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_2237 Dsui_2237 ABC-type dipeptide/oligopeptide/nickel transport system, permease component
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__PS:Dsui_2237 Length = 322 Score = 162 bits (409), Expect = 1e-44 Identities = 107/331 (32%), Positives = 168/331 (50%), Gaps = 29/331 (8%) Query: 25 LKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKG 84 + F+L+RLL A ++ V + + +++ GN EL V DPA A Sbjct: 1 MTFILRRLLHGAWVLLAVSALVFAALYVV-GNPVELL--------VDPQADPADTARTIA 51 Query: 85 FEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILFA 144 GL+ PLW+Q L +L A G SF + LI E+ P T LA S++ A Sbjct: 52 ---ALGLDQPLWRQYLTFLGNAARGDLGTSFIHGVPALS-LILERLPATLELAASALFLA 107 Query: 145 LVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSG--- 201 L++G+PLG+ A L+ + S +G A+P++ V + LIL+F++ L WLP G Sbjct: 108 LLLGIPLGLWAGLRPTSLAGRLIGAASTLGFALPAFWVGLMLILVFAVQLQWLPPGGRGE 167 Query: 202 -------------WEGIRTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGG 248 +G R +LP + LAL A V R R + L QD++R A AKG Sbjct: 168 TREVLGLSLSVFTLDGWRHLLLPALNLALYKAALVVRLVRAGSREALAQDYVRFARAKGL 227 Query: 249 DDRTVIMKHALRPSMIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPL 308 + V+ H L ++IP+VT++G ++ L+ V E +F PG+G+L +A D P+ Sbjct: 228 TESRVVTGHVLPNTLIPVVTVLGMELGALIAFAVVTETVFGWPGMGKLLMDAINALDRPV 287 Query: 309 LVTSTFILALTVMIMNLIVDVLYAILDPRIK 339 +V A +++NL+V++LY LDPR++ Sbjct: 288 VVAYLLFAAALFVVLNLLVELLYGWLDPRVR 318 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: 289 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: 322 Length adjustment: 28 Effective length of query: 313 Effective length of database: 294 Effective search space: 92022 Effective search space used: 92022 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