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 8501682 DvMF_2400 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__Miya:8501682 Length = 373 Score = 182 bits (463), Expect = 8e-51 Identities = 93/250 (37%), Positives = 141/250 (56%) Query: 35 ILIALAILAPYIAPYPYDEPHYIRAFEGPSKDFIFGTDALGRDLFSRILYSLRNACIIGF 94 I++++A+ AP +P P D+ R FE PS + GTD LGR + +R+ + R + Sbjct: 55 IIVSMAVFAPAFSPRPPDDVDITRKFEAPSLEEPLGTDHLGRSVLARLCHGTRVSLFAVG 114 Query: 95 GSQFVVLIIGGILGAVAGFKGGWIDKFIMSIVDIMFAFPTFLFNVILVTALGRGLFTIFL 154 ++ +G G VAG+ GG +D +M D+ FPTF+ + LV LG GL + + Sbjct: 115 AILTCIVAVGLTAGCVAGYAGGRVDSLLMRACDVFMTFPTFILALFLVGVLGSGLTNVII 174 Query: 155 AIGLTGWAGMARLVRGQVLYLKNSEFVEAAKAAGASTFYIIRKHILPNMIGPILVNLAFG 214 A+ T WA AR RG VL LK E+V AA+AAG ++ +HILP ++ +LV Sbjct: 175 AVACTHWAWYARFARGLVLGLKQREYVLAARAAGTRPARLVLRHILPPVLAQLLVMAGLD 234 Query: 215 VPGAMMTESGLAVIGMGVRPPMPSWGNLIGEGIGMMMAFPHLLIFPAVTFAFTLISFTFL 274 V ++ SGL+ +G+GVRPP P WG +IG+ + A P L++P + T+++F L Sbjct: 235 VGHMLLHVSGLSFLGLGVRPPTPEWGVMIGDAREYIGAHPEQLLYPGLMIFVTVMAFNLL 294 Query: 275 ADGLRDAFNP 284 D LRDA +P Sbjct: 295 GDALRDALDP 304 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: 247 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: 373 Length adjustment: 28 Effective length of query: 261 Effective length of database: 345 Effective search space: 90045 Effective search space used: 90045 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 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