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 3610412 Dshi_3793 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__Dino:3610412 Length = 317 Score = 157 bits (396), Expect = 4e-43 Identities = 100/328 (30%), Positives = 169/328 (51%), Gaps = 27/328 (8%) Query: 25 LKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPA-YQATLK 83 L FL++R+ M+ V ++ + L+ ++PG D + + PD Q L Sbjct: 2 LTFLIRRVAYTIPIMLGVSLVCFALVHISPG---------DPLVSILPPDASVELQQQLM 52 Query: 84 GFEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILF 143 YG + +Q + +L AV G S + R + + T LA+++ + Sbjct: 53 AI---YGFDRSYPEQFIRWLGRAVQGDLGNSIAT-GRPVTAEVLNAVGNTLILAVTATII 108 Query: 144 ALVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSG-- 201 G G +A +++WID A T+SV+GV+IP Y + + L++IFS+ LGWLP +G Sbjct: 109 GFTFGGLFGFVAGYFRDSWIDKLASTISVVGVSIPHYWLGMVLVIIFSVQLGWLPATGAG 168 Query: 202 ----------WEGIRTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDR 251 WE ++ ILP + +++ P+ VAR R + D L Q+++ AKG DR Sbjct: 169 PRGSSEWAFDWEHLQYLILPAVTMSVIPMGIVARTVRALVADILQQEYVTGLRAKGLLDR 228 Query: 252 TVIMKHALRPSMIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVT 311 V+ H ++ + + ++G Q+ YL+ G++ +E +F PG G L A RD PLL Sbjct: 229 GVLA-HVIKNAAPTALAVMGLQLGYLLGGSILIETVFSWPGTGFLLGQAIFQRDLPLLQG 287 Query: 312 STFILALTVMIMNLIVDVLYAILDPRIK 339 + +LA+ +I+NL+VDV + LDPR++ Sbjct: 288 TILVLAMFFVILNLLVDVAQSALDPRLQ 315 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: 272 Number of extensions: 14 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: 341 Length of database: 317 Length adjustment: 28 Effective length of query: 313 Effective length of database: 289 Effective search space: 90457 Effective search space used: 90457 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