Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate WP_048086190.1 ARCVE_RS05005 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWS6 (255 letters) >NCBI__GCF_000194625.1:WP_048086190.1 Length = 258 Score = 138 bits (348), Expect = 1e-37 Identities = 79/255 (30%), Positives = 141/255 (55%), Gaps = 26/255 (10%) Query: 5 ILKVENLSMRFGG-LLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQP-----T 58 +L++ N+ + + +L + GV++ +++ +V L+GPNGAGKTT ++G +P T Sbjct: 1 MLELNNVEVVYNDFILVLKGVSIEIEKGSIVTLLGPNGAGKTTTLKSISGLIKPERGEVT 60 Query: 59 GGTILLDGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLF 118 GTI+ +G+ I+ AR G+++ + R+F+++T ENL + NT+F Sbjct: 61 RGTIVYEGKRIENRDPEENARDGIIQVMEGRRIFEELTVEENLRAGSYISGNTDF----- 115 Query: 119 KTPAFRKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLD 178 M Y + NL E N G L+ G+Q+ L I R ++ +P++L+LD Sbjct: 116 -----------DMVYNYF----PNLREKRNLRGGYLSGGEQQMLAIGRALLAKPKLLLLD 160 Query: 179 EPAAGLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTP 238 EP+ GL P +++ +I + E NVT+LL+E + KL + I+D+ ++ G + DG Sbjct: 161 EPSLGLAPIVVKEIFEIIKRINREENVTILLVEQNAKLALEIADYGYIMENGRIVMDGEA 220 Query: 239 EQIRDNPEVIKAYLG 253 E++R N +V + Y+G Sbjct: 221 EKLRQNEDVREFYMG 235 Lambda K H 0.321 0.138 0.398 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: 171 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: 255 Length of database: 258 Length adjustment: 24 Effective length of query: 231 Effective length of database: 234 Effective search space: 54054 Effective search space used: 54054 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: 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