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 PfGW456L13_3344 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3344 Length = 357 Score = 155 bits (391), Expect = 2e-42 Identities = 110/355 (30%), Positives = 180/355 (50%), Gaps = 41/355 (11%) Query: 25 LKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFE-----LQRVRDAIARVT------TP 73 L ++ +RLL I ++ +++I +V++ APG E L+ A +R+ + Sbjct: 2 LAYIFRRLLLIIPTLFGILLINFVIIQAAPGGPVEQMIAKLEGFEGATSRIAGGGAEVSV 61 Query: 74 DDPAYQ-------ATLKGFEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLI 126 AY+ A +K E YG + +++ + +K FG SF A+ I DLI Sbjct: 62 AGSAYRGAQGLDPALIKEIEHMYGFDKSAPERLWIMVKNYASLDFGDSFFRDAKVI-DLI 120 Query: 127 KEKFPITFTLALSSILFALVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFL 186 KEK P++ +L L S L +V +PLGI A + + D + ++G AIP+++ A+ L Sbjct: 121 KEKMPVSISLGLWSTLIMYLVSIPLGIAKAKRHGSHFDVWTSSAIIVGYAIPAFLFAILL 180 Query: 187 ILIFS--IYLGWLPTSGWE-------GIRTKI--------LPTIALALGPLASVARFTRV 229 I++F+ YL W P G + KI LP AL +G A++ T+ Sbjct: 181 IVVFAGGSYLDWFPLRGLTSNNFDELSMGGKILDYFWHLALPVTALVIGNFATMTLLTKN 240 Query: 230 SLLDTLNQDFIRTAYAKGGDDRTVIMKHALRPSMIPLVTIVGPQMAYL---MVGTVWVEN 286 S LD +N+ ++ TA AKG + V+ H R +M L+ I G A++ G++ VE Sbjct: 241 SFLDEINKQYVITARAKGLTNHRVLYGHVFRNAM--LLVIAGFPSAFIGIFFTGSLLVEV 298 Query: 287 IFRIPGLGQLFANAAVTRDYPLLVTSTFILALTVMIMNLIVDVLYAILDPRIKLD 341 IF + GLG + AA+ RDYP++ + FI L +++ LI D+ Y +DPRI + Sbjct: 299 IFSLDGLGLMSFEAAINRDYPVVFGTLFIFTLLGLVVKLIGDLTYTFVDPRIDFE 353 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: 294 Number of extensions: 18 Number of successful extensions: 4 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: 357 Length adjustment: 29 Effective length of query: 312 Effective length of database: 328 Effective search space: 102336 Effective search space used: 102336 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