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Query: [J] COG1097 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain), from COG1018

Results of FFAS03 search in PDB1018
Master-slave alignment(slide right to see more) does not show gaps in the query sequence, use ali links to display alignment between query and templates.
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# Score Template Links and tools%idFirst MDKKIVIPGDLLSENQKKAGYGTYVKNDKIYSSLCGIENLKEDKVGVIPLAGAYIPSANDVVIGIVIVVTPSNWIFDIAAPYDGLLHVSEYPRRVESREMPEILNVGDSVILRVKDVDSSMKVELALRDPSLHKLKTGQIIKVESVKVPRVIGHGGSMISMLKKETNCSIFVGQNGRIWIDGKDEDIELLSKALRKIELEAQRSGLTDRIYNFLKNERIRQKESKPVGFFKNETEGVTATKEDHSEEIYRKIDVLLDPKNLast
1 -84.6002ba0_A mol:protein length:229 Archaeal exosome RNA binding protein RRP4  ali model follow..  42  2..RKIVLPGDLLSTNPRAAGYGTYVEGGKVYAKIIGLFDQTETHVRVIPLKGRYTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKDRICRPIRFGRIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQNGLIWVNGDRRKVSIAEEAIYLIEQEAHTEGLTDRVAEFIKRRKADVGIQ.................................... 223
2 -81.3002z0s_A mol:protein length:235 Probable exosome complex RNA-binding protein 1  ali model follow..  31  7LAGRIVVPGEPLPEEVEASPPYVIDYKGVKRATVVGLLREKGGGRAFVKLKEIYVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDRPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQGEGLGRIVRGKIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARNGRIHLECPNDLEAIAVMAIKIIDEEAYTSGLTKRIIKFIEEERRIREV..................................... 235
3 -78.3002je6_I mol:protein length:251 EXOSOME COMPLEX RNA-BINDING PROTEIN 1  ali model follow..  36  15.PRSIVVPGELLAEGEIPWSPYILKINSKYYSTVVGLFDVKDTQFEVIPLEGFYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGKDLGRVSNGIVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSFSEEILIEAIRKIENESHIKGLTDRIKQFIEEKLGERNASSGETKTNS............................ 251
4 -77.0004oo1_H mol:protein length:363 Exosome complex component RRP4  ali model follow..  20  55.DSQIVTPGELVTDPIWMRGHGTYFLDNMTYSSVAGTVSRVNRLLSVIPLKGRYAPETGDHVVGRIAEVGNKRWKVDIGGKQHAVLMLGRRKSESDELQMRSFLKEGDLLNAEVQSLFQDGSASLHTRSLKYGKLRNGMFCQVPSSLIVRAKNHTHNLP------GNITVVLGVNGYIWLRKTSQMDLARDTPSANNSSSIKSTGPTGAVSLNPSDPSISNNIRQAICRYANVIKALAFCEIGITQQRISAYEASMVYSN 335
5 -76.8005jea_H mol:protein length:316 Exosome complex component RRP4  ali model follow..  20  8.DSQIVTPGELVTDPIWMRGHGTYFLDNMTYSSVAGTVSRVNRLLSVIPLKGRYAPETGDHVVGRIAEVGNKRWKVDIGGKQHAVLMLGSVKSESDELQMRSFLKEGDLLNAEVQSLFQDGSASLHTRSLKYGKLRNGMFCQVPSSLIVRAKNHTHNLP------GNITVVLGVNGYIWLRKTSQMDLARDTPSANNSSSIKSTGPTGAVSLNPSDPSISNNIRQAICRYANVIKALAFCEIGITQQRISAYEASMVYSN 288
6 -70.8002nn6_H mol:protein length:308 Exosome complex exonuclease RRP4  ali model follow..  20  32.KKHLVVPGDTITTTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKALKTRYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKR------QKTHFHDLPCGASVILGNNGFIWIYPTPEHKEEEAGGFIANLEP------------------VSLADREVISRLRNCIISLVTQRMMLYDTSIYCYEASLPHQ. 276
7 -70.8006h25_H mol:protein length:297 Exosome complex component RRP4  ali model follow..  20  27.KKHLVVPGDTITTTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKALKTRYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKR------QKTHFHDLPCGASVILGNNGFIWIYPTPEHKEEEAGGFIANLEP------------------VSLADREVISRLRNCIISLVTQRMMLYDTSIYCYEASLPHQ. 271
8 -69.8005jea_G mol:protein length:244 Exosome complex component RRP40  ali model follow..  19  5.MSTFIFPGDSFPVDPVKLGPGIYCNTQEIRPVNTGVLHVSVQTAYIDYSSKRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSY-MAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIECFDSGFGILEDGMIIDVNLNFARQLLFNDFPLLKVLAAHTKFEVAIGLNGKIWVKCEESNTLACYRTIMECCQKNDTAAFKDIAKRQFKEILTVKEE..................................... 244
9 -69.5004oo1_G mol:protein length:244 Exosome complex component RRP40  ali model follow..  20  4HMSTFIFPGDSFPVDPVKLGPGIYCNTQEIRPVNTGVLHVSVQTAYIDYSSKRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSY-MAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIECRDAGFGILEDGMIIDVNLNFARQLLFNDFPLLKVLAAHTKFEVAIGLNGKIWVKCEESNTLACYRTIMECCQKNDTAAFKDIAKRQFKEILTVKEE..................................... 244
10 -68.5006h25_G mol:protein length:293 Exosome complex component RRP40  ali model follow..  22  41VLGQVVLPGEELSRVRVVCGPGLRRCGDRLLVTKCGRLRHKGGVYWVDSQQKRYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYL--SFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDSCGRANQDGLLFKVTLGLIRKLLAPDCEIIQEVGKLYPLEIVFGMNGRIWVKAKTQQTLILANILEACEHSDQRKQIFSRLAE................................................ 292
11 -68.1002nn6_G mol:protein length:289 Exosome complex exonuclease RRP40  ali model follow..  19  31VLGQVVLPGEELSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEGVYWVDSQQKRYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYL--SFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDSCGRAGQDGLLFKVTLGLIRKLLAPDCEIIQEVGKLYPLEIVFGMNGRIWVKAKTIQQTLILANILEACEHMTSDQRKQIFSRLAES............................................ 283
12 -47.0002ba1_A mol:protein length:179 Archaeal exosome RNA binding protein CSL4  ali model follow..  15  2...RFVMPGDRIGSEEYVKGEGVYEEGGELFAAVAGKLIIKDRVAKVESISPIPEIVKGDVVLGRVVDLRNSIALIEVSSKKGENRGPSSNVDEGYVKEISEAVGYLDILKARVIG----DNLRLSTKEEEM-----GVLRALCSNCKTEMVREGDILKCPECGRVEKRKISTDYGKG.................................................................................. 177
13 -43.5002nn6_I mol:protein length:209 3`-5` exoribonuclease CSL4 homolog  ali model follow..  16  12.PVRYCIPGERLCNEEGSPGSGTYTRHGYIFSSLAGCLMKSSENGALPETESQLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSYLLTTAENEL-----GVVVAHSESGIQMVPISWCEMQCPKTHTKEFRKVARVQPEF.................................................................................. 200
14 -42.8006h25_I mol:protein length:199 Exosome complex component CSL4  ali model follow..  16  8.PVRYCIPGERLCNEEGSPGSGTYTRHGYIFSSLAGCLMKSSENGALPETESQLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSYLLTTAENEL-----GVVVAHSESGIQMVPISWCEMQCPKTHTKEFRKVARVQPEF.................................................................................. 196
15 -31.5004oo1_I mol:protein length:296 Exosome complex component CSL4  ali model follow..  12  81.EREGTDQSTEEESVDASPNDVTRRTVKNILVSVLPGTEKGRKTNKYANNDFANLPKEGDIVLTRVTRLSLQRANVEIGETFRGIIRSQDVSTDRDRVKVIECFKPGDIVRAQVLSLGDGTNYYLTTARNDLGVVFA........................................................................................................................... 261
16 -31.2004ifd_I mol:protein length:301 Exosome complex component CSL4  ali model follow..  12  79EEREGTDQSTEEESVDASPNDVTRRTVKNILVSVLPGTEKGRKTNKYANNDFANLPKEGDIVLTRVTRLSLQRANVEIGETFRGIIRSQDVRTDRDRVKVIECFKPGDIVRAQVLSLGDGTNYYLTTARNDLGVVFA........................................................................................................................... 260
17 -13.9005xq5_A mol:protein length:103 30S ribosomal protein S1  ali model follow..  24  14........................................................NKGDRVEGKIKSITDFGIFIGLDGGIDGLVHLSDISWNVAGEEAVREYKKGDEIAAVVLQVDAERE.......................................................................................................................................... 79
18 -13.8002khi_A mol:protein length:115 30S ribosomal protein S1  ali model follow..  27  23........................................................PEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDEERR.......................................................................................................................................... 88
19 -12.8002k4k_A mol:protein length:130 General stress protein 13  ali model follow..  27  6........................................................EVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHG-FVKDINEHLSVGDEVQVKVLAVDEKGKISLSIRA................................................................................................................................... 78
20 -12.4001wi5_A mol:protein length:119 RRP5 protein homolog  ali model follow..  16  1...................................GSSGSSGKNVNRVLSAEAL--KPGMLLTGTVSSLEDHGYLVDIGDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGG.......................................................................................................................................... 86
21 -12.2004nnh_A mol:protein length:168 30S ribosomal protein S1  ali model follow..  15  15........................................................AIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELSERHVE-VPDQVVQVGDDAMVKVIDIDERRRISLSLKQANEDYTE-----EFDPSKYGMADSYDEQGNYIFPEGFDPETNEWLEGFDKQREEWEARYAEAERRHKMHTA............................................................ 153
22 -12.2004nni_A mol:protein length:161 30S ribosomal protein S1  ali model follow..  17  15........................................................AIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVE-VPDQVVAVGDDAMVKVIDIDLERRRIS----LSLKQANEDYTEEFDPAKYGMADSYDEQGNYIFPEGFDAETNEWLEGFE.................................................................................. 131
23 -12.2004nnk_A mol:protein length:159 30S ribosomal protein S1  ali model follow..  17  17........................................................AIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVE-VPDQVVAVGDDAMVKVIDIDERRRISLSLKQANEDYTE-----EFDPAKYGMADSYDEQGNYIFPEGFDAETNEWLEGFE.................................................................................. 133
24 -11.8002mfi_A mol:protein length:96 30S ribosomal protein S1  ali model follow..  15  15........................................................RPGSIVRGVVVAIDKDVVLVDAGLKSESAIPAEQFK----NAQGELEIQVGDEVDVALDAVEDG............................................................................................................................................ 74
25 -11.7002ckz_B mol:protein length:218 DNA-DIRECTED RNA POLYMERASE III 25 KD POLYPEPTIDE  ali model follow..  11  7IADLVRIPPDQFHRDKIIPNVGLCITIYDLLTVEEGQLKPGDGSSYVTFRAVVFKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGMDEETKLYFDVNEKIRFRIEREVFVDVKPKSPKERELEERAQ----------LENEIEGKNEETPQNEKPPAYALLGSCQGLVW................................................................................. 210
26 -11.5002eqs_A mol:protein length:103 ATP-dependent RNA helicase DHX8  ali model follow..  18  11........................................................TIGDIYNGKVTSIMQFGCFVQLEGLREGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTK........................................................................................................................................... 78
27 -11.5005ie8_A mol:protein length:89 30S ribosomal protein S1  ali model follow..  24  13........................................................AIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERH-VEVPDQVVAVGDDAMVKVIDIDLERR.......................................................................................................................................... 77
28 -11.4002khj_A mol:protein length:109 30S ribosomal protein S1  ali model follow..  26  24........................................................KKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVE-DATLVLSVGDEVEAKFTGVDRKNR.......................................................................................................................................... 88
29 -10.8001kl9_A mol:protein length:182 EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 1  ali model follow..  22  12......................................................FPEVEDVVMVNVRSIAEMGAYVSLLNNIEGMILLSELSRR--IRSINKLIRIGRNECVVVIRVDKEK........................................................................................................................................... 79
30 -10.7003ayh_B mol:protein length:203 DNA-directed RNA polymerase III subunit rpc8  ali model follow..  11  7FSDIISIHPSNFWKPKVIQNIGLAICVYDFLKIGEGIIKYGDGSSYVVFRLIIFRPFRGEVMLGKIKSCSEEGIRVTISFFDDIFIPKDMLEGEDGSEGTELYFDIDEEIRFQIESED.............................................................................................................................................. 158
31 -10.7002a19_A mol:protein length:175 Eukaryotic translation initiation factor 2 alpha subunit  ali model follow..  22  13.......................................................PEIDDIVMVNVQQIAEMGAYVKLLDNIEGMILLSELSRR--IRSIQKLIRVGKNDVAVVLRVDKEGYIDLSKRR................................................................................................................................... 88
32 -10.5005aj3_f mol:protein length:188 MITORIBOSOMAL PROTEIN MS28, MRPS28  ali model follow..  18  96........................................................AKNKLVIGQIFHIVEDDLYIDFGGKFHCVCKRPEVD--------GEKYQKGTRVRLRLLDLELTSRFLGATTDTTILEADAVLL........................................................................................................................ 171
33 -10.3005k0y_P mol:protein length:266 Eukaryotic translation initiation factor 2 subunit 1  ali model follow..  22  9.......................................................PEVEDVVMVNVRSIAEMGAYVSLLNNIEGMILLSELSRR--IRSINKLIRIGRNECVVVIRVDKEGYIDLSKRR................................................................................................................................... 84
34 -10.3002k52_A mol:protein length:80 Uncharacterized protein MJ1198  ali model follow..  22  4........................................................EPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRL-----ENLNVGDEIIVQAIDVRPEKR.......................................................................................................................................... 64
35 -10.3006GSN Entity 27(prereleased)  ali follow..  22  12.......................................................PEIDDIVMVNVQQIAEMGAYVKLLDNIEGMILLSELSRR--IRSIQKLIRVGKNDVAVVLRVDKEGYIDLSKRR................................................................................................................................... 87
36 -10.2002aho_B mol:protein length:266 Translation initiation factor 2 alpha subunit  ali model follow..  21  8......................................................LPSEGEILIATVKQVFDYGSYVSLDGGLQAFLPWSEVSSK--VKNIRDVLKENRKVIVKVIRVDRRGTVDVSLKK................................................................................................................................... 84
37 -10.1003d0f_A mol:protein length:106 Penicillin-binding 1 transmembrane protein MrcA  ali model follow..  10  30......................................................IGNSDDILAAVVLSATPGAVEAFRKNGETIRITGDGLKASNDPKIGEKRIRPGALIRVK................................................................................................................................................... 93
38 -10.1003jd5_f mol:protein length:189 28S ribosomal protein S28, mitochondrial  ali model follow..  17  98..........................................................DKIVIGRIFHIVENDLYIDFGGKFHCVCKRPEVD--------GEKYQKGTRVRLRLLDLELTSRFLGATTDTTILEAEAVLL........................................................................................................................ 171
39 -10.0002mfl_A mol:protein length:182 30S ribosomal protein S1  ali model follow..  13  22........................................................RPGSIVRGVVVAIDKDVVLVDAGLKSESAIPAEQFK----NAQGELEIQVGDEVDVALDAVEDGFGETLLSREKAKRHEA---------ITLEKAYEDAETVTGVINGKVKGGFTVGIRAFLPGSLVDVRPVRDTLHLEGKELEFKVIKLDQKRNNVVVSRRAVIESENS.................................. 182
40 -9.7602cqo_A mol:protein length:119 Nucleolar protein of 40 kDa  ali model follow..  18  21........................................................ALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKND.......................................................................................................................................... 86
41 -9.7302rf4_A mol:protein length:214 DNA-directed RNA polymerase I subunit RPA4  ali model follow..  12  77......VGGVVLGYEGLKILDADPLSKEDTSEKLIKITPDTPFGTWCHVNLYVWQPQVGDVLEGYIFIQSASHIGLLIHDAFNASIKKNNIPVD-GHWVDSNGEPIDGKLRFTVRNVHTTGRVVSVD----------GTLIS...................................................................................................................... 214
42 -9.7101yz6_A mol:protein length:274 Probable translation initiation factor 2 alpha subunit  ali model follow..  20  1................................................PRRAREYPEEGEFVVATVKRIHNYGAFLELDPGKEAFMHISEVAST--VRNIRDYLKEGQKVVAKVIRVDPRGHIDLSLRR................................................................................................................................... 83
43 -9.6101q8k_A mol:protein length:308 Eukaryotic translation initiation factor 2 subunit 1  ali model follow..  24  11.......................................................PEVEDVVMVNVRSIQEMGAYVSL-NNIEGMIHLSELSRR--IRSINKLIRIGRNECVKVIRVDKEGYIDLSKRR................................................................................................................................... 86
44 -9.6002c35_B mol:protein length:172 DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE  ali model follow..  15  7LEHEILLHPRYFGPNTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEKTMDEDIVIQQDDEIRLKIVGTKNDIFAIGSLMDDYLGLVS............................................................................................................................ 172
45 -9.5202y0s_E mol:protein length:180 RNA POLYMERASE SUBUNIT 4  ali model follow..  17  7ARSIVRIPPNEFGQEKILKDLGLVLAILNVKTSEEGMLVFGDGATYHEVEFDMYVPVVQEVVEGEVLQVDNYGVFVNLGPMDGLVHISQITDDTLKGEKSKKVIQKGDKVRARVISVARLPRIALTMRQPYLGKLE............................................................................................................................ 173
46 -9.4802pmz_E mol:protein length:180 DNA-directed RNA polymerase subunit E  ali model follow..  18  7ARSIVRIPPNEFGQEKILKDLGLVLAILNVKTSEEGILVFGDGATYHEVEFDMYVPVVQEVVEGEVLQVDNYGIFVNLGPMDGLVHISQITDDTLKGEKSKKVIQKGDKVRARVISVARLPRIALTMRQPYLGKLE............................................................................................................................ 173
47 -9.3503aev_A mol:protein length:275 Translation initiation factor 2 subunit alpha  ali model follow..  21  9.......................................................PEEGEFVVATVKRIHNYGAFLELDPGKEAFMHISEVAST--VRNIRDYLKEGQKVVAKVIRVDPRGHIDLSLRR................................................................................................................................... 84
48 -9.2901go3_E mol:protein length:187 DNA-DIRECTED RNA POLYMERASE SUBUNIT E  ali model follow..  17  7IADVVKVPPEEFGEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFE-YIPEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVS-KETGKVLEIGDYVRARIVAISRGSKIALTMRQPYLGKLE............................................................................................................................ 174
49 -9.2704qiw_E mol:protein length:190 DNA-directed RNA polymerase, subunit E`  ali model follow..  21  7VKDVVRIPPRMFTEGIYDRDEGVVLAILDVEEISEGVIVPGDGATYHEAIFN-WEPRNQEVVEGEVVEMMPYGAFIRIG-PMDGLVHISQLMDDYVVKETNRVLKLGDYVRARIIGVS.............................................................................................................................................. 150
FFAS is supported by the NIH grant R01-GM087218-01
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Selected papers from Godzik Lab
Ying Zhang, Ines Thiele, Dana Weekes, Zhanwen Li, Lukasz Jaroszewski, Krzysztof Ginalski, Ashley Deacon, John Wooley, Scott Lesley, Ian Wilson, Bernhard Palsson, Andrei Osterman, Adam Godzik. Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima. Science. 2009 Sep 18;325(5947):1544-9.

Mayya Sedova, Mallika Iyer, Zhanwen Li, Lukasz Jaroszewski, Kai W Post, Thomas Hrabe, Eduard Porta-Pardo, Adam Godzik Cancer3D 2.0:: interactive analysis of 3D patterns of cancer mutations in cancer subsets. Nucleic Acids Research, gky1098 2018; Published on November 8 2018.

Pawlowski K, Pio F, Chu Z, Reed JC, Godzik A. PAAD - a new protein domain associated with apoptosis, cancer and autoimmune diseases. Trends Biochem Sci. 2001 Feb;26(2):85-7.