Align CVE1 aka ChvE aka ATU2348 aka AGR_C_4267, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate GFF2145 PS417_10940 sugar ABC transporter substrate-binding protein
Query= TCDB::P25548 (354 letters) >FitnessBrowser__WCS417:GFF2145 Length = 333 Score = 164 bits (415), Expect = 3e-45 Identities = 115/351 (32%), Positives = 182/351 (51%), Gaps = 24/351 (6%) Query: 1 MKSIISLMAACAIGAASFAAPAFAQDKG-SVGIAMPTKSSARWIDDGNNIVKQLQEAGYK 59 MKS + A A+ A A PA A +G ++ RW D + V ++ K Sbjct: 1 MKSFKRTLIATAL--ALLALPAMADSAHPKIGFSIDDLRLERWSRDRDYFVAAAEKLDAK 58 Query: 60 TDLQYADDDIPNQLSQIENMVTKGVKVLVIASIDGTTLSDVLKQAGEQGIKVIAYDRLIR 119 +Q AD + Q+SQIEN++++GV V+VI + T L++ + +A + GIKV++YDRLI Sbjct: 59 VFVQSADANEQKQISQIENLISRGVDVIVIVPFNATVLTNAVAEAKKAGIKVVSYDRLIL 118 Query: 120 NSGDVSYYATFDNFQVGVLQATSITDKLGLKDGKGPFNIELFGGSPDDNNAFFFYDGAMS 179 N+ D+ Y +FDN +VG +QA+ G+ N L GG+P DNNA +G M Sbjct: 119 NA-DIDAYISFDNEKVGEMQAS------GVLQAAPKGNYFLLGGAPTDNNAKVLREGQMK 171 Query: 180 VLKPYIDSGKLVVKSGQMGMDKVGTLRWDPATAQARMDNLLSAYYTDAKVDAVLSPYDGL 239 VL+P ID G + V Q W+P A + ++N L+ + K+DA+++ D Sbjct: 172 VLQPAIDKGDIKVVGQQW------VKEWNPTEALSIVENALTR--NNNKIDAIVASNDAT 223 Query: 240 SIGIISSLKGVGYGTKDQPLPVVSGQDAEVPSVKSIIAGEQYSTIFKDTRELAKVTVNMV 299 + G I +L K +P +SGQDA++ ++K +I G Q T++K + +A + Sbjct: 224 AGGAIQALAAQKLAGK---VP-ISGQDADLAAIKRVIDGTQTMTVYKPLKLIASEAAKLS 279 Query: 300 NAVMEGKEPEVNDTKTYENGVKVVPSYLLKPVAVTKENYKQVLVDGGYYKE 350 + ++P + Y+NG K V + LL P +TK N + DG Y KE Sbjct: 280 VQLARNEKPTY--SSQYDNGSKKVDTILLTPTPLTKANIDLLEKDGFYTKE 328 Lambda K H 0.314 0.133 0.372 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 293 Number of extensions: 18 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 354 Length of database: 333 Length adjustment: 29 Effective length of query: 325 Effective length of database: 304 Effective search space: 98800 Effective search space used: 98800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory