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 WP_086510990.1 BZY95_RS16560 L-arabinose ABC transporter permease AraH
Query= TCDB::Q7BSH3 (333 letters) >NCBI__GCF_002151265.1:WP_086510990.1 Length = 336 Score = 176 bits (446), Expect = 7e-49 Identities = 98/305 (32%), Positives = 165/305 (54%), Gaps = 4/305 (1%) Query: 12 LFLIIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTKSIDLSVAANLA 71 L I V++ V + F T N+ G+ +++ +A M V+ +DLSVA+ +A Sbjct: 35 LIAIFVILFVALAVFIPGFLTGRNMVGLLLSITLIGTIATTMMMVLALGEVDLSVASIVA 94 Query: 72 FTGMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVVTLGTLTIYRG 131 F G+ A++ + + + VL V+ G +GA NGF+V I ++ TL ++ RG Sbjct: 95 FAGVVAAVVTSTSGSVAIGVL--GGVLAGGAVGAFNGFVVAKFGINSLIATLASMEFVRG 152 Query: 132 MAFVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYVLLRYTQFGRSAYA 191 +A++ S G V P F + LGL + W I ++ VLL T FGR+ A Sbjct: 153 LAYITSRGDAVMI--TVPEFFDLGSASFLGLTLPVWTMIACFVIFGVLLNMTAFGRNVLA 210 Query: 192 TGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIANGFELDSVAAC 251 TGGN AA AG++ K + F L G +AG+A L SR + + + G EL ++AC Sbjct: 211 TGGNAEAAALAGVNVRRLKVIVFGLQGVVAGIAGVLLASRMGLGDPNTSMGLELAVISAC 270 Query: 252 VIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVIILAVAFNARRE 311 V+GG++++GGV ++ G ++G L +G ++NA+ ++ + F Q + G +++LAV F+ ++ Sbjct: 271 VLGGVALSGGVATITGVLVGVLIMGCVQNAMGLLNVPTFYQYLVRGAILLLAVMFDRWKQ 330 Query: 312 RNRGR 316 R R Sbjct: 331 TRRQR 335 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: 243 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: 336 Length adjustment: 28 Effective length of query: 305 Effective length of database: 308 Effective search space: 93940 Effective search space used: 93940 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 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