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_003553864.1 RLEG_RS27470 rhamnose ABC transporter substrate-binding protein
Query= TCDB::Q7BSH5 (331 letters) >NCBI__GCF_000023185.1:WP_003553864.1 Length = 331 Score = 622 bits (1604), Expect = 0.0 Identities = 318/331 (96%), Positives = 323/331 (97%) Query: 1 MKLAKTLALGVALAVAMMAGTASAKDIKIGLVVKSLGNGFFDAANKGAQEAAKELGGVEV 60 MKLAK LA+GVA AVAMMAGTASA DIKIGLVVKSLGNGFFDAANKGAQEAAKELGGVEV Sbjct: 1 MKLAKKLAIGVAFAVAMMAGTASAADIKIGLVVKSLGNGFFDAANKGAQEAAKELGGVEV 60 Query: 61 IYTGPTSTTAEGQIEVINSLIAQGVDAIAVSANDPDALVPALKKATQRGIKVISWDSGVA 120 IYTGPT+TTAEGQIEVINSLIAQGV AIAVSANDPDALVPALKKA QRGIKVISWDSGVA Sbjct: 61 IYTGPTTTTAEGQIEVINSLIAQGVSAIAVSANDPDALVPALKKAAQRGIKVISWDSGVA 120 Query: 121 PEGRILQLNPSSNELIGKMCLTLAKDHLEGGKGDFAILSATTTSTNQNIWIDQMKKQLKD 180 PEGRILQLNPSSNELIGKMCLTL KDHL+GGKGDFAILSATTTSTNQNIWIDQMKKQLKD Sbjct: 121 PEGRILQLNPSSNELIGKMCLTLVKDHLDGGKGDFAILSATTTSTNQNIWIDQMKKQLKD 180 Query: 181 FPGLNLVTTVYGDDLSDKSYREAEGLLKSNPNVKVIVAPTTVGVLAASKVVEDKGLVGKV 240 FPGLNLVTTVYGDDLSDKSYREAEGLLK+NPN+KVIVAPTTVGVLAASKVVEDKGLVGKV Sbjct: 181 FPGLNLVTTVYGDDLSDKSYREAEGLLKANPNIKVIVAPTTVGVLAASKVVEDKGLVGKV 240 Query: 241 YVTGLGLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGETDGKPGSEINAGRM 300 YVTGLGLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGETDGKPGSEI GRM Sbjct: 241 YVTGLGLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGETDGKPGSEIEVGRM 300 Query: 301 GKIKVGDNGEAAMADPFVYNASNIDQFSKVF 331 GKIKVGDNGEAAMADPFVYNASNIDQFSKVF Sbjct: 301 GKIKVGDNGEAAMADPFVYNASNIDQFSKVF 331 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: 533 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: 331 Length of database: 331 Length adjustment: 28 Effective length of query: 303 Effective length of database: 303 Effective search space: 91809 Effective search space used: 91809 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 Apr 09 2024. 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