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_083529437.1 AS188_RS12245 ATP-binding cassette domain-containing protein
Query= TCDB::Q8DQH8 (254 letters) >NCBI__GCF_001482365.1:WP_083529437.1 Length = 313 Score = 104 bits (260), Expect = 2e-27 Identities = 73/238 (30%), Positives = 112/238 (47%), Gaps = 21/238 (8%) Query: 3 LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62 +LE + L++ FGG T V DV+ + G + G +G NGAGKTT +LTGV + G V Sbjct: 22 VLEARGLSRAFGGRTVVEDVSFRVEPGRMTGFVGANGAGKTTTMRMLTGVLRTTAGEVLW 81 Query: 63 DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFY 122 DG + G G + L+ VLD L G H Sbjct: 82 DGRPVTAAD-----RAGFGYMPEERGLYPRQPVLDQ-LCYLGRLHGM------------- 122 Query: 123 KSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGM 182 + A+A LL+ DL G LS G Q+R++I AL P L LDEP +G+ Sbjct: 123 -DRRAALAEARRLLERLDLAGRERDPLGTLSLGNQQRVQIAAALLHGPTALVLDEPFSGL 181 Query: 183 NPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIK 240 +P +T L+R + E + ++ H ++LV + + + VL GR++A G ++++ Sbjct: 182 DPVAVDAMTGLLRE-RLEQGVPVLFSSHQLDLVDRLCDSLVVLSAGRVLAAGAVEDLR 238 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: 161 Number of extensions: 8 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: 254 Length of database: 313 Length adjustment: 26 Effective length of query: 228 Effective length of database: 287 Effective search space: 65436 Effective search space used: 65436 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 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