Align citrate synthase (unknown stereospecificity) (EC 2.3.3.16) (characterized)
to candidate WP_017358571.1 BA79_RS12705 citryl-CoA lyase
Query= BRENDA::P45858 (372 letters) >NCBI__GCF_000691145.1:WP_017358571.1 Length = 285 Score = 78.2 bits (191), Expect = 3e-19 Identities = 63/215 (29%), Positives = 97/215 (45%), Gaps = 13/215 (6%) Query: 155 LSYSANFLYMMTGKLPSSLEEQIFDRSLVLYSEHEMPNSTFAARVIASTHSDLYGALTGA 214 LSY ++ G+L + +F+ LV ++H + AA +A T + + Sbjct: 47 LSYPQMLYLLLVGELLDDSKAALFESVLVAGADHGPRAPSIAAARMAVTCGISFNSSVAT 106 Query: 215 VASLKGNLHGGANEAVMYLLLEAKTTSD--------FEQLLQTKLKRKEKIMGFGHRVYM 266 +L G++HGGA E M +L EAK D +Q+ QT L RKEKI G GH+++ Sbjct: 107 GVNLLGDIHGGAGEKAMRMLYEAKAAYDEHEDIKSAAKQVCQTWLARKEKIPGIGHQLH- 165 Query: 267 KKMDPRALMMKEALQQLCDKAGDHRLY-EMCEAGERLMEKEKG--LYPNLDYYAAPVYWM 323 DPR + E Q + Y + EA +E+ KG + N+D +A + Sbjct: 166 -DDDPRVRRLYELSQTYVQQGDISGTYLRLAEAIRHELEQLKGKKITMNIDGVSAAIQCE 224 Query: 324 LGIPIPLYTPIFFSARTSGLCAHVIEQHANNRLFR 358 L IP IF +R G+ AH E+ L + Sbjct: 225 LSIPAEAAKGIFSLSRGMGIVAHAYEELTKGALVK 259 Lambda K H 0.317 0.134 0.381 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: 240 Number of extensions: 9 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: 372 Length of database: 285 Length adjustment: 28 Effective length of query: 344 Effective length of database: 257 Effective search space: 88408 Effective search space used: 88408 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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