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 15637 b1516 AI2 transporter (NCBI)
Query= TCDB::Q7BSH5 (331 letters) >FitnessBrowser__Keio:15637 Length = 340 Score = 187 bits (474), Expect = 4e-52 Identities = 111/336 (33%), Positives = 186/336 (55%), Gaps = 17/336 (5%) Query: 5 KTLALGVALAVAMMAGTASAKDIKIGLVVKSLGNGFFDAANKGAQEAAKELGGVEVIYTG 64 K +AL AL +A ++ A + +I + K +G GFF + GAQ+A KELG V+V Y G Sbjct: 7 KKIALLSALGIAAISMNVQAAE-RIAFIPKLVGVGFFTSGGNGAQQAGKELG-VDVTYDG 64 Query: 65 PTSTTAEGQIEVINSLIAQGVDAIAVSANDPDALVPALKKATQRGIKVISWDSGVAPEGR 124 PT + GQ+++IN+ + QG +AI VSA PD L PALK+A QRG++V++WDS PE R Sbjct: 65 PTEPSVSGQVQLINNFVNQGYNAIIVSAVSPDGLCPALKRAMQRGVRVLTWDSDTKPECR 124 Query: 125 ILQLNPSSNELIGKMCLTLAKDHLEGGKGDFAILSATTTSTNQNIWIDQMKKQL-KDFPG 183 +N + +G M + +A + K A ++ T T+QN W+ + K ++ K+ PG Sbjct: 125 SYYINQGTPAQLGGMLVDMAARQVNKDKAKVAFFYSSPTVTDQNQWVKEAKAKIAKEHPG 184 Query: 184 LNLVTTVYGDDLSDKSYREAEGLLKSNPNVKVIVAPTTVGVLAASKVVEDKGLVGKVYVT 243 +VTT +G + + KS + AEG+LK+ ++ I+AP + AA++ E+ KV + Sbjct: 185 WEIVTTQFGYNDATKSLQTAEGILKAYSDLDAIIAPDANALPAAAQAAENL-KNDKVAIV 243 Query: 244 GLGLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGETDGKPGSEINAGRMGKI 303 G P+ M ++ G KEF +W+ + G + +A L+K + K G +++ +G++ Sbjct: 244 GFSTPNVMRPYVERGTVKEFGLWDVVQQGKISVYVADALLK-KGSMKTGDKLDIKGVGQV 302 Query: 304 KVG------------DNGEAAMADPFVYNASNIDQF 327 +V NG + + ++N NI ++ Sbjct: 303 EVSPNSVQGYDYEADGNGIVLLPERVIFNKENIGKY 338 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: 286 Number of extensions: 14 Number of successful extensions: 5 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: 340 Length adjustment: 28 Effective length of query: 303 Effective length of database: 312 Effective search space: 94536 Effective search space used: 94536 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