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_RS25795 BPHYT_RS25795 LacI family transcription regulator
Query= TCDB::Q7BSH5 (331 letters) >FitnessBrowser__BFirm:BPHYT_RS25795 Length = 334 Score = 129 bits (325), Expect = 8e-35 Identities = 93/289 (32%), Positives = 153/289 (52%), Gaps = 7/289 (2%) Query: 2 KLAKTLALGVALAVAMMAGTASAKDIKIGLVVKSLGNGFFDAANKGAQEAAKELGGVEVI 61 +L LA G AL V ++A +A + I VVK G +F+ + G ++ AK+ + Sbjct: 5 RLGAALAAG-ALTVGVIAAAQAATNETIVTVVKVTGINWFNRMDDGVKQFAKDNPNINAY 63 Query: 62 YTGPTSTTAEGQIEVINSLIAQGVDAIAVSANDPDALVPALKKATQRGIKVISWDSGVAP 121 TGP A Q+++I LIA+ V AIAV DP L PALKKA RGIKV++ ++ A Sbjct: 64 QTGPGRADAAQQLKIIEDLIAKKVTAIAVVPYDPPTLEPALKKAMDRGIKVVTHEADNA- 122 Query: 122 EGRILQLNPSSNELIGK-MCLTLAKDHLEGGKGDFAILSATTTSTNQNIWIDQMKKQLK- 179 + ++ + N G + LA + GK +A+L + S +Q W D K Sbjct: 123 KNTMVDIEAFDNTAYGAGLNERLASCMHDDGK--WAVLVGSLGSRSQVQWADGGIGNAKA 180 Query: 180 DFPGLNLV-TTVYGDDLSDKSYREAEGLLKSNPNVKVIVAPTTVGVLAASKVVEDKGLVG 238 +P +NLV + ++ +++Y A+ +L+ +P++K +++ V+ + VE+ G+ G Sbjct: 181 KYPKMNLVEPKLETNNDGERAYEVAKEVLRKHPDLKGFQGSSSLDVIGIGRAVEEAGMQG 240 Query: 239 KVYVTGLGLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGET 287 K+ V G GLP+E ++SGA A W+P G + ++A LV G+T Sbjct: 241 KICVYGTGLPTEAGKFLESGAINGIAFWDPKLAGIAMNKVAQMLVDGKT 289 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: 272 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: 334 Length adjustment: 28 Effective length of query: 303 Effective length of database: 306 Effective search space: 92718 Effective search space used: 92718 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