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 WP_086508994.1 BZY95_RS05615 peptide ABC transporter permease
Query= TCDB::Q9X270 (289 letters) >NCBI__GCF_002151265.1:WP_086508994.1 Length = 298 Score = 218 bits (556), Expect = 1e-61 Identities = 110/282 (39%), Positives = 173/282 (61%), Gaps = 6/282 (2%) Query: 8 ESIGYWKAFWLRFKKNKMAVIGGVFVLILIALAILAPYIAPYPYDEPHYIRAFEGP---S 64 ES+G + W R K+N+ A++ V ++++ ++ P++ P+ +E ++ AF P + Sbjct: 19 ESLG--RDAWRRLKQNRAAMVSLVLLILIAIACVVGPWLTPWGLNEVNW-NAFRAPPSLA 75 Query: 65 KDFIFGTDALGRDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMS 124 + GTDA GRDL +R LY + + + + V L+IG + GA+AG+ GG +D +M Sbjct: 76 DGHLAGTDANGRDLLTRTLYGGQISLSVALVATLVSLVIGVLYGAIAGYLGGRVDNLMMR 135 Query: 125 IVDIMFAFPTFLFNVILVTALGRGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEFVEAA 184 VDIM++ P ++L+ GR + I+ AIG W M+R+VRGQ L LK EFVEAA Sbjct: 136 FVDIMYSLPFMFLVILLMVVFGRNILLIYAAIGAVEWLDMSRIVRGQTLALKRREFVEAA 195 Query: 185 KAAGASTFYIIRKHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWGNLIG 244 +A G + I+ +H++PN +GP++V + VP ++ ES L+ +G+GV+ PM SWG LI Sbjct: 196 RALGVRSRTIVMRHLIPNTLGPVVVYVTLTVPKVILLESFLSFLGLGVQEPMTSWGVLIS 255 Query: 245 EGIGMMMAFPHLLIFPAVTFAFTLISFTFLADGLRDAFNPRS 286 EG+ MM P +L+ P+ A TL+ FL DGLRDA +PR+ Sbjct: 256 EGVDMMQGAPWMLLVPSTFLAVTLLCLNFLGDGLRDALDPRT 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: 219 Number of extensions: 11 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: 298 Length adjustment: 26 Effective length of query: 263 Effective length of database: 272 Effective search space: 71536 Effective search space used: 71536 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 24 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