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_036833161.1 N784_RS05555 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH8 (254 letters) >NCBI__GCF_000775615.1:WP_036833161.1 Length = 250 Score = 186 bits (471), Expect = 5e-52 Identities = 100/250 (40%), Positives = 157/250 (62%), Gaps = 5/250 (2%) Query: 3 LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62 ++E K +T FGG AV V++++ E + +IGPNGAGKTT FNLL+G +P+ G++ Sbjct: 4 IMETKDVTVSFGGHVAVDQVSVQILERKFTSIIGPNGAGKTTFFNLLSGQMKPTNGSIYF 63 Query: 63 DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFY 122 G + +S + LG+GR+FQ +F +LTV +NV +A + K ++ A + Sbjct: 64 KGADVTKRSATERTRLGIGRSFQITNVFPNLTVFENVRLAVQSQAKVRY-----QMFAHF 118 Query: 123 KSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGM 182 K+ + K E+L + L A +LA NL++G++R+LEI LA E ++L LDEP AGM Sbjct: 119 NQYKQFQEKTDEILALVFLQDKANSLAMNLAHGEKRKLEIAMLLALETELLLLDEPTAGM 178 Query: 183 NPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKTN 242 + +E + ++I IK + TI+LIEH M+++M +++ + VL +G LIA+GTP+EI N Sbjct: 179 SLEEVPAIIDVIHEIKQQGNRTIVLIEHKMDMIMGMSDEVLVLYHGELIAKGTPNEIVHN 238 Query: 243 KRVIEAYLGG 252 + V AYLGG Sbjct: 239 EIVQSAYLGG 248 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: 166 Number of extensions: 7 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: 250 Length adjustment: 24 Effective length of query: 230 Effective length of database: 226 Effective search space: 51980 Effective search space used: 51980 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