Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate WP_015448846.1 R2APBS1_RS16920 NADP-dependent malic enzyme
Query= BRENDA::O52593 (332 letters) >NCBI__GCF_000230695.2:WP_015448846.1 Length = 763 Score = 164 bits (414), Expect = 9e-45 Identities = 104/331 (31%), Positives = 179/331 (54%), Gaps = 13/331 (3%) Query: 4 LEQIIERAKSDVKTIVLPESTDLRVIKAASMIMKKGIAKVVLIGNEKEIKSLAGDIDLE- 62 ++ + ERAKS +V E + V++A +++ +G+A+ +LIG + I+ L Sbjct: 431 MKPVFERAKSAPCRLVYAEGEEETVLRAVQVVVDEGLARPILIGRPEVIEKRIHRAGLRI 490 Query: 63 --GVMIED-SLNSE-KLEDYANTLYELRKSKGMTIEAARETIKD-PLYYGVMMVKKGEAD 117 GV IE ++N + + +DY + L + +G+T A+ ++ P +MV++GEAD Sbjct: 491 RPGVDIEICNINFDPRFDDYWRHYHRLMERRGVTPSMAKAVVRSRPTAIAALMVERGEAD 550 Query: 118 GMVAGAVNSTANTLRPALQILKTAPGTKLVSSFFVMVVPNCEYGHNGTFVYADCGLVENP 177 M+ G V LR I+ G S+ + GTF Y D + ++P Sbjct: 551 AMICGLVGQYQGKLRYIRDIIGLDAGVVEPSAMAAVSTDK------GTFFYLDTHVQDDP 604 Query: 178 DADQLSEIAISASKSFEMLVGAKPQVAMLSYSSYGSAKSELTEKVIKATQLAKEKAPHLA 237 +Q++E + AS + L G P++A+LS ++GS + +K+ KA +L + +AP L Sbjct: 605 CPEQIAEATLQASIRLK-LFGIVPKIALLSGGNFGSRDTCGAKKMRKALELIRARAPRLE 663 Query: 238 IDGELQVDAAIVPEVAKSKAKGSSVAGKANVLIFPDLDAGNIAYKLTQRLAKAEAYGPIT 297 ++GE+Q DAA+VP + + S + GKANV +FP+LDA NIAY +T+ L+ GPI Sbjct: 664 VEGEMQADAALVPALREKLFPHSRLEGKANVFVFPNLDAANIAYNMTRMLSDGVVIGPIL 723 Query: 298 QGLARPVNDLSRGCSAEDIVGVAAITAVQAQ 328 G+A+P + L + +V ++A+ V+AQ Sbjct: 724 MGVAKPAHILMPQSTVRRVVNMSAVACVEAQ 754 Lambda K H 0.313 0.129 0.346 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: 517 Number of extensions: 21 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: 332 Length of database: 763 Length adjustment: 34 Effective length of query: 298 Effective length of database: 729 Effective search space: 217242 Effective search space used: 217242 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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