Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase; Vegetative protein 43; VEG43 (uncharacterized)
to candidate WP_066602966.1 V473_RS09375 NADP-dependent malic enzyme
Query= curated2:P39646 (323 letters) >NCBI__GCF_001046645.1:WP_066602966.1 Length = 755 Score = 143 bits (361), Expect = 1e-38 Identities = 95/324 (29%), Positives = 151/324 (46%), Gaps = 6/324 (1%) Query: 4 LFSTVQEKVAGKDVKIVFPEGLDERILEAVSKLAGNKVLNPIVIGNENEIQAKAKELNLT 63 L V E G +I + EG D+R+L A+ ++ P V+ + K EL L+ Sbjct: 427 LMLPVFEAARGTGCRIAYGEGEDDRVLRAIRDALDEGIVRPTVVARRRILAQKLPELGLS 486 Query: 64 LG---GVKIYDPHT-YEGMEDLVQAF--VERRKGKATEEQARKALLDENYFGTMLVYKGL 117 V++ DP T + M +LV+A+ V R+G +E R ML+ G Sbjct: 487 FDLDRDVEVIDPETDHLVMGELVEAYRTVASRRGVPADEILRHVYRRPTITAAMLLQTGR 546 Query: 118 ADGLVSGAAHSTADTVRPALQIIKTKEGVKKTSGVFIMARGEEQYVFADCAINIAPDSQD 177 D + G V L+II G + + + D + P + Sbjct: 547 VDAALVGGRSEYWGQVEHVLRIIDRTPGHSRVYALSGLILDAGALFITDTHMVPDPTPEQ 606 Query: 178 LAEIAIESANTAKMFDIEPRVAMLSFSTKGSAKSDETEKVADAVKIAKEKAPELTLDGEF 237 +AE+ + +A + F + PR A+LS S G++ +D K+ A KI ++ APEL +DGE Sbjct: 607 IAEMTLLAATEIQHFGLTPRAALLSHSNFGASHTDSARKMRKAFKIVRDAAPELAVDGEM 666 Query: 238 QFDAAFVPSVAEKKAPDSEIKGDANVFVFPSLEAGNIGYKIAQRLGNFEAVGPILQGLNM 297 DAA ++ E+ PDS +G AN+ V P+L+A NI + VGP+L GL+ Sbjct: 667 HADAALSQALRERLIPDSRFEGPANLLVMPNLDAANITLTALSASSSSPTVGPMLMGLSK 726 Query: 298 PVNDLSRGCNAEDVYNLALITAAQ 321 P++ L+ G + + NL I AA+ Sbjct: 727 PIHVLTPGVTSRGILNLTAIAAAE 750 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: 456 Number of extensions: 19 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: 323 Length of database: 755 Length adjustment: 34 Effective length of query: 289 Effective length of database: 721 Effective search space: 208369 Effective search space used: 208369 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