Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate GFF3630 PGA1_262p00340 oligopeptide ABC transporter, ATP binding protein
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Phaeo:GFF3630 Length = 332 Score = 199 bits (507), Expect = 6e-56 Identities = 121/337 (35%), Positives = 196/337 (58%), Gaps = 26/337 (7%) Query: 3 LMELKGVSVIFE---DKVGLFKK---RKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGR 56 +ME+ +S+ F+ V + +K R AL VSL++ +G+ L V+GESG GK+TL R Sbjct: 5 VMEIDDLSLTFQLPRSLVDVIRKQPGRAVRALNGVSLALQKGETLGVVGESGCGKSTLAR 64 Query: 57 VIVGLQKPTSGEVVYDGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPI 116 IV L +P G + + G +I+ + + Y + VQ++ QDPYS+L T +IL + Sbjct: 65 CIVRLYQPQGGSIRHHGQDIFAEGARRDRSYNRRVQMMFQDPYSSLNPRMTCGQILSEAL 124 Query: 117 LRWEKINKDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIV 176 + DE+ R+ LLELV+L PA+ K PH+ SGGQ+QR++IAR+L+V P +++ Sbjct: 125 HVHKMRPADEIPARVEELLELVRL-PADA-AQKLPHEFSGGQRQRIAIARALAVEPEVLI 182 Query: 177 ADEPVTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGR 236 ADE V+ +D S++ ++N L E++ +L+LT++F+ HD+ + R+ H V++ GR Sbjct: 183 ADELVSALDVSVQAQVVNLLLELQEQLDLTILFVAHDLRLVRHVSH-----RVAVIYLGR 237 Query: 237 IVERADLEEILKDPLHPYTNDLIKLTPSID--------NLYKEINVKINYERVEKGCPYR 288 IVE D E + +P HPY+ L+ PS+D L E+ +N V GCP+ Sbjct: 238 IVEIGDSETLFANPAHPYSQALLSAAPSLDPDDTGDAIRLEGELPSPLN---VPPGCPFH 294 Query: 289 LRCPFAMDICKNEEPKLFKYSH--EVACFLYGKVGES 323 +RC A D+C+ + P+L EVAC L ++ ++ Sbjct: 295 VRCAHAADVCRRDVPRLRPLGDRGEVACHLAEEISQN 331 Lambda K H 0.321 0.141 0.410 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: 283 Number of extensions: 13 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: 324 Length of database: 332 Length adjustment: 28 Effective length of query: 296 Effective length of database: 304 Effective search space: 89984 Effective search space used: 89984 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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:
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