Align Homocitrate synthase; EC 2.3.3.14 (uncharacterized)
to candidate PfGW456L13_2506 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39)
Query= curated2:Q01181 (391 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2506 Length = 344 Score = 82.0 bits (201), Expect = 2e-20 Identities = 87/285 (30%), Positives = 125/285 (43%), Gaps = 37/285 (12%) Query: 19 VALCDTTLRDGEQTAGVAFTRAEKRAIAEALQAAGVAEVEV-------------GVPAMG 65 V L D +LRDG + + ++A L AAGV +E+ G PA Sbjct: 8 VRLHDMSLRDGMHAKQHQISIEQMVSVATGLDAAGVPLIEITHGDGLGGASLNYGFPAHS 67 Query: 66 EEERADIRAVAAVLKTA---APVVWCRLRAEDLAAAQRTGVVRLHIGVPVSERQISAK-L 121 +EE AV +K A A ++ + L A GV + + +E +S + + Sbjct: 68 DEEY--FSAVIPKMKQAKVSALLLPGIGTLDHLKMAHEHGVSTIRVATHCTEADVSGQHI 125 Query: 122 GKDAAWVRDKVEKLVRAASWAGHKVSVGAEDASRADPFFLAEIAHVAAEAGAIRFRISDT 181 G A D V L+ A H VS P L E A + GA +D+ Sbjct: 126 GMSAKMGLDTVGFLMMA-----HMVS----------PEKLLEQARLMESYGANCIYCTDS 170 Query: 182 LGVLDPFAAHELVG--RVVTRCPLPVEFHGHNDLGMATANSLAAARAGASHLSVTVNGLG 239 G + P + +G R V FHGH+++GMA ANSLAA AGA+ + +V GLG Sbjct: 171 AGYMLPDEVTQKIGALRAGLNAGTEVGFHGHHNMGMAIANSLAAIEAGAARIDGSVAGLG 230 Query: 240 ERAGNAALEEVAAALEAAGRATGVALGQLCALSE-LVARASGRPL 283 AGN LE A LE G +GV L ++ ++E LV +P+ Sbjct: 231 AGAGNTPLEVFVAVLERMGVNSGVDLYKIMDVAEDLVVPMMDQPI 275 Lambda K H 0.318 0.130 0.371 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: 189 Number of extensions: 5 Number of successful extensions: 1 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: 391 Length of database: 344 Length adjustment: 30 Effective length of query: 361 Effective length of database: 314 Effective search space: 113354 Effective search space used: 113354 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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