Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate WP_028316323.1 G491_RS0123750 ABC transporter ATP-binding protein
Query= TCDB::P0A9S7 (255 letters) >NCBI__GCF_000429905.1:WP_028316323.1 Length = 287 Score = 245 bits (626), Expect = 6e-70 Identities = 130/282 (46%), Positives = 180/282 (63%), Gaps = 30/282 (10%) Query: 3 QPLLSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTI 62 +P+L V L M FGGL A++++++++ P EI +LIGPNGAGKTT FNC+TG Y PT G + Sbjct: 2 KPILDVKNLTMDFGGLRALDSLDIDVRPGEIAALIGPNGAGKTTFFNCVTGMYNPTKGDV 61 Query: 63 LLRDQ-----HLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQH----------- 106 L+ L GL ++ G+ RTFQ++RLF+ MTV+EN+++ +H Sbjct: 62 LVNSPSGYSTRLNGLKPNKVTERGLARTFQNIRLFQNMTVLENVMIGRHCHSGAGHEIIM 121 Query: 107 --------QQLKTGLFSG------LLKTPSFRRAQSEALDRAATWLERIGLLEHANRQAS 152 + + F G LLK F+ + E + + LE++GL + AN A Sbjct: 122 NPDNSPVKRMAASAFFGGMEIAATLLKGKRFKEREQETVQYSYNVLEKVGLEKFANNFAK 181 Query: 153 NLAYGDQRRLEIARCMVTQPEILMLDEPAAGLNPKETKELDELIAELRNHHNTTILLIEH 212 NL YG QRRLEIAR M T+P +L+LDEPAAG+NP+ETKELD+LI +R+ +ILLIEH Sbjct: 182 NLPYGLQRRLEIARAMATEPFLLLLDEPAAGMNPQETKELDDLIQRIRDKEGISILLIEH 241 Query: 213 DMKLVMGISDRIYVVNQGTPLANGTPEQIRNNPDVIRAYLGE 254 DM+LVM IS RI+V++ G +A GTP +IR N VI+AYLGE Sbjct: 242 DMRLVMSISQRIFVMDYGKKIAQGTPGEIRTNDAVIKAYLGE 283 Lambda K H 0.320 0.137 0.395 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: 204 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: 287 Length adjustment: 25 Effective length of query: 230 Effective length of database: 262 Effective search space: 60260 Effective search space used: 60260 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