Tag: SwissProt

Sequence information Variant position:  322 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  360 The length of the canonical sequence. Location on the sequence:   IEVEQALAHPYLEQYYDPSD  E PIAEAPFKFDMELDDLPKEK The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

Sequence information Variant position:  468 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  805 The length of the canonical sequence. Location on the sequence:   GTLPFTYMLEKWRWMVFKGE  I PKDQWMKKWWEMKREIVGVV The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

Sequence information Variant position:  28 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  492 The length of the canonical sequence. Location on the sequence:   PPAIGPYYENHGYQPENPYP  A QPTVVPTVYEVHPAQYYPSP The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

Sequence information Variant position:  205 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  496 The length of the canonical sequence. Location on the sequence:   ERSLDTLLEAVESRGGVPGG  C VLVPRADLRLGGQPAPPQLL The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

Sequence information Variant position:  4075 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  4374 The length of the canonical sequence. Location on the sequence:   GQDAGGLLREWYMIISREMF  N PMYALFRTSPGDRVTYTINP The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

Associated RNAi Experiments Homology BLAST of hypothetical protein DAPPUDRAFT_213302 vs. L. salmonis genes Match: EMLSAG00000000401 (supercontig:LSalAtl2s:LSalAtl2s1063:86108:87342:-1 gene:EMLSAG00000000401 transcript:EMLSAT00000000401 description:”maker-LSalAtl2s1063-snap-gene-0.46″) HSP 1 Score: 149.443 bits (376), Expect = 4.121e-44Identity = 91/196 (46.43%), Postives = 119/196 (60.71%), Query Frame = 0 Query: 14 MDKITDLQVEPLT–NSRFVKPLRLRFKQDGKVKVWDLIQCHASVAVVIFNQTTQKFVFVRQFRPAVYFSALRRAQGDVEPGTQFKGDEIDPKVGITLELCAGIVD-KSKSLIEIAHEEILEETGYDVPMNLIEEIQTFPVGVGVGGENMTLFCAEVTEAMRKGPGGGLAEEGEMIDVIEMGVEETRTLMRAKSVT 206 MDK+ VEPL +SRFV P R+ ++Q+G…

Listing Results Biopython Contact Map Protein Contact Maps using Biopython Warwick 9 hours ago Warwick.ac.uk View All Protein Contact Maps using Biopython. When working with protein 3D structures, a contact map is usually defined as a binary matrix with the rows and columns representing the residues of two different chains….

I am having trouble running the blastp command. When I run this command against the Swiss-prot database installed from the NCBI i get this error $ blastp -db swissprot -query Ecoli_rpoB.fasta -out TEST15.txt BLAST Database error: Error: Not a valid version 4 database. However, when I create my own database…

Associated RNAi Experiments Homology BLAST of probable dimethyladenosine transferase-like vs. L. salmonis genes Match: EMLSAG00000006273 (supercontig:LSalAtl2s:LSalAtl2s341:673186:674124:1 gene:EMLSAG00000006273 transcript:EMLSAT00000006273 description:”augustus_masked-LSalAtl2s341-processed-gene-6.3″) HSP 1 Score: 484.567 bits (1246), Expect = 2.083e-174Identity = 227/310 (73.23%), Postives = 259/310 (83.55%), Query Frame = 0 Query: 9 KVRKTGSGMSTVEAAGSGGGGQQGMVFNTGLGQHILKNPLVVQSIIDKAALRSTDVVLEIGPGTGNLTVRALEKCKKLIACEVDPRMVAELQKRVQGTHFQSKLQIMVGDVIKTDLPFFDACVANVPYQISSPLVFKLLLHRPFFRCAVLMFQREFAQRLVAKPGDKLYCRLSINTQLLARVDHVMKVGKGNFRPPPKVESSVVRIEPRNPPPPINFKEWDGLTRVAFVRKNKTLGAAFNQTTVLMMLEKNYRVHLSLADEPVPEKIDIKSIIETVLAEIAFKEKRARSMDIDDFMKLLHAFNAKGIHFV 318 KV+ T + GG+QG+VFNT LGQHILKNP VV…

How To Use Python Retrieve Results From Uniprot Automatically 3 You can use this: wget –quiet -O- ftp.uniprot.org/pub/databases/uniprot/currentrelease/knowledgebase/complete/uniprotsprot.dat.gz | zcat | python uniprot2go.py GO:0070337 GO:0016021 > out.fasta #!/usr/bin/env python “””Fetch uniprot entries for given go terms””” import sys from Bio import SwissProt #load go terms gos = set(sys.argv[1:]) sys.stderr.write(“Looking for…