Align 4-hydroxy-2-oxovalerate aldolase 2; HOA 2; EC 4.1.3.39; 4-hydroxy-2-keto-pentanoic acid aldolase 2; 4-hydroxy-2-oxopentanoate aldolase 2 (uncharacterized)
to candidate AZOBR_RS05495 AZOBR_RS05495 homocitrate synthase
Query= curated2:A8M6W8 (348 letters) >FitnessBrowser__azobra:AZOBR_RS05495 Length = 381 Score = 94.4 bits (233), Expect = 4e-24 Identities = 98/342 (28%), Positives = 141/342 (41%), Gaps = 38/342 (11%) Query: 7 ICDSTLRDGNHAVAHQLGRADISAYARAAEEAGVDVLEVGHGNGLGASSIQVGIAAVSDA 66 I D+TLRDG + A ARA +EAGV LE+G + + Sbjct: 9 INDTTLRDGEQTAGVAFTLDEKIAIARALDEAGVPELEIG-----------IPAMGPEER 57 Query: 67 EMLRAAKAELRNSRLGVLSIPGFASVERDLKPALDCGVDEVRVGAHCTEADVTRQ----- 121 E +RA A +RL V + DLK ALDC V V + ++ +T++ Sbjct: 58 EGIRAVAALGLKARLMVWC----RMHDTDLKAALDCKVGTVNLSMPVSDIHITKKLKRSR 113 Query: 122 ---------QITMLRSMGVRVKGLLLMSHMASAGKLVEQAGLMQEYGAEAVVLMDSAGAY 172 ++ R G+ V S A L+ A + QE GA D+ G Sbjct: 114 AWALAEIERKVKTARDHGLEVSLGGEDSSRADMDFLIAAATVAQEAGARRFRFADTLGVL 173 Query: 173 TPEMVREKVGELVEKLDIAIGFHAHNNLGLSVINSITAVRAGASIVDVTARGFGAGAGNA 232 P R + L D+ I HAH++LGL+ NS+ AV GA+ V+ T G G AGNA Sbjct: 174 DPFQTRACIERLRRATDLEIEIHAHDDLGLANANSLAAVLGGATHVNTTVNGLGERAGNA 233 Query: 233 PIELVAANLHV---EQIEARIKLFDAL-DAADTAEERFVKHVPTNDGVTIASGIAGVFSG 288 P+E V +L V + + A+ D + A R V + G + + AG+ Sbjct: 234 PLEEVVVSLKVLYGQDCGVDTRALGAISDLVERASNRPVAVNKSIVGDAVFTHEAGIHVD 293 Query: 289 FAAPVRRASRRFGVDPREILLELGRRRVVAGQEDTIIEVAMA 330 R + F DP E+ E R+V G+ V MA Sbjct: 294 GLLRDRATYQNF--DPAEVGRE---HRIVLGKHSGTAGVKMA 330 Lambda K H 0.319 0.133 0.366 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: 313 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: 348 Length of database: 381 Length adjustment: 29 Effective length of query: 319 Effective length of database: 352 Effective search space: 112288 Effective search space used: 112288 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: 49 (23.5 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