Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate WP_011911265.1 PST_RS00075 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA
Query= uniprot:P70970 (276 letters) >NCBI__GCF_000013785.1:WP_011911265.1 Length = 279 Score = 130 bits (328), Expect = 2e-35 Identities = 86/232 (37%), Positives = 128/232 (55%), Gaps = 14/232 (6%) Query: 6 ERLALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQ------ 59 E L ++ ++EG VA+IG +GSGKSTLL+ L L G I + + Sbjct: 37 ELTVLEGLDLDVQEGEKVAIIGPSGSGKSTLLRVLMTLEGIDDGLIEVDGEPLTHMPDGH 96 Query: 60 ---AGKKNKDLKKLRKKVGIVFQFPEHQLFEE-TVLKDISFGPMN-FGVKKEDAEQKARE 114 + L+++R KVG+VFQ LF L+++ P+ G+ K +A ++A E Sbjct: 97 GRLVPANARHLRRVRGKVGMVFQ--SFNLFPHMNALQNVMEAPVQVLGLSKREARERAEE 154 Query: 115 MLQLVGLSEELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDM 174 +L +VGL E+ L+ P +LSGGQ +RVAIA LAM P+V++ DE T+ LDP E++ + Sbjct: 155 LLAMVGL-EDKLEHFPAQLSGGQQQRVAIARALAMRPKVMLFDEVTSALDPELCGEVLSV 213 Query: 175 FYELHQRGNLTTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFLKGEE 226 L + NLT ++VTH M A +AD + H+G I GSP LF +E Sbjct: 214 IRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQGSPDALFNNPQE 265 Lambda K H 0.318 0.136 0.380 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: 198 Number of extensions: 8 Number of successful extensions: 4 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: 276 Length of database: 279 Length adjustment: 25 Effective length of query: 251 Effective length of database: 254 Effective search space: 63754 Effective search space used: 63754 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 Apr 09 2024. 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