Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate WP_097029597.1 CRO07_RS05055 citrate (Si)-synthase
Query= SwissProt::O34002 (379 letters) >NCBI__GCF_900207575.1:WP_097029597.1 Length = 428 Score = 184 bits (466), Expect = 5e-51 Identities = 130/398 (32%), Positives = 189/398 (47%), Gaps = 44/398 (11%) Query: 5 TIHKGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYLLWNSELPNDSEL 64 T G A + I+ ++ D LLYRGYP+++LA + + +V YLL ELPN ++ Sbjct: 41 TYDPGFTSTAACESTITYIDGDKGELLYRGYPIEQLAERSHYLEVCYLLLYGELPNAAQA 100 Query: 65 KAFVNFERSHRKLDENVKGAIDLLSTACHPMDVARTAVSVLGANHARAQDS----SPEAN 120 F H L E + HPM T V V+GA A DS P Sbjct: 101 ADFEYRITRHTMLHEQIHYFFRGFRRDSHPM---ATMVGVVGAMSAFYHDSLDINDPWQR 157 Query: 121 LEKAMSLLATFPSVVAYDQRRRRGEELIEPREDLDYSANFLWMTFGEEAAPEVV-----E 175 A+ ++A P++ A + G+ P+ LDY+ NFL M F A P V + Sbjct: 158 EVAAVRMIAKLPTIAAMAYKYSLGQPFNYPQNHLDYAGNFLHMCFAVPAEPYTVNPILSK 217 Query: 176 AFNVSMILYAEHSFNASTFTARVITSTLADLHSAVTGAIGALKGPLHGGANEAVMHTFEE 235 A + M+L+A+H NAST T R+ S+ A+ + + I L GP HGGAN+A + E Sbjct: 218 AMDRIMMLHADHEQNASTSTVRLAGSSGANPFACIAAGIACLWGPAHGGANQACLEMLRE 277 Query: 236 IGI--RKDESLDEAATRSKAWMVDALAQKKKVMGFGHRVYKNGDSRVPTMKSALDAMIKH 293 IG R E + A + + ++MGFGHRVYKN D R MK + D ++ Sbjct: 278 IGTVDRIPEYIKRAKDKDDPF---------RLMGFGHRVYKNFDPRAKVMKESADEVL-- 326 Query: 294 YDRPEMLGLYNG--LEAAME-----------EAKQIKPNLDYPAGPTYNLMGFDTEMFTP 340 +LG+ N L+ A E +K++ PN+D+ +G + MGF T MFTP Sbjct: 327 ----GLLGIENNPTLQVAKELERIALEDDYFVSKKLYPNVDFYSGIILDAMGFPTSMFTP 382 Query: 341 LFIAARITGWTAHIMEQVAD--NALIRPLSEYNGPEQR 376 +F +R GW + E + D + RP Y G +QR Sbjct: 383 IFAISRTVGWISQWKEMIGDPTQRIGRPRQLYKGEKQR 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: 391 Number of extensions: 18 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