Align glycine C-acetyltransferase (EC 2.3.1.29) (characterized)
to candidate 5209242 Shew_1720 8-amino-7-oxononanoate synthase (RefSeq)
Query= BRENDA::P0AB77 (398 letters) >FitnessBrowser__PV4:5209242 Length = 382 Score = 194 bits (494), Expect = 3e-54 Identities = 127/384 (33%), Positives = 199/384 (51%), Gaps = 12/384 (3%) Query: 7 QQLTNDLETARAEGLFKEERIIT-SAQQADITVADGSHVINFCANNYLGLANHPDLIAAA 65 Q++ + ++ A GL + +++T S A+ V GS NF +N+YLGL+ P+LI A Sbjct: 6 QKIDDKMQRAEQSGLLRRRQLLTQSVGSANRLVHQGSIKHNFASNDYLGLSQSPELIEAL 65 Query: 66 KAGMDSHGFGMASVRFICGTQDSHKELEQKLAAFLGMEDAILYSSCFDANGGLFETLLGA 125 G +G G + + G D+H LEQ L G E A+L+SS F AN L +TLL Sbjct: 66 GEGARLYGVGSGASPLVTGYSDAHAALEQALCEATGHEAALLFSSGFSANSALMKTLLDK 125 Query: 126 EDAIISDALNHASIIDGVRLCKAKRYRYANNDMQELEARLKEAREAGARHVLIATDGVFS 185 E +++D L HAS+IDG+ A+ R+A+ND+ + RL + + + + T+ VFS Sbjct: 126 ESVVVADKLIHASLIDGLLESGAQLKRFAHNDLGAAK-RLVDKHQP----LTVVTESVFS 180 Query: 186 MDGVIANLKGVCDLADKYDALVMVDDSHAVGFVGENGRGSHEYCDVMGRVDIITGTLGKA 245 MDG +A + + +L DA ++VDD+H G + G H D DI T GKA Sbjct: 181 MDGDLAPIDELYELTQANDAWLIVDDAHGFGVL---PLGGHNKVDA-SCCDIQIVTFGKA 236 Query: 246 LGGASGGYTAARKEVVEWLRQRSRPYLFSNSLAPAIVAASIKVLEMVEAGSELRDRLWAN 305 L G G +++L +R Y++S +L+PA ++K + +++ G E RDRL Sbjct: 237 L-GCQGAAILGSNTCIDFLVAHARDYIYSTALSPASAHVALKAVNLIKNG-ECRDRLAQV 294 Query: 306 ARQFREQMSAAGFTLAGADHAIIPVMLGDAVVAQKFARELQKEGIYVTGFFYPVVPKGQA 365 F+ A G L G+ I P+++GD K REL+ G +V P VP+G A Sbjct: 295 IEAFKLAAKARGLRLLGSHTPIQPLVVGDIDKLAKVNRELKTAGFWVGAIRPPTVPQGSA 354 Query: 366 RIRTQMSAAHTPEQITRAVEAFTR 389 R+R ++ HT ++ + R Sbjct: 355 RLRITLNVNHTQAELEALADQLQR 378 Lambda K H 0.320 0.135 0.388 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: 333 Number of extensions: 21 Number of successful extensions: 4 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: 398 Length of database: 382 Length adjustment: 30 Effective length of query: 368 Effective length of database: 352 Effective search space: 129536 Effective search space used: 129536 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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