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 207956 DVU2462 oligopeptide ABC transporter, permease protein
Query= TCDB::Q9X270 (289 letters) >MicrobesOnline__882:207956 Length = 300 Score = 221 bits (564), Expect = 1e-62 Identities = 118/270 (43%), Positives = 162/270 (60%), Gaps = 3/270 (1%) Query: 16 FWLRFKKNKMAVIGGVFVLILIALAILAPYIAPYPYDEPHYIRAFEGPSKDFIFGTDALG 75 FW R N + IG V + LA+LAP+IAPY H GPS + GTDALG Sbjct: 31 FWQR---NILFAIGFAIVGSMSLLALLAPWIAPYDPTALHLDTILSGPSATHLLGTDALG 87 Query: 76 RDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIVDIMFAFPTF 135 RD+ SR+LY R + +GF S + + IG +G VAG+ GG ID+ M +VDIM FP+F Sbjct: 88 RDVLSRLLYGARVSLWVGFVSVGIAVAIGLAVGLVAGYFGGIIDELAMRLVDIMLCFPSF 147 Query: 136 LFNVILVTALGRGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEFVEAAKAAGASTFYII 195 + ++ L L I IGLT W G+ARLVR + L L+ EFV AA+ AGA II Sbjct: 148 FLILAVIAFLEPSLGNIMAVIGLTSWMGVARLVRAETLSLREREFVAAARLAGAGRTRII 207 Query: 196 RKHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWGNLIGEGIGMMMAFPH 255 HILPN + P+LV+ GV GA++TES L+ +G+GV+PP PSWGN++ EG ++ P Sbjct: 208 LTHILPNAMAPVLVSATLGVAGAILTESALSFLGLGVQPPDPSWGNMLLEGKDVLEIAPW 267 Query: 256 LLIFPAVTFAFTLISFTFLADGLRDAFNPR 285 + +FP + T++ + L + LRD +PR Sbjct: 268 MSLFPGLAILVTVLGYNLLGESLRDFLDPR 297 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: 278 Number of extensions: 10 Number of successful extensions: 1 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: 300 Length adjustment: 26 Effective length of query: 263 Effective length of database: 274 Effective search space: 72062 Effective search space used: 72062 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