Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_072909154.1 BUB13_RS12770 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH8 (254 letters) >NCBI__GCF_900142125.1:WP_072909154.1 Length = 254 Score = 221 bits (563), Expect = 1e-62 Identities = 111/249 (44%), Positives = 169/249 (67%), Gaps = 1/249 (0%) Query: 3 LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62 +L+++ ++K+FGGL A+ DV+ E+ +G + LIGPNGAGK+TL N TGV +PS+GTV+ Sbjct: 1 MLKLENVSKNFGGLPALSDVSFEVPQGLVTALIGPNGAGKSTLINCTTGVLQPSKGTVSF 60 Query: 63 DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFY 122 + +++A LG+ RTFQN++LF LTVLDNVL + + LRLP Sbjct: 61 QQKKITALPAHQVARLGIARTFQNLKLFPRLTVLDNVLTGLTCEGGSSMLMAMLRLPYLR 120 Query: 123 KSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGM 182 E++LK +A+E L F L A+ A L+YG ++R+E+ RA ++P +L LDEP AG+ Sbjct: 121 HRERQLKLRAMEALDRFSLSDKADWPAGILAYGDKKRVELARATVSQPDLLLLDEPVAGL 180 Query: 183 NPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKTN 242 N +ETAE+ E +R ++ T++L+EHDM+LVME+ +++ VL+ G+ IA GTP+E++ N Sbjct: 181 NAEETAEVGEQLRLLRSAGH-TMLLVEHDMDLVMEIADQVVVLDSGKCIATGTPEEVRRN 239 Query: 243 KRVIEAYLG 251 V+EAYLG Sbjct: 240 PLVLEAYLG 248 Lambda K H 0.319 0.139 0.385 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: 151 Number of extensions: 5 Number of successful extensions: 2 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: 254 Length of database: 254 Length adjustment: 24 Effective length of query: 230 Effective length of database: 230 Effective search space: 52900 Effective search space used: 52900 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 (21.7 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