Align Homocitrate synthase; HCS; EC 2.3.3.14 (uncharacterized)
to candidate AO353_24260 AO353_24260 hypothetical protein
Query= curated2:O59390 (361 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24260 Length = 309 Score = 213 bits (541), Expect = 7e-60 Identities = 115/297 (38%), Positives = 171/297 (57%), Gaps = 2/297 (0%) Query: 2 ILDSTLREGEQTPGVNYSPEQRLRIALALDEIGVDFIEVGHPAVSKDVFIGIKLIASQDL 61 ++DSTLREG Q PGV + + L IA AL + G+DFIE GHP SK F + + + Sbjct: 6 LVDSTLREGNQAPGVKLTTKSTLTIAYALADAGIDFIEAGHPYASKQEFDRVTALVKSKI 65 Query: 62 NANLLAHSRALLEDIDYVIQADVEWVGIFFCLSNACLRKRFRMSLSQALERISKAIEYAK 121 N+LAHSRA +DID V W+GIF ++ + R R S +Q + I +++ YAK Sbjct: 66 AKNILAHSRAHQDDIDAVAATGANWIGIFAGINETSQKYRIRKSKAQIQDLIKRSVLYAK 125 Query: 122 DHGLKVRFTPEDTTRTEWENLRRAIELAKELKVDRISVADTTGGTHPLRFYTLVKKVVN- 180 GLKVR+T ED +RT ++L ++AK DRI AD+ G P + +K + Sbjct: 126 SLGLKVRYTIEDASRTPSDDLIETFKIAKAAGADRICYADSLGVCDPFKVQATIKLIRQS 185 Query: 181 -FGIPVNVHCHNDLGLALANAIMGIEGGATVVDATVNGLGERAGIVDLAQIVTVLYYHYG 239 I + VH H+D GLA+AN + IE GAT + TVNG+GER GI + ++T L+++ Sbjct: 186 LSDIDLEVHFHDDRGLAMANTLASIEAGATFISCTVNGIGERCGITETCLLITNLHFNSI 245 Query: 240 VKKYRLDKLYEISRMVSEITGIALQPNYPIVGENAFTHKAGLHVSAVLKDPRFYEFL 296 + + K+ ++S +VS+ G A PI+GE +F H A LHV+A ++ Y ++ Sbjct: 246 LCSGKASKVLKLSSIVSKELGDAFDRRRPIIGEYSFVHTAKLHVTANSRNKNCYHWI 302 Lambda K H 0.322 0.139 0.405 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: 248 Number of extensions: 12 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: 361 Length of database: 309 Length adjustment: 28 Effective length of query: 333 Effective length of database: 281 Effective search space: 93573 Effective search space used: 93573 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 (21.9 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