Align RhaS, 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 BPHYT_RS28200 BPHYT_RS28200 sugar ABC transporter substrate-binding protein
Query= TCDB::Q7BSH5 (331 letters) >FitnessBrowser__BFirm:BPHYT_RS28200 Length = 335 Score = 253 bits (647), Expect = 4e-72 Identities = 143/327 (43%), Positives = 201/327 (61%), Gaps = 6/327 (1%) Query: 6 TLALGVAL-AVAMMAGTASAKD-IKIGLVVKSLGNGFFDAANKGAQEAAKELGGVEVIYT 63 T AL VAL A++ A A K +KI V K + N + A+ G A KE GV Sbjct: 10 TAALCVALLAISCAASAADLKSGLKIAFVPKQINNPYEVIADDGGMTAIKEFKGVGKA-V 68 Query: 64 GPTSTTAEGQIEVINSLIAQGVDAIAVSANDPDALVPALKKATQRGIKVISWDSGVAPEG 123 GP+ A Q++ IN+LI Q DAI ++AND +A+VP LKKA +GIKV+++DS APEG Sbjct: 69 GPSDAGASSQVQYINTLITQRQDAIVIAANDANAVVPYLKKAMSQGIKVVTFDSDTAPEG 128 Query: 124 RILQLNPSSNELIGKMCLTLAKDHLEGGKGDFAILSATTTSTNQNIWIDQMKKQLK--DF 181 R L +N ++ E IG+ + L L GG+G+FA+LSAT +TNQN WI M+++LK ++ Sbjct: 129 RQLFVNQANAEGIGRGQVQLVSK-LMGGEGEFAVLSATPNATNQNTWIKWMQEELKKPEY 187 Query: 182 PGLNLVTTVYGDDLSDKSYREAEGLLKSNPNVKVIVAPTTVGVLAASKVVEDKGLVGKVY 241 + LV YG+D KS+ E +GLL++ PN+K IVAPTTVG+ AA++ + GKV Sbjct: 188 SKIKLVKIAYGNDDDQKSFTETQGLLQAYPNLKAIVAPTTVGIAAAARYISTSSSKGKVA 247 Query: 242 VTGLGLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGETDGKPGSEINAGRMG 301 VTGLG P++M +K+G K F +W+P LGY A A L G GK G +AG++G Sbjct: 248 VTGLGTPNQMRAFVKNGTVKAFQLWDPGQLGYLAAYAAAALASGTISGKEGESFDAGKLG 307 Query: 302 KIKVGDNGEAAMADPFVYNASNIDQFS 328 K +G GE + P +++SNID F+ Sbjct: 308 KRTIGPQGEIILGPPTTFDSSNIDNFN 334 Lambda K H 0.313 0.131 0.365 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: 318 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: 331 Length of database: 335 Length adjustment: 28 Effective length of query: 303 Effective length of database: 307 Effective search space: 93021 Effective search space used: 93021 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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