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 AO353_21795 AO353_21795 peptide ABC transporter permease
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21795 Length = 352 Score = 162 bits (411), Expect = 9e-45 Identities = 106/346 (30%), Positives = 188/346 (54%), Gaps = 34/346 (9%) Query: 25 LKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFE-----LQRVR--------DAIARVT 71 L ++++RLL I ++V+++++ +V++ APG E LQ + DAI+ + Sbjct: 2 LAYIVRRLLLIIPTLVIILLVNFVIVQAAPGGPVEQAIAHLQGIGGPAIGSSGDAISHGS 61 Query: 72 TPDDPAYQATLKGFEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFP 131 +K E++YG + P +++ + + FG SF A + DLI EK P Sbjct: 62 RASRGLDPQLIKDIEKQYGFDKPAPERLWLMITSYARLDFGKSFFRGA-TVTDLILEKMP 120 Query: 132 ITFTLALSSILFALVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFS 191 +T +L L + L +V +PLGI A+ + D + T+ VIG A+P+++ A+FLI++F+ Sbjct: 121 VTISLGLWATLITYLVSIPLGIRKAVHHGSLFDIWSSTIIVIGYALPAFLFAMFLIVVFA 180 Query: 192 --IYLGWLPTSG-----WEGIRT----------KILPTIALALGPLASVARFTRVSLLDT 234 L W P G ++ + T +LP AL +G A++ T+ S L+ Sbjct: 181 GGTSLNWFPVRGLVSENFDQLSTLGKVADYFWHLVLPVTALVVGGFATLTILTKNSFLNE 240 Query: 235 LNQDFIRTAYAKGGDDRTVIMKHALRPSMIPLVTIVGPQ--MAYLMVGTVWVENIFRIPG 292 + + ++ TA AKG +R V+ H R +M+ +V+ + PQ ++ G++ +E IF + G Sbjct: 241 ITRQYVVTARAKGLSERRVLYGHVFRNAMLLVVSGI-PQALISVFFAGSLLIEVIFSLDG 299 Query: 293 LGQLFANAAVTRDYPLLVTSTFILALTVMIMNLIVDVLYAILDPRI 338 LG++ AAV+RDYP++ S FI L +++ +I D+ Y ++DPRI Sbjct: 300 LGRMSYEAAVSRDYPVVFGSLFIFTLFGLLIKIIGDLCYTLVDPRI 345 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: 291 Number of extensions: 19 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: 352 Length adjustment: 29 Effective length of query: 312 Effective length of database: 323 Effective search space: 100776 Effective search space used: 100776 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