Align TM1747, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate 8500162 DvMF_0920 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__Miya:8500162 Length = 343 Score = 196 bits (499), Expect = 6e-55 Identities = 117/332 (35%), Positives = 190/332 (57%), Gaps = 26/332 (7%) Query: 25 LKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKG 84 L+ + ++L + + +I++ ++ LAPG+ ++Q TT + A T K Sbjct: 5 LRRMARKLAWMLFVFWGITIISFWVIHLAPGSPTDMQ---------TTMNPLAGAETRKR 55 Query: 85 FEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILFA 144 E YGL+ PL Q + +L FG S S R + D IKE+ P+T + ++S++ Sbjct: 56 LEALYGLDKPLHVQYVQWLGRLSRLDFGNSMSSDPRPVWDKIKERLPLTVGMNVASLVLT 115 Query: 145 LVVGVPLGILAALKKNTWIDYTAMTVSV-IGVAIPSYVVAVFLILIFSIYLGWLPTSG-- 201 ++ +P+G+ +A + D AMTV V IG A+P + +A+ L+L+F I+L WLP SG Sbjct: 116 MLCAIPIGVASAHWQGRLFD-RAMTVLVFIGFAMPGFWLALLLMLLFGIHLQWLPLSGLT 174 Query: 202 -------------WEGIRTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGG 248 W+ + +P G LA ++RF R S+L+ L QD+I TA AKG Sbjct: 175 SLDHAAMSPMGKAWDIMAHLAMPIFIYTFGSLAGLSRFMRASMLEVLRQDYILTARAKGL 234 Query: 249 DDRTVIMKHALRPSMIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPL 308 RTVI +HALR +++P++TI+G + L+ G+V +E+IF +PGLGQLF A + RDYPL Sbjct: 235 PVRTVIFRHALRNALLPVITILGLSLPGLIGGSVIIESIFALPGLGQLFYQAVMARDYPL 294 Query: 309 LVTSTFILALTVMIMNLIVDVLYAILDPRIKL 340 ++ + + A+ ++ NL+ D+ Y + DPRI+L Sbjct: 295 IMGNLVLGAVLTLVGNLLADLCYGLADPRIRL 326 Lambda K H 0.328 0.143 0.429 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: 309 Number of extensions: 16 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: 341 Length of database: 343 Length adjustment: 29 Effective length of query: 312 Effective length of database: 314 Effective search space: 97968 Effective search space used: 97968 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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