Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate Echvi_4081 Echvi_4081 Malic enzyme
Query= curated2:Q9ZKU4 (519 letters) >FitnessBrowser__Cola:Echvi_4081 Length = 757 Score = 207 bits (527), Expect = 1e-57 Identities = 119/318 (37%), Positives = 188/318 (59%), Gaps = 2/318 (0%) Query: 204 KAKKQIKKVVLPESEDERILKAAHRLNLMGAVGLILLGDKEAINSQAKNLNLNLENVEII 263 +AKK K+VV E+++ +ILKAA +N ILLG++E I + +L+L NV II Sbjct: 437 RAKKHPKRVVFAEADNTKILKAAQLINDERICDPILLGNRETILKLIEEHSLDLSNVPII 496 Query: 264 NPNTSHYR-EEFAKSLYELRKSKGLSEQEAERLALDKTYFATMLVHLGYAHAMVSGVNHT 322 +P R E+F LY R+ KGL+ EA++L D+TYF M+V G A A++SG+ Sbjct: 497 DPYEEPERLEKFGNLLYNKRQRKGLTPFEAQKLMRDRTYFGAMMVETGEADALISGLTKD 556 Query: 323 TAETIRPALQIIKTKPGVSLVSSVFLMCLDTQVFVFGDCAIIPNPSPKELAEIATTSAQT 382 +TI PAL +I K V V+ +++M D + F D + +P+ ++ EI +A Sbjct: 557 YPKTILPALHVIGVKKDVDRVAGMYIMNSDKGPYFFADTTVNVDPTADQIVEIIGLTADA 616 Query: 383 AKQFNIAPKVALLSYATGNSAQGEMIDKINEALTIVQKLDPQLEIDGPLQFDASIDKGVA 442 K F++ PKVA+LSY+ SA+G K A ++ P L I+G +Q + +I++ + Sbjct: 617 VKFFDLEPKVAVLSYSNFGSAKGNTPTKTALATAKAKEKFPDLIIEGEMQANVAINEAIQ 676 Query: 443 KKKMPNSQVAG-QASVFIFPDLNAGNIAYKAVQRSAKAVAIGPILQGLNKPINDLSRGAL 501 K+ P S +A +A+ IFP+L++GNIAYK + A AIGP+L G+NKP++ L G+ Sbjct: 677 KENYPFSALANKKANTLIFPNLSSGNIAYKLLAEIGNAEAIGPVLLGMNKPVHILQLGSS 736 Query: 502 VEDIVNTVLISAIQAQDY 519 + +I+N V I+ + AQ + Sbjct: 737 IREIINMVAIAVVDAQSH 754 Lambda K H 0.316 0.132 0.364 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: 729 Number of extensions: 36 Number of successful extensions: 3 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: 519 Length of database: 757 Length adjustment: 38 Effective length of query: 481 Effective length of database: 719 Effective search space: 345839 Effective search space used: 345839 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: 54 (25.4 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