Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate Dsui_2958 Dsui_2958 cobalt transport protein ATP-binding subunit
Query= uniprot:P40735 (281 letters) >FitnessBrowser__PS:Dsui_2958 Length = 279 Score = 158 bits (399), Expect = 1e-43 Identities = 98/256 (38%), Positives = 147/256 (57%), Gaps = 6/256 (2%) Query: 6 LISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGD 65 L+ +E++ +RY + L G SL V G A++G NGSGK+TL + NGL+ P +G Sbjct: 5 LLQLEEVHYRYPDGSA--GLAGCSLSVSRGSRNALIGANGSGKTTLFQHCNGLLRPAAGR 62 Query: 66 IEVAG--IQLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERV 123 + AG + + +R K+G+VFQNPD Q +VR+DV+FG N G+ + RV Sbjct: 63 VHYAGAPVDYGRAGLRALRSKVGLVFQNPDRQLFSASVREDVSFGPLNLGLDEATVAARV 122 Query: 124 DWAVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLE 183 + A++ V M D + +LS GQK+RV IAGV+A P++++LDE + LD +EE+L Sbjct: 123 EAALQAVGMDDLAHKPVQNLSFGQKKRVCIAGVLAMEPELLVLDEPMAGLDQAMQEELLA 182 Query: 184 TVRHLKEQGMATVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEIFKLNKELVRIGLD 242 + L +GM T++ THD++ A + ADRI +M G+ A + EL IGL Sbjct: 183 VLDGLHRRGM-TILLATHDIHFAYRWADRIHLMAAGRCCASFDAPALAGHEAELAAIGLR 241 Query: 243 LPFSFQLSQLLRENGL 258 LP L + LR+ GL Sbjct: 242 LPSVIGLERQLRQRGL 257 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: 196 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: 279 Length adjustment: 26 Effective length of query: 255 Effective length of database: 253 Effective search space: 64515 Effective search space used: 64515 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