Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_083866752.1 FRAAL_RS30325 hypothetical protein
Query= BRENDA::P74569 (600 letters) >NCBI__GCF_000058485.1:WP_083866752.1 Length = 421 Score = 133 bits (334), Expect = 2e-35 Identities = 110/346 (31%), Positives = 167/346 (48%), Gaps = 21/346 (6%) Query: 3 LIVQKFGGTSVGTVERIQAVAQRIKRTVQGGNS--------LVVVVSAMGKSTDVLVDLA 54 ++V KFGG + Q +A+ + ++ G S +VVVSA+ TD L Sbjct: 12 VVVLKFGGAAFAAPGAHQGIARHVADRLRAGGSSASPGGARAIVVVSAVAGETDRLGTAL 71 Query: 55 QQISPNPCRREMDMLLSTGEQVSIALLSLALQEIDQPAISLTGAQVGIVTEAEHSRARIL 114 + +SP P R + L TGE V++AL++ AL++ A++LT A G V E A + Sbjct: 72 RAVSPAPDRDLLAAALMTGETVNVALMTAALRDAGLAAVALTAADTGFVGAGEPHCADLR 131 Query: 115 EIRPDRLEHHLRE-GKVVVVAGFQGISSVEHLEITTLGRGGSDTSAVALAAALKADFCEI 173 I L + G V+VV G Q + + LGR SD SA+A A A+ A CEI Sbjct: 132 RIDGSVLASLVEPAGTVLVVPGGQAVDGDGRPIM--LGRNSSDLSAIAAAIAVGARACEI 189 Query: 174 YTDVPGILTTDPRLVPEAQLMAEITCDEMLELASLGAKVLHPRAVEIARNYGIPLVVRSS 233 ++D PGI T DPRLVP+A+ +A + D M+ ++ GAKVLH AV A+ +G+ + RS Sbjct: 190 FSDSPGICTADPRLVPDARTLAAVDYDTMITMSRHGAKVLHHSAVAWAQRHGVEIRCRSL 249 Query: 234 WSDEPGTKVVAPPVQNRSLVGLEIAKAVDGVEYDADQAKVALL-----RVPDRPGVASKL 288 D VV + + V + V + D +A +A L +P+ V Sbjct: 250 LPDGAVYSVVRAGRTSAAAVLVHGTGTVWAGDPDLVRATLAELGSDAVAIPEAAAVP--- 306 Query: 289 FRDIAQQQVDIDLIIQSIHDGNSNDIAFTVVKDLLNTAEAVTSAIA 334 ++A +V + ++ D D+A T V A A T+ IA Sbjct: 307 --EVAVTEVAAVPEVAAVPDVAVTDVAVTEVAVTEVAAAAATAGIA 350 Lambda K H 0.318 0.132 0.366 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: 553 Number of extensions: 26 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: 600 Length of database: 421 Length adjustment: 34 Effective length of query: 566 Effective length of database: 387 Effective search space: 219042 Effective search space used: 219042 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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