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 BWI76_RS00655 BWI76_RS00655 inner-membrane translocator
Query= TCDB::Q7BSH3 (333 letters) >FitnessBrowser__Koxy:BWI76_RS00655 Length = 334 Score = 384 bits (987), Expect = e-111 Identities = 191/326 (58%), Positives = 242/326 (74%) Query: 3 RLIRKRETLLFLIIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTKSI 62 +L++ RE LL +I++MI +RA F +PGNL +FNDT+ILIILAL QM V+LTK I Sbjct: 4 QLLKHREALLAAVIILMIGAIGSRAPSFVSPGNLVEMFNDTAILIILALGQMMVLLTKGI 63 Query: 63 DLSVAANLAFTGMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVVT 122 DLS+AANLA TGM +A++NA +P +P+ L+ +A ++G +G ING LVW L IP IVVT Sbjct: 64 DLSMAANLALTGMIVALLNAHYPGIPVAALLALATLLGLLMGMINGLLVWRLGIPAIVVT 123 Query: 123 LGTLTIYRGMAFVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYVLLRY 182 LGT++IYRG+ F+LS G WVN+HQM+ FL +PR +LGLP+LSW I ++L+ LRY Sbjct: 124 LGTMSIYRGIIFLLSDGGWVNSHQMSADFLGLPRASLLGLPLLSWCAIAALLLVGYFLRY 183 Query: 183 TQFGRSAYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIANG 242 ++ GR+ Y GGN TAA Y GI+ G +F++F LSGALAG YLW+SR+AVAYVD+ANG Sbjct: 184 SRTGRALYTAGGNATAAYYTGINAGKMQFVSFCLSGALAGFCGYLWISRFAVAYVDVANG 243 Query: 243 FELDSVAACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVIIL 302 FEL VAACVIGGIS GG G V G + GALFLGVI NALPVIGISPF QMAISG VI++ Sbjct: 244 FELQVVAACVIGGISTMGGTGRVLGCLCGALFLGVINNALPVIGISPFWQMAISGAVIVI 303 Query: 303 AVAFNARRERNRGRIILRDRAATEIK 328 AV N R + GR+ILR+ A K Sbjct: 304 AVLLNERSNKTHGRLILRNAALARQK 329 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: 318 Number of extensions: 13 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: 334 Length adjustment: 28 Effective length of query: 305 Effective length of database: 306 Effective search space: 93330 Effective search space used: 93330 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