Align Putative xylitol transport system substrate-binding protein; SubName: Full=Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_037155072.1 RHSP_RS28510 sugar ABC transporter substrate-binding protein
Query= uniprot:A0A1N7UEK0 (335 letters) >NCBI__GCF_000359745.1:WP_037155072.1 Length = 309 Score = 127 bits (319), Expect = 4e-34 Identities = 87/280 (31%), Positives = 144/280 (51%), Gaps = 12/280 (4%) Query: 14 SLLACSIAMAADGKTYKVGAAVYGLKGQFMQNWVRELKEHPAVKDGTVQLTVFDGNYDAL 73 S +A ++ AA +T V A++ F+ ++++ G V L V D D Sbjct: 8 SAMALLLSTAAHAQTIGVSMALFD--DNFLTVLRNGMQDYAKGMSG-VTLQVEDAQNDVA 64 Query: 74 TQNNQIENMVTQRYDAILFVPIDTKAGVGTVKAAMSNDVVVIASNTKVADA-SVP----Y 128 Q +QI+N + + DAI+ P+DT A K A + ++ N + A+ S+P + Sbjct: 65 KQQSQIQNFIASKVDAIIVNPVDTDATAAISKLAADAKIPLVYVNREPANVDSLPDKQAF 124 Query: 129 VGNDDVEGGRLQAQAMVDKLNGKGNVVIIQGPIGQSAQIDREKGELEVLGKH--PDIKII 186 V +++ E G L+ + + L GKG V++ G + A R K +VL IKI+ Sbjct: 125 VASNEQESGTLETKEVCRILGGKGKAVVMMGELSNQAARMRTKDVHDVLATDGCKGIKIV 184 Query: 187 EKKTANWDRAQALALTEDWLNAHPKGINGVIAQNDDMALGAVQALKSHGLTSKDVPVTSI 246 +++TANW R Q L +WL++ + + VI+ ND+MA+GA+QALK+ G + V + Sbjct: 185 QEQTANWQRTQGADLMTNWLSSGLE-FDAVISNNDEMAIGAIQALKAAGKPMDKIVVAGV 243 Query: 247 DGMPDAIQAAKKDEV-TTFLQDAQAQSQGALDVALRALAG 285 D DA+ A + ++ T QDA Q +GA+D AL+ G Sbjct: 244 DATQDALAAMQAGDLKVTVFQDAAGQGKGAVDAALKLAKG 283 Lambda K H 0.314 0.130 0.373 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: 268 Number of extensions: 15 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: 335 Length of database: 309 Length adjustment: 28 Effective length of query: 307 Effective length of database: 281 Effective search space: 86267 Effective search space used: 86267 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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