Align D-lactate transporter, ATP-binding component (characterized)
to candidate 206140 DVU0715 branched-chain amino acid ABC transporter, ATP binding protein
Query= reanno::Phaeo:GFF1248 (251 letters) >MicrobesOnline__882:206140 Length = 255 Score = 180 bits (457), Expect = 2e-50 Identities = 97/252 (38%), Positives = 155/252 (61%), Gaps = 6/252 (2%) Query: 1 MGILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSV 60 M +L ++N+ K FGGL A++ V+ V E ++ +IGPNGAGK+T+ N + G PD+G + Sbjct: 1 MSLLSLRNLTKTFGGLVAVNSVSFDVDEGSIVGLIGPNGAGKTTVFNLITGNYKPDSGDI 60 Query: 61 MFDGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVS 120 FDG+++ G + I QMGI+R FQT +F ++SV+EN++ C R A +A+ + Sbjct: 61 FFDGRAIKGLLTHRIVQMGIARTFQTIRLFQNMSVMENVLAGCHC-RMTAGVFSAMLGTA 119 Query: 121 GQR----DILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPT 176 G R +E+A LE + +AD+ A ++S G++R LEI L+ +PR ++LDEP Sbjct: 120 GHRREEKRAIERAVRELEFVGLADQHDNLAKNLSYGNQRLLEIARALATDPRFIILDEPA 179 Query: 177 AGMARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNI 236 GM +T I ++ I+ +R I++ +IEHDM +V + +++ VL G + E P I Sbjct: 180 GGMNDQETAALIGTIRAIR-DRGISVLLIEHDMSLVMKVCEKLVVLEYGALIAEGTPSVI 238 Query: 237 KGNPKVREAYLG 248 K +P+V EAYLG Sbjct: 239 KRDPRVIEAYLG 250 Lambda K H 0.318 0.135 0.379 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: 166 Number of extensions: 10 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: 251 Length of database: 255 Length adjustment: 24 Effective length of query: 227 Effective length of database: 231 Effective search space: 52437 Effective search space used: 52437 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: 46 (22.3 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