Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate WP_068173974.1 HTA01S_RS17235 citrate synthase
Query= SwissProt::O34002 (379 letters) >NCBI__GCF_001592305.1:WP_068173974.1 Length = 436 Score = 189 bits (481), Expect = 1e-52 Identities = 126/394 (31%), Positives = 198/394 (50%), Gaps = 29/394 (7%) Query: 5 TIHKGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYLLWNSELPNDSEL 64 T G + +AI+ ++ D LLYRGYP+++LA C + YLL N ELPND E Sbjct: 46 TYDPGFLSTASCQSAITYIDGDKGELLYRGYPIEQLATNCDYLDTCYLLLNGELPNDKER 105 Query: 65 KAFVNFERSHRKLDENVKGAIDLLSTACHPMDVARTAVSVLGANHARAQD-SSPEANLEK 123 F +H ++E ++ + HPM V V L A + + D ++PE Sbjct: 106 GDFHKLVINHTMVNEQMQFFLRGFRRDAHPMAVLTGLVGALSAFYHDSTDINNPEHRRIA 165 Query: 124 AMSLLATFPSVVAYDQRRRRGEELIEPREDLDYSANFLWMTFGE-----EAAPEVVEAFN 178 A+ L+A P++VA + G+ + PR DL YS NFL M FG + P + +A + Sbjct: 166 AIRLIAKMPTLVAMAYKYGIGQPYMYPRNDLSYSGNFLRMMFGTPCEEYKVNPVLEKALD 225 Query: 179 VSMILYAEHSFNASTFTARVITSTLADLHSAVTGAIGALKGPLHGGANEAVMHTFEEI-- 236 IL+A+H NAST T R+ S+ + +A+ + L GP HGGANEA ++ E+I Sbjct: 226 RIFILHADHEQNASTSTVRLCGSSGTNPFAAIAAGVACLWGPAHGGANEACLNMLEDIQR 285 Query: 237 --GIRK-DESLDEAATRSKAWMVDALAQKKKVMGFGHRVYKNGDSRVPTMKSALDAMIKH 293 G+ K E +++ ++ K+MGFGHRVYKN D R M+ + ++ Sbjct: 286 QGGVSKVGEFMEKVKDKNSG---------VKLMGFGHRVYKNYDPRAKLMQETCNEVLAE 336 Query: 294 --YDRPEMLGLYNGLE-AAMEE----AKQIKPNLDYPAGPTYNLMGFDTEMFTPLFIAAR 346 + + L LE A+E+ ++++ PN+D+ +G +G +FT +F AR Sbjct: 337 LGLENDPLFKLAKELEKIALEDEYFVSRKLYPNVDFYSGIVQRAIGIPVNLFTGIFALAR 396 Query: 347 ITGWTAHIMEQVAD--NALIRPLSEYNGPEQRQV 378 GW A + E ++D + RP + G E+R V Sbjct: 397 TVGWIAQLNEMISDPEYKIGRPRQLFTGSERRDV 430 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: 358 Number of extensions: 17 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: 436 Length adjustment: 31 Effective length of query: 348 Effective length of database: 405 Effective search space: 140940 Effective search space used: 140940 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