Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate 14980 b0855 ATP-binding component of putrescine transport system (VIMSS)
Query= uniprot:D8J1T6 (255 letters) >FitnessBrowser__Keio:14980 Length = 377 Score = 121 bits (303), Expect = 2e-32 Identities = 77/243 (31%), Positives = 130/243 (53%), Gaps = 23/243 (9%) Query: 5 LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64 LL+IR+++K + G A++ V +TI +G+I+ L+G +G GK+T ++ G QP G L Sbjct: 19 LLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIML 78 Query: 65 DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124 DG S P+ I FQ+ LF MTV +N+ G K + Sbjct: 79 DGVDLSQVPPY---LRPINMMFQSYALFPHMTVEQNIAFGL---------------KQDK 120 Query: 125 EEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGM 184 +A I + ++L V + +FAKR LS G ++R+ +AR+LA P+LL LDEP + Sbjct: 121 LPKAEIASRVNEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGAL 180 Query: 185 NATEKLGLR---ELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQ 241 + +KL R E++ ++ G T +++ HD + M + RI +++ GK + G P ++ Sbjct: 181 D--KKLRDRMQLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIY 238 Query: 242 KNP 244 ++P Sbjct: 239 EHP 241 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: 223 Number of extensions: 14 Number of successful extensions: 4 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: 377 Length adjustment: 27 Effective length of query: 228 Effective length of database: 350 Effective search space: 79800 Effective search space used: 79800 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: 48 (23.1 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