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 CA265_RS20545 CA265_RS20545 2-amino-3-ketobutyrate CoA ligase
Query= SwissProt::Q5SHZ8 (395 letters) >FitnessBrowser__Pedo557:CA265_RS20545 Length = 420 Score = 247 bits (630), Expect = 5e-70 Identities = 140/352 (39%), Positives = 205/352 (58%), Gaps = 5/352 (1%) Query: 41 REVVNLASNNYLGFANHPYLKEKARQYLEKWGAGSGAVRTIAGTFTYHVELEEALARFKG 100 ++ V+L SN+YLGF H +K+ A ++K+G G+GA I G F++H LE+ +A F G Sbjct: 66 KKYVSLVSNDYLGFTQHDLVKKAAIDGIKKFGTGAGASPAIGGHFSFHEMLEQKIAAFFG 125 Query: 101 TESALVLQSGFTANQGVLGALLKEGDVVFSDELNHASIIDGLRLTKATRLVFRHADVAHL 160 E+A+ +G+TAN L LLK+ D+ D HAS+ +G T +F H ++ L Sbjct: 126 REAAITYTTGYTANSASLLCLLKKEDMAILDMAVHASVYEGCMNTNIK--MFLHNNMDAL 183 Query: 161 EELLK-AHDTDGLKLIVTDGVFSMDGDIAPLDKIVPLAKKYKAVVYVDDAHGSGVLGEKG 219 E L+ + DT +++V DGV+S DGD+APLDKI+ L Y A + VDDAHG GVLG G Sbjct: 184 ERALRESRDTHRTRIVVVDGVYSQDGDLAPLDKILELTHFYGAYLMVDDAHGIGVLGRTG 243 Query: 220 KGTVHHFGFHQDPDVVQVATLSKAWAGIGGYAAGARELKDLLINKARPFLFSTSHPPAVV 279 +G + + D++ T SK + +GGY + EL L ++R LFS + PA + Sbjct: 244 RGLIQDYDLLDKVDIIS-GTFSKTFGHVGGYVVASAELIQFLKYQSRQHLFSVTASPASM 302 Query: 280 GALLGALELIEKEPERVERLWENTRYFKRELARLGYDTLGSQTPITPVLFGEAPLAFEAS 339 A+L A++LI++EPE + LWEN YF+ L LG D + + I PV + P E Sbjct: 303 -AILKAIDLIDEEPEWQDMLWENITYFQDGLKGLGLDIGTTASGIVPVKIRDIPKTLEVG 361 Query: 340 RLLLEEGVFAVGIGFPTVPRGKARIRNIVTAAHTKEMLDKALEAYEKVGKRL 391 RLLL GV+A I +P V + +RIR + A HT+ LDK L A+ + K+L Sbjct: 362 RLLLRAGVYANPIMYPAVAKKDSRIRMSLMATHTRPQLDKVLNAFSDIAKKL 413 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: 381 Number of extensions: 22 Number of successful extensions: 3 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: 420 Length adjustment: 31 Effective length of query: 364 Effective length of database: 389 Effective search space: 141596 Effective search space used: 141596 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