Align TreV, component of Trehalose porter (characterized)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__SynE:Synpcc7942_1406 Length = 368 Score = 188 bits (478), Expect = 2e-52 Identities = 101/231 (43%), Positives = 153/231 (66%), Gaps = 10/231 (4%) Query: 18 INGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADITDK----PPEK 73 ++ ++ ++E GE ++GPSG GK+TLL+++AG E L G I G + PPE Sbjct: 24 VDQVSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLAGETVATAQRSLPPET 83 Query: 74 RNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGISEILDKKVTQI 133 R+V MVFQ+YAL+P+++V DN+ F L+ R K + R +A L+G+ + + ++ Sbjct: 84 RSVGMVFQDYALFPHLTVLDNVCFGLRDR--KGSAAVAR--QALALVGLEGLERRYPHEL 139 Query: 134 SGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKELKGTFIYVTHDQ 193 SGGQQQRVALARA+ P LLDEPLSNLD +VR R EL+ I ++ + T I VTHDQ Sbjct: 140 SGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDILRQAQATAILVTHDQ 199 Query: 194 KEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLPGE 244 +EALS+ DR+A++ G+FEQ+ P+ L+++P +++VA+F+ + NFL E Sbjct: 200 EEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFLSQ--ANFLATE 248 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: 275 Number of extensions: 13 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: 324 Length of database: 368 Length adjustment: 29 Effective length of query: 295 Effective length of database: 339 Effective search space: 100005 Effective search space used: 100005 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 Apr 09 2024. 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