Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_019556634.1 F612_RS0104875 ABC transporter ATP-binding protein
Query= uniprot:P40735 (281 letters) >NCBI__GCF_000381085.1:WP_019556634.1 Length = 309 Score = 116 bits (290), Expect = 7e-31 Identities = 75/200 (37%), Positives = 111/200 (55%), Gaps = 7/200 (3%) Query: 18 KDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTEES 77 K + L+ + Y+ E++ +VG +G GKSTLAR + GL E+G I V G +TE Sbjct: 48 KGKTNKVLNKIDFTAYKREFICVVGPSGCGKSTLARLIAGLETQEAGHILVDGKHVTEPG 107 Query: 78 VWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQVNMQDFLD 137 GMVFQ+ + F +V+ +V FGL +G+ R + V + FLD Sbjct: 108 -----PDRGMVFQSY-SLFPWMSVKHNVMFGLTQSGMSRNSAESEAFQWIDLVGLTPFLD 161 Query: 138 QEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQGMATVI 197 PH LSGG KQRVAI +A +P I+++DE + LDP R ++ + + + + TV Sbjct: 162 AYPHQLSGGMKQRVAIIRALANQPKILLMDEPFAALDPQNRLKMQQYLLEIWQNIDITVF 221 Query: 198 SITHDLNEAA-KADRIIVMN 216 ITHDL+EA ADRI+V++ Sbjct: 222 FITHDLDEAIYLADRILVLD 241 Lambda K H 0.316 0.135 0.383 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: 189 Number of extensions: 7 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: 281 Length of database: 309 Length adjustment: 26 Effective length of query: 255 Effective length of database: 283 Effective search space: 72165 Effective search space used: 72165 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 (21.6 bits) S2: 48 (23.1 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