Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate Synpcc7942_0249 Synpcc7942_0249 ATPase
Query= uniprot:P70970 (276 letters) >FitnessBrowser__SynE:Synpcc7942_0249 Length = 261 Score = 121 bits (304), Expect = 1e-32 Identities = 77/217 (35%), Positives = 128/217 (58%), Gaps = 12/217 (5%) Query: 9 ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLK 68 AL ++ +++ G V ++G +GSGKST L+ LN L +G+I + + ++ D+ Sbjct: 37 ALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWIEGHRLSHDRR--DIA 94 Query: 69 KLRKKVGIVFQFPEHQLFEE-TVLKDISFGPMNFGVKK---EDAEQKAREMLQLVGLSEE 124 +R++VG+VFQ + LF TVL+++ P+ V++ AE AR++L+ V ++E+ Sbjct: 95 TIRQEVGMVFQ--QFNLFPHLTVLQNLMLAPVQ--VRRWPVAQAEATARQLLERVRIAEQ 150 Query: 125 LLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNL 184 D+ P +LSGGQ +RVAIA LAM P +L+ DEPT+ LDP +E++D+ +L G + Sbjct: 151 A-DKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVMRDLASEG-M 208 Query: 185 TTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLF 221 T ++ TH + A AD +++M G I P F Sbjct: 209 TMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFF 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: 161 Number of extensions: 9 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: 261 Length adjustment: 25 Effective length of query: 251 Effective length of database: 236 Effective search space: 59236 Effective search space used: 59236 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