Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate WP_011654832.1 RL_RS30155 amino acid ABC transporter ATP-binding protein
Query= uniprot:P70970 (276 letters) >NCBI__GCF_000009265.1:WP_011654832.1 Length = 254 Score = 142 bits (358), Expect = 7e-39 Identities = 87/215 (40%), Positives = 129/215 (60%), Gaps = 8/215 (3%) Query: 9 ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLK 68 AL DIN S++ G + + G +GSGKSTL++ +N L +G+I +G ++ G + K + Sbjct: 28 ALRDINISVRSGERIVLCGPSGSGKSTLIRCINHLETYERGEIRVGGILL--GNQAKTID 85 Query: 69 KLRKKVGIVFQFPEHQLFEE-TVLKDISFGPMN-FGVKKEDAEQKAREMLQLVGLSEELL 126 +R++VG+VFQ + LF TVL++ PM GV + +AE++AR +L+ V + E+ Sbjct: 86 AIRREVGMVFQ--QFNLFPHLTVLQNCMLAPMKAVGVSRAEAEERARGLLERVKILEQA- 142 Query: 127 DRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTT 186 D+ P +LSGGQ +RVAIA L M P+V++ DEPT+ LDP KE++D L G +T Sbjct: 143 DKYPVQLSGGQQQRVAIARALCMRPKVMLFDEPTSALDPEMVKEVLDTMIALADEG-MTM 201 Query: 187 ILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLF 221 I VTH M A AD +I M G I P + F Sbjct: 202 ICVTHEMGFARQVADRVIFMASGAIVEEAPPAEFF 236 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: 156 Number of extensions: 7 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: 254 Length adjustment: 25 Effective length of query: 251 Effective length of database: 229 Effective search space: 57479 Effective search space used: 57479 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