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 AZOBR_RS23020 AZOBR_RS23020 ABC transporter permease
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__azobra:AZOBR_RS23020 Length = 326 Score = 187 bits (474), Expect = 4e-52 Identities = 104/332 (31%), Positives = 183/332 (55%), Gaps = 24/332 (7%) Query: 23 RFLKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATL 82 R F+ +RL+ ++ + V + L+ APG D A + A + Sbjct: 3 RIALFISQRLVKAVFVILAIAVFNFFLVHAAPG---------DPAAVMAGEAGAADAKFV 53 Query: 83 KGFEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSIL 142 + +++GL+ PL++Q+ Y+ V G S+ R + DL+ ++ P+T +L L++ + Sbjct: 54 EQLRQQFGLDRPLYEQLGTYMSKVVQADLGYSYRQQ-RPVFDLLMDRLPVTLSLTLTAFV 112 Query: 143 FALVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSGW 202 AL+ GV LG LAA++ TW D V + A P + + + LIL+FS+ LGWLP G Sbjct: 113 LALLGGVALGTLAAMRAGTWSDTAITVVGLTAYATPIFWIGLMLILLFSVNLGWLPAFGT 172 Query: 203 EGI------------RTK--ILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGG 248 E I R K +LP L L +A R TR S+L+ + DF++TA AKG Sbjct: 173 ESIGAGYTGWDAFLDRAKHLVLPVTTLGLFYMAVYTRLTRASILEVRDMDFVKTARAKGL 232 Query: 249 DDRTVIMKHALRPSMIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPL 308 + ++ H LR +++P++T+ G Q +L+ G++ +E +F +PG+G+L A + RDY + Sbjct: 233 PEWRIVSVHILRNAILPVITVAGFQAGHLIGGSILIETVFALPGIGRLAFEAVLQRDYQV 292 Query: 309 LVTSTFILALTVMIMNLIVDVLYAILDPRIKL 340 L+ + ++ V++ NL+ D++Y+++DPRI++ Sbjct: 293 LLGIFLLTSVVVVVFNLLTDLIYSLVDPRIEV 324 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: 257 Number of extensions: 11 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: 326 Length adjustment: 28 Effective length of query: 313 Effective length of database: 298 Effective search space: 93274 Effective search space used: 93274 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