Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate SM_b20785 SM_b20785 branched-chain amino acid ABC transporter ATP-binding protein
Query= TCDB::Q8DQH8 (254 letters) >lcl|FitnessBrowser__Smeli:SM_b20785 SM_b20785 branched-chain amino acid ABC transporter ATP-binding protein Length = 254 Score = 167 bits (422), Expect = 3e-46 Identities = 98/255 (38%), Positives = 145/255 (56%), Gaps = 11/255 (4%) Query: 2 ALLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVT 61 A+ EV+ L + FGGL DV+L + G+ V LIGPNGAGKTT NL+TG +P G V Sbjct: 3 AIFEVRNLKRSFGGLAVTNDVSLSMAPGDRVALIGPNGAGKTTFVNLVTGNLKPDAGEVR 62 Query: 62 LDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAF--GNHHKQHVFTSFLRLP 119 + G + GL R+FQ RLF+D+T ++V +A + +F +FL +P Sbjct: 63 IGGETVTNVDAIGRVRRGLVRSFQVTRLFQDMTPAEHVALAVLQRDGRAGRMFGNFLAMP 122 Query: 120 AFYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPA 179 + A+A LL L A + ++YGQQR LEI ALA +P++L LDEPA Sbjct: 123 G-------VMAEAGSLLGKLGLRDLAHRPVREIAYGQQRLLEIAVALALKPRVLLLDEPA 175 Query: 180 AGMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEI 239 AG+ +T + + + + D+ + +++IEHDM+LV +R+ VL G +I G+P ++ Sbjct: 176 AGVPQSDTGRIEQALADLPDD--LAVLMIEHDMDLVFRFAKRVIVLAAGTVIFDGSPADV 233 Query: 240 KTNKRVIEAYLGGEA 254 + RV EAYLG A Sbjct: 234 TKDPRVREAYLGSYA 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: 162 Number of extensions: 9 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: 254 Length adjustment: 24 Effective length of query: 230 Effective length of database: 230 Effective search space: 52900 Effective search space used: 52900 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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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