Align citrate synthase (unknown stereospecificity) (EC 2.3.3.16) (characterized)
to candidate WP_009545710.1 CCE_RS09005 citrate (Si)-synthase
Query= BRENDA::P45858 (372 letters) >NCBI__GCF_000017845.1:WP_009545710.1 Length = 369 Score = 196 bits (498), Expect = 9e-55 Identities = 122/362 (33%), Positives = 201/362 (55%), Gaps = 17/362 (4%) Query: 20 HISYLDTQSSQILIRGYDLIELSETKSYLELVHLLLEGRLPEESEMETLERKINSASSLP 79 H+S +D Q +++I G+ EL+ S+ E++ L L LP ++E++ + +K+ S L Sbjct: 7 HLSKIDGQLGKLIILGFPFEELATNASFEEMIFLFLHNHLPNKNELDNVTKKLLSHRYLD 66 Query: 80 ADHLRLLE-LLPEDTHPMDGLRTGLSALAGYDRQIDDRSPSANKER---AYQLLGKMPAL 135 L +L+ D ++G+R G+S L +D +S +KE A +++ +P + Sbjct: 67 EKILDVLKNAAANDIELIEGVRIGVSCLT-----LDMQSHRIDKEGINGALKIIASVPII 121 Query: 136 TAASYRIINKKEPILPLQTLSYSANFLYMMTGKLPSSLEEQIFDRSLVLYSEHEMPNSTF 195 TA+ +R++ + + P L ++AN+LYM+TG+ P+ + + + L EH M STF Sbjct: 122 TASYWRLLKGQPIVEPHLELGHAANYLYMLTGEKPAPEDVKTLEIYLNTVIEHGMNASTF 181 Query: 196 AARVIASTHSDLYGALTGAVASLKGNLHGGANEAVMYLLLEAKTTSDFEQLLQTKLKRKE 255 AARV+ ST SD A+T A+ ++KG LHGGA V+ +LLE + + D E L+ K + +E Sbjct: 182 AARVVMSTRSDFVSAVTAAIGAMKGVLHGGAPGPVLDMLLEMQKSGDIEGYLRHKFENRE 241 Query: 256 KIMGFGHRVYMKKMDPRALMMKEALQQLCDKAGDHRLYEMCEAGE----RLMEKEK---G 308 ++MGFGHRVY K DPRA+++ + + D + + E RL+++ K Sbjct: 242 RLMGFGHRVYRVK-DPRAILLANVSADVWKRREDKEFWGLAVDVETTALRLLKEYKPNRS 300 Query: 309 LYPNLDYYAAPVYWMLGIPIPLYTPIFFSARTSGLCAHVIEQHANNRLFRPRVSYMGPRY 368 + N++YY A V LG+P L+T F +R G AH +EQ +R+ RP Y GP Sbjct: 301 IETNVEYYTALVLHGLGLPSALFTSTFTVSRVVGWLAHCLEQLELDRIIRPSSVYTGPSE 360 Query: 369 QT 370 QT Sbjct: 361 QT 362 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: 318 Number of extensions: 13 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: 369 Length adjustment: 30 Effective length of query: 342 Effective length of database: 339 Effective search space: 115938 Effective search space used: 115938 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: 49 (23.5 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