Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_065398591.1 BBI00_RS09790 ATP-binding cassette domain-containing protein
Query= TCDB::Q8DQH8 (254 letters) >NCBI__GCF_001684965.1:WP_065398591.1 Length = 342 Score = 127 bits (320), Expect = 2e-34 Identities = 81/264 (30%), Positives = 137/264 (51%), Gaps = 33/264 (12%) Query: 3 LLEVKQLTKHFG----GLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEG 58 ++E++ ++K F A+ V+L + +G++VG+IG +GAGK+TL + + P EG Sbjct: 1 MIEIRNISKTFHQKNQSFKALDKVSLNIEKGDIVGIIGFSGAGKSTLIRTVNLLERPDEG 60 Query: 59 TVTLDGHLLNGKSPYKIASLGL-------GRTFQNIRLFKDLTVLDNVLIAFGNHHKQHV 111 + ++NGK K+ S L G FQ+ L TV DNV + H Sbjct: 61 QI-----IINGKDFTKLNSRQLAEERKKIGMIFQHFNLLSSRTVFDNVALPLELDHT--- 112 Query: 112 FTSFLRLPAFYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPK 171 ++++ K ELLKI L+ A ++LS GQ++R+ I RALA +P Sbjct: 113 ------------GKEQINRKVNELLKIVGLEEKANDYPRSLSGGQKQRVAIARALANDPH 160 Query: 172 ILFLDEPAAGMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLI 231 +L DE + ++P T + +L+R I ITI+LI H+M ++ V + V++ G+L+ Sbjct: 161 LLLCDEATSALDPATTQSILQLLRDINQRLGITILLITHEMEVIKTVCNHVAVIDKGKLL 220 Query: 232 AQGTPDEIKTNKR--VIEAYLGGE 253 +GT EI ++K VI ++ + Sbjct: 221 TKGTLSEIISDKEHPVIRQFINSD 244 Lambda K H 0.319 0.139 0.385 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: 190 Number of extensions: 11 Number of successful extensions: 3 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: 254 Length of database: 342 Length adjustment: 26 Effective length of query: 228 Effective length of database: 316 Effective search space: 72048 Effective search space used: 72048 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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