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kfetchdata |
kfetchdata utilizes fetchdata method included dbfetch SOAP service provided
EBI (European Bioinformatics Institute).
Original web-service is located at the following URL:
http://www.ebi.ac.uk/cgi-bin/dbfetch
This tools is a subset of Keio Bioinformatics Web Service (KBWS) package, which contains interfaces to bioinformatics web services through a proxy server at Keio University. kfetchdata is thus an interface of "runFetchData" method included in KBWS SOAP service. This method can be alternatively accessed directly from programming languages as SOAP web service. Please refer to the KBWS online documentations http://soap.g-language.org/kbws/ for more information.
Here is a sample session with kfetchdata % kfetchdata Fetch an entry in a defined format and style dbName:ID: UniProtKB:WAP_RAT Output file [outfile.kfetchdata]: Jobid: kbws_12654644 *** ID WAP_RAT Reviewed; 137 AA. AC P01174; DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot. DT 01-OCT-1989, sequence version 2. DT 24-NOV-2009, entry version 79. DE RecName: Full=Whey acidic protein; DE AltName: Full=Whey phosphoprotein; DE AltName: Full=WAP; DE Flags: Precursor; GN Name=Wap; OS Rattus norvegicus (Rat). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; OC Muroidea; Muridae; Murinae; Rattus. OX NCBI_TaxID=10116; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX MEDLINE=85062841; PubMed=6095207; DOI=10.1093/nar/12.22.8685; RA Campbell S.M., Rosen J.M., Hennighausen L.G., Strech-Jurk U., RA Sippel A.E.; RT "Comparison of the whey acidic protein genes of the rat and mouse."; RL Nucleic Acids Res. 12:8685-8697(1984). RN [2] RP NUCLEOTIDE SEQUENCE [MRNA]. RX MEDLINE=82274212; PubMed=6896749; DOI=10.1093/nar/10.12.3733; RA Hennighausen L.G., Sippel A.E.; RT "Comparative sequence analysis of the mRNAs coding for mouse and rat RT whey protein."; RL Nucleic Acids Res. 10:3733-3744(1982). RN [3] RP NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 20-41, AND DISULFIDE RP BONDS. RX MEDLINE=82275050; PubMed=6955785; DOI=10.1073/pnas.79.13.3987; RA Dandekar A.M., Robinson E.A., Appella E., Qasba P.K.; RT "Complete sequence analysis of cDNA clones encoding rat whey RT phosphoprotein: homology to a protease inhibitor."; RL Proc. Natl. Acad. Sci. U.S.A. 79:3987-3991(1982). CC -!- FUNCTION: Could be a protease inhibitor. CC -!- SUBCELLULAR LOCATION: Secreted. CC -!- TISSUE SPECIFICITY: Milk-specific; major protein component of milk CC whey. CC -!- PTM: Contains 8 disulfide bonds. CC -!- SIMILARITY: Contains 2 WAP domains. CC ----------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution-NoDerivs License CC ----------------------------------------------------------------------- DR EMBL; X01153; CAA25600.2 ; -; Genomic_DNA. DR EMBL; X01154; CAA25600.2 ; JOINED; Genomic_DNA. DR EMBL; X01155; CAA25600.2 ; JOINED; Genomic_DNA. DR EMBL; X01156; CAA25600.2 ; JOINED; Genomic_DNA. DR EMBL; J00801; AAA42346.1 ; -; mRNA. DR IPI; IPI00210939; -. DR PIR; A93920; WYRT. DR RefSeq; NP_446203.1; -. DR UniGene; Rn.9978; -. DR STRING; P01174; -. DR Ensembl; ENSRNOT00000010744 ; ENSRNOP00000010744; ENSRNOG00000008097; Rattus norvegicus. DR GeneID; 114596; -. DR KEGG; rno:114596; -. DR UCSC; NM_053751; rat. DR CTD; 114596; -. DR RGD; 621851; Wap. DR HOVERGEN; P01174; -. DR NextBio; 618763; -. DR ArrayExpress; P01174; -. DR Genevestigator; P01174; -. DR GermOnline; ENSRNOG00000008097; Rattus norvegicus. DR GO; GO:0005576; C:extracellular region; IEA:UniPro tKB-SubCell. DR GO; GO:0030414; F:peptidase inhibitor activity; NA S:RGD. DR InterPro; IPR015874; 4-disulph ide_core. DR InterPro; IPR008197; Whey_acid ic_protein_4-diS_core. DR Gene3D; G3DSA:4.10.75.10; Whey_acidic_protein_4-diS_core; 1 . DR Pfam; PF00095; WAP; 2. DR PRINTS; PR00003; 4DISULPHCORE. DR SMART; SM00217; WAP; 1. DR PROSITE; PS51390; WAP; 2. PE 1: Evidence at protein level; KW Direct protein sequencing; Disulfide bond; Milk protein; KW Protease inhibitor; Repeat; Secreted; < A HREF=http://www.expasy.org/cgi-bin/get-entries?KW=Signal>Signal. FT SIGNAL 1 19 FT CHAIN 20 137 Wh ey acidic protein. FT /FTId=PRO_0000041353. FT DOMAIN 27 73 WA P 1. FT DOMAIN 76 127 WA P 2. FT DISULFID 34 61 Pr obable. FT DISULFID 45 65 Pr obable. FT DISULFID 48 60 Pr obable. FT DISULFID 54 69 Pr obable. FT DISULFID 83 115 Pr obable. FT DISULFID 96 119 P robable. FT DISULFID 102 114 P robable. FT DISULFID 108 123 P robable. FT CONFLICT 4 4 S -> F (in Ref. 3; AAA42347). FT CONFLICT 35 35 S -> P (in Ref. 2 and 3). FT CONFLICT 39 39 F -> S (in Ref. 2 and 3). FT CONFLICT 47 47 N -> K (in Ref. 2; AAA42346). FT CONFLICT 68 68 S -> P (in Ref. 2 and 3). FT CONFLICT 99 99 D -> G (in Ref. 2; AAA42346). FT CONFLICT 116 116 K -> N (in Ref. 2 and 3). FT CONFLICT 127 127 E -> K (in Ref. 2). FT CONFLICT 129 129 K -> D (in Ref. 2). FT CONFLICT 129 129 K -> E (in Ref. 3; AAA42347). FT CONFLICT 134 134 I -> V (in Ref. 3; AAA42347). SQ SEQUENCE 137 AA; 14827 MW; 1C2E8ADA9FD97949 CRC64; MRCSISLVLG LLALEVALAR NLQEHVFNSV QSMCSDDSFS EDTECINCQT NEECAQNDMC CPSSCGRSCK TPVNIEVQKA GRCPWNPIQM IAAGPCPKDN PCSIDSDCSG TMKCCKNGCI MSCMDPEPKS PTVISFQ // |
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-id] (Parameter 1) |
string | dbName:ID | Any string | 2 |
| [-outfile] (Parameter 2) |
outfile | Output file name | Output file | <*>.kfetchdata |
| Additional (Optional) qualifiers | ||||
| -format | string | output format | Any string | default |
| -style | string | output data style | Any string | default |
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
Labarga, A., et al.,(2007) Web Services at the European Bioinformatics
Institute, Nucleic Acids Research, 35, W6-W11.
| Program name | Description |
|---|---|
| seqret | Reads and writes (returns) sequences |