Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_086511852.1 BZY95_RS21065 NADP-dependent malic enzyme
Query= metacyc::PTACLOS-MONOMER (333 letters) >NCBI__GCF_002151265.1:WP_086511852.1 Length = 756 Score = 165 bits (417), Expect = 4e-45 Identities = 101/333 (30%), Positives = 181/333 (54%), Gaps = 11/333 (3%) Query: 2 DLIESIWECAKQDKKRIILAEGEEKRNLIAADKIIKEGLAELVLVGDENKIKEKASELNL 61 +++E ++E A+Q+ R++ AEGE++R L A + + + A+ VL+G I+ + EL L Sbjct: 428 NVMEPVFERARQNPLRLLYAEGEDERVLRAMEVCVSQHYAKPVLIGRRKVIEARIEELGL 487 Query: 62 DISKA---EIMDPETSLKTETYARDFYELRKHKGMTIEKSEKMVRD-PLYFATMALKDGY 117 + E++D T A ++++L +G+ E +EK VR A++ L+ G Sbjct: 488 PVRAGVDFELIDARDYPDCSTLASEYHQLMGRRGVHPEAAEKRVRSRSTILASLLLRRGE 547 Query: 118 VDGMVSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNP 177 VD +++G V T + L L +I GV + ++I+ E L AD VN Sbjct: 548 VDAVIAGPVGTYHEHLDLVLDVIGLREGVSTPAALQLLIL------ERATLFIADPFVNY 601 Query: 178 NPTSDELADIAITTAETARKLCNVEPKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPD 237 +P + ++A+I + AE R+ + P+ A++S S GS+ K+++A+ + ++ PD Sbjct: 602 DPNASQIAEITLLAAEQVRRF-GITPRAALVSHSNFGSSDFASAVKMRDALALIRERDPD 660 Query: 238 LAIDGELQLDAAIDSEVAALKAPSSNVAGNANVLVFPDLQTGNIGYKLVQRFAKAKAIGP 297 L +DGE+Q D+A+ + V P S + G AN+L+ P+L NI + ++ ++GP Sbjct: 661 LVVDGEMQADSALSTGVRGRILPGSLLEGEANLLIMPNLDAANIAFTALKVLGNGVSVGP 720 Query: 298 ICQGFAKPINDLSRGCSSEDIVNVVAITVVQAQ 330 I G AKP++ L+R ++ I N+ A VV+AQ Sbjct: 721 ILLGAAKPVHVLNRTVTARGIANMSAFAVVEAQ 753 Lambda K H 0.316 0.134 0.374 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: 511 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: 333 Length of database: 756 Length adjustment: 34 Effective length of query: 299 Effective length of database: 722 Effective search space: 215878 Effective search space used: 215878 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 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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