Align TreV, component of Trehalose porter (characterized)
to candidate WP_057508907.1 ABB28_RS12160 methionine ABC transporter ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >NCBI__GCF_001431535.1:WP_057508907.1 Length = 335 Score = 131 bits (329), Expect = 3e-35 Identities = 70/216 (32%), Positives = 119/216 (55%), Gaps = 5/216 (2%) Query: 25 IETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADITDKPPE-----KRNVAMV 79 I+ GE F I+G SG GKSTL++++ +E G+++ G D+T +R + M+ Sbjct: 28 IQEGEVFGIIGHSGAGKSTLIRMINRLEDPSGGRLLIAGEDVTALETAGLRTLRRRIGMI 87 Query: 80 FQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGISEILDKKVTQISGGQQQ 139 FQ++ L + +V N+AFPL++ G + +I RV + + +G+ DK Q+SGGQ+Q Sbjct: 88 FQHFNLLSSRTVASNVAFPLELAGTPRAQIDARVAELLQTVGLQAHADKYPAQLSGGQKQ 147 Query: 140 RVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKELKGTFIYVTHDQKEALSL 199 RV +ARA+ P L DE S LD + + L +I +EL T + +TH+ + Sbjct: 148 RVGIARALATGPQILLCDEATSALDPQTTASVLALLSKINRELGLTIVLITHEMDVIRRV 207 Query: 200 ADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGE 235 DR+A+L G+ ++ ++ +P+ +FV E Sbjct: 208 CDRVAVLDAGEMVEMGPVTDVFLHPQHPTTRRFVSE 243 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: 229 Number of extensions: 9 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: 335 Length adjustment: 28 Effective length of query: 296 Effective length of database: 307 Effective search space: 90872 Effective search space used: 90872 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 24 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