Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate WP_048080973.1 EJ01_RS11645 ABC transporter ATP-binding protein
Query= uniprot:P70970 (276 letters) >NCBI__GCF_000745485.1:WP_048080973.1 Length = 222 Score = 125 bits (313), Expect = 1e-33 Identities = 83/208 (39%), Positives = 120/208 (57%), Gaps = 19/208 (9%) Query: 9 ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLK-PTKGQISLGSTVIQAGKKNKDL 67 AL IN + +GS++A++G +GSGKSTLL HL G+L P+KG + L I+ N+ Sbjct: 24 ALRGINLKVNKGSFIAIMGPSGSGKSTLL-HLAGILDIPSKGTVLLNGKNIKEYTGNEQA 82 Query: 68 KKLRKKVGIVFQ----FPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLSE 123 + RK +G +FQ P+ E +L IS +KA+E+L VGLS+ Sbjct: 83 ELRRKNIGFIFQRYNLMPQLTALENVMLPMIS-----------PDSKKAKELLDKVGLSD 131 Query: 124 ELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGN 183 + DR +LSGG+ +RVAIA LA DP +L+ DEPT LD ++IM + +L+Q Sbjct: 132 KY-DRYQTQLSGGEQQRVAIARALANDPSILLADEPTGELDTVNTRKIMGLLKDLNQEKG 190 Query: 184 LTTILVTHSMEDAAAYADEMIVMHKGTI 211 LT I+VTH+ AA + +E+I M G I Sbjct: 191 LTIIIVTHN-PLAAEFVEEVIKMQDGDI 217 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: 139 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: 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