Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate WP_043745954.1 AMB_RS03695 NADP-dependent malic enzyme
Query= curated2:P39197 (318 letters) >NCBI__GCF_000009985.1:WP_043745954.1 Length = 760 Score = 135 bits (340), Expect = 3e-36 Identities = 99/334 (29%), Positives = 161/334 (48%), Gaps = 26/334 (7%) Query: 1 MKPLDRIHEAAKALDRHIILPEGEDPRVAEAARRLLAAGLARVTLMGGPEI--------- 51 MKP + + A+ R ++ EGE RV AA+ ++ GLAR L+G E+ Sbjct: 430 MKP---VFDRARQDMRRVVYCEGEGRRVLHAAQTVVDEGLARPVLIGRREVVEKRIQDLD 486 Query: 52 ------PGAGRIDPAGGPDLAELADHWHRMRAARGMTAERALTEMRDPIRQ-AAMRVRLG 104 DP P E +H + +G++ E A T +R + ++ Sbjct: 487 LRLRIDQDFDLCDPEDDPRFNEYWRLYHSIMERQGVSPEYARTVVRTRNTVIGTLMLKRK 546 Query: 105 QADGTVGGAVATTADTVRAALQIIGKAPGAGIVSSFFLMLSCGPGAPVRGGMIFADCGLV 164 + D + G + + L +IG G + ++ L++ P+ G D + Sbjct: 547 EVDAMICGTIGRYDKHLSHILNVIGTREGVKVPAAMNLLIM-----PI-GTFFICDTYVT 600 Query: 165 IQPDARELAAIALSAADSCRRILAEEPRVALLSFSTAGSAEHPSLGRIREALALIRAAAP 224 +P ++ + L A++ RR EP+VA LS + G+ + S R R+ALAL+R AP Sbjct: 601 PEPTPEQICDMTLLASEEVRRF-GIEPKVAFLSHANFGNRQTASAQRQRDALALLREKAP 659 Query: 225 GLEVDGEMQFDAALDEAIRARKAPESPLTGRPNVFVFPDLADGNIGYKIAERLAGLTAIG 284 LE +GEM DAAL E IR R P S L G N+ V P L NI + + + ++G Sbjct: 660 YLEAEGEMHGDAALSEEIRTRIFPNSKLKGAANLLVMPTLDAANISFNLLKVAGDALSVG 719 Query: 285 PILQGLAKPANDLSRACSVKDIVNATAITAMQTK 318 PIL G+A+PA+ L+ + +V++I+N TA+ A+ + Sbjct: 720 PILMGIAQPAHVLTPSATVRNIINITALAAVDAQ 753 Lambda K H 0.320 0.136 0.391 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: 423 Number of extensions: 16 Number of successful extensions: 1 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: 318 Length of database: 760 Length adjustment: 34 Effective length of query: 284 Effective length of database: 726 Effective search space: 206184 Effective search space used: 206184 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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