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_002723942.1 RSPH17029_RS20335 ABC transporter ATP-binding protein
Query= TCDB::P0A9S7 (255 letters) >NCBI__GCF_000015985.1:WP_002723942.1 Length = 257 Score = 164 bits (414), Expect = 2e-45 Identities = 98/253 (38%), Positives = 150/253 (59%), Gaps = 15/253 (5%) Query: 5 LLSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILL 64 +LS GL FGG AVNNV+L+++ I +LIGPNGAGKTTVFN LT F +PT G I L Sbjct: 12 VLSARGLGKDFGGFTAVNNVDLDVHHARIHALIGPNGAGKTTVFNLLTKFLQPTRGKITL 71 Query: 65 RDQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKTPSFR 124 + ++ARMG+VR+FQ +F +TV+EN+ VA + + + F Sbjct: 72 LGTDITRTRPDKVARMGMVRSFQISAVFPHLTVLENVRVALQRPAELAV--------QFW 123 Query: 125 RAQSEALD----RAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEP 180 + S ALD RA +E +GL + N +A++L+YG +R LEIA + PE+L+LDEP Sbjct: 124 QPLS-ALDRLNGRAEVLIEELGLTPYLNTRAADLSYGRKRVLEIATTLALDPEVLLLDEP 182 Query: 181 AAGLNPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQ 240 AG+ ++ + + +I E+ H +L++EH++ +V I ++ V+ +G LA+G Sbjct: 183 MAGMGQEDVQMVAGIIREVARHR--AVLMVEHNLNVVADICHQVTVLQRGEILAHGDYAT 240 Query: 241 IRNNPDVIRAYLG 253 + +P V AY+G Sbjct: 241 VSTDPRVRTAYMG 253 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: 167 Number of extensions: 6 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: 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 Apr 10 2024. 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