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 CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP
Query= TCDB::Q7BSH3 (333 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 175 bits (444), Expect = 1e-48 Identities = 109/305 (35%), Positives = 168/305 (55%), Gaps = 7/305 (2%) Query: 6 RKRETLLFLIIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTKSIDLS 65 RK T+LFL+++V VF F T N I ++ SI I+A+ VIL ID++ Sbjct: 24 RKHRTILFLLLLV--AVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVA 81 Query: 66 VAANLAFTGMAIA-MMNAAHPDLPLVVLI--LMAVVIGACLGAINGFLVWALEIPPIVVT 122 V + LAF +A A ++ A D P LI L++ +IG G + G V L +P +VT Sbjct: 82 VGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVT 141 Query: 123 LGTLTIYRGMAFVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYVLLRY 182 LG +T++RG +L+ G ++ + +L LPV + ++ +V LRY Sbjct: 142 LGGMTVWRGATLLLNDGGPISG--FNDAYRWWGSGEILFLPVPVVIFALVAAAGHVALRY 199 Query: 183 TQFGRSAYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIANG 242 T++GR YA GGN AA +G++ + + + GALAGL+ +L +R A G Sbjct: 200 TRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTG 259 Query: 243 FELDSVAACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVIIL 302 +EL +A+ VIGG S+ GG G V GTVLGAL +GV+ N L ++ ++ + Q + G +I+ Sbjct: 260 YELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVA 319 Query: 303 AVAFN 307 AVAF+ Sbjct: 320 AVAFD 324 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: 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: 332 Length adjustment: 28 Effective length of query: 305 Effective length of database: 304 Effective search space: 92720 Effective search space used: 92720 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