = 36.2 bits (82), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
+Y+G++ + T + L F G ++ + ++ D +G KG+ +I F S ++ + L
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF-SDKESVRTSLAL 66
Query: 177 NGFELAGRPMKV 188
+ GR +KV
Sbjct: 67 DESLFRGRQIKV 78
>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 = 44.7 bits (104), Expect = 8e-05, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L + +L F +++ ++ +F FG + + D +GRS G + F DA KA +Q
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAXKQ 89
Query: 176 LNGFELAGRPMKVGTVT 192
NG L GRP + VT
Sbjct: 90 YNGVPLDGRPXNIQLVT 106
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 44.7 bits (104), Expect = 8e-05, Method: Composition-based stats.
Identities = 30/88 (34%), Positives = 41/88 (46%), Gaps = 2/88 (2%)
Query: 13 ERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVP 72
E DAR+I+ + +LE F G V V ++ + KG AYIEF D ESV
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 73 LAMGLNGQKLLGIPIIVQPTQAEKNRAG 100
++ L+ G I V P + NR G
Sbjct: 63 TSLALDESLFRGRQIKVIPKRT--NRPG 88
Score = 35.0 bits (79), Expect = 0.063, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
+Y+G++ + T + L F G ++ + ++ D +G KG+ +I F S ++ + L
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF-SDKESVRTSLAL 67
Query: 177 NGFELAGRPMKV 188
+ GR +KV
Sbjct: 68 DESLFRGRQIKV 79
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 44.7 bits (104), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 6/73 (8%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
RL++G+L +ITE+ +R +FE +GK + + D KG+GFI + A+ A+ +
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 77
Query: 176 LNGFELAGRPMKV 188
L+ L G+ ++V
Sbjct: 78 LDNMPLRGKQLRV 90
Score = 31.6 bits (70), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
L + +L ++ ++L F FG+++ ++VD D GR G G + F A+KA
Sbjct: 99 LTVRNLPQYVSNELLEEAFSVFGQVERAVVIVD-DRGRPSGKGIVEFSGKPAARKA 153
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 44.7 bits (104), Expect = 9e-05, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 8/73 (10%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
RL++ ++ E L IF PFG + ++++ G+ F+ F A+ A KA E+
Sbjct: 33 RLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEE 84
Query: 176 LNGFELAGRPMKV 188
++G A +P++V
Sbjct: 85 VHGKSFANQPLEV 97
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/89 (26%), Positives = 47/89 (52%), Gaps = 2/89 (2%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
++++G + N E LR F+ FG + + ++ D + R +G+GFITF +A
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-N 70
Query: 176 LNGFELAGRPMKVGTVTDRNESVGGGPSN 204
++ ++ G+ ++V R +S GPS+
Sbjct: 71 MHFHDIMGKKVEVKRAEPR-DSKSSGPSS 98
Score = 35.4 bits (80), Expect = 0.054, Method: Composition-based stats.
Identities = 17/68 (25%), Positives = 38/68 (55%)
Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLGIPIIVQP 91
+L E+F G V +V +I + +R +G +I F+D +SV A+ ++ ++G + V+
Sbjct: 26 ELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKR 85
Query: 92 TQAEKNRA 99
+ +++
Sbjct: 86 AEPRDSKS 93
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 36/59 (61%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+++G L + E+ +R F FG++++I+L +D T + +G+ FITF + KK E+
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Score = 35.4 bits (80), Expect = 0.058, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 27/57 (47%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM 75
IF LS + E+F G+V + L NKT + +G +I FK+ E V M
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 23/63 (36%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L++G L+ +E+ + +F+PFG ID ++ PD G SKG F+ F S +A+ A
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKFSSHTEAQAAIHA 75
Query: 176 LNG 178
L+G
Sbjct: 76 LHG 78
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 8/72 (11%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L++ +L +TE++L F FGK++ ++ + D Y FI F D A KA E++
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 177 NGFELAGRPMKV 188
NG +L G +++
Sbjct: 66 NGKDLEGENIEI 77
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 32/48 (66%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITF 163
+L++G L ++ T++ LR F +G++ + +M D T +S+G+GF+ F
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 31/73 (42%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLN 78
+F L L +FS G+V D ++ T + +G +++FKDP V +
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 79 GQKLLGIPIIVQP 91
L G I +P
Sbjct: 79 PHTLDGRNIDPKP 91
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 26/95 (27%), Positives = 49/95 (51%), Gaps = 9/95 (9%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
G+ G ++L+IG+L TE +R +FE +GK+ ++ K YGF+ A
Sbjct: 4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAA 55
Query: 170 KKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
+ A L+ ++L G + V +++++ GPS+
Sbjct: 56 EDAIRNLHHYKLHGVNINVEASKNKSKA-SSGPSS 89
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
LY+ +L IT+D L IF +G I ++ D TGR +G F+ ++ ++A++A L
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 177 NGF--ELAGRPMKV 188
N E +P+ V
Sbjct: 76 NNVIPEGGSQPLSV 89
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 29/79 (36%), Positives = 40/79 (50%), Gaps = 2/79 (2%)
Query: 12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESV 71
+E RT+F L R+R L E F G + V I ++ + K ++ FK PESV
Sbjct: 12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVT-ICKDREGKPKSFGFVCFKHPESV 70
Query: 72 PLAMG-LNGQKLLGIPIIV 89
A+ LNG +L G PI V
Sbjct: 71 SYAIALLNGIRLYGRPINV 89
Score = 41.6 bits (96), Expect = 7e-04, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
+++G+L + E++L +F G + + + D + G+ K +GF+ F + A L
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALL 77
Query: 177 NGFELAGRPMKV 188
NG L GRP+ V
Sbjct: 78 NGIRLYGRPINV 89
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 43.1 bits (100), Expect = 3e-04, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 37/73 (50%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L+IG L + +D ++ + FG + L+ D TG SKGY F + + +A
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 176 LNGFELAGRPMKV 188
LNG +L + + V
Sbjct: 63 LNGMQLGDKKLLV 75
>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 = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 41/188 (21%), Positives = 80/188 (42%), Gaps = 18/188 (9%)
Query: 16 ARTIFCMQLSQRIRTRDLEEFFSSVGKV--------RDVRLITCNKTRRFKGIAYIEFKD 67
AR ++ + I + +FF++ ++ V + N+ + F A++EF+
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNF---AFLEFRS 60
Query: 68 PESVPLAMGLNGQKLLGIPI-IVQPTQAEKNRAGNTLPNLQPRGTGGPM------RLYIG 120
+ AM +G G + I +P + + P++ G + +L+IG
Sbjct: 61 VDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIG 120
Query: 121 SLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFE 180
L + +D ++ + FG + L+ D TG SKGY F + + +A LNG +
Sbjct: 121 GLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ 180
Query: 181 LAGRPMKV 188
L + + V
Sbjct: 181 LGDKKLLV 188
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 42/86 (48%), Gaps = 3/86 (3%)
Query: 9 LSPEER---DARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF 65
LS EE+ D R+++ + +DLE FSS G + + ++ + KG AYIEF
Sbjct: 26 LSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEF 85
Query: 66 KDPESVPLAMGLNGQKLLGIPIIVQP 91
+ SV A+ ++ G I V P
Sbjct: 86 AERNSVDAAVAMDETVFRGRTIKVLP 111
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 7/75 (9%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITF---HSADDAKKAQ 173
+Y+G++ + T L F G I+ I ++ D +G KGY +I F +S D A
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMD 98
Query: 174 EQLNGFELAGRPMKV 188
E + GR +KV
Sbjct: 99 ETV----FRGRTIKV 109
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 37/62 (59%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
LY+ L +++ + +F +G+I ++++D TG S+G GFI F +A++A + L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 177 NG 178
NG
Sbjct: 64 NG 65
Score = 37.4 bits (85), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEF-KDPESVPLAMGL 77
++ L + + +++E+ FS G++ R++ T +G+ +I F K E+ GL
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 78 NGQKLLGI--PIIVQ 90
NGQK LG PI V+
Sbjct: 64 NGQKPLGAAEPITVK 78
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
LY+G+L F TE+ + +F G I I + +D + G+ F+ ++S DA+ A +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 177 NGFELAGRPMKV 188
NG L R ++
Sbjct: 102 NGTRLDDRIIRT 113
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
LYI +L + IT + + IF +G I I++ P+T +G ++ + DAK A + L
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAVDHL 67
Query: 177 NGFELAGRPMKV 188
+GF ++ R + V
Sbjct: 68 SGFNVSNRYLVV 79
>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 = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
LYI +L + IT + + IF +G I I++ P+T +G ++ + DAK A + L
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNACDHL 77
Query: 177 NGFELAGRPMKV 188
+GF + R + V
Sbjct: 78 SGFNVCNRYLVV 89
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L + +L F +++ ++ +F FG + + D +GRS G + F DA KA +Q
Sbjct: 90 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQ 148
Query: 176 LNGFELAGRPMKVGTVT 192
G L GRPM + V
Sbjct: 149 YKGVPLDGRPMDIQLVA 165
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 41.6 bits (96), Expect = 6e-04, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
LYI +L + IT + + IF +G I I++ P+T +G ++ + DAK A + L
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNACDHL 71
Query: 177 NGFELAGRPMKV 188
+GF + R + V
Sbjct: 72 SGFNVCNRYLVV 83
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 41.6 bits (96), Expect = 8e-04, Method: Composition-based stats.
Identities = 31/106 (29%), Positives = 51/106 (48%), Gaps = 9/106 (8%)
Query: 99 AGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGY 158
+G LP T P Y+G+L FN + + IF+ I +++L+ D DT + KG+
Sbjct: 6 SGKELP------TEPPYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGF 58
Query: 159 GFITFHSADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
++ F D K+A +G L R ++V R + GPS+
Sbjct: 59 CYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQD-KSGPSS 102
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 2/53 (3%)
Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLNGQKLLG 84
D++ F + +R VRL+ T +FKG Y+EF + +S+ A+ +G LLG
Sbjct: 31 DIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDG-ALLG 81
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 30/87 (34%), Positives = 49/87 (56%), Gaps = 4/87 (4%)
Query: 114 PMRLYIGSLHFNITEDMLR-GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
P L+IG+L+ N + L+ I E F K D +VD TG ++ +G++ F SA+D +KA
Sbjct: 17 PFNLFIGNLNPNKSVAELKVAISELFAKND--LAVVDVRTGTNRKFGYVDFESAEDLEKA 74
Query: 173 QEQLNGFELAGRPMKVGTVTDRNESVG 199
E L G ++ G +K+ R+ + G
Sbjct: 75 LE-LTGLKVFGNEIKLEKPKGRDGTRG 100
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L + +L F +++ ++ +F FG + + D +GRS G + F DA KA +Q
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQ 95
Query: 176 LNGFELAGRPMKVGTVT 192
G L GRPM + V
Sbjct: 96 YKGVPLDGRPMDIQLVA 112
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L + +L F +++ ++ +F FG + + D +GRS G + F DA KA +Q
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQ 95
Query: 176 LNGFELAGRPMKVGTVT 192
G L GRPM + V
Sbjct: 96 YKGVPLDGRPMDIQLVA 112
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 6/71 (8%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
+Y G + +T+ ++R F PFG+I +++ V P+ KGY F+ F + + A A +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQI--MEIRVFPE----KGYSFVRFSTHESAAHAIVSV 81
Query: 177 NGFELAGRPMK 187
NG + G +K
Sbjct: 82 NGTTIEGHVVK 92
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 7/80 (8%)
Query: 125 NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGR 184
++T +LRG F PFG I I L +DP + F+T+ + A +A +LNG ++
Sbjct: 24 DMTPTLLRGAFSPFGNI--IDLSMDP----PRNCAFVTYEKMESADQAVAELNGTQVESV 77
Query: 185 PMKVGTVTDRNESVGGGPSN 204
+KV + + + GPS+
Sbjct: 78 QLKV-NIARKQPMLDSGPSS 96
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
LY+G+L F TE+ + +F G I I + +D + G+ F+ ++S DA+ A +
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD-KMKTACGFCFVEYYSRADAENAMRYI 79
Query: 177 NGFELAGRPMK 187
NG L R ++
Sbjct: 80 NGTRLDDRIIR 90
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQ 173
P LYI +L ++ E L + +PFG++ + +++ D +G S+G GF S + +
Sbjct: 25 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVI 83
Query: 174 EQLNG 178
NG
Sbjct: 84 GHFNG 88
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 26/94 (27%), Positives = 44/94 (46%), Gaps = 10/94 (10%)
Query: 111 TGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAK 170
+G ++++G++ T LR +FE G++ ++ D Y F+ DAK
Sbjct: 6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAK 57
Query: 171 KAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
A QLNG E+ G+ + V T + GPS+
Sbjct: 58 AAIAQLNGKEVKGKRINVELSTKGQKK--SGPSS 89
>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 = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
G P+ I S + + L +F GK+ N++ +D TG++KG+ F+ S +DAKK
Sbjct: 13 GAPV---IPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKK 69
Query: 172 AQEQLNGFEL 181
+ +G L
Sbjct: 70 IIKSFHGKRL 79
>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 = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
G P+ I S + + L +F GK+ N++ +D TG++KG+ F+ S +DAKK
Sbjct: 13 GAPV---IPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKK 69
Query: 172 AQEQLNGFEL 181
+ +G L
Sbjct: 70 IIKSFHGKRL 79
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 49/93 (52%), Gaps = 3/93 (3%)
Query: 112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKK 171
G P LY+G+L ++TE ++ +F G + +++ + + + Y F+ F+ DA
Sbjct: 13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAA 70
Query: 172 AQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
A +NG ++ G+ +KV T + S GPS+
Sbjct: 71 ALAAMNGRKILGKEVKVNWATTPS-SQKSGPSS 102
Score = 28.9 bits (63), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 17 RTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRR-FKGIAYIEFKDPESVPLAM 75
RT++ LS+ + + + FS +G + ++IT + + + + + E +D + AM
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAM 75
Query: 76 GLNGQKLLGIPIIV 89
NG+K+LG + V
Sbjct: 76 --NGRKILGKEVKV 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 = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 6/64 (9%)
Query: 125 NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGR 184
++T +LRG F PFG I I L +DP + F+T+ + A +A +LNG ++
Sbjct: 48 DMTPTLLRGAFSPFGNI--IDLSMDP----PRNCAFVTYEKMESADQAVAELNGTQVESV 101
Query: 185 PMKV 188
+KV
Sbjct: 102 QLKV 105
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 117 LYIGSLHFNIT-EDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+YI +++ I E++ R ++ F + ++ +V T + +G F+ F + A Q
Sbjct: 9 IYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGSSTNALRQ 68
Query: 176 LNGFELAGRPMKV 188
L GF G+PM++
Sbjct: 69 LQGFPFYGKPMRI 81
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 8/86 (9%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDN--------IQLMVDPDTGRSKGYGFITFHSADD 168
+++ L N+T + + F+ G I I L D +TG+ KG ++F
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 169 AKKAQEQLNGFELAGRPMKVGTVTDR 194
AK A + +G E +G P+KV T R
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSFATRR 95
Score = 36.2 bits (82), Expect = 0.032, Method: Composition-based stats.
Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 9/87 (10%)
Query: 12 EERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRD--------VRLITCNKTRRFKGIAYI 63
+ D TIF L + + + ++F +G ++ + L T +T + KG A +
Sbjct: 3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62
Query: 64 EFKDPESVPLAMG-LNGQKLLGIPIIV 89
F DP S A+ +G++ G PI V
Sbjct: 63 SFDDPPSAKAAIDWFDGKEFSGNPIKV 89
>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 = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L I +L + IT + + IF +G I I++ P+T +G ++ + DAK A + L
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNACDHL 77
Query: 177 NGFELAGRPMKV 188
+GF + R + V
Sbjct: 78 SGFNVCNRYLVV 89
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 47/91 (51%), Gaps = 3/91 (3%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVD-PDTGRSKGYGFITFHSADDAKKAQE 174
++ + ++ F + +R +F FG++ ++L TG +G+GF+ F + DAKKA
Sbjct: 17 KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76
Query: 175 QL-NGFELAGRPMKVGTVTDRNESVGGGPSN 204
L + L GR + V D +V GPS+
Sbjct: 77 ALCHSTHLYGRRL-VLEWADSEVTVQSGPSS 106
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 39/88 (44%), Gaps = 8/88 (9%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
+L++G++ T LR FE +G + ++ D Y F+ A+DA +A
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRG 63
Query: 176 LNGFELAGRPMKVGTVTDRNESVGGGPS 203
L+ E G+ M V T R + G S
Sbjct: 64 LDNTEFQGKRMHVQLSTSRLRTASGPSS 91
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
+++ +L + + L+ +F G + ++ D D G+S+G G +TF + +A +A
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAISMF 76
Query: 177 NGFELAGRPMKV 188
NG L RPM V
Sbjct: 77 NGQLLFDRPMHV 88
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 30/59 (50%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
L + L + TE L+ F FG++ +Q+ D TG SKG+GF+ F + K Q
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 76
Score = 29.6 bits (65), Expect = 2.9, Method: Composition-based stats.
Identities = 15/52 (28%), Positives = 29/52 (55%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPES 70
+ + L + +DL+E+FS+ G+V V++ KT KG ++ F + E+
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 69
>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 = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTG--RSKGYGFITFHSADDAKKA 172
+++++G + +E LR +FE +G + I ++ D +SKG F+TF++ A +A
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 173 QEQLNGFEL 181
Q L+ ++
Sbjct: 64 QNALHNMKV 72
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 37.4 bits (85), Expect = 0.015, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 8/84 (9%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDN--------IQLMVDPDTGRSKGYGFITFHSADD 168
+++ L N+T + + F+ G I I L D +TG+ KG ++F
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 169 AKKAQEQLNGFELAGRPMKVGTVT 192
AK A + +G E +G P+KV T
Sbjct: 76 AKAAIDWFDGKEFSGNPIKVSFAT 99
Score = 36.2 bits (82), Expect = 0.033, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 9/84 (10%)
Query: 15 DARTIFCMQLSQRIRTRDLEEFFSSVGKVRD--------VRLITCNKTRRFKGIAYIEFK 66
D TIF L + + + ++F +G ++ + L T +T + KG A + F
Sbjct: 12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 71
Query: 67 DPESVPLAMG-LNGQKLLGIPIIV 89
DP S A+ +G++ G PI V
Sbjct: 72 DPPSAKAAIDWFDGKEFSGNPIKV 95
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 36/68 (52%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
LY+ +L +TE L +F F + + TGR +G FITF + + A +A +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 177 NGFELAGR 184
NG++L G+
Sbjct: 88 NGYKLYGK 95
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 36.6 bits (83), Expect = 0.021, Method: Composition-based stats.
Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 12/90 (13%)
Query: 103 LPNLQPRGTGGPMRLYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGY 158
+P +P T +YI +L+ I +D L+ IF FG+I +I + + + +G
Sbjct: 3 VPETRPNHT-----IYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQ 54
Query: 159 GFITFHSADDAKKAQEQLNGFELAGRPMKV 188
F+ F A A + GF +PM++
Sbjct: 55 AFVIFKEVSSATNALRSMQGFPFYDKPMRI 84
Score = 34.7 bits (78), Expect = 0.094, Method: Composition-based stats.
Identities = 22/89 (24%), Positives = 46/89 (51%), Gaps = 11/89 (12%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
PE R TI+ L+++I+ +L++ FS G++ D I +++ + +G A++ FK
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILD---ILVSRSLKMRGQAFVIFK 60
Query: 67 DPESVPLAMGLNGQKLLGIPIIVQPTQAE 95
+ S A+ + + G P +P + +
Sbjct: 61 EVSSATNAL----RSMQGFPFYDKPMRIQ 85
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 36.6 bits (83), Expect = 0.024, Method: Composition-based stats.
Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 9/70 (12%)
Query: 106 LQPRGTGGPMRLYIGSLHF-NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH 164
L PRG+ RL+IG+L N++++ L IF P+G I I + +GFI F
Sbjct: 14 LVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFD 65
Query: 165 SADDAKKAQE 174
+ + A E
Sbjct: 66 NPQSVRDAIE 75
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 36.2 bits (82), Expect = 0.027, Method: Composition-based stats.
Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 9/70 (12%)
Query: 106 LQPRGTGGPMRLYIGSLHF-NITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFH 164
L PRG+ RL+IG+L N++++ L IF P+G I I + +GFI F
Sbjct: 14 LVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFD 65
Query: 165 SADDAKKAQE 174
+ + A E
Sbjct: 66 NPQSVRDAIE 75
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 36.2 bits (82), Expect = 0.027, Method: Composition-based stats.
Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 12/90 (13%)
Query: 103 LPNLQPRGTGGPMRLYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGY 158
+P +P T +YI +L+ I +D L+ IF FG+I +I + + + +G
Sbjct: 2 VPETRPNHT-----IYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQ 53
Query: 159 GFITFHSADDAKKAQEQLNGFELAGRPMKV 188
F+ F A A + GF +PM++
Sbjct: 54 AFVIFKEVSSATNALRSMQGFPFYDKPMRI 83
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 22/89 (24%), Positives = 46/89 (51%), Gaps = 11/89 (12%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
PE R TI+ L+++I+ +L++ FS G++ D I +++ + +G A++ FK
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFK 59
Query: 67 DPESVPLAMGLNGQKLLGIPIIVQPTQAE 95
+ S A+ + + G P +P + +
Sbjct: 60 EVSSATNAL----RSMQGFPFYDKPMRIQ 84
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 36.2 bits (82), Expect = 0.027, Method: Composition-based stats.
Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 12/90 (13%)
Query: 103 LPNLQPRGTGGPMRLYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGY 158
+P +P T +YI +L+ I +D L+ IF FG+I +I + + + +G
Sbjct: 2 VPETRPNHT-----IYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQ 53
Query: 159 GFITFHSADDAKKAQEQLNGFELAGRPMKV 188
F+ F A A + GF +PM++
Sbjct: 54 AFVIFKEVSSATNALRSMQGFPFYDKPMRI 83
Score = 34.3 bits (77), Expect = 0.11, Method: Composition-based stats.
Identities = 22/89 (24%), Positives = 46/89 (51%), Gaps = 11/89 (12%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
PE R TI+ L+++I+ +L++ FS G++ D I +++ + +G A++ FK
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFK 59
Query: 67 DPESVPLAMGLNGQKLLGIPIIVQPTQAE 95
+ S A+ + + G P +P + +
Sbjct: 60 EVSSATNAL----RSMQGFPFYDKPMRIQ 84
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 36.2 bits (82), Expect = 0.027, Method: Composition-based stats.
Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 12/90 (13%)
Query: 103 LPNLQPRGTGGPMRLYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGY 158
+P +P T +YI +L+ I +D L+ IF FG+I +I + + + +G
Sbjct: 3 VPETRPNHT-----IYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQ 54
Query: 159 GFITFHSADDAKKAQEQLNGFELAGRPMKV 188
F+ F A A + GF +PM++
Sbjct: 55 AFVIFKEVSSATNALRSMQGFPFYDKPMRI 84
Score = 34.3 bits (77), Expect = 0.11, Method: Composition-based stats.
Identities = 22/89 (24%), Positives = 46/89 (51%), Gaps = 11/89 (12%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
PE R TI+ L+++I+ +L++ FS G++ D I +++ + +G A++ FK
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFK 60
Query: 67 DPESVPLAMGLNGQKLLGIPIIVQPTQAE 95
+ S A+ + + G P +P + +
Sbjct: 61 EVSSATNAL----RSMQGFPFYDKPMRIQ 85
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 36.2 bits (82), Expect = 0.027, Method: Composition-based stats.
Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 12/90 (13%)
Query: 103 LPNLQPRGTGGPMRLYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGY 158
+P +P T +YI +L+ I +D L+ IF FG+I +I + + + +G
Sbjct: 2 VPETRPNHT-----IYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQ 53
Query: 159 GFITFHSADDAKKAQEQLNGFELAGRPMKV 188
F+ F A A + GF +PM++
Sbjct: 54 AFVIFKEVSSATNALRSMQGFPFYDKPMRI 83
Score = 34.3 bits (77), Expect = 0.11, Method: Composition-based stats.
Identities = 22/89 (24%), Positives = 46/89 (51%), Gaps = 11/89 (12%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
PE R TI+ L+++I+ +L++ FS G++ D I +++ + +G A++ FK
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFK 59
Query: 67 DPESVPLAMGLNGQKLLGIPIIVQPTQAE 95
+ S A+ + + G P +P + +
Sbjct: 60 EVSSATNAL----RSMQGFPFYDKPMRIQ 84
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 36.2 bits (82), Expect = 0.032, Method: Composition-based stats.
Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 12/90 (13%)
Query: 103 LPNLQPRGTGGPMRLYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGY 158
+P +P T +YI +L+ I +D L+ IF FG+I +I + + + +G
Sbjct: 3 VPETRPNHT-----IYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQ 54
Query: 159 GFITFHSADDAKKAQEQLNGFELAGRPMKV 188
F+ F A A + GF +PM++
Sbjct: 55 AFVIFKEVSSATNALRSMQGFPFYDKPMRI 84
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 22/89 (24%), Positives = 46/89 (51%), Gaps = 11/89 (12%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
PE R TI+ L+++I+ +L++ FS G++ D I +++ + +G A++ FK
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFK 60
Query: 67 DPESVPLAMGLNGQKLLGIPIIVQPTQAE 95
+ S A+ + + G P +P + +
Sbjct: 61 EVSSATNAL----RSMQGFPFYDKPMRIQ 85
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 35.8 bits (81), Expect = 0.036, Method: Composition-based stats.
Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 12/90 (13%)
Query: 103 LPNLQPRGTGGPMRLYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGY 158
+P +P T +YI +L+ I +D L+ IF FG+I +I + + + +G
Sbjct: 2 VPETRPNHT-----IYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQ 53
Query: 159 GFITFHSADDAKKAQEQLNGFELAGRPMKV 188
F+ F A A + GF +PM++
Sbjct: 54 AFVIFKEVSSATNALRSMQGFPFYDKPMRI 83
Score = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 22/89 (24%), Positives = 46/89 (51%), Gaps = 11/89 (12%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
PE R TI+ L+++I+ +L++ FS G++ D I +++ + +G A++ FK
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILD---ILVSRSLKMRGQAFVIFK 59
Query: 67 DPESVPLAMGLNGQKLLGIPIIVQPTQAE 95
+ S A+ + + G P +P + +
Sbjct: 60 EVSSATNAL----RSMQGFPFYDKPMRIQ 84
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 35.8 bits (81), Expect = 0.040, Method: Composition-based stats.
Identities = 25/88 (28%), Positives = 45/88 (51%), Gaps = 7/88 (7%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
LY+ +L + +E+M+ F +NI+ + + Y F+ F + +DA +A + L
Sbjct: 18 LYVRNLMLSTSEEMIEKEF------NNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKAL 71
Query: 177 NGFELAGRPMKVGTVTDRNESVGGGPSN 204
NG L G P++V T+ + GPS+
Sbjct: 72 NGKVLDGSPIEV-TLAKPVDKDSSGPSS 98
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 35.8 bits (81), Expect = 0.040, Method: Composition-based stats.
Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 12/89 (13%)
Query: 104 PNLQPRGTGGPMRLYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGYG 159
P +P T +YI +L+ I +D L+ IF FG+I +I + + + +G
Sbjct: 1 PETRPNHT-----IYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQA 52
Query: 160 FITFHSADDAKKAQEQLNGFELAGRPMKV 188
F+ F A A + GF +PM++
Sbjct: 53 FVIFKEVSSATNALRSMQGFPFYDKPMRI 81
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 22/89 (24%), Positives = 46/89 (51%), Gaps = 11/89 (12%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
PE R TI+ L+++I+ +L++ FS G++ D I +++ + +G A++ FK
Sbjct: 1 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFK 57
Query: 67 DPESVPLAMGLNGQKLLGIPIIVQPTQAE 95
+ S A+ + + G P +P + +
Sbjct: 58 EVSSATNAL----RSMQGFPFYDKPMRIQ 82
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 35.8 bits (81), Expect = 0.041, Method: Composition-based stats.
Identities = 29/101 (28%), Positives = 51/101 (50%), Gaps = 7/101 (6%)
Query: 110 GTGGP-MRLYIGSLHFNITEDMLRGIF-EPFGKIDNIQLMVDPDTGRSKGYGFITFHSAD 167
G+ GP L++G L ++ + ML F + + ++++D TG SKGYGF+ F
Sbjct: 4 GSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDEL 62
Query: 168 DAKKAQEQLNG-FELAGRPMKVGTV---TDRNESVGGGPSN 204
+ K+A + G L +P+++ R + V GPS+
Sbjct: 63 EQKRALTECQGAVGLGSKPVRLSVAIPKASRVKPVESGPSS 103
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 35.4 bits (80), Expect = 0.047, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 117 LYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
+YI +L+ I +D L+ IF FG+I +I + + + +G F+ F A A
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFKEVSSATNA 62
Query: 173 QEQLNGFELAGRPMKV 188
+ GF +PM++
Sbjct: 63 LRSMQGFPFYDKPMRI 78
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 35.4 bits (80), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 37/83 (44%), Gaps = 2/83 (2%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPD--TGRSKGYGFITFHSADDAKKAQE 174
+Y+GS + T+ L + G D ++L + G+SKGY + S + K E
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 175 QLNGFELAGRPMKVGTVTDRNES 197
L G L G + V T +N S
Sbjct: 118 LLPGKVLNGEKVDVRPATRQNLS 140
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 35.4 bits (80), Expect = 0.048, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 117 LYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
+YI +L+ I +D L+ IF FG+I +I + + + +G F+ F A A
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFKEVSSATNA 63
Query: 173 QEQLNGFELAGRPMKV 188
+ GF +PM++
Sbjct: 64 LRSMQGFPFYDKPMRI 79
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 35.4 bits (80), Expect = 0.048, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 117 LYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
+YI +L+ I +D L+ IF FG+I +I + + + +G F+ F A A
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFKEVSSATNA 64
Query: 173 QEQLNGFELAGRPMKV 188
+ GF +PM++
Sbjct: 65 LRSMQGFPFYDKPMRI 80
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 35.4 bits (80), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 117 LYIGSLHFNITEDMLR----GIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
+YI +L+ I +D L+ IF FG+I +I + + + +G F+ F A A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS---RSLKMRGQAFVIFKEVSSATNA 68
Query: 173 QEQLNGFELAGRPMKV 188
+ GF +PM++
Sbjct: 69 LRSMQGFPFYDKPMRI 84
Score = 32.7 bits (73), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 35/61 (57%), Gaps = 7/61 (11%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
PE R TI+ L+++I+ +L++ FS G++ D I +++ + +G A++ FK
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILD---ILVSRSLKMRGQAFVIFK 60
Query: 67 D 67
+
Sbjct: 61 E 61
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 35.4 bits (80), Expect = 0.056, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 8/62 (12%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
L++ +L +TE++L F FGK++ ++ + D Y F+ F A KA +++
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEDRGAAVKAMDEM 69
Query: 177 NG 178
NG
Sbjct: 70 NG 71
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 35.0 bits (79), Expect = 0.072, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 5/51 (9%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRR-FKGIAYIEFKDP 68
I+ L IRT+D+E+ F G +RD+ L K RR A++EF+DP
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDL----KNRRGGPPFAFVEFEDP 71
Score = 31.2 bits (69), Expect = 0.88, Method: Composition-based stats.
Identities = 27/100 (27%), Positives = 44/100 (44%), Gaps = 10/100 (10%)
Query: 109 RGTGG--PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKG--YGFITFH 164
RG G R+Y+G+L +I + +F +G I +I L R G + F+ F
Sbjct: 15 RGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-----KNRRGGPPFAFVEFE 69
Query: 165 SADDAKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
DA+ A +G++ G ++V G GPS+
Sbjct: 70 DPRDAEDAVYGRDGYDYDGYRLRV-EFPRSGRGTGSGPSS 108
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 34.7 bits (78), Expect = 0.086, Method: Composition-based stats.
Identities = 18/52 (34%), Positives = 33/52 (63%), Gaps = 2/52 (3%)
Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLA-MGLNGQKL 82
+LEE + G V+D+RL+T N+ + KG+AY+E+++ A M ++G +
Sbjct: 33 ELEEICKAHGTVKDLRLVT-NRAGKPKGLAYVEYENESQASQAVMKMDGMTI 83
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 34.7 bits (78), Expect = 0.088, Method: Composition-based stats.
Identities = 24/96 (25%), Positives = 46/96 (47%), Gaps = 9/96 (9%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDN--------IQLMVDPDTGRSKGYGFITFHSADD 168
+Y+ L+ ++T D L F+ G + I + +D +TG+ KG +++
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 169 AKKAQEQLNGFELAGRPMKVGTVTDRNESVGGGPSN 204
AK A E +G + G +KV ++ + + GPS+
Sbjct: 78 AKAAVEWFDGKDFQGSKLKV-SLARKKPPMNSGPSS 112
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 34.7 bits (78), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 127 TEDMLRGIFEPFG-KIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
TED +RG + G + ++LM + +G+S+G+ F+ F DA + E
Sbjct: 14 TEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWME 62
>pdb|1URO|A Chain A, Uroporphyrinogen Decarboxylase
pdb|1R3Q|A Chain A, Uroporphyrinogen Decarboxylase In Complex With
Coproporphyrinogen-I
pdb|1R3Y|A Chain A, Uroporphyrinogen Decarboxylase In Complex With
Coproporphyrinogen-Iii
pdb|3GVQ|A Chain A, Urod Single-Chain Dimer
pdb|3GVR|A Chain A, Single-Chain Urod Y164g (Gy) Mutation
Length = 367
Score = 34.7 bits (78), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 6/92 (6%)
Query: 12 EERDARTIFCMQLSQRI-----RTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
EE D ++CM+ + R TR ++FFS+ +T RRF A I F
Sbjct: 26 EETDYTPVWCMRQAGRYLPEFRETRAAQDFFSTCRSPEACCELTLQPLRRFPLDAAIIFS 85
Query: 67 DPESVPLAMGLNGQKLLGI-PIIVQPTQAEKN 97
D VP A+G+ + G P +P + E++
Sbjct: 86 DILVVPQALGMEVTMVPGKGPSFPEPLREEQD 117
>pdb|3GVV|A Chain A, Single-Chain Urod Y164g (Gy) Mutation
pdb|3GVW|A Chain A, Single-Chain Urod F217y (Yf) Mutation
Length = 367
Score = 34.7 bits (78), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 6/92 (6%)
Query: 12 EERDARTIFCMQLSQRI-----RTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
EE D ++CM+ + R TR ++FFS+ +T RRF A I F
Sbjct: 26 EETDYTPVWCMRQAGRYLPEFRETRAAQDFFSTCRSPEACCELTLQPLRRFPLDAAIIFS 85
Query: 67 DPESVPLAMGLNGQKLLGI-PIIVQPTQAEKN 97
D VP A+G+ + G P +P + E++
Sbjct: 86 DILVVPQALGMEVTMVPGKGPSFPEPLREEQD 117
>pdb|3GW3|A Chain A, Human Urod Mutant K297n
Length = 367
Score = 34.7 bits (78), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 6/92 (6%)
Query: 12 EERDARTIFCMQLSQRI-----RTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
EE D ++CM+ + R TR ++FFS+ +T RRF A I F
Sbjct: 26 EETDYTPVWCMRQAGRYLPEFRETRAAQDFFSTCRSPEACCELTLQPLRRFPLDAAIIFS 85
Query: 67 DPESVPLAMGLNGQKLLGI-PIIVQPTQAEKN 97
D VP A+G+ + G P +P + E++
Sbjct: 86 DILVVPQALGMEVTMVPGKGPSFPEPLREEQD 117
>pdb|1R3W|A Chain A, Uroporphyrinogen Decarboxylase Y164f Mutant In Complex
With Coproporphyrinogen-Iii
Length = 367
Score = 34.7 bits (78), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 6/92 (6%)
Query: 12 EERDARTIFCMQLSQRI-----RTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
EE D ++CM+ + R TR ++FFS+ +T RRF A I F
Sbjct: 26 EETDYTPVWCMRQAGRYLPEFRETRAAQDFFSTCRSPEACCELTLQPLRRFPLDAAIIFS 85
Query: 67 DPESVPLAMGLNGQKLLGI-PIIVQPTQAEKN 97
D VP A+G+ + G P +P + E++
Sbjct: 86 DILVVPQALGMEVTMVPGKGPSFPEPLREEQD 117
>pdb|3GW0|A Chain A, Urod Mutant G318r
Length = 367
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 6/92 (6%)
Query: 12 EERDARTIFCMQLSQRI-----RTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
EE D ++CM+ + R TR ++FFS+ +T RRF A I F
Sbjct: 26 EETDYTPVWCMRQAGRYLPEFRETRAAQDFFSTCRSPEACCELTLQPLRRFPLDAAIIFS 85
Query: 67 DPESVPLAMGLNGQKLLGI-PIIVQPTQAEKN 97
D VP A+G+ + G P +P + E++
Sbjct: 86 DILVVPQALGMEVTMVPGKGPSFPEPLREEQD 117
>pdb|1JPH|A Chain A, Ile260thr Mutant Of Human Urod, Human Uroporphyrinogen Iii
Decarboxylase
Length = 388
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 6/92 (6%)
Query: 12 EERDARTIFCMQLSQRI-----RTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
EE D ++CM+ + R TR ++FFS+ +T RRF A I F
Sbjct: 47 EETDYTPVWCMRQAGRYLPEFRETRAAQDFFSTCRSPEACCELTLQPLRRFPLDAAIIFS 106
Query: 67 DPESVPLAMGLNGQKLLGI-PIIVQPTQAEKN 97
D VP A+G+ + G P +P + E++
Sbjct: 107 DILVVPQALGMEVTMVPGKGPSFPEPLREEQD 138
>pdb|1JPI|A Chain A, Phe232leu Mutant Of Human Urod, Human Uroporphyrinogen Iii
Decarboxylase
Length = 388
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 6/92 (6%)
Query: 12 EERDARTIFCMQLSQRI-----RTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
EE D ++CM+ + R TR ++FFS+ +T RRF A I F
Sbjct: 47 EETDYTPVWCMRQAGRYLPEFRETRAAQDFFSTCRSPEACCELTLQPLRRFPLDAAIIFS 106
Query: 67 DPESVPLAMGLNGQKLLGI-PIIVQPTQAEKN 97
D VP A+G+ + G P +P + E++
Sbjct: 107 DILVVPQALGMEVTMVPGKGPSFPEPLREEQD 138
>pdb|1JPK|A Chain A, Gly156asp Mutant Of Human Urod, Human Uroporphyrinogen Iii
Decarboxylase
Length = 388
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 6/92 (6%)
Query: 12 EERDARTIFCMQLSQRI-----RTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
EE D ++CM+ + R TR ++FFS+ +T RRF A I F
Sbjct: 47 EETDYTPVWCMRQAGRYLPEFRETRAAQDFFSTCRSPEACCELTLQPLRRFPLDAAIIFS 106
Query: 67 DPESVPLAMGLNGQKLLGI-PIIVQPTQAEKN 97
D VP A+G+ + G P +P + E++
Sbjct: 107 DILVVPQALGMEVTMVPGKGPSFPEPLREEQD 138
>pdb|2Q71|A Chain A, Uroporphyrinogen Decarboxylase G168r Single Mutant Enzyme
In Complex With Coproporphyrinogen-Iii
pdb|2Q6Z|A Chain A, Uroporphyrinogen Decarboxylase G168r Single Mutant Apo-
Enzyme
Length = 356
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 6/92 (6%)
Query: 12 EERDARTIFCMQLSQRI-----RTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
EE D ++CM+ + R TR ++FFS+ +T RRF A I F
Sbjct: 16 EETDYTPVWCMRQAGRYLPEFRETRAAQDFFSTCRSPEACCELTLQPLRRFPLDAAIIFS 75
Query: 67 DPESVPLAMGLNGQKLLGI-PIIVQPTQAEKN 97
D VP A+G+ + G P +P + E++
Sbjct: 76 DILVVPQALGMEVTMVPGKGPSFPEPLREEQD 107
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 33.9 bits (76), Expect = 0.13, Method: Composition-based stats.
Identities = 31/97 (31%), Positives = 50/97 (51%), Gaps = 10/97 (10%)
Query: 110 GTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDA 169
G+ G +LYIG+L +T D LR +F + +L + GY F+ + + A
Sbjct: 4 GSSGMNKLYIGNLSPAVTADDLRQLF------GDRKLPLAGQVLLKSGYAFVDYPDQNWA 57
Query: 170 KKAQEQLNG-FELAGRPMKVG-TVTDRNESVGGGPSN 204
+A E L+G EL G+ M+V +V+ + S GPS+
Sbjct: 58 IRAIETLSGKVELHGKIMEVDYSVSKKLRS--SGPSS 92
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 6/79 (7%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
++ L +LE F G +R V + R G A++EF+DP A+ L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPRDAADAVRDL 130
Query: 78 NGQKLLGIPIIVQPTQAEK 96
+G+ L G + V+ + EK
Sbjct: 131 DGRTLCGCRVRVELSNGEK 149
>pdb|2E5I|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Heterogeneous Nuclear Ribonucleoprotein L-Like
Length = 124
Score = 33.1 bits (74), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 31/110 (28%), Positives = 49/110 (44%), Gaps = 18/110 (16%)
Query: 98 RAGNTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKG 157
R GNT P G + L I + + IT D+L + P GK+ I + R+
Sbjct: 12 RPGNTD---DPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIF-----KRNGI 63
Query: 158 YGFITFHSADDAKKAQEQLNGFEL-AG---------RPMKVGTVTDRNES 197
+ F S A+KA+ LNG ++ AG RP ++ + + N+S
Sbjct: 64 QAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRLNVIRNDNDS 113
>pdb|1R3V|A Chain A, Uroporphyrinogen Decarboxylase Single Mutant D86e In
Complex With Coproporphyrinogen-I
Length = 367
Score = 32.7 bits (73), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 42/92 (45%), Gaps = 6/92 (6%)
Query: 12 EERDARTIFCMQLSQRI-----RTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
EE D ++CM+ + R TR ++FFS+ +T RRF A I F
Sbjct: 26 EETDYTPVWCMRQAGRYLPEFRETRAAQDFFSTCRSPEACCELTLQPLRRFPLDAAIIFS 85
Query: 67 DPESVPLAMGLNGQKLLGI-PIIVQPTQAEKN 97
+ VP A+G+ + G P +P + E++
Sbjct: 86 EILVVPQALGMEVTMVPGKGPSFPEPLREEQD 117
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 32.7 bits (73), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 6/79 (7%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GL 77
++ L +LE F G +R V + R G A++EF+DP A+ L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPRDAADAVREL 130
Query: 78 NGQKLLGIPIIVQPTQAEK 96
+G+ L G + V+ + EK
Sbjct: 131 DGRTLCGCRVRVELSNGEK 149
>pdb|1R3R|A Chain A, Uroporphyrinogen Decarboxylase With Mutation D86n
Length = 367
Score = 32.7 bits (73), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 42/92 (45%), Gaps = 6/92 (6%)
Query: 12 EERDARTIFCMQLSQRI-----RTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
EE D ++CM+ + R TR ++FFS+ +T RRF A I F
Sbjct: 26 EETDYTPVWCMRQAGRYLPEFRETRAAQDFFSTCRSPEACCELTLQPLRRFPLDAAIIFS 85
Query: 67 DPESVPLAMGLNGQKLLGI-PIIVQPTQAEKN 97
+ VP A+G+ + G P +P + E++
Sbjct: 86 NILVVPQALGMEVTMVPGKGPSFPEPLREEQD 117
>pdb|2E44|A Chain A, Solution Structure Of Rna Binding Domain In Insulin-Like
Growth Factor 2 Mrna Binding Protein 3
Length = 96
Score = 32.3 bits (72), Expect = 0.41, Method: Composition-based stats.
Identities = 13/33 (39%), Positives = 22/33 (66%)
Query: 161 ITFHSADDAKKAQEQLNGFELAGRPMKVGTVTD 193
+T+ S D A++A ++LNGF+L +KV + D
Sbjct: 59 VTYSSKDQARQALDKLNGFQLENFTLKVAYIPD 91
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 32.3 bits (72), Expect = 0.41, Method: Composition-based stats.
Identities = 22/89 (24%), Positives = 45/89 (50%), Gaps = 11/89 (12%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
PE R TI+ L+++I+ +L++ FS G++ D I +++ + +G A++ FK
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKXRGQAFVIFK 59
Query: 67 DPESVPLAMGLNGQKLLGIPIIVQPTQAE 95
+ S A+ + G P +P + +
Sbjct: 60 EVSSATNAL----RSXQGFPFYDKPXRIQ 84
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 32.3 bits (72), Expect = 0.41, Method: Composition-based stats.
Identities = 22/89 (24%), Positives = 45/89 (50%), Gaps = 11/89 (12%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
PE R TI+ L+++I+ +L++ FS G++ D I +++ + +G A++ FK
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKXRGQAFVIFK 60
Query: 67 DPESVPLAMGLNGQKLLGIPIIVQPTQAE 95
+ S A+ + G P +P + +
Sbjct: 61 EVSSATNAL----RSXQGFPFYDKPXRIQ 85
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 32.3 bits (72), Expect = 0.47, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 3/59 (5%)
Query: 131 LRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKVG 189
L IF FG+I +I V T + +G F+ F A A + GF +PM++
Sbjct: 27 LYAIFSQFGQILDI---VALKTLKMRGQAFVIFKEIGSASNALRTMQGFPFYDKPMQIA 82
>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 = 32.3 bits (72), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 40/146 (27%), Positives = 60/146 (41%), Gaps = 23/146 (15%)
Query: 52 NKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQ---PTQAEKNRAGNTLPNLQ 107
N +RRF AYI+ E + LNG K+ G ++ + P + K TL
Sbjct: 156 NTSRRF---AYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATL---- 208
Query: 108 PRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGY----GFITF 163
G +R L + E++LR FE FG I+ I + P + + F F
Sbjct: 209 -EGREIXIRNLSTEL---LDENLLRESFEGFGSIEKINI---PAGQKEHSFNNCCAFXVF 261
Query: 164 HSADDAKKAQEQLNGFELAGRPMKVG 189
+ D A++A Q N L R + V
Sbjct: 262 ENKDSAERAL-QXNRSLLGNREISVS 286
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 32.0 bits (71), Expect = 0.50, Method: Composition-based stats.
Identities = 22/89 (24%), Positives = 45/89 (50%), Gaps = 11/89 (12%)
Query: 11 PEERDARTIFCMQLSQRIRTRDLEE----FFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
PE R TI+ L+++I+ +L++ FS G++ D I +++ + +G A++ FK
Sbjct: 1 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKXRGQAFVIFK 57
Query: 67 DPESVPLAMGLNGQKLLGIPIIVQPTQAE 95
+ S A+ + G P +P + +
Sbjct: 58 EVSSATNAL----RSXQGFPFYDKPXRIQ 82
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 32.0 bits (71), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 6/82 (7%)
Query: 112 GGPMRLYIGSLHFNITEDMLRGIFEPFGKIDNI-QLMVDP----DTGRSKGYGFITFHSA 166
G RLY+G++ F ITE+ + F ++ + Q +P + K + F+ F S
Sbjct: 4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 63
Query: 167 DDAKKAQEQLNGFELAGRPMKV 188
D+ +A +G G+ +K+
Sbjct: 64 DETTQAMA-FDGIIFQGQSLKI 84
>pdb|1R3S|A Chain A, Uroporphyrinogen Decarboxylase Single Mutant D86g In
Complex With Coproporphyrinogen-I
pdb|1R3T|A Chain A, Uroporphyrinogen Decarboxylase Single Mutant D86g In
Complex With Coproporphyrinogen-Iii
Length = 367
Score = 31.6 bits (70), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 41/92 (44%), Gaps = 6/92 (6%)
Query: 12 EERDARTIFCMQLSQRI-----RTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFK 66
EE D ++CM+ + R TR ++FFS+ +T RRF A I F
Sbjct: 26 EETDYTPVWCMRQAGRYLPEFRETRAAQDFFSTCRSPEACCELTLQPLRRFPLDAAIIFS 85
Query: 67 DPESVPLAMGLNGQKLLGI-PIIVQPTQAEKN 97
VP A+G+ + G P +P + E++
Sbjct: 86 GILVVPQALGMEVTMVPGKGPSFPEPLREEQD 117
>pdb|2IIA|A Chain A, Anabaena Sensory Rhodopsin Transducer
Length = 131
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/101 (21%), Positives = 39/101 (38%), Gaps = 2/101 (1%)
Query: 3 PAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAY 62
P Y + P+ T+ + ++ ++S V RL RR K + +
Sbjct: 24 PPYGNGPEPQFISHETVCILNAGDEDAHVEITIYYSDKEPVGPYRLTV--PARRTKHVRF 81
Query: 63 IEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTL 103
+ DP +P +PI+VQ T+ + +A N L
Sbjct: 82 NDLNDPAPIPHDTDFASVIQSNVPIVVQHTRLDSRQAENAL 122
>pdb|2II7|A Chain A, Anabaena Sensory Rhodopsin Transducer
pdb|2II7|B Chain B, Anabaena Sensory Rhodopsin Transducer
pdb|2II7|C Chain C, Anabaena Sensory Rhodopsin Transducer
pdb|2II7|D Chain D, Anabaena Sensory Rhodopsin Transducer
pdb|2II7|E Chain E, Anabaena Sensory Rhodopsin Transducer
pdb|2II7|F Chain F, Anabaena Sensory Rhodopsin Transducer
pdb|2II7|G Chain G, Anabaena Sensory Rhodopsin Transducer
pdb|2II7|H Chain H, Anabaena Sensory Rhodopsin Transducer
pdb|2II8|A Chain A, Anabaena Sensory Rhodopsin Transducer
pdb|2II8|B Chain B, Anabaena Sensory Rhodopsin Transducer
pdb|2II8|C Chain C, Anabaena Sensory Rhodopsin Transducer
pdb|2II8|D Chain D, Anabaena Sensory Rhodopsin Transducer
pdb|2II8|E Chain E, Anabaena Sensory Rhodopsin Transducer
pdb|2II8|F Chain F, Anabaena Sensory Rhodopsin Transducer
pdb|2II8|G Chain G, Anabaena Sensory Rhodopsin Transducer
pdb|2II8|H Chain H, Anabaena Sensory Rhodopsin Transducer
pdb|2II9|A Chain A, Anabaena Sensory Rhodopsin Transducer
pdb|2II9|B Chain B, Anabaena Sensory Rhodopsin Transducer
pdb|2II9|C Chain C, Anabaena Sensory Rhodopsin Transducer
pdb|2II9|D Chain D, Anabaena Sensory Rhodopsin Transducer
Length = 131
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/101 (21%), Positives = 39/101 (38%), Gaps = 2/101 (1%)
Query: 3 PAYSDDLSPEERDARTIFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAY 62
P Y + P+ T+ + ++ ++S V RL RR K + +
Sbjct: 18 PPYGNGPEPQFISHETVCILNAGDEDAHVEITIYYSDKEPVGPYRLTV--PARRTKHVRF 75
Query: 63 IEFKDPESVPLAMGLNGQKLLGIPIIVQPTQAEKNRAGNTL 103
+ DP +P +PI+VQ T+ + +A N L
Sbjct: 76 NDLNDPAPIPHDTDFASVIQSNVPIVVQHTRLDSRQAENAL 116
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKIDNI-QLMVDP----DTGRSKGYGFITFHSADDAK 170
RLY+G++ F ITE+ + F ++ + Q +P + K + F+ F S D+
Sbjct: 3 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62
Query: 171 KAQEQLNGFELAGRPMKV 188
+A +G G+ +K+
Sbjct: 63 QAMA-FDGIIFQGQSLKI 79
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 39/83 (46%), Gaps = 2/83 (2%)
Query: 104 PNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKID--NIQLMVDPDTGRSKGYGFI 161
PN+ TG + LYIG+L + T++ L G D I+ + G+SKG+ +
Sbjct: 58 PNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALV 117
Query: 162 TFHSADDAKKAQEQLNGFELAGR 184
S +KK + L EL G+
Sbjct: 118 GVGSEASSKKLMDLLPKRELHGQ 140
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 8/77 (10%)
Query: 19 IFCMQLSQRIRTRDLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAMGLN 78
+F + ++ + +L++FF G+V DV + + F+ A++ F D + +A L
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAFVTFADDK---VAQSLC 65
Query: 79 GQKLLGIPIIVQPTQAE 95
G+ L+ I V + AE
Sbjct: 66 GEDLIIKGISVHISNAE 82
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 7/73 (9%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ- 175
LY+G L ITE LR F FG+I I ++ + + FI F + A+ A E+
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVV------QRQQCAFIQFATRQAAEVAAEKS 68
Query: 176 LNGFELAGRPMKV 188
N + GR + V
Sbjct: 69 FNKLIVNGRRLNV 81
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 11/81 (13%)
Query: 116 RLYIGSLHFNITEDMLRGIFEPFGKID--------NIQLMVDPDTGRSKGYGFITFHSAD 167
R+Y+ +L ++ E L+ IF + +I+LM + GR KG FI +
Sbjct: 47 RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKE---GRMKGQAFIGLPNEK 103
Query: 168 DAKKAQEQLNGFELAGRPMKV 188
A KA ++ NG+ L G+PM V
Sbjct: 104 AAAKALKEANGYVLFGKPMVV 124
>pdb|3NNJ|A Chain A, Halogenase Domain From Cura Module (Apo Hal)
pdb|3NNJ|B Chain B, Halogenase Domain From Cura Module (Apo Hal)
Length = 344
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 101 NTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKI 141
N L +++P G P + +GS F TED I+ P KI
Sbjct: 124 NALFSVEPNHKGLPWHVGVGSFSFTKTEDFGASIWIPLDKI 164
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 30.0 bits (66), Expect = 2.0, Method: Composition-based stats.
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQE 174
M++Y+G+L + L F +G + + + +P G+ F+ F DA+ A
Sbjct: 1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVR 55
Query: 175 QLNGFELAGRPMKV 188
L+G + G ++V
Sbjct: 56 GLDGKVICGSRVRV 69
Score = 30.0 bits (66), Expect = 2.4, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 6/69 (8%)
Query: 32 DLEEFFSSVGKVRDVRLITCNKTRRFKGIAYIEFKDPESVPLAM-GLNGQKLLGIPIIVQ 90
+LE FS G +R V + R G A++EF+DP A+ GL+G+ + G + V+
Sbjct: 16 ELERAFSYYGPLRTVWI-----ARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVE 70
Query: 91 PTQAEKNRA 99
+ R+
Sbjct: 71 LSTGMPRRS 79
>pdb|3NNF|A Chain A, Halogenase Domain From Cura Module With Fe, Chloride, And
Alpha- Ketoglutarate
pdb|3NNL|A Chain A, Halogenase Domain From Cura Module (Crystal Form Iii)
pdb|3NNL|B Chain B, Halogenase Domain From Cura Module (Crystal Form Iii)
pdb|3NNM|A Chain A, Halogenase Domain From Cura Module (Crystal Form Iv)
pdb|3NNM|B Chain B, Halogenase Domain From Cura Module (Crystal Form Iv)
Length = 344
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 101 NTLPNLQPRGTGGPMRLYIGSLHFNITEDMLRGIFEPFGKI 141
N L +++P G P + +GS F TED I+ P KI
Sbjct: 124 NALFSVEPNHKGLPWHVGVGSFSFTKTEDFGASIWIPLDKI 164
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 30.0 bits (66), Expect = 2.3, Method: Composition-based stats.
Identities = 23/92 (25%), Positives = 44/92 (47%), Gaps = 9/92 (9%)
Query: 117 LYIGSLHFNITEDMLRGIFEPFGK-IDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQ 175
L++G L + E+ + F G+ + +++++ + TG GY F+ F A+K +
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 176 LNGFELAGRPMKVGTVTDR---NESVGGGPSN 204
+N G+P+ T R N + GPS+
Sbjct: 72 IN-----GKPLPGATPAKRFKLNYATYSGPSS 98
>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex
pdb|3P5T|M Chain M, Cfim25-Cfim68 Complex
pdb|3P5T|N Chain N, Cfim25-Cfim68 Complex
pdb|3P5T|O Chain O, Cfim25-Cfim68 Complex
pdb|3P5T|P Chain P, Cfim25-Cfim68 Complex
pdb|3P5T|Q Chain Q, Cfim25-Cfim68 Complex
pdb|3P6Y|C Chain C, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|D Chain D, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|G Chain G, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|H Chain H, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|K Chain K, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|L Chain L, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|O Chain O, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|P Chain P, Cf Im25-Cf Im68-Uguaa Complex
Length = 90
Score = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 115 MRLYIGSLHFNITEDMLRGIFEPFGKID--NIQLMVDPDTGRSKGYGFITFHSADDAKKA 172
+ LYIG+L + T++ L G D I+ + G+SKG+ + S +KK
Sbjct: 2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61
Query: 173 QEQLNGFELAGR 184
+ L EL G+
Sbjct: 62 MDLLPKRELHGQ 73
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 29.3 bits (64), Expect = 3.6, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 141 IDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQLNGFELAGRPMKV 188
++NI+L+ D T +++G+ F+ SA DA + + L P+K+
Sbjct: 38 VNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLH---PPLKI 82
>pdb|1N69|A Chain A, Crystal Structure Of Human Saposin B
pdb|1N69|B Chain B, Crystal Structure Of Human Saposin B
pdb|1N69|C Chain C, Crystal Structure Of Human Saposin B
Length = 81
Score = 29.3 bits (64), Expect = 3.7, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 268 IATQCFLLANMFDPATETNPTWDVEIRDDVIEECNKHGVGASTVC--FI--YSVIFLKLW 323
+ C + A TN T+ + + V EEC++ G G + +C +I YS I +++
Sbjct: 5 VCQDCIQMVTDIQTAVRTNSTFVQALVEHVKEECDRLGPGMADICKNYISQYSEIAIQMM 64
Query: 324 SYVQVNLWC 332
++Q C
Sbjct: 65 MHMQPKEIC 73
>pdb|2CPY|A Chain A, Solution Structure Of Rna Binding Domain 3 In Rna Binding
Motif Protein 12
Length = 114
Score = 28.5 bits (62), Expect = 6.9, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 42/76 (55%), Gaps = 3/76 (3%)
Query: 118 YIGSLHFNITEDMLRGIFEPFGKIDN-IQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL 176
+I ++ F+IT+ + E +N + ++VD + G+ G + F + DDA+K+ E+L
Sbjct: 19 HITNIPFSITKMDVLQFLEGIPVDENAVHVLVD-NNGQGLGQALVQFKNEDDARKS-ERL 76
Query: 177 NGFELAGRPMKVGTVT 192
+ +L GR V VT
Sbjct: 77 HRKKLNGREAFVHVVT 92
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 28.1 bits (61), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDP-DTGRSKGYGFITFH 164
P ++G+L +++TE+ ++ F I ++L +P + R KG+G+ F
Sbjct: 15 PYTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFE 65
>pdb|1X4F|A Chain A, Solution Structure Of The Second Rrm Domain In Matrin 3
Length = 112
Score = 28.1 bits (61), Expect = 8.7, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 9/84 (10%)
Query: 123 HFNITEDMLRGIFEPFGKIDNIQLMVDPDTGRSKGYGFITFHSADDAKKAQEQL--NGFE 180
H ++ + + EP+GKI N LM R K FI + +DA +
Sbjct: 35 HSGYSDSAVLKLAEPYGKIKNYILM------RMKSQAFIEMETREDAMAMVDHCLKKALW 88
Query: 181 LAGRPMKVGTVTDRNESVGGGPSN 204
GR +KV ++++ + + GPS+
Sbjct: 89 FQGRCVKV-DLSEKYKKLVSGPSS 111
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 28.1 bits (61), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 114 PMRLYIGSLHFNITEDMLRGIFEPFGKIDNIQLMVDP-DTGRSKGYGFITFH 164
P ++G+L +++TE+ ++ F I ++L +P + R KG+G+ F
Sbjct: 19 PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFE 69
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
0.319 0.136 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,590,361
Number of Sequences: 62578
Number of extensions: 437269
Number of successful extensions: 1448
Number of sequences better than 100.0: 225
Number of HSP's better than 100.0 without gapping: 157
Number of HSP's successfully gapped in prelim test: 68
Number of HSP's that attempted gapping in prelim test: 1100
Number of HSP's gapped (non-prelim): 343
length of query: 370
length of database: 14,973,337
effective HSP length: 100
effective length of query: 270
effective length of database: 8,715,537
effective search space: 2353194990
effective search space used: 2353194990
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)