Align TreV, component of Trehalose porter (characterized)
to candidate WP_011020381.1 MA_RS01715 ATP-binding cassette domain-containing protein
Query= TCDB::Q97ZC0 (324 letters) >NCBI__GCF_000007345.1:WP_011020381.1 Length = 353 Score = 172 bits (435), Expect = 1e-47 Identities = 88/232 (37%), Positives = 146/232 (62%), Gaps = 1/232 (0%) Query: 3 VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62 +E+ DI G + + GI + E G++ ++GPSG GKS LL+ + G +G + + Sbjct: 4 LEVRDIYLDVG-SFELKGIDLRAEKGDYVALIGPSGSGKSLLLETIIGFYGPRQGSVFLE 62 Query: 63 GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122 G DIT P+KR +++V+Q+ L+P+M + +NIA+ L+ + K++I V + A +LGI Sbjct: 63 GRDITFFSPDKRQISIVYQDNMLFPHMDIFENIAYALRKKLKDKKQIELEVTQIAGVLGI 122 Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182 E+L +K +SGG++QR +LAR++V P LLDEP S LDAR R R LK+ + Sbjct: 123 RELLHRKPDTLSGGEKQRASLARSLVARPKLLLLDEPFSALDARTREKLREMLKKAIADY 182 Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVG 234 T ++VTHD ++ +LA+R+ ++ KG+ QV DP++++ P +VA+F+G Sbjct: 183 STTVLHVTHDFEDVWALANRVVVIRKGEVMQVGDPESVFRRPSPDFVAEFLG 234 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: 289 Number of extensions: 14 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: 353 Length adjustment: 28 Effective length of query: 296 Effective length of database: 325 Effective search space: 96200 Effective search space used: 96200 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