Align D-lactate transporter, ATP-binding component (characterized)
to candidate WP_043744331.1 AMB_RS11770 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF1248 (251 letters) >NCBI__GCF_000009985.1:WP_043744331.1 Length = 256 Score = 177 bits (450), Expect = 1e-49 Identities = 99/248 (39%), Positives = 148/248 (59%), Gaps = 8/248 (3%) Query: 3 ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62 I+E +++ K F G A+SDVNL VR +T+HA+IGPNGAGK+T N + L P G ++F Sbjct: 6 IVETRSLTKEFKGFVAVSDVNLKVRRHTIHALIGPNGAGKTTCFNLVTKFLTPTRGQILF 65 Query: 63 DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSGQ 122 +G + P I + G+ R FQ +FG L+VLEN+ + K+ +F+ SG+ Sbjct: 66 NGNDITHTQPAAIARQGMVRSFQISAVFGHLTVLENVRVALQRKQGKSFQFWR----SGE 121 Query: 123 --RDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGMA 180 ++ +AE ++E + +A+ R A +S G KR LEI L+ +P +LLLDEP AGM Sbjct: 122 CLNELNARAEELIEAVGVAEYRDTPAGELSYGRKRALEIATTLALDPEMLLLDEPMAGMG 181 Query: 181 RADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKGNP 240 D T +L++++ + R TI ++EH++ VV L+D ITVL G L E I NP Sbjct: 182 TEDVRRTAELIRRVAANR--TILMVEHNLSVVADLSDTITVLKLGRVLAEGSYAEITDNP 239 Query: 241 KVREAYLG 248 +V EAY+G Sbjct: 240 EVVEAYMG 247 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: 174 Number of extensions: 6 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: 256 Length adjustment: 24 Effective length of query: 227 Effective length of database: 232 Effective search space: 52664 Effective search space used: 52664 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 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