Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate WP_048082401.1 EI99_RS13040 ATP-binding cassette domain-containing protein
Query= uniprot:P70970 (276 letters) >NCBI__GCF_000746075.1:WP_048082401.1 Length = 279 Score = 201 bits (512), Expect = 1e-56 Identities = 111/259 (42%), Positives = 164/259 (63%), Gaps = 5/259 (1%) Query: 9 ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLK 68 AL +IN S G +A++G G+GKSTL H NG+L+PT G + + + + K +DL Sbjct: 19 ALENINFSAPTGKIIALLGPNGAGKSTLFLHFNGILQPTSGSVMVDNACLNY--KKEDLM 76 Query: 69 KLRKKVGIVFQFPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLSEELLDR 128 LR+KVGIVFQ P+ QLF TV++D++FGP+N G+ KE+ +++ E L+ V + E + Sbjct: 77 NLRQKVGIVFQNPDDQLFAPTVVEDVAFGPVNLGLSKEEVKKRVDESLRRVEMIE-FKHK 135 Query: 129 SPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTTIL 188 +P LSGGQ +RVAIAG+LAM P+++VLDEPT+GLDPRG +IM + YEL++ G +T I+ Sbjct: 136 APHHLSGGQKKRVAIAGILAMHPKIMVLDEPTSGLDPRGASKIMKLLYELNREG-ITIII 194 Query: 189 VTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFLKGEEMAGWGLDLPETIKFQRHLEAAL 248 TH ++ YA + ++ KG I GSP+++F E + L LP L+ Sbjct: 195 STHDVDLVPLYAHSVYIISKGNIIKKGSPQEVFEDAETIRKANLRLPRIAHLVEILQKED 254 Query: 249 GVRFNEPM-LTIEDAAAEI 266 V F++P LTI +A I Sbjct: 255 KVPFDKPYPLTIGEARKRI 273 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: 222 Number of extensions: 9 Number of successful extensions: 4 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: 279 Length adjustment: 25 Effective length of query: 251 Effective length of database: 254 Effective search space: 63754 Effective search space used: 63754 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