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_108223487.1 C8J29_RS19490 ABC transporter permease subunit
Query= TCDB::Q9X270 (289 letters) >NCBI__GCF_003046325.1:WP_108223487.1 Length = 379 Score = 201 bits (511), Expect = 2e-56 Identities = 100/219 (45%), Positives = 145/219 (66%) Query: 67 FIFGTDALGRDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIV 126 F+FGTDA+GRDL SRI +R + IG + + L++G GA++G+ GG +D +M IV Sbjct: 159 FLFGTDAVGRDLMSRIFIGVRISLAIGLLASAMALLLGVTYGAISGYLGGRVDNVMMRIV 218 Query: 127 DIMFAFPTFLFNVILVTALGRGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEFVEAAKA 186 D++++ P F ++LV GR L IF+AIG T W MAR+VRGQ L LK EFV+AA+A Sbjct: 219 DVLYSLPFIFFVILLVVFFGRNLVIIFIAIGATEWLDMARIVRGQTLSLKRQEFVQAAEA 278 Query: 187 AGASTFYIIRKHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWGNLIGEG 246 GA+ I+ +H++PN +GP++V + VP A++ ES L+ +G+GV+ P+ S G LI EG Sbjct: 279 LGATRAGILMRHVVPNTLGPVIVFVTLLVPKAILLESLLSFLGLGVQEPLTSLGLLISEG 338 Query: 247 IGMMMAFPHLLIFPAVTFAFTLISFTFLADGLRDAFNPR 285 M P LLI+PA+T L + FL DGLRD+ +P+ Sbjct: 339 AANMRGAPWLLIWPALTLTAILFALNFLGDGLRDSLDPK 377 Score = 35.4 bits (80), Expect = 2e-06 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 2/49 (4%) Query: 13 WKAFWLRFKKNKMAVIGGVFVLILIALAILAPYIAPYPYDE--PHYIRA 59 W+ W+R ++N+ AV + + L + I P ++P+ Y P ++RA Sbjct: 25 WQDAWIRLRRNRAAVASALVLAFLGLVGIFGPMLSPHDYTRVYPQFVRA 73 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: 269 Number of extensions: 14 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 289 Length of database: 379 Length adjustment: 28 Effective length of query: 261 Effective length of database: 351 Effective search space: 91611 Effective search space used: 91611 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: 49 (23.5 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