Align TreV, component of Trehalose porter (characterized)
to candidate WP_047092042.1 AAV99_RS00435 ABC transporter ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >NCBI__GCF_001013305.1:WP_047092042.1 Length = 233 Score = 115 bits (289), Expect = 8e-31 Identities = 68/199 (34%), Positives = 103/199 (51%), Gaps = 9/199 (4%) Query: 17 VINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADITDKPPE---- 72 ++ GI + GE +LGPSG GKS+L+ +L+G+E+ GK+ G D T + Sbjct: 29 ILRGIDLDVARGETLALLGPSGSGKSSLMSVLSGLERATSGKLTVAGEDFTALNEDALAM 88 Query: 73 --KRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGISEILDKKV 130 + + +V Q + L P M+ +N+A PL++ G ++ ER + +G+ L Sbjct: 89 ARRGRIGIVLQAFHLLPTMTAVENVATPLELAG--EDGAWERATAELEAVGLGHRLTHYP 146 Query: 131 TQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKELKGTFIYVT 190 Q+SGG+QQRVA+ARAIV P DEP NLD + L + E T I +T Sbjct: 147 AQLSGGEQQRVAIARAIVSRPPLIFADEPTGNLDTNTGASVEDALFERRAETGATLIIIT 206 Query: 191 HDQKEALSLADRIAILHKG 209 HD+K A +R+ L G Sbjct: 207 HDRKLA-ERCNRVVTLGDG 224 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: 163 Number of extensions: 7 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: 233 Length adjustment: 25 Effective length of query: 299 Effective length of database: 208 Effective search space: 62192 Effective search space used: 62192 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: 47 (22.7 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