Align TreV, component of Trehalose porter (characterized)
to candidate WP_008410843.1 DESHY_RS13325 ABC transporter ATP-binding protein
Query= TCDB::Q97ZC0 (324 letters) >NCBI__GCF_000315365.1:WP_008410843.1 Length = 363 Score = 138 bits (347), Expect = 2e-37 Identities = 79/211 (37%), Positives = 123/211 (58%), Gaps = 2/211 (0%) Query: 25 IETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADITDKPPE-KRNVAMVFQNY 83 + GE ++GP+G GKS+L+K+LA +EK +G+II DG +T P + +R +AMVFQ Sbjct: 30 LHKGETIALIGPNGAGKSSLVKLLALLEKPWQGEIIFDGRQVTGSPLQVRRQMAMVFQE- 88 Query: 84 ALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGISEILDKKVTQISGGQQQRVAL 143 AL + SV N+A L+ RG+ +++I RV K L I+ + D+ + +SGG+ QRV++ Sbjct: 89 ALLLSGSVFGNVAQGLRFRGLPRDQIARRVNYWLKKLQIAHLADRHIRYLSGGEAQRVSI 148 Query: 144 ARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKELKGTFIYVTHDQKEALSLADRI 203 ARA+ P LDEP + LD R T E+ I K +++TH+ +E LA R+ Sbjct: 149 ARALALEPQVLFLDEPFAALDLPTRITLIEEIGEIIKATATATVFITHNVEEIPLLAGRV 208 Query: 204 AILHKGKFEQVSDPKTLYEYPKTKWVAQFVG 234 + GK Q + ++ YP + VA+ VG Sbjct: 209 CAMSAGKIVQDCSTEDIFRYPVNEEVARLVG 239 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: 282 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: 363 Length adjustment: 29 Effective length of query: 295 Effective length of database: 334 Effective search space: 98530 Effective search space used: 98530 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