Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate WP_089322249.1 CHB58_RS01095 LPS export ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWS6 (255 letters) >NCBI__GCF_900188395.1:WP_089322249.1 Length = 245 Score = 155 bits (391), Expect = 1e-42 Identities = 88/250 (35%), Positives = 136/250 (54%), Gaps = 16/250 (6%) Query: 5 ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64 +L NL +G V V+L VKE +VV L+GPNGAGKTT F C+ G +P G + + Sbjct: 8 VLSAVNLKKVYGSRTVVENVSLKVKEGEVVGLLGPNGAGKTTTFYCIIGLVKPEDGKVFI 67 Query: 65 DGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPAFR 124 E I P + ARKG+ Q +F+ +T ENL+ H Sbjct: 68 GEEEITNDPTYIRARKGLSYLPQEASIFRKLTVEENLIAVMEMH---------------N 112 Query: 125 KSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184 +RE + E L++ + A TL+ G++RRLEIAR + +P+ L+LDEP AG+ Sbjct: 113 YPKREIEKTTETLLEEFGIKHLRKNRADTLSGGERRRLEIARALTIKPKFLLLDEPFAGV 172 Query: 185 NPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIRDN 244 +P D++ LI L+ + ++ +L+ +H+++ + I D +I+ G LA+GTPE+I + Sbjct: 173 DPIAVADIQNLIKELK-KRDIGILITDHNVRETLRIIDRAYIISHGKVLAEGTPEEIISS 231 Query: 245 PEVIKAYLGE 254 +V K YLGE Sbjct: 232 EKVKKVYLGE 241 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: 183 Number of extensions: 10 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: 245 Length adjustment: 24 Effective length of query: 231 Effective length of database: 221 Effective search space: 51051 Effective search space used: 51051 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