Align TreV, component of Trehalose porter (characterized)
to candidate WP_024852149.1 N745_RS0110835 ABC transporter ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >NCBI__GCF_000526715.1:WP_024852149.1 Length = 263 Score = 147 bits (372), Expect = 2e-40 Identities = 93/233 (39%), Positives = 135/233 (57%), Gaps = 6/233 (2%) Query: 3 VELIDIVKKYGKNI--VINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKII 60 V + ++ Y K + V+ I I G+ ++G SG GKSTLL+++AG+ G + Sbjct: 8 VWIAELSHSYKKQLPPVLTNINLNIPKGQLTAMIGRSGCGKSTLLQMIAGLLLPSDGVVR 67 Query: 61 ADGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLL 120 +G + KP K N M+FQ +LYP MSVR+N A L G K++ +RVE+ ++ Sbjct: 68 INGKTVV-KPSAKWN--MMFQKPSLYPWMSVRENAALGLVFAGTYKQKQ-DRVEELLDMV 123 Query: 121 GISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQK 180 G+SE DK V ++SGGQQQRVALAR++ P LLDEP S LDA RT + E+ +I Sbjct: 124 GLSEHKDKNVQELSGGQQQRVALARSLATEPEILLLDEPFSALDAFTRTALQTEVAQICH 183 Query: 181 ELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFV 233 E T I VTHD +EA+++AD++ I+ E V D YP+ + A F+ Sbjct: 184 EQGITMIMVTHDIEEAIAMADKVVIMSHNPGEIVGDLDVPLTYPRDRSAADFI 236 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: 207 Number of extensions: 8 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: 263 Length adjustment: 26 Effective length of query: 298 Effective length of database: 237 Effective search space: 70626 Effective search space used: 70626 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 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