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 Ac3H11_2050 Dipeptide transport system permease protein DppC (TC 3.A.1.5.2)
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2050 Length = 303 Score = 177 bits (449), Expect = 3e-49 Identities = 101/289 (34%), Positives = 157/289 (54%), Gaps = 27/289 (9%) Query: 20 FKKNKMAVIGGVFVLILIALAILAPYIAPY-PYD-----------EPHYIRAFEGPSKDF 67 F+ + MA++ LI + ++ A ++AP+ P+D P + + EG K + Sbjct: 17 FRTSPMAMVAAAIALICVFCSVFAGWVAPHNPFDLATLELSDARLPPAW--SAEGSMK-Y 73 Query: 68 IFGTDALGRDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIVD 127 GTD GRD+ S ++Y R + ++G S + +++G G +AGFKGGWID +M + D Sbjct: 74 PLGTDDQGRDILSALIYGARISLVVGLASVVLSVLVGVAFGLLAGFKGGWIDAVLMRLCD 133 Query: 128 IMFAFPTFLFNVILVTALGRGLF----------TIFLAIGLTGWAGMARLVRGQVLYLKN 177 +M +FP L +L+ +GR LF + ++I LTGW AR VRG L +N Sbjct: 134 VMLSFPAILV-ALLIAGVGRALFPNAHESLAFGVLIISISLTGWVQYARTVRGSTLVERN 192 Query: 178 SEFVEAAKAAGASTFYIIRKHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMP 237 E+V+AA+ G S I+RKH+LPN++GP++V V A++TE+ L+ +G+G P P Sbjct: 193 KEYVQAARVTGVSPLRIMRKHVLPNVMGPVMVLATIQVATAIITEATLSFLGVGAPPTSP 252 Query: 238 SWGNLIGEGIGMMMAFP-HLLIFPAVTFAFTLISFTFLADGLRDAFNPR 285 S G LI G + + + +FP +S L D LRDA NPR Sbjct: 253 SLGTLIRIGNDYLFSGEWWITVFPGAMLVLIALSVNLLGDWLRDALNPR 301 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: 237 Number of extensions: 9 Number of successful extensions: 3 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: 303 Length adjustment: 26 Effective length of query: 263 Effective length of database: 277 Effective search space: 72851 Effective search space used: 72851 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