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_011383886.1 AMB_RS07455 ABC transporter ATP-binding protein
Query= TCDB::P0A9S7 (255 letters) >NCBI__GCF_000009985.1:WP_011383886.1 Length = 261 Score = 185 bits (469), Expect = 9e-52 Identities = 106/252 (42%), Positives = 154/252 (61%), Gaps = 15/252 (5%) Query: 6 LSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILLR 65 LSV GL +GG+ AV NV+ +L P EI++LIGPNGAGK+T FN L G + PT G+I L Sbjct: 7 LSVRGLSKNYGGVAAVTNVDFDLAPGEILALIGPNGAGKSTCFNMLNGQFPPTAGSIKLF 66 Query: 66 DQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENL---LVAQHQQLKT-GLFSGLLKTP 121 + L G ++I R+GV RTFQ F MTV+EN+ L++ H +L+ F+G L Sbjct: 67 GEELVGKKPREIWRLGVGRTFQITATFGSMTVLENVQMALISFHNRLRALWPFAGGLYQ- 125 Query: 122 SFRRAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEPA 181 D A LE +G+ A+R S LAYGD +R+E+A + P++L++DEP Sbjct: 126 ----------DEAFQLLELVGMEAQASRPCSVLAYGDLKRVELAVALANAPKLLLMDEPT 175 Query: 182 AGLNPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQI 241 AG+ PKE EL +L A++ ++L EHDM +V ++RI V+++G +A G P+++ Sbjct: 176 AGMAPKERIELMQLTADIVRERGISVLFTEHDMDVVFTHANRIMVLSRGHVVAEGKPQEV 235 Query: 242 RNNPDVIRAYLG 253 R NP+V YLG Sbjct: 236 RANPEVQATYLG 247 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: 166 Number of extensions: 8 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: 255 Length of database: 261 Length adjustment: 24 Effective length of query: 231 Effective length of database: 237 Effective search space: 54747 Effective search space used: 54747 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 17 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