Align D-lactate transporter, ATP-binding component (characterized)
to candidate WP_057507783.1 ABB28_RS06050 energy-dependent translational throttle protein EttA
Query= reanno::Phaeo:GFF1248 (251 letters) >NCBI__GCF_001431535.1:WP_057507783.1 Length = 554 Score = 65.5 bits (158), Expect = 2e-15 Identities = 67/250 (26%), Positives = 105/250 (42%), Gaps = 31/250 (12%) Query: 3 ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62 ++E KNV K+FG ++N V + IIGPNGAGKSTL + G+ PDTG ++ Sbjct: 324 VMEFKNVSKKFGDRLLFDNLNFLVPGGAIVGIIGPNGAGKSTLFKMITGQEKPDTGEIVV 383 Query: 63 DGKSVLGRAPYEINQM-GISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSG 121 L + + G VFQ EI G L +L +N + Sbjct: 384 GPTVKLSYVDQSRDALEGNHNVFQ--EIAGGLDIL---------------NINGV----- 421 Query: 122 QRDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGMAR 181 +I +A D++ + S+S G++ RL + L Q +LLLDEP+ + Sbjct: 422 --EIQSRAYIGRFNFKGQDQQKL-VGSLSGGERGRLHMAKTLLQGGNVLLLDEPSNDL-- 476 Query: 182 ADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKGNPK 241 T+ L+ E +I HD + +A I +G VE N + + Sbjct: 477 --DIETLRALEDALLEFPGNTFVISHDRWFLDRIATHILAF-EGDSHVEFFQGNYREYEE 533 Query: 242 VREAYLGESA 251 + +G+ A Sbjct: 534 DKRRRMGDDA 543 Score = 47.8 bits (112), Expect = 5e-10 Identities = 56/234 (23%), Positives = 100/234 (42%), Gaps = 43/234 (18%) Query: 17 QALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMFDGKSVLGRAPYEIN 76 Q + D++LS ++G NG+GKST+L + G F+G++ P Sbjct: 21 QIIKDISLSFFPGAKIGLLGLNGSGKSTVLKIMAGV------DNDFEGEA----RPQAGI 70 Query: 77 QMGISRVFQTPEIFGDLSVLENM------MIPCFAKRDGAFEMNAISAVSGQRDILEKAE 130 ++G + Q PE+ +V E++ ++ A D + A + D L K + Sbjct: 71 KVGY--LAQEPELDPTKTVRESVEEGVGEVLQAQAALDAVYL--AYAEEGADFDKLAKEQ 126 Query: 131 HMLEEMNMADKRHMN-------------------AASMSRGDKRRLEIGMCLSQEPRLLL 171 LE + A H ++S G+KRR+ + L Q+P +LL Sbjct: 127 ERLEAILAAGDAHTLENQLDVAADALRLPPWEAIVGTLSGGEKRRVALCRLLLQKPDMLL 186 Query: 172 LDEPTAGMARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQG 225 LDEPT + +++ L+Q + T+ + HD + + + A+ I L +G Sbjct: 187 LDEPTNHL----DAESVEWLEQFLARYTGTVVAVTHDRYFLDNAAEWILELDRG 236 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: 319 Number of extensions: 22 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 4 Length of query: 251 Length of database: 554 Length adjustment: 30 Effective length of query: 221 Effective length of database: 524 Effective search space: 115804 Effective search space used: 115804 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