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 AZOBR_RS31105 AZOBR_RS31105 8-amino-7-oxononanoate synthase
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__azobra:AZOBR_RS31105 Length = 393 Score = 251 bits (640), Expect = 3e-71 Identities = 151/382 (39%), Positives = 214/382 (56%), Gaps = 13/382 (3%) Query: 10 REELERLKREGLYISPKVLEAPQEPVTRVE--GREVVNLASNNYLGFANHPYLKEKARQY 67 R+ L+RL R + +L E R+ GR ++N +SN+YLG A+HP L E+A + Sbjct: 9 RQHLDRLDRR--HTRRTLLPVRPEGAGRIRRGGRTLLNFSSNDYLGLASHPLLVERAGDW 66 Query: 68 LEKWGAGSGAVRTIAGTFTYHVELEEALARFKGTESALVLQSGFTANQGVLGALLKEGDV 127 +WGAG+ A R + GT H E+E LAR KGTE+AL+ SG+ AN VL AL + Sbjct: 67 TRRWGAGATASRLVCGTLELHAEVEAKLARLKGTEAALLFNSGWQANAAVLPALFDRELL 126 Query: 128 -----VFSDELNHASIIDGLRLTKATRLVFRHADVAHLEELLKAHDTD-GLKLIVTDGVF 181 VF+D LNHAS+ G ++ FRH D+ HLE LL + G++ IVT+ VF Sbjct: 127 GVEAQVFTDRLNHASLHHGCAAAGVRQIRFRHNDLDHLETLLSQRTGEPGMRFIVTESVF 186 Query: 182 SMDGDIAPLDKIVPLAKKYKAVVYVDDAHGSGVLGEKGKGTVHHFGFHQDPDVVQVATLS 241 SMDGD A + + LA+++ A +++D+AH +GVLG +G G G D + + T S Sbjct: 187 SMDGDRADVPALAALAERHGAFLFLDEAHATGVLGPRGMGLAALGGGRVD---LAMGTFS 243 Query: 242 KAWAGIGGYAAGARELKDLLINKARPFLFSTSHPPAVVGALLGALELIEKEPERVERLWE 301 KA G G Y AG+REL D L+N+ +++T+ PPAV+GA+ AL+L+ K RL Sbjct: 244 KALGGFGAYVAGSRELCDYLVNRCGGLIYATALPPAVLGAMDAALDLVPKLDAERARLQA 303 Query: 302 NTRYFKRELARLGYDTLGSQTPITPVLFGEAPLAFEASRLLLEEGVFAVGIGFPTVPRGK 361 + L LG T GS T I P + G A R L E G+ + I PTVP G Sbjct: 304 MAERLRTALHGLGVATAGSSTQIVPAITGAEEDALALGRRLEERGILGIAIRPPTVPPGT 363 Query: 362 ARIRNIVTAAHTKEMLDKALEA 383 +R+R ++AAHT L+ + A Sbjct: 364 SRLRFALSAAHTDADLETLVSA 385 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: 324 Number of extensions: 17 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: 395 Length of database: 393 Length adjustment: 31 Effective length of query: 364 Effective length of database: 362 Effective search space: 131768 Effective search space used: 131768 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