Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate WP_035130886.1 Q763_RS02520 ABC transporter ATP-binding protein
Query= uniprot:P70970 (276 letters) >NCBI__GCF_000769915.1:WP_035130886.1 Length = 222 Score = 119 bits (297), Expect = 7e-32 Identities = 76/209 (36%), Positives = 123/209 (58%), Gaps = 14/209 (6%) Query: 10 LYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGK-----KN 64 L ++ IK+G V+++G +G+GK+TLLQ L L KP + G++++ G+ K+ Sbjct: 17 LKGVDLHIKKGEVVSIVGASGAGKTTLLQILGTLDKPKSEK---GTSLLIDGEDVLNMKD 73 Query: 65 KDLKKLRK-KVGIVFQFPEHQLFEE-TVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLS 122 K L K R K+G +FQF HQLF E T L+++ G +K + E +A+++L+ +GLS Sbjct: 74 KALSKFRNLKLGFIFQF--HQLFPEFTALENVCIPAFIAGKQKAETEAEAKKLLEYLGLS 131 Query: 123 EELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRG 182 + + P ELSGG+ +RVA+A L P V+ DEP+ LD + + ++F++L Sbjct: 132 HRI-NHKPGELSGGEQQRVAVARALINKPAVIFADEPSGNLDTHSAENLHNLFFKLRDEM 190 Query: 183 NLTTILVTHSMEDAAAYADEMIVMHKGTI 211 T ++VTH+ E+ A AD +VM G I Sbjct: 191 GQTFVIVTHN-EELANMADRKLVMSDGQI 218 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: 146 Number of extensions: 6 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: 276 Length of database: 222 Length adjustment: 24 Effective length of query: 252 Effective length of database: 198 Effective search space: 49896 Effective search space used: 49896 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: 46 (22.3 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