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_089137090.1 CES79_RS10020 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH8 (254 letters) >NCBI__GCF_002217945.1:WP_089137090.1 Length = 236 Score = 140 bits (353), Expect = 2e-38 Identities = 85/253 (33%), Positives = 145/253 (57%), Gaps = 18/253 (7%) Query: 1 MALLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTV 60 M +LEVK L ++G + AV V+ +N+GE+V LIG NGAGKTT+ ++G+ +P GT+ Sbjct: 1 MTMLEVKDLAVNYGVINAVKGVSFHINKGEIVSLIGANGAGKTTILKTISGLLKPVSGTI 60 Query: 61 TLDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLI-AFGNHHKQHVFTSFLRLP 119 T +G + KI + G+ + + +F ++V +N+ + AF ++ + +SF + Sbjct: 61 TYEGKTIQKHKAPKIVAAGISQVPEGRHIFAGMSVRENLQMGAFLQNNHAEITSSFETVY 120 Query: 120 AFYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPA 179 + + KE ++ DA T LS G+Q+ L + RAL ++PK+L LDEP+ Sbjct: 121 SRFPVLKE------------RINQDAAT----LSGGEQQMLAMGRALMSKPKLLLLDEPS 164 Query: 180 AGMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEI 239 G+ P E+ E+++ IK++ T++LIE + + + +R YVL G++ GT E+ Sbjct: 165 MGLAPIFINEIFEIVKAIKEQ-GTTVLLIEQNAKKALSIADRGYVLASGKVKMTGTGQEL 223 Query: 240 KTNKRVIEAYLGG 252 N+ V +AYLGG Sbjct: 224 LANQDVQKAYLGG 236 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: 135 Number of extensions: 6 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: 236 Length adjustment: 24 Effective length of query: 230 Effective length of database: 212 Effective search space: 48760 Effective search space used: 48760 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: 46 (22.3 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