Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate WP_011188232.1 DP_RS04970 amino acid ABC transporter ATP-binding protein
Query= uniprot:P70970 (276 letters) >NCBI__GCF_000025945.1:WP_011188232.1 Length = 244 Score = 126 bits (317), Expect = 4e-34 Identities = 85/215 (39%), Positives = 125/215 (58%), Gaps = 8/215 (3%) Query: 9 ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLK 68 AL D++ ++K V VIG +GSGKST L+ LN L G I + I K + Sbjct: 20 ALKDVSLTVKPAEVVVVIGPSGSGKSTFLRCLNRLEYADAGSIVIDGVNILDPKCA--IN 77 Query: 69 KLRKKVGIVFQFPEHQLFEE-TVLKDISFGPMNFG-VKKEDAEQKAREMLQLVGLSEELL 126 +R +VG+VFQ LF TVL++I+ ++ +K +A++ + E+L+ VGLS++ Sbjct: 78 AVRAEVGMVFQ--SFNLFPHITVLENITMAQISVRKTRKAEADKISMELLEKVGLSQKAA 135 Query: 127 DRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTT 186 P +LSGGQ +RVAIA LAM P+VL+ DEPT+ LDP E++D+ +L + G +T Sbjct: 136 -AYPDQLSGGQQQRVAIARSLAMSPKVLLFDEPTSALDPEMVGEVLDVMQDLAKEG-MTM 193 Query: 187 ILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLF 221 ++VTH M A AD ++ M G IQ G P F Sbjct: 194 VVVTHEMGFAREVADRVVFMDDGQIQEEGKPEHFF 228 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: 151 Number of extensions: 14 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: 244 Length adjustment: 24 Effective length of query: 252 Effective length of database: 220 Effective search space: 55440 Effective search space used: 55440 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 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