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= 012034
(472 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DYD|A Chain A, Solution Structure Of The Pabc Domain From Triticum
Aevestium Poly(A)-Binding Protein
Length = 85
Score = 124 bits (312), Expect = 8e-29, Method: Compositional matrix adjust.
Identities = 63/79 (79%), Positives = 70/79 (88%)
Query: 374 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 433
PI AL++ALAN+ PE QR +LGE+LYPLV+QLE D AAKVTGMLLEMDQTEVLHLLESP+
Sbjct: 6 PIGALASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLESPD 65
Query: 434 ALKAKVAEAMEVLRSVAQQ 452
ALKAKVAEAMEVLRS Q
Sbjct: 66 ALKAKVAEAMEVLRSAQQH 84
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 118 bits (296), Expect = 5e-27, Method: Compositional matrix adjust.
Identities = 55/90 (61%), Positives = 75/90 (83%), Gaps = 1/90 (1%)
Query: 126 VDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEA 185
+ ++Q +NLY+KNL D IDDE+L++ FS FGTITS KVM + G SKG GFV FS+PEEA
Sbjct: 10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEA 68
Query: 186 SRALAEMNGKMIVSKPLYVAVAQRKEERRA 215
++A+ EMNG+++ +KPLYVA+AQRKEER++
Sbjct: 69 TKAVTEMNGRIVATKPLYVALAQRKEERQS 98
Score = 79.0 bits (193), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 41/82 (50%), Positives = 56/82 (68%), Gaps = 1/82 (1%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
N++VKNLD+ DE L+K F +GTITSA VM +G G+SK FGFV F + ++A KAV +
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFSSPEEATKAVTEM 75
Query: 90 NGKKFDDREWYVGKAQKKSERE 111
NG+ + YV AQ+K ER+
Sbjct: 76 NGRIVATKPLYVALAQRKEERQ 97
>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 = 92.4 bits (228), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 70/200 (35%), Positives = 108/200 (54%), Gaps = 22/200 (11%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
+++V +L T+ L + F G I S V RD +S + +VNF+ DA +A++
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 89 LNGKKFDDREWYVGKAQK--KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 146
+N FD + GK + S+R+ L+ K V N++IKNL SID++
Sbjct: 77 MN---FDVIK---GKPVRIMWSQRDPSLR-------KSGVG-----NIFIKNLDKSIDNK 118
Query: 147 KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV 206
L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +MNG ++ + ++V
Sbjct: 119 ALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177
Query: 207 AQRKEERRARLQAQFSQMRP 226
+ ++ER A L A+ + P
Sbjct: 178 FKSRKEREAELGARAKEFYP 197
Score = 75.5 bits (184), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 40/115 (34%), Positives = 67/115 (58%), Gaps = 1/115 (0%)
Query: 17 QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNF 76
+R+ K+ N+F+KNLD+S ++ L F +G I S V+ D +G SK +GFV+F
Sbjct: 92 SQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHF 150
Query: 77 ENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQG 131
E + A +A+E +NG +DR+ +VG+ + + ERE EL + ++ V + G
Sbjct: 151 ETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPDYAG 205
Score = 32.0 bits (71), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 12/20 (60%), Positives = 17/20 (85%)
Query: 1 MLINDKQVFVGHFLRKQERE 20
ML+ND++VFVG F ++ERE
Sbjct: 166 MLLNDRKVFVGRFKSRKERE 185
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 90.5 bits (223), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 69/194 (35%), Positives = 106/194 (54%), Gaps = 22/194 (11%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
+++V +L T+ L + F G I S V RD +S + +VNF+ DA +A++
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 89 LNGKKFDDREWYVGKAQK--KSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 146
+N FD + GK + S+R+ L+ K V N++IKNL SID++
Sbjct: 72 MN---FDVIK---GKPVRIMWSQRDPSLR-------KSGVG-----NIFIKNLDKSIDNK 113
Query: 147 KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAV 206
L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +MNG ++ + ++V
Sbjct: 114 ALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 172
Query: 207 AQRKEERRARLQAQ 220
+ ++ER A L A+
Sbjct: 173 FKSRKEREAELGAR 186
Score = 74.7 bits (182), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 38/98 (38%), Positives = 61/98 (62%), Gaps = 1/98 (1%)
Query: 17 QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNF 76
+R+ K+ N+F+KNLD+S ++ L F +G I S V+ D +G SK +GFV+F
Sbjct: 87 SQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHF 145
Query: 77 ENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQEL 114
E + A +A+E +NG +DR+ +VG+ + + ERE EL
Sbjct: 146 ETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 183
Score = 31.6 bits (70), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 12/20 (60%), Positives = 17/20 (85%)
Query: 1 MLINDKQVFVGHFLRKQERE 20
ML+ND++VFVG F ++ERE
Sbjct: 161 MLLNDRKVFVGRFKSRKERE 180
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 85.5 bits (210), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 54/178 (30%), Positives = 92/178 (51%), Gaps = 24/178 (13%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
N+ V L ++ T ++ K +FG G I S ++RD G+S +GFVN+ + +DA KA+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 89 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 148
LNG K + V A+ S + NLY+ L ++ +++
Sbjct: 66 LNGLKLQTKTIKVSYARPSSA------------------SIRDANLYVSGLPKTMSQKEM 107
Query: 149 KELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVA 205
++LFS++G I + +++ D +G+S+G GF+ F EA A+ +NG+ KPL A
Sbjct: 108 EQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ----KPLGAA 161
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 46/77 (59%), Gaps = 1/77 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
NL + L ++ ++ K LF G I SCK++RD +G S G GFV +S P +A +A+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 192 MNGKMIVSKPLYVAVAQ 208
+NG + +K + V+ A+
Sbjct: 66 LNGLKLQTKTIKVSYAR 82
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 85.1 bits (209), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 53/180 (29%), Positives = 96/180 (53%), Gaps = 17/180 (9%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
++V NLD++ T++ LK+ F G I + +M D + K+ + FV + + DA A++ LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 91 GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 150
GK+ ++ + A F+ + D F NL++ +L ++DDE L+
Sbjct: 63 GKQIENNIVKINWA-------------FQSQQSSSDDTF---NLFVGDLNVNVDDETLRN 106
Query: 151 LFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQR 209
F +F + S VM D +G S+G GFV+F++ ++A A+ M G+ + +PL + A +
Sbjct: 107 AFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 45/78 (57%), Gaps = 1/78 (1%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
N+FV +L+ + DE L+ F ++ + S VM D G S+ +GFV+F + DDA A+++
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 89 LNGKKFDDREWYVGKAQK 106
+ G+ + R + A K
Sbjct: 149 MQGQDLNGRPLRINWAAK 166
>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 = 83.2 bits (204), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 50/169 (29%), Positives = 87/169 (51%), Gaps = 20/169 (11%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE 87
N+ V L ++ T E+ + +FG G I S ++RD G+S +GFVN+ + DA KA+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 88 ALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEK 147
LNG + + V A+ S + NLY+ L ++ ++
Sbjct: 63 TLNGLRLQTKTIKVSYARPSSA------------------SIRDANLYVSGLPKTMTQKE 104
Query: 148 LKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGK 195
L++LFS++G I + +++ D +G+S+G GF+ F EA A+ +NG+
Sbjct: 105 LEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ 153
Score = 52.4 bits (124), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 46/77 (59%), Gaps = 1/77 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
NL + L ++ E+ + LF G I SCK++RD +G S G GFV + P++A +A+
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 192 MNGKMIVSKPLYVAVAQ 208
+NG + +K + V+ A+
Sbjct: 64 LNGLRLQTKTIKVSYAR 80
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 43/65 (66%), Gaps = 1/65 (1%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
N++V L ++ T ++L+++F +YG ITS +++ G S+ GF+ F+ +A +A++
Sbjct: 90 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 149
Query: 89 LNGKK 93
LNG+K
Sbjct: 150 LNGQK 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 = 81.6 bits (200), Expect = 9e-16, Method: Compositional matrix adjust.
Identities = 51/167 (30%), Positives = 85/167 (50%), Gaps = 20/167 (11%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
N+ V L ++ T ++L+ +F G + SA ++RD G S +GFVN+ A DA +A+
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 89 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 148
LNG + + V A+ SE +K+ NLYI L ++ + +
Sbjct: 64 LNGLRLQSKTIKVSYARPSSE-----------VIKDA-------NLYISGLPRTMTQKDV 105
Query: 149 KELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNG 194
+++FS FG I + +V+ D +G+S+G F+ F EA A+ NG
Sbjct: 106 EDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 52.0 bits (123), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
NL + L ++ ++L+ LFS G + S K++RD +G S G GFV + T ++A RA+
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 192 MNGKMIVSKPLYVAVAQRKEE 212
+NG + SK + V+ A+ E
Sbjct: 64 LNGLRLQSKTIKVSYARPSSE 84
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 81.6 bits (200), Expect = 9e-16, Method: Compositional matrix adjust.
Identities = 51/167 (30%), Positives = 85/167 (50%), Gaps = 20/167 (11%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
N+ V L ++ T ++L+ +F G + SA ++RD G S +GFVN+ A DA +A+
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 89 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 148
LNG + + V A+ SE +K+ NLYI L ++ + +
Sbjct: 64 LNGLRLQSKTIKVSYARPSSE-----------VIKDA-------NLYISGLPRTMTQKDV 105
Query: 149 KELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNG 194
+++FS FG I + +V+ D +G+S+G F+ F EA A+ NG
Sbjct: 106 EDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 52.0 bits (123), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
NL + L ++ ++L+ LFS G + S K++RD +G S G GFV + T ++A RA+
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 192 MNGKMIVSKPLYVAVAQRKEE 212
+NG + SK + V+ A+ E
Sbjct: 64 LNGLRLQSKTIKVSYARPSSE 84
>pdb|1NMR|A Chain A, Solution Structure Of C-Terminal Domain From Trypanosoma
Cruzi Poly(A)-Binding Protein
Length = 85
Score = 81.3 bits (199), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 42/70 (60%), Positives = 52/70 (74%)
Query: 378 LSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKA 437
LST LAN +PEQQ+ +LGE LY + + AAAKVTGMLLEMD E+L+LL++P L A
Sbjct: 11 LSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILNLLDTPGLLDA 70
Query: 438 KVAEAMEVLR 447
KV EA+EVL
Sbjct: 71 KVQEALEVLN 80
>pdb|1G9L|A Chain A, Solution Structure Of The Pabc Domain Of Human Poly(A)
Binding Protein
Length = 144
Score = 80.5 bits (197), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 374 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 433
P+TA + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESPE
Sbjct: 52 PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 109
Query: 434 ALKAKVAEAMEVLRS 448
+L++KV EA+ VL++
Sbjct: 110 SLRSKVDEAVAVLQA 124
>pdb|1JGN|A Chain A, Solution Structure Of The C-Terminal Pabc Domain Of Human
Poly(A)-Binding Protein In Complex With The Peptide From
Paip2
pdb|1JH4|A Chain A, Solution Structure Of The C-Terminal Pabc Domain Of Human
Poly(A)-Binding Protein In Complex With The Peptide From
Paip1
Length = 98
Score = 80.1 bits (196), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 374 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 433
P+TA + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESPE
Sbjct: 6 PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 63
Query: 434 ALKAKVAEAMEVLRS 448
+L++KV EA+ VL++
Sbjct: 64 SLRSKVDEAVAVLQA 78
>pdb|3KUR|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|C Chain C, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|D Chain D, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|E Chain E, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|F Chain F, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|G Chain G, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|H Chain H, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
Length = 79
Score = 79.7 bits (195), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 374 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 433
P+TA + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESPE
Sbjct: 6 PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 63
Query: 434 ALKAKVAEAMEVLRS 448
+L++KV EA+ VL++
Sbjct: 64 SLRSKVDEAVAVLQA 78
>pdb|3KUS|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KUS|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KUT|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(a)-binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KUT|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(a)-binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KTP|A Chain A, Structural Basis Of Gw182 Recognition By Poly(a)-binding
Protein
pdb|3KTR|A Chain A, Structural Basis Of Ataxin-2 Recognition By
Poly(A)-Binding
pdb|3KUI|A Chain A, Crystal Structure Of C-Terminal Domain Of Pabpc1 In
Complex Binding Region Of Erf3a
pdb|3KUJ|A Chain A, Crystal Structure Of C-Terminal Domain Of Pabpc1 In
Complex With Binding Region Of Erf3a
pdb|3PKN|A Chain A, Crystal Structure Of Mlle Domain Of Poly(A) Binding
Protein In Complex With Pam2 Motif Of La-Related Protein
4 (Larp4)
Length = 88
Score = 79.7 bits (195), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 374 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 433
P+TA + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESPE
Sbjct: 6 PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 63
Query: 434 ALKAKVAEAMEVLRS 448
+L++KV EA+ VL++
Sbjct: 64 SLRSKVDEAVAVLQA 78
>pdb|3PTH|A Chain A, The Pabc1 Mlle Domain Bound To The Variant Pam2 Motif Of
Larp4b
Length = 82
Score = 79.3 bits (194), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 374 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 433
P+TA + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESPE
Sbjct: 5 PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 62
Query: 434 ALKAKVAEAMEVLRS 448
+L++KV EA+ VL++
Sbjct: 63 SLRSKVDEAVAVLQA 77
>pdb|2RQG|B Chain B, Structure Of Gspt1ERF3A-Pabc
pdb|2RQH|B Chain B, Structure Of Gspt1ERF3A-Pabc
Length = 83
Score = 79.3 bits (194), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 38/75 (50%), Positives = 60/75 (80%), Gaps = 2/75 (2%)
Query: 374 PITALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPE 433
P+TA + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESPE
Sbjct: 4 PLTA--SMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPE 61
Query: 434 ALKAKVAEAMEVLRS 448
+L++KV EA+ VL++
Sbjct: 62 SLRSKVDEAVAVLQA 76
>pdb|2X04|A Chain A, Crystal Structure Of The Pabc-Tnrc6c Complex
pdb|2X04|B Chain B, Crystal Structure Of The Pabc-Tnrc6c Complex
Length = 80
Score = 78.6 bits (192), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 37/76 (48%), Positives = 61/76 (80%), Gaps = 1/76 (1%)
Query: 374 PITALSTA-LANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESP 432
P+ +L+ + LA+A P++Q+ +LGE L+PL++ + A K+TGMLLE+D +E+LH+LESP
Sbjct: 2 PLGSLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESP 61
Query: 433 EALKAKVAEAMEVLRS 448
E+L++KV EA+ VL++
Sbjct: 62 ESLRSKVDEAVAVLQA 77
>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 = 78.6 bits (192), Expect = 8e-15, Method: Composition-based stats.
Identities = 42/95 (44%), Positives = 61/95 (64%), Gaps = 1/95 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
N++IKNL SID++ L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +M
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 193 NGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRPV 227
NG ++ + ++V + ++ER A L A+ + V
Sbjct: 66 NGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNV 100
Score = 76.6 bits (187), Expect = 3e-14, Method: Composition-based stats.
Identities = 42/111 (37%), Positives = 66/111 (59%), Gaps = 11/111 (9%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
N+F+KNLD+S ++ L F +G I S V+ D +G SK +GFV+FE + A +A+E +
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 90 NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLG 140
NG +DR+ +VG+ + + ERE EL + ++ N+YIKN G
Sbjct: 66 NGMLLNDRKVFVGRFKSRKEREAELGARAKEFT----------NVYIKNFG 106
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 19/43 (44%), Positives = 28/43 (65%), Gaps = 2/43 (4%)
Query: 1 MLINDKQVFVGHFLRKQERETV--AIKTKFNNVFVKNLDESTT 41
ML+ND++VFVG F ++ERE A +F NV++KN +T
Sbjct: 68 MLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGST 110
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 77.8 bits (190), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 54/182 (29%), Positives = 93/182 (51%), Gaps = 22/182 (12%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
N+ V L + TD +L +F G I + +MRD G S + FV+F + D+ +A++
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 89 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 148
LNG ++ V A+ E ++K+T NLY+ NL +I D++L
Sbjct: 65 LNGITVRNKRLKVSYARPGGE-----------SIKDT-------NLYVTNLPRTITDDQL 106
Query: 149 KELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIV--SKPLYVA 205
+F ++G+I ++RD +G +G FV ++ EEA A++ +N + S+PL V
Sbjct: 107 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 166
Query: 206 VA 207
+A
Sbjct: 167 LA 168
Score = 52.4 bits (124), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
NL + L + D +L LF G I +C++MRD +G S G FV F++ ++ RA+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 192 MNGKMIVSKPLYVAVAQ 208
+NG + +K L V+ A+
Sbjct: 65 LNGITVRNKRLKVSYAR 81
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKA 85
K N++V NL + TD+ L IFG+YG+I ++RD G+ + FV + ++A +A
Sbjct: 88 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 147
Query: 86 VEALN 90
+ ALN
Sbjct: 148 ISALN 152
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 75.9 bits (185), Expect = 5e-14, Method: Composition-based stats.
Identities = 39/83 (46%), Positives = 56/83 (67%), Gaps = 1/83 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
N++IKNL SID++ L + FS FG I SCKV+ D +G SKG GFV F T E A RA+ +M
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 71
Query: 193 NGKMIVSKPLYVAVAQRKEERRA 215
NG ++ + ++V + ++ER A
Sbjct: 72 NGMLLNDRKVFVGRFKSRKEREA 94
Score = 72.0 bits (175), Expect = 6e-13, Method: Composition-based stats.
Identities = 36/89 (40%), Positives = 57/89 (64%), Gaps = 1/89 (1%)
Query: 25 KTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
K+ N+F+KNLD+S ++ L F +G I S V+ D +G SK +GFV+FE + A +
Sbjct: 8 KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAER 66
Query: 85 AVEALNGKKFDDREWYVGKAQKKSEREQE 113
A+E +NG +DR+ +VG+ + + ERE E
Sbjct: 67 AIEKMNGMLLNDRKVFVGRFKSRKEREAE 95
Score = 31.6 bits (70), Expect = 1.1, Method: Composition-based stats.
Identities = 12/20 (60%), Positives = 17/20 (85%)
Query: 1 MLINDKQVFVGHFLRKQERE 20
ML+ND++VFVG F ++ERE
Sbjct: 74 MLLNDRKVFVGRFKSRKERE 93
>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 = 75.5 bits (184), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 53/183 (28%), Positives = 93/183 (50%), Gaps = 22/183 (12%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
N+ V L + TD +L +F G I + + RD G S + FV+F + D+ +A++
Sbjct: 16 NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
Query: 89 LNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 148
LNG ++ V A+ E ++K+T NLY+ NL +I D++L
Sbjct: 76 LNGITVRNKRLKVSYARPGGE-----------SIKDT-------NLYVTNLPRTITDDQL 117
Query: 149 KELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIV--SKPLYVA 205
+F ++G+I ++RD +G +G FV ++ EEA A++ +N + S+PL V
Sbjct: 118 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 177
Query: 206 VAQ 208
+A+
Sbjct: 178 LAE 180
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKA 85
K N++V NL + TD+ L IFG+YG+I ++RD G+ + FV + ++A +A
Sbjct: 99 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 158
Query: 86 VEALN 90
+ ALN
Sbjct: 159 ISALN 163
>pdb|4IVE|A Chain A, Crystal Structure Of A Polyadenylate-binding Protein 3
(pabpc3) From Homo Sapiens At 2.30 A Resolution
pdb|4IVE|B Chain B, Crystal Structure Of A Polyadenylate-binding Protein 3
(pabpc3) From Homo Sapiens At 2.30 A Resolution
pdb|4IVE|C Chain C, Crystal Structure Of A Polyadenylate-binding Protein 3
(pabpc3) From Homo Sapiens At 2.30 A Resolution
pdb|4IVE|D Chain D, Crystal Structure Of A Polyadenylate-binding Protein 3
(pabpc3) From Homo Sapiens At 2.30 A Resolution
Length = 98
Score = 70.1 bits (170), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 36/83 (43%), Positives = 58/83 (69%)
Query: 376 TALSTALANASPEQQRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEAL 435
T ++ LA+A P++Q+ LGE L+PL++ A K+TG LLE+D +E+L+ LESPE+L
Sbjct: 6 TLTASRLASAPPQKQKQXLGERLFPLIQAXHPTLAGKITGXLLEIDNSELLYXLESPESL 65
Query: 436 KAKVAEAMEVLRSVAQQQANNPA 458
++KV EA+ VL++ ++A A
Sbjct: 66 RSKVDEAVAVLQAHQAKEATQKA 88
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 70.1 bits (170), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 45/164 (27%), Positives = 87/164 (53%), Gaps = 28/164 (17%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFE---NADDAAKAV 86
+F+ L+ TT+++L++ FG+YGT+T +M+D G+S+ FGF++FE + D+ K
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 87 EALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDE 146
L+GK D + +A + E+++ K +++ +G + +
Sbjct: 66 HILDGKVIDPK-----RAIPRDEQDKTGK------------------IFVGGIGPDVRPK 102
Query: 147 KLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 189
+ +E FS++GTI ++M D +G S+G GFV + + + R
Sbjct: 103 EFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC 146
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 43/72 (59%), Gaps = 4/72 (5%)
Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTP---EEA 185
+ ++I L ++ L+E F ++GT+T K+M+DP +G S+G GF++F P +E
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 186 SRALAEMNGKMI 197
+ ++GK+I
Sbjct: 62 VKTQHILDGKVI 73
Score = 38.5 bits (88), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 5/71 (7%)
Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKA 85
K +FV + ++ ++ F ++GTI A +M D D G+S+ FGFV +++AD A
Sbjct: 86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSAD----A 141
Query: 86 VEALNGKKFDD 96
V+ + KF D
Sbjct: 142 VDRVCQNKFID 152
>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 = 66.2 bits (160), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 46/180 (25%), Positives = 86/180 (47%), Gaps = 14/180 (7%)
Query: 17 QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVN 75
Q + +AI + V+V ++ ++ +++ F +G I S + D K K F FV
Sbjct: 5 QRQRALAIMCR---VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE 61
Query: 76 FENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN-L 134
+E + A A+E +N R VG+ GQ + + + ++ + N +
Sbjct: 62 YEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRI 113
Query: 135 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 193
Y+ ++ + D+ +K +F FG I SC + RDP +G KG GF+ + + + A++ MN
Sbjct: 114 YVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 173
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAV 86
FN ++V ++ + +D+D+K +F +G I S + RD GK K +GF+ +E A + AV
Sbjct: 110 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 169
Query: 87 EALNGKKFDDREWYVGKA 104
++N + VGKA
Sbjct: 170 SSMNLFDLGGQYLRVGKA 187
Score = 36.6 bits (83), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEASRALAEM 192
+Y+ ++ + ++ +++ F+ FG I S + D + KG FV + PE A AL +M
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 193 NGKMI------VSKPLYVAVAQ 208
N M+ V +P + AQ
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQ 97
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 64.7 bits (156), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 49/188 (26%), Positives = 82/188 (43%), Gaps = 30/188 (15%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG---KSKCFGFVNFENADDAAKAVE 87
+FV + + +++DL+++F +YG + V+RD +SK FV F A +A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 88 ALNGKKFDDREWYVGKAQKKSEREQELKG-----QFEQAMKETVDKFQGLNLYIKNLGDS 142
AL+ K L G Q + A E + + L+I +
Sbjct: 78 ALHNMKV-------------------LPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKK 118
Query: 143 IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI---VS 199
+ ++ +FS FG I C+++R P G+S+G FV F+T A A+ M+ S
Sbjct: 119 CTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCS 178
Query: 200 KPLYVAVA 207
P+ V A
Sbjct: 179 SPMVVKFA 186
Score = 35.0 bits (79), Expect = 0.100, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 6/68 (8%)
Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI---SKGSGFVAFSTPE---E 184
+ +++ + + ++ L+ELF ++G + V+RD S SKG FV F T + E
Sbjct: 15 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 74
Query: 185 ASRALAEM 192
A AL M
Sbjct: 75 AQNALHNM 82
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 64.7 bits (156), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 49/188 (26%), Positives = 82/188 (43%), Gaps = 30/188 (15%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG---KSKCFGFVNFENADDAAKAVE 87
+FV + + +++DL+++F +YG + V+RD +SK FV F A +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 88 ALNGKKFDDREWYVGKAQKKSEREQELKG-----QFEQAMKETVDKFQGLNLYIKNLGDS 142
AL+ K L G Q + A E + + L+I +
Sbjct: 66 ALHNMKV-------------------LPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKK 106
Query: 143 IDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI---VS 199
+ ++ +FS FG I C+++R P G+S+G FV F+T A A+ M+ S
Sbjct: 107 CTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCS 166
Query: 200 KPLYVAVA 207
P+ V A
Sbjct: 167 SPMVVKFA 174
Score = 35.0 bits (79), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 6/68 (8%)
Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI---SKGSGFVAFSTPE---E 184
+ +++ + + ++ L+ELF ++G + V+RD S SKG FV F T + E
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62
Query: 185 ASRALAEM 192
A AL M
Sbjct: 63 AQNALHNM 70
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 64.3 bits (155), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 34/80 (42%), Positives = 52/80 (65%), Gaps = 1/80 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 89
+FV L T ++ L+++F +YG I+ VV++D + +S+ FGFV FEN DDA A+ A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 90 NGKKFDDREWYVGKAQKKSE 109
NGK D R+ V +A K S+
Sbjct: 75 NGKSVDGRQIRVDQAGKSSD 94
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 48/83 (57%), Gaps = 1/83 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 192
L++ L +++ L+++FS++G I+ V++D + S+G GFV F ++A A+ M
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 193 NGKMIVSKPLYVAVAQRKEERRA 215
NGK + + + V A + + R+
Sbjct: 75 NGKSVDGRQIRVDQAGKSSDNRS 97
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 63.2 bits (152), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 46/164 (28%), Positives = 69/164 (42%), Gaps = 29/164 (17%)
Query: 26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 85
T+ +FV NL T+ED K++F YG + + RD + FGF+ E+ A A
Sbjct: 20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIA 74
Query: 86 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 145
L+G R + A G L +KNL + +
Sbjct: 75 KAELDGTILKSRPLRIRFAT------------------------HGAALTVKNLSPVVSN 110
Query: 146 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
E L++ FS+FG + V+ D G + G GFV F+ A +AL
Sbjct: 111 ELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKAL 154
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
Q L++ NL I +E K LF +G + + RD +G GF+ + A A
Sbjct: 21 QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAK 75
Query: 190 AEMNGKMIVSKPLYVAVA 207
AE++G ++ S+PL + A
Sbjct: 76 AELDGTILKSRPLRIRFA 93
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 33/62 (53%)
Query: 33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 92
VKNL ++E L++ F ++G + AVV+ D G++ GFV F A KA+E
Sbjct: 101 VKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDG 160
Query: 93 KF 94
F
Sbjct: 161 AF 162
>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 = 62.8 bits (151), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 45/180 (25%), Positives = 83/180 (46%), Gaps = 14/180 (7%)
Query: 17 QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVN 75
Q + +AI + V+V ++ ++ +++ F +G I S D K K F FV
Sbjct: 4 QRQRALAIXCR---VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVE 60
Query: 76 FENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN-L 134
+E + A A+E N R VG+ GQ + + + ++ + N +
Sbjct: 61 YEVPEAAQLALEQXNSVXLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRI 112
Query: 135 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 193
Y+ ++ + D+ +K +F FG I SC + RDP +G KG GF+ + + + A++ N
Sbjct: 113 YVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN 172
Score = 52.4 bits (124), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAV 86
FN ++V ++ + +D+D+K +F +G I S + RD GK K +GF+ +E A + AV
Sbjct: 109 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
Query: 87 EALNGKKFDDREWYVGKA 104
+ N + VGKA
Sbjct: 169 SSXNLFDLGGQYLRVGKA 186
>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 = 62.4 bits (150), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 45/180 (25%), Positives = 86/180 (47%), Gaps = 14/180 (7%)
Query: 17 QERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVN 75
Q + +AI ++ V+V ++ ++ +++ F +G I S + D K K F FV
Sbjct: 20 QRQGALAIMSR---VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE 76
Query: 76 FENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLN-L 134
+E + A A+E +N R VG+ GQ + + + ++ + N +
Sbjct: 77 YEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRI 128
Query: 135 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMN 193
Y+ ++ + D+ +K +F FG I S + RDP +G KG GF+ + + + A++ MN
Sbjct: 129 YVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188
Score = 56.2 bits (134), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 45/78 (57%), Gaps = 1/78 (1%)
Query: 28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAV 86
FN ++V ++ + +D+D+K +F +G I SA + RD GK K +GF+ +E A + AV
Sbjct: 125 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV 184
Query: 87 EALNGKKFDDREWYVGKA 104
++N + VGKA
Sbjct: 185 SSMNLFDLGGQYLRVGKA 202
Score = 36.6 bits (83), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI-SKGSGFVAFSTPEEASRALAEM 192
+Y+ ++ + ++ +++ F+ FG I S + D + KG FV + PE A AL +M
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 193 NGKMI------VSKPLYVAVAQ 208
N M+ V +P + AQ
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQ 112
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 60.8 bits (146), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 44/166 (26%), Positives = 73/166 (43%), Gaps = 27/166 (16%)
Query: 32 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG---KSKCFGFVNFENADDAAKAVEA 88
FV + + +++DL+++F +YG + V+RD +SK FV F A +A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 89 LNGKKFDDREWYVGKAQKKSEREQELKG-----QFEQAMKETVDKFQGLNLYIKNLGDSI 143
L+ K L G Q + A E + + L+I +
Sbjct: 67 LHNXKV-------------------LPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKC 107
Query: 144 DDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
+ ++ FS FG I C+++R P G+S+G FV F+T A A+
Sbjct: 108 TENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 58.9 bits (141), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 41/69 (59%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
NLYI NL S+D+++L+ + FG + S +++RD SG S+G GF + E+ +
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 193 NGKMIVSKP 201
NGK I + P
Sbjct: 87 NGKFIKTPP 95
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
N+++ NL S +++L+ + +G + S ++RD G S+ GF E+ + +
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 85
Query: 89 LNGK 92
NGK
Sbjct: 86 FNGK 89
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 58.9 bits (141), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 47/78 (60%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
+F+ L+ T ++ LK +FG++G I+ ++++D KS+ F F+ FEN DA A + +N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 91 GKKFDDREWYVGKAQKKS 108
GK + V +A+K S
Sbjct: 70 GKSLHGKAIKVEQAKKPS 87
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 42/76 (55%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
L+I L +++ LK +F + G I+ +++D + S+G F+ F P +A A +MN
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 194 GKMIVSKPLYVAVAQR 209
GK + K + V A++
Sbjct: 70 GKSLHGKAIKVEQAKK 85
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 58.5 bits (140), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 49/82 (59%), Gaps = 1/82 (1%)
Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALA 190
NL++ +L ++DDE L+ F +F + S VM D +G S+G GFV+F++ ++A A+
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 191 EMNGKMIVSKPLYVAVAQRKEE 212
M G+ + +PL + A + E
Sbjct: 62 SMQGQDLNGRPLRINWAAKLEH 83
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 45/78 (57%), Gaps = 1/78 (1%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
N+FV +L+ + DE L+ F ++ + S VM D G S+ +GFV+F + DDA A+++
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 89 LNGKKFDDREWYVGKAQK 106
+ G+ + R + A K
Sbjct: 63 MQGQDLNGRPLRINWAAK 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 = 58.2 bits (139), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 85
+ +F+ L TTDE L+ F ++GT+T VVMRD + K S+ FGFV + ++ A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 86 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 145
+ A K D R V + ++ RE + +K+ +++ + + ++
Sbjct: 72 MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 118
Query: 146 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 179
L++ F ++G I ++M D SG +G FV F
Sbjct: 119 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 43/167 (25%), Positives = 80/167 (47%), Gaps = 15/167 (8%)
Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 85
+ +F+ L TTDE L+ F ++GT+T VVMRD + K S+ FGFV + ++ A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 86 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 145
+ A K D R V + ++ RE + +K+ +++ + + ++
Sbjct: 72 MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 118
Query: 146 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
L++ F ++G I ++M D SG +G FV F + + + +
Sbjct: 119 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 85
+ +F+ L TTDE L+ F ++GT+T VVMRD + K S+ FGFV + ++ A
Sbjct: 11 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 70
Query: 86 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 145
+ A K D R V + ++ RE + +K+ +++ + + ++
Sbjct: 71 MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 117
Query: 146 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 179
L++ F ++G I ++M D SG +G FV F
Sbjct: 118 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 43/167 (25%), Positives = 80/167 (47%), Gaps = 15/167 (8%)
Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 85
+ +F+ L TTDE L+ F ++GT+T VVMRD + K S+ FGFV + ++ A
Sbjct: 10 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 69
Query: 86 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 145
+ A K D R V + ++ RE + +K+ +++ + + ++
Sbjct: 70 MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 116
Query: 146 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
L++ F ++G I ++M D SG +G FV F + + + +
Sbjct: 117 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 163
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 43/165 (26%), Positives = 79/165 (47%), Gaps = 15/165 (9%)
Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 85
+ +F+ L TTDE L+ F ++GT+T VVMRD + K S+ FGFV + ++ A
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64
Query: 86 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 145
+ A K D R V + ++ RE + +K+ +++ + + ++
Sbjct: 65 MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 111
Query: 146 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 189
L++ F ++G I ++M D SG +G FV F + + +
Sbjct: 112 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 15/155 (9%)
Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKA 85
+ +F+ L TTDE L+ F ++GT+T VVMRD + K S+ FGFV + ++ A
Sbjct: 13 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 72
Query: 86 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 145
+ A K D R V + ++ RE + +K+ +++ + + ++
Sbjct: 73 MNA-RPHKVDGR---VVEPKRAVSREDSQRPGAHLTVKK---------IFVGGIKEDTEE 119
Query: 146 EKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAF 179
L++ F ++G I ++M D SG +G FV F
Sbjct: 120 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 57.4 bits (137), Expect = 2e-08, Method: Composition-based stats.
Identities = 30/82 (36%), Positives = 53/82 (64%), Gaps = 2/82 (2%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTI-TSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
++I NL ID++ L + FS FG I + K+MRDP +G SKG F+ F++ + + A+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 192 MNGKMIVSKPLYVAVAQRKEER 213
MNG+ + ++P+ V+ A +K+ +
Sbjct: 68 MNGQYLCNRPITVSYAFKKDSK 89
Score = 49.3 bits (116), Expect = 5e-06, Method: Composition-based stats.
Identities = 29/84 (34%), Positives = 46/84 (54%), Gaps = 2/84 (2%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTI-TSAVVMRDGD-GKSKCFGFVNFENADDAAKAV 86
+ +F+ NLD ++ L F +G I + +MRD D G SK + F+NF + D + A+
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 87 EALNGKKFDDREWYVGKAQKKSER 110
EA+NG+ +R V A KK +
Sbjct: 66 EAMNGQYLCNRPITVSYAFKKDSK 89
>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 = 56.2 bits (134), Expect = 4e-08, Method: Composition-based stats.
Identities = 31/81 (38%), Positives = 49/81 (60%), Gaps = 1/81 (1%)
Query: 129 FQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASR 187
FQG NL + L + ++L+ LFS G + S K++RD +G S G GFV + T ++A R
Sbjct: 17 FQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
Query: 188 ALAEMNGKMIVSKPLYVAVAQ 208
A+ +NG + SK + V+ A+
Sbjct: 77 AINTLNGLRLQSKTIKVSYAR 97
Score = 48.5 bits (114), Expect = 7e-06, Method: Composition-based stats.
Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
N+ V L ++ T ++L+ +F G + SA ++RD G S +GFVN+ A DA +A+
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 89 LNGKKFDDREWYVGKAQ 105
LNG + + V A+
Sbjct: 81 LNGLRLQSKTIKVSYAR 97
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 56.2 bits (134), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 28/63 (44%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA 88
N+F+ +L + TD DL F +G + SA V D SKCFGFV+F+N D A A++A
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 89 LNG 91
+NG
Sbjct: 102 MNG 104
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 188
+G NL+I +L D L F FG + S KV D + +SK GFV+F P+ A A
Sbjct: 39 EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98
Query: 189 LAEMNGKMIVSKPLYV 204
+ MNG + +K L V
Sbjct: 99 IKAMNGFQVGTKRLKV 114
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 55.1 bits (131), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 43/82 (52%), Gaps = 3/82 (3%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
L++ LG DE ++++F FGTI C V+R P G SKG FV F T EA A+ ++
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
Query: 194 GKMIV---SKPLYVAVAQRKEE 212
+ S L V A ++E
Sbjct: 75 SSRTLPGASSSLVVKFADTEKE 96
Score = 48.1 bits (113), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 36/63 (57%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
+FV L + TDED++K+F +GTI V+R DG SK FV F+ +A A+ L+
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
Query: 91 GKK 93
+
Sbjct: 75 SSR 77
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 50/82 (60%), Gaps = 2/82 (2%)
Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 190
+ LY+ +L +I ++ L+ +F FG I S ++M D +G SKG GF+ FS E A +AL
Sbjct: 27 MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86
Query: 191 EMNGKMIVSKPLYVA-VAQRKE 211
++NG + +P+ V V +R +
Sbjct: 87 QLNGFELAGRPMKVGHVTERTD 108
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 49/80 (61%), Gaps = 1/80 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
++V +L + T++ L+ IF +G I S +M D + G+SK +GF+ F +++ A KA+E L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 90 NGKKFDDREWYVGKAQKKSE 109
NG + R VG ++++
Sbjct: 89 NGFELAGRPMKVGHVTERTD 108
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 41/73 (56%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
+ VFV NLD + LK++F G + A ++ D DGKS+ G V FE + +A +A+
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 89 LNGKKFDDREWYV 101
NG+ DR +V
Sbjct: 76 FNGQLLFDRPMHV 88
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 46/79 (58%)
Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
G +++ NL + +KLKE+FS G + ++ D G S+G G V F EA +A++
Sbjct: 15 GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAIS 74
Query: 191 EMNGKMIVSKPLYVAVAQR 209
NG+++ +P++V + +R
Sbjct: 75 MFNGQLLFDRPMHVKMDER 93
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 50/82 (60%), Gaps = 1/82 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
NL + + ++D+ +L++LF +G I S K++ D + S+G GFV F + A +A+A
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 192 MNGKMIVSKPLYVAVAQRKEER 213
+NG I++K L VA+A +R
Sbjct: 104 LNGFNILNKRLKVALAASGHQR 125
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 1/84 (1%)
Query: 28 FNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAV 86
N+ V + + + L+++F YG I S ++ D + + S+ +GFV F++ A +A+
Sbjct: 42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
Query: 87 EALNGKKFDDREWYVGKAQKKSER 110
LNG ++ V A +R
Sbjct: 102 AGLNGFNILNKRLKVALAASGHQR 125
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 44/164 (26%), Positives = 70/164 (42%), Gaps = 29/164 (17%)
Query: 26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 85
T+ + +FV NL T+E+++K+F +YG + +D K FGF+ E A A
Sbjct: 20 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIA 74
Query: 86 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD 145
L+ R ++L+ +F +L ++NL + +
Sbjct: 75 KVELDNMPL---------------RGKQLRVRF---------ACHSASLTVRNLPQYVSN 110
Query: 146 EKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
E L+E FS FG + V+ D G G G V FS A +AL
Sbjct: 111 ELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKAL 154
Score = 34.7 bits (78), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 32/62 (51%)
Query: 33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 92
V+NL + ++E L++ F +G + AVV+ D G+ G V F A KA++ +
Sbjct: 101 VRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCSEG 160
Query: 93 KF 94
F
Sbjct: 161 SF 162
Score = 33.5 bits (75), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 5/78 (6%)
Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
Q L++ NL I +E++++LF ++G + +D KG GF+ T A A
Sbjct: 21 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAK 75
Query: 190 AEMNGKMIVSKPLYVAVA 207
E++ + K L V A
Sbjct: 76 VELDNMPLRGKQLRVRFA 93
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/91 (32%), Positives = 49/91 (53%), Gaps = 1/91 (1%)
Query: 23 AIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADD 81
A+ +VFV N+ T+E LK IF E G + S ++ D + GK K +GF +++ +
Sbjct: 3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62
Query: 82 AAKAVEALNGKKFDDREWYVGKAQKKSEREQ 112
A A+ LNG++F R V A + +E+
Sbjct: 63 ALSAMRNLNGREFSGRALRVDNAASEKNKEE 93
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 48/87 (55%), Gaps = 4/87 (4%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
++++ N+ +E+LK++FSE G + S +++ D +G KG GF + E A A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 192 MNGKMIVSKPLYV---AVAQRKEERRA 215
+NG+ + L V A + KEE ++
Sbjct: 70 LNGREFSGRALRVDNAASEKNKEELKS 96
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 53.5 bits (127), Expect = 3e-07, Method: Composition-based stats.
Identities = 28/77 (36%), Positives = 46/77 (59%), Gaps = 1/77 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
NL + L ++ ++ K LF G I SCK++RD +G S G GFV +S P +A +A+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 192 MNGKMIVSKPLYVAVAQ 208
+NG + +K + V+ A+
Sbjct: 66 LNGLKLQTKTIKVSYAR 82
Score = 52.8 bits (125), Expect = 4e-07, Method: Composition-based stats.
Identities = 29/80 (36%), Positives = 45/80 (56%), Gaps = 1/80 (1%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
N+ V L ++ T ++ K +FG G I S ++RD G+S +GFVN+ + +DA KA+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 89 LNGKKFDDREWYVGKAQKKS 108
LNG K + V A+ S
Sbjct: 66 LNGLKLQTKTIKVSYARPSS 85
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 53.1 bits (126), Expect = 3e-07, Method: Composition-based stats.
Identities = 29/80 (36%), Positives = 46/80 (57%), Gaps = 4/80 (5%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSG----ISKGSGFVAFSTPEEASRAL 189
L+IKNL S +E LK +FS+ G I SC + + + +S G GFV + PE+A +AL
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 190 AEMNGKMIVSKPLYVAVAQR 209
++ G + L V +++R
Sbjct: 68 KQLQGHTVDGHKLEVRISER 87
Score = 45.1 bits (105), Expect = 8e-05, Method: Composition-based stats.
Identities = 26/85 (30%), Positives = 47/85 (55%), Gaps = 4/85 (4%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK----SKCFGFVNFENADDAAK 84
+ +F+KNL+ STT+E LK +F + G I S + + + S FGFV ++ + A K
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 85 AVEALNGKKFDDREWYVGKAQKKSE 109
A++ L G D + V +++ ++
Sbjct: 66 ALKQLQGHTVDGHKLEVRISERATK 90
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 53.1 bits (126), Expect = 3e-07, Method: Composition-based stats.
Identities = 28/73 (38%), Positives = 45/73 (61%), Gaps = 1/73 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
LY+ +L +I ++ L+ +F FG I + +M+D +G SKG GF+ FS E A RAL ++
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 193 NGKMIVSKPLYVA 205
NG + +P+ V
Sbjct: 68 NGFELAGRPMRVG 80
Score = 52.0 bits (123), Expect = 6e-07, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 50/80 (62%), Gaps = 1/80 (1%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVE 87
+ ++V +L + T++ L+ IF +G I + V+M+D D G+SK +GF+ F +++ A +A+E
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 88 ALNGKKFDDREWYVGKAQKK 107
LNG + R VG ++
Sbjct: 66 QLNGFELAGRPMRVGHVTER 85
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In
Cytotoxic Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 53.1 bits (126), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
+VFV +L T ED+K F +G I+ A V++D GKSK +GFV+F N DA A++
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 89 LNGKKFDDRE 98
+ G+ R+
Sbjct: 77 MGGQWLGGRQ 86
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 49/89 (55%), Gaps = 4/89 (4%)
Query: 123 KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFST 181
K+T + F +++ +L I E +K F+ FG I+ +V++D +G SKG GFV+F
Sbjct: 10 KDTSNHFH---VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 66
Query: 182 PEEASRALAEMNGKMIVSKPLYVAVAQRK 210
+A A+ +M G+ + + + A RK
Sbjct: 67 KWDAENAIQQMGGQWLGGRQIRTNWATRK 95
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 52.0 bits (123), Expect = 8e-07, Method: Composition-based stats.
Identities = 30/79 (37%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
+VFV +L T ED+K F +G I+ A V++D GKSK +GFV+F N DA A+
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 89 LNGKKFDDREWYVGKAQKK 107
+ G+ R+ A +K
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
Score = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 28/89 (31%), Positives = 49/89 (55%), Gaps = 4/89 (4%)
Query: 123 KETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFST 181
K+T + F ++++ +L I E +K F+ FG I+ +V++D +G SKG GFV+F
Sbjct: 10 KDTSNHF---HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYN 66
Query: 182 PEEASRALAEMNGKMIVSKPLYVAVAQRK 210
+A A+ M G+ + + + A RK
Sbjct: 67 KLDAENAIVHMGGQWLGGRQIRTNWATRK 95
>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 = 52.0 bits (123), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 30/87 (34%), Positives = 47/87 (54%), Gaps = 1/87 (1%)
Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 188
+G NL+I +L D+ L ++F FG + S KV D + +SK GFV++ P A A
Sbjct: 24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 189 LAEMNGKMIVSKPLYVAVAQRKEERRA 215
+ MNG I K L V + + K + ++
Sbjct: 84 IQSMNGFQIGMKRLKVQLKRSKNDSKS 110
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 40/63 (63%), Gaps = 1/63 (1%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEA 88
N+F+ +L + D+DL ++F +G + SA V D SKCFGFV+++N A A+++
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 89 LNG 91
+NG
Sbjct: 87 MNG 89
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 51.2 bits (121), Expect = 1e-06, Method: Composition-based stats.
Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
NL + L + D +L LF G I +C++MRD +G S G FV F++ ++ RA+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 192 MNGKMIVSKPLYVAVAQ 208
+NG + +K L V+ A+
Sbjct: 65 LNGITVRNKRLKVSYAR 81
Score = 42.7 bits (99), Expect = 4e-04, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 1/81 (1%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
N+ V L + TD +L +F G I + +MRD G S + FV+F + D+ +A++
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 89 LNGKKFDDREWYVGKAQKKSE 109
LNG ++ V A+ E
Sbjct: 65 LNGITVRNKRLKVSYARPGGE 85
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 51.2 bits (121), Expect = 1e-06, Method: Composition-based stats.
Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 40 TTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNGKKFDDR 97
TT+ DL+++F +YG I ++ D + S+ F FV FEN DDA +A E NG + D R
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR 85
Score = 31.6 bits (70), Expect = 0.92, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 189
GL+LY + L+E+FS++G I ++ D S S+G FV F ++A A
Sbjct: 22 GLSLYTT-------ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 190 AEMNG 194
NG
Sbjct: 75 ERANG 79
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 51.2 bits (121), Expect = 1e-06, Method: Composition-based stats.
Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 40 TTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNGKKFDDR 97
TT+ DL+++F +YG I ++ D + S+ F FV FEN DDA +A E NG + D R
Sbjct: 24 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR 82
Score = 31.6 bits (70), Expect = 0.96, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 189
GL+LY + L+E+FS++G I ++ D S S+G FV F ++A A
Sbjct: 19 GLSLYTT-------ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 71
Query: 190 AEMNG 194
NG
Sbjct: 72 ERANG 76
>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 = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKA 85
K N++V NL + TD+ L IFG+YG+I ++RD G+ + FV + ++A +A
Sbjct: 12 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 71
Query: 86 VEALN 90
+ ALN
Sbjct: 72 ISALN 76
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 48/79 (60%), Gaps = 3/79 (3%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
NLY+ NL +I D++L +F ++G+I ++RD +G +G FV ++ EEA A++
Sbjct: 15 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 192 MNGKMIV--SKPLYVAVAQ 208
+N + S+PL V +A+
Sbjct: 75 LNNVIPEGGSQPLSVRLAE 93
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 50.8 bits (120), Expect = 2e-06, Method: Composition-based stats.
Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 40 TTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNGKKFDDR 97
TT+ DL+++F +YG I ++ D + S+ F FV FEN DDA +A E NG + D R
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR 85
Score = 31.2 bits (69), Expect = 1.2, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 189
GL+LY + L+E+FS++G I ++ D S S+G FV F ++A A
Sbjct: 22 GLSLYTT-------ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 190 AEMNG 194
NG
Sbjct: 75 ERANG 79
>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 = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 46/187 (24%), Positives = 85/187 (45%), Gaps = 18/187 (9%)
Query: 31 VFVKNLDESTTDEDLKKIFG---EYGTITSAV---VMRDGDGKSKCFGFVNFENADDAAK 84
++V N+ T+E + F G +T A V+ + K F F+ F + D+ +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 85 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ------AMKETVDKFQGLNLYIKN 138
A+ A +G F + + ++ Q L G E + TV L+I
Sbjct: 67 AM-AFDGIIFQGQSLKI----RRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGG 121
Query: 139 LGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMI 197
L + ++D+++KEL + FG + + +++D +G+SKG F + +A+A +NG +
Sbjct: 122 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 181
Query: 198 VSKPLYV 204
K L V
Sbjct: 182 GDKKLLV 188
>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 = 50.4 bits (119), Expect = 2e-06, Method: Composition-based stats.
Identities = 28/77 (36%), Positives = 47/77 (61%), Gaps = 1/77 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
NL + L ++ ++L+ LFS G + S K++RD +G S G GFV + T ++A RA+
Sbjct: 6 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 65
Query: 192 MNGKMIVSKPLYVAVAQ 208
+NG + SK + V+ A+
Sbjct: 66 LNGLRLQSKTIKVSYAR 82
Score = 48.1 bits (113), Expect = 1e-05, Method: Composition-based stats.
Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
N+ V L ++ T ++L+ +F G + SA ++RD G S +GFVN+ A DA +A+
Sbjct: 6 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 65
Query: 89 LNGKKFDDREWYVGKAQ 105
LNG + + V A+
Sbjct: 66 LNGLRLQSKTIKVSYAR 82
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 46/74 (62%), Gaps = 5/74 (6%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
NLY+ L ++ +++++LFS++G I + +++ D +G+S+G GF+ F EA A+
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 192 MNGKMIVSKPLYVA 205
+NG+ KPL A
Sbjct: 63 LNGQ----KPLGAA 72
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 43/65 (66%), Gaps = 1/65 (1%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
N++V L ++ + ++++++F +YG ITS +++ G S+ GF+ F+ +A +A++
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 89 LNGKK 93
LNG+K
Sbjct: 63 LNGQK 67
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNG 91
V L TT+ DL+++F +YG I ++ D + S+ F FV FEN DDA +A E NG
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 92 KKFDDREWYV 101
+ D R V
Sbjct: 111 MELDGRRIRV 120
Score = 31.6 bits (70), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 8/65 (12%)
Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRAL 189
GL+LY + L+E+FS++G I ++ D S S+G FV F ++A A
Sbjct: 53 GLSLYTT-------ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105
Query: 190 AEMNG 194
NG
Sbjct: 106 ERANG 110
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 50.1 bits (118), Expect = 2e-06, Method: Composition-based stats.
Identities = 26/70 (37%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVE 87
+ V+V NL S T+ DL +IF +YG + +M+D D KSK F+ F + D A
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 88 ALNGKKFDDR 97
A+N K+ R
Sbjct: 77 AINNKQLFGR 86
Score = 38.5 bits (88), Expect = 0.009, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
+Y+ NL S+ + L +FS++G + +M+D + SKG F+ F + A +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 193 NGKMIVSKPLYVAVA 207
N K + + + ++A
Sbjct: 79 NNKQLFGRVIKASIA 93
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 38/67 (56%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
+ V NLD +D D++++F E+GT+ A V D G+S V+FE DA KA++ N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 91 GKKFDDR 97
G D R
Sbjct: 91 GVPLDGR 97
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 39/71 (54%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
L + NL + D ++ELF+EFGT+ V D SG S G+ V F +A +A+ + N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 194 GKMIVSKPLYV 204
G + +P+ +
Sbjct: 91 GVPLDGRPMNI 101
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 54/90 (60%), Gaps = 11/90 (12%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
L+++NL +++ +E L++ FS+FG + K ++D + F+ F + A +A+ EMN
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYA-------FIHFDERDGAVKAMEEMN 66
Query: 194 GKMIVSKPLYVAVA----QRKEERRARLQA 219
GK + + + + A Q+++ER+A+ QA
Sbjct: 67 GKDLEGENIEIVFAKPPDQKRKERKAQRQA 96
Score = 45.4 bits (106), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 50/96 (52%), Gaps = 7/96 (7%)
Query: 26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 85
K +FV+NL + T+E L+K F ++G + ++D + F++F+ D A KA
Sbjct: 9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKA 61
Query: 86 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQA 121
+E +NGK + + A+ ++ +E K Q + A
Sbjct: 62 MEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAA 97
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 40/82 (48%), Gaps = 3/82 (3%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
L++ L +E + LF FG I C V+R P G SKG FV FS+ EA A+ ++
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 194 GKMIV---SKPLYVAVAQRKEE 212
G + S L V A +E
Sbjct: 78 GSQTMPGASSSLVVKFADTDKE 99
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 37/63 (58%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
+FV L++ ++ED+ ++F +G I V+R DG SK FV F + +A A+ AL+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 91 GKK 93
G +
Sbjct: 78 GSQ 80
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 33/85 (38%), Positives = 48/85 (56%), Gaps = 6/85 (7%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSC---KVMRDPSGISKGSGFVAFSTPEEASRAL 189
+L++ +L +DD L E F + SC KV+ D +G+SKG GFV F+ E RAL
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVK--VYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRAL 68
Query: 190 AEMNGKM-IVSKPLYVAVAQRKEER 213
E G + + SKP+ ++VA K R
Sbjct: 69 TECQGAVGLGSKPVRLSVAIPKASR 93
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 49.3 bits (116), Expect = 5e-06, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 40/72 (55%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
+++ NL + +E L ELF + G +T + +D G K GFV F PE S A+A +N
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 194 GKMIVSKPLYVA 205
G + +P+ V+
Sbjct: 79 GIRLYGRPINVS 90
Score = 48.1 bits (113), Expect = 1e-05, Method: Composition-based stats.
Identities = 24/67 (35%), Positives = 39/67 (58%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
VFV NL+ +E L ++F + G +T + +D +GK K FGFV F++ + + A+ LN
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 91 GKKFDDR 97
G + R
Sbjct: 79 GIRLYGR 85
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 49.3 bits (116), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 92
V N+ D DL+++FG++G I ++ + G SK FGFV FEN+ DA +A E L+G
Sbjct: 34 VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGT 92
Query: 93 KFDDREWYVGKAQKK 107
+ R+ V A +
Sbjct: 93 VVEGRKIEVNNATAR 107
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 45/83 (54%), Gaps = 1/83 (1%)
Query: 125 TVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEE 184
T +K Q L++ N+ D L+++F +FG I +++ + G SKG GFV F +
Sbjct: 23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSAD 81
Query: 185 ASRALAEMNGKMIVSKPLYVAVA 207
A RA +++G ++ + + V A
Sbjct: 82 ADRAREKLHGTVVEGRKIEVNNA 104
>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 = 48.9 bits (115), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 37/67 (55%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
+ V NLD +D D++++F E+GT+ A V D G+S V+FE DA KA + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 91 GKKFDDR 97
G D R
Sbjct: 92 GVPLDGR 98
Score = 45.1 bits (105), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 36/68 (52%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
L + NL + D ++ELF+EFGT+ V D SG S G+ V F +A +A + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 194 GKMIVSKP 201
G + +P
Sbjct: 92 GVPLDGRP 99
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 48.5 bits (114), Expect = 7e-06, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 41/64 (64%), Gaps = 1/64 (1%)
Query: 33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEALNG 91
V NL E T + DL+++F +G+I+ + +D G+SK F F++F +DAA+A+ ++G
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
Query: 92 KKFD 95
+D
Sbjct: 80 FGYD 83
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 38/60 (63%), Gaps = 1/60 (1%)
Query: 136 IKNLGDSIDDEKLKELFSEFGTITSCKVMRDPS-GISKGSGFVAFSTPEEASRALAEMNG 194
+ NL + + L+ELF FG+I+ + +D + G SKG F++F E+A+RA+A ++G
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 48.5 bits (114), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGK 92
V N+ D DL+++FG++G I ++ + G SK FGFV FEN+ DA +A E L+G
Sbjct: 20 VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGT 78
Query: 93 KFDDREWYVGKAQKK 107
+ R+ V A +
Sbjct: 79 VVEGRKIEVNNATAR 93
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
L++ N+ D L+++F +FG I +++ + G SKG GFV F +A RA +++
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH 76
Query: 194 GKMIVSKPLYVAVA 207
G ++ + + V A
Sbjct: 77 GTVVEGRKIEVNNA 90
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 48.1 bits (113), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 42/175 (24%), Positives = 74/175 (42%), Gaps = 31/175 (17%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
+ ++ L T++++ + +Y V K K FV N + A A+ A +
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAFVTLLNGEQAEAAINAFH 78
Query: 91 GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 150
+ RE+EL Q + D L + NL S+ ++ +E
Sbjct: 79 QSRL---------------RERELSVQLQ-----PTDAL----LCVANLPPSLTQQQFEE 114
Query: 151 LFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV 204
L FG++ C V + +G SKG GF + + A+RA +++ GK + + LYV
Sbjct: 115 LVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 48.1 bits (113), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 89
+FV+NL ++++EDL+K+F YG ++ D K K F FV F + A KA +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 90 NGKKFDDREWYVGKAQKKSEREQ 112
+G+ F R +V + K E Q
Sbjct: 71 DGQVFQGRMLHVLPSTIKKEASQ 93
Score = 45.4 bits (106), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
L+++NL + +E L++LFS +G ++ D + KG FV F PE A +A AE+
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 193 NGKMIVSKPLYVAVAQRKEE 212
+G++ + L+V + K+E
Sbjct: 71 DGQVFQGRMLHVLPSTIKKE 90
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 42/175 (24%), Positives = 74/175 (42%), Gaps = 31/175 (17%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
+ ++ L T++++ + +Y V K K FV N + A A+ A +
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAFVTLLNGEQAEAAINAFH 78
Query: 91 GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 150
+ RE+EL Q + D L + NL S+ ++ +E
Sbjct: 79 QSRL---------------RERELSVQLQ-----PTDAL----LCVANLPPSLTQQQFEE 114
Query: 151 LFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV 204
L FG++ C V + +G SKG GF + + A+RA +++ GK + + LYV
Sbjct: 115 LVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
>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 = 1e-05, Method: Compositional matrix adjust.
Identities = 43/181 (23%), Positives = 82/181 (45%), Gaps = 26/181 (14%)
Query: 31 VFVKNLDESTTDEDLKKIFG---EYGTITSAV---VMRDGDGKSKCFGFVNFENADDAAK 84
++V N+ T+E + F G +T A V+ + K F F+ F + D+ +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 85 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSID 144
A+ A +G F + + ++ Q L G + L+I L + ++
Sbjct: 69 AM-AFDGIIFQGQSLKI----RRPHDYQPLPGAHK--------------LFIGGLPNYLN 109
Query: 145 DEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY 203
D+++KEL + FG + + +++D +G+SKG F + +A+A +NG + K L
Sbjct: 110 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 169
Query: 204 V 204
V
Sbjct: 170 V 170
>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 = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 42/175 (24%), Positives = 74/175 (42%), Gaps = 31/175 (17%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
+ ++ L T++++ + +Y V K K FV N + A A+ A +
Sbjct: 23 ILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAFVTLLNGEQAEAAINAFH 76
Query: 91 GKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKE 150
+ RE+EL Q + D L + NL S+ ++ +E
Sbjct: 77 QSRL---------------RERELSVQLQ-----PTDAL----LCVANLPPSLTQQQFEE 112
Query: 151 LFSEFGTITSC-KVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYV 204
L FG++ C V + +G SKG GF + + A+RA +++ GK + + LYV
Sbjct: 113 LVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 167
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 3/82 (3%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
L++ L ++ ++ LF FG I C ++R P G SKG FV +S+ EA A+ ++
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 194 GKMIV---SKPLYVAVAQRKEE 212
G + S L V A +E
Sbjct: 78 GSQTMPGASSSLVVKFADTDKE 99
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 38/63 (60%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
+FV L++ +++D++++F +G I ++R DG SK FV + + +A A+ AL+
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 91 GKK 93
G +
Sbjct: 78 GSQ 80
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 43/181 (23%), Positives = 82/181 (45%), Gaps = 26/181 (14%)
Query: 31 VFVKNLDESTTDEDLKKIFG---EYGTITSAV---VMRDGDGKSKCFGFVNFENADDAAK 84
++V N+ T+E + F G +T A V+ + K F F+ F + D+ +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 85 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSID 144
A+ A +G F + + ++ Q L G + L+I L + ++
Sbjct: 67 AM-AFDGIIFQGQSLKI----RRPHDYQPLPGAHK--------------LFIGGLPNYLN 107
Query: 145 DEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLY 203
D+++KEL + FG + + +++D +G+SKG F + +A+A +NG + K L
Sbjct: 108 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 167
Query: 204 V 204
V
Sbjct: 168 V 168
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 5/76 (6%)
Query: 14 LRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFG 72
L +++RE K +F +F+ L TT+E L+ + ++G +T VVMRD +S+ FG
Sbjct: 17 LERKKRE----KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFG 72
Query: 73 FVNFENADDAAKAVEA 88
FV F + + A+ A
Sbjct: 73 FVTFSSMAEVDAAMAA 88
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 43/76 (56%), Gaps = 5/76 (6%)
Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 185
+K Q L+I L +E L+ + ++G +T C VMRDP S S+G GFV FS+ E
Sbjct: 23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 82
Query: 186 SRALA----EMNGKMI 197
A+A ++G+++
Sbjct: 83 DAAMAARPHSIDGRVV 98
>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 = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNG 91
V NL T+ + L+++F +YG + + RD K S+ F FV F + DA A++A++G
Sbjct: 52 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111
Query: 92 KKFDDREWYVGKAQ 105
D RE V A+
Sbjct: 112 AVLDGRELRVQMAR 125
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
+L + NL + L+ +F ++G + + RD + S+G FV F +A A+
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 192 MNGKMIVSKPLYVAVAQ 208
M+G ++ + L V +A+
Sbjct: 109 MDGAVLDGRELRVQMAR 125
>pdb|3NTW|A Chain A, Structure Of The Mlle Domain Of Edd In Complex With A Pam2
Peptide From Paip1
pdb|3NTW|C Chain C, Structure Of The Mlle Domain Of Edd In Complex With A Pam2
Peptide From Paip1
Length = 65
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 41/57 (71%)
Query: 390 QRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVL 446
R LGE LYP V+ ++ A+K+TGMLLE+ ++L LL S ++L+A+V EAME++
Sbjct: 6 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVEEAMELI 62
>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 = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 34/125 (27%), Positives = 57/125 (45%), Gaps = 6/125 (4%)
Query: 12 HFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKC- 70
HF E + +K K ++V NL TT+E + ++F + G I ++ D K+ C
Sbjct: 24 HFRGDNEEQEKLLK-KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 82
Query: 71 FGFVNFENADDAAKAVEALNGKKFDDR----EWYVGKAQKKSEREQELKGQFEQAMKETV 126
F FV + + DA A+ +NG + DDR +W G + + GQ ++
Sbjct: 83 FCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDY 142
Query: 127 DKFQG 131
D +G
Sbjct: 143 DAGRG 147
Score = 30.0 bits (66), Expect = 2.8, Method: Composition-based stats.
Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 4/86 (4%)
Query: 110 REQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-S 168
R+Q +G E+ +E + K + LY+ NL +E++ ELFS+ G I + D
Sbjct: 21 RDQHFRGDNEE--QEKLLK-KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMK 77
Query: 169 GISKGSGFVAFSTPEEASRALAEMNG 194
+ G FV + + +A A+ +NG
Sbjct: 78 KTACGFCFVEYYSRADAENAMRYING 103
>pdb|1I2T|A Chain A, X-Ray Structure Of The Human Hyperplastic Discs Protein:
An Ortholog Of The C-Terminal Domain Of Poly(A)-Binding
Protein
Length = 61
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 41/57 (71%)
Query: 390 QRTLLGESLYPLVEQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEVL 446
R LGE LYP V+ ++ A+K+TGMLLE+ ++L LL S ++L+A+V EAME++
Sbjct: 1 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELI 57
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 37/67 (55%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
+ V NLD +D D++++F E+GT+ A V D G+S V+FE DA KA++
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 91 GKKFDDR 97
G D R
Sbjct: 151 GVPLDGR 157
Score = 45.1 bits (105), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 39/74 (52%)
Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
G L + NL + D ++ELF+EFGT+ V D SG S G+ V F +A +A+
Sbjct: 88 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 147
Query: 191 EMNGKMIVSKPLYV 204
+ G + +P+ +
Sbjct: 148 QYKGVPLDGRPMDI 161
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 46.6 bits (109), Expect = 3e-05, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
N VFV +D + +++ F YG++ ++ D G SK +GFV+F N D K VE+
Sbjct: 11 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 70
Query: 89 ---LNGKKF 94
+GKK
Sbjct: 71 QINFHGKKL 79
Score = 39.7 bits (91), Expect = 0.004, Method: Composition-based stats.
Identities = 13/46 (28%), Positives = 31/46 (67%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAF 179
+++ + +D+ +++ F+ +G++ K++ D +G+SKG GFV+F
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 58
>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 = 46.2 bits (108), Expect = 4e-05, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
N VFV +D + +++ F YG++ ++ D G SK +GFV+F N D K VE+
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 89 ---LNGKKF 94
+GKK
Sbjct: 70 QINFHGKKL 78
Score = 39.7 bits (91), Expect = 0.004, Method: Composition-based stats.
Identities = 13/46 (28%), Positives = 31/46 (67%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAF 179
+++ + +D+ +++ F+ +G++ K++ D +G+SKG GFV+F
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
>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 = 46.2 bits (108), Expect = 4e-05, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
N VFV +D + +++ F YG++ ++ D G SK +GFV+F N D K VE+
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 89 ---LNGKKF 94
+GKK
Sbjct: 70 QINFHGKKL 78
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 13/46 (28%), Positives = 31/46 (67%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAF 179
+++ + +D+ +++ F+ +G++ K++ D +G+SKG GFV+F
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 30/85 (35%), Positives = 41/85 (48%), Gaps = 5/85 (5%)
Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRAL 189
G ++I L E L+E F +FG + C VMRDP + S+G GFV F + L
Sbjct: 25 GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
Query: 190 A----EMNGKMIVSKPLYVAVAQRK 210
A E++ K I K + AQ K
Sbjct: 85 AQSRHELDSKTIDPKVAFPRRAQPK 109
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 42/83 (50%), Gaps = 5/83 (6%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAV-- 86
+F+ L TT E L++ FG++G + +VMRD +S+ FGFV F + K +
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 87 --EALNGKKFDDREWYVGKAQKK 107
L+ K D + + +AQ K
Sbjct: 87 SRHELDSKTIDPKVAFPRRAQPK 109
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 27/65 (41%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
+FVK L E TT+E LK+ F G++ + +V G SK FGFV+F + +DA A EA+
Sbjct: 18 LFVKGLSEDTTEETLKESF--DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME 75
Query: 91 GKKFD 95
+ D
Sbjct: 76 DGEID 80
Score = 35.0 bits (79), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
L++K L + +E LKE F G++ + V +G SKG GFV F++ E+A A M
Sbjct: 18 LFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 45.1 bits (105), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 37/67 (55%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
+ V NLD +D D++++F E+GT+ A V D G+S V+FE DA KA++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 91 GKKFDDR 97
G D R
Sbjct: 98 GVPLDGR 104
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 39/74 (52%)
Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
G L + NL + D ++ELF+EFGT+ V D SG S G+ V F +A +A+
Sbjct: 35 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
Query: 191 EMNGKMIVSKPLYV 204
+ G + +P+ +
Sbjct: 95 QYKGVPLDGRPMDI 108
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 45.1 bits (105), Expect = 8e-05, Method: Composition-based stats.
Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
V+V NL + +L++ FG YG + S V R+ G F FV FE+ DAA AV L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRELD 131
Query: 91 GK 92
G+
Sbjct: 132 GR 133
Score = 42.0 bits (97), Expect = 7e-04, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 38/64 (59%), Gaps = 4/64 (6%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
+Y+ NLG++ + +L+ F +G + S V R+P G + FV F P +A+ A+ E++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFA----FVEFEDPRDAADAVRELD 131
Query: 194 GKMI 197
G+ +
Sbjct: 132 GRTL 135
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 45.1 bits (105), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 37/67 (55%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
+ V NLD +D D++++F E+GT+ A V D G+S V+FE DA KA++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 91 GKKFDDR 97
G D R
Sbjct: 98 GVPLDGR 104
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 39/74 (52%)
Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALA 190
G L + NL + D ++ELF+EFGT+ V D SG S G+ V F +A +A+
Sbjct: 35 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
Query: 191 EMNGKMIVSKPLYV 204
+ G + +P+ +
Sbjct: 95 QYKGVPLDGRPMDI 108
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
V+V NL + +L++ FG YG + S V R+ G F FV FE+ DAA AV L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRDLD 131
Query: 91 GK 92
G+
Sbjct: 132 GR 133
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 38/64 (59%), Gaps = 4/64 (6%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
+Y+ NLG++ + +L+ F +G + S V R+P G + FV F P +A+ A+ +++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFA----FVEFEDPRDAADAVRDLD 131
Query: 194 GKMI 197
G+ +
Sbjct: 132 GRTL 135
>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 = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 45/93 (48%), Gaps = 6/93 (6%)
Query: 133 NLYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 188
+YI NL + I ++LK+ +FS+FG I V R S +G FV F A+ A
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNA 68
Query: 189 LAEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 221
L M G KP+ + A+ + A+++ F
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 101
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 47/94 (50%), Gaps = 6/94 (6%)
Query: 29 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
+ +++ NL+E ++LKK IF ++G I +V R + + FV F+ A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQA--FVIFKEVSSATN 67
Query: 85 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
A+ ++ G F D+ + A+ S+ ++KG F
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 101
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 5/76 (6%)
Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKA 85
+ +FV LD STT E L+ F +YG + V+M+D +S+ FGFV F++ +
Sbjct: 15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 74
Query: 86 VEA----LNGKKFDDR 97
+ + L+G+ D +
Sbjct: 75 LASRPHTLDGRNIDPK 90
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE- 191
L++ L S E L+ FS++G + C +M+D + S+G GFV F P LA
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 192 ---MNGKMIVSKP 201
++G+ I KP
Sbjct: 79 PHTLDGRNIDPKP 91
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 43.5 bits (101), Expect = 3e-04, Method: Composition-based stats.
Identities = 29/82 (35%), Positives = 43/82 (52%), Gaps = 5/82 (6%)
Query: 26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAK 84
T F +FV L TTD L+K F +G I AVV+ D GKS+ +GFV + A +
Sbjct: 15 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAER 74
Query: 85 AVE----ALNGKKFDDREWYVG 102
A + ++G+K + Y+G
Sbjct: 75 ACKDPNPIIDGRKANVNLAYLG 96
Score = 30.4 bits (67), Expect = 2.1, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 192
+++ L D L++ F FG I V+ D +G S+G GFV + A RA +
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 193 N 193
N
Sbjct: 80 N 80
>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 = 43.1 bits (100), Expect = 4e-04, Method: Composition-based stats.
Identities = 28/95 (29%), Positives = 46/95 (48%), Gaps = 5/95 (5%)
Query: 12 HFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCF 71
HF E + +K K ++V NL TT+E + ++F + G I ++ D + F
Sbjct: 3 HFRGDNEEQEKLLK-KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGF 61
Query: 72 GFVNFENADDAAKAVEALNGKKFDDR----EWYVG 102
FV + + DA A+ +NG + DDR +W G
Sbjct: 62 CFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAG 96
Score = 33.1 bits (74), Expect = 0.34, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 42/84 (50%), Gaps = 3/84 (3%)
Query: 111 EQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI 170
+Q +G E+ +E + K + LY+ NL +E++ ELFS+ G I + D
Sbjct: 1 DQHFRGDNEE--QEKLLK-KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKT 57
Query: 171 SKGSGFVAFSTPEEASRALAEMNG 194
+ G FV + + +A A+ +NG
Sbjct: 58 ACGFCFVEYYSRADAENAMRYING 81
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNFENADDAAKAVEALNG 91
V NL T+ + L+++F +YG + + RD K S+ F FV F + DA A++A++G
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 92 KKFDDREWYVGKAQ 105
D RE V A+
Sbjct: 135 AVLDGRELRVQMAR 148
Score = 33.9 bits (76), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE 191
+L + NL + L+ +F ++G + + RD + S+G FV F +A A+
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 192 MNGKMIVSKPLYVAVAQ 208
M+G ++ + L V +A+
Sbjct: 132 MDGAVLDGRELRVQMAR 148
>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 = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 44/92 (47%), Gaps = 6/92 (6%)
Query: 134 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 68
Query: 190 AEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 221
M G KP+ + A+ + A+++ F
Sbjct: 69 RSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 46/94 (48%), Gaps = 6/94 (6%)
Query: 29 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 66
Query: 85 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
A+ ++ G F D+ + A+ S+ ++KG F
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 45/92 (48%), Gaps = 6/92 (6%)
Query: 134 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
+YI NL + I ++LK+ +FS+FG I V R S +G FV F A+ AL
Sbjct: 11 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 68
Query: 190 AEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 221
M G KP+ + A+ + A+++ F
Sbjct: 69 RSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 47/94 (50%), Gaps = 6/94 (6%)
Query: 29 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
+ +++ NL+E ++LKK IF ++G I +V R K + FV F+ A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATN 66
Query: 85 AVEALNGKKFDDREWYVGKAQKKSEREQELKGQF 118
A+ ++ G F D+ + A+ S+ ++KG F
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 42/86 (48%), Gaps = 12/86 (13%)
Query: 12 HFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCF 71
H +QE E + +FV+ + +L +IFG +G + ++ F
Sbjct: 20 HMHHRQEGELSNTR-----LFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-------F 67
Query: 72 GFVNFENADDAAKAVEALNGKKFDDR 97
FV FE A+ AAKA+E ++GK F ++
Sbjct: 68 AFVEFEEAESAAKAIEEVHGKSFANQ 93
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 7/80 (8%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
L+++ + + +L E+F FG + K++ G FV F E A++A+ E++
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVH 86
Query: 194 GKMIVSKPLYVAVAQRKEER 213
GK ++PL V ++ +R
Sbjct: 87 GKSFANQPLEVVYSKLPAKR 106
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 190
++I L E L+E F +FG + C VMRDP + S+G GFV F + LA
Sbjct: 1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
Query: 191 ----EMNGKMI 197
E++ K I
Sbjct: 61 QSRHELDSKTI 71
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGK-SKCFGFVNF 76
+F+ L TT E L++ FG++G + +VMRD K S+ FGFV F
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 7/69 (10%)
Query: 24 IKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAA 83
+ K +FV+NL + T+E L+K F E+G + ++D + FV+FE+ A
Sbjct: 11 VMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEDRGAAV 63
Query: 84 KAVEALNGK 92
KA++ +NGK
Sbjct: 64 KAMDEMNGK 72
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 48/82 (58%), Gaps = 7/82 (8%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
L+++NL ++ +E L++ FSEFG + K ++D + FV F A +A+ EMN
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYA-------FVHFEDRGAAVKAMDEMN 70
Query: 194 GKMIVSKPLYVAVAQRKEERRA 215
GK I + + + +A+ +++R+
Sbjct: 71 GKEIEGEEIEIVLAKPPDKKRS 92
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 28 FNNVFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAV 86
F +FV ++ TT+ L++ F YG I +V GK + + F+ +E+ D A
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 87 EALNGKKFDDR 97
+ +GKK D R
Sbjct: 162 KHADGKKIDGR 172
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 46/174 (26%), Positives = 79/174 (45%), Gaps = 23/174 (13%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
N+FV NL+ + + +LK + V+ G ++ FG+V+FE+A+D KA+E L
Sbjct: 9 NLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKALE-L 67
Query: 90 NGKKFDDREWYVGKAQ-KKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKL 148
G K E + K + K S++E++ + L KNL + ++L
Sbjct: 68 TGLKVFGNEIKLEKPKGKDSKKERDAR-----------------TLLAKNLPYKVTQDEL 110
Query: 149 KELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPL 202
KE+F + I + G SKG ++ F T +A + E G I + +
Sbjct: 111 KEVFEDAAEIR----LVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSI 160
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 42.4 bits (98), Expect = 6e-04, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
L+I L + ++D+++KEL + FG + + +++D +G+SKG F + +A+A +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 193 NGKMIVSKPLYVAVA 207
NG + K L V A
Sbjct: 64 NGMQLGDKKLLVQRA 78
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 42.4 bits (98), Expect = 6e-04, Method: Composition-based stats.
Identities = 22/58 (37%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE 87
+FV L +TT ED+K F ++G + A++M D + + FGFV FE+ D K E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
>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 = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 46/168 (27%), Positives = 77/168 (45%), Gaps = 21/168 (12%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
N+F+ NL+ + + +LK E V+ G ++ FG+V+FE+A+D KA+E L
Sbjct: 15 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-L 73
Query: 90 NGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLK 149
G K E + K KG+ + ++ L KNL +I +++LK
Sbjct: 74 TGLKVFGNEIKLEKP----------KGRDSKKVR------AARTLLAKNLSFNITEDELK 117
Query: 150 ELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMI 197
E+F + I + G SKG ++ F + +A + L E G I
Sbjct: 118 EVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI 161
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 7/71 (9%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
+ V N+ + T+++L+ F EYG + +++D + FV+ E A+DA +A+ L+
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGLD 65
Query: 91 GKKFDDREWYV 101
+F + +V
Sbjct: 66 NTEFQGKRMHV 76
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/77 (19%), Positives = 38/77 (49%), Gaps = 7/77 (9%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
L++ N+ + +++L+ F E+G + C +++D + FV E+A A+ ++
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYA-------FVHMERAEDAVEAIRGLD 65
Query: 194 GKMIVSKPLYVAVAQRK 210
K ++V ++ +
Sbjct: 66 NTEFQGKRMHVQLSTSR 82
>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 = 42.0 bits (97), Expect = 7e-04, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE- 191
++I L + LK+ FS+FG + C + DP +G S+G GFV F E + + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 192 ---MNGKMIVSK 200
+NGK+I K
Sbjct: 62 EHKLNGKVIDPK 73
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE-- 87
+F+ L TT +DLK F ++G + + D G+S+ FGFV F+ ++ K ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 88 --ALNGKKFDDR 97
LNGK D +
Sbjct: 62 EHKLNGKVIDPK 73
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 33 VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKS-KCFGFVNFENADDAAKAVEALNG 91
V NL T+ + L+++F +YG + + R+ K+ + F FV F + DA A A++G
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 92 KKFDDREWYV 101
+ D RE V
Sbjct: 78 AELDGRELRV 87
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 45/80 (56%), Gaps = 2/80 (2%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
N+Y+ NL S E++KELFS+FG + + K++ D + KG GFV E S A+A+
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 192 MNGKMIVSKPLYVAVAQRKE 211
++ + + + V A K+
Sbjct: 62 LDNTDFMGRTIRVTEANPKK 81
Score = 38.1 bits (87), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 44/83 (53%), Gaps = 2/83 (2%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKS-KCFGFVNFENADDAAKAVEA 88
N++V NL S T E +K++F ++G + + ++ D + K K FGFV + + ++A+
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61
Query: 89 LNGKKFDDREWYVGKAQKKSERE 111
L+ F R V +A K E
Sbjct: 62 LDNTDFMGRTIRVTEANPKKSLE 84
>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 = 42.0 bits (97), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 37/149 (24%), Positives = 67/149 (44%), Gaps = 21/149 (14%)
Query: 68 SKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVD 127
S+ F +++ + +DA VE LNG K E Y + + E++ +
Sbjct: 158 SRRFAYIDVTSKEDARYCVEKLNGLKI---EGYTLVTK--------VSNPLEKSKRTDSA 206
Query: 128 KFQGLNLYIKNLGDSIDDEK-LKELFSEFGTITSCKVMRDPSG-----ISKGSGFVAFST 181
+G + I+NL + DE L+E F FG+I + P+G + F F
Sbjct: 207 TLEGREIXIRNLSTELLDENLLRESFEGFGSIEKINI---PAGQKEHSFNNCCAFXVFEN 263
Query: 182 PEEASRALAEMNGKMIVSKPLYVAVAQRK 210
+ A RAL + N ++ ++ + V++A +K
Sbjct: 264 KDSAERAL-QXNRSLLGNREISVSLADKK 291
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 42.0 bits (97), Expect = 8e-04, Method: Composition-based stats.
Identities = 24/62 (38%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVE 87
+ ++++ L TTD+DL K+ YG I S + D K K +GFV+F++ A KAV
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 88 AL 89
AL
Sbjct: 66 AL 67
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 28 FNNVFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAV 86
F +FV ++ TT+ L++ F YG I +V GK + + F+ +E+ D A
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 87 EALNGKKFDDR 97
+ +GKK D R
Sbjct: 162 KHADGKKIDGR 172
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 7/81 (8%)
Query: 117 QFEQAMKETVDKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGF 176
+FE + ++ K +Y + + D+ +++ FS FG I +V + KG F
Sbjct: 13 RFEDVVNQSSPK--NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSF 65
Query: 177 VAFSTPEEASRALAEMNGKMI 197
V FST E A+ A+ +NG I
Sbjct: 66 VRFSTHESAAHAIVSVNGTTI 86
>pdb|1IFW|A Chain A, Solution Structure Of C-Terminal Domain Of Poly(A) Binding
Protein From Saccharomyces Cerevisiae
Length = 92
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 37/68 (54%), Gaps = 2/68 (2%)
Query: 388 EQQRTLLGESLYPLV--EQLERDAAAKVTGMLLEMDQTEVLHLLESPEALKAKVAEAMEV 445
++QR LGE LY V + +AA K+TGM+L++ EV LLES E + EA
Sbjct: 18 QKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLESDELFEQHYKEASAA 77
Query: 446 LRSVAQQQ 453
S ++Q
Sbjct: 78 YESFKKEQ 85
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 7/67 (10%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
+FV+ + +L +IFG +G + ++ F FV FE A+ AAKA+E ++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-------FAFVEFEEAESAAKAIEEVH 59
Query: 91 GKKFDDR 97
GK F ++
Sbjct: 60 GKSFANQ 66
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 7/75 (9%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
L+++ + + +L E+F FG + K++ G FV F E A++A+ E++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEVH 59
Query: 194 GKMIVSKPLYVAVAQ 208
GK ++PL V ++
Sbjct: 60 GKSFANQPLEVVYSK 74
>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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 134 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 69
Query: 190 AEMNGKMIVSKPLYVAVAQRKEERRARLQ 218
M G KP+ + A+ + A+++
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 98
Score = 35.8 bits (81), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 23/91 (25%), Positives = 44/91 (48%), Gaps = 6/91 (6%)
Query: 29 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 67
Query: 85 AVEALNGKKFDDREWYVGKAQKKSEREQELK 115
A+ ++ G F D+ + A+ S+ ++K
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 134 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 66
Query: 190 AEMNGKMIVSKPLYVAVAQRKEERRARLQ 218
M G KP+ + A+ + A+++
Sbjct: 67 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 95
Score = 35.4 bits (80), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 29 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 7 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 64
Query: 85 AVEALNGKKFDDREWYVGKAQKKSE 109
A+ ++ G F D+ + A+ S+
Sbjct: 65 ALRSMQGFPFYDKPMRIQYAKTDSD 89
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 134 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 68
Query: 190 AEMNGKMIVSKPLYVAVAQRKEERRARLQ 218
M G KP+ + A+ + A+++
Sbjct: 69 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97
Score = 35.4 bits (80), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 29 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 66
Query: 85 AVEALNGKKFDDREWYVGKAQKKSE 109
A+ ++ G F D+ + A+ S+
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSD 91
>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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 134 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 69
Query: 190 AEMNGKMIVSKPLYVAVAQRKEERRARLQ 218
M G KP+ + A+ + A+++
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 98
Score = 38.1 bits (87), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 45/92 (48%), Gaps = 6/92 (6%)
Query: 29 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 67
Query: 85 AVEALNGKKFDDREWYVGKAQKKSEREQELKG 116
A+ ++ G F D+ + A+ S+ ++KG
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKG 99
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 134 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
+YI NL + I ++LK+ +FS+FG I V R S +G FV F A+ AL
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 69
Query: 190 AEMNGKMIVSKPLYVAVAQ 208
M G KP+ + A+
Sbjct: 70 RSMQGFPFYDKPMRIQYAK 88
Score = 36.6 bits (83), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 42/85 (49%), Gaps = 6/85 (7%)
Query: 29 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
+ +++ NL+E ++LKK IF ++G I +V R + + FV F+ A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 67
Query: 85 AVEALNGKKFDDREWYVGKAQKKSE 109
A+ ++ G F D+ + A+ S+
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSD 92
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 26/68 (38%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
+FV+NL T + LK F E G + A + + +GKSK G V FE+ + A +A +N
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMN 69
Query: 91 GKKFDDRE 98
G K RE
Sbjct: 70 GMKLSGRE 77
Score = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
++++NL + LK+ F+E G + + + +G SKG G V F +PE A RA MN
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMN 69
Query: 194 GKMIVSKPLYVAV 206
G + + + V +
Sbjct: 70 GMKLSGREIDVRI 82
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 26/70 (37%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
+ +FV+NL T + LK F E G + A + + +GKSK G V FE+ + A +A
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRM 64
Query: 89 LNGKKFDDRE 98
+NG K RE
Sbjct: 65 MNGMKLSGRE 74
Score = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
++++NL + LK+ F+E G + + + +G SKG G V F +PE A RA MN
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMN 66
Query: 194 GKMIVSKPLYVAV 206
G + + + V +
Sbjct: 67 GMKLSGREIDVRI 79
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 190
+ L+I + ++D++ LK LF EFG I V++D +G+ KG F+ + E A +A +
Sbjct: 14 IKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQS 73
Query: 191 EMN 193
++
Sbjct: 74 ALH 76
Score = 33.1 bits (74), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 34 KNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEALNGK 92
+NLDE +DLK +F E+G I V++D G K F+ + + A KA AL+ +
Sbjct: 23 RNLDE----KDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQ 78
Query: 93 K 93
K
Sbjct: 79 K 79
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 192
LY+ L + +DD+ L F FG IT ++ D + +G FV F E+A+ A+ M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 193 NGKMIVSKPLYVAVA 207
N + + + V +A
Sbjct: 126 NESELFGRTIRVNLA 140
Score = 37.4 bits (85), Expect = 0.018, Method: Composition-based stats.
Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 89
++V L E D+ L F +G IT + D + K + F FV FE A+DAA A++ +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 90 N 90
N
Sbjct: 126 N 126
>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 = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 42/88 (47%), Gaps = 6/88 (6%)
Query: 134 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 68
Query: 190 AEMNGKMIVSKPLYVAVAQRKEERRARL 217
M G KP+ + A+ + A++
Sbjct: 69 RSMQGFPFYDKPMRIQYAKTDSDIIAKM 96
Score = 35.8 bits (81), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 29 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 66
Query: 85 AVEALNGKKFDDREWYVGKAQKKSE 109
A+ ++ G F D+ + A+ S+
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSD 91
>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 = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 134 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 65
Query: 190 AEMNGKMIVSKPLYVAVAQRKEERRARLQ 218
M G KP+ + A+ + A+++
Sbjct: 66 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 94
Score = 34.3 bits (77), Expect = 0.15, Method: Composition-based stats.
Identities = 23/91 (25%), Positives = 44/91 (48%), Gaps = 6/91 (6%)
Query: 29 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 6 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 63
Query: 85 AVEALNGKKFDDREWYVGKAQKKSEREQELK 115
A+ ++ G F D+ + A+ S+ ++K
Sbjct: 64 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 94
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 44/86 (51%), Gaps = 5/86 (5%)
Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 191
+ +Y+ NLG +L+ FS +G + + + R+P G + FV F P +A A+
Sbjct: 1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFA----FVEFEDPRDAEDAVRG 56
Query: 192 MNGKMIVSKPLYVAVAQRKEERRARL 217
++GK+I + V ++ RR+R
Sbjct: 57 LDGKVICGSRVRVELST-GMPRRSRF 81
Score = 38.5 bits (88), Expect = 0.009, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
V+V NL +L++ F YG + + + R+ G F FV FE+ DA AV L+
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG----FAFVEFEDPRDAEDAVRGLD 58
Query: 91 GK 92
GK
Sbjct: 59 GK 60
>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 = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEA 88
+VFV +L T + F +G I+ A V++D GKSK +GFV+F N DA A++
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 89 LNGKKFDDRE 98
+ G+ R+
Sbjct: 68 MGGQWLGGRQ 77
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 155 FGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRK 210
FG I+ +V++D +G SKG GFV+F +A A+ +M G+ + + + A RK
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86
>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 = 39.7 bits (91), Expect = 0.004, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 41/74 (55%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
L+I L S E+L+E+ GT+ +++ + +G KG +V + +AS+A+ +M+
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 194 GKMIVSKPLYVAVA 207
G I + VA++
Sbjct: 80 GMTIKENIIKVAIS 93
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 36/63 (57%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
+ +F+ L S T E+L++I +GT+ ++ + GK K +V +EN A++AV
Sbjct: 18 HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMK 77
Query: 89 LNG 91
++G
Sbjct: 78 MDG 80
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 192
LY+ L + +DD+ L F FG IT ++ D + +G FV F E+A+ A+ M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 193 NGKMIVSKPLYVAVAQ 208
N + + + V +A+
Sbjct: 68 NESELFGRTIRVNLAK 83
Score = 36.2 bits (82), Expect = 0.042, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 89
++V L E D+ L F +G IT + D + K + F FV FE A+DAA A++ +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 90 NGKKFDDREWYVGKAQ 105
N + R V A+
Sbjct: 68 NESELFGRTIRVNLAK 83
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 192
LY+ L + +DD+ L F FG IT ++ D + +G FV F E+A+ A+ M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 193 NGKMIVSKPLYVAVAQ 208
N + + + V +A+
Sbjct: 70 NESELFGRTIRVNLAK 85
Score = 35.8 bits (81), Expect = 0.047, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 89
++V L E D+ L F +G IT + D + K + F FV FE A+DAA A++ +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 90 NGKKFDDREWYVGKAQ 105
N + R V A+
Sbjct: 70 NESELFGRTIRVNLAK 85
>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 = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 134 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 64
Query: 190 AEMNGKMIVSKPLYVAVAQ 208
M G KP+ + A+
Sbjct: 65 RSMQGFPFYDKPMRIQYAK 83
Score = 34.7 bits (78), Expect = 0.13, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 29 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 5 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 62
Query: 85 AVEALNGKKFDDREWYVGKAQKKSE 109
A+ ++ G F D+ + A+ S+
Sbjct: 63 ALRSMQGFPFYDKPMRIQYAKTDSD 87
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 10/81 (12%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
+FV N+ + T ++L+ +F G + V++D + FV+ E DA A+ LN
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQLN 64
Query: 91 GKKFDDREWYV---GKAQKKS 108
GK+ + V K QKKS
Sbjct: 65 GKEVKGKRINVELSTKGQKKS 85
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 40/65 (61%), Gaps = 5/65 (7%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
++V+NL ST++E ++K E+ I V R K + + FV+F N +DA +A++ALN
Sbjct: 18 LYVRNLMLSTSEEMIEK---EFNNIKPGAVERVK--KIRDYAFVHFSNREDAVEAMKALN 72
Query: 91 GKKFD 95
GK D
Sbjct: 73 GKVLD 77
Score = 38.1 bits (87), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 9/77 (11%)
Query: 134 LYIKNLGDSIDDEKLKELFSEF--GTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAE 191
LY++NL S +E +++ F+ G + K +RD + FV FS E+A A+
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYA-------FVHFSNREDAVEAMKA 70
Query: 192 MNGKMIVSKPLYVAVAQ 208
+NGK++ P+ V +A+
Sbjct: 71 LNGKVLDGSPIEVTLAK 87
>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 = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 134 LYIKNLGDSIDDEKLKE----LFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
+YI NL + I ++LK+ +FS FG I V R S +G FV F A+ AL
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 63
Query: 190 AEMNGKMIVSKPLYVAVAQ 208
M G KP+ + A+
Sbjct: 64 RSMQGFPFYDKPMRIQYAK 82
Score = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 29 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 4 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 61
Query: 85 AVEALNGKKFDDREWYVGKAQKKSE 109
A+ ++ G F D+ + A+ S+
Sbjct: 62 ALRSMQGFPFYDKPMRIQYAKTDSD 86
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 38.9 bits (89), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 192
LY+ L + +DD+ L F FG IT ++ D + +G FV F E+A+ A+ M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 193 NGKMIVSKPLYVAVAQ 208
N + + + V +A+
Sbjct: 75 NESELFGRTIRVNLAK 90
Score = 35.4 bits (80), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 89
++V L E D+ L F +G IT + D + K + F FV FE A+DAA A++ +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 90 NGKKFDDREWYVGKAQ 105
N + R V A+
Sbjct: 75 NESELFGRTIRVNLAK 90
>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 = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAEM 192
LY+ L + +DD+ L F FG IT ++ D + +G FV F E+A+ A+ M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 193 NGKMIVSKPLYVAVA 207
N + + + V +A
Sbjct: 65 NESELFGRTIRVNLA 79
Score = 35.8 bits (81), Expect = 0.049, Method: Composition-based stats.
Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 89
++V L E D+ L F +G IT + D + K + F FV FE A+DAA A++ +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 90 N 90
N
Sbjct: 65 N 65
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 132 LNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 190
+ L++ + +D++ LK LF EFG I V++D +G+ KG F+ + + A +A +
Sbjct: 16 IKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQS 75
Query: 191 EMN 193
++
Sbjct: 76 ALH 78
Score = 34.7 bits (78), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
+FV + ++DLK +F E+G I V++D G K F+ + D A KA A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 89 LNGKK 93
L+ +K
Sbjct: 77 LHEQK 81
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 28/93 (30%), Positives = 46/93 (49%), Gaps = 7/93 (7%)
Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEA 185
D +G ++I+NL ++E L E+ +FG + +V+ P + SKG F F T E A
Sbjct: 11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70
Query: 186 SRAL------AEMNGKMIVSKPLYVAVAQRKEE 212
+ L AE G + + L V +A ++E
Sbjct: 71 QKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 103
Score = 28.9 bits (63), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 40/91 (43%), Gaps = 7/91 (7%)
Query: 26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSA-VVMRDGDGKSKCFGFVNFENADDAAK 84
T+ VF++NL + +E L ++ ++G + VV+ SK F F + A K
Sbjct: 13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72
Query: 85 AVEALN------GKKFDDREWYVGKAQKKSE 109
+ A + G K D R+ V A + E
Sbjct: 73 CLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 103
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 38.5 bits (88), Expect = 0.008, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTIT--SAVVMRDGDGKSKCFGFVNFENADDAAK 84
K V + L + T + + +IF YG I V R SK + +V FEN D+A K
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62
Query: 85 AVEALNGKKFDDRE 98
A++ ++G + D +E
Sbjct: 63 ALKHMDGGQIDGQE 76
Score = 38.5 bits (88), Expect = 0.008, Method: Composition-based stats.
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTIT--SCKVMRDPSGISKGSGFVAFSTPEEASRALAE 191
++I L ++ + + E+FS +G I V R +SKG +V F P+EA +AL
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 192 MNGKMI 197
M+G I
Sbjct: 67 MDGGQI 72
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 38.5 bits (88), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 1/83 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKV-MRDPSGISKGSGFVAFSTPEEASRALAEM 192
LY+KNL + + L LF+ F + R +G +G F+ F E A +AL +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 193 NGKMIVSKPLYVAVAQRKEERRA 215
NG + K L + + K++R +
Sbjct: 88 NGYKLYGKILVIEFGKNKKQRSS 110
Score = 32.0 bits (71), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 1/81 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVV-MRDGDGKSKCFGFVNFENADDAAKAVEAL 89
+++KNL T+ DL +F + + R G+ + F+ F N + A +A+ +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 90 NGKKFDDREWYVGKAQKKSER 110
NG K + + + K +R
Sbjct: 88 NGYKLYGKILVIEFGKNKKQR 108
>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 = 38.5 bits (88), Expect = 0.009, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
+FV + E T+ED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 90 NGK 92
NG+
Sbjct: 70 NGQ 72
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 38.1 bits (87), Expect = 0.011, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
+FV + E T+ED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 90 NGK 92
NG+
Sbjct: 70 NGQ 72
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 38.1 bits (87), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 41/88 (46%), Gaps = 9/88 (10%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP---------SGISKGSGFVAFSTPEE 184
++++ LG+++ E + + F + G I + K P +G KG V+F P
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 185 ASRALAEMNGKMIVSKPLYVAVAQRKEE 212
A A+ +GK P+ V+ A R+ +
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSFATRRAD 97
>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 = 37.7 bits (86), Expect = 0.012, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
+FV + E T+ED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 90 NGK 92
NG+
Sbjct: 70 NGQ 72
>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 = 37.7 bits (86), Expect = 0.012, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
+FV + E T+ED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 90 NGK 92
NG+
Sbjct: 72 NGQ 74
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 37.7 bits (86), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 40/67 (59%), Gaps = 3/67 (4%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
+ + NL S T+E L+++F + I V ++ +GKSK + F+ F + +DA +A+ + N
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFIK---VPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 91 GKKFDDR 97
++ + R
Sbjct: 75 KREIEGR 81
Score = 36.2 bits (82), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
L + NL S +E L+E+F + T KV ++ +G SKG F+ F++ E+A AL N
Sbjct: 18 LVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 194 GKMI 197
+ I
Sbjct: 75 KREI 78
>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 = 37.4 bits (85), Expect = 0.016, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 32 FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEA-- 88
FV L T+ +DLK F ++G + + D + G+S+ FGF+ F++A K ++
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 89 --LNGKKFDDRE 98
L+G+ D ++
Sbjct: 75 HRLDGRVIDPKK 86
Score = 36.2 bits (82), Expect = 0.046, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 135 YIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAE-- 191
++ L + LK+ F++FG + C + DP +G S+G GF+ F + L +
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 192 --MNGKMIVSK 200
++G++I K
Sbjct: 75 HRLDGRVIDPK 85
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 37.4 bits (85), Expect = 0.016, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
+FV + E T+ED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 90 NGK 92
NG+
Sbjct: 85 NGQ 87
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 37.4 bits (85), Expect = 0.020, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKAVEAL 89
+FV + E T+ED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 90 NGK 92
NG+
Sbjct: 86 NGQ 88
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 37.0 bits (84), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEA 185
++ Q +Y+ L + + + L ELF + G + + + +D +G +G GFV F + E+A
Sbjct: 11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70
Query: 186 SRALAEMNGKMIVSKPLYV 204
A+ M+ + KP+ V
Sbjct: 71 DYAIKIMDMIKLYGKPIRV 89
Score = 32.7 bits (73), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 89
V+V LDE ++ L ++F + G + + + +D G+ + +GFV F + +DA A++ +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 90 NGKKFDDREWYVGKA 104
+ K + V KA
Sbjct: 78 DMIKLYGKPIRVNKA 92
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 37.0 bits (84), Expect = 0.027, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
+Y+ ++ +E++ +L S G + + K+M DP +G SKG F+ F E ++ A+ +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 193 NGKMIVSKPL 202
NG + S+ L
Sbjct: 66 NGYQLGSRFL 75
Score = 33.5 bits (75), Expect = 0.27, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
V++ ++ T+E + + G + + +M D G+SK + F+ F + + +A AV L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 90 NGKKFDDR 97
NG + R
Sbjct: 66 NGYQLGSR 73
>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 = 36.6 bits (83), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 188
+G L++ ++ + +++++E F ++G I + + D +G SKG V + T ++A A
Sbjct: 71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130
Query: 189 LAEMNGKMIVSKPLYV 204
+NG I+ + + V
Sbjct: 131 KEALNGAEIMGQTIQV 146
Score = 32.7 bits (73), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 89
+FV ++ E ++++++ F +YG I + + D G SK + V +E A A EAL
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 90 NG 91
NG
Sbjct: 135 NG 136
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 36.6 bits (83), Expect = 0.030, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
+Y+ ++ +E++ +L S G + + K+M DP +G SKG F+ F E ++ A+ +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 193 NGKMIVSKPL 202
NG + S+ L
Sbjct: 65 NGYQLGSRFL 74
Score = 33.1 bits (74), Expect = 0.31, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
V++ ++ T+E + + G + + +M D G+SK + F+ F + + +A AV L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 90 NGKKFDDR 97
NG + R
Sbjct: 65 NGYQLGSR 72
>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 = 36.6 bits (83), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 7/81 (8%)
Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
+G LY+ G+ + L+ FS FG I + DP + FV + E A +A+
Sbjct: 38 KGNTLYV--YGEDMTPTLLRGAFSPFGNIIDLSM--DPP---RNCAFVTYEKMESADQAV 90
Query: 190 AEMNGKMIVSKPLYVAVAQRK 210
AE+NG + S L V +A+++
Sbjct: 91 AELNGTQVESVQLKVNIARKQ 111
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 36.2 bits (82), Expect = 0.038, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRALAEM 192
+Y+ ++ +E++ +L S G + + K+M DP +G SKG F+ F E ++ A+ +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 193 NGKMIVSKPL 202
NG + S+ L
Sbjct: 67 NGYQLGSRFL 76
Score = 33.1 bits (74), Expect = 0.37, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGD-GKSKCFGFVNFENADDAAKAVEAL 89
V++ ++ T+E + + G + + +M D G+SK + F+ F + + +A AV L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 90 NGKKFDDR 97
NG + R
Sbjct: 67 NGYQLGSR 74
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 36.2 bits (82), Expect = 0.045, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 35/65 (53%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEAL 89
N+F+ NL+ + + +LK E V+ G ++ FG+V+FE+A+D KA+E
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELT 78
Query: 90 NGKKF 94
K F
Sbjct: 79 GLKVF 83
>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 = 36.2 bits (82), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 6/68 (8%)
Query: 131 GLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGI---SKGSGFVAFSTPE---E 184
+ +++ + + ++ L+ELF ++G + V+RD S SKG FV F T + E
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62
Query: 185 ASRALAEM 192
A AL M
Sbjct: 63 AQNALHNM 70
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD---GDGKSKCFGFVNFENADDAAKAVE 87
+FV + + +++DL+++F +YG + V+RD +SK FV F A +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 88 ALNGKK 93
AL+ K
Sbjct: 66 ALHNMK 71
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 35.8 bits (81), Expect = 0.049, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 39/65 (60%), Gaps = 7/65 (10%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYG-TITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
N +++ NL + T +DL+++FG+ + V+++ G + FV++ + + A +A+E
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSG------YAFVDYPDQNWAIRAIE 62
Query: 88 ALNGK 92
L+GK
Sbjct: 63 TLSGK 67
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 35.8 bits (81), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 29/98 (29%), Positives = 45/98 (45%), Gaps = 7/98 (7%)
Query: 133 NLYIKNLGDSIDDE----KLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRA 188
+YI NL + I E L +FS+FG I ++ +G FV F AS A
Sbjct: 8 TIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLK--MRGQAFVIFKEIGSASNA 65
Query: 189 LAEMNGKMIVSKPLYVAVAQRKEERRARLQAQFSQMRP 226
L M G KP+ +A ++ + A+++ F + RP
Sbjct: 66 LRTMQGFPFYDKPMQIAYSKSDSDIVAKIKGTFKE-RP 102
Score = 32.3 bits (72), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 21/95 (22%), Positives = 45/95 (47%), Gaps = 6/95 (6%)
Query: 30 NVFVKNLDEST----TDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKA 85
+++ NL+E + L IF ++G I V ++ + + FV F+ A+ A
Sbjct: 8 TIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQA--FVIFKEIGSASNA 65
Query: 86 VEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQ 120
+ + G F D+ + ++ S+ ++KG F++
Sbjct: 66 LRTMQGFPFYDKPMQIAYSKSDSDIVAKIKGTFKE 100
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 35.8 bits (81), Expect = 0.056, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 7/76 (9%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALN 90
+ KNL + T+++LK++F + + + DGKSK ++ F++ DA K +E
Sbjct: 19 LLAKNLSFNITEDELKEVFED----ALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQ 74
Query: 91 GKKFDDRE---WYVGK 103
G + D R +Y G+
Sbjct: 75 GAEIDGRSVSLYYTGE 90
Score = 29.3 bits (64), Expect = 4.5, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 4/64 (6%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
L KNL +I +++LKE+F + I + G SKG ++ F + +A + L E
Sbjct: 19 LLAKNLSFNITEDELKEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQ 74
Query: 194 GKMI 197
G I
Sbjct: 75 GAEI 78
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 35.8 bits (81), Expect = 0.060, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 27 KFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD-GDGKSKCFGFVNFENADDAAKA 85
K +++ V L TT++DLK+ F +G + V +D G SK FGFV F + K
Sbjct: 14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 73
Query: 86 V 86
+
Sbjct: 74 M 74
Score = 34.7 bits (78), Expect = 0.12, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 145 DEKLKELFSEFGTITSCKVMRD-PSGISKGSGFVAFSTPEEASRALAE 191
++ LKE FS FG + +V +D +G SKG GFV F+ E + +++
Sbjct: 29 EQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 76
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 35.4 bits (80), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 7/81 (8%)
Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRAL 189
+G LY+ G+ + L+ FS FG I + DP + FV + E A +A+
Sbjct: 14 KGNTLYV--YGEDMTPTLLRGAFSPFGNIIDLSM--DPP---RNCAFVTYEKMESADQAV 66
Query: 190 AEMNGKMIVSKPLYVAVAQRK 210
AE+NG + S L V +A+++
Sbjct: 67 AELNGTQVESVQLKVNIARKQ 87
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 35.4 bits (80), Expect = 0.071, Method: Composition-based stats.
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSK----CFGFVNFENADDAAKAV 86
++V NL +D++ +F +YG I RD D K++ F FV FE+ DA AV
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAI------RDIDLKNRRGGPPFAFVEFEDPRDAEDAV 78
Query: 87 EALNGKKFD 95
+G +D
Sbjct: 79 YGRDGYDYD 87
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp-
Interacting Repressor, Siahbp1
Length = 119
Score = 35.0 bits (79), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 49/98 (50%), Gaps = 15/98 (15%)
Query: 11 GHFLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSK- 69
G LRKQE + ++ N V K++D+ E + + G++G + ++ ++ G+ +
Sbjct: 7 GKLLRKQESTVMVLR---NMVDPKDIDDDLEGE-VTEECGKFGAVNRVIIYQEKQGEEED 62
Query: 70 ----CFGFVNFENADDAAKAVEALNGKKFDDREWYVGK 103
FV F A + KA++ALNG+ W+ G+
Sbjct: 63 AEIIVKIFVEFSIASETHKAIQALNGR------WFAGR 94
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 35.0 bits (79), Expect = 0.084, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
LYI+NL I E++ ++F ++G I +V P ++G+ +V + +A A ++
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNACDHLS 72
Query: 194 GKMIVSKPLYV 204
G + ++ L V
Sbjct: 73 GFNVCNRYLVV 83
Score = 33.1 bits (74), Expect = 0.33, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 19 RETVAIKTKFNNV-FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNF 76
R + + + N + +++NL T E++ IFG+YG I +R G+ +++ +V +
Sbjct: 2 RANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVY 58
Query: 77 ENADDAAKAVEALNG 91
E+ DA A + L+G
Sbjct: 59 EDIFDAKNACDHLSG 73
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 35.0 bits (79), Expect = 0.089, Method: Composition-based stats.
Identities = 27/89 (30%), Positives = 46/89 (51%), Gaps = 1/89 (1%)
Query: 127 DKFQGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEAS 186
D Q LY+ NL + + + +LFS+ G SCK++ + + + FV F +A+
Sbjct: 11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAA 69
Query: 187 RALAEMNGKMIVSKPLYVAVAQRKEERRA 215
ALA MNG+ I+ K + V A +++
Sbjct: 70 AALAAMNGRKILGKEVKVNWATTPSSQKS 98
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 35.0 bits (79), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 33/114 (28%), Positives = 55/114 (48%), Gaps = 14/114 (12%)
Query: 108 SEREQELKGQFEQAMKETVDKFQG-------LNLYIKNLGDSIDDEKLKELFSEFGTITS 160
S RE E KG+ + ET+ F+ +Y+KNL + ++ LK +F + +S
Sbjct: 16 SRRELE-KGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSS 74
Query: 161 --CKVMRD----PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQ 208
++M D G KG F+ + A++AL E NG ++ KP+ V A+
Sbjct: 75 ETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFAR 128
Score = 32.0 bits (71), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 46/90 (51%), Gaps = 12/90 (13%)
Query: 14 LRKQERETVAIKTKFN------NVFVKNLDESTTDEDLKKIFGEYGTITSAV--VMRD-- 63
+ ++E ET+++ + ++VKNL + ++DLK IFG Y +S +M D
Sbjct: 25 ISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIR 84
Query: 64 --GDGKSKCFGFVNFENADDAAKAVEALNG 91
+G+ K F+ N AAKA++ NG
Sbjct: 85 LMKEGRMKGQAFIGLPNEKAAAKALKEANG 114
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 35.0 bits (79), Expect = 0.092, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 2/70 (2%)
Query: 22 VAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRD--GDGKSKCFGFVNFENA 79
V K + + V+N+ +++++F +G + + + + G G + FGFV+F
Sbjct: 9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 68
Query: 80 DDAAKAVEAL 89
DA KA AL
Sbjct: 69 QDAKKAFNAL 78
Score = 33.9 bits (76), Expect = 0.21, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGIS--KGSGFVAFSTPEEASRAL 189
+ ++N+ + +++ELFS FG + + ++ + +G +G GFV F T ++A +A
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 35.0 bits (79), Expect = 0.096, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 5/66 (7%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
LY+ LGD+I + L+ F +FG I + V++ + F+ F+T + A A +
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQ-----RQQCAFIQFATRQAAEVAAEKSF 69
Query: 194 GKMIVS 199
K+IV+
Sbjct: 70 NKLIVN 75
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 35.0 bits (79), Expect = 0.100, Method: Composition-based stats.
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 9/83 (10%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP---------SGISKGSGFVAFSTPEE 184
++++ LG+++ E + + F + G I + K P +G KG V+F P
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 185 ASRALAEMNGKMIVSKPLYVAVA 207
A A+ +GK P+ V+ A
Sbjct: 76 AKAAIDWFDGKEFSGNPIKVSFA 98
Score = 28.5 bits (62), Expect = 9.4, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 9/75 (12%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSA---------VVMRDGDGKSKCFGFVNFENA 79
N +FV+ L E+ T E + F + G I + + GK K V+F++
Sbjct: 14 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73
Query: 80 DDAAKAVEALNGKKF 94
A A++ +GK+F
Sbjct: 74 PSAKAAIDWFDGKEF 88
>pdb|3UE2|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.23 A Resolution
pdb|3US5|A Chain A, Crystal Structure Of A Rna-Binding Domain Of A Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.38 A Resolution
Length = 118
Score = 34.7 bits (78), Expect = 0.12, Method: Composition-based stats.
Identities = 25/91 (27%), Positives = 46/91 (50%), Gaps = 9/91 (9%)
Query: 13 FLRKQERETVAIKTKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSK--- 69
LRKQE ++ N V K++D+ E ++ G++G + ++ ++ G+ +
Sbjct: 14 LLRKQESTVXVLR---NXVDPKDIDDDLEGEVTEEC-GKFGAVNRVIIYQEKQGEEEDAE 69
Query: 70 --CFGFVNFENADDAAKAVEALNGKKFDDRE 98
FV F A + KA++ALNG+ F R+
Sbjct: 70 IIVKIFVEFSIASETHKAIQALNGRWFAGRK 100
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 34.7 bits (78), Expect = 0.12, Method: Composition-based stats.
Identities = 19/76 (25%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 130 QGLNLYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP-SGISKGSGFVAFSTPEEASRA 188
+G L++ ++ + +++++E F ++G I + + D +G SKG V + T ++A A
Sbjct: 25 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84
Query: 189 LAEMNGKMIVSKPLYV 204
+NG I+ + + V
Sbjct: 85 KEALNGAEIMGQTIQV 100
Score = 33.5 bits (75), Expect = 0.25, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEAL 89
+FV ++ E ++++++ F +YG I + + D G SK + V +E A A EAL
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 90 NGKK 93
NG +
Sbjct: 89 NGAE 92
>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 = 0.12, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAV-VMRD-GDGKSKCFGFVNFENADDAAKAV 86
N V ++ L ++ T++D++ +G V +MR+ G+S+ F FV F + DA + +
Sbjct: 2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWM 61
Query: 87 EA 88
EA
Sbjct: 62 EA 63
>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 = 34.7 bits (78), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 5/53 (9%)
Query: 26 TKFNNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFEN 78
T+ + +FV NL T+E+++K+F +YG + +D K FGF+ E
Sbjct: 13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLET 60
Score = 31.6 bits (70), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
L++ NL I +E++++LF ++G + +D KG GF+ T A A E++
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELD 72
Query: 194 GKMIVSKPLYVAVA 207
+ K L V A
Sbjct: 73 NMPLRGKQLRVRFA 86
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 34.3 bits (77), Expect = 0.16, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
LYI+NL I E++ ++F ++G I +V P ++G+ +V + +A A+ ++
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNAVDHLS 68
Query: 194 GKMIVSKPLYV 204
G + ++ L V
Sbjct: 69 GFNVSNRYLVV 79
Score = 34.3 bits (77), Expect = 0.17, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 4/68 (5%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCFGFVNFENADDAAKAVEAL 89
++++NL T E++ IFG+YG I +R G+ +++ +V +E+ DA AV+ L
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 90 NGKKFDDR 97
+G +R
Sbjct: 68 SGFNVSNR 75
>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2
Length = 108
Score = 33.9 bits (76), Expect = 0.18, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 30/70 (42%), Gaps = 6/70 (8%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
N V V L S + +DLK E G + A V RDG G V F +D AV
Sbjct: 16 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGT------GVVEFVRKEDMTYAVRK 69
Query: 89 LNGKKFDDRE 98
L+ KF E
Sbjct: 70 LDNTKFRSHE 79
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 33.9 bits (76), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 9/86 (10%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDP---------SGISKGSGFVAFSTPEE 184
+Y++ L DS+ + L + F + G + K P +G KG V++ P
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 185 ASRALAEMNGKMIVSKPLYVAVAQRK 210
A A+ +GK L V++A++K
Sbjct: 78 AKAAVEWFDGKDFQGSKLKVSLARKK 103
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 9/86 (10%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITS---------AVVMRDGDGKSKCFGFVNFENADD 81
++V+ L++S T +DL F + G + + + GK K V++E+
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 82 AAKAVEALNGKKFDDREWYVGKAQKK 107
A AVE +GK F + V A+KK
Sbjct: 78 AKAAVEWFDGKDFQGSKLKVSLARKK 103
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 33.9 bits (76), Expect = 0.22, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
LYI+NL I E++ ++F ++G I +V P ++G+ +V + +A A ++
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNACDHLS 78
Query: 194 GKMIVSKPLYV 204
G + ++ L V
Sbjct: 79 GFNVCNRYLVV 89
Score = 32.3 bits (72), Expect = 0.53, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 44/80 (55%), Gaps = 5/80 (6%)
Query: 14 LRKQERETVAIKTKFNNV-FVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCF 71
++ +R + + + N + +++NL T E++ IFG+YG I +R G+ +++
Sbjct: 3 MQAAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGT 59
Query: 72 GFVNFENADDAAKAVEALNG 91
+V +E+ DA A + L+G
Sbjct: 60 AYVVYEDIFDAKNACDHLSG 79
>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2)
Length = 113
Score = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 30/70 (42%), Gaps = 6/70 (8%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
N V V L S + +DLK E G + A V RDG G V F +D AV
Sbjct: 16 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGT------GVVEFVRKEDMTYAVRK 69
Query: 89 LNGKKFDDRE 98
L+ KF E
Sbjct: 70 LDNTKFRSHE 79
>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To
Its Substrate AsfSF2
Length = 115
Score = 33.5 bits (75), Expect = 0.26, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 30/70 (42%), Gaps = 6/70 (8%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
N V V L S + +DLK E G + A V RDG G V F +D AV
Sbjct: 17 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGT------GVVEFVRKEDMTYAVRK 70
Query: 89 LNGKKFDDRE 98
L+ KF E
Sbjct: 71 LDNTKFRSHE 80
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 33.1 bits (74), Expect = 0.38, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 6/85 (7%)
Query: 29 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 7 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQ--AFVIFKEVSSATN 64
Query: 85 AVEALNGKKFDDREWYVGKAQKKSE 109
A+ + G F D+ + A+ S+
Sbjct: 65 ALRSXQGFPFYDKPXRIQYAKTDSD 89
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 33.1 bits (74), Expect = 0.38, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 6/85 (7%)
Query: 29 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQ--AFVIFKEVSSATN 66
Query: 85 AVEALNGKKFDDREWYVGKAQKKSE 109
A+ + G F D+ + A+ S+
Sbjct: 67 ALRSXQGFPFYDKPXRIQYAKTDSD 91
>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 = 33.1 bits (74), Expect = 0.38, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 6/85 (7%)
Query: 29 NNVFVKNLDESTTDEDLKK----IFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAK 84
+ +++ NL+E ++LKK IF +G I +V R + + FV F+ A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQ--AFVIFKEVSSATN 67
Query: 85 AVEALNGKKFDDREWYVGKAQKKSE 109
A+ + G F D+ + A+ S+
Sbjct: 68 ALRSXQGFPFYDKPXRIQYAKTDSD 92
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 32.7 bits (73), Expect = 0.43, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 2/65 (3%)
Query: 133 NLYIKNLGDSIDDEKLKELFSEFG-TITSCKVMRDP-SGISKGSGFVAFSTPEEASRALA 190
+L++ +L +D+ + F+ G T+ S K++R+ +GI G FV F+ A + L
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 191 EMNGK 195
++NGK
Sbjct: 71 KINGK 75
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 32.3 bits (72), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 31 VFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
+F+ NL ++ + EDL +IF YG I + FGF+ F+N A+E
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 75
>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 = 0.66, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 134 LYIKNLGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMN 193
L I+N+ + E L L ++G + SC+ + S + + V +S+ ++A +AL ++N
Sbjct: 18 LQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVN--VTYSSKDQARQALDKLN 75
Query: 194 GKMIVSKPLYVA 205
G + + L VA
Sbjct: 76 GFQLENFTLKVA 87
>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 = 31.6 bits (70), Expect = 1.1, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNF--ENADDAAKAV 86
+V+V N+D +T +DL+ F G+I ++ D G K + ++ F N+ DAA A+
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAM 97
Query: 87 E 87
+
Sbjct: 98 D 98
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 31.2 bits (69), Expect = 1.2, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 45 LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWY 100
+ KIF ++G IT+ + DGK+K + F+ + + A AV+ +G K D + +
Sbjct: 24 IHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 78
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of
The Spliceosomal Protein P14 Bound To A Region Of
Sf3b155
Length = 125
Score = 31.2 bits (69), Expect = 1.2, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 43/80 (53%), Gaps = 5/80 (6%)
Query: 14 LRKQERETVAIKTKFNNVF-VKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDG-KSKCF 71
++ +R + + + N + ++NL T E++ IFG+YG I +R G+ +++
Sbjct: 3 MQAAKRANIRLPPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGT 59
Query: 72 GFVNFENADDAAKAVEALNG 91
+V +E+ DA A + L+G
Sbjct: 60 AYVVYEDIFDAKNACDHLSG 79
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 31.2 bits (69), Expect = 1.5, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 45 LKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWY 100
+ KIF ++G IT+ + DGK+K + F+ + + A AV+ +G K D + +
Sbjct: 38 IHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 92
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/67 (22%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 145 DEKLKELFSE----FGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIVSK 200
DE +E+F+E +G + V + G+ +V F E+A +A+ ++N + +
Sbjct: 37 DEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ 96
Query: 201 PLYVAVA 207
P++ ++
Sbjct: 97 PIHAELS 103
>pdb|2CPY|A Chain A, Solution Structure Of Rna Binding Domain 3 In Rna Binding
Motif Protein 12
Length = 114
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 60 VMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGKAQKKSEREQE 113
V+ D +G+ V F+N DDA K+ E L+ KK + RE +V + RE E
Sbjct: 48 VLVDNNGQGLGQALVQFKNEDDARKS-ERLHRKKLNGREAFVHVVTLEDMREIE 100
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 30.4 bits (67), Expect = 2.1, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
+FV L T +E +++ FG +G + S + M + K + F F+ F+ + K +E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
>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 = 30.4 bits (67), Expect = 2.4, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 31 VFVKNLDESTTDEDLKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
+FV L T +E +++ FG +G + S + M + K + F F+ F+ + K +E
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 30.0 bits (66), Expect = 2.6, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 8/60 (13%)
Query: 29 NNVFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
+ +F+ NL ++ + EDL +IF YG I + FGF+ F+N A+E
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 75
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 30.0 bits (66), Expect = 2.7, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 8/60 (13%)
Query: 29 NNVFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
+ +F+ NL ++ + EDL +IF YG I + FGF+ F+N A+E
Sbjct: 11 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 63
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 30.0 bits (66), Expect = 3.2, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 8/60 (13%)
Query: 29 NNVFVKNLD-ESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVE 87
+ +F+ NL ++ + EDL +IF YG I + FGF+ F+N A+E
Sbjct: 3 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 55
>pdb|3UX8|A Chain A, Crystal Structure Of Uvra
Length = 670
Score = 29.6 bits (65), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 9/55 (16%)
Query: 167 PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 221
P G +G VA TPEE + G+ + KP+ E RAR+QA++
Sbjct: 620 PEGGDRGGQIVAVGTPEEVAEVKESHTGRYL--KPIL-------ERDRARMQARY 665
>pdb|3UWX|A Chain A, Crystal Structure Of Uvra-Uvrb Complex
Length = 972
Score = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 9/55 (16%)
Query: 167 PSGISKGSGFVAFSTPEEASRALAEMNGKMIVSKPLYVAVAQRKEERRARLQAQF 221
P G +G VA TPEE + G+ + KP+ E RAR+QA++
Sbjct: 922 PEGGDRGGQIVAVGTPEEVAEVKESHTGRYL--KPIL-------ERDRARMQARY 967
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 28.9 bits (63), Expect = 5.7, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 45 LKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFDDREWYVGK 103
L +F + G + + + + GK+K F FV + +DA K +++ +GK+ D +
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLY 88
Query: 104 AQKKSER 110
K ER
Sbjct: 89 TMKDVER 95
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 28.9 bits (63), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 8/64 (12%)
Query: 29 NNVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDGDGKSKCFGFVNFENADDAAKAVEA 88
+ VFV E T E+L++ F +YG + + + + F FV F ADD K ++
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK----PFRAFAFVTF--ADD--KVAQS 63
Query: 89 LNGK 92
L G+
Sbjct: 64 LCGE 67
>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 = 28.9 bits (63), Expect = 6.3, Method: Composition-based stats.
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 45 LKKIFGEYGTITS-AVVMRDGDGKSKCFGFVNFENADDAAKAVEALNGKKFD 95
L +F + G + + + + GK+K F FV + +DA K +++ +GK+ D
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>pdb|4EGB|A Chain A, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|B Chain B, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|C Chain C, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|D Chain D, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|E Chain E, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|F Chain F, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|G Chain G, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
pdb|4EGB|H Chain H, 3.0 Angstrom Resolution Crystal Structure Of Dtdp-Glucose
4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str.
Ames In Complex With Nad
Length = 346
Score = 28.9 bits (63), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 26/47 (55%)
Query: 84 KAVEALNGKKFDDREWYVGKAQKKSEREQELKGQFEQAMKETVDKFQ 130
K +E + + DR + + + K+E + E K FEQ ++ETV ++
Sbjct: 289 KDIEYVTDRLGHDRRYAINAEKXKNEFDWEPKYTFEQGLQETVQWYE 335
>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 = 28.9 bits (63), Expect = 6.5, Method: Composition-based stats.
Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 2/70 (2%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
+++V N+D T E+L+ F G++ ++ D G K F ++ F + + ++ A
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 66
Query: 89 LNGKKFDDRE 98
L+ F R+
Sbjct: 67 LDESLFRGRQ 76
>pdb|1B8D|A Chain A, Crystal Structure Of A Phycourobilin-Containing
Phycoerythrin
pdb|1B8D|K Chain K, Crystal Structure Of A Phycourobilin-Containing
Phycoerythrin
Length = 164
Score = 28.9 bits (63), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 101 VGKAQKKSEREQELKGQFEQAMKETVDKFQGLNLYIKNLGDSIDD-EKLKELFSEF 155
+ +A + E Q+L G E +KE D Y+KN G++ D EK+ + + +
Sbjct: 31 IQRAAARLEAAQKLSGNHEAVVKEAGDACFAKYSYLKNAGEAGDSPEKINKCYRDI 86
>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 = 28.9 bits (63), Expect = 7.4, Method: Composition-based stats.
Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 2/70 (2%)
Query: 30 NVFVKNLDESTTDEDLKKIFGEYGTITSAVVMRDG-DGKSKCFGFVNFENADDAAKAVEA 88
+++V N+D T E+L+ F G++ ++ D G K F ++ F + + ++ A
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 65
Query: 89 LNGKKFDDRE 98
L+ F R+
Sbjct: 66 LDESLFRGRQ 75
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 28.5 bits (62), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 17/84 (20%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 134 LYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
L + NL + + + L LF +G + K++ + K + V + +A A++ +
Sbjct: 37 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSHL 92
Query: 193 NGKMIVSKPLYVAVAQRKEERRAR 216
NG + KP+ + +++ + + R
Sbjct: 93 NGHKLHGKPIRITLSKHQNVQLPR 116
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 28.5 bits (62), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 17/84 (20%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 134 LYIKNLG-DSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEM 192
L + NL + + + L LF +G + K++ + K + V + +A A++ +
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSHL 61
Query: 193 NGKMIVSKPLYVAVAQRKEERRAR 216
NG + KP+ + +++ + + R
Sbjct: 62 NGHKLHGKPIRITLSKHQNVQLPR 85
>pdb|3THP|A Chain A, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
Length = 345
Score = 28.5 bits (62), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 22/96 (22%), Positives = 43/96 (44%), Gaps = 19/96 (19%)
Query: 139 LGDSIDDEKLKELFSEFGTITSCKVMRDPSGISKGSGFVAFSTPEEASRALAEMNGKMIV 198
LG+ + +L + + G + + ++ P+ K F + T EE+ RA +NGK +V
Sbjct: 28 LGNGVSRNQLLPVLEKCGLVDA--LLXPPN---KPYSFARYRTTEESKRAYVTLNGKEVV 82
Query: 199 SK-----PLYVAVAQRKEERRARLQAQFSQMRPVAM 229
LY+ ++ Q+ ++RP A+
Sbjct: 83 DDLGQKITLYLNFVEK---------VQWKELRPQAL 109
>pdb|3DXB|A Chain A, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|B Chain B, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|C Chain C, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|D Chain D, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|E Chain E, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|F Chain F, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|G Chain G, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|H Chain H, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
Length = 222
Score = 28.1 bits (61), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 41/87 (47%), Gaps = 15/87 (17%)
Query: 36 LDESTTDEDLK----KIFGEYGTITSAVVMRDGDGKSK-----CFGFVNFENADDAAKAV 86
+D D+DL+ + G++G + ++ ++ G+ + FV F A + KA+
Sbjct: 133 VDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAI 192
Query: 87 EALNGKKFDDREWYVGKAQKKSEREQE 113
+ALNG+ W+ G+ +QE
Sbjct: 193 QALNGR------WFAGRKVVAEVYDQE 213
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.132 0.373
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,663,197
Number of Sequences: 62578
Number of extensions: 447861
Number of successful extensions: 2032
Number of sequences better than 100.0: 243
Number of HSP's better than 100.0 without gapping: 138
Number of HSP's successfully gapped in prelim test: 105
Number of HSP's that attempted gapping in prelim test: 1574
Number of HSP's gapped (non-prelim): 402
length of query: 472
length of database: 14,973,337
effective HSP length: 102
effective length of query: 370
effective length of database: 8,590,381
effective search space: 3178440970
effective search space used: 3178440970
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)