Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; CS; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate WP_028950703.1 Q385_RS0105475 citrate/2-methylcitrate synthase
Query= SwissProt::H8F0D7 (393 letters) >NCBI__GCF_000619805.1:WP_028950703.1 Length = 375 Score = 231 bits (588), Expect = 3e-65 Identities = 128/361 (35%), Positives = 199/361 (55%), Gaps = 5/361 (1%) Query: 28 IKKGLAGVVVDTTAISKVVPQTNSLTYRGYPVQDLAARCSFEQVAFLLWRGELPTDAELA 87 + +GLAG+ V ++IS V + L YRG P+Q+L +F +V++LL G++P + EL Sbjct: 3 VYEGLAGIPVVKSSISYVDGENGILEYRGIPIQELVENSNFLEVSYLLIFGKIPDEKELL 62 Query: 88 LFSQRERASRRVDRSMLSLLAKLPDNCHPMDVVRTAISYLGAEDPDEDDAAANRA--KAM 145 F + + + +L +L LP N HPM ++++ I +D D D + + Sbjct: 63 KFELDIKENLKYSERILDILKSLPKNLHPMKILQSLIPVFAFDDIDTDIMKEENKYRQTV 122 Query: 146 RMMAVLPTIVAIDMRRRRGLPPIAPHSGLGYAQNFLHMCFGEVPETAVVSAFEQSMILYA 205 R+MA++P ++A R + G + P+ Y +NFL+M G+ E ++++IL+A Sbjct: 123 RIMAIVPVVIAFSKRLKEGKEIVFPNKNFYYTENFLYMLKGKPVEKIYWQTLDKTLILHA 182 Query: 206 EHGFNASTFAARVVTSTQSDIYSAVTGAIGALKGRLHGGANEAVMHDMIEI-GDPANARE 264 EH NASTF A VV ST +D+Y+ V+ A+G+L GRLHGGANE V + + D RE Sbjct: 183 EHTINASTFTAMVVVSTLADLYACVSSAVGSLSGRLHGGANEEVYKMLSSLPNDEKIIRE 242 Query: 265 WLRAKLARKEKIMGFGHRVYRHGDSRVPTMKRALERVGTVRDGQ--RWLDIYQVLAAEMA 322 +++ KL K+KIMGFGHR+Y+ D R MK LE++ + +I++ +A E Sbjct: 243 YIKEKLKNKDKIMGFGHRIYKTYDPRAKIMKYLLEKLQKEKSTPLLEKAEIFEKIALEYL 302 Query: 323 SATGILPNLDFPTGPAYYLMGFDIASFTPIFVMSRITGWTAHIMEQATANALIRPLSAYC 382 I N+DF +G Y M +T IF M+R+ GW +H +E N L RP Y Sbjct: 303 EEKKIYTNIDFYSGVLYSQMEIPSDFYTTIFAMARVPGWISHCIEYVRNNKLFRPTQVYD 362 Query: 383 G 383 G Sbjct: 363 G 363 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: 301 Number of extensions: 23 Number of successful extensions: 4 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: 375 Length adjustment: 30 Effective length of query: 363 Effective length of database: 345 Effective search space: 125235 Effective search space used: 125235 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 Apr 09 2024. 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