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 WP_013092021.1 BC1002_RS21090 rhamnose ABC transporter substrate-binding protein
Query= TCDB::Q7BSH5 (331 letters) >NCBI__GCF_000092885.1:WP_013092021.1 Length = 336 Score = 251 bits (642), Expect = 1e-71 Identities = 141/323 (43%), Positives = 200/323 (61%), Gaps = 8/323 (2%) Query: 12 ALAVAMMAGTASAKDIKIGL----VVKSLGNGFFDAANKGAQEAAKELGGVEVIYTGPTS 67 A +A+ G A A D+K GL V K + N + A+ G A KE GGV GP+ Sbjct: 15 AALLAISCGGAFAADLKSGLKIAFVPKQINNPYEVIADDGGLAAIKEFGGVGKA-VGPSD 73 Query: 68 TTAEGQIEVINSLIAQGVDAIAVSANDPDALVPALKKATQRGIKVISWDSGVAPEGRILQ 127 A Q+ IN+LI Q DAI ++AND +A+VP LKKA +GIKV+++DS APEGR L Sbjct: 74 AGASSQVSYINTLITQHQDAIVIAANDANAVVPYLKKAMGQGIKVVTFDSDTAPEGRQLF 133 Query: 128 LNPSSNELIGKMCLTLAKDHLEGGKGDFAILSATTTSTNQNIWIDQMKKQLK--DFPGLN 185 +N ++ E IG+ + L L GG+G+FAILSAT +TNQN WI M+++LK ++ + Sbjct: 134 VNQANAEGIGRGQVQLVAK-LMGGEGEFAILSATPNATNQNTWIKWMQEELKKPEYSKIK 192 Query: 186 LVTTVYGDDLSDKSYREAEGLLKSNPNVKVIVAPTTVGVLAASKVVEDKGLVGKVYVTGL 245 LV YG+D KS+ E +GLL++ PN+K IVAPTTVG+ AA++ + GKV VTGL Sbjct: 193 LVKIAYGNDDDQKSFVETQGLLQAYPNLKAIVAPTTVGIAAAARYISSSSSKGKVAVTGL 252 Query: 246 GLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGETDGKPGSEINAGRMGKIKV 305 G P++M +K+G F +W+P +LGY A A L G+ GK G +AG++GK + Sbjct: 253 GTPNQMRAFVKNGTVTAFQLWDPSELGYLAAYAAASLASGKIAGKEGESFDAGKLGKRTI 312 Query: 306 GDNGEAAMADPFVYNASNIDQFS 328 G GE + P ++ASNID+++ Sbjct: 313 GAQGEIILGPPTTFDASNIDKYN 335 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: 338 Number of extensions: 20 Number of successful extensions: 4 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: 336 Length adjustment: 28 Effective length of query: 303 Effective length of database: 308 Effective search space: 93324 Effective search space used: 93324 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 24 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