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Query: [A] KOG3013 Exosomal 3`-5` exoribonuclease complex, subunit Rrp4, from COG1018

Results of FFAS03 search in SCOP207
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 MVTILKPEEFYVSSEADIVNDVSMTEMEDEIMEDEQMGLVDGEDVLEEFDKSIHQNLVTPGQLVTDDPQFMRGHGTYFEDGGIYASVAGSVQRVNKLISVKPLRSKYVPEIGDLIIGKIAEVQPKRWKVDIGAKQNAVLMLSSINLPGGIQRRKLETDELQMRSFFQEGDLLVAEVQQYFSDGSVSIHTRSLKYGKLRNGVFLKVPPALVVRSKSHAYALAGGVDIILSVNGYVWVSKHNENQHSSVSITRLEEEASESIYSNENDEIDGYTRLNISRVSICIKGLASRSLPLTQASITNFYESSLVFSNLQDLTVPKNMDQIAMEAMQLast
1 -45.100d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  60  1.......................................................................................................KTRYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKL.................................................................................................................................... 94
2 -42.300d2nn6h3 d.51.1.1 (H:168-293) Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  32  1......................................................................................................................................................................................................QGVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWIYPTPEH-----------KEEEAGGFIANLEPVSLADREVISRLRNCIISLVTQRMMLYDTSILYCYEASLPH-QIKDILKPEIMEEIVMETRQ 119
3 -37.300d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  18  1........................................................................................................SQLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSYLLTTAENELGVVVAHSESGIQM--VPISWCEMQCPKTH.......................................................................................................... 118
4 -36.500d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}  ali model 3D-neighbors follow..  21  1........................................................................................................KRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSY----------MAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIECFDSTTGRDAGFGILE............................................................................................................................. 90
5 -35.700d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}  ali model 3D-neighbors follow..  24  1........................................................................................................SFYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLL-------GRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGKDLGRVS................................................................................................................................... 87
6 -29.000d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}  ali model 3D-neighbors follow..  26  1..........................................................................................................YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSEN---------PEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKDRICRPIR................................................................................................................................... 83
7 -23.100d2nn6h2 b.84.4.2 (H:25-72) Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  62  1.......................................................HLVVPGDTITTDTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKAL.................................................................................................................................................................................................................................. 48
8 -22.700d2nn6i2 b.84.4.2 (I:6-60) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  25  1.......................................................RYCIPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKSNGALPVVSVVRET.............................................................................................................................................................................................................................. 54
9 -22.600d2je6i2 b.84.4.2 (I:7-65) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}  ali model 3D-neighbors follow..  17  1...............................................QEIVLQPRSIVVPGELLAEGEFQIPSPYILKINSKYYSTVVGLFDVKDTQFEVIPLEG................................................................................................................................................................................................................................ 59
10 -21.900d2ba0a2 b.84.4.2 (A:2-52) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}  ali model 3D-neighbors follow..  31  1......................................................RKIVLPGDLLST-NPRAAGYGTYVEGGKVYAKIIGLFDQTETHVRVIPLKGR............................................................................................................................................................................................................................... 51
11 -17.700d2ja9a2 d.51.1.1 (A:152-236) Ribosomal RNA-processing protein 40, RRP40 {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}  ali model 3D-neighbors follow..  9  1......................................................................................................................................................................................................DGMIIDVNLNFARQLLFNNDFPHTKFEVAIGLNGKIWVKCEELSNTLACYRTIMECCQKND-----TAAFKDIAKRQFKEILT................................................ 85
12 -15.300d2nn6g3 d.51.1.1 (G:195-274) Ribosomal RNA-processing protein 40, RRP40 {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  19  1......................................................................................................................................................................................................DGLLFKVTLGLIRKLLAPDCEILYPLEIVFGMNGRIWVKAKTIQQTLILANILEACEHMTS...................................................................... 67
13 -14.700d2nn6g2 b.84.4.2 (G:16-106) Ribosomal RNA-processing protein 40, RRP40 {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  12  1..............................................ARAARTVLGQVVLPGEELCSRVRVVCGPGLRRCGDRLLVTKCGRLRHKE.......................................................................................................................................................................................................................................... 74
14 -13.500d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}  ali model 3D-neighbors follow..  7  1............................................................................................................PFKGEVVDGTVVSCSQHGFEVQVGPM-KVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISSIHAIGSIKEDYLGAI.................................................................................................................................... 91
15 -12.500d3bzca4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]}  ali model 3D-neighbors follow..  20  17.............................................................................................................KPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALS----------EKFVKDPYEVVKAGDIVKVKVMEVDPRNRVGLSMRMSD........................................................................................................................................ 91
16 -12.300d2khja1 b.40.4.0 (A:2-89) automated matches {Escherichia coli [TaxId: 562]}  ali model 3D-neighbors follow..  17  9.............................................................................................................KKGAIVTGKVTAVDAKGATVELADGVEGYLRASEAS----------RDRVEDATLVLSVGDEVEAKFTGVDKNRAISLSVRA.......................................................................................................................................... 81
17 -12.200d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Methanococcus jannaschii [TaxId: 2190]}  ali model 3D-neighbors follow..  16  1............................................................................................................PEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAEIALTMRQPYLGKLE................................................................................................................................... 96
18 -11.200d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  13  11............................................................................................................PEVEDVVMVNVRSIAEMGAYVSLLEYNEGMILLSELS----------RRRIRSINKLIRIGRNECVVVIRVDEKGYIDLSKRR.......................................................................................................................................... 86
19 -11.200d5ie8a_ b.40.4.0 (A:) automated matches {Mycobacterium leprae [TaxId: 272631]}  ali model 3D-neighbors follow..  16  13.............................................................................................................AIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELA----------ERHVEVPDQVVAVGDDAMVKVIDIDERRRISLSLKQ.......................................................................................................................................... 85
20 -11.100d3cw2c1 b.40.4.5 (C:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]}  ali model 3D-neighbors follow..  17  9............................................................................................................PSEGEILIATVKQVFDYGSYVSLDEYGQAFLPWSEVS----------SKWVKNIRDVLKENRKVIVKVIRVDRKGTVDVSLKK.......................................................................................................................................... 84
21 -10.000d1wi5a1 b.40.4.5 (A:186-291) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]}  ali model 3D-neighbors follow..  20  13.............................................................................................................KPGMLLTGTVSSLEDHGYLVDIGVDGRAFLPLLKA---------QEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVSLSVGHSEVST..................................................................................................................................... 92
22 -9.270d1luza_ b.40.4.5 (A:) Viral structural mimic of eIF2alpha {Vaccinia virus [TaxId: 10245]}  ali model 3D-neighbors follow..  13  6............................................................................................................PNAGDVIKGRV-YEKDYALYIYLFDYPHFE----------LAESVKMHMDRYVEYRDKLVGKTVKVKVIRVDTKGYIDVNYKR.......................................................................................................................................... 80
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.

Schwarzenbacher R, Godzik A, Jaroszewski L. The JCSG MR pipeline: optimized alignments, multiple models and parallel searches. Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):133-40. Epub 2007 Dec 5.