Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate Dsui_1398 Dsui_1398 ABC-type transport system involved in resistance to organic solvents, ATPase component
Query= uniprot:P40735 (281 letters) >FitnessBrowser__PS:Dsui_1398 Length = 273 Score = 124 bits (312), Expect = 2e-33 Identities = 76/235 (32%), Positives = 136/235 (57%), Gaps = 7/235 (2%) Query: 1 MNQNQLISVEDIVFRYRKDA-ERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLI 59 M L+ + + F Y D+ R+ L+G+ + ++G+ +AI+G +G GK+TL R + G + Sbjct: 1 MPTESLVEIRGLNFAYDTDSGPRKVLEGIDMSFHKGKVVAIMGGSGCGKTTLLRLIGGQL 60 Query: 60 LPESGDIEVAGI---QLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGL-ENNGVP 115 P +G+++VAG ++ ++ +R+++GM+FQ F +V D+VAF + E+ +P Sbjct: 61 RPSAGEVKVAGHAVHRMNTRELYALRRRMGMLFQF-GALFTDMSVFDNVAFQMREHTDLP 119 Query: 116 REEMIERVDWAVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDP 175 E + + V ++ V ++ P+ LSGG +RVA+A +A P +I+ DE + LDP Sbjct: 120 EELIRDMVLLKLQAVGLRGAAGLMPNELSGGMARRVALARAVALDPMLIMYDEPFTGLDP 179 Query: 176 IGREEVLETVRHLKEQGMATVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEI 229 I + + +R L + AT I +THD+ E+ + D I M+ G+ A+G P+EI Sbjct: 180 ISLGVIGQLIRKLNDALGATSIMVTHDIQESLQIVDYIYFMSAGRVVAQGTPDEI 234 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: 173 Number of extensions: 8 Number of successful extensions: 3 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: 273 Length adjustment: 25 Effective length of query: 256 Effective length of database: 248 Effective search space: 63488 Effective search space used: 63488 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 Sep 17 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