Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein
Query= uniprot:P40735 (281 letters) >FitnessBrowser__Dyella79:N515DRAFT_1085 Length = 336 Score = 132 bits (333), Expect = 8e-36 Identities = 84/231 (36%), Positives = 130/231 (56%), Gaps = 7/231 (3%) Query: 6 LISVEDIVFRYRKDAER-RALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESG 64 +I D+ YR D + AL SL + +GE I+GH+G+GKSTL R +N L P G Sbjct: 1 MIRFVDVHKSYRVDGKDIPALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGG 60 Query: 65 DIEVAGIQLT---EESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIE 121 I + G ++T + ++ R++IGM+FQ+ N TV D++AF L G I+ Sbjct: 61 SILIDGTEMTALGDAALRAQRRRIGMIFQH-FNLLSSQTVADNIAFPLRLAGETDAGKIK 119 Query: 122 -RVDWAVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREE 180 RVD +++V ++ + P LSGGQKQRV IA +A RP I++ DEATS LDP Sbjct: 120 ARVDELLRRVGLEAHASKYPAQLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTAS 179 Query: 181 VLETVRHLKEQGMATVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEIF 230 VLE + + + T++ ITH+++ + DR+ V++ G+ G ++F Sbjct: 180 VLELLAEINRELKLTIVLITHEMDVVRRVCDRVAVLDAGRIVEHGAVADVF 230 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: 208 Number of extensions: 8 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: 336 Length adjustment: 27 Effective length of query: 254 Effective length of database: 309 Effective search space: 78486 Effective search space used: 78486 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 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