Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein
Query= uniprot:P40735 (281 letters) >NCBI__GCF_000016765.1:WP_041378948.1 Length = 252 Score = 139 bits (349), Expect = 8e-38 Identities = 85/212 (40%), Positives = 125/212 (58%), Gaps = 3/212 (1%) Query: 20 AERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTEESVW 79 A R LD VSL + G ++A+VG +G+GK+TL +A+N L+ ++G I + G + + V Sbjct: 12 AGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIEGRDVAAQPVA 71 Query: 80 EVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQVNMQ-DFLDQ 138 E+R++IG VFQ F +V ++VA GVPREE RV + V + DF ++ Sbjct: 72 ELRRRIGYVFQGI-GLFPHMSVAENVALVPRLQGVPREERAARVAELLDLVALPADFAER 130 Query: 139 EPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQGMATVIS 198 P LSGGQ QRV A +AARP I+++DE LDP+ R+E+ R L E T + Sbjct: 131 RPAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRALHEAMGLTSLI 190 Query: 199 ITHDLNEA-AKADRIIVMNGGKKYAEGPPEEI 229 +THD+ EA ADR+IV+ G+ A+ PP + Sbjct: 191 VTHDMAEALLLADRVIVIGEGRILADQPPRAL 222 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: 147 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: 281 Length of database: 252 Length adjustment: 25 Effective length of query: 256 Effective length of database: 227 Effective search space: 58112 Effective search space used: 58112 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: 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