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 PP_3343 PP_3343 nickel ABC transporter permease subunit
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__Putida:PP_3343 Length = 313 Score = 174 bits (441), Expect = 3e-48 Identities = 107/317 (33%), Positives = 171/317 (53%), Gaps = 9/317 (2%) Query: 25 LKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKG 84 L+++L RL + M+ ++ +VL+ L + A+ + P A + Sbjct: 2 LRYILLRLALLVPVMLGASLLVFVLLHLGSTD--------PALDYLRLSHIPPTDAAIAE 53 Query: 85 FEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILFA 144 GL+ PL+ Q L +L AV FG S+ ++DL+ P T L ++ Sbjct: 54 VRHTLGLDRPLYAQYLSWLWNAVHLDFGISYITGRPVLDDLLYY-LPATLQLGGLALACT 112 Query: 145 LVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSGWEG 204 L++ +PLG+LAA + W D+ V+ +GV++P++ +A LI +FS++LGWLP G G Sbjct: 113 LLLSIPLGLLAARWQGRWPDHAVRAVTFLGVSMPNFWLAFLLIALFSLWLGWLPPLGRGG 172 Query: 205 IRTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTVIMKHALRPSMI 264 ++P +A+AL ++ AR R SLLD Q + A A+G +R V H LR + + Sbjct: 173 AGHLVMPVLAIALMSMSINARLLRASLLDAGGQRHVTYARARGLPERHVWRDHILRNAWL 232 Query: 265 PLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTSTFILALTVMIMN 324 PLVT G + L+ G + +E IF PG+G+ +A + RD+P++ T +L +MI N Sbjct: 233 PLVTATGMHIGELLGGALVIETIFAWPGVGRFAVSAVLNRDFPVMQCFTLLLTGLLMICN 292 Query: 325 LIVDVLYAILDPRIKLD 341 LIVDV YA LDPR +L+ Sbjct: 293 LIVDVCYAWLDPRSRLE 309 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: 290 Number of extensions: 9 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: 313 Length adjustment: 28 Effective length of query: 313 Effective length of database: 285 Effective search space: 89205 Effective search space used: 89205 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: 48 (23.1 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