Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate WP_013402971.1 CALHY_RS05375 energy-coupling factor transporter ATPase
Query= uniprot:P70970 (276 letters) >NCBI__GCF_000166355.1:WP_013402971.1 Length = 278 Score = 166 bits (420), Expect = 5e-46 Identities = 102/263 (38%), Positives = 157/263 (59%), Gaps = 17/263 (6%) Query: 2 KTPFERLALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAG 61 KTP AL DIN I+ G +VA++G GSGKSTL + +NGLL P KG + + S Sbjct: 21 KTP----ALIDINLKIERGEFVAILGLNGSGKSTLAKLINGLLIPEKGDVIVDSM----- 71 Query: 62 KKNKDLKKL---RKKVGIVFQFPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAREMLQL 118 KD++K+ R+K G +FQ P++QL V +D++FGP N G+ +E + L Sbjct: 72 -NTKDVEKIWDIRRKCGYIFQNPDNQLVASIVEEDVAFGPENLGMPREKIRKAVDSALLT 130 Query: 119 VGLSEELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYEL 178 V + E + + ++LSGGQ +RVAIAGVLAM PE ++LDEPT+ LDP+GRKE++ L Sbjct: 131 VEMME-YKNHATYKLSGGQKQRVAIAGVLAMKPECIILDEPTSMLDPKGRKEVIATVERL 189 Query: 179 HQRGNLTTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFLKGEEMAGWGLDLPETI 238 ++ T +LVTH++ D + IV+ KG I+ G +L LK + G D+P+ + Sbjct: 190 NKEEKKTIVLVTHNI-DEMLLSQRSIVLDKGHIKFDGPSFEL-LKLDWFYEMGFDMPQIL 247 Query: 239 KFQRHLEAALGVRFNEPMLTIED 261 K L+ GV+ ++ + ++++ Sbjct: 248 KLSIELKKR-GVKIDKEIWSVDE 269 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: 206 Number of extensions: 17 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: 278 Length adjustment: 25 Effective length of query: 251 Effective length of database: 253 Effective search space: 63503 Effective search space used: 63503 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 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