Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_041100369.1 SUTH_RS14935 NADP-dependent malic enzyme
Query= SwissProt::P77844 (329 letters) >NCBI__GCF_000828635.1:WP_041100369.1 Length = 760 Score = 165 bits (417), Expect = 4e-45 Identities = 106/320 (33%), Positives = 173/320 (54%), Gaps = 11/320 (3%) Query: 14 ARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERATELGLHLNTA---Y 70 A+ + + +V EG+D+R+L AA + D+ + ++G P +++R GL + Sbjct: 436 AKKKPARVVFAEGEDERVLRAAQAVCDEGLARPILIGRPEVVEQRIARYGLRIRPGDHFE 495 Query: 71 LVNPLTDPRLEEFAEQFAELRKSKSVTIDEA-REIMKDISYFGTMMVHNGDADGMVSGAA 129 LVNP +DPR +E + + EL K V I+ A RE+ + + G M+V + AD ++ G Sbjct: 496 LVNPDSDPRYKELWQDYYELTCRKGVGIEYAKREMRRRTTLIGAMLVRHNYADALLCGTF 555 Query: 130 NTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTAEQLGEIAVVSA 189 + ++ +I P ++ L++L R GD VN +P+AEQ+ E A + A Sbjct: 556 GKHSLHLRYIADVIGLKPGIENFYAMNLLILPKRTLFIGDTYVNYDPSAEQIAEFARLGA 615 Query: 190 KTAAQFGIDPRVAILSYSTGNSGGGSDVDRAID---ALAEARRLNPELCVDGPLQFDAAV 246 + +FG+ PR A+LS+S + G D +I AL R + PEL VDG + D A+ Sbjct: 616 EEVRRFGLAPRAALLSHS---NFGAEDTPTSIKMRRALEILREVAPELEVDGEMHGDTAL 672 Query: 247 DPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRT-GHALAVGPILQGLNKPVNDL 305 + R+ P+S + GQAN+ I P L+A NI + + + G L VGP+L G +PV+ L Sbjct: 673 SDDIRRQVFPNSTLKGQANLLIMPTLDAANIAFNLIKTSAGDGLTVGPMLLGAARPVHIL 732 Query: 306 SRGATVPDIVNTVAITAIQA 325 + ATV IVN A+ +++A Sbjct: 733 TPTATVRRIVNVTALLSVEA 752 Lambda K H 0.318 0.134 0.386 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: 583 Number of extensions: 24 Number of successful extensions: 5 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: 329 Length of database: 760 Length adjustment: 34 Effective length of query: 295 Effective length of database: 726 Effective search space: 214170 Effective search space used: 214170 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 (21.7 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