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 Pf6N2E2_524 Inositol transport system permease protein
Query= TCDB::Q7BSH3 (333 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_524 Length = 340 Score = 157 bits (396), Expect = 5e-43 Identities = 93/281 (33%), Positives = 153/281 (54%), Gaps = 17/281 (6%) Query: 44 SILIILALAQMTVILTKSIDLSVAANLAFTGMAIAMM-------NAAHP---DLPLVVLI 93 SI+ +LA+ VI+T IDLS + LA + M A + A P DLP+ + + Sbjct: 64 SIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWIPV 123 Query: 94 LMAVVIGACLGAINGFLVWALEIPPIVVTLGTLTIYRGMAFVLSGGAWVNAHQMTPIFLS 153 + + +G GAING ++ IPP + TLG + RG+A + G V+ + + Sbjct: 124 VAGLGVGLLAGAINGSIIAITGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIG 183 Query: 154 VPRTPVLGLPVLSWVGIIIVILMYVLLRYTQFGRSAYATGGNPTAAVYAGIDTGWTKFLA 213 PV+ + +++ ++ ++ LRYT++G+ YA GGN AA +GI+ + Sbjct: 184 HGAMPVI-------IFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIV 236 Query: 214 FVLSGALAGLASYLWVSRYAVAYVDIANGFELDSVAACVIGGISIAGGVGSVAGTVLGAL 273 + ++G LAGLA + +R A + +ELD++AA VIGG S+AGGVG + GTV+GAL Sbjct: 237 YSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGAL 296 Query: 274 FLGVIKNALPVIGISPFTQMAISGTVIILAVAFNARRERNR 314 LGV+ + +G+ + Q I G +I++AV + R + + Sbjct: 297 ILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQYRNKRK 337 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: 288 Number of extensions: 17 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: 340 Length adjustment: 28 Effective length of query: 305 Effective length of database: 312 Effective search space: 95160 Effective search space used: 95160 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