Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate WP_012277058.1 SHAL_RS10215 2-methylcitrate synthase
Query= SwissProt::Q8EJW2 (375 letters) >NCBI__GCF_000019185.1:WP_012277058.1 Length = 379 Score = 590 bits (1521), Expect = e-173 Identities = 285/372 (76%), Positives = 318/372 (85%) Query: 4 AKKLTGAGLRGQSAGETALSTVGVSGSGLTYRGYDVKDLAENATFEEVAYLILYGELPTT 63 +KK+ GAGLRGQSAGETAL TVG SGSGLTY GYDV DLA+NATFEEVAYL+ GELP Sbjct: 8 SKKIGGAGLRGQSAGETALCTVGKSGSGLTYCGYDVSDLADNATFEEVAYLLFNGELPNQ 67 Query: 64 AQLAAYKTKLKGMRGLPQALKEVLERIPADAHPMDVMRTGCSMLGNLEAEHSFSEQSQIA 123 QL YKT+L R LPQALKEVL+RIPA+AHPMDVMRTGCS LGNLE E+ FSEQ++ A Sbjct: 68 TQLDHYKTELFAHRDLPQALKEVLQRIPAEAHPMDVMRTGCSFLGNLEPENDFSEQNRAA 127 Query: 124 DRLLAAFPSIICYWYRFSHDGVRIDTETDDDQIGAHFLHLLHGKAPSALHTKVMDVSLIL 183 +RLLAAFP+I+CYWY+FSH+GV ID TD+D IG HFLHLL+GKAPS H +VMDVSLIL Sbjct: 128 NRLLAAFPAIMCYWYKFSHEGVEIDCVTDEDSIGGHFLHLLNGKAPSEQHRRVMDVSLIL 187 Query: 184 YAEHEFNASTFTARVCASTLSDMHSCVTGAIGSLRGPLHGGANEAAMELIQDMKDEADAR 243 YAEHEFNASTFTARVCASTLSDM+SC+TGAIG+LRGPLHGGANEAAM++IQ DA+ Sbjct: 188 YAEHEFNASTFTARVCASTLSDMYSCITGAIGTLRGPLHGGANEAAMDMIQKFSSPEDAK 247 Query: 244 DVLMGKLERKEKIMGFGHAIYRDSDPRNAIIKEWSEKLAADYGDDRLYRVSVACEALMWE 303 + + G LERKEKIMGFGHAIYR SDPRN IIK WS+KL A++GD LY +SVACE MW+ Sbjct: 248 EQMAGMLERKEKIMGFGHAIYRTSDPRNVIIKAWSKKLGAEFGDSSLYDISVACEEFMWD 307 Query: 304 QKKLFCNADFFHASAYHFMGIPTKLFTPIFVCSRVTGWTAHVMEQRSNNRIIRPSADYVG 363 KKLFCNADFFHASAYHFMGIPTKLFTPIFVCSR+TGW AHVMEQRSNNRIIRPSADY G Sbjct: 308 TKKLFCNADFFHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVMEQRSNNRIIRPSADYTG 367 Query: 364 VSPRKVIPIANR 375 PR V PI+ R Sbjct: 368 SEPRTVTPISER 379 Lambda K H 0.320 0.134 0.401 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: 494 Number of extensions: 10 Number of successful extensions: 1 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: 375 Length of database: 379 Length adjustment: 30 Effective length of query: 345 Effective length of database: 349 Effective search space: 120405 Effective search space used: 120405 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 (21.8 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