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 GFF665 PGA1_c06790 putative peptide ABC transporter, permease protein
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__Phaeo:GFF665 Length = 326 Score = 178 bits (452), Expect = 1e-49 Identities = 105/331 (31%), Positives = 186/331 (56%), Gaps = 29/331 (8%) Query: 25 LKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKG 84 L ++++R++ + + VV ++ + M+ G+ E ++ TT D +A L Sbjct: 2 LAYIIRRIMQSVLVLFVVGLVAFS-MFRFVGDPIENMLGQER----TTEDVVRLRADL-- 54 Query: 85 FEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILFA 144 GL+ P Q +L+ A FG S+ R + D++ E+ P T LAL S A Sbjct: 55 -----GLDQPFPVQYWRFLENAAQGNFGLSYRQ-GRPVADILIERAPATLELALVSGTLA 108 Query: 145 LVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSG--- 201 +V+G+ LG+L A++++ W+ T MT S+IGV++P++++ + LI +FS+ LGWLP+ G Sbjct: 109 MVLGIGLGVLTAIRRDGWLANTIMTASLIGVSLPTFLIGILLIYVFSVELGWLPSFGRGE 168 Query: 202 ------WE-------GIRTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGG 248 W G+ + +LP+I L L + + R R +L+ L D+IR A A+G Sbjct: 169 TVMLGQWSTGFLTKSGLMSLVLPSITLGLYQMTLIMRLVRSEMLEVLRTDYIRFARARGL 228 Query: 249 DDRTVIMKHALRPSMIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPL 308 +R V +HAL +M+P++TI+G Q+ ++ + E +F+ PG+G LF NA D P+ Sbjct: 229 GERAVYFRHALVNTMVPVITIIGLQLGSIIAFAIITETVFQWPGVGLLFINAVQFVDIPV 288 Query: 309 LVTSTFILALTVMIMNLIVDVLYAILDPRIK 339 + ++++ + +NLIVD+LY ++DPR++ Sbjct: 289 MAAYLMLISVLFVGINLIVDLLYFLIDPRLR 319 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: 268 Number of extensions: 13 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: 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