Align glycine C-acetyltransferase (EC 2.3.1.29) (characterized)
to candidate 208061 DVU2564 8-amino-7-oxononanoate synthase
Query= BRENDA::P0AB77 (398 letters) >MicrobesOnline__882:208061 Length = 424 Score = 150 bits (378), Expect = 9e-41 Identities = 118/419 (28%), Positives = 180/419 (42%), Gaps = 38/419 (9%) Query: 1 MRGEFYQQLTNDLETARAEGLFKEERIIT-SAQQADITVADGSHVINFCANNYLGLANHP 59 M F +LT L+ RA GL + ++T + + DG + NF +N+YLGLA+ Sbjct: 1 MAHPFLHRLTLRLDAQRAAGL--DRTVMTPETRTTRHVILDGQRLCNFASNDYLGLADDA 58 Query: 60 DLIAAAKAGMDSHGFGMASVRFICGTQDSHKELEQKLAAFLGMEDAILYSSCFDANGGLF 119 A H + R G E E A G E + S + AN + Sbjct: 59 AWRAEVADCFARHPASGTASRLAAGHSALVAEAEAAWAEHFGYESCLFLPSGYQANLAVV 118 Query: 120 ETLLGAEDAIISDALNHASIIDGVRLCKAKRYRYANNDMQELEARLKEAREA-------- 171 LL D + D HAS+ V LC A Y + D+ L+ RL R Sbjct: 119 TGLLHTGDTLFIDRRIHASMARAVPLCGAHPVTYPHGDLARLDRRLTAWRHETTAETASA 178 Query: 172 ------------------------GARHVLIATDGVFSMDGVIANLKGVCDLADKYDALV 207 G +I T+ +FSMDG + ++ + L ++ A V Sbjct: 179 APLTEGAPLSSPPATCPTASPPPHGDASPVILTESLFSMDGTVTSMDALATLRSRHGAFV 238 Query: 208 MVDDSHAVGFVGENGRG-SHEYCDVMGRVDIITGTLGKALGGASGGYTAARKEVVEWLRQ 266 ++D++HA G +G+ GRG + + D+I GTLGK G G + + V E L Sbjct: 239 ILDEAHACGALGQGGRGLAWGQTENAPAADVIVGTLGKG-PGFFGAFVLMPRIVRESLEN 297 Query: 267 RSRPYLFSNSLAPAIVAASIKVLEMVEAGSELRDRLWANARQFREQMSAAGFTLAGADHA 326 + + S +L A AA +++L + + R RL NAR RE ++ G + G H Sbjct: 298 FASAVMHSTALPEAHAAAVLRLLPRMAGMDDARARLARNARALREGLAGCGLPVHGDAH- 356 Query: 327 IIPVMLGDAVVAQKFARELQKEGIYVTGFFYPVVPKGQARIRTQMSAAHTPEQITRAVE 385 I+ + GD A + AR L+ +G+ +P VP G A +R ++AAHT + IT E Sbjct: 357 ILCIETGDEAQATQLARRLRTQGVLALSARHPTVPHGHAIVRFSVTAAHTDDDITYCKE 415 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: 373 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 398 Length of database: 424 Length adjustment: 31 Effective length of query: 367 Effective length of database: 393 Effective search space: 144231 Effective search space used: 144231 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