Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate WP_050462656.1 AKL27_RS09910 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= uniprot:D8IUY5 (404 letters) >NCBI__GCF_001189915.1:WP_050462656.1 Length = 408 Score = 274 bits (700), Expect = 4e-78 Identities = 166/389 (42%), Positives = 230/389 (59%), Gaps = 61/389 (15%) Query: 9 KRNPQQARISLLLLLALMIVFPFVAQQFGNSWVRIMDVALLYIMLALGLNVVVGFAGLLD 68 K P Q R +L++LLA+ +V+PF + GN V ++ +AL+Y++L LGLN+VVGFAGLLD Sbjct: 74 KLQPTQQRYALMVLLAVALVWPFFGSR-GN--VDVVTLALIYVVLGLGLNIVVGFAGLLD 130 Query: 69 LGYIAFYAIGAYSAGLLASPQFAAVIESFVNTYPSVGNFLVWLCGPEIVQNGIHLSLWLI 128 LGY+ FYA+G Y+ LL N Y LS W Sbjct: 131 LGYVGFYAVGGYTYALL-------------NQY-------------------FGLSFWEC 158 Query: 129 VPISAFLAALFGALLGAPTLKLRGDYLAIVTLGFGEIIRIFMNNLNAPVNITNGPQGINL 188 +P++A ++ALFG LLG P L+LRGDYLAIVTLGFGEIIR+ +NNL + +T GP G++ Sbjct: 159 LPLAAGMSALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLLLNNLTS---LTGGPDGVSG 215 Query: 189 IDPIKVFGVSLA---GEPGSGSMVKVFGMSMPS---VNAYYFLFLLLCIGVIFFSVRLQD 242 I VFG+ +A G + + G++ V YFL LLL + F + RL Sbjct: 216 IPKPTVFGIEMARTASVEGGTTFHDMLGLTYQGGHMVIFLYFLGLLLVLFTYFVTSRLIR 275 Query: 243 SRLGRAWVAIREDEIAAKAMGINTRNVKLLAFAMGASFGGVAGAMFGAFQGFVSPESFSL 302 +GRAW A+R+DEIA +++GIN +KL AF +GA+F G+AG+ F A QG V+PESF+ Sbjct: 276 MPMGRAWEALRDDEIACRSLGINPTKIKLSAFTLGAAFAGLAGSFFAARQGLVNPESFTF 335 Query: 303 TESIAVLAMVVLGGIGHIPGVVLGGVILAALPEVLRHVVEPVQMAIFGKVWIDAEVLRQL 362 ES +LA+VVLGG+G GV+L ++L LPEV R E R L Sbjct: 336 IESALILAIVVLGGMGSQLGVILAAILLTILPEVARSFAE----------------YRML 379 Query: 363 LYGLAMVVIMLTRPAGLWPSPR-HEDRPE 390 ++GL MV++M+ RP GL P+ R H + P+ Sbjct: 380 IFGLVMVLMMIWRPQGLLPATRPHVELPQ 408 Lambda K H 0.327 0.143 0.430 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: 426 Number of extensions: 27 Number of successful extensions: 6 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: 404 Length of database: 408 Length adjustment: 31 Effective length of query: 373 Effective length of database: 377 Effective search space: 140621 Effective search space used: 140621 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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