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 3609042 Dshi_2431 Monosaccharide-transporting ATPase (RefSeq)
Query= TCDB::Q7BSH3 (333 letters) >FitnessBrowser__Dino:3609042 Length = 328 Score = 145 bits (365), Expect = 2e-39 Identities = 94/313 (30%), Positives = 163/313 (52%), Gaps = 19/313 (6%) Query: 1 MARLIRKRETLLFLIIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTK 60 M + ++ ETLL L+ + + V S + F NL+ + + ++A A +I++ Sbjct: 16 MEQRLKSWETLLLLVAIGIFVANSFASPYFLNAWNLSDATFNFTEKAMIAFAMALLIISG 75 Query: 61 SIDLSVAANLAFTGMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIV 120 IDLSVA+ +A + AM A + L+L+ + +G GA NG LV + +P IV Sbjct: 76 EIDLSVASIIALA--STAMGAAVQMGVGTPGLVLIGLGVGLLCGAFNGVLVTRMGLPSIV 133 Query: 121 VTLGTLTIYRGMAFVLSGGAWVNAHQMTPIFLSVPRT-PVLGLPVLSWV-------GIII 172 VT+GT++++RG+++++ G F P + G + WV II Sbjct: 134 VTIGTMSLFRGISYIVLGDQ---------AFRGYPESFSWFGQGYVWWVISFELVLFAII 184 Query: 173 VILMYVLLRYTQFGRSAYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRY 232 ++ +LL T FGR+ YA G N T A+++GI KF+ F+L+G ++G+A+ +R Sbjct: 185 AVIYAMLLHKTNFGRAVYAIGNNATGAMFSGIRVQRVKFILFLLTGLMSGVAAICLTARL 244 Query: 233 AVAYVDIANGFELDSVAACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQ 292 IA G+EL+ V V+GG+SI GG G++ G V+ A +G++ L ++ + Sbjct: 245 GSTRPSIAMGWELEVVTMVVLGGVSILGGSGTILGVVIAAFVMGLVTFGLGLLNVPGIVM 304 Query: 293 MAISGTVIILAVA 305 + G ++I +A Sbjct: 305 SIVIGALLIGVIA 317 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: 266 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: 328 Length adjustment: 28 Effective length of query: 305 Effective length of database: 300 Effective search space: 91500 Effective search space used: 91500 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