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 Pf6N2E2_1810 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1810 Length = 305 Score = 193 bits (490), Expect = 5e-54 Identities = 108/316 (34%), Positives = 184/316 (58%), Gaps = 13/316 (4%) Query: 25 LKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKG 84 L FLL+RL + V VI++ L+ L+ D + P+ + Q ++ Sbjct: 2 LGFLLRRLGIAICVAITVSVISFSLLHLSG----------DLATAIGGPEATSEQ--IEQ 49 Query: 85 FEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILFA 144 +YGL+ PL Q +L + G SF ++ +L+ + PIT L ++ A Sbjct: 50 IRVQYGLDKPLPTQYFNWLGDLLRLDLGDSFFFQ-ESVYNLVASRLPITLGLGAMALGIA 108 Query: 145 LVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSGWEG 204 L+V +PLG+LAA+K++TW+D A++++V+G A+PS+ A+ LI++F++ L WLP SG Sbjct: 109 LLVAIPLGVLAAVKRDTWVDRLALSIAVLGQAMPSFWFALMLIVVFAVTLKWLPVSGNST 168 Query: 205 IRTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTVIMKHALRPSMI 264 + ++P IAL ++ R TR +LD L+ D+IRTA AKG V+ KHALR ++I Sbjct: 169 LLHFVMPAIALGYYATPAIMRLTRAGMLDVLSSDYIRTARAKGLRPARVLFKHALRNALI 228 Query: 265 PLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTSTFILALTVMIMN 324 P+V + + +++ G+V +E +F + G+GQL +A D+P++ ++A+ +I+ Sbjct: 229 PVVALAAVEFGFMLGGSVVIETVFSLQGIGQLAWDAIARDDFPVVQAVVLLIAVIYIILT 288 Query: 325 LIVDVLYAILDPRIKL 340 L+ DVL A+LDPRI++ Sbjct: 289 LLADVLNALLDPRIRV 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: 267 Number of extensions: 12 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: 305 Length adjustment: 28 Effective length of query: 313 Effective length of database: 277 Effective search space: 86701 Effective search space used: 86701 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