Align D-lactate transporter, ATP-binding component (characterized)
to candidate Synpcc7942_2493 Synpcc7942_2493 ATPase
Query= reanno::Phaeo:GFF1248 (251 letters) >FitnessBrowser__SynE:Synpcc7942_2493 Length = 253 Score = 165 bits (418), Expect = 7e-46 Identities = 91/252 (36%), Positives = 146/252 (57%), Gaps = 3/252 (1%) Query: 1 MGILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSV 60 M +L+++ V +RFGGL A++ V+ V + +IGPNGAGK+TL N + G G + Sbjct: 1 MSLLQLEQVTRRFGGLVAVNQVSFKVEVGEIFGLIGPNGAGKTTLFNLITGLQPLSGGEI 60 Query: 61 MFDGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAK-RDGAFE--MNAIS 117 F G + + P +I Q GI+R FQ +F LSV EN+++ + R ++ + + Sbjct: 61 CFQGDRLDRQRPDQIAQRGIARTFQNLRLFNQLSVFENVLVARHRQARTSLWDELIGSSR 120 Query: 118 AVSGQRDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTA 177 A R + + +LE + ++D+ AAS++ GD+RRLEI L+ EP+LLLLDEP A Sbjct: 121 ATRQSRGDRRRVQELLELLELSDQADQPAASLAYGDRRRLEIARALALEPQLLLLDEPAA 180 Query: 178 GMARADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIK 237 G+ + + D ++ I+ + +T+ +IEH + +V L DRI VL G + DP ++ Sbjct: 181 GLNPREKQDLSDRIRAIREQFQLTVVLIEHHVPLVMGLCDRIAVLDFGQLIALGDPATVR 240 Query: 238 GNPKVREAYLGE 249 +P V EAYLG+ Sbjct: 241 QDPAVIEAYLGD 252 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: 183 Number of extensions: 12 Number of successful extensions: 2 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: 253 Length adjustment: 24 Effective length of query: 227 Effective length of database: 229 Effective search space: 51983 Effective search space used: 51983 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