Align TM1748, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate HSERO_RS09205 HSERO_RS09205 glutathione ABC transporter permease
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__HerbieS:HSERO_RS09205 Length = 296 Score = 215 bits (547), Expect = 1e-60 Identities = 106/274 (38%), Positives = 163/274 (59%), Gaps = 1/274 (0%) Query: 13 WKAFWLRFKKNKMAVIGGVFVLILIALAILAPYIAPY-PYDEPHYIRAFEGPSKDFIFGT 71 W+ FW +FKK +AV GVF+L L+A+AILAP+I P+ P + Y P+ FG Sbjct: 19 WREFWRKFKKQHLAVYAGVFILFLVAVAILAPWIVPFDPENFFDYDALNSPPTWVHWFGV 78 Query: 72 DALGRDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIVDIMFA 131 D+LGRD+FSRI+ R + GF S + +IG + G +AG+ GW D+ M I D++FA Sbjct: 79 DSLGRDIFSRIVMGTRISLAAGFFSVAIGAVIGTVFGLLAGYYEGWWDRITMRICDVLFA 138 Query: 132 FPTFLFNVILVTALGRGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEFVEAAKAAGAST 191 FP L + +V LG G+ + +++ + ARLVRG L LKN ++EA ++ GAS Sbjct: 139 FPGILLAIGIVAILGGGMINVIISVSVFSIPAFARLVRGNTLQLKNLTYIEATRSIGASD 198 Query: 192 FYIIRKHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWGNLIGEGIGMMM 251 I+ KHI P I I+V + +++T +GL+ +G+G + P P WG ++ E M+ Sbjct: 199 MTIMWKHIFPGTISAIVVYFTMRIGTSIITAAGLSFLGLGAQSPTPEWGLMLNEARADMV 258 Query: 252 AFPHLLIFPAVTFAFTLISFTFLADGLRDAFNPR 285 PH+ + P++ T+++F L DGLRDA +P+ Sbjct: 259 TSPHVALVPSIAIFLTVLAFNLLGDGLRDALDPK 292 Lambda K H 0.331 0.147 0.457 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: 244 Number of extensions: 14 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: 289 Length of database: 296 Length adjustment: 26 Effective length of query: 263 Effective length of database: 270 Effective search space: 71010 Effective search space used: 71010 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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