Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate WP_011382725.1 AMB_RS01410 cobalt ABC transporter
Query= uniprot:P70970 (276 letters) >NCBI__GCF_000009985.1:WP_011382725.1 Length = 264 Score = 165 bits (418), Expect = 8e-46 Identities = 96/251 (38%), Positives = 145/251 (57%), Gaps = 12/251 (4%) Query: 9 ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLK 68 AL ++ ++ G +AV+G G+GK+TLL HLNG LKP+ G + LG ++ G L Sbjct: 18 ALSGLDLGVERGRRLAVLGPNGAGKTTLLLHLNGTLKPSAGTVRLGGEIM--GYSRAALT 75 Query: 69 KLRKKVGIVFQFPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLSEELLDR 128 R++VG+V Q P+ QLF TV +D+SFGP+N G+ + + ++ L +G+S+ L R Sbjct: 76 GWRRRVGLVLQEPDDQLFAATVAEDVSFGPLNLGLSEAETRRRVEAALDALGISD-LAGR 134 Query: 129 SPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTTIL 188 + LS GQ +RVAIAG LAM+PEVL+LDEP AGLD +G K ++ L + G T + Sbjct: 135 ATHMLSFGQKKRVAIAGALAMEPEVLLLDEPLAGLDHQGGKRLLAALDALARAGT-TLVF 193 Query: 189 VTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFLKGEEMAGWGLDLPETIKFQRHLEAAL 248 TH ++ A +AD + + G + A G ++ E +A GL++P L L Sbjct: 194 TTHEVDLAHGFADRVALFRDGRVIAQGEAAEVLSDRECLAACGLEMP--------LLLEL 245 Query: 249 GVRFNEPMLTI 259 GVR + L + Sbjct: 246 GVRTRDEALAL 256 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: 185 Number of extensions: 10 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: 264 Length adjustment: 25 Effective length of query: 251 Effective length of database: 239 Effective search space: 59989 Effective search space used: 59989 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