Align citrate synthase (unknown stereospecificity) (EC 2.3.3.16) (characterized)
to candidate CCNA_03758 CCNA_03758 citrate synthase
Query= BRENDA::P45858 (372 letters) >FitnessBrowser__Caulo:CCNA_03758 Length = 392 Score = 87.0 bits (214), Expect = 8e-22 Identities = 66/188 (35%), Positives = 95/188 (50%), Gaps = 16/188 (8%) Query: 180 RSLVLYSEHEMPNSTFAARVIASTHSDLYGALTGAVASLKGNLHGGANEAVMYLLLEAKT 239 R+LVL ++HE+ STFAARV AST + L A +++L G LHGG V L+ EA Sbjct: 205 RALVLMADHELNASTFAARVAASTGASLSAACLAGLSALSGPLHGGMAARVEALVEEA-D 263 Query: 240 TSDFEQLLQTKLKRKEKIMGFGHRVYMKKMDPRALMMKEALQQLCDKAGDHRLYEMCEAG 299 D + + ++L++ + GF H +Y DPRA + + E A Sbjct: 264 RRDAARAVSSRLEQGASLPGFDHPLY-PGGDPRAAALLARFEP----------PEPLTAL 312 Query: 300 ERLMEKEKGLYPNLDYYAAPVYWMLGIPIPLYTP--IFFSARTSGLCAHVIEQHANNRLF 357 + GL PN+D+ A V G+ +P P +F +AR++G AH IEQ RL Sbjct: 313 WQATRAATGLAPNIDF--ALVALARGLALPQDAPFILFATARSAGWTAHAIEQLQTGRLI 370 Query: 358 RPRVSYMG 365 RPR Y+G Sbjct: 371 RPRARYIG 378 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: 275 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: 372 Length of database: 392 Length adjustment: 30 Effective length of query: 342 Effective length of database: 362 Effective search space: 123804 Effective search space used: 123804 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: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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