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_034276209.1 AMYHA_RS07110 ABC transporter ATP-binding protein
Query= TCDB::P0A9S7 (255 letters) >NCBI__GCF_000504245.1:WP_034276209.1 Length = 257 Score = 204 bits (520), Expect = 1e-57 Identities = 101/245 (41%), Positives = 162/245 (66%), Gaps = 2/245 (0%) Query: 10 GLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILLRDQHL 69 G+ + FGG+ A+++V+L++ P +++ +IGPNGAGKTT+FN GF +P GT+ RD+ L Sbjct: 3 GINVNFGGIAALSDVSLDVAPNQVLGVIGPNGAGKTTLFNVACGFVQPDTGTLTWRDREL 62 Query: 70 EGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKTPSFRRAQSE 129 + L Q+A +G+ RT Q + LF MTV+EN++V + + G FSGLL P + + Sbjct: 63 KRLRPHQLAGLGIGRTLQGLGLFDRMTVLENVIVGADRHARAGFFSGLLGLPRSAKEERA 122 Query: 130 ALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEPAAGLNPKET 189 DRA L+ +G +HA + S+L Y ++R+ +AR +V++P++L+LDEPAAGL+ + Sbjct: 123 LRDRAMALLDELGAAKHAGQLPSSLPYPVRKRVALARALVSEPDLLLLDEPAAGLSGDDM 182 Query: 190 KELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQIRNNPDVIR 249 EL ELI L +++L+EH M LVM + D I V++ G +A+G P+Q++ +P V+ Sbjct: 183 AELGELIRGL--SRRMSVMLVEHHMDLVMSVCDHIVVLDFGKNIASGPPQQVKEDPAVLA 240 Query: 250 AYLGE 254 AYLG+ Sbjct: 241 AYLGD 245 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: 199 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: 257 Length adjustment: 24 Effective length of query: 231 Effective length of database: 233 Effective search space: 53823 Effective search space used: 53823 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