Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate BPHYT_RS22535 BPHYT_RS22535 methionine ABC transporter ATP-binding protein
Query= uniprot:P40735 (281 letters) >FitnessBrowser__BFirm:BPHYT_RS22535 Length = 386 Score = 135 bits (339), Expect = 2e-36 Identities = 82/222 (36%), Positives = 125/222 (56%), Gaps = 5/222 (2%) Query: 13 VFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGI- 71 VF + AL V+L V GE I+G +G+GKSTL R +NGL P SG + V G+ Sbjct: 40 VFADARGVSTAALANVTLNVARGEVFGIIGRSGAGKSTLLRLVNGLEKPSSGAVRVNGVS 99 Query: 72 --QLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQ 129 +L E + +R++IGMVFQ+ N TVR+++A L+ GVP+ + ++VD ++ Sbjct: 100 VGELDERGLVALRRRIGMVFQH-FNLLSAKTVRENIALPLKIAGVPKAAIDKKVDALLEL 158 Query: 130 VNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLK 189 V + D P LSGGQKQRV IA + PDI++ DEATS LDP + +L +R + Sbjct: 159 VGLSAKRDAYPASLSGGQKQRVGIARALVTDPDILLCDEATSALDPETTQAILALLRDIN 218 Query: 190 EQGMATVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEIF 230 ++ T++ ITH++ + D + V+ G+ G +F Sbjct: 219 QRLNLTIVLITHEMQVIREVCDTVAVIERGEVVETGAVWRVF 260 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: 250 Number of extensions: 13 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: 386 Length adjustment: 28 Effective length of query: 253 Effective length of database: 358 Effective search space: 90574 Effective search space used: 90574 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: 49 (23.5 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