Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate CCNA_03663 CCNA_03663 NADP-dependent malic enzyme
Query= BRENDA::O52593 (332 letters) >lcl|FitnessBrowser__Caulo:CCNA_03663 CCNA_03663 NADP-dependent malic enzyme Length = 766 Score = 137 bits (346), Expect = 7e-37 Identities = 99/327 (30%), Positives = 158/327 (48%), Gaps = 14/327 (4%) Query: 3 FLEQIIERAKSDVKTIVLPESTDLRVIKAASMIMKKGIAKVVLIGNE----KEIKSLAGD 58 FL++I ++ K IV E D VI+AA G K +L G E + +K + D Sbjct: 439 FLQKISGSVLANPKRIVFAEGEDPSVIRAAYAYQSGGFGKAILCGRENLVHENMKLVGLD 498 Query: 59 IDLEGVMIEDSLNSEKLEDYANTLYELRKSKGMTIEAARETI-KDPLYYGVMMVKKGEAD 117 D G+ I ++ S++ DY + LY + +G + I +D + MV GEAD Sbjct: 499 PDTAGLEIINARLSDRNPDYVDALYARLQRQGYLKRDVQRLINQDRNSFAASMVTLGEAD 558 Query: 118 GMVAGAVNSTANTLRPALQILKTAPGTKLVSSFFVMVVPNCEYGHNGTFVYADCGLVENP 177 GMV G S L L+++ APG +++ V+ T AD + E P Sbjct: 559 GMVTGVTRSFDQALEEVLRVVDPAPGGRIMGMSVVLA-------KGRTIFVADTNVTELP 611 Query: 178 DADQLSEIAISASKSFEMLVGAKPQVAMLSYSSYGSAKSELTEKVIKATQLAKEKAPHLA 237 +A++L EIA A+++ L G KP+VA +SYS++G+ +EKV +A + E Sbjct: 612 EAEELVEIACEAARAVRRL-GFKPRVAFMSYSTFGNPMGLRSEKVREAVAMLDEMEVDFE 670 Query: 238 IDGELQVDAAIVPEVAKSKAKGSSVAGKANVLIFPDLDAGNIAYKLTQRLAKAEAYGPIT 297 +GE+ + A+ PE ++ + AN+LI P + A +I+ KL Q L A GP+ Sbjct: 671 YEGEMPPELALDPE-KRANYPFMRLTDSANILIMPAIHAASISTKLVQSLGGATVIGPVL 729 Query: 298 QGLARPVNDLSRGCSAEDIVGVAAITA 324 GL++ V S I+ +A + A Sbjct: 730 LGLSKSVQIAPLSASVSKILNMAMMAA 756 Lambda K H 0.313 0.129 0.346 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: 469 Number of extensions: 19 Number of successful extensions: 5 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: 332 Length of database: 766 Length adjustment: 34 Effective length of query: 298 Effective length of database: 732 Effective search space: 218136 Effective search space used: 218136 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 52 (24.6 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