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 BWI76_RS24645 BWI76_RS24645 autoinducer 2 ABC transporter substrate-binding protein
Query= TCDB::Q7BSH5 (331 letters) >FitnessBrowser__Koxy:BWI76_RS24645 Length = 333 Score = 184 bits (467), Expect = 3e-51 Identities = 106/299 (35%), Positives = 172/299 (57%), Gaps = 5/299 (1%) Query: 11 VALAVAMMAGTASAKDIKIGLVVKSLGNGFFDAANKGAQEAAKELGGVEVIYTGPTSTTA 70 + LA+A+ +A A D +I + K +G GFF + GA+EA K LG V+V Y GPT + Sbjct: 6 MVLAMALGMASAQAAD-RIAFIPKLVGVGFFTSGGNGAKEAGKALG-VDVTYDGPTEPSV 63 Query: 71 EGQIEVINSLIAQGVDAIAVSANDPDALVPALKKATQRGIKVISWDSGVAPEGRILQLNP 130 GQ+++IN+ + QG +AI VSA PD L PALK+A QRG+KV++WDS PE R + +N Sbjct: 64 SGQVQLINNFVNQGYNAIIVSAVSPDGLCPALKRAMQRGVKVLTWDSDTKPECRSIYINQ 123 Query: 131 SSNELIGKMCLTLAKDHLEGGKGDFAILSATTTSTNQNIWIDQMKKQL-KDFPGLNLVTT 189 + + +G + + +A+ + A ++ T T+QN W+ + K ++ K+ P +VTT Sbjct: 124 GTPQQLGGLLVEMAEKQVTKPTAKVAFFYSSPTVTDQNQWVKEAKAKIEKEHPQWEVVTT 183 Query: 190 VYGDDLSDKSYREAEGLLKSNPNVKVIVAPTTVGVLAASKVVEDKGLVGKVYVTGLGLPS 249 +G + + KS + AEG+LK+ P++ I+AP + AA++ E+ G V + G P+ Sbjct: 184 QFGYNDATKSLQTAEGILKAYPDLDAIIAPDANALPAAAQAAENLKRQG-VAIVGFSTPN 242 Query: 250 EMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGETDGKPGSEINAGRMGKIKVGDN 308 M + G K F +W+ + G A +A RL+K + D G ++ +G +KV N Sbjct: 243 VMRPYVDRGTVKAFGLWDVVQQGKIAVNVADRLLK-KGDLNVGDSVDVKDLGALKVEPN 300 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: 278 Number of extensions: 13 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: 333 Length adjustment: 28 Effective length of query: 303 Effective length of database: 305 Effective search space: 92415 Effective search space used: 92415 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