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 BWI76_RS17230 BWI76_RS17230 peptide ABC transporter permease
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__Koxy:BWI76_RS17230 Length = 302 Score = 206 bits (525), Expect = 4e-58 Identities = 107/285 (37%), Positives = 171/285 (60%), Gaps = 4/285 (1%) Query: 4 KNKTESIGYWKAFWLRFKKNKMAVIGGVFVLILIALAI-LAPYIAPYPYDEPHYIRAFEG 62 K + E W+ RF N+ AV + VL++IAL + +AP ++ + Y + + Sbjct: 17 KLEVEGRSLWQDARRRFMHNRAAV-ASLIVLVIIALFVTIAPMVSQFSYYDTDWGMMSSA 75 Query: 63 PSKD--FIFGTDALGRDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDK 120 P + FGTD+ GRDL R+ R + ++G + V +I+G + G+++G+ GG +D Sbjct: 76 PDTESGHYFGTDSSGRDLLVRVAIGGRISLMVGVAAALVAVILGTLYGSLSGYLGGKVDS 135 Query: 121 FIMSIVDIMFAFPTFLFNVILVTALGRGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEF 180 +M +++I+ +FP F ++LVT G+ + IF+AIG+ W MAR+VRGQ L LK EF Sbjct: 136 VMMRLLEILNSFPFMFFVILLVTFFGQNILLIFVAIGMVSWLDMARIVRGQTLSLKRKEF 195 Query: 181 VEAAKAAGASTFYIIRKHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWG 240 +EAA+ G ST I+ +HI+PN++G ++V + VP ++ ES L+ +G+G + P+ SWG Sbjct: 196 IEAAQVGGVSTGNIVIRHIVPNVLGVVVVYASLLVPSMILFESFLSFLGLGTQEPLSSWG 255 Query: 241 NLIGEGIGMMMAFPHLLIFPAVTFAFTLISFTFLADGLRDAFNPR 285 L+ +G M P LL+FPA TL F F+ DGLRDA +P+ Sbjct: 256 ALLSDGANSMEVSPWLLLFPAGFLVVTLFCFNFIGDGLRDALDPK 300 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: 236 Number of extensions: 11 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: 302 Length adjustment: 26 Effective length of query: 263 Effective length of database: 276 Effective search space: 72588 Effective search space used: 72588 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