Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate RR42_RS11265 RR42_RS11265 methylcitrate synthase
Query= SwissProt::Q937N9 (385 letters) >FitnessBrowser__Cup4G11:RR42_RS11265 Length = 385 Score = 739 bits (1909), Expect = 0.0 Identities = 361/385 (93%), Positives = 372/385 (96%) Query: 1 MSEAQPLVTPKPKKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEFEEIAHL 60 MSEAQPLV PKPKKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEFEEIAHL Sbjct: 1 MSEAQPLVAPKPKKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEFEEIAHL 60 Query: 61 LVHGKLPTKSELAAYKAKLKSLRGLPANVKAALEWVPASAHPMDVMRTGVSVLGTVLPEK 120 LVHGKLPT++ELAAYKAKLK+LRGLPANVKAALEWVPASAHPMDVMRTGVSVLGTVLPEK Sbjct: 61 LVHGKLPTRAELAAYKAKLKALRGLPANVKAALEWVPASAHPMDVMRTGVSVLGTVLPEK 120 Query: 121 EDHNTPGARDIADRLMASLGSMLLYWYHYSHNGRRIEVETDDDSIGGHFLHLLHGEKPSA 180 +DHNTPGARDIADRLMASLGSMLLYWYHYSHNGRRIEVETDDD+IG HFLHLLHG+KPSA Sbjct: 121 DDHNTPGARDIADRLMASLGSMLLYWYHYSHNGRRIEVETDDDTIGAHFLHLLHGQKPSA 180 Query: 181 LWERAMNTSLNLYAEHEFNASTFTARVIAGTGSDMYSSISGAIGALRGPKHGGANEVAFE 240 LWERAM TSLNLYAEHEFNASTF RVIAGTGSDMYSSI GAIGALRGPKHGGANEVAFE Sbjct: 181 LWERAMQTSLNLYAEHEFNASTFAGRVIAGTGSDMYSSICGAIGALRGPKHGGANEVAFE 240 Query: 241 IQKRYDNPDEAQADITRRVENKEVVIGFGHPVYTTGDPRNQVIKEVAKKLSKDAGSMKMF 300 IQKRYD+PDEA DI+RRVENKEVVIGFGHPVYTTGDPRNQVIKEVA++LSKDAGSMKMF Sbjct: 241 IQKRYDSPDEAHIDISRRVENKEVVIGFGHPVYTTGDPRNQVIKEVARRLSKDAGSMKMF 300 Query: 301 DIAEALETVMWDIKKMFPNLDWFSAVSYHMMGVPTAMFTALFVIARTSGWAAHIIEQRID 360 DIAE LET MWD KKMFPNLDWFSAVSYHMMGVPTAMFT LFVIARTSGWAAHIIEQRID Sbjct: 301 DIAERLETTMWDAKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRID 360 Query: 361 NKIIRQSANYTGPENLKFVPLKDRK 385 NKIIR SANYTGPENLKFVP+KDRK Sbjct: 361 NKIIRPSANYTGPENLKFVPIKDRK 385 Lambda K H 0.317 0.133 0.394 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: 653 Number of extensions: 9 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: 385 Length of database: 385 Length adjustment: 30 Effective length of query: 355 Effective length of database: 355 Effective search space: 126025 Effective search space used: 126025 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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