RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15676
(309 letters)
>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 = 108 bits (270), Expect = 7e-27
Identities = 39/205 (19%), Positives = 66/205 (32%), Gaps = 11/205 (5%)
Query: 115 DPYEDLPELVYPPSPE----------PTRELLANGLIGADEDIDETAGLSAQEIEELRAE 164
DP LP L P + P + ET + + E
Sbjct: 17 DPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKRREKIE 76
Query: 165 REAKARATILEIVGDLPEADAAP-PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIR 223
R + T L++ + +A LFV ++N T++ L F +G + ++
Sbjct: 77 RRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVY 136
Query: 224 DKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEI 283
K +G YAF+E+++ + AY D ID RR+ E K +
Sbjct: 137 SKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGL 196
Query: 284 DEKKEEEEKEDRAMIGDRMEDGLRE 308
+ + G E
Sbjct: 197 GGTRRGGADVNIRHSGRDDTSRYDE 221
>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 = 100 bits (250), Expect = 1e-26
Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 8/79 (10%)
Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
A P L+V L P TS L F RFG + + ++ +A++++++ + +
Sbjct: 14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD------SFAYIQYESLDAAQ 67
Query: 246 DAYLKMDNVLID--DRRIH 262
A KM + DRR+
Sbjct: 68 AACAKMRGFPLGGPDRRLR 86
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 83.6 bits (207), Expect = 2e-20
Identities = 15/78 (19%), Positives = 32/78 (41%)
Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
P + +LN + L+ + ++G+V E++ T L A V F + + ++
Sbjct: 4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKE 63
Query: 247 AYLKMDNVLIDDRRIHAR 264
+ + IHA+
Sbjct: 64 TVKNLHLTSVMGNIIHAQ 81
>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 = 78.8 bits (195), Expect = 5e-18
Identities = 23/106 (21%), Positives = 46/106 (43%), Gaps = 16/106 (15%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
L V L + ++ +F G++ C+++RDK+TG SL Y FV + +PK E A +
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 252 DNVLIDDRRIHARGEEWNMWKRREEEEEKE----------EIDEKK 287
+ + + + I + R ++ + +K+
Sbjct: 65 NGLRLQTKTIKV------SYARPSSASIRDANLYVSGLPKTMTQKE 104
Score = 66.1 bits (162), Expect = 2e-13
Identities = 18/66 (27%), Positives = 33/66 (50%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
L+V L + +LE +FS++G++ ++ D+VTG S F+ FD E+A +
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 252 DNVLID 257
+
Sbjct: 151 NGQKPS 156
>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 = 74.5 bits (184), Expect = 3e-17
Identities = 20/70 (28%), Positives = 34/70 (48%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
L++ L P T+D DL + +GK+ + I DK T Y FV+FD+P + + A +
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 252 DNVLIDDRRI 261
+ +
Sbjct: 68 KASGVQAQMA 77
>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 = 76.8 bits (190), Expect = 3e-17
Identities = 25/106 (23%), Positives = 45/106 (42%), Gaps = 16/106 (15%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
L V L +D +L +F G +N C ++RD TG S YAFV+F + + A +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 252 DNVLIDDRRIHARGEEWNMWKRREEEEEKE----------EIDEKK 287
+ + + ++R+ + R E K+ I + +
Sbjct: 66 NGITVRNKRLKV------SYARPGGESIKDTNLYVTNLPRTITDDQ 105
Score = 66.8 bits (164), Expect = 1e-13
Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
P ++ N L+V L +DD L+ IF ++G + ++RDK+TG AFV ++
Sbjct: 82 PGGESIKDTN-LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNK 140
Query: 241 PKSCEDAYLKMDNVLID 257
+ ++A ++NV+ +
Sbjct: 141 REEAQEAISALNNVIPE 157
>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 = 75.5 bits (186), Expect = 4e-17
Identities = 22/81 (27%), Positives = 41/81 (50%)
Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
P L V L+ T++ DL +FS++G + ++ D+ + S +AFV F+N
Sbjct: 38 GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 97
Query: 241 PKSCEDAYLKMDNVLIDDRRI 261
++A + + + +D RRI
Sbjct: 98 VDDAKEAKERANGMELDGRRI 118
>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 = 72.6 bits (179), Expect = 1e-16
Identities = 22/78 (28%), Positives = 41/78 (52%)
Query: 184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
P L V L+ T++ DL +FS++G + ++ D+ + S +AFV F+N
Sbjct: 10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 69
Query: 244 CEDAYLKMDNVLIDDRRI 261
++A + + + +D RRI
Sbjct: 70 AKEAKERANGMELDGRRI 87
>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 = 72.6 bits (179), Expect = 1e-16
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 1/79 (1%)
Query: 183 ADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
+ +FV L+P + + F+ FG+++ V++D TG S Y FV F N
Sbjct: 1 GPLGSHFH-VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKW 59
Query: 243 SCEDAYLKMDNVLIDDRRI 261
E+A +M + R+I
Sbjct: 60 DAENAIQQMGGQWLGGRQI 78
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 73.2 bits (180), Expect = 2e-16
Identities = 25/70 (35%), Positives = 34/70 (48%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
LF+ L +D DL F FG V +V DK T S + FV FDNP S + A M
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 252 DNVLIDDRRI 261
+ + +R+
Sbjct: 103 NGFQVGTKRL 112
>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 = 72.7 bits (179), Expect = 2e-16
Identities = 27/84 (32%), Positives = 37/84 (44%), Gaps = 3/84 (3%)
Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
P LF+ L D DL +F FG V +V DK T S + FV +DNP S +
Sbjct: 23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQA 82
Query: 247 AYLKMDNVLIDDRRI---HARGEE 267
A M+ I +R+ R +
Sbjct: 83 AIQSMNGFQIGMKRLKVQLKRSKN 106
>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 = 72.8 bits (179), Expect = 2e-16
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 1/81 (1%)
Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
+ D + + +FV L+P + +D++ F+ FG+++ V++D TG S Y FV F N
Sbjct: 8 QKKDTSNHFH-VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 66
Query: 241 PKSCEDAYLKMDNVLIDDRRI 261
E+A +M + R+I
Sbjct: 67 KWDAENAIQQMGGQWLGGRQI 87
>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 = 73.2 bits (180), Expect = 3e-16
Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 3/86 (3%)
Query: 185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
L V + + L +F R+G + +++ D+ T S Y FV+F + S
Sbjct: 38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97
Query: 245 EDAYLKMDNVLIDDRRI---HARGEE 267
+ A ++ I ++R+ A
Sbjct: 98 QQAIAGLNGFNILNKRLKVALAASGH 123
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 70.9 bits (174), Expect = 8e-16
Identities = 16/86 (18%), Positives = 30/86 (34%), Gaps = 8/86 (9%)
Query: 179 DLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEF 238
+ + P V+ + L + DL FG ++ V+ K + A VEF
Sbjct: 11 NYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK------RQALVEF 64
Query: 239 DNPKSCEDA--YLKMDNVLIDDRRIH 262
++ +A Y + + I
Sbjct: 65 EDVLGACNAVNYAADNQIYIAGHPAF 90
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 70.4 bits (173), Expect = 9e-16
Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 6/82 (7%)
Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEV--IRDKVTGDSLQYAFVEFDNPKSC 244
+ + + + P T D + S + + + I+DK T + +AFV+ +
Sbjct: 7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDA 66
Query: 245 EDAYLKMDNV----LIDDRRIH 262
+ ++ ID + I
Sbjct: 67 SQLLQILQSLHPPLKIDGKTIG 88
>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 = 70.0 bits (172), Expect = 2e-15
Identities = 27/84 (32%), Positives = 47/84 (55%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
G + A E LFV L+ T++ LE +FS++G+++ V++D+ T S + FV
Sbjct: 1 GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVT 60
Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
F+N +DA + M+ +D R+I
Sbjct: 61 FENIDDAKDAMMAMNGKSVDGRQI 84
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 72.3 bits (178), Expect = 2e-15
Identities = 19/82 (23%), Positives = 40/82 (48%)
Query: 180 LPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFD 239
A + ++V + +D + F+ FG + ++ D VT +AFVE++
Sbjct: 19 AQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYE 78
Query: 240 NPKSCEDAYLKMDNVLIDDRRI 261
P++ + A +M++V++ R I
Sbjct: 79 VPEAAQLALEQMNSVMLGGRNI 100
Score = 65.0 bits (159), Expect = 1e-12
Identities = 22/87 (25%), Positives = 43/87 (49%), Gaps = 1/87 (1%)
Query: 175 EIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYA 234
+ + D +A + +V ++ SDDD++ +F FGK+ + RD TG Y
Sbjct: 112 QPIIDQLAEEARAFNRI-YVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYG 170
Query: 235 FVEFDNPKSCEDAYLKMDNVLIDDRRI 261
F+E++ +S +DA M+ + + +
Sbjct: 171 FIEYEKAQSSQDAVSSMNLFDLGGQYL 197
>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 = 69.2 bits (170), Expect = 3e-15
Identities = 18/81 (22%), Positives = 40/81 (49%), Gaps = 3/81 (3%)
Query: 185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGD---SLQYAFVEFDNP 241
+ + LF+ LN T+++ L+ +FS+ G + C + + K S+ + FVE+ P
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 242 KSCEDAYLKMDNVLIDDRRIH 262
+ + A ++ +D ++
Sbjct: 61 EQAQKALKQLQGHTVDGHKLE 81
>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 = 69.2 bits (170), Expect = 3e-15
Identities = 23/78 (29%), Positives = 39/78 (50%)
Query: 185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
+ LFV L+ +S++DLE +FS +G ++ D +T +AFV F P+
Sbjct: 4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63
Query: 245 EDAYLKMDNVLIDDRRIH 262
AY ++D + R +H
Sbjct: 64 VKAYAEVDGQVFQGRMLH 81
>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 = 73.1 bits (180), Expect = 5e-15
Identities = 19/96 (19%), Positives = 33/96 (34%), Gaps = 3/96 (3%)
Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
P + +L V L P + E + FG + C ++ + TG S Y F E+ S
Sbjct: 92 QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAA 151
Query: 246 DAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKE 281
A + + R ++ W +
Sbjct: 152 RAKSDLLGKPLGPRTLYVH---WTDAGQLTPALLHS 184
Score = 60.4 bits (147), Expect = 1e-10
Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 2/82 (2%)
Query: 181 PEADAAPPENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFD 239
A L V +L P D L S C++ + G +A +E++
Sbjct: 176 QLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYE 234
Query: 240 NPKSCEDAYLKMDNVLIDDRRI 261
+ E+A + D + + +
Sbjct: 235 TAEMAEEAQQQADGLSLGGSHL 256
Score = 50.0 bits (120), Expect = 3e-07
Identities = 13/73 (17%), Positives = 28/73 (38%), Gaps = 7/73 (9%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+ + L ++ ++ + S + + C V + K G AFV N + E A
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYK--G----TAFVTLLNGEQAEAAINAF 77
Query: 252 DNVLIDDRRIHAR 264
+ +R + +
Sbjct: 78 HQSRLRERELSVQ 90
>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 = 69.4 bits (170), Expect = 9e-15
Identities = 25/125 (20%), Positives = 49/125 (39%), Gaps = 18/125 (14%)
Query: 184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
L+V L+ T+++ + +FS+ G + + DK+ + + FVE+ +
Sbjct: 34 KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRAD 93
Query: 244 CEDAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEKKEEEEKEDRAMIGDRME 303
E+A ++ +DDR I W D +E + R G ++
Sbjct: 94 AENAMRYINGTRLDDRIIRT------DW------------DAGFKEGRQYGRGRSGGQVR 135
Query: 304 DGLRE 308
D R+
Sbjct: 136 DEYRQ 140
>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 = 68.0 bits (167), Expect = 9e-15
Identities = 22/74 (29%), Positives = 34/74 (45%)
Query: 188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
L V L TS D L +F ++G+V + R+ T +AFV F + + +DA
Sbjct: 12 GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDA 71
Query: 248 YLKMDNVLIDDRRI 261
MD +D R +
Sbjct: 72 EAAMDGAELDGREL 85
>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 = 68.0 bits (167), Expect = 1e-14
Identities = 19/77 (24%), Positives = 34/77 (44%)
Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
A + V L+ T + DL+ +F FG ++ + +DK TG S +AF+ F +
Sbjct: 12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 71
Query: 246 DAYLKMDNVLIDDRRIH 262
A + D ++
Sbjct: 72 RAIAGVSGFGYDHLILN 88
>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 = 67.6 bits (166), Expect = 1e-14
Identities = 23/79 (29%), Positives = 42/79 (53%)
Query: 183 ADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
AP ++ ++V L +++DL IFS++GKV +++DK T S AF+ F +
Sbjct: 10 GGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKD 69
Query: 243 SCEDAYLKMDNVLIDDRRI 261
S ++ ++N + R I
Sbjct: 70 SAQNCTRAINNKQLFGRVI 88
>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 = 67.6 bits (166), Expect = 1e-14
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 1/79 (1%)
Query: 185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKV-NCCEVIRDKVTGDSLQYAFVEFDNPKS 243
+ + +F+ L+P + L FS FG + +++RD TG+S YAF+ F + +
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 244 CEDAYLKMDNVLIDDRRIH 262
+ A M+ + +R I
Sbjct: 61 SDAAIEAMNGQYLCNRPIT 79
>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 = 68.1 bits (167), Expect = 1e-14
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
A LF+ LN T++ L+ +F + G ++ +I+D+ T S +AF+ F+NP +
Sbjct: 4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAK 62
Query: 246 DAYLKMDNVLIDDRRI 261
+A M+ + + I
Sbjct: 63 NAAKDMNGKSLHGKAI 78
>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 = 70.4 bits (173), Expect = 2e-14
Identities = 29/105 (27%), Positives = 46/105 (43%), Gaps = 6/105 (5%)
Query: 177 VGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFV 236
+G + + + P L+V L+P ++ L FS G + V RD +T SL YA+V
Sbjct: 3 LGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 62
Query: 237 EFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKE 281
F P E A M+ +I + + MW +R+ K
Sbjct: 63 NFQQPADAERALDTMNFDVIKGKPVRI------MWSQRDPSLRKS 101
Score = 66.9 bits (164), Expect = 2e-13
Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+F+ L+ + L FS FG + C+V+ D S Y FV F+ ++ E A KM
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 163
Query: 252 DNVLIDDRRIH 262
+ +L++DR++
Sbjct: 164 NGMLLNDRKVF 174
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 68.3 bits (167), Expect = 2e-14
Identities = 27/121 (22%), Positives = 40/121 (33%), Gaps = 8/121 (6%)
Query: 149 ETAGLSAQEIEEL--------RAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPV 200
+ LS + E L R G +A + VL+V L
Sbjct: 15 KCENLSDEMYEILSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEE 74
Query: 201 TSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRR 260
D L F FG + ++ D T +AFVEF+ + A M+ + R
Sbjct: 75 VDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRT 134
Query: 261 I 261
I
Sbjct: 135 I 135
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 67.5 bits (165), Expect = 3e-14
Identities = 25/76 (32%), Positives = 38/76 (50%)
Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
L V L TS D L +F ++G+V + RD+ T +S +AFV F + + E
Sbjct: 44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 103
Query: 246 DAYLKMDNVLIDDRRI 261
DA MD ++D R +
Sbjct: 104 DAMDAMDGAVLDGREL 119
>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 = 66.4 bits (162), Expect = 4e-14
Identities = 16/84 (19%), Positives = 29/84 (34%), Gaps = 8/84 (9%)
Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
V+ V L + DL +FG + ++ K + A VEF+N
Sbjct: 7 GSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK------RQALVEFEN 60
Query: 241 PKSCEDA--YLKMDNVLIDDRRIH 262
S ++ + V I ++
Sbjct: 61 IDSAKECVTFAADVPVYIAGQQAF 84
>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 = 65.6 bits (161), Expect = 4e-14
Identities = 21/70 (30%), Positives = 29/70 (41%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
LFV LN D+ L F F V+ D TG S Y FV F + ++A M
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 252 DNVLIDDRRI 261
++ R +
Sbjct: 64 QGQDLNGRPL 73
>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 = 66.5 bits (163), Expect = 4e-14
Identities = 27/96 (28%), Positives = 47/96 (48%), Gaps = 7/96 (7%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+F+ L+ + L FS FG + C+V+ D S Y FV F+ ++ E A KM
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65
Query: 252 DNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEKK 287
+ +L++DR++ +K R+E E + K+
Sbjct: 66 NGMLLNDRKVFV-----GRFKSRKEREAELGARAKE 96
>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 = 68.0 bits (167), Expect = 4e-14
Identities = 21/98 (21%), Positives = 43/98 (43%), Gaps = 8/98 (8%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGD--SLQYAFVEFDNPKSCEDAYL 249
+FV ++ S+ DL +F ++G V V+RD+ S FV F K+ +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 250 KMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEKK 287
+ N+ + H + + + E+ ++++K
Sbjct: 66 ALHNMKVLPGMHHP------IQMKPADSEKNNAVEDRK 97
Score = 58.4 bits (142), Expect = 1e-10
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
LF+ ++ +++D+ ++FS FG++ C ++R G S AFV F + A M
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAM 156
Query: 252 DNVLI 256
Sbjct: 157 HQAQT 161
>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 = 66.1 bits (162), Expect = 5e-14
Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 2/84 (2%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
G + L+V L+ ++ + +FS+ G C++I + + D Y FVE
Sbjct: 4 GSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVE 61
Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
F + A M+ I + +
Sbjct: 62 FYEHRDAAAALAAMNGRKILGKEV 85
>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 = 65.3 bits (160), Expect = 7e-14
Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 1/70 (1%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+FV + + +L F +FG V +I D + F+ F++ +S + A + M
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQA-VNM 71
Query: 252 DNVLIDDRRI 261
I +++
Sbjct: 72 HFHDIMGKKV 81
>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 = 65.8 bits (161), Expect = 8e-14
Identities = 25/70 (35%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+FV L T+D L F FG + VI D+ TG S Y FV + + E A K
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA-CKD 78
Query: 252 DNVLIDDRRI 261
N +ID R+
Sbjct: 79 PNPIIDGRKA 88
>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 = 65.4 bits (160), Expect = 8e-14
Identities = 16/62 (25%), Positives = 30/62 (48%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
LF+ ++ + DL+ +F FGK+ V++D+ TG AF+ + +S A +
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 252 DN 253
Sbjct: 76 HE 77
>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 = 65.5 bits (160), Expect = 9e-14
Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 9/80 (11%)
Query: 184 DAAPPENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
D + +F+ LN + D+E IFS++G+V C V + YAFV++ N +
Sbjct: 22 DPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKG--------YAFVQYSNER 73
Query: 243 SCEDAYLKMDNVLIDDRRIH 262
A L + ++ + +
Sbjct: 74 HARAAVLGENGRVLAGQTLD 93
>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-13
Identities = 21/84 (25%), Positives = 37/84 (44%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
G + ++V L+ S+ L +F + G V + +D+VTG Y FVE
Sbjct: 4 GSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVE 63
Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
F + + + A MD + + + I
Sbjct: 64 FLSEEDADYAIKIMDMIKLYGKPI 87
>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 = 66.9 bits (164), Expect = 1e-13
Identities = 17/70 (24%), Positives = 37/70 (52%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
LF+ L +DD ++ + + FG + +++D TG S YAF E+ + + A +
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 252 DNVLIDDRRI 261
+ + + D+++
Sbjct: 157 NGMQLGDKKL 166
Score = 58.0 bits (141), Expect = 2e-10
Identities = 9/75 (12%), Positives = 27/75 (36%), Gaps = 6/75 (8%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCC-----EVIRDKVTGDSLQYAFVEFDNPKSCED 246
L+V + +++ + F+ ++ + +AF+EF +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 247 AYLKMDNVLIDDRRI 261
A + D ++ + +
Sbjct: 67 A-MAFDGIIFQGQSL 80
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 65.0 bits (159), Expect = 1e-13
Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 1/79 (1%)
Query: 184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
+ ++ LF+ L + ++LE I G V ++ ++ G A+VE++N
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQ 70
Query: 244 CEDAYLKMDNVLIDDRRIH 262
A +KMD + I + I
Sbjct: 71 ASQAVMKMDGMTIKENIIK 89
>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 = 64.6 bits (158), Expect = 1e-13
Identities = 16/85 (18%), Positives = 38/85 (44%), Gaps = 6/85 (7%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
G + LFV L P +++++ +F ++GK + +DK + F+
Sbjct: 4 GSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIR 57
Query: 238 FDNPKSCEDAYLKMDNVLIDDRRIH 262
+ E A +++DN+ + +++
Sbjct: 58 LETRTLAEIAKVELDNMPLRGKQLR 82
>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 = 65.0 bits (159), Expect = 1e-13
Identities = 17/78 (21%), Positives = 35/78 (44%)
Query: 184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
+ P VL++ L+P ++ DL +F+RF + + +TG AF+ F N +
Sbjct: 20 NPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEI 79
Query: 244 CEDAYLKMDNVLIDDRRI 261
A ++ + + +
Sbjct: 80 AWQALHLVNGYKLYGKIL 97
>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 = 64.6 bits (158), Expect = 1e-13
Identities = 17/74 (22%), Positives = 36/74 (48%)
Query: 188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
P V+++ + +++ + + S G V +++ D TG S YAF+EF + +S A
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 248 YLKMDNVLIDDRRI 261
++ + R +
Sbjct: 61 VRNLNGYQLGSRFL 74
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 63.6 bits (156), Expect = 1e-13
Identities = 18/70 (25%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+FV L+ T+ +D++ F +FGKV+ ++ DK T + FV F++ E ++
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV-CEI 60
Query: 252 DNVLIDDRRI 261
I+++ +
Sbjct: 61 HFHEINNKMV 70
>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 = 67.0 bits (164), Expect = 2e-13
Identities = 18/100 (18%), Positives = 42/100 (42%), Gaps = 1/100 (1%)
Query: 162 RAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEV 221
+ + + G + LF+ L +DD ++ + + FG + +
Sbjct: 88 YQPLPGMSENPSVYVPGVVSTVVPDSAHK-LFIGGLPNYLNDDQVKELLTSFGPLKAFNL 146
Query: 222 IRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI 261
++D TG S YAF E+ + + A ++ + + D+++
Sbjct: 147 VKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 186
Score = 55.0 bits (133), Expect = 3e-09
Identities = 10/78 (12%), Positives = 28/78 (35%), Gaps = 6/78 (7%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCC-----EVIRDKVTGDSLQYAFVEFDNPKSCED 246
L+V + +++ + F+ ++ + +AF+EF +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 247 AYLKMDNVLIDDRRIHAR 264
A + D ++ + + R
Sbjct: 67 A-MAFDGIIFQGQSLKIR 83
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 66.4 bits (162), Expect = 2e-13
Identities = 26/106 (24%), Positives = 44/106 (41%), Gaps = 6/106 (5%)
Query: 162 RAEREAKARATILEIVGDLPEADAAPPENV-----LFVCKLNPVTSDDDLEIIFSRFGKV 216
R ++ + + DL ++ E V L V L+ SD D++ +F+ FG +
Sbjct: 56 RPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTL 115
Query: 217 NCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
V D+ +G SL A V F+ A + V +D R +
Sbjct: 116 KKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMD 160
>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 = 64.1 bits (157), Expect = 2e-13
Identities = 19/77 (24%), Positives = 38/77 (49%)
Query: 185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
+ + L+V L+ ++D L IF FGK++ +++D TG S Y F+ F + +
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 245 EDAYLKMDNVLIDDRRI 261
A +++ + R +
Sbjct: 61 RRALEQLNGFELAGRPM 77
>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 = 64.6 bits (158), Expect = 2e-13
Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 1/71 (1%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
L++ L + +LE + FG+V ++RD +G S F ++ + CE
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHF 86
Query: 252 DNVLIDDRRIH 262
+ I
Sbjct: 87 NGKFIKTPPGV 97
>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 = 63.7 bits (156), Expect = 2e-13
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKV-TGDSLQYAFVEFDNPKSC 244
+ + + +L + D + IFS +GK+ ++ +++ S YA+VEF+NP
Sbjct: 1 SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60
Query: 245 EDAYLKMDNVLIDDRRI 261
E A MD ID + I
Sbjct: 61 EKALKHMDGGQIDGQEI 77
>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 = 64.7 bits (158), Expect = 3e-13
Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 1/81 (1%)
Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
+ L V L+ SD D++ +F+ FG + V D+ +G SL A V F+
Sbjct: 28 GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERR 86
Query: 242 KSCEDAYLKMDNVLIDDRRIH 262
A + V +D R +
Sbjct: 87 ADALKAMKQYKGVPLDGRPMD 107
>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 = 62.9 bits (154), Expect = 3e-13
Identities = 14/70 (20%), Positives = 29/70 (41%), Gaps = 1/70 (1%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+FV L+P T ++ + F FG+V E+ D T + F+ F + + ++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI-MEK 60
Query: 252 DNVLIDDRRI 261
+ +
Sbjct: 61 KYHNVGLSKC 70
>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 = 63.4 bits (155), Expect = 4e-13
Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 11/79 (13%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+FV ++ + +L +F R G+V C+V++D YAFV + + A ++
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQL 63
Query: 252 DNVLIDDRRI---HARGEE 267
+ + +RI + +
Sbjct: 64 NGKEVKGKRINVELSTKGQ 82
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 63.4 bits (155), Expect = 4e-13
Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 9/82 (10%)
Query: 182 EADAAPPENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
E PP++ LF+ L S +DL IFS +G + + + F++FDN
Sbjct: 3 EMHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA--------FGFIQFDN 54
Query: 241 PKSCEDAYLKMDNVLIDDRRIH 262
P+S DA + +++
Sbjct: 55 PQSVRDAIECESQEMNFGKKLI 76
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 64.9 bits (158), Expect = 4e-13
Identities = 16/127 (12%), Positives = 42/127 (33%), Gaps = 7/127 (5%)
Query: 137 ANGLIGADEDIDETAGLSAQEIEELRAEREAKARATILEIVGDLPEADAAPPENVLFVCK 196
++G+ E++ + + + + + IL + ++V
Sbjct: 8 SSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILY-----TYSGLRNRRAAVYVGS 62
Query: 197 LNPVTSDDDLEIIFSRFGKVNCCE--VIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNV 254
+ T+D L + G + E ++ G S YA V + S +
Sbjct: 63 FSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGK 122
Query: 255 LIDDRRI 261
+++ ++
Sbjct: 123 VLNGEKV 129
>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 = 65.2 bits (159), Expect = 4e-13
Identities = 25/74 (33%), Positives = 38/74 (51%)
Query: 188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
L V L TS D L +F ++G+V + RD+ T +S +AFV F + + EDA
Sbjct: 69 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 128
Query: 248 YLKMDNVLIDDRRI 261
MD ++D R +
Sbjct: 129 MDAMDGAVLDGREL 142
>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 = 63.5 bits (155), Expect = 5e-13
Identities = 20/76 (26%), Positives = 32/76 (42%), Gaps = 1/76 (1%)
Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
+ LFV LN S++D+ +F FG ++ C V+R G S AFV+F +
Sbjct: 7 GSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSS 65
Query: 241 PKSCEDAYLKMDNVLI 256
+ A +
Sbjct: 66 HTEAQAAIHALHGSQT 81
>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 = 63.0 bits (154), Expect = 5e-13
Identities = 21/79 (26%), Positives = 32/79 (40%)
Query: 183 ADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
+ A + VL+V L D L F FG + ++ D T +AFVEF+ +
Sbjct: 6 SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 65
Query: 243 SCEDAYLKMDNVLIDDRRI 261
A M+ + R I
Sbjct: 66 DAAAAIDNMNESELFGRTI 84
>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 = 64.5 bits (158), Expect = 6e-13
Identities = 22/82 (26%), Positives = 33/82 (40%), Gaps = 1/82 (1%)
Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
++ + N LFV LN D+ L F F V+ D TG S Y FV F +
Sbjct: 80 QQSSSDDTFN-LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTS 138
Query: 241 PKSCEDAYLKMDNVLIDDRRIH 262
++A M ++ R +
Sbjct: 139 QDDAQNAMDSMQGQDLNGRPLR 160
Score = 61.8 bits (151), Expect = 6e-12
Identities = 17/90 (18%), Positives = 38/90 (42%), Gaps = 7/90 (7%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
L+V L+ ++D L+ F G + +++ DK ++ YAFVE+ A +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61
Query: 252 DNVLIDDRRIHARGEEWNMWKRREEEEEKE 281
+ I++ + W + ++ +
Sbjct: 62 NGKQIENNIVKI------NWAFQSQQSSSD 85
>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 = 63.1 bits (154), Expect = 7e-13
Identities = 21/84 (25%), Positives = 34/84 (40%), Gaps = 1/84 (1%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
L V L+ SD D++ +F+ FG + V D+ +G SL A V
Sbjct: 18 SGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVH 76
Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
F+ A + + V +D R +
Sbjct: 77 FERKADALKAMKQYNGVPLDGRPM 100
>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 = 62.6 bits (153), Expect = 8e-13
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
L V L T++ DL+ FS FG+V +V +D TG S + FV F ++ +
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV-MSQ 76
Query: 252 DNVLIDDRRI 261
++ ID R
Sbjct: 77 RHM-IDGRWC 85
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 62.7 bits (153), Expect = 9e-13
Identities = 22/86 (25%), Positives = 37/86 (43%), Gaps = 8/86 (9%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
++V L +LE FS +G + + R+ +AFVEF++P+ EDA +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 252 DNVLIDDRRI---HARGEEWNMWKRR 274
D +I R+ + G R
Sbjct: 58 DGKVICGSRVRVELSTGMPRRSRFDR 83
>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 = 62.3 bits (152), Expect = 9e-13
Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 9/80 (11%)
Query: 184 DAAPPENVLFVCKLNPVT-SDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
+ ++ LF+ L S +DL IFS +G + + + F++FDNP+
Sbjct: 17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA--------FGFIQFDNPQ 68
Query: 243 SCEDAYLKMDNVLIDDRRIH 262
S DA + +++
Sbjct: 69 SVRDAIEXESQEMNFGKKLI 88
>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 = 65.5 bits (159), Expect = 1e-12
Identities = 12/82 (14%), Positives = 26/82 (31%), Gaps = 2/82 (2%)
Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFG--KVNCCEVIRDKVTGDSLQYAFVEFD 239
L++ L T+D+DL G + + ++ G S +A V
Sbjct: 61 VYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVG 120
Query: 240 NPKSCEDAYLKMDNVLIDDRRI 261
+ S + + + +
Sbjct: 121 SEASSKKLMDLLPKRELHGQNP 142
>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 = 63.2 bits (154), Expect = 1e-12
Identities = 18/85 (21%), Positives = 39/85 (45%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
GD P + +LFV ++ +++D+ F+ +G++ + D+ TG Y VE
Sbjct: 11 GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 70
Query: 238 FDNPKSCEDAYLKMDNVLIDDRRIH 262
++ K + A ++ + + I
Sbjct: 71 YETYKEAQAAMEGLNGQDLMGQPIS 95
>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 = 61.9 bits (151), Expect = 1e-12
Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 8/71 (11%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
L V ++P ++ +L F +G V C++++D YAFV + + +A +
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGL 64
Query: 252 DNVLIDDRRIH 262
DN +R+H
Sbjct: 65 DNTEFQGKRMH 75
>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 = 62.7 bits (153), Expect = 1e-12
Identities = 21/87 (24%), Positives = 34/87 (39%), Gaps = 1/87 (1%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
G A + +FV L+ L+ +FS G V +++ DK G S V
Sbjct: 4 GSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVT 62
Query: 238 FDNPKSCEDAYLKMDNVLIDDRRIHAR 264
F+ A + L+ DR +H +
Sbjct: 63 FEQSIEAVQAISMFNGQLLFDRPMHVK 89
>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 = 63.4 bits (154), Expect = 1e-12
Identities = 22/108 (20%), Positives = 41/108 (37%), Gaps = 8/108 (7%)
Query: 161 LRAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCE 220
+ D+ P + ++V L + +LE F +G +
Sbjct: 45 YDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVW 104
Query: 221 VIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI---HARG 265
V R+ G +AFVEF++P+ DA ++D + R+ + G
Sbjct: 105 VARNP-PG----FAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNG 147
>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 = 61.4 bits (150), Expect = 1e-12
Identities = 21/76 (27%), Positives = 31/76 (40%)
Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
A + VL+V L D L F FG + ++ D T +AFVEF+ +
Sbjct: 4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63
Query: 246 DAYLKMDNVLIDDRRI 261
A M+ + R I
Sbjct: 64 AAIDNMNESELFGRTI 79
>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 = 62.4 bits (152), Expect = 1e-12
Identities = 18/111 (16%), Positives = 48/111 (43%), Gaps = 11/111 (9%)
Query: 187 PPE--NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
PPE +L++ L + +++ IF ++G + IR T ++ A+V +++
Sbjct: 4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPI---RQIRVGNTPETRGTAYVVYEDIFDA 60
Query: 245 EDAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEKKEEEEKEDR 295
++A + + +R + ++ +K + +K+E+ +
Sbjct: 61 KNAVDHLSGFNVSNRYLVV------LYYNANRAFQKMDTKKKEEQLKLLKE 105
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 60.6 bits (148), Expect = 2e-12
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+F+ L+ T+ + L F +FG+V C V+RD +T S + FV F + + L
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-LAQ 61
Query: 252 DNVLIDDRRI 261
+D + I
Sbjct: 62 SRHELDSKTI 71
>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 = 61.2 bits (149), Expect = 3e-12
Identities = 17/80 (21%), Positives = 36/80 (45%), Gaps = 1/80 (1%)
Query: 183 ADAAPPENVLFVCKLNPVTSDDDLEIIFSRFG-KVNCCEVIRDKVTGDSLQYAFVEFDNP 241
+ ++ L++ L P ++ + F+ G V ++IR+++TG Y FVEF +
Sbjct: 3 SGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADL 62
Query: 242 KSCEDAYLKMDNVLIDDRRI 261
+ E K++ +
Sbjct: 63 ATAEKCLHKINGKPLPGATP 82
>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 = 61.1 bits (149), Expect = 3e-12
Identities = 21/85 (24%), Positives = 41/85 (48%), Gaps = 7/85 (8%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
L+V L+ D+ L FS FG + +V+ + G S + FV F +P+ A +M
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 252 DNVLIDDRRIHARGEEWNMWKRREE 276
+ ++ + ++ + +R+EE
Sbjct: 76 NGRIVATKPLYV-----ALAQRKEE 95
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 61.2 bits (149), Expect = 3e-12
Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 7/78 (8%)
Query: 185 AAPPENV-LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
+APP ++ + ++ DL +F FG + + +K F+++D +
Sbjct: 22 SAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK------GCCFIKYDTHEQ 75
Query: 244 CEDAYLKMDNVLIDDRRI 261
+ + N R +
Sbjct: 76 AAVCIVALANFPFQGRNL 93
>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 = 61.1 bits (149), Expect = 3e-12
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+F+ L+ T+ + L F +FG+V C V+RD +T S + FV F + + L
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-LAQ 86
Query: 252 DNVLIDDRRI 261
+D + I
Sbjct: 87 SRHELDSKTI 96
>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 = 61.2 bits (149), Expect = 3e-12
Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 6/78 (7%)
Query: 184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
++P ++ + +D + FS FG++ V +K Y+FV F +S
Sbjct: 20 QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHES 73
Query: 244 CEDAYLKMDNVLIDDRRI 261
A + ++ I+ +
Sbjct: 74 AAHAIVSVNGTTIEGHVV 91
>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 = 60.7 bits (148), Expect = 3e-12
Identities = 20/87 (22%), Positives = 40/87 (45%), Gaps = 2/87 (2%)
Query: 175 EIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYA 234
++ D E + LF+ LNP S +L++ S N + D TG + ++
Sbjct: 3 HMLEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFG 61
Query: 235 FVEFDNPKSCEDAYLKMDNVLIDDRRI 261
+V+F++ + E A L++ + + I
Sbjct: 62 YVDFESAEDLEKA-LELTGLKVFGNEI 87
>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 = 61.2 bits (149), Expect = 4e-12
Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 6/86 (6%)
Query: 185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
A + ++V L P D+E +F ++G + ++ + +AFVEF++P+
Sbjct: 18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRDA 74
Query: 245 EDAYLKMDNVLIDDRRI---HARGEE 267
EDA D D R+ R
Sbjct: 75 EDAVYGRDGYDYDGYRLRVEFPRSGR 100
>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 = 61.1 bits (149), Expect = 4e-12
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
LFV L+ T+ + L FS++G+V C +++DK T S + FV+F +P L
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV-LAS 77
Query: 252 DNVLIDDRRI 261
+D R I
Sbjct: 78 RPHTLDGRNI 87
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 60.7 bits (148), Expect = 4e-12
Identities = 18/85 (21%), Positives = 39/85 (45%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
GD P + +LFV ++ +++D+ F+ +G++ + D+ TG Y VE
Sbjct: 12 GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 71
Query: 238 FDNPKSCEDAYLKMDNVLIDDRRIH 262
++ K + A ++ + + I
Sbjct: 72 YETYKEAQAAMEGLNGQDLMGQPIS 96
>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 = 62.2 bits (152), Expect = 5e-12
Identities = 19/101 (18%), Positives = 42/101 (41%), Gaps = 8/101 (7%)
Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
E + LF+ LNP S +L++ S N V+ + TG + ++ +V+F++
Sbjct: 6 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESA 64
Query: 242 KSCEDAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKEE 282
+ E A L++ + + I + + ++
Sbjct: 65 EDLEKA-LELTGLKVFGNEIKL------EKPKGRDSKKVRA 98
Score = 51.8 bits (125), Expect = 2e-08
Identities = 14/81 (17%), Positives = 27/81 (33%), Gaps = 6/81 (7%)
Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
L L+ ++D+L+ +F ++ G S A++EF +
Sbjct: 92 DSKKVRAART-LLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKS 145
Query: 241 PKSCEDAYLKMDNVLIDDRRI 261
E + ID R +
Sbjct: 146 EADAEKNLEEKQGAEIDGRSV 166
>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 = 60.4 bits (147), Expect = 5e-12
Identities = 15/80 (18%), Positives = 34/80 (42%), Gaps = 4/80 (5%)
Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
+ + L + L+ +++ L+ +F + + + G S YAF+EF +
Sbjct: 8 NSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEFASF 63
Query: 242 KSCEDAYLKMDNVLIDDRRI 261
+ ++A + I+ R I
Sbjct: 64 EDAKEALNSCNKREIEGRAI 83
>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 = 59.9 bits (146), Expect = 5e-12
Identities = 16/79 (20%), Positives = 37/79 (46%), Gaps = 11/79 (13%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
LF+ L ++ ++ +F ++GKV C++I++ Y FV ++ + EDA +
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRNL 62
Query: 252 DNVLIDDRRI---HARGEE 267
+ + I ++ +
Sbjct: 63 HHYKLHGVNINVEASKNKS 81
>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 = 60.4 bits (147), Expect = 5e-12
Identities = 17/102 (16%), Positives = 37/102 (36%), Gaps = 14/102 (13%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
G E A N L+V + + L FS FG + + + AFV
Sbjct: 4 GSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVT 55
Query: 238 FDNPKSCEDAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEE 279
++ +S + A +++ ++ ++ R++ +
Sbjct: 56 YEKMESADQAVAELNGTQVESVQLKV------NIARKQPMLD 91
>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 = 63.1 bits (153), Expect = 6e-12
Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 6/83 (7%)
Query: 181 PEADAAPPENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFD 239
A +VL V LNP + L I+F +G V +++ +K A V+
Sbjct: 26 IPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMA 80
Query: 240 NPKSCEDAYLKMDNVLIDDRRIH 262
+ + A ++ + + I
Sbjct: 81 DGNQAQLAMSHLNGHKLHGKPIR 103
Score = 52.3 bits (125), Expect = 3e-08
Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 4/78 (5%)
Query: 183 ADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
+ PP L + + P S++DL+++FS G V K A ++ + +
Sbjct: 145 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK----MALIQMGSVE 200
Query: 243 SCEDAYLKMDNVLIDDRR 260
A + + N + +
Sbjct: 201 EAVQALIDLHNHDLGENH 218
>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 = 60.0 bits (146), Expect = 7e-12
Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 8/80 (10%)
Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
+ VLFV L +++ LE FS+FGK+ + ++D YAF+ FD
Sbjct: 4 GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDER 55
Query: 242 KSCEDAYLKMDNVLIDDRRI 261
A +M+ ++ I
Sbjct: 56 DGAVKAMEEMNGKDLEGENI 75
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 59.8 bits (145), Expect = 9e-12
Identities = 11/85 (12%), Positives = 27/85 (31%), Gaps = 3/85 (3%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
G L + + P + L+ + ++G V CE + V
Sbjct: 4 GSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVT 60
Query: 238 FDNPKSCEDAYLKMDNVLIDDRRIH 262
+ + A K++ +++ +
Sbjct: 61 YSSKDQARQALDKLNGFQLENFTLK 85
>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 = 59.6 bits (145), Expect = 1e-11
Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 3/84 (3%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
G + P LFV L+ T+++ L+ F + ++ D+ TG S + FV+
Sbjct: 4 GSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRAR---IVTDRETGSSKGFGFVD 60
Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
F++ + + A M++ ID ++
Sbjct: 61 FNSEEDAKAAKEAMEDGEIDGNKV 84
>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 = 61.9 bits (151), Expect = 1e-11
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
LF+ L+ T+D+ L F ++G + C V+RD T S + FV + + + A +
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA-MNA 74
Query: 252 DNVLIDDRRI 261
+D R +
Sbjct: 75 RPHKVDGRVV 84
Score = 59.2 bits (144), Expect = 9e-11
Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+FV + T + L F ++GK+ E++ D+ +G +AFV FD+ S + +
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI-VIQ 165
Query: 252 DNVLIDDRRIHAR 264
++ R
Sbjct: 166 KYHTVNGHNCEVR 178
>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 = 58.7 bits (143), Expect = 1e-11
Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+FV L+ TS DL+ F++FG+V C + D TG S + F+ F + S E L
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKV-LDQ 72
Query: 252 DNVLIDDRRI 261
+D R I
Sbjct: 73 KEHRLDGRVI 82
>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 = 58.8 bits (143), Expect = 2e-11
Identities = 19/85 (22%), Positives = 34/85 (40%), Gaps = 6/85 (7%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
G + D +L+V L TS++ +E F+ V + + YAFV
Sbjct: 4 GSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR------DYAFVH 57
Query: 238 FDNPKSCEDAYLKMDNVLIDDRRIH 262
F N + +A ++ ++D I
Sbjct: 58 FSNREDAVEAMKALNGKVLDGSPIE 82
>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 = 59.4 bits (144), Expect = 2e-11
Identities = 16/81 (19%), Positives = 33/81 (40%), Gaps = 8/81 (9%)
Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
PE A N L+V + + L FS FG + + + AFV ++
Sbjct: 31 PERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEK 82
Query: 241 PKSCEDAYLKMDNVLIDDRRI 261
+S + A +++ ++ ++
Sbjct: 83 MESADQAVAELNGTQVESVQL 103
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 58.7 bits (142), Expect = 2e-11
Identities = 14/80 (17%), Positives = 33/80 (41%), Gaps = 8/80 (10%)
Query: 185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
+ P V+ + KL ++ ++ + FGKV +++ K AF+E + ++
Sbjct: 12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAA 65
Query: 245 EDA--YLKMDNVLIDDRRIH 262
Y ++ + I+
Sbjct: 66 NTMVNYYTSVTPVLRGQPIY 85
>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 = 58.4 bits (142), Expect = 2e-11
Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 1/75 (1%)
Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
+ +FV L ++ L +F + G + + +D+ G + FV F +P+S
Sbjct: 14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSY 72
Query: 247 AYLKMDNVLIDDRRI 261
A ++ + + R I
Sbjct: 73 AIALLNGIRLYGRPI 87
>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 = 59.2 bits (143), Expect = 2e-11
Identities = 15/80 (18%), Positives = 33/80 (41%), Gaps = 8/80 (10%)
Query: 185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
A P V+ + KL ++ ++ + FGKV +++ K AF+E + ++
Sbjct: 27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAA 80
Query: 245 EDA--YLKMDNVLIDDRRIH 262
Y ++ + I+
Sbjct: 81 NTMVNYYTSVTPVLRGQPIY 100
>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 = 58.5 bits (142), Expect = 2e-11
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 2/84 (2%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
G +++ L V + D DL +F +FGK+ E+I ++ S + FV
Sbjct: 4 GSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVT 61
Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
F+N + A K+ +++ R+I
Sbjct: 62 FENSADADRAREKLHGTVVEGRKI 85
>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 = 58.4 bits (142), Expect = 3e-11
Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 5/82 (6%)
Query: 180 LPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFD 239
LPE P N +FV ++ + ++ F+R+G V ++I D+ TG S Y FV F
Sbjct: 2 LPEGKIMP--NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFY 58
Query: 240 NPKSCEDAYLKMDNVLIDDRRI 261
N + N +++
Sbjct: 59 NDVDVQKIVESQIN--FHGKKL 78
>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 = 58.1 bits (141), Expect = 4e-11
Identities = 20/84 (23%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
+ + +A P L+V L+ ++D L IF FG++ +++ D TG S Y F+
Sbjct: 16 ANNLQKGSAGPMR-LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFIT 74
Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
F + + + A +++ + R +
Sbjct: 75 FSDSECAKKALEQLNGFELAGRPM 98
>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 = 58.5 bits (142), Expect = 4e-11
Identities = 20/81 (24%), Positives = 31/81 (38%), Gaps = 1/81 (1%)
Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
+ +F +L DLE FS GKV +I D+ + S A+VEF
Sbjct: 17 NLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCE 76
Query: 241 PKSCEDAYLKMDNVLIDDRRI 261
+S A + + + I
Sbjct: 77 IQSVPLA-IGLTGQRLLGVPI 96
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 57.6 bits (140), Expect = 4e-11
Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 2/73 (2%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+FV L + L+ F+ G V ++ + G S V+F++P+ E A M
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMM 68
Query: 252 DNVLIDDRRIHAR 264
+ + + R I R
Sbjct: 69 NGMKLSGREIDVR 81
>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 = 58.1 bits (141), Expect = 5e-11
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
LF+ L+ T+++ L + ++GK+ C V+RD + S + FV F + + A +
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA-MAA 88
Query: 252 DNVLIDDRRI 261
ID R +
Sbjct: 89 RPHSIDGRVV 98
>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 = 57.1 bits (139), Expect = 6e-11
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
++V ++ + ++LE F G VN ++ DK +G +A++EF + +S + L +
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS-LAL 67
Query: 252 DNVLIDDRRI 261
D L R+I
Sbjct: 68 DESLFRGRQI 77
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 57.7 bits (140), Expect = 6e-11
Identities = 15/81 (18%), Positives = 30/81 (37%), Gaps = 8/81 (9%)
Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
+ LFV + +L IF FG + +++ +AFVEF+
Sbjct: 24 RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG--------FAFVEFEEA 75
Query: 242 KSCEDAYLKMDNVLIDDRRIH 262
+S A ++ ++ +
Sbjct: 76 ESAAKAIEEVHGKSFANQPLE 96
>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 = 59.1 bits (144), Expect = 6e-11
Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 1/81 (1%)
Query: 184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
D +FV + P + E FS++G + +++ DK TG S + FV +D+ +
Sbjct: 82 DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141
Query: 244 CEDAYLKMDNVLIDDRRIHAR 264
+ + + DR+I +
Sbjct: 142 VDRV-CQNKFIDFKDRKIEIK 161
Score = 57.5 bits (140), Expect = 2e-10
Identities = 20/70 (28%), Positives = 41/70 (58%), Gaps = 2/70 (2%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+F+ LN T++D+L F ++G V ++++D TG S + F+ F+ P S ++ +K
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV-VKT 64
Query: 252 DNVLIDDRRI 261
++ +D + I
Sbjct: 65 QHI-LDGKVI 73
>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 = 59.1 bits (143), Expect = 6e-11
Identities = 19/82 (23%), Positives = 37/82 (45%)
Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
P + +LFV ++ +D+++ F +G++ + D+ TG S YA VE++
Sbjct: 64 PGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET 123
Query: 241 PKSCEDAYLKMDNVLIDDRRIH 262
K A ++ I + I
Sbjct: 124 HKQALAAKEALNGAEIMGQTIQ 145
>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 = 56.9 bits (138), Expect = 8e-11
Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 5/87 (5%)
Query: 175 EIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYA 234
++ D + L L+ ++D+L+ +F E+ G S A
Sbjct: 2 HMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIA 56
Query: 235 FVEFDNPKSCEDAYLKMDNVLIDDRRI 261
++EF + E + ID R +
Sbjct: 57 YIEFKSEADAEKNLEEKQGAEIDGRSV 83
>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 = 57.6 bits (139), Expect = 8e-11
Identities = 18/80 (22%), Positives = 36/80 (45%), Gaps = 6/80 (7%)
Query: 190 NVLFVCKLNPVTSDDDL---EIIFSRFGKVNCCEVIRDKVTGDSLQ---YAFVEFDNPKS 243
N++FV L+ +D ++ F +FGK++ + S A+V + +
Sbjct: 16 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75
Query: 244 CEDAYLKMDNVLIDDRRIHA 263
A ++NV++D R + A
Sbjct: 76 ALRAIQCVNNVVVDGRTLKA 95
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 58.0 bits (140), Expect = 8e-11
Identities = 15/129 (11%), Positives = 37/129 (28%), Gaps = 10/129 (7%)
Query: 161 LRAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDL----EIIFSRFGKV 216
++ AK ++ P V+ + +NP + L + S G +
Sbjct: 1 MKETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDI 60
Query: 217 NCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH---ARGEEWNMWKR 273
I ++ D+ A++ F +S + + + + + +
Sbjct: 61 LD---IVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAED 117
Query: 274 REEEEEKEE 282
E
Sbjct: 118 GSLEHHHHH 126
>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 = 60.4 bits (147), Expect = 9e-11
Identities = 8/93 (8%), Positives = 32/93 (34%), Gaps = 6/93 (6%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
L++ P + ++ + V + S ++A+++ + + K+
Sbjct: 120 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 179
Query: 252 DNVLIDDRRIHARGEEWNMWKRREEEEEKEEID 284
+ + I+ + + E+ ++ +
Sbjct: 180 NGLKIEGYTLVTK------VSNPLEKSKRTDSA 206
Score = 60.0 bits (146), Expect = 1e-10
Identities = 19/84 (22%), Positives = 34/84 (40%), Gaps = 3/84 (3%)
Query: 181 PEADAAPPENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRD-KVTGDSLQYAFVEF 238
A + + L+ + ++ L F FG + + K + AF+ F
Sbjct: 202 RTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVF 261
Query: 239 DNPKSCEDAYLKMDNVLIDDRRIH 262
+N S E A L+M+ L+ +R I
Sbjct: 262 ENKDSAERA-LQMNRSLLGNREIS 284
Score = 56.5 bits (137), Expect = 2e-09
Identities = 10/70 (14%), Positives = 24/70 (34%), Gaps = 3/70 (4%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+ V L + + + F G + +V + ++A +EF A +
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAA-ITK 100
Query: 252 DNVLIDDRRI 261
+ ++ I
Sbjct: 101 THKVVGQNEI 110
>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 = 57.4 bits (139), Expect = 9e-11
Identities = 27/108 (25%), Positives = 45/108 (41%), Gaps = 2/108 (1%)
Query: 155 AQEIEELRAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFG 214
A ++ ++ A A E +V +V ++ ++ DLE FS G
Sbjct: 3 APCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSV-YVGNVDYGSTAQDLEAHFSSCG 61
Query: 215 KVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
+N ++ DK +G YA++EF S DA + MD + R I
Sbjct: 62 SINRITILCDKFSGHPKGYAYIEFAERNS-VDAAVAMDETVFRGRTIK 108
>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 = 60.1 bits (146), Expect = 1e-10
Identities = 25/101 (24%), Positives = 42/101 (41%), Gaps = 5/101 (4%)
Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
A L V L+PV S++ LE FS+FG V V+ D G + FVEF
Sbjct: 93 ATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPAR 151
Query: 246 DAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEK 286
A + + + + + E+ ++++ + EK
Sbjct: 152 KALERCGDGAF----LLTTTPRPVIVEPMEQFDDEDGLPEK 188
Score = 59.3 bits (144), Expect = 2e-10
Identities = 17/81 (20%), Positives = 36/81 (44%), Gaps = 6/81 (7%)
Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
P LFV L +++D + +F R+G+ + + RD+ G + F+ ++
Sbjct: 14 PGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR--G----FGFIRLES 67
Query: 241 PKSCEDAYLKMDNVLIDDRRI 261
E A ++D ++ R +
Sbjct: 68 RTLAEIAKAELDGTILKSRPL 88
>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 = 56.8 bits (137), Expect = 1e-10
Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 8/79 (10%)
Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
P VL + KL ++ ++ + FGKV +++ K AF+E ++
Sbjct: 12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQAFLELATEEAAI 65
Query: 246 DA--YLKMDNVLIDDRRIH 262
Y + ++ I+
Sbjct: 66 TMVNYYSAVTPHLRNQPIY 84
>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 = 56.9 bits (138), Expect = 1e-10
Identities = 19/82 (23%), Positives = 37/82 (45%)
Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
P + +LFV ++ +D+++ F +G++ + D+ TG S YA VE++
Sbjct: 18 PGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET 77
Query: 241 PKSCEDAYLKMDNVLIDDRRIH 262
K A ++ I + I
Sbjct: 78 HKQALAAKEALNGAEIMGQTIQ 99
>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 = 56.7 bits (137), Expect = 1e-10
Identities = 20/105 (19%), Positives = 37/105 (35%), Gaps = 9/105 (8%)
Query: 190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
V+ L T +++ FSRFG + + +T A VEF P A+
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGIT------AIVEFLEPLEARKAFR 64
Query: 250 KMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEKKEEEEKED 294
+ ++ EW +K++ ++ E+ E
Sbjct: 65 HLAYSKFHHVPLYL---EWAPIGVFGAAPQKKDSQHEQPAEKAES 106
>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 = 56.6 bits (137), Expect = 1e-10
Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 6/77 (7%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+F+ L+ + ++ L + +FG + V+ T S AF +F ++ +
Sbjct: 18 VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 77
Query: 252 DNVL------IDDRRIH 262
+D R++
Sbjct: 78 SLEAEGGGLKLDGRQLK 94
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 56.3 bits (136), Expect = 2e-10
Identities = 15/101 (14%), Positives = 36/101 (35%), Gaps = 8/101 (7%)
Query: 189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAY 248
+++ + DD++ G+V ++ R FV FD+ +S +
Sbjct: 11 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKF- 68
Query: 249 LKMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEKKEE 289
++ + + ++K ++ EE + K E
Sbjct: 69 VETPGQKYKETDLLI------LFKDDYFAKKNEERKQNKVE 103
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 55.8 bits (135), Expect = 2e-10
Identities = 18/73 (24%), Positives = 25/73 (34%), Gaps = 6/73 (8%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+FV L F FG V V+ DK G +A VE + + E L
Sbjct: 11 VFVSGFPRGVDSAQLSEYFLAFGPVA--SVVMDKDKG---VFAIVEMGDVGAREAV-LSQ 64
Query: 252 DNVLIDDRRIHAR 264
+ R+ R
Sbjct: 65 SQHSLGGHRLRVR 77
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 56.2 bits (136), Expect = 2e-10
Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 2/84 (2%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
G + L V + D DL +F +FGK+ E+I ++ S + FV
Sbjct: 18 GSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVT 75
Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
F+N + A K+ +++ R+I
Sbjct: 76 FENSADADRAREKLHGTVVEGRKI 99
>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 = 58.2 bits (140), Expect = 3e-10
Identities = 9/75 (12%), Positives = 23/75 (30%)
Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
P NVL ++++ I G V + +E+D+ +
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALE 180
Query: 247 AYLKMDNVLIDDRRI 261
+++ + +
Sbjct: 181 TLGFLNHYQMKNPNG 195
Score = 57.4 bits (138), Expect = 4e-10
Identities = 16/125 (12%), Positives = 41/125 (32%), Gaps = 12/125 (9%)
Query: 186 APPENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
VL V L+ + D + +F +G V + ++ K A VE + +
Sbjct: 1 GADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPG-----AAMVEMADGYAV 55
Query: 245 EDAYLKMDNVLIDDRRI------HARGEEWNMWKRREEEEEKEEIDEKKEEEEKEDRAMI 298
+ A ++N + +++ + + ++ E +
Sbjct: 56 DRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAA 115
Query: 299 GDRME 303
+R++
Sbjct: 116 KNRIQ 120
>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 = 55.3 bits (134), Expect = 3e-10
Identities = 20/101 (19%), Positives = 41/101 (40%), Gaps = 8/101 (7%)
Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
+ +FV + +++ L+ IFS G V ++ D+ TG Y F E+ +
Sbjct: 1 DPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQ 60
Query: 242 KSCEDAYLKMDNVLIDDRRI---HARGEEWNMWKRREEEEE 279
++ A ++ R + +A E+ +EE +
Sbjct: 61 ETALSAMRNLNGREFSGRALRVDNAASEK-----NKEELKS 96
>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 = 56.0 bits (135), Expect = 4e-10
Identities = 28/153 (18%), Positives = 57/153 (37%), Gaps = 16/153 (10%)
Query: 139 GLIGADEDIDETAGLSAQEIEELRAEREAKARATILEIVGDLPEADAAPPENVLFVCKLN 198
G +G+D D + +S +E+E+ R RE ++ + P ++V L
Sbjct: 1 GPLGSDSDEMPSECISRRELEKGRISREEMETLSVFRSY------EPGEPNCRIYVKNLA 54
Query: 199 PVTSDDDLEIIFSRFGKVNCCEV-----IRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDN 253
+ DL+ IF R+ + IR G AF+ N K+ A + +
Sbjct: 55 KHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANG 114
Query: 254 VLIDDRRIHARGEEWNMWKRREEEEEKEEIDEK 286
++ + + + +++ +E K
Sbjct: 115 YVLFGKPMVV-----QFARSARPKQDPKEGKRK 142
>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 = 54.1 bits (131), Expect = 6e-10
Identities = 12/72 (16%), Positives = 26/72 (36%), Gaps = 2/72 (2%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFG--KVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
L++ L T+D+DL G + + ++ G S +A V + S +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 250 KMDNVLIDDRRI 261
+ + +
Sbjct: 64 LLPKRELHGQNP 75
>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 = 58.0 bits (139), Expect = 7e-10
Identities = 27/119 (22%), Positives = 50/119 (42%), Gaps = 10/119 (8%)
Query: 186 APPENVLFVCKLNPVTSDDDLE----IIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
P + +++ LN D+L+ IFS+FG++ V R + AFV F
Sbjct: 6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEV 62
Query: 242 KSCEDAYLKMDNVLIDDRRIH---ARGEEWNMWKRREEEEEKEEIDEKKEEEEKEDRAM 297
S +A M D+ + A+ + + K + E++ EK++ + +E A
Sbjct: 63 SSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPAT 121
Score = 44.5 bits (104), Expect = 2e-05
Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 5/74 (6%)
Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
PP ++LF+ L T++ L ++F++F ++ + AFVEFDN
Sbjct: 205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD-----IAFVEFDNEVQAGA 259
Query: 247 AYLKMDNVLIDDRR 260
A + I
Sbjct: 260 ARDALQGFKITQNN 273
>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 = 54.6 bits (132), Expect = 8e-10
Identities = 13/82 (15%), Positives = 34/82 (41%), Gaps = 2/82 (2%)
Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDK-VTGDSLQYAFVEFDN 240
+ + + V + + ++ +FS FG++ + + TG + FV+F
Sbjct: 8 QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 67
Query: 241 PKSCEDAYLKMDN-VLIDDRRI 261
+ + A+ + + + RR+
Sbjct: 68 KQDAKKAFNALCHSTHLYGRRL 89
>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 = 56.4 bits (136), Expect = 9e-10
Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 6/73 (8%)
Query: 191 VLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
VL V LNP + L I+F +G V +++ +K A V+ + + A
Sbjct: 5 VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQLAMS 59
Query: 250 KMDNVLIDDRRIH 262
++ + + I
Sbjct: 60 HLNGHKLHGKPIR 72
Score = 50.7 bits (121), Expect = 8e-08
Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 4/78 (5%)
Query: 183 ADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
+ PP L + + P S++DL+++FS G V K A ++ + +
Sbjct: 114 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK----MALIQMGSVE 169
Query: 243 SCEDAYLKMDNVLIDDRR 260
A + + N + +
Sbjct: 170 EAVQALIDLHNHDLGENH 187
>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 = 53.5 bits (129), Expect = 1e-09
Identities = 19/94 (20%), Positives = 31/94 (32%), Gaps = 8/94 (8%)
Query: 177 VGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNC--------CEVIRDKVTG 228
+G + N +FV L + + + F + G + + D+ TG
Sbjct: 1 MGHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETG 60
Query: 229 DSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
A V FD+P S + A D I
Sbjct: 61 KLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIK 94
>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 = 53.6 bits (129), Expect = 2e-09
Identities = 11/74 (14%), Positives = 31/74 (41%), Gaps = 4/74 (5%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGK-VNCCEVIRD-KVTGDSLQYAFVEFDNPKSCEDAYL 249
LF+ + + +++ ++ + V V + +AFVE+++ ++ A
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70
Query: 250 KM--DNVLIDDRRI 261
K+ + + +I
Sbjct: 71 KLMPGRIQLWGHQI 84
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 53.2 bits (128), Expect = 2e-09
Identities = 14/72 (19%), Positives = 24/72 (33%)
Query: 190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
+ L +FS+ GKV E D+ TG + + FVE + +
Sbjct: 13 GAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72
Query: 250 KMDNVLIDDRRI 261
+D +
Sbjct: 73 SFHGKRLDLKHR 84
>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 = 51.9 bits (125), Expect = 4e-09
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
L+V L ++ DL F +FG++ V++ + Q AF++F ++ E A K
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAFIQFATRQAAEVAAEKS 68
Query: 252 DN-VLIDDRRI 261
N ++++ RR+
Sbjct: 69 FNKLIVNGRRL 79
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 52.8 bits (127), Expect = 4e-09
Identities = 18/84 (21%), Positives = 28/84 (33%), Gaps = 8/84 (9%)
Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNC--------CEVIRDKVTGDSLQYAFVEF 238
N +FV L + + + F + G + + D+ TG A V F
Sbjct: 5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 64
Query: 239 DNPKSCEDAYLKMDNVLIDDRRIH 262
D+P S + A D I
Sbjct: 65 DDPPSAKAAIDWFDGKEFSGNPIK 88
>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 = 51.9 bits (125), Expect = 5e-09
Identities = 12/82 (14%), Positives = 30/82 (36%)
Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
+ P ++ V + S D++ F + + ++ G A V F++
Sbjct: 7 GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 66
Query: 241 PKSCEDAYLKMDNVLIDDRRIH 262
A + +++ I R++
Sbjct: 67 RDEATAAVIDLNDRPIGSRKVK 88
>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 = 49.9 bits (120), Expect = 2e-08
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
++V L + + ++ +FS+FGKV ++I D+ T + FVE +S +A K+
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 252 DNVLIDDRRI 261
DN R I
Sbjct: 63 DNTDFMGRTI 72
>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 = 50.0 bits (120), Expect = 2e-08
Identities = 13/82 (15%), Positives = 30/82 (36%)
Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
+ P V+ V + S D++ F + + ++ G A V F++
Sbjct: 7 GSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 66
Query: 241 PKSCEDAYLKMDNVLIDDRRIH 262
A + +++ I R++
Sbjct: 67 RDEATAAVIDLNDRPIGSRKVK 88
>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 = 49.6 bits (119), Expect = 3e-08
Identities = 15/82 (18%), Positives = 33/82 (40%), Gaps = 10/82 (12%)
Query: 190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
N L++ L+P + DDL +F +V+ YAFV++ + A
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS------GYAFVDYPDQNWAIRAIE 62
Query: 250 KMD-NVLIDDRRI---HARGEE 267
+ V + + + ++ ++
Sbjct: 63 TLSGKVELHGKIMEVDYSVSKK 84
>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 = 49.5 bits (119), Expect = 4e-08
Identities = 20/80 (25%), Positives = 32/80 (40%), Gaps = 7/80 (8%)
Query: 187 PPENVLFVCKLNPVTSDDDLE----IIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
P + +++ LN D+L+ IFSRFG++ I + AFV F
Sbjct: 6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQI---LDILVSRSLKMRGQAFVIFKEVS 62
Query: 243 SCEDAYLKMDNVLIDDRRIH 262
S +A M D+ +
Sbjct: 63 SATNALRSMQGFPFYDKPMR 82
>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 = 49.1 bits (118), Expect = 4e-08
Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 7/73 (9%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+FV + ++D+L FS++G V + + +AFV F + + +
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSL-CGE 61
Query: 252 DNVLIDDRRIHAR 264
D + I +H
Sbjct: 62 DLI-IKGISVHIS 73
>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 = 4e-08
Identities = 20/93 (21%), Positives = 34/93 (36%), Gaps = 8/93 (8%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVN--------CCEVIRDKVTGD 229
G + D + ++V LN + DDL F + G V + DK TG
Sbjct: 4 GSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGK 63
Query: 230 SLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
A V +++P + + A D ++
Sbjct: 64 PKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLK 96
>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 = 49.5 bits (118), Expect = 5e-08
Identities = 13/77 (16%), Positives = 28/77 (36%), Gaps = 8/77 (10%)
Query: 186 APPENVLFVC--KLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
+ L V L S + L + + G V+ + +K Y+F + +
Sbjct: 22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEE 75
Query: 244 CEDAYLKMDNVLIDDRR 260
+ AY+ ++ + D
Sbjct: 76 SKRAYVTLNGKEVVDDL 92
>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 = 49.0 bits (117), Expect = 7e-08
Identities = 20/95 (21%), Positives = 32/95 (33%), Gaps = 4/95 (4%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
G + + + + L S +++ FS V + G S AFV+
Sbjct: 4 GSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQ 63
Query: 238 FDNPKSCEDAYLKMDNVLIDDRRIH---ARGEEWN 269
F + + E A LK I R I + E
Sbjct: 64 FASQEIAEKA-LKKHKERIGHRYIEIFKSSRAEVR 97
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 48.4 bits (116), Expect = 9e-08
Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 2/75 (2%)
Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
P +V L T D++ IF + ++RDK T + +VEFD S ++
Sbjct: 13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKE 71
Query: 247 AYLKMDNVLIDDRRI 261
A L D L+ DR +
Sbjct: 72 A-LTYDGALLGDRSL 85
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 47.3 bits (113), Expect = 2e-07
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 3/76 (3%)
Query: 188 PENVLFVCKLNPVTSDDDLEIIFS-RFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
PE LFV L P D L F + +V+ D+ TG S Y FV+F + +
Sbjct: 8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKR 66
Query: 247 AYLKMDN-VLIDDRRI 261
A + V + + +
Sbjct: 67 ALTECQGAVGLGSKPV 82
>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 = 47.4 bits (113), Expect = 3e-07
Identities = 10/80 (12%), Positives = 22/80 (27%), Gaps = 1/80 (1%)
Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
E D + + + + D+ + G L A V+F N
Sbjct: 8 EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 67
Query: 242 KSCEDAYLKMDNVLIDDRRI 261
+ ++ ++ R
Sbjct: 68 DDARKS-ERLHRKKLNGREA 86
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 46.7 bits (111), Expect = 4e-07
Identities = 13/82 (15%), Positives = 29/82 (35%), Gaps = 7/82 (8%)
Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQ-YAFVEFD 239
P + AP ++V L DL+ G V ++T + AF+ +
Sbjct: 11 PPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPL------RLTWQGPRRRAFLHYP 64
Query: 240 NPKSCEDAYLKMDNVLIDDRRI 261
+ + + A + + + +
Sbjct: 65 DSAAAQQAVSCLQGLRLGTDTL 86
>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 = 47.1 bits (112), Expect = 4e-07
Identities = 14/82 (17%), Positives = 24/82 (29%), Gaps = 1/82 (1%)
Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
+++ L + + F + V I G + FVEF N
Sbjct: 17 RSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRN 76
Query: 241 PKSCEDAYLKMDNVLIDDRRIH 262
+ A L + +R I
Sbjct: 77 EADYKAA-LCRHKQYMGNRFIQ 97
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 46.3 bits (110), Expect = 5e-07
Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 8/79 (10%)
Query: 189 ENVLFVCKLNPVTSD------DDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
++V+ V + V D + + IFS+FGK+ + G + Y F+E+ +P
Sbjct: 15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKIT--NDFYPEEDGKTKGYIFLEYASPA 72
Query: 243 SCEDAYLKMDNVLIDDRRI 261
DA D +D +
Sbjct: 73 HAVDAVKNADGYKLDKQHT 91
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 45.5 bits (108), Expect = 6e-07
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 10/80 (12%)
Query: 189 ENVLFVCKLNPVTSDDDLEI-------IFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
++V+ V + P D LE IFS+FGK+ + G + Y F+E+ +P
Sbjct: 1 DSVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKIT--NDFYPEEDGKTKGYIFLEYASP 57
Query: 242 KSCEDAYLKMDNVLIDDRRI 261
DA D +D +
Sbjct: 58 AHAVDAVKNADGYKLDKQHT 77
>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 = 46.4 bits (110), Expect = 7e-07
Identities = 16/84 (19%), Positives = 29/84 (34%), Gaps = 1/84 (1%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
G + + + + + L + +++ FS V + G AFV+
Sbjct: 31 GRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQ 90
Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
F + + E A L I R I
Sbjct: 91 FASQELAEKA-LGKHKERIGHRYI 113
>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 = 45.3 bits (108), Expect = 8e-07
Identities = 14/73 (19%), Positives = 30/73 (41%), Gaps = 7/73 (9%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+FV + + ++L+ F ++G+V + + +AFV F + K +
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK-----PFRAFAFVTFADDKVAQSL-CGE 67
Query: 252 DNVLIDDRRIHAR 264
D + I +H
Sbjct: 68 DLI-IKGISVHIS 79
>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 = 45.7 bits (109), Expect = 9e-07
Identities = 13/75 (17%), Positives = 32/75 (42%), Gaps = 3/75 (4%)
Query: 188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQ-YAFVEFDNPKSCED 246
P F+ L +++ ++ F + R+ + L+ + + EF++ S
Sbjct: 14 PPYTAFLGNLPYDVTEESIKEFFRGLNISAVR-LPREPSNPERLKGFGYAEFEDLDSLLS 72
Query: 247 AYLKMDNVLIDDRRI 261
A L ++ + ++RI
Sbjct: 73 A-LSLNEESLGNKRI 86
>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 = 45.1 bits (107), Expect = 1e-06
Identities = 17/85 (20%), Positives = 38/85 (44%), Gaps = 6/85 (7%)
Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
P + + V + ++D+ F +V+ +++D G + V+F +P+ +
Sbjct: 14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFE 71
Query: 247 AYLKMDNVLIDDRRIH---ARGEEW 268
A LK + +L+ R + A +W
Sbjct: 72 A-LKRNRMLMIQRYVEVSPATERQW 95
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 45.0 bits (106), Expect = 2e-06
Identities = 19/86 (22%), Positives = 32/86 (37%), Gaps = 13/86 (15%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDK--VTGDSLQYAFVEFDNPKSCEDA-- 247
+FV L P +D++ F RFG + + + YAF+ F S +
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70
Query: 248 ---------YLKMDNVLIDDRRIHAR 264
YL + + I D+ + R
Sbjct: 71 ACLEEDGKLYLCVSSPTIKDKPVQIR 96
>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 = 45.9 bits (108), Expect = 3e-06
Identities = 20/86 (23%), Positives = 29/86 (33%), Gaps = 6/86 (6%)
Query: 181 PEADAAPPENVLFVCKLNPVTS--DDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEF 238
A VL + N D L IFS+FG V A +++
Sbjct: 36 AGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF----QALLQY 91
Query: 239 DNPKSCEDAYLKMDNVLIDDRRIHAR 264
+P S + A L +D I + R
Sbjct: 92 ADPVSAQHAKLSLDGQNIYNACCTLR 117
>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 = 44.4 bits (105), Expect = 3e-06
Identities = 20/73 (27%), Positives = 25/73 (34%), Gaps = 7/73 (9%)
Query: 189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAY 248
EN + V L P S DL+ G V +V RD VEF + A
Sbjct: 15 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-------TGVVEFVRKEDMTYAV 67
Query: 249 LKMDNVLIDDRRI 261
K+DN
Sbjct: 68 RKLDNTKFRSHEG 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 = 44.0 bits (104), Expect = 5e-06
Identities = 23/85 (27%), Positives = 28/85 (32%), Gaps = 11/85 (12%)
Query: 181 PEADAAPP----ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFV 236
P PP EN + V L P S DL+ G V +V RD V
Sbjct: 4 PRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-------TGVV 56
Query: 237 EFDNPKSCEDAYLKMDNVLIDDRRI 261
EF + A K+DN
Sbjct: 57 EFVRKEDMTYAVRKLDNTKFRSHEG 81
>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 = 43.2 bits (102), Expect = 5e-06
Identities = 9/75 (12%), Positives = 27/75 (36%), Gaps = 6/75 (8%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEV-----IRDKVTGDSLQYAFVEFDNPKSCED 246
L+V + +++ + F+ ++ + +AF+EF +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 247 AYLKMDNVLIDDRRI 261
A + D ++ + +
Sbjct: 69 A-MAFDGIIFQGQSL 82
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 44.2 bits (104), Expect = 5e-06
Identities = 22/81 (27%), Positives = 31/81 (38%), Gaps = 8/81 (9%)
Query: 181 PEADAAPPENVLFVCKLN---PVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
A VL + N PVT D L IFS+FG V A ++
Sbjct: 18 AGMAMAGQSPVLRIIVENLFYPVT-LDVLHQIFSKFGTVLKIITFTKNNQF----QALLQ 72
Query: 238 FDNPKSCEDAYLKMDNVLIDD 258
+ +P S + A L +D I +
Sbjct: 73 YADPVSAQHAKLSLDGQNIYN 93
>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 = 42.4 bits (100), Expect = 8e-06
Identities = 7/70 (10%), Positives = 23/70 (32%), Gaps = 7/70 (10%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
+ V L ++ ++ + + ++ + + AFV N + ++A
Sbjct: 8 ILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMF 60
Query: 252 DNVLIDDRRI 261
+ +
Sbjct: 61 HQYSFRGKDL 70
>3bkp_A Cyclophilin; malaria, isomerase, structural GENO structural
genomics consortium, SGC; 1.80A {Toxoplasma gondii}
Length = 232
Score = 44.7 bits (106), Expect = 1e-05
Identities = 10/46 (21%), Positives = 13/46 (28%), Gaps = 1/46 (2%)
Query: 102 KNDIRITHAVILEDPYEDLPELVYPP-SPEPTRELLANGLIGADED 146
I +L +P+EDL P P E G
Sbjct: 181 MTPPFIKSVDVLWNPFEDLVPRRLPDAPPAQKDERKRARAAGGRTT 226
>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 = 42.2 bits (100), Expect = 1e-05
Identities = 14/75 (18%), Positives = 32/75 (42%), Gaps = 3/75 (4%)
Query: 188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQ-YAFVEFDNPKSCED 246
P F+ L +++ ++ F + R+ + L+ + + EF++ S
Sbjct: 18 PPYTAFLGNLPYDVTEESIKEFFRGLNISAVR-LPREPSNPERLKGFGYAEFEDLDSLLS 76
Query: 247 AYLKMDNVLIDDRRI 261
A L ++ + +RRI
Sbjct: 77 A-LSLNEESLGNRRI 90
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 42.5 bits (100), Expect = 1e-05
Identities = 11/79 (13%), Positives = 24/79 (30%), Gaps = 5/79 (6%)
Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFG-KVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
+ + L S DL+ + + V G +EF + +
Sbjct: 26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDG----TGALEFPSEEILV 81
Query: 246 DAYLKMDNVLIDDRRIHAR 264
+A +++N+ I
Sbjct: 82 EALERLNNIEFRGSVITVE 100
>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 = 41.6 bits (98), Expect = 3e-05
Identities = 13/84 (15%), Positives = 27/84 (32%), Gaps = 3/84 (3%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
G + + + + + L +++D+ FS + G A VE
Sbjct: 4 GSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGP-DGRVTGEADVE 61
Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
F + A + D + R +
Sbjct: 62 FATHEDAVAA-MAKDKANMQHRYV 84
>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 = 42.5 bits (99), Expect = 4e-05
Identities = 21/143 (14%), Positives = 47/143 (32%), Gaps = 9/143 (6%)
Query: 140 LIGADEDIDETAGLSAQEIEELRAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNP 199
L I E S E+ E+ ++ R+ + E +++
Sbjct: 60 LTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPT 119
Query: 200 VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDR 259
+ DD++ G+V ++ R FV FD+ +S + ++ +
Sbjct: 120 DATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKF-VETPGQKYKET 177
Query: 260 RIHARGEEWNMWKRREEEEEKEE 282
+ ++K + +K E
Sbjct: 178 DLLI------LFK-DDYFAKKNE 193
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 41.2 bits (96), Expect = 5e-05
Identities = 17/92 (18%), Positives = 31/92 (33%), Gaps = 7/92 (7%)
Query: 175 EIVGDLPEADAAPPENVLFVCKLNPV--TSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQ 232
I D + VL + NP+ + D L + + GKV + +
Sbjct: 9 RITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGI----- 63
Query: 233 YAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR 264
A VEF++ + A ++ I +
Sbjct: 64 QAMVEFESVLCAQKAKAALNGADIYAGCCTLK 95
>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 = 43.3 bits (101), Expect = 7e-05
Identities = 55/393 (13%), Positives = 102/393 (25%), Gaps = 146/393 (37%)
Query: 23 WTMRKKEEKYLESF--EM------WLWRRMEK------------IKWSDKI--------- 53
WT+ K+E+ ++ F E+ +L ++ I+ D++
Sbjct: 69 WTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAK 128
Query: 54 ----RNEEV--LRRGFSFLEDFEIVS-----GISKVCNKTHRYKLAVKCVQSNIIVFKRK 102
R + LR+ L + V G K +A+ S + K
Sbjct: 129 YNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTW-------VALDVCLSYKVQCKMD 181
Query: 103 NDI--------RITHAVI---------LEDPYEDLPELVYPPSPEPT-------RELLA- 137
I V+ ++ + + R LL
Sbjct: 182 FKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNI-KLRIHSIQAELRRLLKS 240
Query: 138 ----NGLIGADE---------------------DIDETAGLSAQEIEELR--------AE 164
N L+ T LSA +
Sbjct: 241 KPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTP 300
Query: 165 REAKAR-ATILEI-VGDLPEADAAPPENVLFVCKLNPV------TSDDDLEIIFSRFGKV 216
E K+ L+ DLP V NP S D + + V
Sbjct: 301 DEVKSLLLKYLDCRPQDLPRE----------VLTTNPRRLSIIAESIRDGLATWDNWKHV 350
Query: 217 NCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM----DNVLIDDRRIHARGEEWNMWK 272
NC DK+T ++ + + P + ++ + I + +W
Sbjct: 351 NC-----DKLT--TIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSL------IWF 397
Query: 273 RREEEEEKEEIDE--KK---EEEEKEDRAMIGD 300
+ + +++ K E++ KE I
Sbjct: 398 DVIKSDVMVVVNKLHKYSLVEKQPKESTISIPS 430
>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 = 39.4 bits (92), Expect = 3e-04
Identities = 15/82 (18%), Positives = 26/82 (31%), Gaps = 3/82 (3%)
Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
+ + + + L +++D+ FS V I G A VEF
Sbjct: 38 EFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVH--IEIGPDGRVTGEADVEFAT 95
Query: 241 PKSCEDAYLKMDNVLIDDRRIH 262
+ A + D + R I
Sbjct: 96 HEEAVAA-MSKDRANMQHRYIE 116
>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 = 38.8 bits (90), Expect = 4e-04
Identities = 17/86 (19%), Positives = 28/86 (32%), Gaps = 3/86 (3%)
Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIR--DKVTGDSLQYAF 235
G + V+ + L S +D++ S + + G AF
Sbjct: 33 GSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAF 92
Query: 236 VEFDNPKSCEDAYLKMDNVLIDDRRI 261
VE + + A LK D + R I
Sbjct: 93 VELGSEDDVKMA-LKKDRESMGHRYI 117
>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 = 37.3 bits (87), Expect = 6e-04
Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 3/77 (3%)
Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
+ + + ++ ++ + K ++R+ G+ Y FV+F N + +
Sbjct: 7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNA-HGNKTGYIFVDFSNEEEVK 64
Query: 246 DAYLKMDNVLIDDRRIH 262
A LK + + R I
Sbjct: 65 QA-LKCNREYMGGRYIE 80
>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 = 36.8 bits (85), Expect = 0.001
Identities = 16/82 (19%), Positives = 27/82 (32%), Gaps = 3/82 (3%)
Query: 183 ADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIR--DKVTGDSLQYAFVEFDN 240
V+ + L S +D++ S + + G AFVE ++
Sbjct: 11 GPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELES 70
Query: 241 PKSCEDAYLKMDNVLIDDRRIH 262
+ A LK D + R I
Sbjct: 71 EDDVKLA-LKKDRESMGHRYIE 91
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 36.8 bits (85), Expect = 0.002
Identities = 12/84 (14%), Positives = 31/84 (36%), Gaps = 4/84 (4%)
Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCE---VIRDKVTGDSLQYAFVE 237
+ + + ++ + L + +++ F + + + + G AFV
Sbjct: 15 AQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVL 74
Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
F + ++A L+ L+ R I
Sbjct: 75 FACEEYAQNA-LRKHKDLLGKRYI 97
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 37.8 bits (87), Expect = 0.003
Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 6/60 (10%)
Query: 197 LNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLI 256
L P + + +FSR G ++ + K FV+F + E A M N +
Sbjct: 151 LKPAQIESRIRFVFSRLGDIDRIRYVESK------NCGFVKFKYQANAEFAKEAMSNQTL 204
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 37.8 bits (87), Expect = 0.003
Identities = 11/68 (16%), Positives = 24/68 (35%), Gaps = 8/68 (11%)
Query: 188 PENVLFVCKLNPVT--SDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
L V S + L + + G V+ + +K Y+F + + +
Sbjct: 17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESK 70
Query: 246 DAYLKMDN 253
AY+ ++
Sbjct: 71 RAYVTLNG 78
>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 = 35.2 bits (81), Expect = 0.004
Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 3/63 (4%)
Query: 201 TSDDDLEIIFSRFGKVNCCEVIR--DKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDD 258
+ +D+ FS N I G A +E ++ + + A L+ + +
Sbjct: 23 CTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKA-LEKHRMYMGQ 81
Query: 259 RRI 261
R +
Sbjct: 82 RYV 84
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 34.5 bits (79), Expect = 0.007
Identities = 14/76 (18%), Positives = 25/76 (32%), Gaps = 4/76 (5%)
Query: 189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAY 248
+ V L P D+ L + F + V+ + G + F P E
Sbjct: 8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCG---GVLTFREPADAERVL 64
Query: 249 LKMDNVLIDDRRIHAR 264
+ D+ L ++ R
Sbjct: 65 AQADHEL-HGAQLSLR 79
>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 = 37.0 bits (85), Expect = 0.009
Identities = 26/108 (24%), Positives = 35/108 (32%), Gaps = 31/108 (28%)
Query: 116 PYEDLPELVYPPSPEPTRELLANGLIGADEDIDETAGLSA-----------QEIEELRAE 164
E L E+V+ R + + DE G+ A QE + E
Sbjct: 1778 SIESLVEVVF------YRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVE 1831
Query: 165 REAKARATILEIV------------GDLPEADAAPPENVLFVCKLNPV 200
R K ++EIV GDL D NVL KL +
Sbjct: 1832 RVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTV--TNVLNFIKLQKI 1877
Score = 29.6 bits (66), Expect = 1.8
Identities = 32/225 (14%), Positives = 66/225 (29%), Gaps = 73/225 (32%)
Query: 122 ELVYPPSPEPTRELLANGLIGADEDIDETAGLSAQEI-----EEL----RAEREAKARAT 172
+L Y S +++ AD +T G S +I L E+ + R
Sbjct: 1634 DL-YKTSKA-AQDVWNR----ADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIREN 1687
Query: 173 ILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSR-FGKVN-------------- 217
++ + D +F ++N ++ F G ++
Sbjct: 1688 YSAMIFETI-VDGKLKTEKIFK-EINEHSTS----YTFRSEKGLLSATQFTQPALTLMEK 1741
Query: 218 -CCEVIRDK--------VTGDSL-QY-AFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE 266
E ++ K G SL +Y A + S E +++ + RG
Sbjct: 1742 AAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESL-VEV---------VFYRG- 1790
Query: 267 EWNMWKRREEEEEKEEIDEKKEEEEKEDRAMIG---DRMEDGLRE 308
++ ++E + + MI R+ +
Sbjct: 1791 ------------MTMQVAVPRDELGRSNYGMIAINPGRVAASFSQ 1823
>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 = 33.1 bits (76), Expect = 0.029
Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 4/61 (6%)
Query: 204 DDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA 263
+DL + S+FG++ + G A V F +P+ + +D R+I A
Sbjct: 41 EDLRVECSKFGQIRKLLLFDRHPDGV----ASVSFRDPEEADYCIQTLDGRWFGGRQITA 96
Query: 264 R 264
+
Sbjct: 97 Q 97
>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 = 32.5 bits (74), Expect = 0.036
Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 2/63 (3%)
Query: 204 DDLEIIFSRFGKVNCCEVIR--DKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI 261
+D+ S++G V E+ R D V FVEF + C+ A + +R +
Sbjct: 30 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 89
Query: 262 HAR 264
+
Sbjct: 90 VTK 92
>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 = 31.5 bits (72), Expect = 0.088
Identities = 10/61 (16%), Positives = 22/61 (36%), Gaps = 4/61 (6%)
Query: 204 DDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA 263
DD+ ++ G V V ++ G+ +V+ + + A + + I A
Sbjct: 32 DDVIEECNKHGGVIHIYVDKNSAQGN----VYVKCPSIAAAIAAVNALHGRWFAGKMITA 87
Query: 264 R 264
Sbjct: 88 A 88
>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 = 31.4 bits (71), Expect = 0.095
Identities = 11/61 (18%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 203 DDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
++ + ++G+V + D + + +V+F + E A + ++N + + IH
Sbjct: 41 EEVFTEMEEKYGEVEEM-NVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99
Query: 263 A 263
A
Sbjct: 100 A 100
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 32.4 bits (73), Expect = 0.12
Identities = 9/35 (25%), Positives = 17/35 (48%), Gaps = 4/35 (11%)
Query: 263 ARGEEWNMWKRREEE----EEKEEIDEKKEEEEKE 293
E ++ K REE+ +E + + E+E +E
Sbjct: 80 LTQEPESIRKWREEQRKRLQELDAASKVMEQEWRE 114
Score = 29.7 bits (66), Expect = 0.87
Identities = 8/58 (13%), Positives = 22/58 (37%), Gaps = 11/58 (18%)
Query: 258 DRRIHARGEEWNMWKRREEEEEKEEID-------EKKEEEEKEDR----AMIGDRMED 304
+R+ + ++ E+ K++++ E+ E+ + +R A D
Sbjct: 95 RKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAFYQQPDAD 152
>3bo7_A Peptidyl-prolyl CIS-trans isomerase cyclophilin-T;
isomerase-immunosuppressant complex, immunosuppressant,
cyclophilin, structural G structural genomics
consortium, SGC; HET: BMT; 2.35A {Toxoplasma gondii}
Length = 201
Score = 31.9 bits (73), Expect = 0.15
Identities = 5/34 (14%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 102 KNDIRITHAVILEDPYEDLPELVYPP-SPEPTRE 134
++ ++ ++P+ED + + E +E
Sbjct: 161 LKPPKVEEIIVFKNPFEDARKEMEDEKREEEEKE 194
>2poe_A Cyclophilin-like protein, putative; cryptosporidium parvum
cyclophilin isomerase, structural genomics; 2.01A
{Cryptosporidium parvum iowa II} PDB: 2qer_A
Length = 185
Score = 31.1 bits (71), Expect = 0.24
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 102 KNDIRITHAVILEDPYEDLPEL 123
++I I VI +P D L
Sbjct: 163 IDEIIIKDIVIHSNPIADQEIL 184
>2hq6_A Serologically defined colon cancer antigen 10; protein folding,
peptidyl-prolyl CIS-trans isomerase, struct genomics;
1.75A {Homo sapiens}
Length = 185
Score = 31.1 bits (71), Expect = 0.27
Identities = 5/18 (27%), Positives = 10/18 (55%)
Query: 102 KNDIRITHAVILEDPYED 119
N +I +L +P++D
Sbjct: 168 HNPHKIKSCEVLFNPFDD 185
>3afv_A DYP; DYE-decolorizing peroxidase, beta barrel, oxidoreductas
aspartic acid; HET: HEM NAG; 1.40A {Bjerkandera adusta}
PDB: 2d3q_A* 3mm2_A* 3mm3_A* 3mm1_A*
Length = 442
Score = 30.5 bits (68), Expect = 0.79
Identities = 7/47 (14%), Positives = 16/47 (34%)
Query: 259 RRIHARGEEWNMWKRREEEEEKEEIDEKKEEEEKEDRAMIGDRMEDG 305
R + E+N + + ++E + A + R + G
Sbjct: 221 RHFQQKVPEFNAYTLANAIPANSAGNLTQQEGAEFLGARMFGRWKSG 267
>1zkc_A Peptidyl-prolyl CIS-trans isomerase like 2; CIS-trans
isomerization, peptidylprolyl isomerase, protein-
folding, structural genomics consortium; 1.65A {Homo
sapiens} SCOP: b.62.1.1
Length = 197
Score = 29.6 bits (67), Expect = 0.95
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 102 KNDIRITHAVILEDPYEDLPE 122
K +IRI + DPYE+
Sbjct: 163 KEEIRIDATTVFVDPYEEADA 183
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 28.6 bits (63), Expect = 1.0
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 5/46 (10%)
Query: 202 SDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
S D L + ++G+V V+ K G A VEF K+ E A
Sbjct: 30 SKDVLLRLLQKYGEVLNL-VLSSKKPG----TAVVEFATVKAAELA 70
>2pnd_A V-SET and immunoglobulin domain containing 4; complement receptor,
IG-like domain, immune system; 1.00A {Mus musculus} PDB:
2icc_A 2ice_S* 2icf_S*
Length = 119
Score = 28.8 bits (64), Expect = 1.1
Identities = 14/75 (18%), Positives = 31/75 (41%), Gaps = 5/75 (6%)
Query: 189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAF----VEFDNPKSC 244
+V C +P+ + + + + + TGD +Q A ++ + K
Sbjct: 17 GDVKIQCIYDPLRGYRQVLVKWLVRHGSDSVTIFLRDSTGDHIQQAKYRGRLKVSH-KVP 75
Query: 245 EDAYLKMDNVLIDDR 259
D L+++ + +DDR
Sbjct: 76 GDVSLQINTLQMDDR 90
>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 = 28.2 bits (63), Expect = 1.4
Identities = 12/65 (18%), Positives = 23/65 (35%), Gaps = 4/65 (6%)
Query: 204 DDLEIIFSRFGKVNCCEVIRDKVTGDSLQYA----FVEFDNPKSCEDAYLKMDNVLIDDR 259
++ +FG VN + ++K + FVEF A ++ R
Sbjct: 40 GEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR 99
Query: 260 RIHAR 264
++ A
Sbjct: 100 KVVAE 104
>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold,
hydro; HET: ADP; 2.91A {Escherichia coli}
Length = 500
Score = 29.7 bits (67), Expect = 1.4
Identities = 10/68 (14%), Positives = 23/68 (33%), Gaps = 1/68 (1%)
Query: 125 YPPSPEPTRELLANGLIGADEDIDETAGLSAQEIEELRAE-REAKARATILEIVGDLPEA 183
R +L + D + + ++ +E E + E E + E++ L +
Sbjct: 181 KVQDKANFRSMLTSQQDENDNPVPDALQVTDEEYERWQKEIGEITLPDHVFELIFMLRQQ 240
Query: 184 DAAPPENV 191
P+
Sbjct: 241 LDKLPDAP 248
>3rg0_A Calreticulin; beta-sandwich, chaperone, monoglucosylated proteins
binding, carbohydrate binding, calcium binding,
endoplasmic reticulu; 2.57A {Mus musculus}
Length = 332
Score = 28.9 bits (64), Expect = 2.2
Identities = 9/44 (20%), Positives = 19/44 (43%)
Query: 251 MDNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEKKEEEEKED 294
DN LI + +A W + E++ + + +E+ K +
Sbjct: 283 FDNFLITNDEAYAEEFGNETWGVTKAAEKQMKDKQDEEQRLKLE 326
>3izy_P Translation initiation factor IF-2, mitochondrial; E coli, RNA,
ribosomal; 10.80A {Bos taurus}
Length = 537
Score = 28.7 bits (65), Expect = 2.4
Identities = 6/19 (31%), Positives = 11/19 (57%)
Query: 157 EIEELRAEREAKARATILE 175
E+ EL+A+ T++E
Sbjct: 167 EMLELKADPTGAVEGTVIE 185
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 28.0 bits (61), Expect = 2.6
Identities = 7/32 (21%), Positives = 12/32 (37%), Gaps = 13/32 (40%)
Query: 156 QEIEELRAEREAKARATILEIVGDLPEADAAP 187
Q +++L + K A D+AP
Sbjct: 20 QALKKL--QASLKLYA---------D--DSAP 38
>2ok3_A Peptidyl-prolyl CIS-trans isomerase-like 3; beta-barrel, helix,
disulfide bridge; 2.00A {Homo sapiens} SCOP: b.62.1.1
PDB: 1xyh_A 2oju_A*
Length = 161
Score = 27.9 bits (63), Expect = 3.0
Identities = 5/17 (29%), Positives = 8/17 (47%)
Query: 102 KNDIRITHAVILEDPYE 118
ND+ I I +P+
Sbjct: 144 LNDVHIKDITIHANPFA 160
>3ix3_A Transcriptional activator protein LASR; quorum sensing receptor,
triphenyl mimics, DNA- binding, quorum sensing; HET:
OHN; 1.40A {Pseudomonas aeruginosa} PDB: 3ix4_A* 3ix8_A*
3jpu_A* 2uv0_E*
Length = 173
Score = 27.8 bits (61), Expect = 3.2
Identities = 8/59 (13%), Positives = 13/59 (22%), Gaps = 2/59 (3%)
Query: 20 SETWTMRKKEEKYLES--FEMWLWRRMEKIKWSDKIRNEEVLRRGFSFLEDFEIVSGIS 76
W Y + + I W I F +V G++
Sbjct: 57 PAAWREHYDRAGYARVDPTVSHCTQSVLPIFWEPSIYQTRKQHEFFEEASAAGLVYGLT 115
>1vq8_G Acidic ribosomal protein P0 homolog; ribosome 50S, protein-protein
complex, RNA-RNA complex, PROT complex, peptidyl
transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS;
2.20A {Haloarcula marismortui} SCOP: j.84.1.1 PDB:
1k73_I* 1k8a_I* 1k9m_I* 1kc8_I* 1kd1_I* 1kqs_G* 1m1k_I*
1m90_I* 1n8r_I* 1nji_I* 1q7y_I* 1q81_I* 1q82_I* 1q86_I*
1qvf_G 1qvg_G 1s72_G* 1vq4_G* 1vq5_G* 1vq6_G* ...
Length = 348
Score = 27.9 bits (61), Expect = 4.9
Identities = 7/35 (20%), Positives = 14/35 (40%)
Query: 275 EEEEEKEEIDEKKEEEEKEDRAMIGDRMEDGLREM 309
++ +++ D EE +D + D L M
Sbjct: 313 DDTASEDDADADDAAEEADDDDDDDEDAGDALGAM 347
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 26.3 bits (58), Expect = 5.3
Identities = 13/78 (16%), Positives = 31/78 (39%), Gaps = 1/78 (1%)
Query: 203 DDDLEIIFSRFGKVNCCEVIRDKVTGD-SLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI 261
+ + + ++GKV C + D F+EF+ +S A + ++ R +
Sbjct: 27 EVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV 86
Query: 262 HARGEEWNMWKRREEEEE 279
A + ++ + E+
Sbjct: 87 KACFYNLDKFRVLDLAEQ 104
>3pow_A Calreticulin; legume lectin fold, CNX/CRT family, multi-functional,
carboh binding, peptide binding, multi-compartmental,
chaperone; 1.55A {Homo sapiens} PDB: 3pos_A 3o0w_A*
3o0v_A* 3o0x_A*
Length = 265
Score = 27.0 bits (59), Expect = 7.8
Identities = 9/48 (18%), Positives = 19/48 (39%)
Query: 245 EDAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEKKEEEEK 292
+ DN LI + +A W + E++ + + +E+ K
Sbjct: 218 VKSGTIFDNFLITNDEAYAEEFGNETWGVTKAAEKQMKDKQDEEQRLK 265
>1e7w_A Pteridine reductase; dihydrofolate reductase, shortchain
dehydrogenase, methotrexate resistance, oxidoreductase;
HET: NDP MTX; 1.75A {Leishmania major} SCOP: c.2.1.2
PDB: 1w0c_A* 1e92_A* 2bf7_A* 2bfa_A* 2bfm_A* 2bfo_A*
2bfp_A* 2p8k_A* 3h4v_A* 2xox_A 1p33_A*
Length = 291
Score = 26.9 bits (60), Expect = 9.5
Identities = 13/64 (20%), Positives = 23/64 (35%), Gaps = 1/64 (1%)
Query: 154 SAQEIEELRAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDL-EIIFSR 212
SA E L A A+ + + + DL AP + T +L ++
Sbjct: 43 SAAEANALSATLNARRPNSAITVQADLSNVATAPVSGADGSAPVTLFTRCAELVAACYTH 102
Query: 213 FGKV 216
+G+
Sbjct: 103 WGRC 106
>1qy5_A Endoplasmin; GRP94, NECA, HSP90, chaperone; HET: NEC; 1.75A {Canis
lupus familiaris} SCOP: d.122.1.1 PDB: 1qy8_A* 1qye_A*
1u0y_A* 1yt2_A*
Length = 269
Score = 26.8 bits (60), Expect = 10.0
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 270 MWKRREEEEEKEEIDEKKEEEEKEDRAM 297
+W + E E+ +E+ +EEKED
Sbjct: 213 VWSSKTETVEEPMEEEEAAKEEKEDSDD 240
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
0.316 0.135 0.400
Gapped
Lambda K H
0.267 0.0439 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,195,968
Number of extensions: 337940
Number of successful extensions: 1811
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1637
Number of HSP's successfully gapped: 266
Length of query: 309
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 216
Effective length of database: 4,105,140
Effective search space: 886710240
Effective search space used: 886710240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (26.5 bits)