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 GFF3595 PS417_18405 LacI family transcriptional regulator
Query= TCDB::Q7BSH5 (331 letters) >FitnessBrowser__WCS417:GFF3595 Length = 318 Score = 97.4 bits (241), Expect = 4e-25 Identities = 91/306 (29%), Positives = 135/306 (44%), Gaps = 29/306 (9%) Query: 10 GVALAVAMMAGTASAKDI-----------KIGLVVKSLGNGFFDAANKGAQEAAKE-LGG 57 G LAVA++A ++A + K+GLV+KSL N FF GA+ KE Sbjct: 7 GRLLAVAVLAAASAALPLSSAFADDAAKPKVGLVMKSLANEFFVTMQDGAKTYQKEHAAD 66 Query: 58 VEVIYTG-PTSTTAEGQIEVINSLIAQGVDAIAVSANDPDALVPALKKATQRGIKVISWD 116 ++I G T QI+++N +I V+AI ++ D ALV LKKA+ GIKV++ D Sbjct: 67 FDMITNGIKNETDTSAQIDIVNQMILAKVNAIVIAPADSKALVTVLKKASDAGIKVVNID 126 Query: 117 SGVAPE---GRILQL------NPSSNELIGKMCLTLAKDHLEGGKGDFAILSATTTSTNQ 167 + + P+ + L + N ++L+G LAK G K TTT+ Q Sbjct: 127 NRLDPDVLKSKNLDIPFVGPDNRKGSKLVGDY---LAKQLASGDKVGIIEGVPTTTNAQQ 183 Query: 168 NIWIDQMKKQLKDFPGLNLVTTVYGDDLSDKSYREAEGLLKSNPNVKVIVAPTTVGVLAA 227 K D G+ +V+T G+ D+ + A +L P++K ++A L A Sbjct: 184 R---TAGYKDAMDAAGMKIVSTQSGNWEIDQGQKVASAMLSEYPDLKALLAGNDNMALGA 240 Query: 228 SKVVEDKGLVGKVYVTGLGLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGE- 286 V G GKV V G + ++ G A Q A +LVKGE Sbjct: 241 VSAVRAAGKAGKVLVVGYDNIEAIKPMLQDGRVLATADQAAAQQAVFGIQNALKLVKGEK 300 Query: 287 TDGKPG 292 D K G Sbjct: 301 VDSKDG 306 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: 252 Number of extensions: 17 Number of successful extensions: 2 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: 318 Length adjustment: 28 Effective length of query: 303 Effective length of database: 290 Effective search space: 87870 Effective search space used: 87870 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: 48 (23.1 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