Align Leucine ABC transporter subunit substrate-binding protein LivK (characterized, see rationale)
to candidate WP_043750690.1 MNOD_RS08385 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A160A0J6 (375 letters) >NCBI__GCF_000022085.1:WP_043750690.1 Length = 372 Score = 295 bits (756), Expect = 1e-84 Identities = 156/353 (44%), Positives = 220/353 (62%), Gaps = 2/353 (0%) Query: 15 MVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGSKMAIEQINAKGGVNGKQLVAV 74 ++ AG+A A IK+ +AGP TGP A +G +G+ A+E IN GG+ GK++ V Sbjct: 7 VLAAGLAWAGSAQAQIKLAVAGPITGPNAAFGAQLKNGATQAVEDINKAGGILGKKIEIV 66 Query: 75 EYDDACDPKQAVAVANKVVNDGIKFVVGHLCSSSTQPASDIYEDEGVVMITPAATSPDIT 134 YDDA DPKQ V+VA+K ++ + VVGH S + PAS++Y + G+V ITPA+T+P T Sbjct: 67 IYDDASDPKQGVSVASKAGSEKVVAVVGHFNSGVSIPASEVYAESGIVEITPASTNPKFT 126 Query: 135 ARGYKMIFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEGIASAVKKTLEDKGV 194 R FRT G D QG AG Y+A H K K +A++HDK YG G+A K L+ KG Sbjct: 127 DRKLWNTFRTCGRDDQQGAVAGAYLAQHFKGKNIAIVHDKTPYGRGLADETLKALKAKGG 186 Query: 195 KVAVFEGVNAGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQSQEKGLKAKFMGPEG 254 K +FEG+N G+KD+S++++KLKQA D VYYGG H E GLI+RQ ++GL A M +G Sbjct: 187 KEVLFEGINPGEKDYSALVSKLKQAKADVVYYGGLHTEAGLIVRQMHDQGLNAPLMSGDG 246 Query: 255 VGNDSISQIAKESSEGLLVTLPKSFDQDPANIALADAFKAKKEDPSGPFVFPSYSAVTVI 314 + + +QIA ++G L+T ++P + AFKAK DP + SY+AV ++ Sbjct: 247 ITDKEFAQIAGPGADGTLMTFSPDARKNPNAKDVVAAFKAKNIDPEA-YTLYSYAAVQIL 305 Query: 315 ADAIKAAKSEDAGKVAEAIHAG-TFKTPTGDLSFDKNGDLKDFKFVVYEWHFG 366 A++ AKS D KVAE + +G TFKT GD+S+DK GD+ +V+Y W G Sbjct: 306 KTAMEDAKSTDGKKVAEVMRSGKTFKTVIGDISYDKKGDITRPDYVMYMWKKG 358 Lambda K H 0.314 0.132 0.372 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: 415 Number of extensions: 21 Number of successful extensions: 4 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: 375 Length of database: 372 Length adjustment: 30 Effective length of query: 345 Effective length of database: 342 Effective search space: 117990 Effective search space used: 117990 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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