Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate Synpcc7942_2493 Synpcc7942_2493 ATPase
Query= uniprot:D8J1T6 (255 letters) >FitnessBrowser__SynE:Synpcc7942_2493 Length = 253 Score = 231 bits (588), Expect = 1e-65 Identities = 122/250 (48%), Positives = 171/250 (68%), Gaps = 1/250 (0%) Query: 4 TLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFE 63 +LL++ V++RFGGL A+N V +E G+I+GLIGPNGAGKTT FN+ITGL G Sbjct: 2 SLLQLEQVTRRFGGLVAVNQVSFKVEVGEIFGLIGPNGAGKTTLFNLITGLQPLSGGEIC 61 Query: 64 LDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAA 123 G P ++A+ GIARTFQN+RLF +++V ENV+V H + + +++ + A Sbjct: 62 FQGDRLDRQRPDQIAQRGIARTFQNLRLFNQLSVFENVLVARHRQARTSLWDELIGSSRA 121 Query: 124 REEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAG 183 + R + Q+LL+ + + A + A L+YGD+RRLEIARALA +PQLL LDEPAAG Sbjct: 122 TRQSRGDRRRVQELLELLELSDQADQPAASLAYGDRRRLEIARALALEPQLLLLDEPAAG 181 Query: 184 MNATEKLGLRELLVKIQAEGK-TILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQK 242 +N EK L + + I+ + + T++LIEH V L+MGLC+RI VLD+G+ IA G PA V++ Sbjct: 182 LNPREKQDLSDRIRAIREQFQLTVVLIEHHVPLVMGLCDRIAVLDFGQLIALGDPATVRQ 241 Query: 243 NPAVIEAYLG 252 +PAVIEAYLG Sbjct: 242 DPAVIEAYLG 251 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: 204 Number of extensions: 9 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: 253 Length adjustment: 24 Effective length of query: 231 Effective length of database: 229 Effective search space: 52899 Effective search space used: 52899 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