Align Leucine ABC transporter subunit substrate-binding protein LivK (characterized, see rationale)
to candidate WP_043748392.1 MNOD_RS09350 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A160A0J6 (375 letters) >NCBI__GCF_000022085.1:WP_043748392.1 Length = 367 Score = 227 bits (579), Expect = 3e-64 Identities = 118/352 (33%), Positives = 196/352 (55%), Gaps = 1/352 (0%) Query: 15 MVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGSKMAIEQINAKGGVNGKQLVAV 74 +V+AG+ + A + +G+A P++G VA G+ G + A++ N +GG+ G+ +V Sbjct: 11 LVIAGLFCAAPACAEVVVGVAVPRSGAVAGIGEQVLQGVQAAVKDANGRGGLAGEPIVLD 70 Query: 75 EYDDACDPKQAVAVANKVVNDGIKFVVGHLCSSSTQPASDIYEDEGVVMITPAATSPDIT 134 DDAC+P QAV VA + V G++ VVGH+CSS++ ASD+Y GVVMI+PA+ + +T Sbjct: 71 IEDDACEPGQAVEVAERFVRTGVRLVVGHVCSSASLAASDVYAANGVVMISPASNAARLT 130 Query: 135 ARGYKMIFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEGIASAVKKTLEDKGV 194 RG IFR G + QG + +A+ + K +A+L+D +A + K L G Sbjct: 131 DRGLSTIFRVSGREDDQGRLSATILAERFRDKKIAILYDDTPLSRSLADSTKANLNKIGQ 190 Query: 195 KVAVFEGVNAGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQSQEKGLKAKFMGPEG 254 A+F + G D +++I +L+ + ++ VYYGG++ E+G ++R + E+G + ++ G G Sbjct: 191 NEALFAAIVPGQTDDAALIKRLQASGIEVVYYGGHYQEMGKLVRTAAEQGYRPQWFGTSG 250 Query: 255 VGNDSISQIAKESSEGLLVTLPKSFDQDPANIALADAFKAKKEDPSGPFVFPSYSAVTVI 314 + +A +S G+L+T + P A A +A DP G FV Y+A+ + Sbjct: 251 IATKEFGTLAGPASNGVLMTFNPDLRRKPEAAAAVKALQADGIDPGG-FVLYGYAAMQAL 309 Query: 315 ADAIKAAKSEDAGKVAEAIHAGTFKTPTGDLSFDKNGDLKDFKFVVYEWHFG 366 +A AKS D +A +HA F G++ FD+ GD+ +V+Y W G Sbjct: 310 VEAGNFAKSTDPKAIAATLHAERFNLVLGNVGFDQKGDVTAPGYVLYVWRDG 361 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: 335 Number of extensions: 10 Number of successful extensions: 2 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: 367 Length adjustment: 30 Effective length of query: 345 Effective length of database: 337 Effective search space: 116265 Effective search space used: 116265 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: 49 (23.5 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