Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate WP_029132263.1 A3GO_RS0103745 citrate synthase
Query= SwissProt::O34002 (379 letters) >NCBI__GCF_000428045.1:WP_029132263.1 Length = 431 Score = 202 bits (514), Expect = 1e-56 Identities = 136/393 (34%), Positives = 199/393 (50%), Gaps = 27/393 (6%) Query: 5 TIHKGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYLLWNSELPNDSEL 64 T G + +AI+ ++ D L YRGYP+++LA + SF +VAYLL +LP+ E+ Sbjct: 44 TYDPGFVATASCRSAITYIDGDKGILRYRGYPIEQLAKEASFLEVAYLLMYGDLPSAEEM 103 Query: 65 KAFVNFERSHRKLDENVKGAIDLLSTACHPMDVARTAVSVLGANHARAQD-SSPEANLEK 123 F N R H + E +K D HPM + V L A + + D ++P Sbjct: 104 AKFDNTIRHHTMIKETLKNFFDGFQYDAHPMGIMVGVVGSLSAFYHDSLDINNPRHREIS 163 Query: 124 AMSLLATFPSVVAYDQRRRRGEELIEPREDLDYSANFLWMTFG---EEAAPE--VVEAFN 178 A L+A P++ A + GE I PR DLDY NFL M F EE +P+ V+A N Sbjct: 164 AHRLIAKMPTIAAASYKHNVGEPFIYPRNDLDYCENFLRMMFSNPCEEYSPDPVAVKAIN 223 Query: 179 VSMILYAEHSFNASTFTARVITSTLADLHSAVTGAIGALKGPLHGGANEAVMHTFEEIG- 237 IL+A+H NAST T R+ S+ A+ + + I +L GP HGGANEAV+ EIG Sbjct: 224 TLFILHADHEQNASTSTVRLSGSSQANPFACIAAGIASLWGPSHGGANEAVLDMLNEIGD 283 Query: 238 -IRKDESLDEAATRSKAWMVDALAQKKKVMGFGHRVYKNGDSRVPTMKSALDAMI---KH 293 + D+ + +A + + ++MGFGHRVYKN D R ++ ++ K Sbjct: 284 VSQIDKYIAKAKDKDDPF---------RLMGFGHRVYKNFDPRATLIREVCHEVLENMKD 334 Query: 294 YDRPEMLGLYNGLEAAMEE----AKQIKPNLDYPAGPTYNLMGFDTEMFTPLFIAARITG 349 D P + A+E+ +++ PN+D+ +G Y +G T MFT +F AR G Sbjct: 335 NDNPLFELALRLEQVALEDEYFVERKLYPNVDFYSGIIYQALGIPTSMFTVMFAVARTVG 394 Query: 350 WTAHIMEQVADN--ALIRPLSEYNG-PEQRQVP 379 W AH ME + D + RP Y G P++ VP Sbjct: 395 WVAHWMEMMDDPEFRIGRPRQLYTGAPKRDYVP 427 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: 355 Number of extensions: 15 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: 431 Length adjustment: 31 Effective length of query: 348 Effective length of database: 400 Effective search space: 139200 Effective search space used: 139200 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 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