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 RR42_RS32895 RR42_RS32895 ABC transporter permease
Query= TCDB::Q7BSH3 (333 letters) >FitnessBrowser__Cup4G11:RR42_RS32895 Length = 318 Score = 163 bits (413), Expect = 5e-45 Identities = 96/293 (32%), Positives = 162/293 (55%), Gaps = 10/293 (3%) Query: 15 IIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTKSIDLSVAANLAFTG 74 +++++ + FS F + NL I ++IL+++AL +I+T+ +DLS+ A L G Sbjct: 24 VLLLLSLGFSVTGPGFLSVENLLNIGAQSTILLLIALPMTLIIMTEGLDLSMGAVLTLCG 83 Query: 75 MAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVVTLGTLTIYRGMAF 134 + +AM+ A LPL + A++ G G +NG LV LEIPP V TLGTL + +G+A Sbjct: 84 VVLAMVMVATESLPLA--LGAALLTGLAFGLLNGALVSWLEIPPFVATLGTLGVAQGLAL 141 Query: 135 VLSGGAWVNAHQMTPIFLSVPRT---PVLGLPVLSWVGIIIVILMYVLLRYTQFGRSAYA 191 V + G +T I ++P +LG+P+ W+ + L + LL +T+FG +A Sbjct: 142 VATDG-----QSVTGIGEAIPLIYAGQLLGVPLPIWIAAVFYGLFHWLLYHTRFGAYVFA 196 Query: 192 TGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIANGFELDSVAAC 251 GGN A ++G+ + L G +AG+A+ L +R + A G E D++AA Sbjct: 197 LGGNREALKFSGVRINVYLIAVYALGGLMAGVAALLLTARMNAGHPTAAIGLEFDAIAAV 256 Query: 252 VIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVIILAV 304 +GG + G G + GTVLG L +GV++N L ++G+ Q+A G ++++ + Sbjct: 257 AVGGTTFDRGNGWLPGTVLGVLAVGVLRNGLNLVGVPSSVQVAAIGLLVLVVL 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: 277 Number of extensions: 15 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: 318 Length adjustment: 28 Effective length of query: 305 Effective length of database: 290 Effective search space: 88450 Effective search space used: 88450 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: 48 (23.1 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