Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; CS; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate WP_047269777.1 C1M55_RS25465 bifunctional 2-methylcitrate synthase/citrate synthase
Query= SwissProt::H8F0D7 (393 letters) >NCBI__GCF_002893965.1:WP_047269777.1 Length = 373 Score = 543 bits (1400), Expect = e-159 Identities = 272/369 (73%), Positives = 305/369 (82%), Gaps = 2/369 (0%) Query: 23 DERPDIKKGLAGVVVDTTAISKVVPQTNSLTYRGYPVQDLAARCSFEQVAFLLWRGELPT 82 ++ P I KGLAGVVVDTTAISKVVP+TNSLTYRGY VQDLAA CSFE+VA LLW GELPT Sbjct: 3 EQIPTIYKGLAGVVVDTTAISKVVPETNSLTYRGYAVQDLAANCSFEEVAHLLWYGELPT 62 Query: 83 DAELALFSQRERASRRVDRSMLSLLAKLPDNCHPMDVVRTAISYLGAEDPDEDDAA--AN 140 +L L RERA+RR DRS+LSLL K+PDNCHPMDVVRTAISYLGAEDP EDD + AN Sbjct: 63 PEQLELLCLRERAARRADRSLLSLLTKMPDNCHPMDVVRTAISYLGAEDPAEDDNSEKAN 122 Query: 141 RAKAMRMMAVLPTIVAIDMRRRRGLPPIAPHSGLGYAQNFLHMCFGEVPETAVVSAFEQS 200 AKA+RM AVLPTIVA D RRRRG PIAP S LG+A+NFL+MCFG VPE+A+V AFE S Sbjct: 123 LAKALRMTAVLPTIVAADFRRRRGQDPIAPQSDLGFAENFLNMCFGAVPESAIVKAFEVS 182 Query: 201 MILYAEHGFNASTFAARVVTSTQSDIYSAVTGAIGALKGRLHGGANEAVMHDMIEIGDPA 260 +ILYAEH FNASTFAARVVTST SDIYSAVT AIG LKG LHGGANEAVMHDM+EI DP Sbjct: 183 LILYAEHSFNASTFAARVVTSTLSDIYSAVTAAIGTLKGPLHGGANEAVMHDMLEIDDPD 242 Query: 261 NAREWLRAKLARKEKIMGFGHRVYRHGDSRVPTMKRALERVGTVRDGQRWLDIYQVLAAE 320 A W+ KLA KEK+MGFGHRVY++GDSRVPTMK+AL V DG++W+ +Y++L Sbjct: 243 RAEAWMSEKLAAKEKVMGFGHRVYKNGDSRVPTMKQALLDVAAATDGEKWVQMYEILEKT 302 Query: 321 MASATGILPNLDFPTGPAYYLMGFDIASFTPIFVMSRITGWTAHIMEQATANALIRPLSA 380 M SATGI PNLDFPTGPAY+LMGFD+ FTPIFVMSRITGWTAHI+EQ +NALIRPLS Sbjct: 303 MVSATGIKPNLDFPTGPAYFLMGFDVEMFTPIFVMSRITGWTAHIIEQGQSNALIRPLSQ 362 Query: 381 YCGHEQRVL 389 Y G QR + Sbjct: 363 YSGVPQRTV 371 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: 455 Number of extensions: 8 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: 393 Length of database: 373 Length adjustment: 30 Effective length of query: 363 Effective length of database: 343 Effective search space: 124509 Effective search space used: 124509 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 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