Align TreV, component of Trehalose porter (characterized)
to candidate Ga0059261_0341 Ga0059261_0341 ABC-type antimicrobial peptide transport system, ATPase component
Query= TCDB::Q97ZC0 (324 letters) >lcl|FitnessBrowser__Korea:Ga0059261_0341 Ga0059261_0341 ABC-type antimicrobial peptide transport system, ATPase component Length = 224 Score = 103 bits (257), Expect = 4e-27 Identities = 64/202 (31%), Positives = 99/202 (49%), Gaps = 7/202 (3%) Query: 17 VINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADITDKPPEKRNV 76 V+ GI + GE +LGPSG GKSTLL+ + +E +G I G ++ R V Sbjct: 24 VLRGIDLTVGQGEIVALLGPSGSGKSTLLQAVGLLEGGFEGSIRISGVEVGKLESHARTV 83 Query: 77 A------MVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGISEILDKKV 130 V+Q + L P+ + +N+ P ++ + R E LG+ L + Sbjct: 84 TRRDKLGFVYQFHHLLPDFNALENVELPQLIQNATLADARARSEGLLTALGLGARLTHRP 143 Query: 131 TQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKELKGTFIYVT 190 +Q+SGG+QQRVA+ARA+ P+ L DEP NLD E R+ + + T Sbjct: 144 SQLSGGEQQRVAVARALANRPALVLADEPTGNLDEHTADIVLAEFLRLVRGEGAAALIAT 203 Query: 191 HDQKEALSLADRIAILHKGKFE 212 H+++ A + DR+ LH+G E Sbjct: 204 HNERLAAKM-DRVVRLHEGVLE 224 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: 171 Number of extensions: 5 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: 324 Length of database: 224 Length adjustment: 25 Effective length of query: 299 Effective length of database: 199 Effective search space: 59501 Effective search space used: 59501 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: 47 (22.7 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