Align RhaP, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate BPHYT_RS28210 BPHYT_RS28210 ATPase
Query= TCDB::Q7BSH3 (333 letters) >FitnessBrowser__BFirm:BPHYT_RS28210 Length = 352 Score = 211 bits (537), Expect = 2e-59 Identities = 114/321 (35%), Positives = 177/321 (55%) Query: 2 ARLIRKRETLLFLIIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTKS 61 A + + RET LF+++V++IV F NL + + SI+ +L VIL + Sbjct: 29 ASIAKSRETTLFVVLVLLIVGTGLAKPQFLNLQNLRDVLLNVSIISLLTAGMTVVILMRH 88 Query: 62 IDLSVAANLAFTGMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVV 121 IDLSV + + + A+ + A P +P++V + + IG G IN LV +P +V Sbjct: 89 IDLSVGSTVGISAYAVGSLYVAFPHMPVIVALAAGLAIGLVAGTINALLVGVGRVPSLVA 148 Query: 122 TLGTLTIYRGMAFVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYVLLR 181 TL TL I+RG + G +NA + F + +LG+P L+ + ++++I + V L+ Sbjct: 149 TLSTLYIFRGADYAWVHGGQINATSLPDAFSRLATGTLLGIPTLALIAVVVLIGLAVYLK 208 Query: 182 YTQFGRSAYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIAN 241 + GR YA G NP AA AG++ F+LSGA+AG A LW++R+ A Sbjct: 209 QFRGGREHYAIGSNPEAARLAGVNVERRVMAGFLLSGAIAGFAGALWLARFGTVDASTAK 268 Query: 242 GFELDSVAACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVII 301 G EL VAA V+G ++I GGVG++ G LGAL LGVI AL V+ +SPF + AI G +I+ Sbjct: 269 GIELQVVAAAVVGSVAITGGVGTILGATLGALVLGVISIALVVLHVSPFWEQAIEGALIV 328 Query: 302 LAVAFNARRERNRGRIILRDR 322 A+ + R+ + ++R R Sbjct: 329 AAITADTLLARSVAKRMMRKR 349 Lambda K H 0.328 0.141 0.413 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: 282 Number of extensions: 9 Number of successful extensions: 1 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: 333 Length of database: 352 Length adjustment: 29 Effective length of query: 304 Effective length of database: 323 Effective search space: 98192 Effective search space used: 98192 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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