RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7847
(170 letters)
>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation
factors PAIP1 and PAIP2, translation-RNA complex; 2.00A
{Homo sapiens} PDB: 1cvj_A*
Length = 213
Score = 126 bits (319), Expect = 2e-37
Identities = 49/167 (29%), Positives = 75/167 (44%), Gaps = 26/167 (15%)
Query: 7 GPISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGF 66
GP+ S + + L+ GDL DVT+ +L FS L +V RD T ++ G+
Sbjct: 1 GPLGS-MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGY 59
Query: 67 GFVSFKDPQDFIRANKEMN-----------------------DDFRLFCGDLGNDVTDEL 103
+V+F+ P D RA MN +F +L + ++
Sbjct: 60 AYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKA 119
Query: 104 LIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
L TFS + + L KVV D N +KG+GFV F+ + RA ++MN
Sbjct: 120 LYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMN 164
>1b7f_A Protein (SXL-lethal protein), RNA
(5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing
regulation, RNP domain, RNA complex; 2.60A {Drosophila
melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A*
1sxl_A 2sxl_A
Length = 168
Score = 122 bits (308), Expect = 4e-36
Identities = 38/151 (25%), Positives = 62/151 (41%), Gaps = 21/151 (13%)
Query: 21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
++ L L D+TD L F +++RD +T + G+ FV F D RA
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 81 NKEMN---------------------DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKV 119
K +N D L+ +L +TD+ L F KY S ++ +
Sbjct: 62 IKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
Query: 120 VRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
+RDK T + +G FV + ++ A +N
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Score = 75.7 bits (187), Expect = 5e-18
Identities = 21/75 (28%), Positives = 37/75 (49%)
Query: 11 SWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVS 70
S+ + E D L+ +L +TD+ L F KY S ++ ++RDK T + +G FV
Sbjct: 78 SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 137
Query: 71 FKDPQDFIRANKEMN 85
+ ++ A +N
Sbjct: 138 YNKREEAQEAISALN 152
>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP,
RBD, poly(U) binding, tandem, acetylation, cytopla
nucleus; 2.70A {Saccharomyces cerevisiae}
Length = 166
Score = 119 bits (301), Expect = 3e-35
Identities = 42/149 (28%), Positives = 64/149 (42%), Gaps = 24/149 (16%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ G+L +T+++L + F K++ D + NK + FV + D A + +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 85 N-----------------------DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVR 121
N D F LF GDL +V DE L F +PS+L V+
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 121
Query: 122 DKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
D +T ++G+GFVSF D A M
Sbjct: 122 DMQTGSSRGYGFVSFTSQDDAQNAMDSMQ 150
Score = 79.9 bits (198), Expect = 1e-19
Identities = 26/72 (36%), Positives = 37/72 (51%)
Query: 14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
+ ++ F LF GDL +V DE L F +PS+L V+ D +T ++G+GFVSF
Sbjct: 79 SQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTS 138
Query: 74 PQDFIRANKEMN 85
D A M
Sbjct: 139 QDDAQNAMDSMQ 150
Score = 59.1 bits (144), Expect = 1e-11
Identities = 21/94 (22%), Positives = 36/94 (38%), Gaps = 24/94 (25%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ G+L +T+++L + F K++ D + NK + FV + D A + +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 150 NEFP-----------------------HLFVGDL 160
N +LFVGDL
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDL 95
>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex,
AU-rich element, transcription/RNA complex; 1.80A {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H
1d8z_A 1d9a_A 3hi9_A
Length = 167
Score = 118 bits (297), Expect = 2e-34
Identities = 37/147 (25%), Positives = 64/147 (43%), Gaps = 21/147 (14%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L L ++T E F K+VRDK T ++ G+GFV++ DP+D +A +
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 85 N---------------------DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDK 123
N D L+ L +T + L + FS+Y + ++++ D+
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ 124
Query: 124 RTNKTKGFGFVSFKDPQDFIRANKEMN 150
T ++G GF+ F + A K +N
Sbjct: 125 VTGVSRGVGFIRFDKRIEAEEAIKGLN 151
Score = 71.8 bits (177), Expect = 1e-16
Identities = 18/75 (24%), Positives = 37/75 (49%)
Query: 11 SWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVS 70
S+ + + D L+ L +T + L + FS+Y + ++++ D+ T ++G GF+
Sbjct: 77 SYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIR 136
Query: 71 FKDPQDFIRANKEMN 85
F + A K +N
Sbjct: 137 FDKRIEAEEAIKGLN 151
Score = 65.7 bits (161), Expect = 2e-14
Identities = 23/92 (25%), Positives = 36/92 (39%), Gaps = 21/92 (22%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L L ++T E F K+VRDK T ++ G+GFV++ DP+D +A +
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 150 NEFP---------------------HLFVGDL 160
N +L+V L
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIRDANLYVSGL 96
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 115 bits (290), Expect = 6e-33
Identities = 33/171 (19%), Positives = 65/171 (38%), Gaps = 32/171 (18%)
Query: 14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
++ R++ G + ++ ++ + + F+ + + D T K KGF FV ++
Sbjct: 20 QRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEV 79
Query: 74 PQDFIRANKEMN--------------------------------DDFRLFCGDLGNDVTD 101
P+ A ++MN R++ + D++D
Sbjct: 80 PEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSD 139
Query: 102 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
+ + F + A + RD T K KG+GF+ ++ Q A MN F
Sbjct: 140 DDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLF 190
>3sde_A Paraspeckle component 1; RRM, anti parallel right handed
coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A
{Homo sapiens} PDB: 3sde_B
Length = 261
Score = 112 bits (282), Expect = 3e-31
Identities = 42/173 (24%), Positives = 67/173 (38%), Gaps = 23/173 (13%)
Query: 5 RPGPISSWIKKTCEDENDF-RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKT 63
I S++K + RLF G+L D+T+E R F +Y + + RD+
Sbjct: 4 FTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR----- 58
Query: 64 KGFGFVSFKDPQDFIRANKEMND---------------DFRLFCGDLGNDVTDELLIRTF 108
GFGF+ + A E++ L +L V++ELL + F
Sbjct: 59 -GFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAF 117
Query: 109 SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLK 161
S++ KA VV D + G GFV F +A + + L +
Sbjct: 118 SQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPR 169
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA
recognition motif, vincu alpha-actinin, nucleus, RNA
binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E
Length = 284
Score = 110 bits (276), Expect = 3e-30
Identities = 25/156 (16%), Positives = 50/156 (32%), Gaps = 26/156 (16%)
Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
D L +L +T + + S + +V +RT ++KG+GF + R
Sbjct: 93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152
Query: 80 ANKEMND------------------------DFRLFCGDLGNDVTD-ELLIRTFSKYPSF 114
A ++ L L D + L R S S
Sbjct: 153 AKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSP 212
Query: 115 LKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
++ + + KGF + ++ + A ++ +
Sbjct: 213 TFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQAD 247
Score = 109 bits (275), Expect = 5e-30
Identities = 32/166 (19%), Positives = 59/166 (35%), Gaps = 23/166 (13%)
Query: 4 LRPGPISSWIKKTCEDENDFR-LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNK 62
L P I ++ T + R + L DVT++ + S Y ++ +K
Sbjct: 3 LDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDK 55
Query: 63 TKGFGFVSFKDPQDFIRANKEMN---------------DDFRLFCGDLGNDVTDELLIRT 107
KG FV+ + + A + D L +L +T +
Sbjct: 56 YKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEEL 115
Query: 108 FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFP 153
+ S + +V +RT ++KG+GF + RA ++ P
Sbjct: 116 VRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKP 161
Score = 57.3 bits (139), Expect = 1e-10
Identities = 15/97 (15%), Positives = 31/97 (31%), Gaps = 22/97 (22%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
++ + ++ L DVT++ + S Y ++ +K KG FV+ +
Sbjct: 14 HTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLN 66
Query: 139 PQDFIRANKEMN---------------EFPHLFVGDL 160
+ A + L V +L
Sbjct: 67 GEQAEAAINAFHQSRLRERELSVQLQPTDALLCVANL 103
Score = 56.5 bits (137), Expect = 2e-10
Identities = 11/69 (15%), Positives = 24/69 (34%), Gaps = 2/69 (2%)
Query: 18 EDENDFRLFCGDLGNDVTD-ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
+ L L D + L R S S ++ + + KGF + ++ +
Sbjct: 180 ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEM 238
Query: 77 FIRANKEMN 85
A ++ +
Sbjct: 239 AEEAQQQAD 247
>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA
splicing factor, RNA recognition motif, RNA binding
protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A
Length = 172
Score = 105 bits (263), Expect = 2e-29
Identities = 27/152 (17%), Positives = 58/152 (38%), Gaps = 25/152 (16%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKY-----PSFLKAKVVRDKRTNKTKGFGFVSFKDPQD-- 76
RL+ G++ +T+E ++ F+ + V + N+ K F F+ F+ +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 77 -------------FIRANK-----EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAK 118
++ + + +LF G L N + D+ + + +
Sbjct: 66 QAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFN 125
Query: 119 VVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
+V+D T +KG+ F + D +A +N
Sbjct: 126 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 157
Score = 70.7 bits (174), Expect = 4e-16
Identities = 15/68 (22%), Positives = 28/68 (41%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+LF G L N + D+ + + + +V+D T +KG+ F + D
Sbjct: 90 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 149
Query: 78 IRANKEMN 85
+A +N
Sbjct: 150 DQAIAGLN 157
>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain,
RNA-protein complex, nucleolus, structural protein/RNA
complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1
d.58.7.1 PDB: 1rkj_A 2krr_A
Length = 175
Score = 99 bits (250), Expect = 2e-27
Identities = 32/157 (20%), Positives = 58/157 (36%), Gaps = 28/157 (17%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
E F LF G+L + + L S+ + VV D RT + FG+V F+ +D
Sbjct: 9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDL 67
Query: 78 IRA----------------------NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFL 115
+A +K++ L +L ++T++ L F
Sbjct: 68 EKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDA---- 123
Query: 116 KAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
++ + K+KG ++ FK D + +E
Sbjct: 124 -LEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGA 159
Score = 61.5 bits (150), Expect = 1e-12
Identities = 12/72 (16%), Positives = 28/72 (38%), Gaps = 5/72 (6%)
Query: 14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
+ + + L +L ++T++ L F ++ + K+KG ++ FK
Sbjct: 91 RDSKKVRAARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKS 145
Query: 74 PQDFIRANKEMN 85
D + +E
Sbjct: 146 EADAEKNLEEKQ 157
Score = 56.5 bits (137), Expect = 8e-11
Identities = 22/101 (21%), Positives = 36/101 (35%), Gaps = 23/101 (22%)
Query: 82 KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
E F LF G+L + + L S+ + VV D RT + FG+V F+ +D
Sbjct: 8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAED 66
Query: 142 FIRA----------------------NKEMNEFPHLFVGDL 160
+A +K++ L +L
Sbjct: 67 LEKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNL 107
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 97.0 bits (242), Expect = 5e-27
Identities = 29/69 (42%), Positives = 36/69 (52%), Gaps = 2/69 (2%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSK-YPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
++ LF GDL DV D +L F K YPS KVV D+ T +KG+GFV F D +
Sbjct: 5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELE 63
Query: 77 FIRANKEMN 85
RA E
Sbjct: 64 QKRALTECQ 72
Score = 96.2 bits (240), Expect = 9e-27
Identities = 29/72 (40%), Positives = 38/72 (52%), Gaps = 2/72 (2%)
Query: 80 ANKEMNDDFRLFCGDLGNDVTDELLIRTFSK-YPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
++ ++ LF GDL DV D +L F K YPS KVV D+ T +KG+GFV F D
Sbjct: 2 SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTD 60
Query: 139 PQDFIRANKEMN 150
+ RA E
Sbjct: 61 ELEQKRALTECQ 72
>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA
binding domain, RBD, RNA splicing, apoptosis,
phosphoprotein, RNA-binding; 1.95A {Homo sapiens}
Length = 87
Score = 95.7 bits (239), Expect = 1e-26
Identities = 23/67 (34%), Positives = 37/67 (55%)
Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
+ F +F GDL ++T + F+ + A+VV+D T K+KG+GFVSF + D
Sbjct: 3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62
Query: 79 RANKEMN 85
A ++M
Sbjct: 63 NAIQQMG 69
Score = 95.3 bits (238), Expect = 1e-26
Identities = 23/67 (34%), Positives = 37/67 (55%)
Query: 84 MNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 143
+ F +F GDL ++T + F+ + A+VV+D T K+KG+GFVSF + D
Sbjct: 3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62
Query: 144 RANKEMN 150
A ++M
Sbjct: 63 NAIQQMG 69
>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA
binding protein-RNA complex; 1.85A {Homo sapiens} PDB:
3nna_A 3nnc_A 2dhs_A 3nnh_A
Length = 175
Score = 98.1 bits (245), Expect = 1e-26
Identities = 30/153 (19%), Positives = 61/153 (39%), Gaps = 28/153 (18%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSFKDPQDFIRANK 82
+F G + +++ L F +Y + + V+RD+ N ++KG FV+F + + A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 83 EMN-------------------------DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKA 117
++ +D +LF G + T+ + FS + +
Sbjct: 66 ALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEEC 125
Query: 118 KVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
+++R ++G FV+F A K M+
Sbjct: 126 RILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMH 157
Score = 60.3 bits (147), Expect = 3e-12
Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 3/79 (3%)
Query: 85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSFKDPQDF 142
+D ++F G + +++ L F +Y + + V+RD+ N ++KG FV+F +
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 143 IRANKEMNEFPHLFVGDLK 161
+ A ++ + G
Sbjct: 61 LEAQNALHNM-KVLPGMHH 78
Score = 58.4 bits (142), Expect = 2e-11
Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 1/68 (1%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
D +LF G + T+ + FS + + +++R ++G FV+F
Sbjct: 91 NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMA 149
Query: 78 IRANKEMN 85
A K M+
Sbjct: 150 QTAIKAMH 157
>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA
binding domain, RNA recognition motif, SP factor, snRNP,
spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP:
d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A
Length = 292
Score = 98.1 bits (245), Expect = 1e-25
Identities = 14/139 (10%), Positives = 37/139 (26%), Gaps = 15/139 (10%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+ +L + + F + V K F + F + A +
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAITKT 101
Query: 85 N-------------DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGF 131
+ + L+ + T + + + R N ++ F
Sbjct: 102 HKVVGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRF 161
Query: 132 GFVSFKDPQDFIRANKEMN 150
++ +D +++N
Sbjct: 162 AYIDVTSKEDARYCVEKLN 180
Score = 93.9 bits (234), Expect = 5e-24
Identities = 21/167 (12%), Positives = 51/167 (30%), Gaps = 31/167 (18%)
Query: 14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
+ + L+ + T + + + R N ++ F ++
Sbjct: 109 EIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTS 168
Query: 74 PQDFIRANKEMND----------------------------DFRLFCGDLGNDVTDELLI 105
+D +++N + +L ++ DE L+
Sbjct: 169 KEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLL 228
Query: 106 R-TFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRANKEMN 150
R +F + S K + ++ + F+ F++ RA +MN
Sbjct: 229 RESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA-LQMN 274
>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing,
transcription, RNA binding protein, mRNA processing; NMR
{Homo sapiens} PDB: 2yh1_A
Length = 198
Score = 95.1 bits (237), Expect = 3e-25
Identities = 28/172 (16%), Positives = 57/172 (33%), Gaps = 45/172 (26%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKY-----PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
RL+ G++ +T+E ++ F+ + V + N+ K F F+ F+ +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 79 RA----------------------------------------NKEMNDDFRLFCGDLGND 98
+A + +LF G L N
Sbjct: 66 QAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNY 125
Query: 99 VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
+ D+ + + + +V+D T +KG+ F + D +A +N
Sbjct: 126 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 177
Score = 69.7 bits (171), Expect = 1e-15
Identities = 17/81 (20%), Positives = 33/81 (40%)
Query: 5 RPGPISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK 64
P + T ++ +LF G L N + D+ + + + +V+D T +K
Sbjct: 97 NPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK 156
Query: 65 GFGFVSFKDPQDFIRANKEMN 85
G+ F + D +A +N
Sbjct: 157 GYAFCEYVDINVTDQAIAGLN 177
>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain,
structural genomics, NPPSFA; NMR {Mus musculus} PDB:
2rne_A 2dh7_A
Length = 115
Score = 92.4 bits (230), Expect = 4e-25
Identities = 25/68 (36%), Positives = 39/68 (57%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+ N F +F GDL ++T E + F+ + A+VV+D T K+KG+GFVSF + D
Sbjct: 11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 70
Query: 78 IRANKEMN 85
A ++M
Sbjct: 71 ENAIQQMG 78
Score = 91.6 bits (228), Expect = 9e-25
Identities = 25/69 (36%), Positives = 41/69 (59%)
Query: 82 KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
K+ ++ F +F GDL ++T E + F+ + A+VV+D T K+KG+GFVSF + D
Sbjct: 10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 69
Query: 142 FIRANKEMN 150
A ++M
Sbjct: 70 AENAIQQMG 78
>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding,
RNA processing, mRNA processing, nonsense-mediated mRNA
decay, cleavage; NMR {Saccharomyces cerevisiae} PDB:
2km8_C
Length = 167
Score = 93.0 bits (232), Expect = 9e-25
Identities = 36/140 (25%), Positives = 67/140 (47%), Gaps = 19/140 (13%)
Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
+ ++F G L D T++ L F KY + K+++D T +++GFGF+SF+ P
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60
Query: 80 A-------------------NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVV 120
E + ++F G +G DV + FS++ + + A+++
Sbjct: 61 VVKTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLM 120
Query: 121 RDKRTNKTKGFGFVSFKDPQ 140
DK T +++GFGFV++
Sbjct: 121 LDKDTGQSRGFGFVTYDSAD 140
Score = 56.0 bits (136), Expect = 1e-10
Identities = 19/76 (25%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
E + ++F G +G DV + FS++ + + A+++ DK T +++GFGFV++
Sbjct: 83 EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA- 141
Query: 78 IRANKEMNDDFRLFCG 93
++ + F F
Sbjct: 142 --VDRVCQNKFIDFKD 155
Score = 55.2 bits (134), Expect = 2e-10
Identities = 20/66 (30%), Positives = 35/66 (53%)
Query: 86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
+ ++F G L D T++ L F KY + K+++D T +++GFGF+SF+ P
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 146 NKEMNE 151
K +
Sbjct: 62 VKTQHI 67
>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD,
RNP, poly(U) binding, nucleus, RNA-binding, binding
protein; 1.60A {Saccharomyces cerevisiae}
Length = 83
Score = 85.6 bits (213), Expect = 8e-23
Identities = 26/63 (41%), Positives = 34/63 (53%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
F LF GDL +V DE L F +PS+L V+ D +T ++G+GFVSF D A
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 83 EMN 85
M
Sbjct: 62 SMQ 64
Score = 85.6 bits (213), Expect = 8e-23
Identities = 26/63 (41%), Positives = 34/63 (53%)
Query: 88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
F LF GDL +V DE L F +PS+L V+ D +T ++G+GFVSF D A
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 148 EMN 150
M
Sbjct: 62 SMQ 64
>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP
A1, RNA-recognition motif, RNA- binding, UP1, RNA
binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1
d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A
1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A*
1up1_A
Length = 196
Score = 86.6 bits (215), Expect = 7e-22
Identities = 35/149 (23%), Positives = 60/149 (40%), Gaps = 26/149 (17%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
E E +LF G L + TDE L F ++ + V+RD T +++GFGFV++ ++
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 78 IRA--------------------------NKEMNDDFRLFCGDLGNDVTDELLIRTFSKY 111
A ++F G + D + L F +Y
Sbjct: 69 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 128
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
+++ D+ + K +GF FV+F D
Sbjct: 129 GKIEVIEIMTDRGSGKKRGFAFVTFDDHD 157
Score = 58.1 bits (141), Expect = 4e-11
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 82 KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
KE +LF G L + TDE L F ++ + V+RD T +++GFGFV++ ++
Sbjct: 8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 67
Query: 142 FIRANKEMNEFPH 154
+ MN PH
Sbjct: 68 ---VDAAMNARPH 77
>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 101
Score = 80.4 bits (199), Expect = 1e-20
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 2/68 (2%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
E F LF G+L + + L S+ + V D RT + FG+V F+ +D
Sbjct: 13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAK-NDLAVVDVRTGTNRKFGYVDFESAEDL 71
Query: 78 IRANKEMN 85
+A E+
Sbjct: 72 EKA-LELT 78
Score = 77.7 bits (192), Expect = 2e-19
Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 2/65 (3%)
Query: 86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
F LF G+L + + L S+ + V D RT + FG+V F+ +D +A
Sbjct: 16 TPFNLFIGNLNPNKSVAELKVAISELFAK-NDLAVVDVRTGTNRKFGYVDFESAEDLEKA 74
Query: 146 NKEMN 150
E+
Sbjct: 75 -LELT 78
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 78.6 bits (194), Expect = 1e-19
Identities = 28/71 (39%), Positives = 37/71 (52%)
Query: 82 KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
E + LF L + TD L TF + + + AKV DK+T+ +K FGFVSF +P
Sbjct: 35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDS 94
Query: 142 FIRANKEMNEF 152
A K MN F
Sbjct: 95 AQVAIKAMNGF 105
Score = 77.8 bits (192), Expect = 2e-19
Identities = 27/68 (39%), Positives = 35/68 (51%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
E LF L + TD L TF + + + AKV DK+T+ +K FGFVSF +P
Sbjct: 36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95
Query: 78 IRANKEMN 85
A K MN
Sbjct: 96 QVAIKAMN 103
>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1 PDB: 2rq4_A 2rqc_A
Length = 115
Score = 70.8 bits (174), Expect = 1e-16
Identities = 24/63 (38%), Positives = 36/63 (57%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF L + D+ L++ F + + + AKV DK+TN +K FGFVS+ +P A + M
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 150 NEF 152
N F
Sbjct: 88 NGF 90
Score = 69.7 bits (171), Expect = 3e-16
Identities = 23/61 (37%), Positives = 35/61 (57%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF L + D+ L++ F + + + AKV DK+TN +K FGFVS+ +P A + M
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 85 N 85
N
Sbjct: 88 N 88
>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA
binding protein, structure, protein-RNA complex, RNA
stem-loop, structural protein/RNA complex; NMR {Homo
sapiens}
Length = 116
Score = 68.9 bits (169), Expect = 5e-16
Identities = 22/68 (32%), Positives = 41/68 (60%), Gaps = 1/68 (1%)
Query: 83 EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 142
E + +LF G L + +++L F K+ + +++D RT+K++GF F++F++P D
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADA 61
Query: 143 IRANKEMN 150
A K+MN
Sbjct: 62 KNAAKDMN 69
Score = 68.5 bits (168), Expect = 8e-16
Identities = 22/68 (32%), Positives = 42/68 (61%), Gaps = 1/68 (1%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
E ++ +LF G L + +++L F K+ + +++D RT+K++GF F++F++P D
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADA 61
Query: 78 IRANKEMN 85
A K+MN
Sbjct: 62 KNAAKDMN 69
>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 68.4 bits (168), Expect = 7e-16
Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 6/81 (7%)
Query: 70 SFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK 129
S D I + +N L+ +L + + DE L + FS + + AKV+ + ++K
Sbjct: 2 SSGSSGDRITRYQVVN----LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSK 55
Query: 130 GFGFVSFKDPQDFIRANKEMN 150
GFGFV F P++ +A EMN
Sbjct: 56 GFGFVCFSSPEEATKAVTEMN 76
Score = 67.2 bits (165), Expect = 2e-15
Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
L+ +L + + DE L + FS + + AKV+ + ++KGFGFV F P++ +
Sbjct: 13 YQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATK 70
Query: 80 ANKEMN 85
A EMN
Sbjct: 71 AVTEMN 76
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 68.7 bits (168), Expect = 1e-15
Identities = 20/74 (27%), Positives = 31/74 (41%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+ L+ G L +V D++L F + ++ D T K +GF FV F+
Sbjct: 55 GSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 114
Query: 139 PQDFIRANKEMNEF 152
+D A MNE
Sbjct: 115 AEDAAAAIDNMNES 128
Score = 67.5 bits (165), Expect = 4e-15
Identities = 19/68 (27%), Positives = 29/68 (42%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
L+ G L +V D++L F + ++ D T K +GF FV F+ +D
Sbjct: 59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 118
Query: 78 IRANKEMN 85
A MN
Sbjct: 119 AAAIDNMN 126
>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 96
Score = 67.2 bits (165), Expect = 1e-15
Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLK-AKVVRDKRTNKTKGFGFVSFKDPQDFI 143
+ +F G+L ++ ++LL TFS + L+ K++RD T +KG+ F++F
Sbjct: 3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62
Query: 144 RANKEMN 150
A + MN
Sbjct: 63 AAIEAMN 69
Score = 67.2 bits (165), Expect = 1e-15
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLK-AKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
+F G+L ++ ++LL TFS + L+ K++RD T +KG+ F++F
Sbjct: 4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63
Query: 80 ANKEMN 85
A + MN
Sbjct: 64 AIEAMN 69
>1x4e_A RNA binding motif, single-stranded interacting protein 2;
structural genomics, RRM domain, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 85
Score = 66.8 bits (164), Expect = 2e-15
Identities = 20/64 (31%), Positives = 29/64 (45%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
L+ L TD+ L++ Y + K + DK TNK KG+GFV F P +A
Sbjct: 7 GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66
Query: 149 MNEF 152
+
Sbjct: 67 LKAS 70
Score = 65.6 bits (161), Expect = 4e-15
Identities = 20/62 (32%), Positives = 29/62 (46%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
L+ L TD+ L++ Y + K + DK TNK KG+GFV F P +A
Sbjct: 7 GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66
Query: 84 MN 85
+
Sbjct: 67 LK 68
>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 115
Score = 67.3 bits (165), Expect = 3e-15
Identities = 12/65 (18%), Positives = 29/65 (44%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
L+ +L VT+ L+ F+++ + T + +G F++F + + +A
Sbjct: 27 VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86
Query: 149 MNEFP 153
+N +
Sbjct: 87 VNGYK 91
Score = 65.0 bits (159), Expect = 2e-14
Identities = 12/62 (19%), Positives = 28/62 (45%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
L+ +L VT+ L+ F+++ + T + +G F++F + + +A
Sbjct: 27 VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86
Query: 84 MN 85
+N
Sbjct: 87 VN 88
>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and
splicing factor,...; protein-RNA complex RRM alpha-beta
sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR
{Streptococcus SP} PDB: 2i38_A
Length = 150
Score = 67.6 bits (165), Expect = 5e-15
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 5/67 (7%)
Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
D +++ G+LGN+ L R F Y V R+ GF FV F+DP+D
Sbjct: 70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAA 124
Query: 79 RANKEMN 85
A +E++
Sbjct: 125 DAVRELD 131
Score = 67.2 bits (164), Expect = 5e-15
Identities = 26/109 (23%), Positives = 40/109 (36%), Gaps = 7/109 (6%)
Query: 44 SKYPSFLKAKVVRDKRTNK--TKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTD 101
+ + V + T TK F D +++ G+LGN+
Sbjct: 28 KVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNK 87
Query: 102 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
L R F Y V R+ GF FV F+DP+D A +E++
Sbjct: 88 TELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAVRELD 131
>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding
protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi}
SCOP: d.58.7.1
Length = 139
Score = 67.1 bits (164), Expect = 5e-15
Identities = 19/74 (25%), Positives = 34/74 (45%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+ N E + L + V + L + F +Y K+V D+ T +++G+GFV F+
Sbjct: 34 QMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS 93
Query: 139 PQDFIRANKEMNEF 152
+A +N F
Sbjct: 94 GSSAQQAIAGLNGF 107
Score = 64.8 bits (158), Expect = 3e-14
Identities = 17/68 (25%), Positives = 31/68 (45%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
E + L + V + L + F +Y K+V D+ T +++G+GFV F+
Sbjct: 38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97
Query: 78 IRANKEMN 85
+A +N
Sbjct: 98 QQAIAGLN 105
>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; 1.54A {Homo sapiens}
Length = 95
Score = 65.3 bits (160), Expect = 8e-15
Identities = 22/72 (30%), Positives = 32/72 (44%), Gaps = 1/72 (1%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+ D +F G+L V +E+L F + K + +D R K K FGFV FK
Sbjct: 8 MFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVCFKH 66
Query: 139 PQDFIRANKEMN 150
P+ A +N
Sbjct: 67 PESVSYAIALLN 78
Score = 65.3 bits (160), Expect = 8e-15
Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
++E D +F G+L V +E+L F + K + +D R K K FGFV FK P+
Sbjct: 12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVCFKHPESV 70
Query: 78 IRANKEMN 85
A +N
Sbjct: 71 SYAIALLN 78
>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49)
(SAP 49) (SF3B50)...; structure genomics,RRM
domain,splicing factor 3B; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 105
Score = 65.4 bits (160), Expect = 1e-14
Identities = 20/68 (29%), Positives = 34/68 (50%)
Query: 83 EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 142
E N D ++ G L V++ LL F + + + +D+ T + +G+GFV F +D
Sbjct: 11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70
Query: 143 IRANKEMN 150
A K M+
Sbjct: 71 DYAIKIMD 78
Score = 65.0 bits (159), Expect = 1e-14
Identities = 19/68 (27%), Positives = 33/68 (48%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
E D ++ G L V++ LL F + + + +D+ T + +G+GFV F +D
Sbjct: 11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70
Query: 78 IRANKEMN 85
A K M+
Sbjct: 71 DYAIKIMD 78
>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 65.3 bits (160), Expect = 1e-14
Identities = 25/68 (36%), Positives = 40/68 (58%)
Query: 83 EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 142
+D+ +LF G L D ++ L + FSKY + VV+D+ T +++GFGFV+F++ D
Sbjct: 8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 67
Query: 143 IRANKEMN 150
A MN
Sbjct: 68 KDAMMAMN 75
Score = 63.8 bits (156), Expect = 4e-14
Identities = 24/68 (35%), Positives = 39/68 (57%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
++ +LF G L D ++ L + FSKY + VV+D+ T +++GFGFV+F++ D
Sbjct: 8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 67
Query: 78 IRANKEMN 85
A MN
Sbjct: 68 KDAMMAMN 75
>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger,
CYP33, MLL, RNA binding protein, ALT splicing, mRNA
processing, mRNA splicing; 1.85A {Homo sapiens} PDB:
2kyx_A 3lpy_A*
Length = 85
Score = 63.7 bits (156), Expect = 2e-14
Identities = 20/68 (29%), Positives = 30/68 (44%)
Query: 85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
L+ G L +V D++L F + ++ D T K +GF FV F+ +D
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64
Query: 145 ANKEMNEF 152
A MNE
Sbjct: 65 AIDNMNES 72
Score = 62.2 bits (152), Expect = 1e-13
Identities = 19/67 (28%), Positives = 30/67 (44%)
Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
L+ G L +V D++L F + ++ D T K +GF FV F+ +D
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64
Query: 80 ANKEMND 86
A MN+
Sbjct: 65 AIDNMNE 71
>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 63.0 bits (154), Expect = 6e-14
Identities = 19/72 (26%), Positives = 35/72 (48%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
N+ +D+ + +L D + L F + S + + +DK T ++KGF F+SF
Sbjct: 7 GPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHR 66
Query: 139 PQDFIRANKEMN 150
+D RA ++
Sbjct: 67 REDAARAIAGVS 78
Score = 59.9 bits (146), Expect = 1e-12
Identities = 17/68 (25%), Positives = 33/68 (48%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+++ + +L D + L F + S + + +DK T ++KGF F+SF +D
Sbjct: 11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDA 70
Query: 78 IRANKEMN 85
RA ++
Sbjct: 71 ARAIAGVS 78
>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25,
CFIM68, CPSF5, CPSF6, CPSF, 3' END processing,
processing, cleavage factor; 2.90A {Homo sapiens} PDB:
3q2t_C
Length = 229
Score = 65.1 bits (158), Expect = 2e-13
Identities = 13/64 (20%), Positives = 22/64 (34%), Gaps = 2/64 (3%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKY--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
L+ G+L TDE L L+ K ++ ++KGF V +
Sbjct: 70 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129
Query: 82 KEMN 85
+
Sbjct: 130 DLLP 133
Score = 65.1 bits (158), Expect = 2e-13
Identities = 13/64 (20%), Positives = 22/64 (34%), Gaps = 2/64 (3%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKY--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 146
L+ G+L TDE L L+ K ++ ++KGF V +
Sbjct: 70 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129
Query: 147 KEMN 150
+
Sbjct: 130 DLLP 133
>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
PDB: 2dgq_A
Length = 106
Score = 62.3 bits (152), Expect = 2e-13
Identities = 13/68 (19%), Positives = 36/68 (52%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+D + +LF G + ++ ++ L F ++ + V++D+ T KG F+++ + +
Sbjct: 9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA 68
Query: 78 IRANKEMN 85
++A ++
Sbjct: 69 LKAQSALH 76
Score = 60.8 bits (148), Expect = 5e-13
Identities = 14/66 (21%), Positives = 35/66 (53%)
Query: 86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
D +LF G + ++ ++ L F ++ + V++D+ T KG F+++ + + ++A
Sbjct: 12 DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
Query: 146 NKEMNE 151
++E
Sbjct: 72 QSALHE 77
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 62.8 bits (153), Expect = 2e-13
Identities = 23/107 (21%), Positives = 41/107 (38%)
Query: 44 SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDEL 103
S + + +V + G + + R ++ L +L + +
Sbjct: 4 SHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDT 63
Query: 104 LIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
L R F KY + RD+ T +++GF FV F D +D A M+
Sbjct: 64 LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMD 110
Score = 59.8 bits (145), Expect = 3e-12
Identities = 20/68 (29%), Positives = 31/68 (45%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+ E L +L + + L R F KY + RD+ T +++GF FV F D +D
Sbjct: 43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 102
Query: 78 IRANKEMN 85
A M+
Sbjct: 103 EDAMDAMD 110
>2kn4_A Immunoglobulin G-binding protein G, splicing FACT
arginine/serine-rich 2, S35, splicing factor SC35,; RRM
domain, cell WALL; NMR {Streptococcus SP}
Length = 158
Score = 63.3 bits (154), Expect = 2e-13
Identities = 19/72 (26%), Positives = 32/72 (44%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+ ++ L +L + + L R F KY + RD+ T +++GF FV F D
Sbjct: 62 HHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 121
Query: 139 PQDFIRANKEMN 150
+D A M+
Sbjct: 122 KRDAEDAMDAMD 133
Score = 61.4 bits (149), Expect = 1e-12
Identities = 20/68 (29%), Positives = 31/68 (45%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+ E L +L + + L R F KY + RD+ T +++GF FV F D +D
Sbjct: 66 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 125
Query: 78 IRANKEMN 85
A M+
Sbjct: 126 EDAMDAMD 133
>2div_A TRNA selenocysteine associated protein; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 99
Score = 62.0 bits (151), Expect = 2e-13
Identities = 15/69 (21%), Positives = 30/69 (43%), Gaps = 1/69 (1%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
L+ GDL + + + R F+ + + K++R++ T G+ FV F D
Sbjct: 5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLAT 64
Query: 77 FIRANKEMN 85
+ ++N
Sbjct: 65 AEKCLHKIN 73
Score = 61.6 bits (150), Expect = 2e-13
Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 90 LFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
L+ GDL + + + R F+ + + K++R++ T G+ FV F D + +
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 149 MN 150
+N
Sbjct: 72 IN 73
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 61.4 bits (150), Expect = 2e-13
Identities = 18/66 (27%), Positives = 31/66 (46%)
Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
+ + L L T+ L FSKY +V D+++ +++GF FV F++ D
Sbjct: 13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72
Query: 80 ANKEMN 85
A + N
Sbjct: 73 AKERAN 78
Score = 61.4 bits (150), Expect = 3e-13
Identities = 18/66 (27%), Positives = 31/66 (46%)
Query: 85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
+ + L L T+ L FSKY +V D+++ +++GF FV F++ D
Sbjct: 13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72
Query: 145 ANKEMN 150
A + N
Sbjct: 73 AKERAN 78
>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain,
RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 61.1 bits (149), Expect = 3e-13
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 2/68 (2%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+D L+ G+L DVT+ L+++ FS+ K++ + +N + FV F + +D
Sbjct: 11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDA 68
Query: 78 IRANKEMN 85
A MN
Sbjct: 69 AAALAAMN 76
Score = 60.7 bits (148), Expect = 6e-13
Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 81 NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
++ L+ G+L DVT+ L+++ FS+ K++ + +N + FV F + +
Sbjct: 9 MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHR 66
Query: 141 DFIRANKEMN 150
D A MN
Sbjct: 67 DAAAALAAMN 76
>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 61.1 bits (149), Expect = 3e-13
Identities = 20/69 (28%), Positives = 30/69 (43%)
Query: 83 EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 142
L+ G L +V D++L F + ++ D T K +GF FV F+ +D
Sbjct: 8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67
Query: 143 IRANKEMNE 151
A MNE
Sbjct: 68 AAAIDNMNE 76
Score = 60.3 bits (147), Expect = 7e-13
Identities = 19/69 (27%), Positives = 30/69 (43%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
L+ G L +V D++L F + ++ D T K +GF FV F+ +D
Sbjct: 8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67
Query: 78 IRANKEMND 86
A MN+
Sbjct: 68 AAAIDNMNE 76
>4f25_A Polyadenylate-binding protein 1; RRM fold, translation
initiation, RNA-binding, EIF4G-binding translation;
1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A
Length = 115
Score = 61.5 bits (150), Expect = 4e-13
Identities = 22/61 (36%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+F +L + ++ L TFS + + L KVV D N +KG+GFV F+ + RA ++M
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65
Query: 85 N 85
N
Sbjct: 66 N 66
Score = 61.5 bits (150), Expect = 4e-13
Identities = 22/61 (36%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+F +L + ++ L TFS + + L KVV D N +KG+GFV F+ + RA ++M
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65
Query: 150 N 150
N
Sbjct: 66 N 66
>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1;
RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 94
Score = 60.7 bits (148), Expect = 4e-13
Identities = 19/67 (28%), Positives = 32/67 (47%)
Query: 86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
++ +L +T+ L R FSKY +K +++DK T K+KG F+ F D
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Query: 146 NKEMNEF 152
+ +N
Sbjct: 75 TRAINNK 81
Score = 60.7 bits (148), Expect = 5e-13
Identities = 19/68 (27%), Positives = 33/68 (48%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+ ++ +L +T+ L R FSKY +K +++DK T K+KG F+ F D
Sbjct: 12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
Query: 78 IRANKEMN 85
+ +N
Sbjct: 72 QNCTRAIN 79
>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 61.2 bits (149), Expect = 4e-13
Identities = 14/83 (16%), Positives = 27/83 (32%)
Query: 82 KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
++ + +F +L D +E L ++ +VV T +KG F F +
Sbjct: 10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 69
Query: 142 FIRANKEMNEFPHLFVGDLKTRS 164
+ + L R
Sbjct: 70 AQKCLAAASLEAEGGGLKLDGRQ 92
Score = 59.7 bits (145), Expect = 2e-12
Identities = 13/80 (16%), Positives = 25/80 (31%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+ +F +L D +E L ++ +VV T +KG F F +
Sbjct: 11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70
Query: 78 IRANKEMNDDFRLFCGDLGN 97
+ + + L
Sbjct: 71 QKCLAAASLEAEGGGLKLDG 90
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 61.3 bits (149), Expect = 4e-13
Identities = 12/62 (19%), Positives = 23/62 (37%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+ L ++V + L KY + +++ RT K G V F + K
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67
Query: 84 MN 85
++
Sbjct: 68 LH 69
Score = 61.3 bits (149), Expect = 4e-13
Identities = 12/62 (19%), Positives = 23/62 (37%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+ L ++V + L KY + +++ RT K G V F + K
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67
Query: 149 MN 150
++
Sbjct: 68 LH 69
>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 61.1 bits (149), Expect = 4e-13
Identities = 18/72 (25%), Positives = 30/72 (41%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+ +++ L +L + + L R F KY + R+ T +GF FV F D
Sbjct: 5 SSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHD 64
Query: 139 PQDFIRANKEMN 150
+D A M+
Sbjct: 65 RRDAQDAEAAMD 76
Score = 58.8 bits (143), Expect = 3e-12
Identities = 18/68 (26%), Positives = 28/68 (41%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+ + L +L + + L R F KY + R+ T +GF FV F D +D
Sbjct: 9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA 68
Query: 78 IRANKEMN 85
A M+
Sbjct: 69 QDAEAAMD 76
>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing
factor, RNA protein complex, SMN, binding protein-RNA
complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A
Length = 129
Score = 61.7 bits (150), Expect = 4e-13
Identities = 18/72 (25%), Positives = 31/72 (43%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+ + L L T+ L FSKY +V D+++ +++GF FV F++
Sbjct: 38 GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 97
Query: 139 PQDFIRANKEMN 150
D A + N
Sbjct: 98 VDDAKEAKERAN 109
Score = 60.9 bits (148), Expect = 8e-13
Identities = 18/62 (29%), Positives = 29/62 (46%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
L L T+ L FSKY +V D+++ +++GF FV F++ D A +
Sbjct: 48 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
Query: 84 MN 85
N
Sbjct: 108 AN 109
>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A
Length = 87
Score = 60.3 bits (147), Expect = 5e-13
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 78 IRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 137
I A+K D ++F G L D + + L F+K+ + + D T +++GFGF+ FK
Sbjct: 2 INASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFK 61
Query: 138 DPQDFIRANKEMNEFPH 154
D K +++ H
Sbjct: 62 DAAS---VEKVLDQKEH 75
Score = 58.0 bits (141), Expect = 4e-12
Identities = 18/73 (24%), Positives = 35/73 (47%)
Query: 13 IKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 72
I + +E+ ++F G L D + + L F+K+ + + D T +++GFGF+ FK
Sbjct: 2 INASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFK 61
Query: 73 DPQDFIRANKEMN 85
D + +
Sbjct: 62 DAASVEKVLDQKE 74
>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 105
Score = 60.3 bits (147), Expect = 8e-13
Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 3/76 (3%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
N ++ +LF G L T E L FS+Y + +++DK TN+++GFGFV FKD
Sbjct: 8 MNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
Query: 139 PQDFIRANKEMNEFPH 154
P + PH
Sbjct: 68 PNC---VGTVLASRPH 80
Score = 57.2 bits (139), Expect = 1e-11
Identities = 23/59 (38%), Positives = 33/59 (55%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
+ +LF G L T E L FS+Y + +++DK TN+++GFGFV FKDP
Sbjct: 12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNC 70
>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 98
Score = 60.0 bits (146), Expect = 9e-13
Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 3/67 (4%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKT---KGFGFVSFKDPQDFIRA 145
LF +L T+E L FSK + + + K GFGFV +K P+ +A
Sbjct: 7 GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66
Query: 146 NKEMNEF 152
K++
Sbjct: 67 LKQLQGH 73
Score = 60.0 bits (146), Expect = 9e-13
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 3/65 (4%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKT---KGFGFVSFKDPQDFIRA 80
LF +L T+E L FSK + + + K GFGFV +K P+ +A
Sbjct: 7 GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66
Query: 81 NKEMN 85
K++
Sbjct: 67 LKQLQ 71
>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper),
RRM2 domain, solution structure, structural genomics,
PSI-2; NMR {Homo sapiens}
Length = 108
Score = 60.0 bits (146), Expect = 1e-12
Identities = 19/74 (25%), Positives = 39/74 (52%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
K RL+ G L ++T+++L F + +++ D T ++KG+GF++F D
Sbjct: 18 NLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSD 77
Query: 139 PQDFIRANKEMNEF 152
+ +A +++N F
Sbjct: 78 SECAKKALEQLNGF 91
Score = 59.2 bits (144), Expect = 2e-12
Identities = 17/69 (24%), Positives = 37/69 (53%)
Query: 17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
RL+ G L ++T+++L F + +++ D T ++KG+GF++F D +
Sbjct: 21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSEC 80
Query: 77 FIRANKEMN 85
+A +++N
Sbjct: 81 AKKALEQLN 89
>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex,
mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB:
2x1b_A 2x1a_A 2km8_B
Length = 96
Score = 59.2 bits (144), Expect = 2e-12
Identities = 15/64 (23%), Positives = 34/64 (53%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
++ G + D T+E ++ S + K++ D +T ++KG+ F+ F+D + A +
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 149 MNEF 152
+N +
Sbjct: 64 LNGY 67
Score = 58.8 bits (143), Expect = 3e-12
Identities = 15/62 (24%), Positives = 33/62 (53%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
++ G + D T+E ++ S + K++ D +T ++KG+ F+ F+D + A +
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 84 MN 85
+N
Sbjct: 64 LN 65
>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics,
RRM domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 116
Score = 59.6 bits (145), Expect = 2e-12
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 3/76 (3%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
R +E +LF G L + T+E L + ++ V+RD + +++GFGFV+F
Sbjct: 19 RKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS 78
Query: 139 PQDFIRANKEMNEFPH 154
+ + M PH
Sbjct: 79 MAE---VDAAMAARPH 91
Score = 55.4 bits (134), Expect = 8e-11
Identities = 18/59 (30%), Positives = 31/59 (52%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
E E +LF G L + T+E L + ++ V+RD + +++GFGFV+F +
Sbjct: 23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE 81
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 60.3 bits (146), Expect = 2e-12
Identities = 11/81 (13%), Positives = 26/81 (32%), Gaps = 2/81 (2%)
Query: 74 PQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKY--PSFLKAKVVRDKRTNKTKGF 131
P + N ++ G TD+ LI+ ++ K ++ ++KG+
Sbjct: 42 PAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGY 101
Query: 132 GFVSFKDPQDFIRANKEMNEF 152
V + + +
Sbjct: 102 AEVVVASENSVHKLLELLPGK 122
Score = 58.0 bits (140), Expect = 2e-11
Identities = 9/65 (13%), Positives = 23/65 (35%), Gaps = 2/65 (3%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKY--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
++ G TD+ LI+ ++ K ++ ++KG+ V +
Sbjct: 56 AAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKL 115
Query: 81 NKEMN 85
+ +
Sbjct: 116 LELLP 120
>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 58.8 bits (143), Expect = 3e-12
Identities = 17/72 (23%), Positives = 32/72 (44%)
Query: 80 ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
+ + L L T++ L FS + L +V +D +T +KGFGFV F +
Sbjct: 8 VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEY 67
Query: 140 QDFIRANKEMNE 151
+ ++ + +
Sbjct: 68 ETQVKVMSQRHM 79
Score = 56.9 bits (138), Expect = 2e-11
Identities = 17/68 (25%), Positives = 31/68 (45%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+ L L T++ L FS + L +V +D +T +KGFGFV F + +
Sbjct: 11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 70
Query: 78 IRANKEMN 85
++ + +
Sbjct: 71 VKVMSQRH 78
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 58.5 bits (142), Expect = 3e-12
Identities = 11/72 (15%), Positives = 28/72 (38%), Gaps = 2/72 (2%)
Query: 25 LFCGDLGNDVTDELLIRTFSKY--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
+ ++ + ++ S Y + ++++DK+T + +GF FV D + +
Sbjct: 12 IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71
Query: 83 EMNDDFRLFCGD 94
+ D
Sbjct: 72 ILQSLHPPLKID 83
Score = 57.7 bits (140), Expect = 6e-12
Identities = 11/72 (15%), Positives = 28/72 (38%), Gaps = 2/72 (2%)
Query: 90 LFCGDLGNDVTDELLIRTFSKY--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
+ ++ + ++ S Y + ++++DK+T + +GF FV D + +
Sbjct: 12 IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71
Query: 148 EMNEFPHLFVGD 159
+ D
Sbjct: 72 ILQSLHPPLKID 83
>2cqd_A RNA-binding region containing protein 1; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 116
Score = 58.8 bits (143), Expect = 4e-12
Identities = 22/68 (32%), Positives = 36/68 (52%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+D ++F G L TD L + F + +A V+ D++T K++G+GFV+ D
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 78 IRANKEMN 85
RA K+ N
Sbjct: 73 ERACKDPN 80
Score = 57.3 bits (139), Expect = 2e-11
Identities = 21/71 (29%), Positives = 37/71 (52%)
Query: 80 ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
+++ ++F G L TD L + F + +A V+ D++T K++G+GFV+ D
Sbjct: 10 GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR 69
Query: 140 QDFIRANKEMN 150
RA K+ N
Sbjct: 70 AAAERACKDPN 80
>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens}
Length = 95
Score = 58.3 bits (142), Expect = 4e-12
Identities = 18/64 (28%), Positives = 37/64 (57%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
L+ G L ++T+++L F + +++D T ++KG+GF++F D + RA ++
Sbjct: 7 GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
Query: 149 MNEF 152
+N F
Sbjct: 67 LNGF 70
Score = 57.6 bits (140), Expect = 6e-12
Identities = 17/62 (27%), Positives = 36/62 (58%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
L+ G L ++T+++L F + +++D T ++KG+GF++F D + RA ++
Sbjct: 7 GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
Query: 84 MN 85
+N
Sbjct: 67 LN 68
>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition
motif, RRM, RNA binding domain, RBD, RNP, structural
genomics; NMR {Mus musculus} SCOP: d.58.7.1
Length = 99
Score = 58.0 bits (141), Expect = 5e-12
Identities = 21/62 (33%), Positives = 32/62 (51%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
RLF +L ++E L + FS Y + D T K KGF FV+F P+ ++A E
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 84 MN 85
++
Sbjct: 70 VD 71
Score = 58.0 bits (141), Expect = 5e-12
Identities = 21/62 (33%), Positives = 32/62 (51%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
RLF +L ++E L + FS Y + D T K KGF FV+F P+ ++A E
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 149 MN 150
++
Sbjct: 70 VD 71
>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition
motif, RRM, RNA binding domain, RBD, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 58.5 bits (142), Expect = 6e-12
Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 1/72 (1%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
A + +F +L V + L FS ++A ++ D + K++G G V+F+
Sbjct: 7 GALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQ 65
Query: 139 PQDFIRANKEMN 150
+ ++A N
Sbjct: 66 SIEAVQAISMFN 77
Score = 58.1 bits (141), Expect = 7e-12
Identities = 15/66 (22%), Positives = 30/66 (45%), Gaps = 1/66 (1%)
Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
+F +L V + L FS ++A ++ D + K++G G V+F+ + ++
Sbjct: 13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAVQ 71
Query: 80 ANKEMN 85
A N
Sbjct: 72 AISMFN 77
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA
complex, RRM, RBD, RNA binding protein- complex; NMR
{Mus musculus}
Length = 109
Score = 57.3 bits (139), Expect = 1e-11
Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 4/83 (4%)
Query: 73 DPQDFIRANKEMNDDFR-LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGF 131
+ M +F G L T E L F ++ + V+RD T +++GF
Sbjct: 10 HSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGF 69
Query: 132 GFVSFKDPQDFIRANKEMNEFPH 154
GFV+F D +K + + H
Sbjct: 70 GFVTFMDQAG---VDKVLAQSRH 89
Score = 53.4 bits (129), Expect = 4e-10
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 3/71 (4%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+ ++F G L T E L F ++ + V+RD T +++GFGFV+F D
Sbjct: 21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG- 79
Query: 78 IRANKEMNDDF 88
+K +
Sbjct: 80 --VDKVLAQSR 88
>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 99
Score = 56.8 bits (138), Expect = 2e-11
Identities = 16/79 (20%), Positives = 37/79 (46%), Gaps = 3/79 (3%)
Query: 80 ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
+ + ++F G + ++ + L F K+ + ++ D + +GFGF++F+D
Sbjct: 3 SGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDE 62
Query: 140 QDFIRANKEMNEFPHLFVG 158
Q ++ +N H +G
Sbjct: 63 QS---VDQAVNMHFHDIMG 78
Score = 56.0 bits (136), Expect = 3e-11
Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 3/76 (3%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
++F G + ++ + L F K+ + ++ D + +GFGF++F+D Q
Sbjct: 6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQS- 64
Query: 78 IRANKEMNDDFRLFCG 93
++ +N F G
Sbjct: 65 --VDQAVNMHFHDIMG 78
>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
Length = 102
Score = 56.9 bits (138), Expect = 2e-11
Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+ LF L D T+E L +F ++A++V D+ T +KGFGFV F +D
Sbjct: 11 RSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDA 67
Query: 78 IRANKEMND 86
A + M D
Sbjct: 68 KAAKEAMED 76
Score = 56.5 bits (137), Expect = 2e-11
Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 3/70 (4%)
Query: 81 NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
N LF L D T+E L +F ++A++V D+ T +KGFGFV F +
Sbjct: 9 NARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEE 65
Query: 141 DFIRANKEMN 150
D A + M
Sbjct: 66 DAKAAKEAME 75
>1x5o_A RNA binding motif, single-stranded interacting protein 1;
structure genomics, RRM domain, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 56.9 bits (138), Expect = 2e-11
Identities = 9/68 (13%), Positives = 28/68 (41%), Gaps = 1/68 (1%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
++++ L+ +L + ++ L + + +++RD + ++G GF + +
Sbjct: 21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKC 79
Query: 78 IRANKEMN 85
N
Sbjct: 80 EAVIGHFN 87
Score = 56.5 bits (137), Expect = 3e-11
Identities = 9/61 (14%), Positives = 24/61 (39%), Gaps = 1/61 (1%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ +L + ++ L + + +++RD + ++G GF + +
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHF 86
Query: 150 N 150
N
Sbjct: 87 N 87
>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition
motif, C-terminal helix, N-terminal helix, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 56.1 bits (136), Expect = 3e-11
Identities = 19/68 (27%), Positives = 37/68 (54%)
Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
D + +F G++ + T+E L FS+ + ++V D+ T K KG+GF ++D + +
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64
Query: 79 RANKEMND 86
A + +N
Sbjct: 65 SAMRNLNG 72
Score = 55.7 bits (135), Expect = 5e-11
Identities = 18/64 (28%), Positives = 35/64 (54%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+F G++ + T+E L FS+ + ++V D+ T K KG+GF ++D + + A +
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 149 MNEF 152
+N
Sbjct: 70 LNGR 73
>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural
genomi center for structural genomics, JCSG, protein
structure INI PSI-biology; 2.54A {Homo sapiens} PDB:
1no8_A
Length = 107
Score = 56.1 bits (136), Expect = 3e-11
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+L +L V+D + F+++ + KA V D R+ ++ G V F+ D ++A K+
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 89
Query: 149 MNEFP 153
N P
Sbjct: 90 YNGVP 94
Score = 56.1 bits (136), Expect = 3e-11
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+L +L V+D + F+++ + KA V D R+ ++ G V F+ D ++A K+
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 89
Query: 84 MN 85
N
Sbjct: 90 YN 91
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 55.2 bits (134), Expect = 4e-11
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 3/66 (4%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
++F G L T E L F ++ + V+RD T +++GFGFV+F D +K
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG---VDKV 58
Query: 149 MNEFPH 154
+ + H
Sbjct: 59 LAQSRH 64
Score = 52.5 bits (127), Expect = 4e-10
Identities = 18/53 (33%), Positives = 28/53 (52%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
++F G L T E L F ++ + V+RD T +++GFGFV+F D
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG 54
>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A
{Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A
Length = 102
Score = 55.7 bits (135), Expect = 4e-11
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+F G + + + + F++Y S + K++ D RT +KG+GFVSF + D + +
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 149 MNEF 152
F
Sbjct: 70 QINF 73
Score = 53.8 bits (130), Expect = 3e-10
Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+F G + + + + F++Y S + K++ D RT +KG+GFVSF + D + +
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 84 MND 86
+
Sbjct: 70 QIN 72
>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 55.4 bits (134), Expect = 6e-11
Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 2/72 (2%)
Query: 81 NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
++ + RL ++ D L + F ++ L +++ ++R + KGFGFV+F++
Sbjct: 9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSA 66
Query: 141 DFIRANKEMNEF 152
D RA ++++
Sbjct: 67 DADRAREKLHGT 78
Score = 53.8 bits (130), Expect = 2e-10
Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
RL ++ D L + F ++ L +++ ++R + KGFGFV+F++ D RA ++
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADRAREK 74
Query: 84 MN 85
++
Sbjct: 75 LH 76
>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 93
Score = 54.9 bits (133), Expect = 7e-11
Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 6/68 (8%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+L+ G+L VT + L + F K+ + G+ FV + D IRA +
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDR------KLPLAGQVLLKSGYAFVDYPDQNWAIRAIET 63
Query: 84 MNDDFRLF 91
++ L
Sbjct: 64 LSGKVELH 71
Score = 53.4 bits (129), Expect = 2e-10
Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 6/68 (8%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+L+ G+L VT + L + F K+ + G+ FV + D IRA +
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDR------KLPLAGQVLLKSGYAFVDYPDQNWAIRAIET 63
Query: 149 MNEFPHLF 156
++ L
Sbjct: 64 LSGKVELH 71
>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA
processing, mRNA splicing, transport, nucleus,
RNA-binding, spliceosome, transport; NMR {Mus musculus}
Length = 124
Score = 55.8 bits (135), Expect = 7e-11
Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+L +L V+D + F+++ + KA V D R+ ++ G V F+ D ++A K+
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQ 95
Query: 149 MNEFP 153
P
Sbjct: 96 YKGVP 100
Score = 55.5 bits (134), Expect = 1e-10
Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+L +L V+D + F+++ + KA V D R+ ++ G V F+ D ++A K+
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQ 95
Query: 84 MN 85
Sbjct: 96 YK 97
>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP
domain, MIF4G domain, RNA maturation, RNA export,
nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP:
d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B
3fey_B 1h6k_X
Length = 156
Score = 56.4 bits (136), Expect = 8e-11
Identities = 19/70 (27%), Positives = 28/70 (40%)
Query: 81 NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
K + L+ G+L T+E + FSK K + DK GF FV +
Sbjct: 33 EKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRA 92
Query: 141 DFIRANKEMN 150
D A + +N
Sbjct: 93 DAENAMRYIN 102
Score = 55.6 bits (134), Expect = 1e-10
Identities = 18/62 (29%), Positives = 26/62 (41%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
L+ G+L T+E + FSK K + DK GF FV + D A +
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 84 MN 85
+N
Sbjct: 101 IN 102
>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition
motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 99
Score = 55.0 bits (133), Expect = 8e-11
Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 6/75 (8%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
K RLF G+L D+T+E + + F KY + + +D KGFGF+ +
Sbjct: 7 GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLET 60
Query: 139 PQDFIRANKEMNEFP 153
A E++ P
Sbjct: 61 RTLAEIAKVELDNMP 75
Score = 54.6 bits (132), Expect = 1e-10
Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 6/69 (8%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
RLF G+L D+T+E + + F KY + + +D KGFGF+ +
Sbjct: 11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLA 64
Query: 78 IRANKEMND 86
A E+++
Sbjct: 65 EIAKVELDN 73
>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain,
poly(A) site recognition, RNA, nuclear, RNA BIND
protein; 2.70A {Homo sapiens} PDB: 3p6y_C
Length = 90
Score = 54.5 bits (132), Expect = 9e-11
Identities = 13/66 (19%), Positives = 22/66 (33%), Gaps = 2/66 (3%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKY--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
L+ G+L TDE L L+ K ++ ++KGF V +
Sbjct: 2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61
Query: 81 NKEMND 86
+
Sbjct: 62 MDLLPK 67
Score = 54.5 bits (132), Expect = 1e-10
Identities = 13/66 (19%), Positives = 23/66 (34%), Gaps = 2/66 (3%)
Query: 88 FRLFCGDLGNDVTDELLIRTFSKY--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
L+ G+L TDE L L+ K ++ ++KGF V +
Sbjct: 2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61
Query: 146 NKEMNE 151
+ +
Sbjct: 62 MDLLPK 67
>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related
protein, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 55.0 bits (133), Expect = 1e-10
Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 6/65 (9%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
++CG + + +TD+L+ +TFS + ++ +V + KG+ FV F + A
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVS 80
Query: 149 MNEFP 153
+N
Sbjct: 81 VNGTT 85
Score = 53.9 bits (130), Expect = 3e-10
Identities = 16/68 (23%), Positives = 33/68 (48%), Gaps = 6/68 (8%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+ ++CG + + +TD+L+ +TFS + ++ +V + KG+ FV F +
Sbjct: 21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESA 74
Query: 78 IRANKEMN 85
A +N
Sbjct: 75 AHAIVSVN 82
>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 54.8 bits (132), Expect = 1e-10
Identities = 15/80 (18%), Positives = 28/80 (35%), Gaps = 2/80 (2%)
Query: 16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKR-TNKTKGFGFVSFKD 73
+ + RLF G + E ++ +K L V K +GF FV ++
Sbjct: 2 SSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYES 61
Query: 74 PQDFIRANKEMNDDFRLFCG 93
+ A +++ G
Sbjct: 62 HRAAAMARRKLMPGRIQLWG 81
Score = 49.8 bits (119), Expect = 1e-08
Identities = 15/72 (20%), Positives = 26/72 (36%), Gaps = 2/72 (2%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRAN 146
RLF G + E ++ +K L V K +GF FV ++ + A
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69
Query: 147 KEMNEFPHLFVG 158
+++ G
Sbjct: 70 RKLMPGRIQLWG 81
>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing,
mRNA splicing, mRNA transport, nonsense-mediated mRNA
decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB:
2j0q_D*
Length = 126
Score = 55.1 bits (133), Expect = 2e-10
Identities = 14/62 (22%), Positives = 29/62 (46%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
LF + + T+E + F++Y + D+RT KG+ V ++ ++ A +
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83
Query: 84 MN 85
+N
Sbjct: 84 LN 85
Score = 55.1 bits (133), Expect = 2e-10
Identities = 14/62 (22%), Positives = 29/62 (46%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
LF + + T+E + F++Y + D+RT KG+ V ++ ++ A +
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83
Query: 149 MN 150
+N
Sbjct: 84 LN 85
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 54.2 bits (131), Expect = 2e-10
Identities = 14/65 (21%), Positives = 31/65 (47%)
Query: 86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
+ + LF + + T+E + F++Y + D+RT KG+ V ++ ++ A
Sbjct: 22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81
Query: 146 NKEMN 150
+ +N
Sbjct: 82 MEGLN 86
Score = 54.2 bits (131), Expect = 2e-10
Identities = 14/63 (22%), Positives = 30/63 (47%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
+ LF + + T+E + F++Y + D+RT KG+ V ++ ++ A +
Sbjct: 24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83
Query: 83 EMN 85
+N
Sbjct: 84 GLN 86
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 53.7 bits (130), Expect = 2e-10
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 2/73 (2%)
Query: 80 ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
+ + ++F +L D T ++L F++ L A + + K+KG G V F+ P
Sbjct: 1 GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESP 58
Query: 140 QDFIRANKEMNEF 152
+ RA + MN
Sbjct: 59 EVAERACRMMNGM 71
Score = 52.6 bits (127), Expect = 5e-10
Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
++F +L D T ++L F++ L A + + K+KG G V F+ P+ RA +
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRM 67
Query: 84 MN 85
MN
Sbjct: 68 MN 69
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 54.2 bits (131), Expect = 2e-10
Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 79 RANKEMNDDF-RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 137
N E RL ++ D L + F ++ L +++ ++R +KGFGFV+F+
Sbjct: 20 HMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFE 77
Query: 138 DPQDFIRANKEMNEF 152
+ D RA ++++
Sbjct: 78 NSADADRAREKLHGT 92
Score = 53.9 bits (130), Expect = 3e-10
Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
RL ++ D L + F ++ L +++ ++R +KGFGFV+F++ D RA ++
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREK 88
Query: 84 MN 85
++
Sbjct: 89 LH 90
>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar
mRNA localization, translation; 1.90A {Drosophila
melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A
Length = 165
Score = 55.2 bits (133), Expect = 2e-10
Identities = 12/62 (19%), Positives = 27/62 (43%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
LF + + ++ + F Y + D+RT +KG+ V ++ + + A +
Sbjct: 74 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133
Query: 84 MN 85
+N
Sbjct: 134 LN 135
Score = 55.2 bits (133), Expect = 2e-10
Identities = 12/62 (19%), Positives = 27/62 (43%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
LF + + ++ + F Y + D+RT +KG+ V ++ + + A +
Sbjct: 74 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133
Query: 149 MN 150
+N
Sbjct: 134 LN 135
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 52.9 bits (128), Expect = 2e-10
Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 3/66 (4%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
++F G L + T E + F ++ A ++ DK TN+ +GFGFV+F+ K
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDI---VEKV 57
Query: 149 MNEFPH 154
H
Sbjct: 58 CEIHFH 63
Score = 52.1 bits (126), Expect = 5e-10
Identities = 17/52 (32%), Positives = 29/52 (55%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
++F G L + T E + F ++ A ++ DK TN+ +GFGFV+F+
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52
>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A
Length = 282
Score = 56.4 bits (135), Expect = 3e-10
Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 11/89 (12%)
Query: 89 RLFCGDLGNDVTDE----LLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
++ +L + + L FS++ L V R+ K +G FV FK+
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIFKEVSSATN 67
Query: 145 ANKEMNEFP----HLFVGDLKTRSSITLK 169
A + M FP + + KT S I K
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 96
Score = 54.9 bits (131), Expect = 1e-09
Identities = 16/74 (21%), Positives = 27/74 (36%), Gaps = 9/74 (12%)
Query: 24 RLFCGDLGNDVTDE----LLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
++ +L + + L FS++ L V R+ K +G FV FK+
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIFKEVSSATN 67
Query: 80 ANKEMNDDFRLFCG 93
A + M F
Sbjct: 68 ALRSMQG--FPFYD 79
Score = 50.6 bits (120), Expect = 3e-08
Identities = 14/83 (16%), Positives = 29/83 (34%), Gaps = 5/83 (6%)
Query: 71 FKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKG 130
+ E + LF +L + + +L F+++P F + ++V +
Sbjct: 191 MPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HD 245
Query: 131 FGFVSFKDPQDFIRANKEMNEFP 153
FV F + A + F
Sbjct: 246 IAFVEFDNEVQAGAARDALQGFK 268
Score = 49.5 bits (117), Expect = 9e-08
Identities = 11/60 (18%), Positives = 24/60 (40%), Gaps = 5/60 (8%)
Query: 26 FCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
F +L + + +L F+++P F + ++V + FV F + A +
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQ 265
>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A)
binding, structural genomics, protein structure
initiative, PSI-2; NMR {Xenopus laevis}
Length = 124
Score = 54.3 bits (131), Expect = 3e-10
Identities = 21/100 (21%), Positives = 40/100 (40%), Gaps = 3/100 (3%)
Query: 52 AKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKY 111
A ++ + T G + PQ K+ D ++ G++ T + L FS
Sbjct: 3 APCMQTTHSKMTAGAY--TEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC 60
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNE 151
S + ++ DK + KG+ ++ F + A M+E
Sbjct: 61 GSINRITILCDKFSGHPKGYAYIEFAERNSVDAA-VAMDE 99
Score = 49.3 bits (118), Expect = 2e-08
Identities = 13/69 (18%), Positives = 31/69 (44%), Gaps = 1/69 (1%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
++ + ++ G++ T + L FS S + ++ DK + KG+ ++ F +
Sbjct: 32 KEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSV 91
Query: 78 IRANKEMND 86
A M++
Sbjct: 92 DAA-VAMDE 99
>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 96
Score = 52.7 bits (127), Expect = 5e-10
Identities = 13/74 (17%), Positives = 29/74 (39%), Gaps = 5/74 (6%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+K++ L +L ++T++ L F ++ + K+KG ++ FK
Sbjct: 8 CTSKKVRAARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKS 62
Query: 139 PQDFIRANKEMNEF 152
D + +E
Sbjct: 63 EADAEKNLEEKQGA 76
Score = 52.3 bits (126), Expect = 8e-10
Identities = 12/72 (16%), Positives = 27/72 (37%), Gaps = 5/72 (6%)
Query: 14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
+ + L +L ++T++ L F ++ + K+KG ++ FK
Sbjct: 8 CTSKKVRAARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKS 62
Query: 74 PQDFIRANKEMN 85
D + +E
Sbjct: 63 EADAEKNLEEKQ 74
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 52.7 bits (127), Expect = 7e-10
Identities = 16/76 (21%), Positives = 31/76 (40%), Gaps = 1/76 (1%)
Query: 10 SSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFV 69
SS + + +LF L T E L + + ++V + R K KG +V
Sbjct: 5 SSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYV 63
Query: 70 SFKDPQDFIRANKEMN 85
+++ +A +M+
Sbjct: 64 EYENESQASQAVMKMD 79
Score = 51.5 bits (124), Expect = 2e-09
Identities = 14/62 (22%), Positives = 27/62 (43%), Gaps = 1/62 (1%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+LF L T E L + + ++V + R K KG +V +++ +A +
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYENESQASQAVMK 77
Query: 149 MN 150
M+
Sbjct: 78 MD 79
>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding
protein, hnRNP, telomere, DNA-binding protein, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wtb_A 1x0f_A
Length = 75
Score = 51.3 bits (124), Expect = 9e-10
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
++F G L D +E + F + ++ D +TNK +GF F++FK+ + K
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEP---VKKI 57
Query: 149 MNEFPHLFVG 158
M + H
Sbjct: 58 MEKKYHNVGL 67
Score = 51.0 bits (123), Expect = 1e-09
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 3/70 (4%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
++F G L D +E + F + ++ D +TNK +GF F++FK+ + K
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEP---VKKI 57
Query: 84 MNDDFRLFCG 93
M +
Sbjct: 58 MEKKYHNVGL 67
>4a8x_A RNA-binding protein with serine-rich domain 1; transcription,
splicing, RNA processing, nonsense mediated D NMD, HDAC,
histone deacetylation; 1.90A {Homo sapiens}
Length = 88
Score = 51.8 bits (125), Expect = 1e-09
Identities = 15/65 (23%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRANK 147
++ G L +VT + ++ FS Y + ++ + +KG+ +V F++P + +A K
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 148 EMNEF 152
M+
Sbjct: 66 HMDGG 70
Score = 51.0 bits (123), Expect = 2e-09
Identities = 15/63 (23%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRANK 82
++ G L +VT + ++ FS Y + ++ + +KG+ +V F++P + +A K
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 83 EMN 85
M+
Sbjct: 66 HMD 68
>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing,
protein complex, EXON junct complex, signaling protein;
1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB:
2hyi_B* 2j0s_D* 2xb2_D*
Length = 110
Score = 51.9 bits (125), Expect = 1e-09
Identities = 12/62 (19%), Positives = 27/62 (43%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
LF + + ++ + F Y + D+RT +KG+ V ++ + + A +
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 84 MN 85
+N
Sbjct: 88 LN 89
Score = 51.9 bits (125), Expect = 1e-09
Identities = 12/62 (19%), Positives = 27/62 (43%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
LF + + ++ + F Y + D+RT +KG+ V ++ + + A +
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 149 MN 150
+N
Sbjct: 88 LN 89
>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 51.9 bits (125), Expect = 1e-09
Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 1/64 (1%)
Query: 18 EDENDFR-LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
+E D R +FC L + L FS +++ D+ + ++KG +V F + Q
Sbjct: 20 PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 79
Query: 77 FIRA 80
A
Sbjct: 80 VPLA 83
Score = 50.8 bits (122), Expect = 5e-09
Identities = 15/66 (22%), Positives = 27/66 (40%)
Query: 80 ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
+ E D +FC L + L FS +++ D+ + ++KG +V F +
Sbjct: 18 LSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEI 77
Query: 140 QDFIRA 145
Q A
Sbjct: 78 QSVPLA 83
>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA
splicing, adenine, mRNA processing, nucleus,
phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo
sapiens} PDB: 2f9d_A 2f9j_A 2fho_B
Length = 115
Score = 51.6 bits (124), Expect = 2e-09
Identities = 20/76 (26%), Positives = 34/76 (44%), Gaps = 5/76 (6%)
Query: 78 IRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 137
IR E+N L+ +L +T E + F KY + +R T +T+G +V ++
Sbjct: 1 IRLPPEVNR--ILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYE 55
Query: 138 DPQDFIRANKEMNEFP 153
D D A ++ F
Sbjct: 56 DIFDAKNAVDHLSGFN 71
Score = 47.4 bits (113), Expect = 8e-08
Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 3/62 (4%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ +L +T E + F KY + +R T +T+G +V ++D D A +
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 85 ND 86
+
Sbjct: 68 SG 69
>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural
genomics, joint center for struc genomics, JCSG,
protein structure initiative; HET: PGE; 1.95A {Homo
sapiens} PDB: 3b4d_A 3b4m_A
Length = 89
Score = 51.0 bits (123), Expect = 2e-09
Identities = 15/72 (20%), Positives = 32/72 (44%), Gaps = 2/72 (2%)
Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
+ + ++ G++ T E L F S + ++ DK + KGF ++ F D +
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 79 RANKEMND-DFR 89
+ +++ FR
Sbjct: 63 TS-LALDESLFR 73
Score = 51.0 bits (123), Expect = 2e-09
Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 1/66 (1%)
Query: 86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
D ++ G++ T E L F S + ++ DK + KGF ++ F D + +
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64
Query: 146 NKEMNE 151
++E
Sbjct: 65 -LALDE 69
>2la6_A RNA-binding protein FUS; structural genomics, northeast
structural genomics consortiu PSI-biology, protein
structure initiative, RNA recognition; NMR {Homo
sapiens}
Length = 99
Score = 51.2 bits (123), Expect = 2e-09
Identities = 19/75 (25%), Positives = 27/75 (36%), Gaps = 9/75 (12%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKY--------PSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
+F LG +VT E + F + + D+ T K KG VSF DP
Sbjct: 15 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74
Query: 76 DFIRANKEMND-DFR 89
A + +F
Sbjct: 75 SAKAAIDWFDGKEFS 89
Score = 50.4 bits (121), Expect = 5e-09
Identities = 19/80 (23%), Positives = 29/80 (36%), Gaps = 8/80 (10%)
Query: 80 ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKY--------PSFLKAKVVRDKRTNKTKGF 131
+ +D+ +F LG +VT E + F + + D+ T K KG
Sbjct: 6 HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE 65
Query: 132 GFVSFKDPQDFIRANKEMNE 151
VSF DP A +
Sbjct: 66 ATVSFDDPPSAKAAIDWFDG 85
>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
PDB: 2dnk_A 2dno_A
Length = 105
Score = 51.1 bits (123), Expect = 2e-09
Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 1/68 (1%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
D +LF G L ++E ++R F + + V+R +KG FV F +
Sbjct: 11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEA 69
Query: 78 IRANKEMN 85
A ++
Sbjct: 70 QAAIHALH 77
Score = 50.7 bits (122), Expect = 3e-09
Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 1/71 (1%)
Query: 80 ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
+ D +LF G L ++E ++R F + + V+R +KG FV F
Sbjct: 8 SESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSH 66
Query: 140 QDFIRANKEMN 150
+ A ++
Sbjct: 67 TEAQAAIHALH 77
>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A
Length = 103
Score = 51.1 bits (123), Expect = 3e-09
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 8/70 (11%)
Query: 81 NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
+ M LF +L N VT+E+L + FS++ + K ++D + F+ F +
Sbjct: 5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERD 56
Query: 141 DFIRANKEMN 150
++A +EMN
Sbjct: 57 GAVKAMEEMN 66
Score = 50.0 bits (120), Expect = 7e-09
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 8/63 (12%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
LF +L N VT+E+L + FS++ + K ++D + F+ F + ++A +E
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEE 64
Query: 84 MND 86
MN
Sbjct: 65 MNG 67
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 51.2 bits (123), Expect = 3e-09
Identities = 19/79 (24%), Positives = 30/79 (37%), Gaps = 8/79 (10%)
Query: 82 KEMNDDFRLFCGDLGNDVTDELLIRTFSKY--------PSFLKAKVVRDKRTNKTKGFGF 133
++ +D+ +F LG +VT E + F + + D+ T K KG
Sbjct: 2 QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61
Query: 134 VSFKDPQDFIRANKEMNEF 152
VSF DP A +
Sbjct: 62 VSFDDPPSAKAAIDWFDGK 80
Score = 51.2 bits (123), Expect = 3e-09
Identities = 19/75 (25%), Positives = 27/75 (36%), Gaps = 9/75 (12%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKY--------PSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
+F LG +VT E + F + + D+ T K KG VSF DP
Sbjct: 9 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68
Query: 76 DFIRANKEMND-DFR 89
A + +F
Sbjct: 69 SAKAAIDWFDGKEFS 83
>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2,
alternate splicing factor)...; structure genomics, SURP
domain, splicing factor SF2; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 50.4 bits (121), Expect = 5e-09
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 3/67 (4%)
Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
ND R++ G+L D+ + + F KY + + + F FV F+DP+D
Sbjct: 19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG---PPFAFVEFEDPRDAE 75
Query: 79 RANKEMN 85
A +
Sbjct: 76 DAVYGRD 82
Score = 50.4 bits (121), Expect = 5e-09
Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 3/66 (4%)
Query: 85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
N+D R++ G+L D+ + + F KY + + + F FV F+DP+D
Sbjct: 20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG---PPFAFVEFEDPRDAED 76
Query: 145 ANKEMN 150
A +
Sbjct: 77 AVYGRD 82
>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A
Length = 205
Score = 52.4 bits (125), Expect = 5e-09
Identities = 19/152 (12%), Positives = 44/152 (28%), Gaps = 9/152 (5%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
N+ +F + V+ + I Y + +D ++ F +
Sbjct: 60 THLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFS------TPEQ 113
Query: 78 IRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 137
N+ + L + +VT+E + V ++ G + +
Sbjct: 114 AAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWD 173
Query: 138 DPQDFIRANKEMNEFPHLFVGDLKTRSSITLK 169
D + +N + + + TLK
Sbjct: 174 SKSDALETLGFLNHYQ---MKNPNGPYPYTLK 202
Score = 41.6 bits (97), Expect = 3e-05
Identities = 19/126 (15%), Positives = 37/126 (29%), Gaps = 7/126 (5%)
Query: 25 LFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
L L + + + F Y + K K ++ K G V D RA
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKP-----GAAMVEMADGYAVDRAITH 61
Query: 84 MNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 143
+N + +F + V+ + I Y + +D ++ F
Sbjct: 62 LN-NNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQ 120
Query: 144 RANKEM 149
+ +
Sbjct: 121 HPSNVL 126
Score = 39.7 bits (92), Expect = 1e-04
Identities = 13/65 (20%), Positives = 20/65 (30%), Gaps = 6/65 (9%)
Query: 90 LFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
L L + + + F Y + K K ++ K G V D RA
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKP-----GAAMVEMADGYAVDRAITH 61
Query: 149 MNEFP 153
+N
Sbjct: 62 LNNNF 66
>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A
Length = 229
Score = 52.3 bits (125), Expect = 6e-09
Identities = 24/181 (13%), Positives = 49/181 (27%), Gaps = 56/181 (30%)
Query: 25 LFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRT-------------------NKTK 64
L +L + VT + L F Y + K++ +K+ N K
Sbjct: 37 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHK 96
Query: 65 GFG-----FVSFKDPQDFIRANKEMNDDFR---------------------------LFC 92
G +S R +E + L
Sbjct: 97 LHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHL 156
Query: 93 GDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
++ V++E L FS +K K + + ++ ++A +++
Sbjct: 157 SNIPPSVSEEDLKVLFSSNGGVVKGFK----FFQKDRKMALIQMGSVEEAVQALIDLHNH 212
Query: 153 P 153
Sbjct: 213 D 213
Score = 48.8 bits (116), Expect = 1e-07
Identities = 14/89 (15%), Positives = 33/89 (37%), Gaps = 15/89 (16%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L ++ V++E L FS +K K + + ++ ++A ++
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFK----FFQKDRKMALIQMGSVEEAVQALIDL 209
Query: 85 NDDFRLFCGDLGNDVTDELLIR-TFSKYP 112
+ +D+ + +R +FSK
Sbjct: 210 H----------NHDLGENHHLRVSFSKST 228
>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif,
U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein;
2.50A {Homo sapiens}
Length = 143
Score = 51.0 bits (122), Expect = 6e-09
Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 5/70 (7%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKV-----VRDKRTNKTKGFGFVSFKDPQDFI 143
R++ +L V ++ L F +Y F +R + + KG F+ + +
Sbjct: 47 RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106
Query: 144 RANKEMNEFP 153
+A KE N +
Sbjct: 107 KALKEANGYV 116
Score = 48.3 bits (115), Expect = 5e-08
Identities = 15/67 (22%), Positives = 28/67 (41%), Gaps = 5/67 (7%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKV-----VRDKRTNKTKGFGFVSFKDPQDFI 78
R++ +L V ++ L F +Y F +R + + KG F+ + +
Sbjct: 47 RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106
Query: 79 RANKEMN 85
+A KE N
Sbjct: 107 KALKEAN 113
>1x5p_A Negative elongation factor E; structure genomics, RRM domain,
PARP14, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 97
Score = 49.6 bits (119), Expect = 7e-09
Identities = 14/63 (22%), Positives = 26/63 (41%), Gaps = 8/63 (12%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ G D+T LL FS + + D + + FV+++ + +A E+
Sbjct: 18 LYVY--GEDMTPTLLRGAFSPF------GNIIDLSMDPPRNCAFVTYEKMESADQAVAEL 69
Query: 150 NEF 152
N
Sbjct: 70 NGT 72
Score = 49.6 bits (119), Expect = 9e-09
Identities = 14/68 (20%), Positives = 26/68 (38%), Gaps = 8/68 (11%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
L+ G D+T LL FS + + D + + FV+++ +
Sbjct: 11 APRKGNTLYVY--GEDMTPTLLRGAFSPF------GNIIDLSMDPPRNCAFVTYEKMESA 62
Query: 78 IRANKEMN 85
+A E+N
Sbjct: 63 DQAVAELN 70
>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
Length = 101
Score = 49.6 bits (119), Expect = 7e-09
Identities = 16/62 (25%), Positives = 23/62 (37%), Gaps = 4/62 (6%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
L +L T+E L F K V + K+KG+ F+ F +D A
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKA----TFIKVPQNQNGKSKGYAFIEFASFEDAKEALNS 72
Query: 84 MN 85
N
Sbjct: 73 CN 74
Score = 49.6 bits (119), Expect = 7e-09
Identities = 16/62 (25%), Positives = 23/62 (37%), Gaps = 4/62 (6%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
L +L T+E L F K V + K+KG+ F+ F +D A
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKA----TFIKVPQNQNGKSKGYAFIEFASFEDAKEALNS 72
Query: 149 MN 150
N
Sbjct: 73 CN 74
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 49.6 bits (119), Expect = 9e-09
Identities = 10/67 (14%), Positives = 21/67 (31%), Gaps = 6/67 (8%)
Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
+ G++ + T+ LI F + L K + KG F+ + +
Sbjct: 24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAA 77
Query: 79 RANKEMN 85
+
Sbjct: 78 VCIVALA 84
Score = 48.8 bits (117), Expect = 2e-08
Identities = 12/65 (18%), Positives = 23/65 (35%), Gaps = 6/65 (9%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+ G++ + T+ LI F + L K + KG F+ + +
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVA 82
Query: 149 MNEFP 153
+ FP
Sbjct: 83 LANFP 87
>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 113
Score = 49.7 bits (119), Expect = 1e-08
Identities = 20/81 (24%), Positives = 33/81 (40%), Gaps = 9/81 (11%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKY--------PSFLKAKVVRDKRTNKTKGFGFV 69
ED ++ ++ L + VT + L F + + DK T K KG V
Sbjct: 11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 70
Query: 70 SFKDPQDFIRANKEMND-DFR 89
S++DP A + + DF+
Sbjct: 71 SYEDPPTAKAAVEWFDGKDFQ 91
Score = 48.6 bits (116), Expect = 3e-08
Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 8/79 (10%)
Query: 81 NKEMNDDFRLFCGDLGNDVTDELLIRTFSKY--------PSFLKAKVVRDKRTNKTKGFG 132
E +D+ ++ L + VT + L F + + DK T K KG
Sbjct: 9 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 68
Query: 133 FVSFKDPQDFIRANKEMNE 151
VS++DP A + +
Sbjct: 69 TVSYEDPPTAKAAVEWFDG 87
>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding
proteins, RNA binding protein/SS-DNA binding protein
complex; NMR {Helicobacter pylori}
Length = 90
Score = 48.7 bits (117), Expect = 1e-08
Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
++ G+L T E + FS++ K++ D+ T K KGFGFV ++ + A +
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61
Query: 84 MND 86
+++
Sbjct: 62 LDN 64
Score = 48.7 bits (117), Expect = 2e-08
Identities = 16/50 (32%), Positives = 27/50 (54%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
++ G+L T E + FS++ K++ D+ T K KGFGFV ++
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE 52
>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 99
Score = 48.8 bits (117), Expect = 1e-08
Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 6/62 (9%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L+ +L ++E++ + F+ K +R K + + FV F + +D + A K +
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNI------KPGAVERVKKIRDYAFVHFSNREDAVEAMKAL 71
Query: 85 ND 86
N
Sbjct: 72 NG 73
Score = 48.8 bits (117), Expect = 2e-08
Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ +L ++E++ + F+ K +R K + + FV F + +D + A K +
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNI------KPGAVERVKKIRDYAFVHFSNREDAVEAMKAL 71
Query: 150 N 150
N
Sbjct: 72 N 72
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 48.8 bits (117), Expect = 2e-08
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+++ G+LG L R FS Y + R+ GF FV F+DP+D A +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAVRG 56
Query: 84 MN 85
++
Sbjct: 57 LD 58
Score = 48.8 bits (117), Expect = 2e-08
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+++ G+LG L R FS Y + R+ GF FV F+DP+D A +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAVRG 56
Query: 149 MN 150
++
Sbjct: 57 LD 58
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 48.8 bits (117), Expect = 2e-08
Identities = 18/84 (21%), Positives = 32/84 (38%), Gaps = 10/84 (11%)
Query: 67 GFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN 126
G V + + N RLF DV + L F + + K++
Sbjct: 13 GLVPRGSHMHHRQEGELSNT--RLFVRPFPLDVQESELNEIFGPFGPMKEVKIL------ 64
Query: 127 KTKGFGFVSFKDPQDFIRANKEMN 150
GF FV F++ + +A +E++
Sbjct: 65 --NGFAFVEFEEAESAAKAIEEVH 86
Score = 47.3 bits (113), Expect = 7e-08
Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 8/63 (12%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
RLF DV + L F + + K++ GF FV F++ + +A +E
Sbjct: 33 RLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEE 84
Query: 84 MND 86
++
Sbjct: 85 VHG 87
>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 48.4 bits (116), Expect = 2e-08
Identities = 14/66 (21%), Positives = 27/66 (40%), Gaps = 8/66 (12%)
Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
N +++F G++ T + L F + ++ VV K + FV + D
Sbjct: 7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKA 58
Query: 80 ANKEMN 85
A ++N
Sbjct: 59 AIAQLN 64
Score = 47.6 bits (114), Expect = 4e-08
Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 8/63 (12%)
Query: 88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
+++F G++ T + L F + ++ VV K + FV + D A
Sbjct: 10 WKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIA 61
Query: 148 EMN 150
++N
Sbjct: 62 QLN 64
>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear
ribonucleoprotein, R binding domain, RNA binding
protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1
PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A*
3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P*
3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A*
...
Length = 97
Score = 48.4 bits (116), Expect = 2e-08
Identities = 21/89 (23%), Positives = 37/89 (41%), Gaps = 11/89 (12%)
Query: 89 RLFCGDLGNDVTDELLIRT----FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
++ +L + + L ++ FS++ L + R+ K +G FV FK+
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 145 ANKEMNEFP----HLFVGDLKTRSSITLK 169
A + M FP + + KT S I K
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 95
Score = 45.3 bits (108), Expect = 4e-07
Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 9/74 (12%)
Query: 24 RLFCGDLGNDVTDELLIRT----FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
++ +L + + L ++ FS++ L + R+ K +G FV FK+
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 80 ANKEMNDDFRLFCG 93
A + M F
Sbjct: 67 ALRSMQG--FPFYD 78
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 48.4 bits (116), Expect = 2e-08
Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 1/62 (1%)
Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
E + + G+L + + F S ++VRDK T+K KGF +V F +
Sbjct: 12 TEPPYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLK 70
Query: 79 RA 80
A
Sbjct: 71 EA 72
Score = 48.4 bits (116), Expect = 3e-08
Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
+ + G+L + + F S ++VRDK T+K KGF +V F + A
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEA 72
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 49.8 bits (119), Expect = 3e-08
Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+L +L V+D + F+++ + KA V D R+ ++ G V F+ D ++A K+
Sbjct: 90 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQ 148
Query: 84 MN 85
Sbjct: 149 YK 150
Score = 49.8 bits (119), Expect = 3e-08
Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+L +L V+D + F+++ + KA V D R+ ++ G V F+ D ++A K+
Sbjct: 90 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQ 148
Query: 149 MN 150
Sbjct: 149 YK 150
>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 97
Score = 48.0 bits (115), Expect = 3e-08
Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 6/65 (9%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
RL+ G LG + + L R F ++ S V+ F ++ ++ A +
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAK 72
Query: 149 MNEFP 153
M FP
Sbjct: 73 MRGFP 77
Score = 47.6 bits (114), Expect = 5e-08
Identities = 13/62 (20%), Positives = 24/62 (38%), Gaps = 6/62 (9%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
RL+ G LG + + L R F ++ S V+ F ++ ++ A +
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAK 72
Query: 84 MN 85
M
Sbjct: 73 MR 74
>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 92
Score = 47.6 bits (114), Expect = 4e-08
Identities = 13/75 (17%), Positives = 32/75 (42%), Gaps = 10/75 (13%)
Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
+ +L G++ T++ L F +Y ++ +V+ + FV + +D +
Sbjct: 7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAV 58
Query: 79 RANKEMNDDFRLFCG 93
A + +++ F G
Sbjct: 59 EAIRGLDN--TEFQG 71
Score = 46.8 bits (112), Expect = 8e-08
Identities = 11/62 (17%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+L G++ T++ L F +Y ++ +V+ + FV + +D + A +
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRG 63
Query: 149 MN 150
++
Sbjct: 64 LD 65
>2bz2_A Negative elongation factor E; NELF E, RNA recognition motif,
alternative splicing, nuclear protein, phosphorylation,
repeat, repressor; NMR {Homo sapiens} SCOP: d.58.7.1
PDB: 2jx2_A
Length = 121
Score = 48.2 bits (115), Expect = 4e-08
Identities = 13/64 (20%), Positives = 26/64 (40%), Gaps = 8/64 (12%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
L+ G D+T LL FS + + + + + FV+++ + +A E
Sbjct: 41 TLYVY--GEDMTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAVAE 92
Query: 149 MNEF 152
+N
Sbjct: 93 LNGT 96
Score = 48.2 bits (115), Expect = 5e-08
Identities = 13/68 (19%), Positives = 26/68 (38%), Gaps = 8/68 (11%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
L+ G D+T LL FS + + + + + FV+++ +
Sbjct: 35 APRKGNTLYVY--GEDMTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESA 86
Query: 78 IRANKEMN 85
+A E+N
Sbjct: 87 DQAVAELN 94
>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*
Length = 437
Score = 49.8 bits (118), Expect = 7e-08
Identities = 17/61 (27%), Positives = 29/61 (47%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
LF + D T+ L R F Y + +V KR+ K +G+ F+ ++ +D A K
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 85 N 85
+
Sbjct: 165 D 165
Score = 49.8 bits (118), Expect = 7e-08
Identities = 17/61 (27%), Positives = 29/61 (47%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
LF + D T+ L R F Y + +V KR+ K +G+ F+ ++ +D A K
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 150 N 150
+
Sbjct: 165 D 165
>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 46.4 bits (111), Expect = 1e-07
Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 8/62 (12%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
+LF G+L + T++ + F +Y L+ ++ K +GFV +D A +
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN 61
Query: 84 MN 85
++
Sbjct: 62 LH 63
Score = 46.4 bits (111), Expect = 1e-07
Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 8/62 (12%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+LF G+L + T++ + F +Y L+ ++ K +GFV +D A +
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN 61
Query: 149 MN 150
++
Sbjct: 62 LH 63
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 46.6 bits (111), Expect = 1e-07
Identities = 16/61 (26%), Positives = 22/61 (36%)
Query: 93 GDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
V + L FSK + + D+ T KTKGF FV D + K +
Sbjct: 18 PSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGK 77
Query: 153 P 153
Sbjct: 78 R 78
Score = 46.3 bits (110), Expect = 2e-07
Identities = 16/58 (27%), Positives = 22/58 (37%)
Query: 28 GDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
V + L FSK + + D+ T KTKGF FV D + K +
Sbjct: 18 PSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75
>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA,
spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1
d.58.7.1
Length = 198
Score = 48.4 bits (115), Expect = 1e-07
Identities = 22/181 (12%), Positives = 49/181 (27%), Gaps = 56/181 (30%)
Query: 25 LFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDK------------------------- 58
L +L + VT + L F Y + K++ +K
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHK 65
Query: 59 ------RTNKTKGFGFVSFKDPQDFIRANKEMNDDF--------------------RLFC 92
R +K ++ Q+ K+ + L
Sbjct: 66 LHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHL 125
Query: 93 GDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
++ V++E L FS +K K + + ++ ++A +++
Sbjct: 126 SNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALIDLHNH 181
Query: 153 P 153
Sbjct: 182 D 182
Score = 46.8 bits (111), Expect = 5e-07
Identities = 14/90 (15%), Positives = 33/90 (36%), Gaps = 15/90 (16%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
L ++ V++E L FS +K K + + ++ ++A +
Sbjct: 122 TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALID 177
Query: 84 MNDDFRLFCGDLGNDVTDELLIR-TFSKYP 112
++ +D+ + +R +FSK
Sbjct: 178 LH----------NHDLGENHHLRVSFSKST 197
>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
Length = 85
Score = 46.1 bits (110), Expect = 1e-07
Identities = 15/73 (20%), Positives = 29/73 (39%), Gaps = 6/73 (8%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
ED+ L+ G LG+ +T+ L F ++ VV+ + F+ F Q
Sbjct: 8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAA 61
Query: 78 IRANKEMNDDFRL 90
A ++ + +
Sbjct: 62 EVAAEKSFNKLIV 74
Score = 43.4 bits (103), Expect = 1e-06
Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 6/60 (10%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L+ G LG+ +T+ L F ++ VV+ + F+ F Q A ++
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKS 68
>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 107
Score = 46.1 bits (110), Expect = 2e-07
Identities = 13/78 (16%), Positives = 28/78 (35%), Gaps = 1/78 (1%)
Query: 14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFK 72
+ + + ++ ++ + FS + ++ + T +GFGFV F
Sbjct: 7 GQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFI 66
Query: 73 DPQDFIRANKEMNDDFRL 90
QD +A + L
Sbjct: 67 TKQDAKKAFNALCHSTHL 84
Score = 44.6 bits (106), Expect = 8e-07
Identities = 14/68 (20%), Positives = 26/68 (38%), Gaps = 1/68 (1%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRANK 147
++ ++ + FS + ++ + T +GFGFV F QD +A
Sbjct: 17 KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76
Query: 148 EMNEFPHL 155
+ HL
Sbjct: 77 ALCHSTHL 84
>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif,
RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 111
Score = 45.2 bits (107), Expect = 5e-07
Identities = 11/70 (15%), Positives = 27/70 (38%), Gaps = 6/70 (8%)
Query: 90 LFCGDLGNDVTDELLIRT---FSKYPSFLKAKVVRDKRTNKTK---GFGFVSFKDPQDFI 143
+F L + D +++ F K+ K + ++ +V++ +D +
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 144 RANKEMNEFP 153
RA + +N
Sbjct: 78 RAIQCVNNVV 87
Score = 44.5 bits (105), Expect = 9e-07
Identities = 11/67 (16%), Positives = 27/67 (40%), Gaps = 6/67 (8%)
Query: 25 LFCGDLGNDVTDELLIRT---FSKYPSFLKAKVVRDKRTNKTK---GFGFVSFKDPQDFI 78
+F L + D +++ F K+ K + ++ +V++ +D +
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 79 RANKEMN 85
RA + +N
Sbjct: 78 RAIQCVN 84
>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B;
protein biosynthesis, RNA recognition motif, RNA
binding domain, RRM, RBD, RNP; NMR {Homo sapiens}
Length = 100
Score = 44.9 bits (107), Expect = 5e-07
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRT-NKTKGFGFVSFKDPQDFIRA 80
+ F G+L DVT+E + F + ++ R+ + KGFG+ F+D + A
Sbjct: 20 YTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 77
Score = 44.9 bits (107), Expect = 5e-07
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRT-NKTKGFGFVSFKDPQDFIRA 145
+ F G+L DVT+E + F + ++ R+ + KGFG+ F+D + A
Sbjct: 20 YTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 77
>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions,
RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus
musculus}
Length = 89
Score = 44.5 bits (106), Expect = 6e-07
Identities = 15/73 (20%), Positives = 28/73 (38%), Gaps = 5/73 (6%)
Query: 80 ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
++ + ++F G D+T E L + F +Y + + + R F FV+F D
Sbjct: 4 SHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFR-----AFAFVTFADD 58
Query: 140 QDFIRANKEMNEF 152
+ E
Sbjct: 59 KVAQSLCGEDLII 71
Score = 44.5 bits (106), Expect = 6e-07
Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 5/58 (8%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
+ ++F G D+T E L + F +Y + + + R F FV+F D +
Sbjct: 7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFR-----AFAFVTFADDK 59
>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA
recognition motif, RRM, RNA binding domain, RBD, RNP,
structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 44.6 bits (106), Expect = 8e-07
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRA 80
+ F G+L DVT+E + F + ++ R+ + KGFG+ F+D + A
Sbjct: 16 YTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 73
Score = 44.6 bits (106), Expect = 8e-07
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRA 145
+ F G+L DVT+E + F + ++ R+ + KGFG+ F+D + A
Sbjct: 16 YTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 73
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 44.5 bits (105), Expect = 1e-06
Identities = 11/89 (12%), Positives = 26/89 (29%), Gaps = 11/89 (12%)
Query: 89 RLFCGDLGNDVTDELLIRT----FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
+ ++ +V E L S L + ++ G ++ F +
Sbjct: 31 VVLITNINPEVPKEKLQALLYALASSQGDILD---IVVDLSDDNSGKAYIVFATQESAQA 87
Query: 145 ANKEMNEFP----HLFVGDLKTRSSITLK 169
+ +P L + +T S +
Sbjct: 88 FVEAFQGYPFQGNPLVITFSETPQSQVAE 116
Score = 42.2 bits (99), Expect = 8e-06
Identities = 7/67 (10%), Positives = 18/67 (26%), Gaps = 7/67 (10%)
Query: 24 RLFCGDLGNDVTDELLIRT----FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
+ ++ +V E L S L + ++ G ++ F +
Sbjct: 31 VVLITNINPEVPKEKLQALLYALASSQGDILD---IVVDLSDDNSGKAYIVFATQESAQA 87
Query: 80 ANKEMND 86
+
Sbjct: 88 FVEAFQG 94
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 43.6 bits (103), Expect = 1e-06
Identities = 9/70 (12%), Positives = 22/70 (31%), Gaps = 3/70 (4%)
Query: 83 EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 142
+ +L ++ + E+L +Y + V V++
Sbjct: 11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS---ETAVVNVTYSSKDQA 67
Query: 143 IRANKEMNEF 152
+A ++N F
Sbjct: 68 RQALDKLNGF 77
Score = 43.2 bits (102), Expect = 2e-06
Identities = 8/68 (11%), Positives = 22/68 (32%), Gaps = 3/68 (4%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+ + +L ++ + E+L +Y + V V++
Sbjct: 11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS---ETAVVNVTYSSKDQA 67
Query: 78 IRANKEMN 85
+A ++N
Sbjct: 68 RQALDKLN 75
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 43.2 bits (102), Expect = 2e-06
Identities = 10/77 (12%), Positives = 25/77 (32%), Gaps = 2/77 (2%)
Query: 14 KKTCEDENDFR-LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 72
+ +++ R ++ D T + + L ++ R KG FV F
Sbjct: 2 RWILKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFD 60
Query: 73 DPQDFIRANKEMNDDFR 89
+ + + ++
Sbjct: 61 SIESAKKFVETPGQKYK 77
Score = 39.3 bits (92), Expect = 7e-05
Identities = 10/69 (14%), Positives = 20/69 (28%), Gaps = 1/69 (1%)
Query: 82 KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
K + ++ D T + + L ++ R KG FV F +
Sbjct: 6 KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIES 64
Query: 142 FIRANKEMN 150
+ +
Sbjct: 65 AKKFVETPG 73
>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM
domain, riken structural genomics/proteomics initiative
RSGI, RNA binding protein; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 88
Score = 42.6 bits (101), Expect = 3e-06
Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 5/64 (7%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+F G D+T++ L FS+Y + + + R F FV+F D Q E
Sbjct: 7 GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQIAQSLCGE 61
Query: 149 MNEF 152
Sbjct: 62 DLII 65
Score = 42.2 bits (100), Expect = 4e-06
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 5/52 (9%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
+F G D+T++ L FS+Y + + + R F FV+F D Q
Sbjct: 7 GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQ 53
>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA
recognition, alternative conformation binding protein;
HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A
Length = 87
Score = 41.3 bits (97), Expect = 9e-06
Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 8/75 (10%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKV-----VRDKRTNKTKGFGFVSFKDPQDFI 78
RL+ G++ +T+E ++ F+ V + N+ K F F+ F+ +
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE-- 65
Query: 79 RANKEMNDDFRLFCG 93
+ M D +F G
Sbjct: 66 -TTQAMAFDGIIFQG 79
Score = 40.5 bits (95), Expect = 2e-05
Identities = 13/67 (19%), Positives = 28/67 (41%), Gaps = 6/67 (8%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKV-----VRDKRTNKTKGFGFVSFKDPQDFI 143
RL+ G++ +T+E ++ F+ V + N+ K F F+ F+ +
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 144 RANKEMN 150
+A +
Sbjct: 68 QA-MAFD 73
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 41.4 bits (97), Expect = 9e-06
Identities = 9/69 (13%), Positives = 18/69 (26%), Gaps = 5/69 (7%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
++ G+L D L R + V + F+ + D
Sbjct: 15 GAPLAADVYVGNLPRDARVSDLKRALREL-----GSVPLRLTWQGPRRRAFLHYPDSAAA 69
Query: 78 IRANKEMND 86
+A +
Sbjct: 70 QQAVSCLQG 78
Score = 40.2 bits (94), Expect = 3e-05
Identities = 9/64 (14%), Positives = 18/64 (28%), Gaps = 5/64 (7%)
Query: 87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 146
++ G+L D L R + V + F+ + D +A
Sbjct: 19 AADVYVGNLPRDARVSDLKRALREL-----GSVPLRLTWQGPRRRAFLHYPDSAAAQQAV 73
Query: 147 KEMN 150
+
Sbjct: 74 SCLQ 77
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 41.8 bits (98), Expect = 9e-06
Identities = 13/73 (17%), Positives = 25/73 (34%), Gaps = 6/73 (8%)
Query: 13 IKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 72
I+ + G LGN V+ L+ K + +K + F ++
Sbjct: 18 IETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYR 71
Query: 73 DPQDFIRANKEMN 85
++ RA +N
Sbjct: 72 TTEESKRAYVTLN 84
Score = 41.5 bits (97), Expect = 1e-05
Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 6/61 (9%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+ G LGN V+ L+ K + +K + F ++ ++ RA +
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAYVTL 83
Query: 150 N 150
N
Sbjct: 84 N 84
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken
structural genomics/proteomics initiative, RSGI; NMR
{Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A
Length = 110
Score = 40.8 bits (96), Expect = 2e-05
Identities = 18/71 (25%), Positives = 26/71 (36%), Gaps = 11/71 (15%)
Query: 24 RLFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
R+F G+L V + FSKY V KG+ FV + + + A
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAAVL 80
Query: 83 EMNDDFRLFCG 93
N R+ G
Sbjct: 81 GENG--RVLAG 89
Score = 40.1 bits (94), Expect = 3e-05
Identities = 16/63 (25%), Positives = 23/63 (36%), Gaps = 9/63 (14%)
Query: 89 RLFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
R+F G+L V + FSKY V KG+ FV + + + A
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAAVL 80
Query: 148 EMN 150
N
Sbjct: 81 GEN 83
>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding
domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 98
Score = 40.7 bits (96), Expect = 2e-05
Identities = 9/67 (13%), Positives = 24/67 (35%)
Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
+ ++ V+ + ++ F Y + ++ G V+F+ +
Sbjct: 13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72
Query: 80 ANKEMND 86
A ++ND
Sbjct: 73 AVIDLND 79
Score = 39.2 bits (92), Expect = 6e-05
Identities = 9/68 (13%), Positives = 25/68 (36%)
Query: 86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
+ ++ V+ + ++ F Y + ++ G V+F+ + A
Sbjct: 14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
Query: 146 NKEMNEFP 153
++N+ P
Sbjct: 74 VIDLNDRP 81
>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; 2.00A {Homo
sapiens} PDB: 2ek6_A
Length = 95
Score = 40.0 bits (94), Expect = 3e-05
Identities = 9/68 (13%), Positives = 24/68 (35%)
Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
+ ++ V+ + ++ F Y + ++ G V+F+ +
Sbjct: 12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 71
Query: 79 RANKEMND 86
A ++ND
Sbjct: 72 AAVIDLND 79
Score = 39.6 bits (93), Expect = 5e-05
Identities = 9/68 (13%), Positives = 25/68 (36%)
Query: 86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
+ ++ V+ + ++ F Y + ++ G V+F+ + A
Sbjct: 14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
Query: 146 NKEMNEFP 153
++N+ P
Sbjct: 74 VIDLNDRP 81
>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 108
Score = 40.2 bits (94), Expect = 3e-05
Identities = 13/77 (16%), Positives = 23/77 (29%), Gaps = 7/77 (9%)
Query: 74 PQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGF 133
+ R+ L + + L + A V RD G G
Sbjct: 2 SSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGV 54
Query: 134 VSFKDPQDFIRANKEMN 150
V F +D A ++++
Sbjct: 55 VEFVRKEDMTYAVRKLD 71
Score = 39.8 bits (93), Expect = 4e-05
Identities = 13/65 (20%), Positives = 24/65 (36%), Gaps = 7/65 (10%)
Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
+ R+ L + + L + A V RD G G V F +D A
Sbjct: 15 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAV 67
Query: 82 KEMND 86
+++++
Sbjct: 68 RKLDN 72
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 39.4 bits (92), Expect = 5e-05
Identities = 10/69 (14%), Positives = 19/69 (27%), Gaps = 6/69 (8%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+ L + V + L+ ++ V+ K V F+D A
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYA 77
Query: 150 NEFPHLFVG 158
+ G
Sbjct: 78 ADNQIYIAG 86
Score = 37.0 bits (86), Expect = 4e-04
Identities = 11/69 (15%), Positives = 20/69 (28%), Gaps = 6/69 (8%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+ L + V + L+ ++ V+ K V F+D A
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYA 77
Query: 85 NDDFRLFCG 93
D+ G
Sbjct: 78 ADNQIYIAG 86
>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription
termination, RNA processi recognition, RRM; HET: CAF;
1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A
Length = 97
Score = 39.2 bits (92), Expect = 6e-05
Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 11/71 (15%)
Query: 24 RLFCGDL-GNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
RLF G+L +V+ E L R FS Y ++ + FGF+ F +PQ A +
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIE 75
Query: 83 EMNDDFRLFCG 93
+ + G
Sbjct: 76 XESQ--EMNFG 84
Score = 37.7 bits (88), Expect = 2e-04
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 9/63 (14%)
Query: 89 RLFCGDL-GNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
RLF G+L +V+ E L R FS Y ++ + FGF+ F +PQ A +
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIE 75
Query: 148 EMN 150
+
Sbjct: 76 XES 78
>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wi6_A
Length = 88
Score = 38.9 bits (91), Expect = 6e-05
Identities = 7/66 (10%), Positives = 20/66 (30%), Gaps = 7/66 (10%)
Query: 21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
+ +L D + + Y ++ ++ K FV+ + + A
Sbjct: 4 GSSGILVKNLPQDSNCQEVHDLLKDY-------DLKYCYVDRNKRTAFVTLLNGEQAQNA 56
Query: 81 NKEMND 86
+ +
Sbjct: 57 IQMFHQ 62
Score = 38.9 bits (91), Expect = 7e-05
Identities = 7/62 (11%), Positives = 20/62 (32%), Gaps = 7/62 (11%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+ +L D + + Y ++ ++ K FV+ + + A +
Sbjct: 7 GILVKNLPQDSNCQEVHDLLKDY-------DLKYCYVDRNKRTAFVTLLNGEQAQNAIQM 59
Query: 149 MN 150
+
Sbjct: 60 FH 61
>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kg0_A
Length = 126
Score = 38.3 bits (89), Expect = 2e-04
Identities = 13/63 (20%), Positives = 21/63 (33%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+ ND + L T E +++ FS + K G FV F +
Sbjct: 38 DSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELA 97
Query: 78 IRA 80
+A
Sbjct: 98 EKA 100
Score = 37.6 bits (87), Expect = 3e-04
Identities = 12/65 (18%), Positives = 22/65 (33%)
Query: 81 NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
+ + +D + L T E +++ FS + K G FV F +
Sbjct: 36 SADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQE 95
Query: 141 DFIRA 145
+A
Sbjct: 96 LAEKA 100
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
2adb_A
Length = 164
Score = 38.5 bits (89), Expect = 3e-04
Identities = 13/69 (18%), Positives = 26/69 (37%), Gaps = 4/69 (5%)
Query: 85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
+ R+ +L VT ++L + FSK+ + LK + + + DP
Sbjct: 44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQH 99
Query: 145 ANKEMNEFP 153
A ++
Sbjct: 100 AKLSLDGQN 108
Score = 37.8 bits (87), Expect = 6e-04
Identities = 13/63 (20%), Positives = 25/63 (39%), Gaps = 4/63 (6%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
R+ +L VT ++L + FSK+ + LK + + + DP A
Sbjct: 47 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKL 102
Query: 83 EMN 85
++
Sbjct: 103 SLD 105
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 37.2 bits (87), Expect = 3e-04
Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 11/71 (15%)
Query: 24 RLFCGDL-GNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
RLF G+L +V+ E L R FS Y ++ + FGF+ F +PQ A +
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAIE 63
Query: 83 EMNDDFRLFCG 93
+ + G
Sbjct: 64 CESQ--EMNFG 72
Score = 36.0 bits (84), Expect = 9e-04
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 9/63 (14%)
Query: 89 RLFCGDL-GNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
RLF G+L +V+ E L R FS Y ++ + FGF+ F +PQ A +
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAIE 63
Query: 148 EMN 150
+
Sbjct: 64 CES 66
>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 37.0 bits (86), Expect = 4e-04
Identities = 11/63 (17%), Positives = 22/63 (34%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+ ND + L + E +++ FS + ++ G FV F +
Sbjct: 11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70
Query: 78 IRA 80
+A
Sbjct: 71 EKA 73
Score = 36.3 bits (84), Expect = 7e-04
Identities = 10/63 (15%), Positives = 22/63 (34%)
Query: 83 EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 142
+ +D + L + E +++ FS + ++ G FV F +
Sbjct: 11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70
Query: 143 IRA 145
+A
Sbjct: 71 EKA 73
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 36.6 bits (85), Expect = 4e-04
Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 8/59 (13%)
Query: 98 DVTDELLIRTFSKYPSFLKAKVVR---DKRTNKTKGFGFVSFKDPQDFIRANKEMNEFP 153
+ ++ + FSK+ K+ + KTKG+ F+ + P + A K + +
Sbjct: 18 EKLKNVIHKIFSKF-----GKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYK 71
Score = 35.8 bits (83), Expect = 7e-04
Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 8/56 (14%)
Query: 33 DVTDELLIRTFSKYPSFLKAKVVR---DKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
+ ++ + FSK+ K+ + KTKG+ F+ + P + A K +
Sbjct: 18 EKLKNVIHKIFSKF-----GKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNAD 68
>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 36.3 bits (84), Expect = 8e-04
Identities = 9/66 (13%), Positives = 20/66 (30%)
Query: 80 ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
+ ++ +T +++ P A V + G V FK+
Sbjct: 8 EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 67
Query: 140 QDFIRA 145
D ++
Sbjct: 68 DDARKS 73
Score = 36.3 bits (84), Expect = 8e-04
Identities = 9/63 (14%), Positives = 20/63 (31%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+ ++ +T +++ P A V + G V FK+ D
Sbjct: 11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 70
Query: 78 IRA 80
++
Sbjct: 71 RKS 73
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 36.2 bits (84), Expect = 0.001
Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 8/59 (13%)
Query: 98 DVTDELLIRTFSKYPSFLKAKVVR---DKRTNKTKGFGFVSFKDPQDFIRANKEMNEFP 153
+ ++ + FSK+ K+ + KTKG+ F+ + P + A K + +
Sbjct: 32 EKLKNVIHKIFSKF-----GKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYK 85
Score = 35.9 bits (83), Expect = 0.001
Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 8/56 (14%)
Query: 33 DVTDELLIRTFSKYPSFLKAKVVR---DKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
+ ++ + FSK+ K+ + KTKG+ F+ + P + A K +
Sbjct: 32 EKLKNVIHKIFSKF-----GKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNAD 82
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 36.1 bits (83), Expect = 0.001
Identities = 9/63 (14%), Positives = 28/63 (44%), Gaps = 2/63 (3%)
Query: 80 ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSFK 137
+ + ++F G L D+ ++ + +F ++ + + + + KG+ F+ F+
Sbjct: 1 GSSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60
Query: 138 DPQ 140
+
Sbjct: 61 EES 63
Score = 36.1 bits (83), Expect = 0.001
Identities = 9/54 (16%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSFKDPQ 75
++F G L D+ ++ + +F ++ + + + + KG+ F+ F++
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEES 63
>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 35.9 bits (83), Expect = 0.001
Identities = 10/69 (14%), Positives = 20/69 (28%), Gaps = 6/69 (8%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+ L V + L+ K+ + ++ KR V F++
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFENIDSAKECVTFA 71
Query: 150 NEFPHLFVG 158
+ P G
Sbjct: 72 ADVPVYIAG 80
Score = 32.8 bits (75), Expect = 0.013
Identities = 10/69 (14%), Positives = 19/69 (27%), Gaps = 6/69 (8%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+ L V + L+ K+ + ++ KR V F++
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFENIDSAKECVTFA 71
Query: 85 NDDFRLFCG 93
D G
Sbjct: 72 ADVPVYIAG 80
>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase,
SR protein, PRE-mRNA splicing, at binding, chromosome
partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP:
d.58.7.1 PDB: 2o3d_A 1wg4_A
Length = 115
Score = 36.0 bits (83), Expect = 0.001
Identities = 13/72 (18%), Positives = 23/72 (31%), Gaps = 7/72 (9%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+ R+ L + + L + A V RD G G V F
Sbjct: 8 YGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVR 60
Query: 139 PQDFIRANKEMN 150
+D A ++++
Sbjct: 61 KEDMTYAVRKLD 72
Score = 36.0 bits (83), Expect = 0.001
Identities = 13/65 (20%), Positives = 24/65 (36%), Gaps = 7/65 (10%)
Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
+ R+ L + + L + A V RD G G V F +D A
Sbjct: 16 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAV 68
Query: 82 KEMND 86
+++++
Sbjct: 69 RKLDN 73
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 35.6 bits (82), Expect = 0.001
Identities = 8/69 (11%), Positives = 18/69 (26%), Gaps = 6/69 (8%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+ L DVT+ +I + +++ K F+ +
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYY 72
Query: 150 NEFPHLFVG 158
+ G
Sbjct: 73 TSVTPVLRG 81
Score = 34.8 bits (80), Expect = 0.002
Identities = 8/69 (11%), Positives = 18/69 (26%), Gaps = 6/69 (8%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+ L DVT+ +I + +++ K F+ +
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYY 72
Query: 85 NDDFRLFCG 93
+ G
Sbjct: 73 TSVTPVLRG 81
>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 124
Score = 35.6 bits (82), Expect = 0.002
Identities = 14/67 (20%), Positives = 26/67 (38%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
R+ F ++ L + ++ +I F K + + K G GFV F++
Sbjct: 17 RSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRN 76
Query: 139 PQDFIRA 145
D+ A
Sbjct: 77 EADYKAA 83
Score = 34.0 bits (78), Expect = 0.007
Identities = 14/63 (22%), Positives = 25/63 (39%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
E F ++ L + ++ +I F K + + K G GFV F++ D+
Sbjct: 21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADY 80
Query: 78 IRA 80
A
Sbjct: 81 KAA 83
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM
domain, RNA- binding, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 104
Score = 35.3 bits (81), Expect = 0.002
Identities = 14/63 (22%), Positives = 21/63 (33%), Gaps = 3/63 (4%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+ L V DELL F V+ +R G ++F++P D
Sbjct: 4 GSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRL---GCGGVLTFREPADA 60
Query: 78 IRA 80
R
Sbjct: 61 ERV 63
Score = 34.9 bits (80), Expect = 0.002
Identities = 14/66 (21%), Positives = 23/66 (34%), Gaps = 3/66 (4%)
Query: 80 ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
+ + + L V DELL F V+ +R G ++F++P
Sbjct: 1 GSSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRL---GCGGVLTFREP 57
Query: 140 QDFIRA 145
D R
Sbjct: 58 ADAERV 63
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 35.2 bits (81), Expect = 0.002
Identities = 10/72 (13%), Positives = 22/72 (30%), Gaps = 3/72 (4%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+K +R+ +L + + L + T G G + F
Sbjct: 20 HMSKLPAKRYRITMKNLPEGCSWQDLKDLARENS---LETTFSSVNTRDFDGTGALEFPS 76
Query: 139 PQDFIRANKEMN 150
+ + A + +N
Sbjct: 77 EEILVEALERLN 88
Score = 35.2 bits (81), Expect = 0.002
Identities = 9/66 (13%), Positives = 21/66 (31%), Gaps = 3/66 (4%)
Query: 21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
+R+ +L + + L + T G G + F + + A
Sbjct: 27 KRYRITMKNLPEGCSWQDLKDLARENS---LETTFSSVNTRDFDGTGALEFPSEEILVEA 83
Query: 81 NKEMND 86
+ +N+
Sbjct: 84 LERLNN 89
>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding
factor, RNA binding domain, STRU genomics, joint center
for structural genomics, JCSG; NMR {Homo sapiens}
Length = 107
Score = 34.1 bits (78), Expect = 0.006
Identities = 14/73 (19%), Positives = 28/73 (38%), Gaps = 2/73 (2%)
Query: 82 KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVR--DKRTNKTKGFGFVSFKDP 139
+E++D F + L T E ++ FS + R K +G + +
Sbjct: 6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESE 65
Query: 140 QDFIRANKEMNEF 152
QD +A ++ +
Sbjct: 66 QDVQKALEKHRMY 78
Score = 31.4 bits (71), Expect = 0.053
Identities = 13/67 (19%), Positives = 24/67 (35%), Gaps = 2/67 (2%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVR--DKRTNKTKGFGFVSFKDPQ 75
E ++ F + L T E ++ FS + R K +G + + Q
Sbjct: 7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQ 66
Query: 76 DFIRANK 82
D +A +
Sbjct: 67 DVQKALE 73
>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 119
Score = 34.1 bits (78), Expect = 0.006
Identities = 10/69 (14%), Positives = 18/69 (26%), Gaps = 6/69 (8%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
+ L DVT+ +I + V + K K F+ +
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFGK------VTNLLMLKGKNQAFIEMNTEEAANTMVNYY 87
Query: 150 NEFPHLFVG 158
+ G
Sbjct: 88 TSVTPVLRG 96
Score = 33.7 bits (77), Expect = 0.008
Identities = 10/69 (14%), Positives = 18/69 (26%), Gaps = 6/69 (8%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+ L DVT+ +I + V + K K F+ +
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFGK------VTNLLMLKGKNQAFIEMNTEEAANTMVNYY 87
Query: 85 NDDFRLFCG 93
+ G
Sbjct: 88 TSVTPVLRG 96
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 34.2 bits (78), Expect = 0.006
Identities = 13/65 (20%), Positives = 25/65 (38%), Gaps = 4/65 (6%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
R+ +L VT ++L + FSK+ + LK + + + DP A
Sbjct: 30 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKLS 85
Query: 149 MNEFP 153
++
Sbjct: 86 LDGQN 90
Score = 33.5 bits (76), Expect = 0.013
Identities = 13/62 (20%), Positives = 25/62 (40%), Gaps = 4/62 (6%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
R+ +L VT ++L + FSK+ + LK + + + DP A
Sbjct: 30 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKLS 85
Query: 84 MN 85
++
Sbjct: 86 LD 87
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 33.6 bits (77), Expect = 0.007
Identities = 10/69 (14%), Positives = 18/69 (26%), Gaps = 6/69 (8%)
Query: 90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
L L +VT+ +I + V + K K F+ + I
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGK------VTNILMLKGKNQAFLELATEEAAITMVNYY 71
Query: 150 NEFPHLFVG 158
+
Sbjct: 72 SAVTPHLRN 80
Score = 32.1 bits (73), Expect = 0.021
Identities = 10/69 (14%), Positives = 18/69 (26%), Gaps = 6/69 (8%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
L L +VT+ +I + V + K K F+ + I
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGK------VTNILMLKGKNQAFLELATEEAAITMVNYY 71
Query: 85 NDDFRLFCG 93
+
Sbjct: 72 SAVTPHLRN 80
>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif,
systemic lupus erythematosus, phosphoprotein, RNA
maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1
PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A
Length = 193
Score = 34.8 bits (79), Expect = 0.007
Identities = 9/69 (13%), Positives = 21/69 (30%), Gaps = 1/69 (1%)
Query: 21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
+ ++ D T + + L ++ R KG FV F + +
Sbjct: 108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKF 166
Query: 81 NKEMNDDFR 89
+ ++
Sbjct: 167 VETPGQKYK 175
Score = 33.7 bits (76), Expect = 0.016
Identities = 11/81 (13%), Positives = 23/81 (28%), Gaps = 1/81 (1%)
Query: 71 FKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKG 130
K + K + ++ D T + + L ++ R KG
Sbjct: 93 SKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKG 151
Query: 131 FGFVSFKDPQDFIRANKEMNE 151
FV F + + + +
Sbjct: 152 SIFVVFDSIESAKKFVETPGQ 172
>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative,
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kfy_A
Length = 136
Score = 34.2 bits (78), Expect = 0.007
Identities = 15/76 (19%), Positives = 21/76 (27%), Gaps = 2/76 (2%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVR--DKRTNKTKGFGFVSF 136
E + F + L + E + S A V R + G FV
Sbjct: 36 MLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVEL 95
Query: 137 KDPQDFIRANKEMNEF 152
D A K+ E
Sbjct: 96 GSEDDVKMALKKDRES 111
Score = 33.8 bits (77), Expect = 0.009
Identities = 13/65 (20%), Positives = 17/65 (26%), Gaps = 2/65 (3%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVR--DKRTNKTKGFGFVSFKDPQ 75
E F + L + E + S A V R + G FV
Sbjct: 40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSED 99
Query: 76 DFIRA 80
D A
Sbjct: 100 DVKMA 104
>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus}
Length = 118
Score = 33.7 bits (77), Expect = 0.009
Identities = 13/76 (17%), Positives = 21/76 (27%), Gaps = 2/76 (2%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVR--DKRTNKTKGFGFVSF 136
E + + + L + E + S V R + G FV
Sbjct: 9 MLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVEL 68
Query: 137 KDPQDFIRANKEMNEF 152
+ D A K+ E
Sbjct: 69 ESEDDVKLALKKDRES 84
Score = 32.2 bits (73), Expect = 0.024
Identities = 11/65 (16%), Positives = 17/65 (26%), Gaps = 2/65 (3%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVR--DKRTNKTKGFGFVSFKDPQ 75
E + + L + E + S V R + G FV +
Sbjct: 13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESED 72
Query: 76 DFIRA 80
D A
Sbjct: 73 DVKLA 77
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 33.1 bits (75), Expect = 0.014
Identities = 11/75 (14%), Positives = 20/75 (26%), Gaps = 5/75 (6%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
N L + +T ++L + KV R + V F+
Sbjct: 17 DDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPV-----GKVQRIVIFKRNGIQAMVEFES 71
Query: 139 PQDFIRANKEMNEFP 153
+A +N
Sbjct: 72 VLCAQKAKAALNGAD 86
Score = 32.0 bits (72), Expect = 0.035
Identities = 9/57 (15%), Positives = 17/57 (29%), Gaps = 5/57 (8%)
Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND 86
+T ++L + KV R + V F+ +A +N
Sbjct: 33 PLYPITVDVLYTVCNPV-----GKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNG 84
>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 32.5 bits (74), Expect = 0.019
Identities = 8/65 (12%), Positives = 20/65 (30%), Gaps = 6/65 (9%)
Query: 86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
+ +L + TFS++ + + V F +P + +A
Sbjct: 9 SKTVILAKNLPAGTLAAEIQETFSRF------GSLGRVLLPEGGITAIVEFLEPLEARKA 62
Query: 146 NKEMN 150
+ +
Sbjct: 63 FRHLA 67
Score = 32.1 bits (73), Expect = 0.030
Identities = 8/61 (13%), Positives = 20/61 (32%), Gaps = 6/61 (9%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
+ +L + TFS++ + + V F +P + +A + +
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRF------GSLGRVLLPEGGITAIVEFLEPLEARKAFRHL 66
Query: 85 N 85
Sbjct: 67 A 67
>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif,
G-tract, G-quadruplex, alternative splicing, RNA binding
protein; NMR {Homo sapiens} PDB: 2kg1_A
Length = 139
Score = 32.9 bits (75), Expect = 0.020
Identities = 12/78 (15%), Positives = 26/78 (33%), Gaps = 2/78 (2%)
Query: 3 GLRPGPISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNK 62
G + G S + T + + L T+ + FS + ++ + +
Sbjct: 27 GQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPL-NPVRVHIEIGPD-GR 84
Query: 63 TKGFGFVSFKDPQDFIRA 80
G V F ++ + A
Sbjct: 85 VTGEADVEFATHEEAVAA 102
Score = 31.0 bits (70), Expect = 0.081
Identities = 9/79 (11%), Positives = 21/79 (26%), Gaps = 2/79 (2%)
Query: 67 GFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN 126
G + + L T+ + FS + ++ +
Sbjct: 26 GGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPL-NPVRVHIEIGPD-G 83
Query: 127 KTKGFGFVSFKDPQDFIRA 145
+ G V F ++ + A
Sbjct: 84 RVTGEADVEFATHEEAVAA 102
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 31.9 bits (73), Expect = 0.024
Identities = 14/70 (20%), Positives = 19/70 (27%), Gaps = 8/70 (11%)
Query: 89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
+F V L F + A VV DK F V D
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPV--ASVVMDKDKGV---FAIVEMGDVGA---REAV 61
Query: 149 MNEFPHLFVG 158
+++ H G
Sbjct: 62 LSQSQHSLGG 71
Score = 31.1 bits (71), Expect = 0.052
Identities = 12/52 (23%), Positives = 14/52 (26%), Gaps = 5/52 (9%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
+F V L F + A VV DK F V D
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPV--ASVVMDKDKGV---FAIVEMGDVG 56
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 33.3 bits (75), Expect = 0.031
Identities = 18/133 (13%), Positives = 40/133 (30%), Gaps = 36/133 (27%)
Query: 41 RTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLF-CGDLGNDV 99
R ++ F K V R + K + +A E+ + G LG
Sbjct: 118 RLYNDNQVFAKYNVSRLQPYLKLR--------------QALLELRPAKNVLIDGVLG--- 160
Query: 100 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFG-F-VSF---KDPQDFIRANKEMNEFPH 154
K +++ V + F F ++ P+ + + + + +
Sbjct: 161 --------SGK--TWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVL---EMLQKLLY 207
Query: 155 LFVGDLKTRSSIT 167
+ +RS +
Sbjct: 208 QIDPNWTSRSDHS 220
Score = 30.6 bits (68), Expect = 0.25
Identities = 28/189 (14%), Positives = 50/189 (26%), Gaps = 60/189 (31%)
Query: 5 RPGPISSWIKKTCEDENDFRLF-CGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKT 63
R P + E + G LG K +++ V +
Sbjct: 133 RLQPYLKLRQALLELRPAKNVLIDGVLG-----------SGK--TWVALDVCLSYKVQCK 179
Query: 64 KGFG-F-VSFK-------------------DPQDFIRANKEMNDDFRLFCGDLGNDVTDE 102
F F ++ K DP R++ N R+ + + E
Sbjct: 180 MDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRI------HSIQAE 233
Query: 103 LLIRTFS--KYP-SFLKAKVVRDKRTNKT-KGFGF-----VSFKDPQ--DFIRANKE--- 148
L R Y L V+ + + K F ++ + Q DF+ A
Sbjct: 234 LR-RLLKSKPYENCLL---VLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHI 289
Query: 149 -MNEFPHLF 156
++
Sbjct: 290 SLDHHSMTL 298
Score = 29.1 bits (64), Expect = 0.75
Identities = 20/148 (13%), Positives = 40/148 (27%), Gaps = 31/148 (20%)
Query: 9 ISSWIKKTCEDENDFRLFCGD------LG-------NDVTDELLIRTFSKYPSFLKAKVV 55
+ + D +D D +G + L F + FL+ K+
Sbjct: 450 VDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDF-RFLEQKIR 508
Query: 56 RDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFL 115
D G Q + D ND E L+ + +
Sbjct: 509 HDSTAWNASGS---ILNTLQQLKFYKPYICD----------NDPKYERLVNAILDFLPKI 555
Query: 116 KAKVVRDKRTNKTKGFGFVSFKDPQDFI 143
+ ++ K T+ + ++ + I
Sbjct: 556 EENLICSKYTDLLR----IALMAEDEAI 579
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 33.1 bits (75), Expect = 0.043
Identities = 18/82 (21%), Positives = 26/82 (31%), Gaps = 10/82 (12%)
Query: 33 DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN-----KEMNDD 87
DV + Y F +V + N T FG K IR N E D
Sbjct: 1644 DVWNRADNHFKDTY-GFSILDIVINNPVNLTIHFGGEKGKR----IRENYSAMIFETIVD 1698
Query: 88 FRLFCGDLGNDVTDELLIRTFS 109
+L + ++ + TF
Sbjct: 1699 GKLKTEKIFKEINEHSTSYTFR 1720
Score = 26.9 bits (59), Expect = 4.1
Identities = 20/83 (24%), Positives = 26/83 (31%), Gaps = 15/83 (18%)
Query: 98 DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFV 157
DV + Y F +V + N T FG K IR N F +
Sbjct: 1644 DVWNRADNHFKDTY-GFSILDIVINNPVNLTIHFGGEKGKR----IRENYSAMIFETIVD 1698
Query: 158 GDLKTR----------SSITLKG 170
G LKT +S T +
Sbjct: 1699 GKLKTEKIFKEINEHSTSYTFRS 1721
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 109
Score = 30.9 bits (70), Expect = 0.062
Identities = 11/63 (17%), Positives = 21/63 (33%), Gaps = 2/63 (3%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+ +D + + + + F +++D + G G V F PQD
Sbjct: 12 INPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKD-HVGRNNGNGLVKFLSPQDT 69
Query: 78 IRA 80
A
Sbjct: 70 FEA 72
Score = 30.9 bits (70), Expect = 0.066
Identities = 12/60 (20%), Positives = 20/60 (33%), Gaps = 2/60 (3%)
Query: 86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
DD + + + + F +++D + G G V F PQD A
Sbjct: 15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKD-HVGRNNGNGLVKFLSPQDTFEA 72
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 123
Score = 31.0 bits (70), Expect = 0.082
Identities = 12/65 (18%), Positives = 21/65 (32%), Gaps = 3/65 (4%)
Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVR--DKRTNKTKGFGFVSFKDPQ 75
EN + L T E ++ F ++ P + + + G FV F +
Sbjct: 20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEE 79
Query: 76 DFIRA 80
A
Sbjct: 80 YAQNA 84
Score = 29.1 bits (65), Expect = 0.40
Identities = 9/51 (17%), Positives = 17/51 (33%), Gaps = 3/51 (5%)
Query: 98 DVTDELLIRTFSKY-PSFLKAKVVR--DKRTNKTKGFGFVSFKDPQDFIRA 145
T E ++ F ++ P + + + G FV F + A
Sbjct: 34 TATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNA 84
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 31.3 bits (70), Expect = 0.11
Identities = 17/100 (17%), Positives = 32/100 (32%), Gaps = 16/100 (16%)
Query: 61 NKTKGFGFVSFKDPQDFIRANKEMNDDFR-LFCGDLGNDVT---------DELLIRTFSK 110
FG F D ++ + + L+ G + + + + FS+
Sbjct: 107 EVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSR 166
Query: 111 YPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
+ + V K GFV FK + A + M+
Sbjct: 167 LGDIDRIRYVESK------NCGFVKFKYQANAEFAKEAMS 200
Score = 30.9 bits (69), Expect = 0.16
Identities = 13/70 (18%), Positives = 24/70 (34%), Gaps = 15/70 (21%)
Query: 25 LFCGDLGNDVT---------DELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
L+ G + + + + FS+ + + V K GFV FK
Sbjct: 137 LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK------NCGFVKFKYQA 190
Query: 76 DFIRANKEMN 85
+ A + M+
Sbjct: 191 NAEFAKEAMS 200
>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H';
structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 102
Score = 28.9 bits (65), Expect = 0.29
Identities = 9/67 (13%), Positives = 22/67 (32%), Gaps = 2/67 (2%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
++ + + L T+ + FS + ++ + + G V F
Sbjct: 7 GSSFQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPD-GRVTGEADVEFAT 64
Query: 139 PQDFIRA 145
+D + A
Sbjct: 65 HEDAVAA 71
Score = 28.5 bits (64), Expect = 0.45
Identities = 9/61 (14%), Positives = 19/61 (31%), Gaps = 2/61 (3%)
Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
+ L T+ + FS + ++ + + G V F +D +
Sbjct: 13 TTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPD-GRVTGEADVEFATHEDAVA 70
Query: 80 A 80
A
Sbjct: 71 A 71
>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 91
Score = 28.0 bits (63), Expect = 0.50
Identities = 9/67 (13%), Positives = 26/67 (38%), Gaps = 2/67 (2%)
Query: 79 RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
+ + +VT++ ++ + + ++VR+ G+ FV F +
Sbjct: 2 SSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAH-GNKTGYIFVDFSN 59
Query: 139 PQDFIRA 145
++ +A
Sbjct: 60 EEEVKQA 66
Score = 27.7 bits (62), Expect = 0.75
Identities = 9/63 (14%), Positives = 25/63 (39%), Gaps = 2/63 (3%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+ +VT++ ++ + + ++VR+ G+ FV F + ++
Sbjct: 6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAH-GNKTGYIFVDFSNEEEV 63
Query: 78 IRA 80
+A
Sbjct: 64 KQA 66
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 27.9 bits (62), Expect = 0.78
Identities = 11/40 (27%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 54 VVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCG 93
V D + G +V F+ +D +A ++N+ R F G
Sbjct: 58 NVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNN--RWFNG 95
Score = 27.1 bits (60), Expect = 1.5
Identities = 13/70 (18%), Positives = 26/70 (37%), Gaps = 9/70 (12%)
Query: 81 NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
+ EM + + F ++ KY + V D + G +V F+ +
Sbjct: 29 DVEMQEHYDEFFEEV--------FTEMEEKYGEVEEMNVC-DNLGDHLVGNVYVKFRREE 79
Query: 141 DFIRANKEMN 150
D +A ++N
Sbjct: 80 DAEKAVIDLN 89
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 27.7 bits (62), Expect = 1.1
Identities = 17/78 (21%), Positives = 28/78 (35%), Gaps = 11/78 (14%)
Query: 16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
D D L ++ D+ E SK+ K + G VSF+DP+
Sbjct: 25 HPMDFEDDPLVLNEIREDLRVE-----CSKFGQIRKLLLFD----RHPDGVASVSFRDPE 75
Query: 76 DFIRANKEMNDDFRLFCG 93
+ + ++ R F G
Sbjct: 76 EADYCIQTLDG--RWFGG 91
Score = 26.6 bits (59), Expect = 2.2
Identities = 13/69 (18%), Positives = 26/69 (37%), Gaps = 10/69 (14%)
Query: 82 KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
+ DD + ++ D+ E SK+ K + G VSF+DP++
Sbjct: 27 MDFEDDPLVL-NEIREDLRVE-----CSKFGQIRKLLLFD----RHPDGVASVSFRDPEE 76
Query: 142 FIRANKEMN 150
+ ++
Sbjct: 77 ADYCIQTLD 85
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding
protein, RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 27.1 bits (60), Expect = 1.4
Identities = 18/78 (23%), Positives = 26/78 (33%), Gaps = 9/78 (11%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVR--DKRTNKTKGFGFVSFKDPQ 75
+E ++ DV DE SKY ++ R D G FV F
Sbjct: 16 PEELLDDEEYEEIVEDVRDE-----CSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVF 70
Query: 76 DFIRANKEMNDDFRLFCG 93
D +A + + R F
Sbjct: 71 DCQKAMQGLTG--RKFAN 86
Score = 26.7 bits (59), Expect = 2.0
Identities = 18/71 (25%), Positives = 27/71 (38%), Gaps = 9/71 (12%)
Query: 82 KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVR--DKRTNKTKGFGFVSFKDP 139
+E+ DD ++ DV DE SKY ++ R D G FV F
Sbjct: 17 EELLDD--EEYEEIVEDVRDE-----CSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSV 69
Query: 140 QDFIRANKEMN 150
D +A + +
Sbjct: 70 FDCQKAMQGLT 80
>1hg3_A Triosephosphate isomerase; thermostability, tetrameric; 2.7A
{Pyrococcus woesei} SCOP: c.1.1.1
Length = 225
Score = 27.2 bits (61), Expect = 2.6
Identities = 8/37 (21%), Positives = 16/37 (43%), Gaps = 8/37 (21%)
Query: 60 TNKTKGFGFVSFKDPQ---DFIRANKEMNDDFRLFCG 93
T VS P+ + + K++N + ++ CG
Sbjct: 151 TGIP-----VSKAKPEVITNTVELVKKVNPEVKVLCG 182
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif,
RRM, RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 26.3 bits (58), Expect = 3.3
Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 11/69 (15%)
Query: 29 DLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFG----FVSFKDPQDFIRANKEM 84
DL +VT+E K+ + + + ++K+ + FV F + +A + +
Sbjct: 37 DLEGEVTEE-----CGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL 91
Query: 85 NDDFRLFCG 93
N R F G
Sbjct: 92 NG--RWFAG 98
Score = 25.1 bits (55), Expect = 7.1
Identities = 12/61 (19%), Positives = 26/61 (42%), Gaps = 9/61 (14%)
Query: 94 DLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFG----FVSFKDPQDFIRANKEM 149
DL +VT+E K+ + + + ++K+ + FV F + +A + +
Sbjct: 37 DLEGEVTEE-----CGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL 91
Query: 150 N 150
N
Sbjct: 92 N 92
>1u02_A Trehalose-6-phosphate phosphatase related protein; structural
genomics, PSI; 1.92A {Thermoplasma acidophilum} SCOP:
c.108.1.15
Length = 239
Score = 26.2 bits (58), Expect = 5.3
Identities = 6/19 (31%), Positives = 8/19 (42%), Gaps = 3/19 (15%)
Query: 84 MNDDFRLFCGDLGNDVTDE 102
+ + GD D TDE
Sbjct: 169 RGERPAIIAGD---DATDE 184
>3l5a_A NADH/flavin oxidoreductase/NADH oxidase; OLD yellow enzyme family,
OYE-like FMN-binding domain, TIM B oxidoreductase; HET:
PGE; 1.65A {Staphylococcus aureus}
Length = 419
Score = 26.5 bits (59), Expect = 5.8
Identities = 6/41 (14%), Positives = 8/41 (19%), Gaps = 7/41 (17%)
Query: 130 GFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLKG 170
G + M + L SI L
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMYRYKPLL-------QSIHLPN 35
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics,
joint center for struc genomics, JCSG, protein
structure initiative, PSI-biology; HET: MSE CIT; 0.95A
{Mus musculus} PDB: 2lq5_A
Length = 114
Score = 25.4 bits (56), Expect = 6.3
Identities = 11/68 (16%), Positives = 25/68 (36%), Gaps = 10/68 (14%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
+ E + ++ +DV +E +K+ + V + N +G +V
Sbjct: 19 QTEEEVGWD-TEIKDDVIEE-----CNKHGGVIHIYVDK----NSAQGNVYVKCPSIAAA 68
Query: 78 IRANKEMN 85
I A ++
Sbjct: 69 IAAVNALH 76
Score = 25.4 bits (56), Expect = 6.9
Identities = 11/71 (15%), Positives = 24/71 (33%), Gaps = 12/71 (16%)
Query: 80 ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
E + ++ +DV +E +K+ + V + N +G +V
Sbjct: 18 PQTEEEVGWDT---EIKDDVIEE-----CNKHGGVIHIYVDK----NSAQGNVYVKCPSI 65
Query: 140 QDFIRANKEMN 150
I A ++
Sbjct: 66 AAAIAAVNALH 76
>2wb7_A PT26-6P; extra chromosomal elements, unknown function; 2.60A
{Thermococcus SP}
Length = 526
Score = 26.0 bits (56), Expect = 7.7
Identities = 14/77 (18%), Positives = 27/77 (35%), Gaps = 1/77 (1%)
Query: 61 NKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVV 120
N T + F+ +P F AN +++D++R + EL T +
Sbjct: 279 NSTAMYKFLITPNPGYFQPANPKISDEYRFVTLRVIEGGRMELADTTTGHIGDLTEPTFF 338
Query: 121 RDKRTNKTKGFGFVSFK 137
+ T G + +
Sbjct: 339 -GLTAHYTDAPGTLDYH 354
>1ddw_A GLGF-domain protein homer; pleckstrin homology domain fold,
signaling protein; 1.70A {Rattus norvegicus} SCOP:
b.55.1.4 PDB: 1ddv_A 2p8v_A 1i7a_A*
Length = 120
Score = 25.1 bits (54), Expect = 8.0
Identities = 15/72 (20%), Positives = 24/72 (33%)
Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
N +R+ D + + + + + K D R N G GF S F
Sbjct: 41 TRNVYRIISLDGSKAIINSTITPNMTFTKTSQKFGQWADSRANTVYGLGFSSEHHLSKFA 100
Query: 79 RANKEMNDDFRL 90
+E + RL
Sbjct: 101 EKFQEFKEAARL 112
>3hl6_A Pathogenicity island protein; unknown functio; 2.50A
{Staphylococcus aureus subsp}
Length = 225
Score = 25.5 bits (55), Expect = 9.0
Identities = 11/36 (30%), Positives = 16/36 (44%)
Query: 133 FVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL 168
F + DP D + F H+++ D K R S L
Sbjct: 35 FKLYNDPFDMVYVMMNSKLFSHVYIKDCKVRQSFEL 70
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.323 0.141 0.426
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,599,433
Number of extensions: 146370
Number of successful extensions: 989
Number of sequences better than 10.0: 1
Number of HSP's gapped: 768
Number of HSP's successfully gapped: 388
Length of query: 170
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 83
Effective length of database: 4,272,666
Effective search space: 354631278
Effective search space used: 354631278
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.5 bits)