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_011972867.1 MAEO_RS00720 ATP-binding cassette domain-containing protein
Query= TCDB::Q8DQH8 (254 letters) >NCBI__GCF_000017185.1:WP_011972867.1 Length = 281 Score = 109 bits (273), Expect = 5e-29 Identities = 77/251 (30%), Positives = 135/251 (53%), Gaps = 19/251 (7%) Query: 1 MALLEVKQLT-KHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGT 59 MA++E K + K+ G A+ + + +G++V L+GPNGAGK+TLF G+ +P G Sbjct: 1 MAIIEAKDIVYKYPDGTLALDRANISVEKGDMVALLGPNGAGKSTLFLHFNGILKPKSGK 60 Query: 60 VTLDGHLL--NGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLR 117 + L G + + KS ++ +G FQN D+ L F KQ V L Sbjct: 61 ILLKGAPIKYDAKSLMEVRKT-VGIVFQNS---------DDQL--FAPTVKQDVAFGPLN 108 Query: 118 LPAFYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDE 177 L E+E++ + E LK ++G +LS GQ++R+ I LA P+I+ LDE Sbjct: 109 LGL---KEEEVEKRVKEALKEVGMEGFENKPPHHLSGGQKKRVAIAGILAMHPEIMVLDE 165 Query: 178 PAAGMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPD 237 P AG++P +++ +L+ ++ E ITI++ HD++LV +I+V+ +++ GT + Sbjct: 166 PTAGLDPMGASKIMKLLYKLNKE-GITIIISTHDVDLVPIYANKIFVMGKTKIVKSGTVE 224 Query: 238 EIKTNKRVIEA 248 E+ ++ + I + Sbjct: 225 EVFSDIKTIRS 235 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: 150 Number of extensions: 5 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: 281 Length adjustment: 25 Effective length of query: 229 Effective length of database: 256 Effective search space: 58624 Effective search space used: 58624 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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