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 Dsui_0412 Dsui_0412 ABC-type dipeptide/oligopeptide/nickel transport system, permease component
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__PS:Dsui_0412 Length = 317 Score = 159 bits (402), Expect = 9e-44 Identities = 101/324 (31%), Positives = 168/324 (51%), Gaps = 25/324 (7%) Query: 27 FLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKGFE 86 ++LKRL+ + V V+++VL++LAPG+ +AIA P++ ++ + Sbjct: 4 YILKRLIYAIPIALSVTVVSFVLVYLAPGDPL------NAIAPADAPEE-----VIQALK 52 Query: 87 ERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILFALV 146 YGL+ P+ Q ++L AV G S + R + + T LA + +V Sbjct: 53 SAYGLDKPVPVQYGLWLMRAVQGDLGLSIAS-GREVTAEVLSAVSNTLLLAGMAAAIGVV 111 Query: 147 VGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSG----- 201 +G LG LA + TWID A +SV+GV+IP Y + + L ++FSI+L W P G Sbjct: 112 LGCILGALAGYRHGTWIDKAATALSVVGVSIPHYWLGLVLTILFSIWLPWFPAMGAGPGG 171 Query: 202 -----W--EGIRTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTVI 254 W E +R +LP + L++ P+ + R R + D L Q+F+ A+G V Sbjct: 172 SGEWLWDLEHLRYLVLPALTLSVIPMGIITRTVRALVADMLGQEFVTALRARGLSGGAVF 231 Query: 255 MKHALRPSMIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTSTF 314 +H + + ++ + G Q+ YLM G++ VE +F PG G L A RD PLL + Sbjct: 232 -RHVAKNTAPTVLAVAGLQIGYLMGGSILVETVFAWPGTGFLLNTAIFQRDIPLLQGTIL 290 Query: 315 ILALTVMIMNLIVDVLYAILDPRI 338 +L + +++NL+VD+L ++DPR+ Sbjct: 291 VLCMFFVVLNLLVDILQPLIDPRM 314 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: 300 Number of extensions: 12 Number of successful extensions: 4 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