Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; CS; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate CCNA_03757 CCNA_03757 citrate synthase
Query= SwissProt::H8F0D7 (393 letters) >lcl|FitnessBrowser__Caulo:CCNA_03757 CCNA_03757 citrate synthase Length = 361 Score = 194 bits (492), Expect = 4e-54 Identities = 134/369 (36%), Positives = 180/369 (48%), Gaps = 24/369 (6%) Query: 31 GLAGVVVDTTAISKVVPQTNSLTYRGYPVQDLAARCSFEQVAFLLWRG---ELPTDAELA 87 GL GV+ T +S V L RGY V+DLA R FE A LL G + P+D A Sbjct: 4 GLEGVIAAQTVLSDVDGAHGRLVIRGYAVEDLAGRTRFEDAAHLLLDGFFDDAPSDLSSA 63 Query: 88 LFSQRERASRRVDRSMLSLLAKLPDNCHPMDVVRTAISYLGAEDPDEDDAAANRAKAMRM 147 L R + + +A L + D V A+ L A PD DD A+R+ Sbjct: 64 LGEARV--------GVFAEVAALDEGLARRDPVE-ALRALLARIPDGDDLKT----ALRL 110 Query: 148 MAVLPTIVAIDMRRRRGLPPIAPHSGLGYAQNFLHMCFGEVPETAVVSAFEQSMILYAEH 207 +A +R G PIAP L +A + L M G A +A + ++ +H Sbjct: 111 IAAPAVFTPAVLRVANGDAPIAPDPALSHAADILRMIRGVPATDAEAAALDAYLVTVCDH 170 Query: 208 GFNASTFAARVVTSTQSDIYSAVTGAIGALKGRLHGGANEAVMHDMIEIGDPANAREWLR 267 G NASTFAARVV ST++ + SAV + ALKG LHGGA V+ + IG P NAR WL Sbjct: 171 GLNASTFAARVVASTRAGLTSAVLAGLSALKGPLHGGAPGPVIDMLDAIGTPENARPWLE 230 Query: 268 AKLARKEKIMGFGHRVYRHGDSRVPTMKRALERVGTVRDG----QRWLDIYQVLAAEMAS 323 LAR +++MGFGHR+YR D R +K A+ R+ + G + + + A E+ Sbjct: 231 RALARGDRLMGFGHRIYRVRDPRADALKAAVRRLSSASGGLPGRLAFAEAVERAALEILR 290 Query: 324 A----TGILPNLDFPTGPAYYLMGFDIASFTPIFVMSRITGWTAHIMEQATANALIRPLS 379 + N++F T +G +SFT +F M R+ GW AH EQ LIRP S Sbjct: 291 EHKPDRPLDTNVEFYTALLLEALGLPPSSFTCVFAMGRVAGWLAHAREQLAGGRLIRPQS 350 Query: 380 AYCGHEQRV 388 Y G E RV Sbjct: 351 VYVGPEVRV 359 Lambda K H 0.321 0.134 0.397 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: 309 Number of extensions: 12 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: 393 Length of database: 361 Length adjustment: 30 Effective length of query: 363 Effective length of database: 331 Effective search space: 120153 Effective search space used: 120153 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 (21.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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