Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_008814119.1 M988_RS06145 NADP-dependent oxaloacetate-decarboxylating malate dehydrogenase
Query= metacyc::PTACLOS-MONOMER (333 letters) >NCBI__GCF_001655005.1:WP_008814119.1 Length = 759 Score = 177 bits (448), Expect = 1e-48 Identities = 102/332 (30%), Positives = 187/332 (56%), Gaps = 12/332 (3%) Query: 4 IESIWECAKQDKKRIILAEGEEKRNLIAADKIIKEGLAELVLVGDENKIKEKASELNLDI 63 ++ I+ AK++KKR++LAEGEE+R L A +++ G+A +LVG + I+ + +L L I Sbjct: 431 MKPIFSQAKKEKKRVVLAEGEEERVLHATQELVTLGIASPILVGRPDVIEMRLKKLGLQI 490 Query: 64 SKA---EIMDPETSLKTETYARDFYELRKHKGMTIEKSEK-MVRDPLYFATMALKDGYVD 119 EI++ E+ + Y R++Y++ K +G++ E++ + ++ +P A + L+ G D Sbjct: 491 EAGKDFEIVNNESDPRFNEYWREYYDIMKRRGVSQEQARRAVIGNPTLIAAIMLQRGEAD 550 Query: 120 GMVSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNPNP 179 M+ G + + + G + +++P G AD VN +P Sbjct: 551 AMICGTIGNYHEHYEVVHNVFGFREGAHVAGAMNALLLPS------GNTFIADTYVNDDP 604 Query: 180 TSDELADIAITTAETARKLCNVEPKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPDLA 239 T+++LA+I + AET R+ +EPKVA+LS S+ G++ K++ +E+ + P+L Sbjct: 605 TAEQLAEITLMAAETVRRF-GIEPKVALLSHSSFGASDCPAARKMRRTLELVNEAAPELE 663 Query: 240 IDGELQLDAAIDSEVAALKAPSSNVAGNANVLVFPDLQTGNIGYKLVQ-RFAKAKAIGPI 298 IDGE+ DAA+ + P S + G AN+L+ P+++ I Y L++ ++ +GP+ Sbjct: 664 IDGEMHGDAALVESIRNDVMPDSPLKGAANILIMPNMEAARISYNLLRVSSSEGVTVGPV 723 Query: 299 CQGFAKPINDLSRGCSSEDIVNVVAITVVQAQ 330 G +KP++ L+ S IVN+VA++VV+AQ Sbjct: 724 LMGVSKPVHILTSIASVRRIVNMVALSVVEAQ 755 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: 540 Number of extensions: 23 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: 759 Length adjustment: 34 Effective length of query: 299 Effective length of database: 725 Effective search space: 216775 Effective search space used: 216775 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