Align 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase; AONS/AKB ligase; 7-keto-8-amino-pelargonic acid synthase; 7-KAP synthase; KAPA synthase; 8-amino-7-ketopelargonate synthase; Alpha-oxoamine synthase; Glycine acetyltransferase; EC 2.3.1.29; EC 2.3.1.47 (characterized)
to candidate GFF2541 HP15_2485 8-amino-7-oxononanoate synthase
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__Marino:GFF2541 Length = 391 Score = 280 bits (716), Expect = 5e-80 Identities = 156/372 (41%), Positives = 222/372 (59%), Gaps = 2/372 (0%) Query: 12 ELERLKREGLYISPKVLEAPQEPVTRVEGREVVNLASNNYLGFANHPYLKEKARQYLEKW 71 ELE K+ GLY + + + PQ P +G+ +++ SN+YLG AN+P E R L + Sbjct: 7 ELEERKQAGLYRTRRHVAGPQRPSLIADGKPLLSFCSNDYLGLANNPANIEALRDALSET 66 Query: 72 GAGSGAVRTIAGTFTYHVELEEALARFKGTESALVLQSGFTANQGVLGALLKEGDVVFSD 131 G G A I G H +LE LA F G SAL +G+ AN GV+ AL GD +FSD Sbjct: 67 GLGGAASHLICGHHDAHHQLELRLAEFTGRSSALFFSTGYMANMGVISALAGRGDTIFSD 126 Query: 132 ELNHASIIDGLRLTKATRLVFRHADVAHLEELLKAHDTDGLKLIVTDGVFSMDGDIAPLD 191 LNHASIIDG L++A + H DVA LE +L +T G KL+VTDGVFSMDGDIAPL Sbjct: 127 RLNHASIIDGCILSRARVRRYAHGDVAALEAMLA--ETSGHKLVVTDGVFSMDGDIAPLA 184 Query: 192 KIVPLAKKYKAVVYVDDAHGSGVLGEKGKGTVHHFGFHQDPDVVQVATLSKAWAGIGGYA 251 ++ + + + ++ VDDAHG GVLG +G+G+V G ++ V + TL K G + Sbjct: 185 ELARVCRFHDTLLVVDDAHGIGVLGPEGRGSVAEAGLSEEDVPVLIGTLGKGVGTSGAFV 244 Query: 252 AGARELKDLLINKARPFLFSTSHPPAVVGALLGALELIEKEPERVERLWENTRYFKRELA 311 AG L D L+ KAR ++++T+ PPA+ A + +L+LIE++ R E + F+RE + Sbjct: 245 AGPSLLMDYLVQKARTYIYTTAMPPALAMATISSLDLIERDQGRREHVLGLVSRFRREAS 304 Query: 312 RLGYDTLGSQTPITPVLFGEAPLAFEASRLLLEEGVFAVGIGFPTVPRGKARIRNIVTAA 371 +GY+ + S+TPI P++ G+ A S+ L E G+ I PTVP G+AR+R +AA Sbjct: 305 AMGYELMPSRTPIQPIMVGDNHDALALSQALEERGLLVSAIRPPTVPAGEARLRVTFSAA 364 Query: 372 HTKEMLDKALEA 383 H++ LD L A Sbjct: 365 HSQANLDCLLTA 376 Lambda K H 0.319 0.137 0.394 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: 13 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: 395 Length of database: 391 Length adjustment: 31 Effective length of query: 364 Effective length of database: 360 Effective search space: 131040 Effective search space used: 131040 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 (21.7 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