Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase; Vegetative protein 43; VEG43 (uncharacterized)
to candidate WP_013451146.1 CALNI_RS05115 NADP-dependent malic enzyme
Query= curated2:P39646 (323 letters) >NCBI__GCF_000183405.1:WP_013451146.1 Length = 758 Score = 221 bits (563), Expect = 4e-62 Identities = 114/307 (37%), Positives = 186/307 (60%), Gaps = 2/307 (0%) Query: 18 KIVFPEGLDERILEAVSKLAGNKVLNPIVIGNENEIQAKAKELNLTLGGVKIYDPHTYEG 77 KIVFPEG E+I++A +K+ PI++G+++ I A++ N+ L G++I P + Sbjct: 446 KIVFPEGEYEKIIKAAAKIVEEGFGTPILLGDKDTILKIAEKANVNLDGIEIVCPGSSPN 505 Query: 78 MEDLVQAFVERRKGKATEEQARKALLDE--NYFGTMLVYKGLADGLVSGAAHSTADTVRP 135 ++ Q + R+ K E LL + NY+G +++ G AD LV+G + ++VRP Sbjct: 506 LDKYAQQLFKMRQRKGVTEVEAYRLLTKITNYYGALMILNGEADCLVTGYSRDYGNSVRP 565 Query: 136 ALQIIKTKEGVKKTSGVFIMARGEEQYVFADCAINIAPDSQDLAEIAIESANTAKMFDIE 195 L+ I ++ K SG + M + + AD +N+ P ++ LA+IA++SA+T + FDI+ Sbjct: 566 LLETIPFEKDYKTVSGSYFMIFKDRLLLCADTTVNLNPTAEQLAQIALQSADTVEKFDIK 625 Query: 196 PRVAMLSFSTKGSAKSDETEKVADAVKIAKEKAPELTLDGEFQFDAAFVPSVAEKKAPDS 255 P++AML+F+ GS K + + + DA+K+ K K P++ +DG+ Q D A +AE+ P S Sbjct: 626 PKIAMLNFTNFGSVKCERVKVIQDAIKLVKAKRPDIIIDGDMQADTATYAPIAEEAFPFS 685 Query: 256 EIKGDANVFVFPSLEAGNIGYKIAQRLGNFEAVGPILQGLNMPVNDLSRGCNAEDVYNLA 315 EIKGDAN+ +FP+LE+GNI YK+ R+G+ A+GPILQG V+ L RG + ++ LA Sbjct: 686 EIKGDANILIFPNLESGNIAYKLLYRVGSGTAIGPILQGFKKSVHVLQRGSDVHEIVYLA 745 Query: 316 LITAAQA 322 A Sbjct: 746 AYAVVDA 752 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: 547 Number of extensions: 28 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: 758 Length adjustment: 34 Effective length of query: 289 Effective length of database: 724 Effective search space: 209236 Effective search space used: 209236 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