Align TreV, component of Trehalose porter (characterized)
to candidate Ac3H11_4180 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4180 Length = 367 Score = 221 bits (562), Expect = 3e-62 Identities = 110/234 (47%), Positives = 162/234 (69%), Gaps = 1/234 (0%) Query: 3 VELIDIVKKY-GKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIA 61 V + K Y G+ +V+ + I+ GEF +LGPSG GK+T L +LAG E G I+ Sbjct: 9 VRFTGVQKTYDGEQLVVRALDLDIQRGEFLSLLGPSGSGKTTTLMMLAGFESPTAGDILL 68 Query: 62 DGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLG 121 DG IT PP KRN MVFQNYAL+P+++V +N+A+PL +R + K E ERV+KA ++ Sbjct: 69 DGKQITRTPPHKRNFGMVFQNYALFPHLTVGENVAYPLTVRKVPKAEQAERVKKALDMVR 128 Query: 122 ISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKE 181 ++ + D+ ++SGGQQQRVALARA+V NP L+DEPL LD ++R + ELK + ++ Sbjct: 129 LTGMADRLPARLSGGQQQRVALARALVFNPQLVLMDEPLGALDKQLREHMQIELKELHRQ 188 Query: 182 LKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGE 235 L TF+YVTHDQ EAL+++DR+A+ ++G +Q++D ++LYE P ++VA FVG+ Sbjct: 189 LGVTFVYVTHDQGEALTMSDRVAVFNEGVIQQLADVESLYETPSNRFVAGFVGD 242 Lambda K H 0.318 0.137 0.385 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: 296 Number of extensions: 7 Number of successful extensions: 1 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: 367 Length adjustment: 29 Effective length of query: 295 Effective length of database: 338 Effective search space: 99710 Effective search space used: 99710 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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