Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate WP_065400337.1 BBI00_RS18690 citrate synthase
Query= SwissProt::O34002 (379 letters) >NCBI__GCF_001684965.1:WP_065400337.1 Length = 428 Score = 188 bits (477), Expect = 3e-52 Identities = 123/385 (31%), Positives = 203/385 (52%), Gaps = 19/385 (4%) Query: 5 TIHKGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYLLWNSELPNDSEL 64 T+ G A ++ I+ ++ D L YRGYP++++A K +F +V YLL + ELP + Sbjct: 42 TLDLGYKNTGATISDITYLDGDKGELFYRGYPIEQIAEKSNFTEVMYLLLHGELPTQDQF 101 Query: 65 KAFVNFERSHRKLDENVKGAIDLLSTACHPMDVARTAVSVLGANHARAQDSSPEANLEKA 124 +F N + + + + +K ID+ + HPM V + S L A + +A + + + ++ A Sbjct: 102 TSFDNNIKKYNFIADEMKKIIDVFPRSAHPMGVLSSLTSALTAFNPKAVNVNSKEEMDHA 161 Query: 125 MSL-LATFPSVVAYDQRRRRGEELIEPREDLDYSANFLWMTF-----GEEAAPEVVEAFN 178 L +A F + A+ R+ +G L +L+Y NF M F E P VV A + Sbjct: 162 AELMIAKFSHLCAWTYRKTQGLPLNHGDNNLNYVENFYKMAFRLPNADFEIDPVVVNALD 221 Query: 179 VSMILYAEHSFNASTFTARVITSTLADLHSAVTGAIGALKGPLHGGANEAVMHTFEEIGI 238 +IL+A+H N ST T R++ S L ++++ + AL GPLHGGAN+AV+ E I Sbjct: 222 KLLILHADHEQNCSTSTVRMVGSAHTGLFASISAGVSALWGPLHGGANQAVIEMLELI-- 279 Query: 239 RKDESLDEAATRSKAWMVDALAQKKKVMGFGHRVYKNGDSRVPTMKSALDAMIKHYD-RP 297 + + D + +KA + ++MGFGHRVYKN D R +K A D ++ + Sbjct: 280 -EKDGGDVSKYVAKA---KDKSDNFRLMGFGHRVYKNFDPRAKIIKKAADDILTALGIQD 335 Query: 298 EMLGLYNGLE-AAMEE----AKQIKPNLDYPAGPTYNLMGFDTEMFTPLFIAARITGWTA 352 + L + LE A+E+ +++ PN+D+ +G Y +G TEMFT +F R+ GW + Sbjct: 336 KALDIAMQLERVALEDEYFVERKLYPNVDFYSGIIYRALGIPTEMFTVMFALGRLPGWIS 395 Query: 353 HIME-QVADNALIRPLSEYNGPEQR 376 E ++ + + RP Y G +QR Sbjct: 396 QWKEMRLKGDPIGRPRQVYQGAQQR 420 Lambda K H 0.316 0.130 0.376 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: 364 Number of extensions: 21 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: 379 Length of database: 428 Length adjustment: 31 Effective length of query: 348 Effective length of database: 397 Effective search space: 138156 Effective search space used: 138156 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 (21.6 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