Align CVE1 aka ChvE aka ATU2348 aka AGR_C_4267, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate BPHYT_RS32820 BPHYT_RS32820 xylose ABC transporter substrate-binding protein
Query= TCDB::P25548 (354 letters) >FitnessBrowser__BFirm:BPHYT_RS32820 Length = 342 Score = 181 bits (459), Expect = 2e-50 Identities = 121/350 (34%), Positives = 190/350 (54%), Gaps = 24/350 (6%) Query: 6 SLMAACAIGAASFAAPAF--AQDKGSVGIAMPTKSSARWIDDGNNIVKQLQEAGYKTDLQ 63 SL+ + + S AP ++D +G + RW D + V ++ G K +Q Sbjct: 12 SLVCGAVLASLSLVAPLAHASKDHPEIGFCIDDLRVERWSRDRDYFVAAAEKLGAKVSVQ 71 Query: 64 YADDDIPNQLSQIENMVTKGVKVLVIASIDGTTLSDVLKQAGEQGIKVIAYDRLIRNSGD 123 AD Q+SQIEN++++GV V+VI + TL +V+ +A + GIKV++YDRLI ++ D Sbjct: 72 SADASEARQISQIENLISRGVDVIVIVPFNSKTLGNVVAEAKKAGIKVVSYDRLILDA-D 130 Query: 124 VSYYATFDNFQVGVLQATSITDKLGLKDGKGPFNIELFGGSPDDNNAFFFYDGAMSVLKP 183 V Y +FDN +VG LQA G+ + + N L GG+P DNNA +G + +LKP Sbjct: 131 VDAYISFDNEKVGELQAQ------GVYNAQPKGNYFLLGGAPTDNNAKMLREGQLKILKP 184 Query: 184 YIDSGKLVVKSGQMGMDKVGTLRWDPATAQARMDNLLSAYYTDAKVDAVLSPYDGLSIGI 243 ID G + V Q W +TA +++ L+A + K+DA+++ DG + G Sbjct: 185 AIDKGDIKVVGQQW------VPEWSASTALRIVEDALTA--NNNKIDAIVASNDGTAGGA 236 Query: 244 ISSLKGVGYGTKDQPLPVVSGQDAEVPSVKSIIAGEQYSTIFKDTRELAKVTVNMVNAVM 303 I +L K +P VSGQDA++ +VK +IAG Q T++K + +A + A+ Sbjct: 237 IQALAAQHMAGK---VP-VSGQDADLAAVKRVIAGTQTMTVYKPLKLIAGEAAKLSVALA 292 Query: 304 EGKEPEVNDTKTYENGVKVVPSYLLKPVAVTKENYKQVLVDGGYYKEDQL 353 +G++P N Y+NG K V + LL+P +TK N V+V G+Y + QL Sbjct: 293 KGEKPAFN--SQYDNGKKKVDTVLLQPTLLTKSNV-DVVVKDGFYSQAQL 339 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: 301 Number of extensions: 17 Number of successful extensions: 6 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: 342 Length adjustment: 29 Effective length of query: 325 Effective length of database: 313 Effective search space: 101725 Effective search space used: 101725 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