Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_020176259.1 A3OQ_RS0115155 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >NCBI__GCF_000385335.1:WP_020176259.1 Length = 255 Score = 131 bits (329), Expect = 1e-35 Identities = 85/253 (33%), Positives = 128/253 (50%), Gaps = 14/253 (5%) Query: 6 MTGQPLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQART 65 M P+L G+ +G AL V+V +G + ++IG NGAGKST + G+ Sbjct: 1 MNSAPVLAAEGIGKRFGGFTALDDVNVAFERGRLTAIIGPNGAGKSTFFSLLSGAVAPSK 60 Query: 66 GSVVFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGL----------DN 115 G + FEG D+ P H AR+ IA+S + +FP++TV EN+++ + Sbjct: 61 GHIRFEGADVAGEPQHRFARMGIARSYQITNLFPQLTVHENVRLACQAMHAPARRSLWRD 120 Query: 116 LKHFAEDVEKIFTLFPR--LKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLG 173 H+ ++ + L R + +L+ GEQ+ L I AL +RPKLLLLDEP+ G Sbjct: 121 RTHYTGLADEADAALAQVGLTSRRKRLAASLAHGEQRALEIAVALASRPKLLLLDEPTAG 180 Query: 174 LAPLIVKGIFEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLA 233 ++P K + I +L A TV LVE + L+ R V+ GK+ SG+ E+ A Sbjct: 181 MSPEETKEMMALIGRL--AAERTVLLVEHKMKMVMGLADRIVVLHQGKLLASGTPDEIRA 238 Query: 234 NPEVRAAYLEGGR 246 + VR YL GR Sbjct: 239 DASVRRVYLGEGR 251 Lambda K H 0.320 0.137 0.387 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: 190 Number of extensions: 6 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: 247 Length of database: 255 Length adjustment: 24 Effective length of query: 223 Effective length of database: 231 Effective search space: 51513 Effective search space used: 51513 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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