Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase; Vegetative protein 43; VEG43 (uncharacterized)
to candidate WP_023433704.1 N177_RS17335 NADP-dependent malic enzyme
Query= curated2:P39646 (323 letters) >NCBI__GCF_000496075.1:WP_023433704.1 Length = 761 Score = 171 bits (432), Expect = 7e-47 Identities = 105/327 (32%), Positives = 170/327 (51%), Gaps = 9/327 (2%) Query: 1 MADLFSTVQEKVAGKDVKIVFPEGLDERILEAVSKLAGNKVLNPIVIGNENEIQAKAKEL 60 M ++FST K A K +I+F EG DERIL AV ++ K+ PI++G + I+ + K Sbjct: 434 MKEIFSTA--KAAPK--RIIFAEGEDERILRAVQVVSEEKLAQPILVGRPSVIETRLKRY 489 Query: 61 NLTLG---GVKIYDPHTYEGMEDLVQAFVER--RKGKATEEQARKALLDENYFGTMLVYK 115 LT+ +I +P D V+ F++R RKG + + VY+ Sbjct: 490 GLTIRPGIDFEIVNPEDDPRYRDYVETFLDRTCRKGVTPDLARTLVRTSTTVIAAISVYR 549 Query: 116 GLADGLVSGAAHSTADTVRPALQIIKTKEGVKKTSGVFIMARGEEQYVFADCAINIAPDS 175 G AD ++ G +R II +EG++ S + ++ Y AD + P S Sbjct: 550 GEADAMICGVEGRFDSHLRWVRNIIGLREGIRDFSALSLLILPRGAYFLADTFVTHDPGS 609 Query: 176 QDLAEIAIESANTAKMFDIEPRVAMLSFSTKGSAKSDETEKVADAVKIAKEKAPELTLDG 235 DLA++A +A + F + P++A+LS S+ GS+ S+ +K+ AV+I + APEL ++G Sbjct: 610 ADLADMARSAAEHVRRFGLTPKIALLSHSSFGSSDSESAQKMRSAVQILRRMAPELEVEG 669 Query: 236 EFQFDAAFVPSVAEKKAPDSEIKGDANVFVFPSLEAGNIGYKIAQRLGNFEAVGPILQGL 295 E DAA + + P S + G+ANV + P+L+A NI Y++ + L + VGPIL G Sbjct: 670 EMHGDAALDEVLRNRIFPRSRLTGEANVLILPNLDAANIAYELLKSLADALPVGPILIGA 729 Query: 296 NMPVNDLSRGCNAEDVYNLALITAAQA 322 N P + L+ A + N+ + A+A Sbjct: 730 NKPAHILTPSVTARGIVNMTAVAVAEA 756 Lambda K H 0.314 0.132 0.359 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: 489 Number of extensions: 27 Number of successful extensions: 2 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: 323 Length of database: 761 Length adjustment: 34 Effective length of query: 289 Effective length of database: 727 Effective search space: 210103 Effective search space used: 210103 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