Align TM1747, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate HSERO_RS09200 HSERO_RS09200 glutathione ABC transporter permease
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__HerbieS:HSERO_RS09200 Length = 306 Score = 195 bits (496), Expect = 1e-54 Identities = 109/313 (34%), Positives = 187/313 (59%), Gaps = 12/313 (3%) Query: 27 FLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKGFE 86 F++KRLL + ++++V V+ ++ + L PG+ L +A DD T+ Sbjct: 4 FVIKRLLGLIPTLLLVAVLVFLFVHLLPGDPARLAAGPEA-------DDK----TVALVR 52 Query: 87 ERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILFALV 146 GL+ PL +Q + + A FG S R + + I +F T L + ++++A++ Sbjct: 53 ADLGLDKPLPEQFVNFFLNAARGDFGHSIRTK-RPVSEEISARFWPTLWLTVVAMVWAVL 111 Query: 147 VGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSGWEGIR 206 G+ +GI +A+ +N W D MT++V G++ P++ + + L+ +FS+ LGWLPT G + Sbjct: 112 FGLIIGISSAVWRNQWPDRLGMTLAVSGISFPAFSLGILLVQVFSVKLGWLPTVGDDTWL 171 Query: 207 TKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTVIMKHALRPSMIPL 266 ILP+I L A +ARFTR S ++ L +DF+RTA AKG + V++KH LR ++IP+ Sbjct: 172 HYILPSITLGAAVAAVMARFTRSSFIEILQEDFVRTARAKGLTETVVVIKHCLRNALIPV 231 Query: 267 VTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTSTFILALTVMIMNLI 326 VT++G Q +L+ G++ VE +F PG+G+L +A RDYP++ + +L + +NL+ Sbjct: 232 VTMMGLQFGFLLGGSILVEVVFNWPGMGRLLVDAVEMRDYPVIQAEILLFSLEFIFINLV 291 Query: 327 VDVLYAILDPRIK 339 VDVLYA+++P I+ Sbjct: 292 VDVLYAVINPSIR 304 Lambda K H 0.328 0.143 0.429 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: 295 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: 341 Length of database: 306 Length adjustment: 28 Effective length of query: 313 Effective length of database: 278 Effective search space: 87014 Effective search space used: 87014 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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