Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_011386686.1 AMB_RS21945 ABC transporter ATP-binding protein
Query= uniprot:P40735 (281 letters) >NCBI__GCF_000009985.1:WP_011386686.1 Length = 232 Score = 127 bits (319), Expect = 2e-34 Identities = 78/216 (36%), Positives = 124/216 (57%), Gaps = 8/216 (3%) Query: 6 LISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGD 65 LI +E + + D LDGV Q+ +GE +A++G NGSGK+TL + GLI P++G Sbjct: 3 LIRLEQVTHAF--DTTHPVLDGVDFQLGKGERVALLGANGSGKTTLLHVMVGLIRPKAGT 60 Query: 66 IEVAGIQLTEESVW-EVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVD 124 + G + E+ + EVR K G++FQ+ D+Q TV +DVAFG N G + E E V Sbjct: 61 VHAFGRERRAEADFVEVRAKAGLLFQDADDQLFCPTVAEDVAFGPLNLGKSKAEAREIVH 120 Query: 125 WAVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLET 184 + ++ + D+ H LSGGQK+ V++A V+A PD ++LDE T+ LD RE +L+ Sbjct: 121 AVLARLGLAALEDRVTHKLSGGQKRLVSLAAVLAMEPDALLLDEPTNALDEATRERLLDI 180 Query: 185 VRHLKEQGMATVISITHDLNEAAK-ADRIIVMNGGK 219 + L + ++ ++HD + A R + + GG+ Sbjct: 181 LAGLPQ----AMVIVSHDREVIERLATRRVTLAGGR 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: 179 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: 232 Length adjustment: 24 Effective length of query: 257 Effective length of database: 208 Effective search space: 53456 Effective search space used: 53456 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