Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate 3610306 Dshi_3686 ABC transporter related (RefSeq)
Query= uniprot:P40735 (281 letters) >FitnessBrowser__Dino:3610306 Length = 221 Score = 142 bits (358), Expect = 6e-39 Identities = 76/208 (36%), Positives = 123/208 (59%), Gaps = 9/208 (4%) Query: 22 RRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTEESVWEV 81 R L +++ + E + I+G NGSGKST AR NGL P SG I + G + ++ Sbjct: 14 RPILSDINIDLNEKR-IGIIGRNGSGKSTFARLFNGLEKPSSGSITLEG----SAELKDL 68 Query: 82 RKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQVNMQDFLDQEPH 141 R+K+G VFQNPDNQ V V +D+AFGL+N +P + ER+ + + ++ D+ H Sbjct: 69 RRKVGFVFQNPDNQIVYPIVDEDLAFGLKNLKLPSATIKERITEVMARFQIEHLKDRLTH 128 Query: 142 HLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQGMATVISITH 201 LSGG++Q VA+AGV+ +P +I+ DE T++LD ++ ++ + LKE V+ ++H Sbjct: 129 QLSGGERQMVALAGVLVMQPQMIVFDEPTTLLDLWNKKRLMRAIADLKEH----VVLVSH 184 Query: 202 DLNEAAKADRIIVMNGGKKYAEGPPEEI 229 DL+ + DR+I + G+ +G P + Sbjct: 185 DLDLLREFDRVIHIEAGRIVGDGEPNAV 212 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: 174 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: 221 Length adjustment: 24 Effective length of query: 257 Effective length of database: 197 Effective search space: 50629 Effective search space used: 50629 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 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