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 RR42_RS11225 RR42_RS11225 peptide ABC transporter permease
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__Cup4G11:RR42_RS11225 Length = 300 Score = 177 bits (448), Expect = 3e-49 Identities = 91/269 (33%), Positives = 151/269 (56%), Gaps = 1/269 (0%) Query: 17 WLRFKKNKMAVIGGVFVLILIALAILAPYIAPYPYDEPHYIRAFEGPSKDFIFGTDALGR 76 W +K+ ++G + ++ + AL+I AP+IA + + + + PS + FGTDALGR Sbjct: 28 WHWARKHPTLIVGALLLVAIAALSIGAPWIATFDPQDIDPLARMQPPSAEHWFGTDALGR 87 Query: 77 DLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIVDIMFAFPTFL 136 D+FSR ++ R + ++G + G +LG AGF W D F+M ++D + A P L Sbjct: 88 DVFSRAVWGGRVSMVVGGSVGLLATGFGVLLGLAAGFVR-WADSFVMRVMDGLMAIPGIL 146 Query: 137 FNVILVTALGRGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEFVEAAKAAGASTFYIIR 196 + L+ L + +AI + + RLVR L L+ +VEAA A G I+ Sbjct: 147 LAIALMAVTQASLTAVIVAITIPEVPRVVRLVRSLALTLREQLYVEAAHAVGTRLPVILA 206 Query: 197 KHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWGNLIGEGIGMMMAFPHL 256 +H++PNM+ P++V F A++TE+ L+ +G+GV PSWGN++ EG + H+ Sbjct: 207 RHVVPNMVAPLIVQATFVAAAAVLTEAALSFLGVGVPGQTPSWGNMMAEGRNFVAVAFHI 266 Query: 257 LIFPAVTFAFTLISFTFLADGLRDAFNPR 285 +++P + A T+++ L DGLRDA +PR Sbjct: 267 ILYPGILLAATVLAINLLGDGLRDALDPR 295 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: 212 Number of extensions: 13 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: 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