Align 4-hydroxy-2-oxovalerate aldolase; HOA; EC 4.1.3.39; 4-hydroxy-2-keto-pentanoic acid aldolase; 4-hydroxy-2-oxopentanoate aldolase (uncharacterized)
to candidate 14220 b0074 2-isopropylmalate synthase (NCBI)
Query= curated2:A5D523 (339 letters) >FitnessBrowser__Keio:14220 Length = 523 Score = 95.5 bits (236), Expect = 3e-24 Identities = 79/264 (29%), Positives = 130/264 (49%), Gaps = 44/264 (16%) Query: 6 EIRIMDTTLRDGMHAMAHQFTPEQMAQVAAALDEAGVDVIEVTHGDGLAGSSFQYGFAAA 65 ++ I DTTLRDG A+ + ++ Q+A AL+ GVDV+EV GF + Sbjct: 4 QVIIFDTTLRDGEQALQASLSVKEKLQIALALERMGVDVMEV-------------GFPVS 50 Query: 66 T--DEEYLEAVAPVLKKAKLAALILPGIGTC--RDMRMAVQA--GVKVFRIATHVTEA-- 117 + D E ++ +A +K +++ AL C +D+ +A ++ + FRI T + + Sbjct: 51 SPGDFESVQTIARQVKNSRVCAL-----ARCVEKDIDVAAESLKVAEAFRIHTFIATSPM 105 Query: 118 -----------DISEEHMGLAKEMGAEVVGFLMMSHTVGKEKIAEQAKLMESY---GADV 163 ++ E + + K G+ IA+ A+++E+ GA Sbjct: 106 HIATKLRSTLDEVIERAIYMVKRARNYTDDVEFSCEDAGRTPIADLARVVEAAINAGATT 165 Query: 164 VYMVDSAGAMIPPEVTEKI-GYLKEVLNIP---VGFHAHNNLGLAVGNTLAAVAAGATAV 219 + + D+ G +P E I G + V NI + H H++LGLAVGN+LAAV AGA V Sbjct: 166 INIPDTVGYTMPFEFAGIISGLYERVPNIDKAIISVHTHDDLGLAVGNSLAAVHAGARQV 225 Query: 220 DGTLRGLGAGAGNTSTEVLVAALK 243 +G + G+G AGN S E ++ A+K Sbjct: 226 EGAMNGIGERAGNCSLEEVIMAIK 249 Lambda K H 0.319 0.134 0.373 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: 325 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: 339 Length of database: 523 Length adjustment: 32 Effective length of query: 307 Effective length of database: 491 Effective search space: 150737 Effective search space used: 150737 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