Align TM1748, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate GFF203 HP15_202 oligopeptide/dipeptide ABC transporter, permease protein
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__Marino:GFF203 Length = 310 Score = 159 bits (403), Expect = 6e-44 Identities = 93/290 (32%), Positives = 150/290 (51%), Gaps = 20/290 (6%) Query: 16 FWLRFKKNKMAVIGGVFVLILIALAILAPYIAPY-PYD--EPHYIRA------FEGPSKD 66 FW FK++K+A++ +L+++ A+ AP +AP PYD + + + + G Sbjct: 17 FWYSFKRDKVAIVSFAVLLLMVLAAVFAPLLAPADPYDLAQINIMNSELPPVGMSGADPA 76 Query: 67 FIFGTDALGRDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIV 126 F GTDA GRDL S ILY R + +IGFG+ + +G + G +AG+ GG +D +M I Sbjct: 77 FPLGTDAQGRDLLSTILYGTRVSLMIGFGAVVLQAFLGILFGLLAGYLGGKVDAVLMRIA 136 Query: 127 DIMFAFPTFLFNVILVTALGRG----------LFTIFLAIGLTGWAGMARLVRGQVLYLK 176 D+ +F T + +I+ ++ + IG+ W +AR VR VL K Sbjct: 137 DVQLSFSTLMVAIIVGAVFKASFGNLMFGEIAIYMLIFIIGVAEWPQIARTVRASVLAEK 196 Query: 177 NSEFVEAAKAAGASTFYIIRKHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPM 236 E+V+AAK G T I+ +HILPN + PI V + A+++E+ L+ +G+G+ Sbjct: 197 KKEYVDAAKVMGFGTRRIMFRHILPNTLSPIFVIATVQIANAIISEAALSFLGLGMPETQ 256 Query: 237 PSWGNLIGEGIGMMMAFP-HLLIFPAVTFAFTLISFTFLADGLRDAFNPR 285 PS G+LI G + + + + P + ++ L D LRD NPR Sbjct: 257 PSLGSLIKSGFDYIQSGSWWITLIPGLVLVVLVLVINLLGDWLRDVMNPR 306 Lambda K H 0.331 0.147 0.457 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: 229 Number of extensions: 12 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: 289 Length of database: 310 Length adjustment: 27 Effective length of query: 262 Effective length of database: 283 Effective search space: 74146 Effective search space used: 74146 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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