Align TM0030, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate GFF665 PGA1_c06790 putative peptide ABC transporter, permease protein
Query= TCDB::Q9WXN7 (338 letters) >lcl|FitnessBrowser__Phaeo:GFF665 PGA1_c06790 putative peptide ABC transporter, permease protein Length = 326 Score = 157 bits (398), Expect = 3e-43 Identities = 104/331 (31%), Positives = 179/331 (54%), Gaps = 15/331 (4%) Query: 6 MFKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTL 65 M Y++RR + ++ V + F + R + G+P+ +L G R + + +R L Sbjct: 1 MLAYIIRRIMQSVLVLFVVGLVAFSMFRFV-GDPIENML-GQERTTE---DVVR-----L 50 Query: 66 MEEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAW 125 + GL +P+ VQY+ F+ A +G+ G S R V D++I P TL L L + +A Sbjct: 51 RADLGLDQPFPVQYWRFLENAAQGNFGLSYR-QGRPVADILIERAPATLELALVSGTLAM 109 Query: 126 ILGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQ 185 +LG LG L A +R+ W+ ++T SLI +P + +G++ I++F V+LGWLP G Sbjct: 110 VLGIGLGVLTAIRRDGWLANTIMTASLIGVSLPTFLIGILLIYVFSVELGWLPSFGRGET 169 Query: 186 GTIPNLSWSFFVDV-LKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMK 244 + S F L ++P ++ + M +R ++ L +DY F+ G+ Sbjct: 170 VMLGQWSTGFLTKSGLMSLVLPSITLGLYQMTLIMRLVRSEMLEVLRTDYIRFARARGLG 229 Query: 245 DKRI-FKYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLI 303 ++ + F++ N+++P IT + L LG ++ A+ITE VF +PG G L A+ +D P + Sbjct: 230 ERAVYFRHALVNTMVPVITIIGLQLGSIIAFAIITETVFQWPGVGLLFINAVQFVDIP-V 288 Query: 304 QGIFVILIASIYLA-NFIVDFLYALIDPRIR 333 +++LI+ +++ N IVD LY LIDPR+R Sbjct: 289 MAAYLMLISVLFVGINLIVDLLYFLIDPRLR 319 Lambda K H 0.329 0.146 0.449 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: 301 Number of extensions: 18 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: 338 Length of database: 326 Length adjustment: 28 Effective length of query: 310 Effective length of database: 298 Effective search space: 92380 Effective search space used: 92380 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 (21.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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