Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate AZOBR_RS25630 AZOBR_RS25630 ABC transporter
Query= uniprot:D8J1T6 (255 letters) >FitnessBrowser__azobra:AZOBR_RS25630 Length = 255 Score = 217 bits (552), Expect = 2e-61 Identities = 115/249 (46%), Positives = 163/249 (65%), Gaps = 1/249 (0%) Query: 5 LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64 LL IR+VS+RFGG+ A+N V ++ G++ GLIGPNGAGKTT FN+I+G +GT Sbjct: 4 LLDIRNVSRRFGGVLAVNDVTGHVDEGELVGLIGPNGAGKTTLFNLISGFTPLSSGTVAF 63 Query: 65 DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124 DG+ S ++VA+ GI+RTFQN+R+F M+V +NV VG Q GA+F A Sbjct: 64 DGRTISGLKTNQVARLGISRTFQNLRVFPNMSVFDNVSVGAVGALPQGALGALFGSLAGG 123 Query: 125 EEEAA-IREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAG 183 +A I ++ + L+ VG+ A A +L YG ++ LEIARALA P+ L LDEPAAG Sbjct: 124 GARSAEISRRTWEALEAVGLTHVAGELAANLPYGQRKYLEIARALAMQPRFLILDEPAAG 183 Query: 184 MNATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQKN 243 +N TE L + + ++ G TI+L+EHD+ L+M +C RI VL G+ IA+G P ++++ Sbjct: 184 LNDTETRALADFIKRLHGTGLTIMLVEHDMTLVMSICQRILVLASGRKIADGPPDAIRRD 243 Query: 244 PAVIEAYLG 252 PAV+EAYLG Sbjct: 244 PAVLEAYLG 252 Lambda K H 0.320 0.138 0.394 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: 200 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: 255 Length of database: 255 Length adjustment: 24 Effective length of query: 231 Effective length of database: 231 Effective search space: 53361 Effective search space used: 53361 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 (21.8 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:
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