Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate PP_4751 PP_4751 Amino acid ABC transporter, ATP-binding protein
Query= uniprot:P70970 (276 letters) >FitnessBrowser__Putida:PP_4751 Length = 269 Score = 138 bits (347), Expect = 1e-37 Identities = 83/210 (39%), Positives = 131/210 (62%), Gaps = 8/210 (3%) Query: 10 LYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGK--KNKDL 67 L+D+ + +G VA+IG +GSGKSTLL+ +N L PTKG++S+ I+AGK +L Sbjct: 40 LHDVCFEMNKGEVVAIIGPSGSGKSTLLRCINQLEPPTKGRVSMDGVHIEAGKALPRTEL 99 Query: 68 KKLRKKVGIVFQFPEHQLFEE-TVLKDISFGPM-NFGVKKEDAEQKAREMLQLVGLSEEL 125 KLR+++G+VFQ LF TVL+++S + G ++A+ ++ ++L+ VGL+++ Sbjct: 100 LKLRRRIGMVFQ--SFNLFPHLTVLRNVSLAQIRTLGRSAKEADARSLQLLERVGLADK- 156 Query: 126 LDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLT 185 P SGGQ +R+AIA LA+DPE+++ DEPT+ LDP E++ + EL G ++ Sbjct: 157 AQHYPARCSGGQQQRIAIARALALDPELMLFDEPTSALDPELGLEVLAVMKELAGEG-MS 215 Query: 186 TILVTHSMEDAAAYADEMIVMHKGTIQASG 215 I+VTH M A +D ++VM G I G Sbjct: 216 MIVVTHEMHFAETVSDRVVVMADGRIIEHG 245 Lambda K H 0.318 0.136 0.380 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: 198 Number of extensions: 12 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: 276 Length of database: 269 Length adjustment: 25 Effective length of query: 251 Effective length of database: 244 Effective search space: 61244 Effective search space used: 61244 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 (21.7 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