Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_198139304.1 XAUT_RS15790 NADP-dependent malic enzyme
Query= metacyc::PTACLOS-MONOMER (333 letters) >NCBI__GCF_000017645.1:WP_198139304.1 Length = 756 Score = 174 bits (440), Expect = 8e-48 Identities = 101/332 (30%), Positives = 178/332 (53%), Gaps = 11/332 (3%) Query: 3 LIESIWECAKQDKKRIILAEGEEKRNLIAADKIIKEGLAELVLVGDENKIKEKASELNLD 62 ++ ++ AK++ KR++ AEGE++R L A +++EG+A ++V N ++ + L Sbjct: 429 IMRPLFAQAKRNIKRVVYAEGEDERVLRAVQAVVEEGIARPIIVARPNVLETRLKRFGLS 488 Query: 63 ISKA---EIMDPETSLKTETYARDFYELRKHKGMTIEKSEKMVRD-PLYFATMALKDGYV 118 + ++++PE + Y RD+ E+ +G+T + + +VR P A +A+K G Sbjct: 489 VRPGHDFDLINPEDDPRYRDYVRDYVEIAGRRGVTPDAARTLVRTHPTVIAALAVKRGEA 548 Query: 119 DGMVSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNPN 178 D M+ G LR II APGVK ++ ++I G D + Sbjct: 549 DAMLCGIEGRFTRHLRQVRDIIGLAPGVKELAALSLLIT------SHGNFFICDTQIQTE 602 Query: 179 PTSDELADIAITTAETARKLCNVEPKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPDL 238 PT+ +LA++ + A R+ +EP+VA+LS S GS + +V++A+ I ++ P+L Sbjct: 603 PTAADLAEMTVLAAAHVRRF-GLEPRVALLSHSNFGSHETLSAKRVRSALSIIREREPNL 661 Query: 239 AIDGELQLDAAIDSEVAALKAPSSNVAGNANVLVFPDLQTGNIGYKLVQRFAKAKAIGPI 298 +DGE+Q D+A+ ++ P+S + G ANVLV PDL +I + +++ A +GPI Sbjct: 662 EVDGEMQADSALLEDIRKRVLPNSTLTGAANVLVMPDLDAADIAFNMLKVLGDALPVGPI 721 Query: 299 CQGFAKPINDLSRGCSSEDIVNVVAITVVQAQ 330 G AKP + L ++ IVN+ A+ V +AQ Sbjct: 722 LMGTAKPAHILGPSVTARGIVNMTAVAVAEAQ 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: 550 Number of extensions: 26 Number of successful extensions: 4 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 Apr 09 2024. 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