Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_013645374.1 METBO_RS08905 ABC transporter ATP-binding protein
Query= uniprot:P40735 (281 letters) >NCBI__GCF_000191585.1:WP_013645374.1 Length = 223 Score = 125 bits (315), Expect = 6e-34 Identities = 80/221 (36%), Positives = 125/221 (56%), Gaps = 4/221 (1%) Query: 1 MNQNQLISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLIL 60 MN N +I ++++ Y +D AL+ V L++ GE ++I+G +GSGKSTL + GL Sbjct: 1 MNDNTIIKIKNLKKEY-EDGSIIALNNVDLEIERGESVSIIGPSGSGKSTLLNMIGGLDK 59 Query: 61 PESGDIEVAGIQLTEESVWEVRK--KIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREE 118 G I VAG+ L + S + +IG VFQ N TV ++V L + ++ Sbjct: 60 ANEGQISVAGVNLMDNSDLSNFRSNEIGFVFQL-HNLIPNLTVLENVQIPLLGTDIDDKK 118 Query: 119 MIERVDWAVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGR 178 M ER +K VN+++ +DQ+P LSGG++QRVAIA + P II+ DE T LD + Sbjct: 119 MEERALKLLKSVNLENKVDQKPTKLSGGERQRVAIARALVNHPSIILADEPTGALDSETQ 178 Query: 179 EEVLETVRHLKEQGMATVISITHDLNEAAKADRIIVMNGGK 219 E +L+ + + ++ T+I +TH+ A +ADR I + GK Sbjct: 179 EVILKLLLDIHKKENVTLIMVTHEPYVAKQADRSIYVLDGK 219 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: 139 Number of extensions: 9 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: 223 Length adjustment: 24 Effective length of query: 257 Effective length of database: 199 Effective search space: 51143 Effective search space used: 51143 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: 46 (22.3 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