Align Homocitrate synthase; EC 2.3.3.14 (uncharacterized)
to candidate WP_028585315.1 G494_RS0115910 hypothetical protein
Query= curated2:Q47884 (351 letters) >NCBI__GCF_000429965.1:WP_028585315.1 Length = 375 Score = 224 bits (571), Expect = 3e-63 Identities = 129/334 (38%), Positives = 193/334 (57%), Gaps = 11/334 (3%) Query: 24 KFCDTTLRDGEQAPGVAFTAAEKLAIAAALDAIGVHQIEAGIPA-MGVTERDVLREILAT 82 K DTTLR+GEQ PG+ F+ +K +I L +GV ++E GI + + ++L Sbjct: 6 KLIDTTLREGEQTPGLNFSLEQKKSIVDHLAQVGVAEVELGIASPLSHQLAELLAYCAGH 65 Query: 83 DPHADIVGWCRADHRDVEAAASCGLVTAHLTIPVSDLHLKSKLGRDRAWARLRVRDCVAD 142 P W R D+ AA G L+IPVSD+HL+ KL RDRAWA + + + Sbjct: 66 HPGLRTSLWARCLDADIRHAAELGGRVVSLSIPVSDIHLRHKLERDRAWACRTLAESIGL 125 Query: 143 ATDRGMRVSVGFEDASRADDAFVTDLAGELRELGVTRLRWADTVGLLDPVSAHDRLGRLV 202 A G+ V+VGFEDA+RA+ FV ++A E G R+R ADTVG+ P S L RLV Sbjct: 126 AIGLGLEVAVGFEDATRAEAGFVREMARLAEEAGAVRIRLADTVGVASPGS----LSRLV 181 Query: 203 R-----AVPGPWEIHAHDDFGLATANTIAAVQAGFTWVSTTVLGLGERAGNAPIEEVAMA 257 + +H H+DFGLA N +AA++AG W +LGLGERAG AP+E++ +A Sbjct: 182 EQVGEVTIRAELGVHTHNDFGLACGNAVAALEAGANWADGALLGLGERAGCAPLEQL-VA 240 Query: 258 LRHLLKLPVDLDTTSFRSLARLVSRAARRPLPAGKAVVGESVFAHESGIHVHGILRHPAT 317 +L+ + +SLA ++ A + + + ++GE++F+ ESG+H+ G+ + P T Sbjct: 241 YLVILRGEGGMQLKPLKSLALYLAAEAGVVIGSREPLLGEAIFSCESGLHLDGLFKEPRT 300 Query: 318 YEPFDPAEVGGRRRLAIGKHSGRASVRYALEQYG 351 YEP+ P +G +RRL IG SG+A++ + LE+ G Sbjct: 301 YEPYPPERIGSKRRLLIGAKSGKAALGHQLERLG 334 Lambda K H 0.321 0.135 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: 399 Number of extensions: 26 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: 351 Length of database: 375 Length adjustment: 29 Effective length of query: 322 Effective length of database: 346 Effective search space: 111412 Effective search space used: 111412 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 10 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