RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16559
(207 letters)
>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 = 93.8 bits (233), Expect = 2e-25
Identities = 29/107 (27%), Positives = 53/107 (49%), Gaps = 5/107 (4%)
Query: 92 SKTLLLNNFFTHLSMDNKSVREYDTDINLEFDETEMHKYFVEFYDDVLPELRS-LGQVTQ 150
S+T+ L N + + + + + + EM +++ EF+++V E+ G+V +
Sbjct: 1 SQTIALLNIYRNPQNSS----QSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEE 56
Query: 151 FKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIRGQFC 197
VC N HL GNVYV + E +A +A L R++ G+ I +
Sbjct: 57 MNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS 103
>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 = 72.4 bits (178), Expect = 7e-17
Identities = 28/117 (23%), Positives = 43/117 (36%), Gaps = 22/117 (18%)
Query: 87 IKPSVSKTLLLNNFFTHLSMDNKSVREYDTDINLEFDETEMHKYFVEFYDDVLPELRSLG 146
++P ++ L+N F E + E DDV+ E G
Sbjct: 2 VQPLATQCFQLSNMFNP-------------------QTEEEVGWDTEIKDDVIEECNKHG 42
Query: 147 QVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIRGQFCNVPLWS 203
V V +GNVYV + A+ A AL GR++ GK I + +P +
Sbjct: 43 GVIHIYVDK---NSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYH 96
>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 = 68.2 bits (167), Expect = 3e-15
Identities = 22/109 (20%), Positives = 41/109 (37%), Gaps = 21/109 (19%)
Query: 88 KPSVSKTLLLNNFFTHLSMDNKSVREYDTDINLEFDETEMHKYFVEFYDDVLPELRSLGQ 147
+ + +++ N F +++ D + E +D+ E GQ
Sbjct: 11 RMRHERVVIIKNMFH--------PMDFEDDPLV----------LNEIREDLRVECSKFGQ 52
Query: 148 VTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIRGQF 196
+ + + H G VS+ + EA L GR++GG+QI Q
Sbjct: 53 IRKLLLF---DRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQA 98
>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 = 54.8 bits (132), Expect = 3e-10
Identities = 13/77 (16%), Positives = 31/77 (40%), Gaps = 5/77 (6%)
Query: 133 EFYDDVLPELRSLGQVTQFKVC-----CNKSPHLRGNVYVSYSNEREALRAFYALTGRFY 187
+ +V E G V + + + + ++V +S E +A AL GR++
Sbjct: 37 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWF 96
Query: 188 GGKQIRGQFCNVPLWSK 204
G+++ + + +
Sbjct: 97 AGRKVVAEVYDQERFDN 113
>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 = 54.0 bits (130), Expect = 4e-10
Identities = 18/116 (15%), Positives = 41/116 (35%), Gaps = 22/116 (18%)
Query: 92 SKTLLLNNFFTHLSMDNKSVREYDTDINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQF 151
++ L L N +E + + E +DV E G V
Sbjct: 5 TEVLCLMNMVLP-------------------EELLDDEEYEEIVEDVRDECSKYGLVKSI 45
Query: 152 KV---CCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIRGQFCNVPLWSK 204
++ G ++V +++ + +A LTGR + + + ++C+ + +
Sbjct: 46 EIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHR 101
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 46.0 bits (109), Expect = 4e-07
Identities = 12/74 (16%), Positives = 30/74 (40%), Gaps = 2/74 (2%)
Query: 133 EFYDDVLPELRSLGQVTQFKVC--CNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGK 190
+ + E G+V + + +++ + A++A L GR++GG+
Sbjct: 25 DLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR 84
Query: 191 QIRGQFCNVPLWSK 204
++ F N+ +
Sbjct: 85 VVKACFYNLDKFRV 98
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 44.0 bits (103), Expect = 8e-06
Identities = 8/38 (21%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 5 EEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDF 42
+W +EQ++ ++E + K + ++ KK +E++
Sbjct: 88 RKWREEQRK--RLQELDAASKVMEQEWREKAKKDLEEW 123
Score = 37.4 bits (86), Expect = 0.001
Identities = 10/45 (22%), Positives = 23/45 (51%), Gaps = 9/45 (20%)
Query: 4 QEEWEKEQKRLRDIEE--KNRQEKEERE-----AQEKEFKKSIED 41
++EW ++ K+ D+EE + + E+ E+ +K F + +
Sbjct: 109 EQEWREKAKK--DLEEWNQRQSEQVEKNKINNRIADKAFYQQPDA 151
Score = 31.3 bits (70), Expect = 0.15
Identities = 10/56 (17%), Positives = 22/56 (39%), Gaps = 4/56 (7%)
Query: 10 EQKRLRDIEEKNRQEKEEREAQ----EKEFKKSIEDFIEGVCNELPDGFRTNVETK 61
+ RL E R+ +EE+ + + K +++ E +L + + E
Sbjct: 76 QADRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQV 131
>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 = 38.8 bits (91), Expect = 2e-04
Identities = 17/77 (22%), Positives = 30/77 (38%), Gaps = 14/77 (18%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NL D TE + + F + G K+ + + +V + R+A
Sbjct: 22 NLSRDVTEVLILQLFSQI-----------GPCKSCKMITEHTSN-DPYCFVEFYEHRDAA 69
Query: 177 RAFYALTGRFYGGKQIR 193
A A+ GR GK+++
Sbjct: 70 AALAAMNGRKILGKEVK 86
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 38.4 bits (90), Expect = 2e-04
Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 13/77 (16%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
L F T+ + + G V ++ N++ +G YV Y NE +A
Sbjct: 24 GLPFSCTKEELEEICKAH-----------GTVKDLRLVTNRAGKPKGLAYVEYENESQAS 72
Query: 177 RAFYALTGRFYGGKQIR 193
+A + G I+
Sbjct: 73 QAVMKMDGMTIKENIIK 89
>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 = 38.7 bits (90), Expect = 2e-04
Identities = 14/90 (15%), Positives = 32/90 (35%), Gaps = 18/90 (20%)
Query: 114 YDTDINLEFDETEM---HKYFVEFYDDVLPELRSLGQVTQFKVC----CNKSPHLRGNVY 166
+ ++ + E+ +YF +F G++ + + S + Y
Sbjct: 19 FVVGLSQRLADPEVLKRPEYFGKF-----------GKIHKVVINNSTSYAGSQGPSASAY 67
Query: 167 VSYSNEREALRAFYALTGRFYGGKQIRGQF 196
V+Y +ALRA + G+ ++
Sbjct: 68 VTYIRSEDALRAIQCVNNVVVDGRTLKASL 97
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 38.5 bits (90), Expect = 2e-04
Identities = 13/84 (15%), Positives = 26/84 (30%), Gaps = 12/84 (14%)
Query: 114 YDTDINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNE 172
+N ET + ++ G+V + ++ + + G V +++
Sbjct: 10 TFARLNDNVRETFLKDMCRKY-----------GEVEEVEILLHPRTRKHLGLARVLFTST 58
Query: 173 REALRAFYALTGRFYGGKQIRGQF 196
R A L G I Q
Sbjct: 59 RGAKETVKNLHLTSVMGNIIHAQL 82
>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 = 37.7 bits (88), Expect = 3e-04
Identities = 12/75 (16%), Positives = 21/75 (28%), Gaps = 16/75 (21%)
Query: 119 NLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRA 178
+ T + F F G + + R +V+Y A +A
Sbjct: 22 GEDMTPTLLRGAFSPF-----------GNIIDLSM-----DPPRNCAFVTYEKMESADQA 65
Query: 179 FYALTGRFYGGKQIR 193
L G Q++
Sbjct: 66 VAELNGTQVESVQLK 80
>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 = 37.6 bits (88), Expect = 3e-04
Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 13/77 (16%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NLE E +++ F++ G +T+ +C ++ + +V + +
Sbjct: 23 NLEARVREEILYELFLQA-----------GPLTKVTICKDREGKPKSFGFVCFKHPESVS 71
Query: 177 RAFYALTGRFYGGKQIR 193
A L G G+ I
Sbjct: 72 YAIALLNGIRLYGRPIN 88
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 38.7 bits (90), Expect = 4e-04
Identities = 16/77 (20%), Positives = 30/77 (38%), Gaps = 13/77 (16%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NL+F ++ + + F EF G + + V ++S G V + +AL
Sbjct: 95 NLDFGVSDADIQELFAEF-----------GTLKKAAVDYDRSGRSLGTADVHFERRADAL 143
Query: 177 RAFYALTGRFYGGKQIR 193
+A G G+ +
Sbjct: 144 KAMKQYKGVPLDGRPMD 160
>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 = 37.7 bits (88), Expect = 4e-04
Identities = 16/77 (20%), Positives = 30/77 (38%), Gaps = 13/77 (16%)
Query: 119 NLEF--DETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NL+F + ++ + F EF G + + V ++S G V + +AL
Sbjct: 42 NLDFGVSDADIQELFAEF-----------GTLKKAAVDYDRSGRSLGTADVHFERRADAL 90
Query: 177 RAFYALTGRFYGGKQIR 193
+A G G+ +
Sbjct: 91 KAMKQYKGVPLDGRPMD 107
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 37.7 bits (88), Expect = 5e-04
Identities = 20/81 (24%), Positives = 33/81 (40%), Gaps = 20/81 (24%)
Query: 119 NL--EFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCC----NKSPHLRGNVYVSYSNE 172
+L EF +T++ F+ F G V KV + S + +VS+ N
Sbjct: 47 HLPQEFTDTDLASTFLPF-----------GNVISAKVFIDKQTSLS---KCFGFVSFDNP 92
Query: 173 REALRAFYALTGRFYGGKQIR 193
A A A+ G G K+++
Sbjct: 93 DSAQVAIKAMNGFQVGTKRLK 113
>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 = 37.4 bits (87), Expect = 6e-04
Identities = 12/75 (16%), Positives = 21/75 (28%), Gaps = 16/75 (21%)
Query: 119 NLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRA 178
+ T + F F G + + R +V+Y A +A
Sbjct: 46 GEDMTPTLLRGAFSPF-----------GNIIDLSM-----DPPRNCAFVTYEKMESADQA 89
Query: 179 FYALTGRFYGGKQIR 193
L G Q++
Sbjct: 90 VAELNGTQVESVQLK 104
>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 = 36.9 bits (86), Expect = 7e-04
Identities = 14/77 (18%), Positives = 33/77 (42%), Gaps = 11/77 (14%)
Query: 117 DINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
+N E +E + F + G +++ + +++ RG ++++ N +A
Sbjct: 14 GLNRETNEKMLKAVFGKH-----------GPISEVLLIKDRTSKSRGFAFITFENPADAK 62
Query: 177 RAFYALTGRFYGGKQIR 193
A + G+ GK I+
Sbjct: 63 NAAKDMNGKSLHGKAIK 79
>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 = 37.5 bits (88), Expect = 8e-04
Identities = 14/77 (18%), Positives = 26/77 (33%), Gaps = 13/77 (16%)
Query: 119 NLEF--DETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NL+ E + +YF G + K+ +K+ +V Y +A
Sbjct: 7 NLDKAITEDILKQYFQVG-----------GPIANIKIMIDKNNKNVNYAFVEYHQSHDAN 55
Query: 177 RAFYALTGRFYGGKQIR 193
A L G+ ++
Sbjct: 56 IALQTLNGKQIENNIVK 72
Score = 35.2 bits (82), Expect = 0.005
Identities = 15/81 (18%), Positives = 30/81 (37%), Gaps = 20/81 (24%)
Query: 119 NLEF--DETEMHKYFVEFYDDVLPELRSLGQVTQFKVCC----NKSPHLRGNVYVSYSNE 172
+L D+ + F +F V S RG +VS++++
Sbjct: 94 DLNVNVDDETLRNAFKDF-----------PSYLSGHVMWDMQTGSS---RGYGFVSFTSQ 139
Query: 173 REALRAFYALTGRFYGGKQIR 193
+A A ++ G+ G+ +R
Sbjct: 140 DDAQNAMDSMQGQDLNGRPLR 160
>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 = 36.4 bits (85), Expect = 8e-04
Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 13/81 (16%)
Query: 123 DETEMHKYFV-----EFYDDVLPEL-RSLGQVTQFKVCC----NKSPHLRGNVYVSYSNE 172
FV E + G+++ +V KS +G +VS+ N+
Sbjct: 2 PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKS---KGYGFVSFFNK 58
Query: 173 REALRAFYALTGRFYGGKQIR 193
+A A + G++ GG+QIR
Sbjct: 59 WDAENAIQQMGGQWLGGRQIR 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 = 38.9 bits (90), Expect = 0.001
Identities = 27/157 (17%), Positives = 44/157 (28%), Gaps = 36/157 (22%)
Query: 13 RLRDIEEKNRQEKEEREAQEKEFKKSIE---DFIEGVCNELPDGFRTNVETKPDKELCPF 69
+L++ K E E A + E E F+ G+ V + +
Sbjct: 32 QLQEQFNKILPEPTEGFAADDEPTTPAELVGKFL---------GY---VSSLVEPSKVGQ 79
Query: 70 YSKV--GACRFFDHC--SRNHI------------KPSVSKTLLLNNFFTHLSMDNKSVRE 113
+ +V F++C N I V L+ N+ T M + +
Sbjct: 80 FDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDK 139
Query: 114 YDTDINLEFDETEMHKYFVEF-----YDDVLPELRSL 145
+ F DD ELR L
Sbjct: 140 KSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDL 176
Score = 34.6 bits (79), Expect = 0.019
Identities = 19/115 (16%), Positives = 38/115 (33%), Gaps = 26/115 (22%)
Query: 36 KKSIEDFIEGVCNELPD----------GFRTNVETKPDKELCPFYS---KVGACRFFD-- 80
++ ++D++ + LP G + V + P + L K A D
Sbjct: 346 QEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQS 405
Query: 81 ---HCSRNHIKPSVSKTLLLNN--FFTHLSMD--NKSVREYDTDINLEFDETEMH 128
R K S L F +HL + + + + N+ F+ ++
Sbjct: 406 RIPFSER---KLKFSNRFLPVASPFHSHL-LVPASDLINKDLVKNNVSFNAKDIQ 456
>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 = 36.1 bits (84), Expect = 0.001
Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 14/78 (17%)
Query: 119 NL--EFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHL-RGNVYVSYSNEREA 175
+L EF + ++ + F+ F G V KV +K +L + +VSY N A
Sbjct: 32 HLPQEFGDQDLLQMFMPF-----------GNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 80
Query: 176 LRAFYALTGRFYGGKQIR 193
A ++ G G K+++
Sbjct: 81 QAAIQSMNGFQIGMKRLK 98
>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 = 36.1 bits (84), Expect = 0.002
Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 13/77 (16%)
Query: 119 NLEF--DETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NL+F + ++ + F EF G + + V ++S G V + + +AL
Sbjct: 36 NLDFGVSDADIQELFAEF-----------GTLKKAAVHYDRSGRSLGTADVHFERKADAL 84
Query: 177 RAFYALTGRFYGGKQIR 193
+A G G+ +
Sbjct: 85 KAMKQYNGVPLDGRPMN 101
>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 = 37.3 bits (87), Expect = 0.002
Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 16/79 (20%)
Query: 117 DINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCC--NKSPHLRGNVYVSYSNERE 174
+++ D ++ F F G + KV C N S +G +V + +
Sbjct: 110 NLDKSIDNKALYDTFSAF-----------GNILSCKVVCDENGS---KGYGFVHFETQEA 155
Query: 175 ALRAFYALTGRFYGGKQIR 193
A RA + G +++
Sbjct: 156 AERAIEKMNGMLLNDRKVF 174
Score = 34.2 bits (79), Expect = 0.014
Identities = 15/78 (19%), Positives = 30/78 (38%), Gaps = 12/78 (15%)
Query: 117 DINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREA 175
D++ + E +++ F G + +VC + + G YV++ +A
Sbjct: 22 DLHPDVTEAMLYEKFSPA-----------GPILSIRVCRDMITRRSLGYAYVNFQQPADA 70
Query: 176 LRAFYALTGRFYGGKQIR 193
RA + GK +R
Sbjct: 71 ERALDTMNFDVIKGKPVR 88
>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 = 35.7 bits (83), Expect = 0.002
Identities = 13/77 (16%), Positives = 28/77 (36%), Gaps = 13/77 (16%)
Query: 119 NLEF--DETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NL++ ++ + F G V + + +K RG V++ EA+
Sbjct: 22 NLDYKVGWKKLKEVFSMA-----------GVVVRADILEDKDGKSRGIGTVTFEQSIEAV 70
Query: 177 RAFYALTGRFYGGKQIR 193
+A G+ + +
Sbjct: 71 QAISMFNGQLLFDRPMH 87
>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 = 35.7 bits (83), Expect = 0.002
Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 18/79 (22%)
Query: 119 NL--EFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCC--NKSPHLRGNVYVSYSNERE 174
NL D+ + K F F G +T KV +S +G +V +S+ E
Sbjct: 22 NLDDGIDDERLRKAFSPF-----------GTITSAKVMMEGGRS---KGFGFVCFSSPEE 67
Query: 175 ALRAFYALTGRFYGGKQIR 193
A +A + GR K +
Sbjct: 68 ATKAVTEMNGRIVATKPLY 86
>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 = 35.8 bits (83), Expect = 0.002
Identities = 18/88 (20%), Positives = 30/88 (34%), Gaps = 24/88 (27%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
+ T+ M + F F GQ+ + +V K G +V +S A
Sbjct: 32 GIASGLTDQLMRQTFSPF-----------GQIMEIRVFPEK-----GYSFVRFSTHESAA 75
Query: 177 RAFYALTGRFYGGKQIRGQFCNVPLWSK 204
A ++ G G ++ C W K
Sbjct: 76 HAIVSVNGTTIEGHVVK---CY---WGK 97
>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 = 34.9 bits (81), Expect = 0.003
Identities = 12/78 (15%), Positives = 33/78 (42%), Gaps = 14/78 (17%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREA 175
NL + +E + K F + G +++ + + +G +V++ A
Sbjct: 15 NLSYTSSEEDLEKLFSAY-----------GPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63
Query: 176 LRAFYALTGRFYGGKQIR 193
++A+ + G+ + G+ +
Sbjct: 64 VKAYAEVDGQVFQGRMLH 81
>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 = 35.6 bits (82), Expect = 0.003
Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 7/80 (8%)
Query: 119 NLEF--DETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NL E ++ F + + S Q F + K ++G ++ NE+ A
Sbjct: 52 NLAKHVQEKDLKYIFGRYV-----DFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106
Query: 177 RAFYALTGRFYGGKQIRGQF 196
+A G GK + QF
Sbjct: 107 KALKEANGYVLFGKPMVVQF 126
>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 = 36.0 bits (84), Expect = 0.003
Identities = 11/78 (14%), Positives = 31/78 (39%), Gaps = 12/78 (15%)
Query: 117 DINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREA 175
+ + + E++ F G + ++ + + + G +V +++E ++
Sbjct: 10 YLPQDMTDRELYALFRAI-----------GPINTCRIMRDYKTGYSYGYAFVDFTSEMDS 58
Query: 176 LRAFYALTGRFYGGKQIR 193
RA L G K+++
Sbjct: 59 QRAIKVLNGITVRNKRLK 76
Score = 30.6 bits (70), Expect = 0.21
Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 14/83 (16%)
Query: 114 YDTDINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCC-NKSPHLRGNVYVSYSNE 172
Y T++ + ++ F ++ G + Q + + RG +V Y+
Sbjct: 93 YVTNLPRTITDDQLDTIFGKY-----------GSIVQKNILRDKLTGRPRGVAFVRYNKR 141
Query: 173 REALRAFYALTGRFYGG--KQIR 193
EA A AL G + +
Sbjct: 142 EEAQEAISALNNVIPEGGSQPLS 164
>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 = 36.4 bits (83), Expect = 0.003
Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 13/82 (15%)
Query: 115 DTDINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNERE 174
+ I + + ++ F +F GQ+ V +S +RG +V +
Sbjct: 18 NEKIKKDELKKSLYAIFSQF-----------GQILDILVS--RSLKMRGQAFVIFKEVSS 64
Query: 175 ALRAFYALTGRFYGGKQIRGQF 196
A A ++ G + K +R Q+
Sbjct: 65 ATNALRSMQGFPFYDKPMRIQY 86
>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 = 34.9 bits (81), Expect = 0.003
Identities = 14/77 (18%), Positives = 22/77 (28%), Gaps = 13/77 (16%)
Query: 119 NL--EFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NL DE E+ F GQV ++ + S RG + + +
Sbjct: 32 NLPLSMDEQELENMLKPF-----------GQVISTRILRDSSGTSRGVGFARMESTEKCE 80
Query: 177 RAFYALTGRFYGGKQIR 193
G+F
Sbjct: 81 AVIGHFNGKFIKTPPGV 97
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 36.1 bits (84), Expect = 0.004
Identities = 10/81 (12%), Positives = 28/81 (34%), Gaps = 18/81 (22%)
Query: 117 DINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCC----NKSPHLRGNVYVSYSNE 172
++ + + ++ F F G++ + K +G ++ Y
Sbjct: 132 SVHQDLSDDDIKSVFEAF-----------GKIKSATLARDPTTGKH---KGYGFIEYEKA 177
Query: 173 REALRAFYALTGRFYGGKQIR 193
+ + A ++ GG+ +R
Sbjct: 178 QSSQDAVSSMNLFDLGGQYLR 198
Score = 33.1 bits (76), Expect = 0.036
Identities = 12/78 (15%), Positives = 26/78 (33%), Gaps = 14/78 (17%)
Query: 119 NLEF--DETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREA 175
++ + E + + F F G + + + + +G +V Y A
Sbjct: 35 SIYYELGEDTIRQAFAPF-----------GPIKSIDMSWDSVTMKHKGFAFVEYEVPEAA 83
Query: 176 LRAFYALTGRFYGGKQIR 193
A + GG+ I+
Sbjct: 84 QLALEQMNSVMLGGRNIK 101
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 34.6 bits (80), Expect = 0.004
Identities = 17/78 (21%), Positives = 34/78 (43%), Gaps = 11/78 (14%)
Query: 117 DINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
D+ + D+ ++++FV+ Y KV +++ +G +V +++E E
Sbjct: 16 DLTPDVDDGMLYEFFVKVY----------PSCRGGKVVLDQTGVSKGYGFVKFTDELEQK 65
Query: 177 RAFYALTGRFY-GGKQIR 193
RA G G K +R
Sbjct: 66 RALTECQGAVGLGSKPVR 83
>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 = 34.5 bits (80), Expect = 0.004
Identities = 13/51 (25%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 146 GQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIRGQF 196
GQ+ V ++S +RG +V + A A ++ G + K +R Q+
Sbjct: 37 GQILDILV--SRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 85
>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 = 35.0 bits (81), Expect = 0.004
Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 18/81 (22%)
Query: 117 DINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCC----NKSPHLRGNVYVSYSNE 172
D++ E ++ F F G+++ +V KS +G +VS+ N+
Sbjct: 22 DLSPEITTEDIKAAFAPF-----------GRISDARVVKDMATGKS---KGYGFVSFFNK 67
Query: 173 REALRAFYALTGRFYGGKQIR 193
+A A + G++ GG+QIR
Sbjct: 68 WDAENAIQQMGGQWLGGRQIR 88
>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 = 35.8 bits (83), Expect = 0.005
Identities = 13/84 (15%), Positives = 30/84 (35%), Gaps = 12/84 (14%)
Query: 117 DINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHL-RGNVYVSYSNEREA 175
+ ++ ++ + F G + F + + + L +G + Y +
Sbjct: 121 GLPNYLNDDQVKELLTSF-----------GPLKAFNLVKDSATGLSKGYAFCEYVDINVT 169
Query: 176 LRAFYALTGRFYGGKQIRGQFCNV 199
+A L G G K++ Q +V
Sbjct: 170 DQAIAGLNGMQLGDKKLLVQRASV 193
>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 = 35.2 bits (82), Expect = 0.005
Identities = 14/78 (17%), Positives = 27/78 (34%), Gaps = 12/78 (15%)
Query: 117 DINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHL-RGNVYVSYSNEREA 175
+ + E F G++ K+ +K G +V+Y + ++A
Sbjct: 9 YLPQNMTQEEFRSLFGSI-----------GEIESCKLVRDKITGQSLGYGFVNYIDPKDA 57
Query: 176 LRAFYALTGRFYGGKQIR 193
+A L G K I+
Sbjct: 58 EKAINTLNGLRLQTKTIK 75
>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 = 33.6 bits (78), Expect = 0.006
Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 18/81 (22%)
Query: 117 DINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCC----NKSPHLRGNVYVSYSNE 172
D+N+ D+ + F +F V S RG +VS++++
Sbjct: 8 DLNVNVDDETLRNAFKDF-----------PSYLSGHVMWDMQTGSS---RGYGFVSFTSQ 53
Query: 173 REALRAFYALTGRFYGGKQIR 193
+A A ++ G+ G+ +R
Sbjct: 54 DDAQNAMDSMQGQDLNGRPLR 74
>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 = 36.4 bits (83), Expect = 0.006
Identities = 31/219 (14%), Positives = 56/219 (25%), Gaps = 66/219 (30%)
Query: 12 KRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIEGVCNELPDGFR------------TNVE 59
+ +RD + + +K IE + P +R ++
Sbjct: 335 ESIRD--GLATWDNWKHVNCDK-LTTIIESSLN---VLEPAEYRKMFDRLSVFPPSAHI- 387
Query: 60 TKPDKELCPFYSKVGACRFFDHCSRNHIKPSVSKTLLLNNFFTHLSMDNKSVREYDTDIN 119
P L + V + +L+ K I
Sbjct: 388 --PTILLSLIWFDVI-----KSDVMVVVNKLHKYSLVEK--------QPKESTISIPSIY 432
Query: 120 LEF-----DETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNK--SPHLRGNVY--VSY- 169
LE +E +H+ V+ Y+ +P+ + P+L Y + +
Sbjct: 433 LELKVKLENEYALHRSIVDHYN--IPK----------TFDSDDLIPPYLDQYFYSHIGHH 480
Query: 170 ------SNEREALRAFYALTGRFYGGKQIR--GQFCNVP 200
R + L RF K IR N
Sbjct: 481 LKNIEHPERMTLFRMVF-LDFRFLEQK-IRHDSTAWNAS 517
>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 = 33.7 bits (78), Expect = 0.007
Identities = 12/76 (15%), Positives = 32/76 (42%), Gaps = 10/76 (13%)
Query: 119 NLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREALR 177
++ +D+TE + +L ++G V K+ + + +G ++ + + +
Sbjct: 9 SIPYDQTE---------EQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 59
Query: 178 AFYALTGRFYGGKQIR 193
A L G G + ++
Sbjct: 60 AVRNLNGYQLGSRFLK 75
>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 = 34.9 bits (81), Expect = 0.008
Identities = 11/78 (14%), Positives = 27/78 (34%), Gaps = 12/78 (15%)
Query: 117 DINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHL-RGNVYVSYSNEREA 175
+ ++ ++ + F G + F + + + L +G + Y +
Sbjct: 101 GLPNYLNDDQVKELLTSF-----------GPLKAFNLVKDSATGLSKGYAFCEYVDINVT 149
Query: 176 LRAFYALTGRFYGGKQIR 193
+A L G G K++
Sbjct: 150 DQAIAGLNGMQLGDKKLL 167
>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 = 33.3 bits (77), Expect = 0.009
Identities = 11/77 (14%), Positives = 24/77 (31%), Gaps = 18/77 (23%)
Query: 121 EFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCC----NKSPHLRGNVYVSYSNEREAL 176
+ ++ K + G++ K NK +G +V + + A
Sbjct: 16 GTTDQDLVKLCQPY-----------GKIVSTKAILDKTTNKC---KGYGFVDFDSPSAAQ 61
Query: 177 RAFYALTGRFYGGKQIR 193
+A AL + +
Sbjct: 62 KAVTALKASGVQAQMAK 78
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 33.2 bits (76), Expect = 0.010
Identities = 13/76 (17%), Positives = 24/76 (31%), Gaps = 13/76 (17%)
Query: 118 INLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALR 177
I + V++ G V + S V V+YS++ +A +
Sbjct: 23 IPPHLQWEVLDSLLVQY-----------GVVESCEQVNTDSE--TAVVNVTYSSKDQARQ 69
Query: 178 AFYALTGRFYGGKQIR 193
A L G ++
Sbjct: 70 ALDKLNGFQLENFTLK 85
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 34.1 bits (78), Expect = 0.011
Identities = 10/51 (19%), Positives = 17/51 (33%), Gaps = 2/51 (3%)
Query: 146 GQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIRGQF 196
G + V S G Y+ ++ + A A G + G + F
Sbjct: 58 GDILDIVVD--LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITF 106
>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 = 33.0 bits (76), Expect = 0.012
Identities = 13/78 (16%), Positives = 33/78 (42%), Gaps = 14/78 (17%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREA 175
NL F T +++ F ++ G+V + + +K + +G ++ + ++ A
Sbjct: 23 NLPFSLTNNDLYRIFSKY-----------GKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
Query: 176 LRAFYALTGRFYGGKQIR 193
A+ + G+ I+
Sbjct: 72 QNCTRAINNKQLFGRVIK 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 = 34.5 bits (79), Expect = 0.012
Identities = 15/53 (28%), Positives = 21/53 (39%), Gaps = 4/53 (7%)
Query: 146 GQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIRGQFCN 198
G V + K+ NK + N V ++ +A A L G GK IR
Sbjct: 29 GDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK 77
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 33.1 bits (76), Expect = 0.013
Identities = 15/77 (19%), Positives = 25/77 (32%), Gaps = 18/77 (23%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
N+ TE + F F G + FK +G ++ Y +A
Sbjct: 34 NIPHFATEADLIPLFQNF-----------GFILDFKH-----YPEKGCCFIKYDTHEQAA 77
Query: 177 RAFYALTGRFYGGKQIR 193
AL + G+ +R
Sbjct: 78 VCIVALANFPFQGRNLR 94
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 32.7 bits (74), Expect = 0.015
Identities = 14/59 (23%), Positives = 20/59 (33%), Gaps = 9/59 (15%)
Query: 142 LRSL----GQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIRGQF 196
LR+L G + F N+ G Y+ EA +A AL I +
Sbjct: 24 LRTLCMQHGPLVSFHPYLNQ-----GIALCKYTTREEANKAQMALNNCVLANTTIFAES 77
>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 = 32.6 bits (75), Expect = 0.020
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 162 RGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
RG +V + + R+A A A+ G G+++R
Sbjct: 55 RGFAFVRFHDRRDAQDAEAAMDGAELDGRELR 86
>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 = 32.6 bits (75), Expect = 0.020
Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 14/78 (17%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREA 175
NL D E + + F F G +++ + +K + +G ++S+ +A
Sbjct: 22 NLSEDTRETDLQELFRPF-----------GSISRIYLAKDKTTGQSKGFAFISFHRREDA 70
Query: 176 LRAFYALTGRFYGGKQIR 193
RA ++G Y +
Sbjct: 71 ARAIAGVSGFGYDHLILN 88
>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 = 32.6 bits (75), Expect = 0.022
Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 14/78 (17%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREA 175
L+ +E + + F++ G V + ++ + +G +V + +E +A
Sbjct: 22 GLDEKVSEPLLWELFLQA-----------GPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70
Query: 176 LRAFYALTGRFYGGKQIR 193
A + GK IR
Sbjct: 71 DYAIKIMDMIKLYGKPIR 88
>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 = 32.7 bits (75), Expect = 0.023
Identities = 14/77 (18%), Positives = 27/77 (35%), Gaps = 15/77 (19%)
Query: 119 NLEFD--ETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NL D ++ F ++ G + + + +V + + R+A
Sbjct: 29 NLPPDIRTKDIEDVFYKY-----------GAIRDIDLKNRRGG--PPFAFVEFEDPRDAE 75
Query: 177 RAFYALTGRFYGGKQIR 193
A Y G Y G ++R
Sbjct: 76 DAVYGRDGYDYDGYRLR 92
>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 = 32.6 bits (75), Expect = 0.024
Identities = 15/77 (19%), Positives = 29/77 (37%), Gaps = 20/77 (25%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NL TE + K F +F G++ + K L+ ++ + A+
Sbjct: 18 NLANTVTEEILEKAFSQF-----------GKLERVKK-------LKDYAFIHFDERDGAV 59
Query: 177 RAFYALTGRFYGGKQIR 193
+A + G+ G+ I
Sbjct: 60 KAMEEMNGKDLEGENIE 76
>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 = 33.8 bits (78), Expect = 0.024
Identities = 12/71 (16%), Positives = 20/71 (28%), Gaps = 11/71 (15%)
Query: 123 DETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYAL 182
D + + T ++ C + L+G + Y A A
Sbjct: 198 DVDALCRALSAV-----------HSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQA 246
Query: 183 TGRFYGGKQIR 193
G GG +R
Sbjct: 247 DGLSLGGSHLR 257
Score = 31.5 bits (72), Expect = 0.17
Identities = 11/81 (13%), Positives = 26/81 (32%), Gaps = 18/81 (22%)
Query: 117 DINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCC----NKSPHLRGNVYVSYSNE 172
++ + + + F G + + + +S +G + Y +
Sbjct: 102 NLPPSLTQQQFEELVRPF-----------GSLERCFLVYSERTGQS---KGYGFAEYMKK 147
Query: 173 REALRAFYALTGRFYGGKQIR 193
A RA L G+ G + +
Sbjct: 148 DSAARAKSDLLGKPLGPRTLY 168
Score = 26.9 bits (60), Expect = 4.5
Identities = 6/32 (18%), Positives = 13/32 (40%)
Query: 162 RGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
+G +V+ N +A A A +++
Sbjct: 57 KGTAFVTLLNGEQAEAAINAFHQSRLRERELS 88
>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 = 33.2 bits (76), Expect = 0.024
Identities = 14/74 (18%), Positives = 30/74 (40%), Gaps = 12/74 (16%)
Query: 121 EFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREALRAF 179
DE ++ + F + G + K+ C++ + RG +V + + A +A
Sbjct: 53 TVDEVQLRQLFERY-----------GPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
Query: 180 YALTGRFYGGKQIR 193
L G K+++
Sbjct: 102 AGLNGFNILNKRLK 115
>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 = 32.2 bits (74), Expect = 0.027
Identities = 18/77 (23%), Positives = 28/77 (36%), Gaps = 18/77 (23%)
Query: 119 NLEFD--ETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NL D E EM K F ++ G+ + + +K +G ++ A
Sbjct: 22 NLPPDITEEEMRKLFEKY-----------GKAGEVFI--HKD---KGFGFIRLETRTLAE 65
Query: 177 RAFYALTGRFYGGKQIR 193
A L GKQ+R
Sbjct: 66 IAKVELDNMPLRGKQLR 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 = 31.9 bits (73), Expect = 0.031
Identities = 17/77 (22%), Positives = 26/77 (33%), Gaps = 18/77 (23%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NL +E + K F +V +R +V +SN +A+
Sbjct: 22 NLMLSTSEEMIEKEFNNI-----------KPGAVERV-----KKIRDYAFVHFSNREDAV 65
Query: 177 RAFYALTGRFYGGKQIR 193
A AL G+ G I
Sbjct: 66 EAMKALNGKVLDGSPIE 82
>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 = 32.2 bits (74), Expect = 0.032
Identities = 15/77 (19%), Positives = 29/77 (37%), Gaps = 14/77 (18%)
Query: 119 NL--EFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NL D ++ F F G + KV C+++ +G +V + + A
Sbjct: 12 NLDKSIDNKALYDTFSAF-----------GNILSCKVVCDENGS-KGYGFVHFETQEAAE 59
Query: 177 RAFYALTGRFYGGKQIR 193
RA + G +++
Sbjct: 60 RAIEKMNGMLLNDRKVF 76
>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 = 32.9 bits (75), Expect = 0.033
Identities = 16/78 (20%), Positives = 29/78 (37%), Gaps = 14/78 (17%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREA 175
NL F TE +++ F + G + + + +K G +V Y + +A
Sbjct: 46 NLSFYTTEEQIYELFSKS-----------GDIKKIIMGLDKMKKTACGFCFVEYYSRADA 94
Query: 176 LRAFYALTGRFYGGKQIR 193
A + G + IR
Sbjct: 95 ENAMRYINGTRLDDRIIR 112
>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 = 31.4 bits (72), Expect = 0.040
Identities = 13/77 (16%), Positives = 25/77 (32%), Gaps = 20/77 (25%)
Query: 119 NLEFD--ETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NL + E E+ F ++ G+V + + ++ +V ++ A
Sbjct: 15 NLPREATEQEIRSLFEQY-----------GKVLECDI-------IKNYGFVHIEDKTAAE 56
Query: 177 RAFYALTGRFYGGKQIR 193
A L G I
Sbjct: 57 DAIRNLHHYKLHGVNIN 73
>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 = 32.0 bits (73), Expect = 0.045
Identities = 10/32 (31%), Positives = 15/32 (46%)
Query: 162 RGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
RG +V + N +A A G G++IR
Sbjct: 88 RGFAFVYFENVDDAKEAKERANGMELDGRRIR 119
>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 = 31.4 bits (72), Expect = 0.047
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 20/81 (24%)
Query: 119 NLEF--DETEMHKYFVEFYDDVLPELRSLGQVTQFKVCC----NKSPHLRGNVYVSYSNE 172
L F +E + + F ++ GQ+++ V +S RG +V++ N
Sbjct: 19 GLSFDTNEQSLEQVFSKY-----------GQISEVVVVKDRETQRS---RGFGFVTFENI 64
Query: 173 REALRAFYALTGRFYGGKQIR 193
+A A A+ G+ G+QIR
Sbjct: 65 DDAKDAMMAMNGKSVDGRQIR 85
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 31.5 bits (72), Expect = 0.062
Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 14/78 (17%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREA 175
+ + TE +H F E+ G++ + ++ + +L+G V Y +EA
Sbjct: 30 GVHEEATEEDIHDKFAEY-----------GEIKNIHLNLDRRTGYLKGYTLVEYETYKEA 78
Query: 176 LRAFYALTGRFYGGKQIR 193
A L G+ G+ I
Sbjct: 79 QAAMEGLNGQDLMGQPIS 96
>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 = 31.1 bits (71), Expect = 0.064
Identities = 15/77 (19%), Positives = 31/77 (40%), Gaps = 16/77 (20%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NL + TE + + F + + KV N++ +G ++ +++ +A
Sbjct: 22 NLSYSATEETLQEVFEKA-----------TFI---KVPQNQNGKSKGYAFIEFASFEDAK 67
Query: 177 RAFYALTGRFYGGKQIR 193
A + R G+ IR
Sbjct: 68 EALNSCNKREIEGRAIR 84
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 31.6 bits (72), Expect = 0.073
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 162 RGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
RG +V + ++R+A A A+ G G+++R
Sbjct: 89 RGFAFVRFHDKRDAEDAMDAMDGAVLDGRELR 120
>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 = 31.8 bits (73), Expect = 0.080
Identities = 14/77 (18%), Positives = 23/77 (29%), Gaps = 14/77 (18%)
Query: 119 NLEF--DETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NL E+ E V ++ R YV + + +
Sbjct: 20 NLNPNKSVAELKVAISEL-----------FAKNDLAVVDVRTGTNRKFGYVDFESAEDLE 68
Query: 177 RAFYALTGRFYGGKQIR 193
+A LTG G +I+
Sbjct: 69 KA-LELTGLKVFGNEIK 84
Score = 29.9 bits (68), Expect = 0.40
Identities = 12/77 (15%), Positives = 26/77 (33%), Gaps = 17/77 (22%)
Query: 119 NLEF--DETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NL F E E+ + F + ++ + +G Y+ + +E +A
Sbjct: 106 NLSFNITEDELKEVFEDA-----------LEIRLVS----QDGKSKGIAYIEFKSEADAE 150
Query: 177 RAFYALTGRFYGGKQIR 193
+ G G+ +
Sbjct: 151 KNLEEKQGAEIDGRSVS 167
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 30.6 bits (70), Expect = 0.080
Identities = 17/79 (21%), Positives = 25/79 (31%), Gaps = 18/79 (22%)
Query: 119 NLEF--DETEMHKYFVEFYDDVLPELRSLGQVTQFKVCC--NKSPHLRGNVYVSYSNERE 174
NL F + F E G V + KS +G V + +
Sbjct: 15 NLPFDFTWKMLKDKFNEC-----------GHVLYADIKMENGKS---KGCGVVKFESPEV 60
Query: 175 ALRAFYALTGRFYGGKQIR 193
A RA + G G++I
Sbjct: 61 AERACRMMNGMKLSGREID 79
>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 = 30.6 bits (70), Expect = 0.085
Identities = 16/78 (20%), Positives = 32/78 (41%), Gaps = 14/78 (17%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREA 175
+L F+ TE + F F G++ + + + +G ++++S+ A
Sbjct: 12 SLHFNITEDMLRGIFEPF-----------GKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 176 LRAFYALTGRFYGGKQIR 193
RA L G G+ +R
Sbjct: 61 RRALEQLNGFELAGRPMR 78
>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 102
Score = 30.7 bits (70), Expect = 0.089
Identities = 7/32 (21%), Positives = 16/32 (50%)
Query: 162 RGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
+G +V +++E +A A A+ G ++
Sbjct: 54 KGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVT 85
>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 = 30.7 bits (70), Expect = 0.090
Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 14/77 (18%)
Query: 119 NL--EFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
N+ F + ++ + F +F G++ ++ N+ +G +V++ N +A
Sbjct: 22 NIPFRFRDPDLRQMFGQF-----------GKILDVEIIFNERGS-KGFGFVTFENSADAD 69
Query: 177 RAFYALTGRFYGGKQIR 193
RA L G G++I
Sbjct: 70 RAREKLHGTVVEGRKIE 86
>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 = 30.7 bits (70), Expect = 0.091
Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 10/76 (13%)
Query: 119 NLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREALR 177
N+ ++ TE + + +G V F++ ++ + +G + Y ++ AL
Sbjct: 15 NIPYEATE---------EQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65
Query: 178 AFYALTGRFYGGKQIR 193
A L GR + G+ +R
Sbjct: 66 AMRNLNGREFSGRALR 81
>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 = 30.6 bits (70), Expect = 0.093
Identities = 15/77 (19%), Positives = 25/77 (32%), Gaps = 20/77 (25%)
Query: 119 NLEFD--ETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
N+ E+ F G+V + V ++ +V E +A
Sbjct: 16 NVSAACTSQELRSLFERR-----------GRVIECDV-------VKDYAFVHMEKEADAK 57
Query: 177 RAFYALTGRFYGGKQIR 193
A L G+ GK+I
Sbjct: 58 AAIAQLNGKEVKGKRIN 74
>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 = 30.6 bits (70), Expect = 0.099
Identities = 5/32 (15%), Positives = 17/32 (53%)
Query: 162 RGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
+G ++++++ + A A+ G++ + I
Sbjct: 48 KGYAFINFASFDASDAAIEAMNGQYLCNRPIT 79
>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 = 30.9 bits (70), Expect = 0.10
Identities = 13/77 (16%), Positives = 22/77 (28%), Gaps = 18/77 (23%)
Query: 119 NLEFD--ETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NL E+ + F F G + + + P V + EA
Sbjct: 17 NLPAGTLAAEIQETFSRF-----------GSLGRVLL-----PEGGITAIVEFLEPLEAR 60
Query: 177 RAFYALTGRFYGGKQIR 193
+AF L + +
Sbjct: 61 KAFRHLAYSKFHHVPLY 77
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 30.7 bits (70), Expect = 0.12
Identities = 13/77 (16%), Positives = 28/77 (36%), Gaps = 20/77 (25%)
Query: 119 NLEFD--ETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
D E+E+++ F F G + + K+ L G +V + A
Sbjct: 38 PFPLDVQESELNEIFGPF-----------GPMKEVKI-------LNGFAFVEFEEAESAA 79
Query: 177 RAFYALTGRFYGGKQIR 193
+A + G+ + + +
Sbjct: 80 KAIEEVHGKSFANQPLE 96
>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, alternative
splicing, FBP interacting repressor, RRM, electron
transport; 2.20A {Escherichia coli O157}
Length = 222
Score = 31.7 bits (72), Expect = 0.12
Identities = 9/31 (29%), Positives = 19/31 (61%)
Query: 165 VYVSYSNEREALRAFYALTGRFYGGKQIRGQ 195
++V +S E +A AL GR++ G+++ +
Sbjct: 178 IFVEFSIASETHKAIQALNGRWFAGRKVVAE 208
>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 = 30.2 bits (69), Expect = 0.14
Identities = 15/81 (18%), Positives = 28/81 (34%), Gaps = 20/81 (24%)
Query: 119 NLEF--DETEMHKYFVEFYDDVLPELRSLGQVTQFKVCC----NKSPHLRGNVYVSYSNE 172
L E ++ + F ++ G + + +S RG +V + N
Sbjct: 22 GLSLYTTERDLREVFSKY-----------GPIADVSIVYDQQSRRS---RGFAFVYFENV 67
Query: 173 REALRAFYALTGRFYGGKQIR 193
+A A G G++IR
Sbjct: 68 DDAKEAKERANGMELDGRRIR 88
>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 = 29.9 bits (68), Expect = 0.14
Identities = 12/77 (15%), Positives = 25/77 (32%), Gaps = 20/77 (25%)
Query: 119 NLEFD--ETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
N+ E+ F E+ G V + + ++ +V +A+
Sbjct: 17 NISPTCTNQELRAKFEEY-----------GPVIECDI-------VKDYAFVHMERAEDAV 58
Query: 177 RAFYALTGRFYGGKQIR 193
A L + GK++
Sbjct: 59 EAIRGLDNTEFQGKRMH 75
>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 = 30.4 bits (69), Expect = 0.15
Identities = 14/78 (17%), Positives = 33/78 (42%), Gaps = 14/78 (17%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREA 175
+L F+ TE + F F G++ ++ + + +G ++++S+ A
Sbjct: 33 SLHFNITEDMLRGIFEPF-----------GRIESIQLMMDSETGRSKGYGFITFSDSECA 81
Query: 176 LRAFYALTGRFYGGKQIR 193
+A L G G+ ++
Sbjct: 82 KKALEQLNGFELAGRPMK 99
>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 = 29.8 bits (68), Expect = 0.15
Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 15/79 (18%)
Query: 119 NLEFDETEMH--KYFVEFYDDVLPELRSLGQVTQFKVCCNK--SPHLRGNVYVSYSNERE 174
L + T+ H + F + G++ + + +G YV + N E
Sbjct: 11 RLTRNVTKDHIMEIFSTY-----------GKIKMIDMPVERMHPHLSKGYAYVEFENPDE 59
Query: 175 ALRAFYALTGRFYGGKQIR 193
A +A + G G++I
Sbjct: 60 AEKALKHMDGGQIDGQEIT 78
>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 = 31.2 bits (71), Expect = 0.18
Identities = 10/77 (12%), Positives = 26/77 (33%), Gaps = 16/77 (20%)
Query: 117 DINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
++ + E + + F + G+ ++ + + RG ++ + A
Sbjct: 29 NLPTDITEEDFKRLFERY-----------GEPSEVFIN--RD---RGFGFIRLESRTLAE 72
Query: 177 RAFYALTGRFYGGKQIR 193
A L G + +R
Sbjct: 73 IAKAELDGTILKSRPLR 89
Score = 27.7 bits (62), Expect = 2.5
Identities = 11/78 (14%), Positives = 24/78 (30%), Gaps = 12/78 (15%)
Query: 117 DINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
+++ + + F +F G V + V + G +V ++ + A
Sbjct: 103 NLSPVVSNELLEQAFSQF-----------GPVEKAVVVVDDRGRATGKGFVEFAAKPPAR 151
Query: 177 RAFYALTGR-FYGGKQIR 193
+A F R
Sbjct: 152 KALERCGDGAFLLTTTPR 169
>2b9s_A Topoisomerase I-like protein; vanadate complex, isomerase/DNA
complex; HET: DNA; 2.27A {Leishmania donovani}
Length = 432
Score = 31.5 bits (71), Expect = 0.18
Identities = 10/37 (27%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 8 EKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIE 44
++E+K R EEK + KE+++A+ + ++ + D
Sbjct: 114 QREKKLSRTKEEK-KAIKEKQDAEAEPYRYCVWDGRR 149
>3lvh_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 9.00A {Bos
taurus}
Length = 205
Score = 31.0 bits (69), Expect = 0.18
Identities = 8/37 (21%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 6 EWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDF 42
+W +EQ++ ++E + K + ++ KK +E++
Sbjct: 104 KWREEQRK--RLQELDAASKVMEQEWREKAKKDLEEW 138
Score = 26.4 bits (57), Expect = 6.8
Identities = 10/41 (24%), Positives = 25/41 (60%), Gaps = 2/41 (4%)
Query: 4 QEEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIE 44
++EW ++ K+ D+EE N+++ E+ E + + + + F +
Sbjct: 124 EQEWREKAKK--DLEEWNQRQSEQVEKNKINNRIADKAFYQ 162
>1ois_A DNA topoisomerase I; DNA-binding protein; HET: DNA; 1.90A
{Saccharomyces cerevisiae} SCOP: e.15.1.1
Length = 223
Score = 31.0 bits (70), Expect = 0.20
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 8 EKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIED 41
+KEQK+ +EK +Q + ERE E+++K D
Sbjct: 104 QKEQKKQLTSQEK-KQIRLEREKFEEDYKFCELD 136
>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 = 30.6 bits (69), Expect = 0.20
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 162 RGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
RG +V + ++R+A A A+ G G+++R
Sbjct: 112 RGFAFVRFHDKRDAEDAMDAMDGAVLDGRELR 143
>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 = 29.8 bits (67), Expect = 0.20
Identities = 15/80 (18%), Positives = 24/80 (30%), Gaps = 14/80 (17%)
Query: 119 NLEFDETEMHKYFVEFYDDVLPELRSLG-QVTQFKVC--CNKSPHLRGNVYVSYSNEREA 175
+ + +++L E+ + V V RG +V Y + R A
Sbjct: 15 GIPKMKKR---------EEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 65
Query: 176 LRAFYALTGRFY--GGKQIR 193
A L G QI
Sbjct: 66 AMARRKLMPGRIQLWGHQIA 85
>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 = 30.0 bits (68), Expect = 0.23
Identities = 19/84 (22%), Positives = 35/84 (41%), Gaps = 14/84 (16%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREA 175
+ + TE +H F E+ G++ + ++ + +L+G V Y +EA
Sbjct: 29 GVHEEATEEDIHDKFAEY-----------GEIKNIHLNLDRRTGYLKGYTLVEYETYKEA 77
Query: 176 LRAFYALTGRFYGGKQIRGQFCNV 199
A L G+ G+ I +C V
Sbjct: 78 QAAMEGLNGQDLMGQPISVDWCFV 101
>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 = 29.6 bits (67), Expect = 0.26
Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 14/78 (17%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREA 175
++ + E + + F ++ G++ + ++ + +G V Y ++A
Sbjct: 33 SIHEEAQEDEIQEKFCDY-----------GEIKNIHLNLDRRTGFSKGYALVEYETHKQA 81
Query: 176 LRAFYALTGRFYGGKQIR 193
L A AL G G+ I+
Sbjct: 82 LAAKEALNGAEIMGQTIQ 99
>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 = 29.6 bits (67), Expect = 0.26
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 11/68 (16%)
Query: 118 INLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALR 177
+N + E ++ + F F G + + V +G +V +S+ EA
Sbjct: 23 LNKQQSEEDVLRLFQPF-----------GVIDECTVLRGPDGSSKGCAFVKFSSHTEAQA 71
Query: 178 AFYALTGR 185
A +AL G
Sbjct: 72 AIHALHGS 79
>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 = 29.5 bits (67), Expect = 0.27
Identities = 16/81 (19%), Positives = 27/81 (33%), Gaps = 20/81 (24%)
Query: 119 NLEF--DETEMHKYFVEFYDDVLPELRSLGQVTQFKVCC----NKSPHLRGNVYVSYSNE 172
L D+ +H F+ F G +T ++ K RG +V +
Sbjct: 19 GLAEEVDDKVLHAAFIPF-----------GDITDIQIPLDYETEKH---RGFAFVEFELA 64
Query: 173 REALRAFYALTGRFYGGKQIR 193
+A A + G+ IR
Sbjct: 65 EDAAAAIDNMNESELFGRTIR 85
>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 = 29.0 bits (66), Expect = 0.30
Identities = 19/93 (20%), Positives = 31/93 (33%), Gaps = 18/93 (19%)
Query: 105 SMDNKSVREYDTDINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCC----NKSPH 160
SM Y + E D+ +H F+ F G +T ++ K
Sbjct: 2 SMATTKRVLYVGGLAEEVDDKVLHAAFIPF-----------GDITDIQIPLDYETEKH-- 48
Query: 161 LRGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
RG +V + +A A + G+ IR
Sbjct: 49 -RGFAFVEFELAEDAAAAIDNMNESELFGRTIR 80
>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 = 29.2 bits (66), Expect = 0.36
Identities = 15/80 (18%), Positives = 33/80 (41%), Gaps = 16/80 (20%)
Query: 119 NLEFD--ETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSP--HLRGNVYVSYSNERE 174
N+ F + E+ + F F G++ ++ + RG +V + +++
Sbjct: 22 NIPFQANQREIRELFSTF-----------GELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 175 ALRAFYALT-GRFYGGKQIR 193
A +AF AL G+++
Sbjct: 71 AKKAFNALCHSTHLYGRRLV 90
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 28.8 bits (65), Expect = 0.50
Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 12/76 (15%)
Query: 118 INLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALR 177
I F + ++ + F +F G++ ++ N+ +G +V++ N +A R
Sbjct: 37 IPFRFRDPDLRQMFGQF-----------GKILDVEIIFNERGS-KGFGFVTFENSADADR 84
Query: 178 AFYALTGRFYGGKQIR 193
A L G G++I
Sbjct: 85 AREKLHGTVVEGRKIE 100
>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 = 29.5 bits (66), Expect = 0.50
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 162 RGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
G +V + + R+A A L GR G ++R
Sbjct: 110 PGFAFVEFEDPRDAADAVRELDGRTLCGCRVR 141
>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 = 28.4 bits (64), Expect = 0.50
Identities = 4/32 (12%), Positives = 11/32 (34%)
Query: 162 RGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
++ + N + A + GK++
Sbjct: 57 NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLI 88
>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 = 28.8 bits (65), Expect = 0.51
Identities = 14/81 (17%), Positives = 30/81 (37%), Gaps = 14/81 (17%)
Query: 119 NLEFD--ETEMHKYFVEFYDDVLPELRSLGQVTQFKV-CCNKSPHLRGNVYVSYSNEREA 175
NL E ++ F F + + + +RG ++++ N+ A
Sbjct: 32 NLSPRVTERDLVSLFARF-----------QEKKGPPIQFRMMTGRMRGQAFITFPNKEIA 80
Query: 176 LRAFYALTGRFYGGKQIRGQF 196
+A + + G GK + +F
Sbjct: 81 WQALHLVNGYKLYGKILVIEF 101
>1ykh_B RNA polymerase II holoenzyme component SRB7; gene regulation; 3.00A
{Saccharomyces cerevisiae} SCOP: a.252.1.1
Length = 132
Score = 29.2 bits (65), Expect = 0.53
Identities = 8/50 (16%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 5 EEWEKEQ-KRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIEGVCNELPDG 53
+ +EQ +++ +++K + ++E+ K+ +K + ++ + + DG
Sbjct: 84 DVSAEEQLRKIDMLQKKLVEVEDEKIEAIKKKEKLMRH-VDSMIEDFVDG 132
>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 = 28.4 bits (64), Expect = 0.57
Identities = 6/32 (18%), Positives = 14/32 (43%)
Query: 162 RGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
+G Y+ + +E +A + G G+ +
Sbjct: 53 KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVS 84
>1a31_A Protein (topoisomerase I); topoisomerase I/DNA, DNA, isomerase/DNA
complex; HET: DNA 5IU PTR; 2.10A {Homo sapiens} SCOP:
d.163.1.2 e.15.1.1 PDB: 1k4t_A* 1k4s_A* 1sc7_A* 1t8i_A*
1tl8_A* 1seu_A* 1a35_A* 1a36_A* 1r49_A* 1rrj_A* 1nh3_A*
1lpq_A* 1rr8_C* 1ej9_A*
Length = 591
Score = 30.1 bits (67), Expect = 0.60
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 8 EKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIED 41
+ E ++ EEK + KEE E KE+ I D
Sbjct: 138 QTEARKQMSKEEK-LKIKEENEKLLKEYGFCIMD 170
>2xs1_A Programmed cell death 6-interacting protein; protein
transport-viral protein complex, cell cycle; 2.30A {Homo
sapiens} PDB: 2xs8_A 2oev_A 2r05_A 2r02_A 2r03_A 2oex_A
2ojq_A
Length = 704
Score = 29.9 bits (66), Expect = 0.61
Identities = 13/63 (20%), Positives = 20/63 (31%)
Query: 4 QEEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIEGVCNELPDGFRTNVETKPD 63
+ + L+ + + K+ERE E + K D L N E
Sbjct: 548 TMQGSEVVNVLKSLLSNLDEVKKEREGLENDLKSVNFDMTSKFLTALAQDGVINEEALSV 607
Query: 64 KEL 66
EL
Sbjct: 608 TEL 610
>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 = 29.0 bits (65), Expect = 0.62
Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 12/77 (15%)
Query: 118 INLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREAL 176
I+ E E E+ + F ++ G++ + ++ + +G V Y ++AL
Sbjct: 80 IHEEAQEDEIQEKFCDY-----------GEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 128
Query: 177 RAFYALTGRFYGGKQIR 193
A AL G G+ I+
Sbjct: 129 AAKEALNGAEIMGQTIQ 145
>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding
protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A
Length = 77
Score = 28.0 bits (62), Expect = 0.63
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 65 ELCPFYSKVGACRFFDHCSRNH 86
ELC YS+ G CR+ C H
Sbjct: 13 ELCRTYSESGRCRYGAKCQFAH 34
Score = 26.5 bits (58), Expect = 2.3
Identities = 7/25 (28%), Positives = 9/25 (36%)
Query: 62 PDKELCPFYSKVGACRFFDHCSRNH 86
ELC + G C + C H
Sbjct: 48 YKTELCHKFKLQGRCPYGSRCHFIH 72
>3efz_A 14-3-3 protein; 14-3-3, cell regulation, structural genom
structural genomics consortium, SGC; HET: SEP; 2.08A
{Cryptosporidium parvum} SCOP: a.118.7.1 PDB: 2ijp_A*
Length = 268
Score = 29.4 bits (65), Expect = 0.77
Identities = 11/57 (19%), Positives = 21/57 (36%), Gaps = 3/57 (5%)
Query: 17 IEEKNRQEKEEREAQE---KEFKKSIEDFIEGVCNELPDGFRTNVETKPDKELCPFY 70
EEK R+EK ++ K+ E+ I ++ N+ ++ F
Sbjct: 88 QEEKLRKEKSLNNEFIQVIEDIKRDFEESILLESEDVIRIIDDNLLMYSEEGARAFC 144
>2nnw_A NOP5/NOP56 related protein; box C/D; 2.70A {Pyrococcus furiosus}
PDB: 3nvi_A 3nmu_A 3nvk_A* 3nvm_A
Length = 376
Score = 29.3 bits (65), Expect = 0.82
Identities = 24/142 (16%), Positives = 47/142 (33%), Gaps = 22/142 (15%)
Query: 9 KEQKRLRDIEEKNRQEKEEREA-QEKEFKKSIEDFIEGVCNELPDG----FRTNVETKPD 63
+ K L ++ +++ + + E + ++ E P+ R+N E
Sbjct: 52 EITKDLEELLNSLKEKGYDEFVFEHPELSRRAKELGFSATTEFPNIAGERLRSNPEEFLG 111
Query: 64 KELCPFYSKVGACRFFDHCSRNHIKPSVSKTLLLNNFFTHLSMDNKSVREYDTDINLEFD 123
+ Y KVG +R I+ + +++ + D INL
Sbjct: 112 ENWFEEYYKVG-----VALTRMRIQEQSGAR------DKMVIQAIEALDDVDKVINL--- 157
Query: 124 ETEMHKYFVEFYDDVLPELRSL 145
+ E+Y PEL L
Sbjct: 158 ---LVARLREWYSLHFPELDEL 176
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 28.0 bits (63), Expect = 0.84
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 162 RGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
G +V + + R+A A L G+ G ++R
Sbjct: 37 PGFAFVEFEDPRDAEDAVRGLDGKVICGSRVR 68
>1i7d_A DNA topoisomerase III; decatenating enzyme, protein-DNA complex,
single-stranded DNA, isomerase/DNA complex; HET: DNA;
2.05A {Escherichia coli} SCOP: e.10.1.1 PDB: 2o5c_A*
2o54_A* 2o59_A* 2o19_A* 2o5e_A* 1d6m_A*
Length = 659
Score = 29.5 bits (67), Expect = 0.91
Identities = 8/72 (11%), Positives = 19/72 (26%), Gaps = 15/72 (20%)
Query: 6 EWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIEGVCNELPDGFRTNVETKPDKE 65
WE L I EK + + ++F + + + + ++
Sbjct: 573 HWES---VLTQISEK--------QCRYQDFMQPLVGTLYQLIDQAKRTPVRQFRGIV--- 618
Query: 66 LCPFYSKVGACR 77
P +
Sbjct: 619 -APGSGGSADKK 629
>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 = 29.2 bits (66), Expect = 0.96
Identities = 13/82 (15%), Positives = 24/82 (29%), Gaps = 18/82 (21%)
Query: 116 TDINLEFDETEMHKYFVEF----YDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSN 171
T+ + + + + LP LR N S R Y+ ++
Sbjct: 123 TNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-----------NTS---RRFAYIDVTS 168
Query: 172 EREALRAFYALTGRFYGGKQIR 193
+ +A L G G +
Sbjct: 169 KEDARYCVEKLNGLKIEGYTLV 190
>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 = 28.3 bits (64), Expect = 1.1
Identities = 12/80 (15%), Positives = 26/80 (32%), Gaps = 14/80 (17%)
Query: 117 DINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
I+ + E ++ F F GQ+ + ++ RG +V+++ A
Sbjct: 102 MISKKCTENDIRVMFSSF-----------GQIEECRILRGPDGLSRGCAFVTFTTRAMAQ 150
Query: 177 RAFYALTGRFY---GGKQIR 193
A A+ +
Sbjct: 151 TAIKAMHQAQTMEGCSSPMV 170
>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin
subfragment 2, heavy meromyosin, essential light chain,
motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP:
i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A
Length = 1184
Score = 29.0 bits (65), Expect = 1.3
Identities = 8/41 (19%), Positives = 24/41 (58%), Gaps = 3/41 (7%)
Query: 4 QEEWEKEQKRLRDIEEKNRQEKEER---EAQEKEFKKSIED 41
+E + + R+ + EE+++Q + E+ + Q + ++ +E+
Sbjct: 926 EEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEE 966
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 27.8 bits (62), Expect = 1.4
Identities = 15/78 (19%), Positives = 28/78 (35%), Gaps = 14/78 (17%)
Query: 119 NLEF--DETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREA 175
L D+ +H F+ F G +T ++ + + RG +V + +A
Sbjct: 70 GLAEEVDDKVLHAAFIPF-----------GDITDIQIPLDYETEKHRGFAFVEFELAEDA 118
Query: 176 LRAFYALTGRFYGGKQIR 193
A + G+ IR
Sbjct: 119 AAAIDNMNESELFGRTIR 136
>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken
structural genomics/proteomics initiative, RSGI, protein
transport; 2.70A {Mus musculus} SCOP: d.58.7.1
Length = 119
Score = 27.8 bits (61), Expect = 1.5
Identities = 7/45 (15%), Positives = 17/45 (37%), Gaps = 7/45 (15%)
Query: 135 YDDVLPELRSLGQVTQFKVCCNKSPHLRGN-VYVSYSNEREALRA 178
+L + G + GN +++ Y ++ +A +A
Sbjct: 37 ASYILLQFAQYGNIL------KHVMSNTGNWMHIRYQSKLQARKA 75
>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 = 27.2 bits (60), Expect = 2.2
Identities = 13/51 (25%), Positives = 20/51 (39%), Gaps = 5/51 (9%)
Query: 135 YDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGR 185
+ +LP L G V + NK + Y E+ RA+ L G+
Sbjct: 41 RNQLLPVLEKCGLVDALLMPPNK-----PYSFARYRTTEESKRAYVTLNGK 86
>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 = 26.5 bits (59), Expect = 2.4
Identities = 8/32 (25%), Positives = 14/32 (43%)
Query: 162 RGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
+G VS+ + A A G+ + G I+
Sbjct: 63 KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIK 94
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp
contractIle protein-transport protein complex; 24.00A
{Gallus gallus}
Length = 1080
Score = 28.2 bits (63), Expect = 2.6
Identities = 7/49 (14%), Positives = 22/49 (44%), Gaps = 8/49 (16%)
Query: 1 LLIQEEW-----EKEQKRLRDIEEKNRQEKEER---EAQEKEFKKSIED 41
+ +Q + ++E K+L+ + K+ E + + ++ I++
Sbjct: 891 VYLQCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDE 939
Score = 27.8 bits (62), Expect = 2.9
Identities = 4/38 (10%), Positives = 16/38 (42%)
Query: 4 QEEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIED 41
+ + + Q+++ + ++ + E+ E + E
Sbjct: 927 ENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEK 964
Score = 27.8 bits (62), Expect = 3.5
Identities = 8/40 (20%), Positives = 20/40 (50%)
Query: 5 EEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIE 44
+ + E+K + + +K + E E+ ++ KE ++ E
Sbjct: 1001 HQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKE 1040
Score = 27.4 bits (61), Expect = 4.0
Identities = 10/42 (23%), Positives = 19/42 (45%)
Query: 3 IQEEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIE 44
+ E E+ L++ + EKEE + + K I + +E
Sbjct: 1017 YKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAKEITETME 1058
>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 = 27.5 bits (60), Expect = 3.0
Identities = 12/58 (20%), Positives = 24/58 (41%), Gaps = 1/58 (1%)
Query: 136 DDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
DD+ L GQV ++ +G+++V + + A + F G+ Y +
Sbjct: 124 DDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA-KKFVETPGQKYKETDLL 180
>2vsw_A Dual specificity protein phosphatase 16; hydrolase, dual
specificity phosphatase, nucleus, cytoplasm, rhodanese
domain, CAsp8; 2.20A {Homo sapiens} PDB: 3tg3_A
Length = 153
Score = 26.7 bits (58), Expect = 4.0
Identities = 15/92 (16%), Positives = 29/92 (31%), Gaps = 2/92 (2%)
Query: 76 CRFFDHCSRNHIKPSVSKTLLLNNFFTHLSMDNKSVREYDTDINLEFDETEMHKYFVEFY 135
R F + +HI +++ L D + E + + + V Y
Sbjct: 27 SRPFVEYNTSHILEAIN-INCSKLMKRRLQQDKVLITELIQHSAKHKVDIDCSQK-VVVY 84
Query: 136 DDVLPELRSLGQVTQFKVCCNKSPHLRGNVYV 167
D ++ SL V K +V++
Sbjct: 85 DQSSQDVASLSSDCFLTVLLGKLEKSFNSVHL 116
>1nzi_A Complement C1S component; calcium, innate immunity, modular
structure, CUB, EGF, hydrolase; 1.50A {Homo sapiens}
SCOP: b.23.1.1 g.3.11.1
Length = 159
Score = 26.7 bits (59), Expect = 4.7
Identities = 10/61 (16%), Positives = 18/61 (29%), Gaps = 11/61 (18%)
Query: 118 INLEFD--ETEMHKY----FVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSN 171
I+L F + E+ + V+ E R G + N + N
Sbjct: 35 IHLYFTHLDIELSENCAYDSVQIISGDTEEGRLCG-----QRSSNNPHSPIVEEFQVPYN 89
Query: 172 E 172
+
Sbjct: 90 K 90
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 26.2 bits (58), Expect = 4.9
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 161 LRGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
L+G VS+ + A A G+ + G I+
Sbjct: 56 LKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIK 88
>3bqp_A Proactivator polypeptide; saposin, sphingolipid activator
protein, lipid binding protein, acid ceramidase,farber
disease, lipid metabolism; 1.30A {Homo sapiens} PDB:
3bqq_C 2rb3_A 2r1q_A 2r0r_A
Length = 80
Score = 25.3 bits (55), Expect = 5.1
Identities = 8/30 (26%), Positives = 16/30 (53%)
Query: 27 EREAQEKEFKKSIEDFIEGVCNELPDGFRT 56
+R ++ K+ I +E C+ LPD ++
Sbjct: 16 DRNLEKNSTKQEILAALEKGCSFLPDPYQK 45
>1y7u_A Acyl-COA hydrolase; structural genomics, coenzyme A, protein
structure initiative, PSI, midwest center for structural
GE MCSG; HET: COA; 2.80A {Bacillus cereus} SCOP:
d.38.1.1
Length = 174
Score = 26.5 bits (59), Expect = 5.4
Identities = 6/31 (19%), Positives = 15/31 (48%)
Query: 9 KEQKRLRDIEEKNRQEKEEREAQEKEFKKSI 39
+E+K I +++ R+A+ K+ +
Sbjct: 142 EEEKESHRIAVLRAEQRHIRKAESKKVATLL 172
>1pj5_A N,N-dimethylglycine oxidase; channelling, FAD binding, folate
binding, amine oxidase, oxidoreductase; HET: FAD; 1.61A
{Arthrobacter globiformis} SCOP: b.44.2.1 c.3.1.2
d.16.1.5 d.250.1.1 PDB: 1pj6_A* 1pj7_A* 3gsi_A*
Length = 830
Score = 27.0 bits (60), Expect = 5.7
Identities = 12/66 (18%), Positives = 18/66 (27%), Gaps = 15/66 (22%)
Query: 124 ETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNER-EALRAFYAL 182
KY VE L G + F G + V+ + R L+
Sbjct: 62 MASFAKYTVEKLL----SLTEDGV-SCFNQV--------GGLEVATTETRLADLKRKLG- 107
Query: 183 TGRFYG 188
+G
Sbjct: 108 YAAAWG 113
>3g5u_A MCG1178, multidrug resistance protein 1A; P-glycoprotein, PGP, cyclic
peptide, membrane protein; 3.80A {Mus musculus} PDB:
3g61_A* 3g60_A*
Length = 1284
Score = 26.5 bits (59), Expect = 7.3
Identities = 8/20 (40%), Positives = 10/20 (50%), Gaps = 4/20 (20%)
Query: 39 IEDFIEGVCNELPDGFRTNV 58
I FI+ LPD + T V
Sbjct: 1150 IHQFIDS----LPDKYNTRV 1165
>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 = 25.4 bits (56), Expect = 7.5
Identities = 14/66 (21%), Positives = 28/66 (42%), Gaps = 12/66 (18%)
Query: 121 EFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHL-RGNVYVSYSNEREALRAF 179
DE ++ F EF G++ + V ++ + +G +++Y AL+A
Sbjct: 24 NLDEKDLKPLFEEF-----------GKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQ 72
Query: 180 YALTGR 185
AL +
Sbjct: 73 SALHEQ 78
>1x79_B RAB GTPase binding effector protein 1; rabaptin5, GGA protein,
GAT domain, intracellular trafficking, protein
transport; 2.41A {Homo sapiens} SCOP: h.1.27.2
Length = 112
Score = 25.6 bits (55), Expect = 7.6
Identities = 9/39 (23%), Positives = 21/39 (53%)
Query: 3 IQEEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIED 41
+++ +K Q LR ++ + ++++ E K+S ED
Sbjct: 4 TRDQVKKLQLMLRQANDQLEKTMKDKQELEDFIKQSSED 42
>1szb_A Mannose binding lectin-associated serine protease-2 related
protein, MAP19 (19KDA)...; calcium, complement, innate
immunity, CUB, EGF; 2.50A {Homo sapiens} SCOP: b.23.1.1
g.3.11.1
Length = 170
Score = 26.1 bits (57), Expect = 7.7
Identities = 7/61 (11%), Positives = 16/61 (26%), Gaps = 11/61 (18%)
Query: 118 INLEFD--ETEMHKY----FVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSN 171
+ L F + E+ FV+ G + + + + S +
Sbjct: 42 LRLYFTHFDLELSHLCEYDFVKLSSGAKVLATLCG-----QESTDTERAPGKDTFYSLGS 96
Query: 172 E 172
Sbjct: 97 S 97
>2xtp_A GTPase IMAP family member 2; immune system, G protein; HET: MSE;
1.50A {Homo sapiens} PDB: 2xto_A* 2xtm_A* 2xtn_A* 3p1j_A
Length = 260
Score = 26.2 bits (57), Expect = 8.7
Identities = 2/38 (5%), Positives = 13/38 (34%)
Query: 3 IQEEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIE 40
+ ++ + +E+ ++ K+ + +
Sbjct: 218 LYSLIQRSKCGPVGSDERVKEFKQSLIKYMETQRSYTA 255
>2kqr_A Asparaginyl-tRNA synthetase, cytoplasmic; aminoacyl-tRNA
synthetase, ATP-binding, ligas nucleotide-binding,
protein biosynthesis; NMR {Brugia malayi}
Length = 113
Score = 25.4 bits (55), Expect = 9.4
Identities = 3/31 (9%), Positives = 11/31 (35%)
Query: 3 IQEEWEKEQKRLRDIEEKNRQEKEEREAQEK 33
+ +E+E + + K ++ +
Sbjct: 64 SWKRYEQEMLKNEKVAAKMLEKDATEVGVKA 94
>2ghi_A Transport protein; multidrug resistance protein, MDR, structural
genomics, structural genomics consortium, SGC; 2.20A
{Plasmodium yoelii yoelii str}
Length = 260
Score = 26.0 bits (58), Expect = 9.7
Identities = 8/20 (40%), Positives = 10/20 (50%), Gaps = 4/20 (20%)
Query: 39 IEDFIEGVCNELPDGFRTNV 58
+ DFIE LP + T V
Sbjct: 134 LYDFIE----ALPKKWDTIV 149
>1v9d_A Diaphanous protein homolog 1; helix bundle, protein binding; 2.60A
{Mus musculus} SCOP: a.207.1.1
Length = 340
Score = 25.9 bits (57), Expect = 9.8
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 9 KEQKRLRDIEEKNRQEKEEREAQEKE 34
KE ++ R+ EEK R+ K +E EKE
Sbjct: 310 KENQKRRETEEKMRRAKLAKEKAEKE 335
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
0.320 0.136 0.416
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: 3,195,340
Number of extensions: 179704
Number of successful extensions: 1028
Number of sequences better than 10.0: 1
Number of HSP's gapped: 979
Number of HSP's successfully gapped: 230
Length of query: 207
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 118
Effective length of database: 4,216,824
Effective search space: 497585232
Effective search space used: 497585232
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.7 bits)