Align leucine-specific-binding protein LivK (characterized)
to candidate WP_013093680.1 BC1002_RS29770 branched-chain amino acid ABC transporter substrate-binding protein
Query= CharProtDB::CH_107418 (369 letters) >NCBI__GCF_000092885.1:WP_013093680.1 Length = 400 Score = 204 bits (519), Expect = 3e-57 Identities = 126/353 (35%), Positives = 184/353 (52%), Gaps = 11/353 (3%) Query: 6 KTIIAGMIALAISHTAMADD--------IKVAVVGAMSGPIAQWGDMEFNGARQAIKDIN 57 +T +AGM A A MA IK+ V +SG A G NGA+ A IN Sbjct: 17 RTAVAGMAAAAALLAGMAPGSALSQGATIKIGVPVPLSGSSANAGTDIVNGAKLAAARIN 76 Query: 58 AKGGIKGDKLVGVEYDDACDPKQAVAVANKIVNDGIKYVIGHLCSSSTQPASDIYEDEGI 117 A GG+ G ++ V DDACD + AV A K+V+ G+ V G CSS+ P S + GI Sbjct: 77 AAGGVLGKQIELVPEDDACDAQTAVQAAQKLVDAGVVAVAGGYCSSAALPESTTFHRAGI 136 Query: 118 LMISPGATNPELTQRGYQHIMRTAGLDSSQGPTAAKYILETVKPQRIAIIHDKQQYGEGL 177 + +TNP+LT+ GY ++ RT G D QGP AA +I + + + +A+I D Y +GL Sbjct: 137 PYVLDASTNPQLTEMGYDNVFRTIGRDDQQGPFAASFIKDVLHAKHVAVIDDNTTYSKGL 196 Query: 178 ARSVQDGLKAANANVVFFDGITAGEKDFSALIARLKKENIDFVYYGGYYPEMGQMLRQAR 237 A++ LK +VV+ + IT G+ D+S + R+ D +YY GY+ E G ++++AR Sbjct: 197 AQNTVQALKKDGVDVVYANSITPGQMDYSPTLTRVSSLKPDVIYYTGYFSEAGLLVKEAR 256 Query: 238 SVGLKTQFMGPEGVGNASLSNIAGDAAEGMLV-TMPKRYDQDPANQGIVDALKADKKDPS 296 +GLK FMG + + +L AG AA+GM++ T P A+ + D KA + P Sbjct: 257 QLGLKMTFMGGDATNDPTLMKTAGPAADGMIITTAPLAQFLSGAHAYVDDYTKAYGQGP- 315 Query: 297 GPYVWITYAAVQSLATALERTGSDEPLALVKDL-KANGANTVIGPLNWDEKGD 348 GPY Y AV A A+ S +P A+ L K G + ++ KGD Sbjct: 316 GPYSVYEYDAVGVTAKAIADAKSTQPAAITAALHKIQNYPGATGTIAFNPKGD 368 Lambda K H 0.315 0.133 0.386 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: 411 Number of extensions: 29 Number of successful extensions: 1 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: 369 Length of database: 400 Length adjustment: 30 Effective length of query: 339 Effective length of database: 370 Effective search space: 125430 Effective search space used: 125430 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.5 bits) S2: 50 (23.9 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