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 HSERO_RS14210 HSERO_RS14210 homocitrate synthase
Query= curated2:Q764S0 (337 letters) >FitnessBrowser__HerbieS:HSERO_RS14210 Length = 376 Score = 93.2 bits (230), Expect = 9e-24 Identities = 81/267 (30%), Positives = 124/267 (46%), Gaps = 41/267 (15%) Query: 6 IRIMDTTLRDGSHAIRHRFTKENVRQIVQALDEAGVPVIEVSHGDGLGGSSLQYGMSLVE 65 + I DTTLRDG FT E I +ALDE GVP +E+ G + G + Sbjct: 2 VTINDTTLRDGEQTAGVAFTAEEKIDIARALDEIGVPEMEI--GIPIMGQA--------- 50 Query: 66 EMELIEEAAKTSRRAKIAALLLPGIGTKKELQQAKDCGIQMVRIATQCSEADVSEQ---- 121 E+E+I+ A R+K ++ G + +L A C +V ++ S+ + + Sbjct: 51 EIEVIQAIAALPLRSKT---MVWGRMCEADLAAAARCNADIVNLSMPVSDIHIQHKLQRD 107 Query: 122 ---------HF-------GLAKELGLETVGFLMMAHMLSPEELAQQAKLMESYGADIVYI 165 HF G+ LG E + ML E AQ A GA Sbjct: 108 RDWVLAQIRHFLPKALDLGMEVCLGGEDSSRADLDFMLRVIETAQAA------GARRFRF 161 Query: 166 VDSAGTMLPQDVIDRVIALKKVLNVPIGFHAHNNLGLAIGNSLAAIQAGATNIDASTRGL 225 D+ G + P + + L++ +++ + HAHN+LGLA N+LAAI AGA++++ + GL Sbjct: 162 ADTLGLLDPFATYEVIRQLRQEVDIELEMHAHNDLGLATANTLAAINAGASHVNTTVNGL 221 Query: 226 GAGSGNTQTEVLVAVLSRM-GIETGID 251 G +GN E +V L + GIET +D Sbjct: 222 GERAGNAPLEEVVMGLRHLHGIETQVD 248 Lambda K H 0.318 0.134 0.375 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: 271 Number of extensions: 11 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: 337 Length of database: 376 Length adjustment: 29 Effective length of query: 308 Effective length of database: 347 Effective search space: 106876 Effective search space used: 106876 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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