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 GFF994 PGA1_c10110 glutathione transport system permease protein GsiC
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__Phaeo:GFF994 Length = 335 Score = 192 bits (489), Expect = 8e-54 Identities = 111/346 (32%), Positives = 188/346 (54%), Gaps = 41/346 (11%) Query: 25 LKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKG 84 L F ++RL+ +++ + ++ ++L+ LAPG D +A+V P + ++ Sbjct: 2 LTFTIRRLVLSVPTLLFISLVIFLLLELAPG---------DPMAQVPLTVPPEVKEKMR- 51 Query: 85 FEERYGLNNP----LWKQILMYL----KGAVVFKFGPSFS---------DPARNIEDLIK 127 E GL P WK I+ + + + FG SFS + D++ Sbjct: 52 --EALGLGQPAHIRFWKWIVQFFWIEPQVLIDHYFGTSFSAGDLRVISWQTRSPVMDIVV 109 Query: 128 EKFPITFTLALSSILFALVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLI 187 ++ P T + ++ L A+ + +P+GI +A ++ +W D VS++G ++P + V +I Sbjct: 110 QRMPQTLWVVGTAYLVAIAIALPIGIYSAYRQYSWFDQVGTFVSMVGFSVPPFFSGVLVI 169 Query: 188 LIFSIYLGWLPT--------SGWEG----IRTKILPTIALALGPLASVARFTRVSLLDTL 235 +IFS+ LGW P+ + W+ ++ ++P + LAL A ++RF R S+LD L Sbjct: 170 VIFSVQLGWFPSIYDTTHVVNSWDSFVKQLQQMVMPVMVLALQITAQLSRFMRASMLDNL 229 Query: 236 NQDFIRTAYAKGGDDRTVIMKHALRPSMIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQ 295 NQD++RTA AKG + V+M H LR SMIP+VT++ + + G + E +F++ G+GQ Sbjct: 230 NQDYVRTARAKGLSEYVVVMVHVLRNSMIPVVTVIALGIPAIFGGAIITEQVFKVNGIGQ 289 Query: 296 LFANAAVTRDYPLLVTSTFILALTVMIMNLIVDVLYAILDPRIKLD 341 L A D P++ T TFI A+ +++ NLI DVLY ILDPRI+ D Sbjct: 290 LLIGAIEANDLPMVQTLTFIFAVLIVLFNLIADVLYGILDPRIRYD 335 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: 326 Number of extensions: 10 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: 341 Length of database: 335 Length adjustment: 28 Effective length of query: 313 Effective length of database: 307 Effective search space: 96091 Effective search space used: 96091 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: 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