Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate SMc00962 SMc00962 ABC transporter ATP-binding protein
Query= uniprot:P40735 (281 letters) >FitnessBrowser__Smeli:SMc00962 Length = 226 Score = 145 bits (366), Expect = 8e-40 Identities = 84/216 (38%), Positives = 125/216 (57%), Gaps = 6/216 (2%) Query: 21 ERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTEESVWE 80 ER AL +SL + E + ++G NGSGK+T AR +NGL+ P +G ++V G+ E+ Sbjct: 14 ERVALHPLSLALDERR-VGVIGLNGSGKTTFARLINGLVKPTTGRVKVNGLDTVEDDR-A 71 Query: 81 VRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQVNMQDFLDQEP 140 V + G +FQNP +Q + V DD+AFGL+N G+P E+ R + + + + + Sbjct: 72 VLTEAGFIFQNPQHQLIMPIVIDDIAFGLKNRGLPAHEISSRTEAVLARFGVSHLARRRV 131 Query: 141 HHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQGMATVISIT 200 H LSGG+ Q VA+A VI P I+ILDE T+ LD R V ET+ L E I IT Sbjct: 132 HELSGGETQLVAMASVIVTGPKILILDEPTNQLDLRNRRMVAETIDTLDED----TIVIT 187 Query: 201 HDLNEAAKADRIIVMNGGKKYAEGPPEEIFKLNKEL 236 HDL A A+R+++ + G+ A+G P+E + E+ Sbjct: 188 HDLALAESAERVLLFHEGRLLADGAPDETIRRYHEV 223 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: 167 Number of extensions: 6 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: 226 Length adjustment: 24 Effective length of query: 257 Effective length of database: 202 Effective search space: 51914 Effective search space used: 51914 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: 46 (22.3 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