Align Homocitrate synthase AksA; EC 2.3.3.14; (R)-homo(2)citrate synthase; EC 2.3.3.-; (R)-homo(3)citrate synthase; EC 2.3.3.- (uncharacterized)
to candidate YP_425786.1 Rru_A0695 alpha-isopropylmalate/homocitrate synthase family transferase
Query= curated2:Q8TW28 (397 letters) >NCBI__GCF_000013085.1:YP_425786.1 Length = 533 Score = 177 bits (449), Expect = 6e-49 Identities = 127/362 (35%), Positives = 185/362 (51%), Gaps = 18/362 (4%) Query: 19 VIVYDTTLRDGEQTPGVSFTPEQKLEIAHLLDELGVQQIEAGFPVVSEGERDAVRRIAHE 78 V +YD+TLRDG QT GV F+ K IA LD LG+ +E G+P + + DA+ Sbjct: 6 VYLYDSTLRDGAQTQGVDFSATDKAAIARELDALGIDYVEGGWPGANPTD-DALFANPPV 64 Query: 79 GLNADILCLARTLRGDVDA-------ALDCDVDGVITFIA-TSELHLKHKLRMSREEVLE 130 A + T R A AL C V+T + T + + + + +E + Sbjct: 65 LRRARLSAFGMTRRSGRSAENDPSLQALFCPGVRVVTMVGKTWDFQCEVAIGVPLDENRK 124 Query: 131 RIADTVEYAKDHGLWVAFSAE---DGTRTEFEFLERVYRTAEECGADRVHATDTVGVMIP 187 IAD++ +A F AE DG ++ ++ R A E GA V DT G +P Sbjct: 125 MIADSIAHAAARVEEAVFDAEHFFDGYKSNPDYALSCVRAAYEAGARWVVLCDTNGGTLP 184 Query: 188 AAMRLFVAKIREVVDLP-IGVHCHDDFGMAVANSLAAVEAGAQAISTTVNGIGERAGNAA 246 + V + V+ +G+HCH+D AVANSLAAV AGA+ + T+NG+GER GNA Sbjct: 185 HQIEAIVGAVAAVIPGDHLGIHCHNDTENAVANSLAAVRAGARQVQGTLNGLGERCGNAN 244 Query: 247 LEEVIMALKELYGIDPGFNTEVLAEL---SRKVSEYSGIDVPPNKAVVGENAFRHESGIH 303 L +I L G + G + L L SR + E N A VG++AF H+ G+H Sbjct: 245 LVSIIPNLMLKMGFETGVSEHDLRHLTHVSRMLDERLNRAPNRNAAFVGDSAFAHKGGLH 304 Query: 304 VAAVLEEPRTYEPIDPKEVGMNRKIVLGKHTGRKAVVAKLEELGVE--PEEEIVEEVLKR 361 V+AV +PR YE I P+ VG R+I++ +GR V+A+ E+G+E P E V ++L Sbjct: 305 VSAVERDPRCYEHIAPETVGNARQILVSNQSGRSNVIARFREIGLEIDPGEPKVNDLLDA 364 Query: 362 IK 363 +K Sbjct: 365 VK 366 Lambda K H 0.317 0.135 0.380 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: 491 Number of extensions: 24 Number of successful extensions: 3 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: 397 Length of database: 533 Length adjustment: 33 Effective length of query: 364 Effective length of database: 500 Effective search space: 182000 Effective search space used: 182000 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 (21.6 bits) S2: 51 (24.3 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