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_041677064.1 R2APBS1_RS14330 ABC transporter ATP-binding protein
Query= TCDB::P0A9S7 (255 letters) >NCBI__GCF_000230695.2:WP_041677064.1 Length = 307 Score = 90.9 bits (224), Expect = 3e-23 Identities = 71/240 (29%), Positives = 120/240 (50%), Gaps = 27/240 (11%) Query: 6 LSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILLR 65 + GL RFG L+AV++V+LE+ + + +GPNG+GK+T L G P+ G I + Sbjct: 1 MRARGLTRRFGKLVAVDHVDLEVPARRVYGFLGPNGSGKSTTIRMLCGLLTPSEGEIEVL 60 Query: 66 DQHLEGLPGQQIA-RMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKTPSFR 124 +P Q A R + Q+ LF ++ V ENL G+ K + R Sbjct: 61 GLR---VPAQADALRPHIGYMTQNFSLFEDLGVRENLEF-------LAAIQGVPKAKTRR 110 Query: 125 RAQSEALDRAATWLERIGLLEHANRQ---ASNLAYGDQRRLEIARCMVTQPEILMLDEPA 181 R E IG +RQ A L+ G ++RL +A ++ +PE+L+LDEP Sbjct: 111 RID-----------ELIGQYHFGDRQKQLAGTLSGGQKQRLALAGAVIHEPELLLLDEPT 159 Query: 182 AGLNPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQI 241 + ++P+ ++ E + EL + TT+L+ H M R+ ++++G +A+GTP ++ Sbjct: 160 SAVDPESRRDFWEKLFELAD-IGTTLLVSTHLMDEAER-CHRLAILDRGVLVADGTPHEL 217 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: 188 Number of extensions: 15 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: 307 Length adjustment: 26 Effective length of query: 229 Effective length of database: 281 Effective search space: 64349 Effective search space used: 64349 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