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 Pf1N1B4_5627 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5627 Length = 353 Score = 164 bits (415), Expect = 3e-45 Identities = 111/349 (31%), Positives = 187/349 (53%), Gaps = 43/349 (12%) Query: 27 FLLKRLLTIAISMVVVIVITYVLMWLAPGNFFE-----LQRVRDAI------------AR 69 ++L+RLL I ++V+++++ +V++ APG E LQ + A +R Sbjct: 4 YILRRLLLIIPTLVIILLVNFVIVQAAPGGPVEQAIAQLQGIGGASVGGGSSETMHGSSR 63 Query: 70 VTTPDDPAYQATLKGFEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEK 129 + DP +K E++YG + P +++ + LK FG SF A + DLI EK Sbjct: 64 ASRGLDPQL---IKEIEKQYGFDKPAPERLWLMLKSYARLDFGKSFFRGA-TVTDLILEK 119 Query: 130 FPITFTLALSSILFALVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILI 189 P+T +L L + L +V +PLGI A+ + D + T +IG A+P+++ A+FLI++ Sbjct: 120 MPVTISLGLWATLITYLVSIPLGIRKAVHHGSHFDIWSSTAIIIGYAMPAFLFAMFLIVV 179 Query: 190 FS--IYLGWLPTSG-----WEGIRT----------KILPTIALALGPLASVARFTRVSLL 232 F+ L W P G +E + T +LP AL +G A++ T+ S L Sbjct: 180 FAGGTSLNWFPVRGLVSDNFESLSTLGKITDYFWHLVLPVTALVVGGFATLTILTKNSFL 239 Query: 233 DTLNQDFIRTAYAKGGDDRTVIMKHALRPSMIPLVTIVGPQMAYLMV---GTVWVENIFR 289 + + + ++ TA AKG +R V+ H R +M L+ + G A++ V G++ +E IF Sbjct: 240 NEITRQYVVTARAKGLSERRVLYGHVFRNAM--LLVVSGIPQAFISVFFAGSLLIEVIFS 297 Query: 290 IPGLGQLFANAAVTRDYPLLVTSTFILALTVMIMNLIVDVLYAILDPRI 338 + GLG++ AAV+RDYP++ S FI L +++ LI D+ Y ++DPRI Sbjct: 298 LDGLGRMSYEAAVSRDYPVVFGSLFIFTLFGLLIKLIGDLCYTLVDPRI 346 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: 276 Number of extensions: 20 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: 353 Length adjustment: 29 Effective length of query: 312 Effective length of database: 324 Effective search space: 101088 Effective search space used: 101088 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