Align Homocitrate synthase; EC 2.3.3.14 (uncharacterized)
to candidate WP_019894518.1 A377_RS0102335 2-isopropylmalate synthase
Query= curated2:P05345 (381 letters) >NCBI__GCF_000384235.1:WP_019894518.1 Length = 545 Score = 54.3 bits (129), Expect = 8e-12 Identities = 84/349 (24%), Positives = 132/349 (37%), Gaps = 46/349 (13%) Query: 11 LRDGEQSPGVAFRTSEKVAIAEALYAAGITAMEVGTPAMGDEEIARIQLVRRQLPDATL- 69 LRDG Q+ +K+ + + L G +E+G P+ E + RR + D + Sbjct: 36 LRDGNQALATPMSVEQKLQLWQVLVEMGFKTIEIGFPSASQPEF---EFTRRLIDDGLIP 92 Query: 70 -------MTWCRMNALEIRQSADLGIDWVDISIPAS------DKLRQYKLREPLAVLLER 116 + R + +E A G+ + + + +++ + E L + ++ Sbjct: 93 EDVNVQVLVQAREHLIEKTFEALKGVKRAVVHVYNTTSTIQRERVFEKSQSEILGMAVQG 152 Query: 117 LAMFIHLAH-------TLGLKVCIGCEDASRASGQTLRAIAEVAQNAPAAR--LRYADTV 167 H A T + + + +A+ +V Q P R L TV Sbjct: 153 AQWVRHYAAQHPDTDWTFQYSPESFSQTETDYALDVCKAVMDVWQPTPEHRCILNLPATV 212 Query: 168 GLLDPFTTAAQISAL------RDVWSGEIEMHAHNDLGMATANTLAAVSAGATSVNTTVL 221 P A QI RD S I +H HND G A A A+ AGA V T+L Sbjct: 213 ESTSPNRFADQIEYFIRHLPNRD--SAIISVHTHNDRGCAVAAAELALLAGADRVEGTLL 270 Query: 222 GLGERAGNAAAWKPSALGLERCLGVETGVHFSALPALCQRVAEAAQRAIDPQQPLVGELV 281 G GER GN A+ L G++ + S + + + + P VGE V Sbjct: 271 GNGERTGN-MDMVTLAMNL-YSEGIDPELDLSRPDDWVPVLEDVTKIPTHLRHPWVGEAV 328 Query: 282 FTHESGVHVAA----LLRDSE------SYQSIAPSLMGRSYRLVLGKHS 320 +T SG H A LLR +Y I P +GR Y ++ +S Sbjct: 329 YTAYSGSHQDAIRKCLLRQQPQEPWQVAYLPIDPKDLGRDYEAIIRVNS 377 Lambda K H 0.319 0.132 0.384 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: 438 Number of extensions: 22 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 381 Length of database: 545 Length adjustment: 33 Effective length of query: 348 Effective length of database: 512 Effective search space: 178176 Effective search space used: 178176 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 (21.8 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