Align TreV, component of Trehalose porter (characterized)
to candidate WP_011384493.1 AMB_RS10565 ABC transporter ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >NCBI__GCF_000009985.1:WP_011384493.1 Length = 257 Score = 134 bits (337), Expect = 2e-36 Identities = 80/239 (33%), Positives = 133/239 (55%), Gaps = 10/239 (4%) Query: 3 VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62 +EL + K +G +V++GI + GE V++G SG GKS +LK + G+ + + G I D Sbjct: 7 IELTGVHKAFGPKVVLDGIDLSVARGESVVVIGGSGTGKSVMLKCILGLLRPESGSIRID 66 Query: 63 GADITDKPPEKRN-----VAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIER---VE 114 G D+ P+ R+ M+FQ AL+ ++ V +N+AF L ++G K E R +E Sbjct: 67 GEDVVGMGPKDRDRIMKKFGMLFQGGALFDSLKVWENVAFGL-IQGQKMERAKARDIAIE 125 Query: 115 KAAKLLGISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGE 174 K A++ + + +++SGG Q+RV+LARAI NP DEP + LD + Sbjct: 126 KLAQVGLAASTGELSPSELSGGMQKRVSLARAIATNPEIIFFDEPTTGLDPIMADVINDL 185 Query: 175 LKRIQKELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFV 233 + + KE+ T + +THD A ++DRIA+L+KG+ V K + ++ ++V QF+ Sbjct: 186 IVKCCKEVGATALSITHDMASARKISDRIAMLYKGRLIWVGPAKDI-DHSGNEYVDQFI 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: 212 Number of extensions: 12 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: 257 Length adjustment: 26 Effective length of query: 298 Effective length of database: 231 Effective search space: 68838 Effective search space used: 68838 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: 48 (23.1 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