Align Leucine ABC transporter subunit substrate-binding protein LivK (characterized, see rationale)
to candidate WP_028316321.1 G491_RS0123735 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A160A0J6 (375 letters) >NCBI__GCF_000429905.1:WP_028316321.1 Length = 394 Score = 234 bits (598), Expect = 2e-66 Identities = 124/345 (35%), Positives = 197/345 (57%), Gaps = 3/345 (0%) Query: 26 AADTIKIGIAGPKTGPVAQYGDMQFSGSKMAIEQINA-KGGVNGKQLVAVEYDDACDPKQ 84 A + +K+ +AG TG +A YG +++ +E +NA +GGV G++++ V DDAC P+ Sbjct: 44 ALEPLKLAVAGAHTGDLASYGIPSVRAAEILVEHVNATQGGVGGRKVILVTEDDACKPEM 103 Query: 85 AVAVANKVVNDGIKFVVGHLCSSSTQPASDIYEDEGVVMITPAATSPDITARG-YKMIFR 143 A A K+V D + VVGH+CS +T+ A IY+D G++ I+P+AT+PD+T G Y FR Sbjct: 104 ATNAATKLVGDDVDLVVGHICSGATKAALGIYKDSGIIAISPSATNPDLTQSGDYPNFFR 163 Query: 144 TIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEGIASAVKKTLEDKG-VKVAVFEGV 202 TI D AQ ++ D + +AVLHDK YG+G+A KK LE+ G +V ++EG+ Sbjct: 164 TIASDDAQARLEVDFALDVLGLTKIAVLHDKGDYGKGLAEFAKKFLEESGKAEVVLYEGI 223 Query: 203 NAGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQSQEKGLKAKFMGPEGVGNDSISQ 262 G D+S+++ K+ ++ V +GGYHPE I+ Q ++K + F+ +GV +D+ + Sbjct: 224 TPGGMDYSAVVQKINRSGAQAVIFGGYHPEASKIVMQMRKKDMDTIFISDDGVKDDTFIK 283 Query: 263 IAKESSEGLLVTLPKSFDQDPANIALADAFKAKKEDPSGPFVFPSYSAVTVIADAIKAAK 322 +A + +EG+ T PK ++P + K K + G F +YSAV + +A+ + Sbjct: 284 VAGDYAEGVYATGPKDTSKNPLAVEADKLHKEKYGEDYGAFYLNAYSAVLALFNAVDKSG 343 Query: 323 SEDAGKVAEAIHAGTFKTPTGDLSFDKNGDLKDFKFVVYEWHFGK 367 S D V+ A+ TP G + FD GD F VY+ GK Sbjct: 344 STDYEAVSNALRNEYVATPLGIIKFDDRGDAIGVGFSVYQVQNGK 388 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: 412 Number of extensions: 18 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: 394 Length adjustment: 30 Effective length of query: 345 Effective length of database: 364 Effective search space: 125580 Effective search space used: 125580 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