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 SMc03000 SMc03000 ABC transporter permease
Query= TCDB::Q7BSH3 (333 letters) >FitnessBrowser__Smeli:SMc03000 Length = 326 Score = 415 bits (1067), Expect = e-121 Identities = 208/324 (64%), Positives = 255/324 (78%) Query: 1 MARLIRKRETLLFLIIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTK 60 MARL++ RE LL + I V++ + + R F P NLA +++DTSIL+ILAL QM VILT+ Sbjct: 2 MARLLKNREILLVVAIAVLLALIALRFPAFVAPSNLARVYSDTSILVILALGQMAVILTR 61 Query: 61 SIDLSVAANLAFTGMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIV 120 IDLS+AANLA GM AM+N A P LP+ ++I+ + +G LG+ING LVW L IPPIV Sbjct: 62 CIDLSMAANLALCGMVAAMLNNAFPGLPIPLIIVAVMALGGFLGSINGTLVWKLNIPPIV 121 Query: 121 VTLGTLTIYRGMAFVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYVLL 180 VTLGTLTIYRG+ FVL+ G W+NAH+M+ F ++PR V G+PVLSW+ ++IV LM++++ Sbjct: 122 VTLGTLTIYRGLIFVLTNGKWINAHEMSDAFKALPRLDVAGMPVLSWLSLVIVALMFLVM 181 Query: 181 RYTQFGRSAYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIA 240 T GR+ YA GGNP AAVY GID G T+F A+ LSGALAGL+ YLWVSRYAVAYVDIA Sbjct: 182 GRTPLGRAFYAVGGNPHAAVYTGIDVGRTRFFAYCLSGALAGLSGYLWVSRYAVAYVDIA 241 Query: 241 NGFELDSVAACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVI 300 GFELD +AACVIGGISIAGG+GSVAG VLGALFLGVIKNALPVI ISPF Q+AISGTVI Sbjct: 242 AGFELDIIAACVIGGISIAGGIGSVAGAVLGALFLGVIKNALPVINISPFAQLAISGTVI 301 Query: 301 ILAVAFNARRERNRGRIILRDRAA 324 I+AVA NAR ER +GR+IL+ A Sbjct: 302 IIAVAVNARAERRKGRVILKKAEA 325 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: 352 Number of extensions: 15 Number of successful extensions: 1 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: 326 Length adjustment: 28 Effective length of query: 305 Effective length of database: 298 Effective search space: 90890 Effective search space used: 90890 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