Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate N515DRAFT_2182 N515DRAFT_2182 malate dehydrogenase (oxaloacetate-decarboxylating)(NADP+)
Query= metacyc::PTACLOS-MONOMER (333 letters) >FitnessBrowser__Dyella79:N515DRAFT_2182 Length = 761 Score = 154 bits (388), Expect = 9e-42 Identities = 99/332 (29%), Positives = 168/332 (50%), Gaps = 11/332 (3%) Query: 3 LIESIWECAKQDKKRIILAEGEEKRNLIAADKIIKEGLAELVLVGDENKIKEKASELNLD 62 L++ ++E A+ D+KR++ AEGEE+ L A +I E LA +L+G + I+ + L L Sbjct: 429 LMKPVYERARADRKRVVYAEGEEETVLRAVQTVIDERLAFPILIGRPSVIETRIQRLGLR 488 Query: 63 ISKA---EIMDPETSLKTETYARDFYELRKHKGMTIEKSEKMVRD-PLYFATMALKDGYV 118 + + E+ + + + Y + ++ L + +G++ ++ ++R P A++ ++ G Sbjct: 489 MKEGVDFELTNIDDDPRFNDYWQQYHALTERRGVSPAAAKNLLRSRPTLIASLMVERGEA 548 Query: 119 DGMVSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNPN 178 D M+ G V L + PGV+ S +I ++G F D V + Sbjct: 549 DAMICGLVGRFHKKLGYMRSVFGLDPGVQCTSAMTGVI------NDQGAWFFLDTHVQVD 602 Query: 179 PTSDELADIAITTAETARKLCNVEPKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPDL 238 P+++++A+ A A KL +EPKVA+LS S GS K++ E+ K P L Sbjct: 603 PSAEQIAE-ATLQASYRLKLFGIEPKVALLSHSNYGSHDNPSAAKMRKVYELLKSRLPKL 661 Query: 239 AIDGELQLDAAIDSEVAALKAPSSNVAGNANVLVFPDLQTGNIGYKLVQRFAKAKAIGPI 298 +DGE+Q D A D + P++ + G AN+ V P+L NI Y +V+ AIGPI Sbjct: 662 EMDGEMQADTAWDEGLRTRMFPNTTLTGRANLFVMPNLDAANITYNMVRVMTDGVAIGPI 721 Query: 299 CQGFAKPINDLSRGCSSEDIVNVVAITVVQAQ 330 G KP + L+ + +VN+ AI V AQ Sbjct: 722 LMGIDKPAHILTPASTPRRVVNMTAIAAVDAQ 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: 500 Number of extensions: 21 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: 761 Length adjustment: 34 Effective length of query: 299 Effective length of database: 727 Effective search space: 217373 Effective search space used: 217373 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 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