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 HSERO_RS22215 HSERO_RS22215 branched-chain amino acid ABC transporter permease
Query= TCDB::Q7BSH3 (333 letters) >FitnessBrowser__HerbieS:HSERO_RS22215 Length = 323 Score = 320 bits (820), Expect = 3e-92 Identities = 167/309 (54%), Positives = 222/309 (71%) Query: 11 LLFLIIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTKSIDLSVAANL 70 LL L+ VV+I++ RA F + ++ + D++I I+LALAQM VILT+ IDLSVA+NL Sbjct: 1 LLALLTVVLILLVGVRAPVFLSAQSMDNLLTDSAITIMLALAQMLVILTRGIDLSVASNL 60 Query: 71 AFTGMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVVTLGTLTIYR 130 A +GM A++ P LP+ V ILMAV+IG LG +NG+L+ LE+PPIVVTLG++++YR Sbjct: 61 ALSGMMSALLAMHFPALPVGVFILMAVLIGLMLGLLNGWLIGYLELPPIVVTLGSMSVYR 120 Query: 131 GMAFVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYVLLRYTQFGRSAY 190 GM FVLSGGAWV++ M F++ P + GL L W+G + V+ ++ L R+T+FGR Y Sbjct: 121 GMVFVLSGGAWVSSRNMPADFIAFPLARLGGLTHLVWLGALAVVAIWFLARHTRFGRDLY 180 Query: 191 ATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIANGFELDSVAA 250 A G +P AA Y GI + + LSGA+AGLA YLWV+RYAVAY +IA GFEL +AA Sbjct: 181 AIGNDPAAAAYVGIASRGRLLWTYGLSGAMAGLAGYLWVARYAVAYTEIAYGFELTVIAA 240 Query: 251 CVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVIILAVAFNARR 310 CVIGG+SIAGGVG V+G VLGALFL VI NALP++ ISPF Q A++G VI+ AV NAR Sbjct: 241 CVIGGVSIAGGVGQVSGAVLGALFLSVINNALPIMRISPFWQSALTGLVILCAVVLNARG 300 Query: 311 ERNRGRIIL 319 ++ R + IL Sbjct: 301 KQGRRKQIL 309 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: 334 Number of extensions: 12 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: 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