Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_041677064.1 R2APBS1_RS14330 ABC transporter ATP-binding protein
Query= uniprot:P40735 (281 letters) >NCBI__GCF_000230695.2:WP_041677064.1 Length = 307 Score = 120 bits (302), Expect = 3e-32 Identities = 74/206 (35%), Positives = 117/206 (56%), Gaps = 3/206 (1%) Query: 24 ALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTEESVWEVRK 83 A+D V L+V +G NGSGKST R L GL+ P G+IEV G+++ ++ +R Sbjct: 15 AVDHVDLEVPARRVYGFLGPNGSGKSTTIRMLCGLLTPSEGEIEVLGLRVPAQAD-ALRP 73 Query: 84 KIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQVNMQDFLDQEPHHL 143 IG + QN + F VR+++ F GVP+ + R+D + Q + D Q L Sbjct: 74 HIGYMTQN-FSLFEDLGVRENLEFLAAIQGVPKAKTRRRIDELIGQYHFGDRQKQLAGTL 132 Query: 144 SGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQGMATVISITHDL 203 SGGQKQR+A+AG + P++++LDE TS +DP R + E + L + G ++S TH + Sbjct: 133 SGGQKQRLALAGAVIHEPELLLLDEPTSAVDPESRRDFWEKLFELADIGTTLLVS-THLM 191 Query: 204 NEAAKADRIIVMNGGKKYAEGPPEEI 229 +EA + R+ +++ G A+G P E+ Sbjct: 192 DEAERCHRLAILDRGVLVADGTPHEL 217 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: 206 Number of extensions: 7 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: 307 Length adjustment: 26 Effective length of query: 255 Effective length of database: 281 Effective search space: 71655 Effective search space used: 71655 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 24 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