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 PfGW456L13_2122 L-arabinose transport system permease protein (TC 3.A.1.2.2)
Query= TCDB::Q7BSH3 (333 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2122 Length = 323 Score = 157 bits (398), Expect = 3e-43 Identities = 97/303 (32%), Positives = 159/303 (52%), Gaps = 7/303 (2%) Query: 12 LFLIIVVMIVVFSTRAAD-FATPGNLAGIFNDTSILIILALAQMTVILTKSIDLSVAANL 70 + L+ V I V T D F +P N+ G+ S I A + + + DLSV + + Sbjct: 26 VMLLAAVGIFVACTLLIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVI 85 Query: 71 AFTGMAIAMMNAAHPDLPLVVL-ILMAVVIGACLGAINGFLVWALEIPPIVVTLGTLTIY 129 A G+ A++ D V L + A+V+G +G ING ++ L + ++ TL T+ I Sbjct: 86 ACAGVVAAVVMR---DTNSVFLGVCAALVMGLIVGLINGIVIAKLRVNALITTLATMQIV 142 Query: 130 RGMAFVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYVLLRYTQFGRSA 189 RG+A++ + G V Q + F + G+PV + I+ + LL YT +GR+ Sbjct: 143 RGLAYIFANGKAVGVSQES--FFVFGNGQMFGVPVPILITIVCFLFFGWLLNYTTYGRNT 200 Query: 190 YATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIANGFELDSVA 249 A GGN AA+ AG++ TK + F + G + LA + SR I GFEL ++ Sbjct: 201 MAIGGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPMIGQGFELTVIS 260 Query: 250 ACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVIILAVAFNAR 309 ACV+GG+S++GG+G + + G L L +I+NA+ + I F Q I G++++LAV + Sbjct: 261 ACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVIDRL 320 Query: 310 RER 312 ++R Sbjct: 321 KQR 323 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: 251 Number of extensions: 15 Number of successful extensions: 2 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: 323 Length adjustment: 28 Effective length of query: 305 Effective length of database: 295 Effective search space: 89975 Effective search space used: 89975 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