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) >FitnessBrowser__Caulo:CCNA_03757 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:
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