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 GFF3462 PS417_17725 ribose ABC transporter permease
Query= TCDB::Q7BSH3 (333 letters) >FitnessBrowser__WCS417:GFF3462 Length = 330 Score = 184 bits (466), Expect = 3e-51 Identities = 112/312 (35%), Positives = 171/312 (54%), Gaps = 4/312 (1%) Query: 1 MARLIRKRETLLFLIIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTK 60 +ARL+R F+ +VV+ +V + F T NL+ I SI I+A+ VILT Sbjct: 23 LARLVRSPAFYPFVGLVVVTLVMILASDTFLTASNLSNIARQVSINAIIAVGMTCVILTG 82 Query: 61 SIDLSVAANLAFTGMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIV 120 IDLSV +A +G A + A LP + I ++IG G NG V L +PPI+ Sbjct: 83 GIDLSVGPVMALSGTLTAGLMVA--GLPPGLAIGAGMLIGVAFGIGNGLFVAYLHMPPII 140 Query: 121 VTLGTLTIYRGMAFVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYVLL 180 VTL T+ I RG+ + + G ++ + F R + G+ V + ++ ++ YVLL Sbjct: 141 VTLATMGIARGLGLMYTDGYPISG--LPDWFAFFGRESLFGIQVPILIMLLTYLVAYVLL 198 Query: 181 RYTQFGRSAYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIA 240 ++T+ GR YA GGN A +G+ K L + +SG A +A + SR + Sbjct: 199 QHTRIGRYIYAIGGNEEAVRLSGVRAARFKLLVYGISGLTAAIAGLVLTSRLMSGQPNAG 258 Query: 241 NGFELDSVAACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVI 300 FELD++AA V+GG SIAGG G + GT+LGA+ LGV+ N L ++G+SP+ Q I G +I Sbjct: 259 VSFELDAIAAVVLGGASIAGGRGVIVGTLLGAMLLGVLNNGLNMLGVSPYVQSVIKGGII 318 Query: 301 ILAVAFNARRER 312 +LA+ + +R + Sbjct: 319 LLAIFISRQRHK 330 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: 294 Number of extensions: 15 Number of successful extensions: 3 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: 330 Length adjustment: 28 Effective length of query: 305 Effective length of database: 302 Effective search space: 92110 Effective search space used: 92110 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