Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate CCNA_03663 CCNA_03663 NADP-dependent malic enzyme
Query= BRENDA::O52593 (332 letters) >FitnessBrowser__Caulo:CCNA_03663 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:
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