Align citrate synthase (unknown stereospecificity) (EC 2.3.3.16) (characterized)
to candidate WP_011373714.1 SUDEN_RS10910 citrate synthase
Query= BRENDA::P45858 (372 letters) >NCBI__GCF_000012965.1:WP_011373714.1 Length = 426 Score = 189 bits (479), Expect = 2e-52 Identities = 121/381 (31%), Positives = 199/381 (52%), Gaps = 19/381 (4%) Query: 7 YSPGLDGVIAAETHISYLDTQSSQILIRGYDLIELSETKSYLELVHLLLEGRLPEESEME 66 Y G + ++ I+Y+D ++ +++ RGYD+ L++ KS+L+ +LL+ G LP + E+E Sbjct: 45 YDEGYTSTASCKSDITYIDGEAGKLMYRGYDIAYLAKKKSFLDSAYLLINGELPSKEELE 104 Query: 67 TLERKINSASSLPADHLRLLELLPEDTHPMDGLRTGLSALAG-YDRQIDDRSPSANKERA 125 ++ S + +L + P+ HPM L G+SAL+ Y ++ ++ E A Sbjct: 105 NFAFEMKKRSFVHEGIKKLFDSFPDSAHPMAILSAGVSALSTFYFDHLNIKNKEEYCEMA 164 Query: 126 YQLLGKMPALTAASYRIINKKEPILPLQTLSYSANFLYMMTGKLPS-----SLEEQIFDR 180 +++ K+P L A SYR N I P ++ NFLYM+ S +E + D Sbjct: 165 NRIVAKIPTLAAFSYRYSNGLPIIYPDMNKGFTENFLYMLRAYPHSYVELKPIEIKALDT 224 Query: 181 SLVLYSEHEMPNSTFAARVIASTHSDLYGALTGAVASLKGNLHGGANEAVMYLLLEAKTT 240 L+++HE ST A R +AST++ Y A++ + +L G HGGANE+V+ L T Sbjct: 225 IFTLHADHEQNASTTAVRNLASTNAHPYAAISAGIGALWGRSHGGANESVIRQLEMIATV 284 Query: 241 SDFEQLLQTKLKRKE---KIMGFGHRVYMKKMDPRALMMKEALQQLCDKAG-DHRLYEMC 296 ++ + + K KE K+MGFGHRVY K DPRA ++K+ +L ++ G L E+ Sbjct: 285 DRVDEFI-ARAKDKEDSFKLMGFGHRVY-KNFDPRATILKDLRNRLVEELGISSELIEVA 342 Query: 297 EAGERLMEKE-----KGLYPNLDYYAAPVYWMLGIPIPLYTPIFFSARTSGLCAH--VIE 349 E++ + + LYPN+D+Y+ + L IP ++ IF RT G A + Sbjct: 343 NKIEKIALNDEYFVSRNLYPNIDFYSGLILQALKIPTEMFAVIFVIGRTPGWIAQWSELN 402 Query: 350 QHANNRLFRPRVSYMGPRYQT 370 Q ++ RPR Y GP +T Sbjct: 403 QQKTVKIARPRQLYRGPIERT 423 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: 334 Number of extensions: 19 Number of successful extensions: 5 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: 426 Length adjustment: 31 Effective length of query: 341 Effective length of database: 395 Effective search space: 134695 Effective search space used: 134695 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 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