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 HSERO_RS15945 HSERO_RS15945 peptide ABC transporter permease
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__HerbieS:HSERO_RS15945 Length = 305 Score = 171 bits (432), Expect = 2e-47 Identities = 93/278 (33%), Positives = 152/278 (54%), Gaps = 6/278 (2%) Query: 13 WKAFWLRFKKNKMAVIGGVFVLILIALAILAPYIAPY-PYDEPHYIRAFEGP-----SKD 66 W+ R ++ +IG + +++ AI AP +AP+ P+D+ R S + Sbjct: 24 WRRKLRRLLGHRGLMIGAAVLAVIVLAAIFAPLLAPHDPFDQDVTARLIPPVWQAQGSWE 83 Query: 67 FIFGTDALGRDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIV 126 I GTD LGRD FSR++Y R + IG + + +IG LG +AG+ GG D I ++ Sbjct: 84 HILGTDKLGRDYFSRLIYGARVSLTIGLAAALISGLIGTTLGVLAGYFGGRTDAVISYLI 143 Query: 127 DIMFAFPTFLFNVILVTALGRGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEFVEAAKA 186 A P L + + + +G L + + +GL W A + R L+++EF+ AAKA Sbjct: 144 TTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIAAAKA 203 Query: 187 AGASTFYIIRKHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWGNLIGEG 246 GAST YI+ + ILPN++G ++V + + A++ E+ L+ +G+GV+PP PSWG ++ EG Sbjct: 204 IGASTPYILLREILPNIMGALIVVVTLEMAHAILLEATLSFLGLGVQPPTPSWGLMVAEG 263 Query: 247 IGMMMAFPHLLIFPAVTFAFTLISFTFLADGLRDAFNP 284 M P +++ P V A +++ + DGLRD P Sbjct: 264 KTYMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNAP 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: 206 Number of extensions: 11 Number of successful extensions: 2 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: 305 Length adjustment: 26 Effective length of query: 263 Effective length of database: 279 Effective search space: 73377 Effective search space used: 73377 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