Align Leucine ABC transporter subunit substrate-binding protein LivK (characterized, see rationale)
to candidate WP_027180502.1 G496_RS0118025 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A160A0J6 (375 letters) >NCBI__GCF_000429985.1:WP_027180502.1 Length = 398 Score = 224 bits (570), Expect = 4e-63 Identities = 120/345 (34%), Positives = 188/345 (54%), Gaps = 3/345 (0%) Query: 26 AADTIKIGIAGPKTGPVAQYGDMQFSGSKMAIEQINAKGGVNGKQLVAVEYDDACDPKQA 85 A I +G+ G +G +A YG + +++ + N KGGVNG ++V DD C P+ A Sbjct: 48 AGGEIILGVPGAHSGDLASYGLPTVAAAELVAKSYNDKGGVNGMKVVVAPQDDQCKPELA 107 Query: 86 VAVANKVVNDGIKFVVGHLCSSSTQPASDIYEDEGVVMITPAATSPDITARG-YKMIFRT 144 A K+V+D + V+GH+CS +T+ A IY++ +V ++P+AT+P +T G Y FRT Sbjct: 108 TNAAFKLVSDKVTIVLGHICSGATKAALPIYKEANIVCLSPSATNPPLTQSGDYPNFFRT 167 Query: 145 IGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEGIASAVKKTLED-KGVKVAVFEGVN 203 I D AQ A + + + K +AV+HDK YG+G A KK +E+ K +V +FEG+ Sbjct: 168 IASDDAQAALAAKFAMEDLHLKKIAVIHDKGDYGKGFAEFAKKFVEEAKDHEVILFEGIT 227 Query: 204 AGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQSQEKGLKAKFMGPEGVGNDSISQI 263 G D+S+++ K+K + D V +GGYHPE I+ Q ++K L F+ +GV + Sbjct: 228 PGAVDYSAVVQKIKSSGADGVIFGGYHPEASKIIMQMRKKTLDIPFISDDGVKAQTFIDT 287 Query: 264 AKESSEGLLVTLPKSFDQDPANIALADAFKAKKEDPS-GPFVFPSYSAVTVIADAIKAAK 322 A ++EG+ T P+ +P F E G F + +YS + +AI+ A Sbjct: 288 AGAAAEGVYATGPRDITANPLYAVAHQGFLDTHEGKEPGAFYYEAYSGAIALLNAIEKAG 347 Query: 323 SEDAGKVAEAIHAGTFKTPTGDLSFDKNGDLKDFKFVVYEWHFGK 367 S D K+ +A+H +TP G + FD GD F VY+ H G+ Sbjct: 348 STDYDKIVDALHNNLVETPVGKIKFDSKGDAIGVGFSVYQVHDGQ 392 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: 403 Number of extensions: 30 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: 398 Length adjustment: 30 Effective length of query: 345 Effective length of database: 368 Effective search space: 126960 Effective search space used: 126960 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