Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_088756986.1 CEJ45_RS20840 2-methylcitrate synthase
Query= BRENDA::Q2Z1A8 (398 letters) >NCBI__GCF_002213425.1:WP_088756986.1 Length = 384 Score = 701 bits (1808), Expect = 0.0 Identities = 339/373 (90%), Positives = 357/373 (95%) Query: 26 KKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEFEEIAHLLVHGKLPTKSEL 85 KKSVALSGVTAGNTALCTVG+TGNDLHYRGYDILD+A++CEFEEIAHLLVHGKLPT +EL Sbjct: 12 KKSVALSGVTAGNTALCTVGKTGNDLHYRGYDILDVADSCEFEEIAHLLVHGKLPTAAEL 71 Query: 86 AAYKAKLKSLRGLPANVKAALEWVPASAHPMDVMRTGVSVLGTVLPEKEDHNTPGARDIA 145 AYKAKLK+LRGLPANVKAALEW+PA++HPMDVMRTGVS LG VLPEK+DHNTPGARDIA Sbjct: 72 RAYKAKLKALRGLPANVKAALEWLPAASHPMDVMRTGVSALGCVLPEKDDHNTPGARDIA 131 Query: 146 DRLMASLGSMLLYWYHYSHNGRRIEVETDDDSIGGHFLHLLHGEKPSALWERAMHTSLNL 205 DRLMASLGSMLLYWYHYSHNG RIEVETDDDSIG HFLHLLHGEKPS WE+AMHTSL L Sbjct: 132 DRLMASLGSMLLYWYHYSHNGNRIEVETDDDSIGAHFLHLLHGEKPSEAWEKAMHTSLIL 191 Query: 206 YAEHEFNASTFTARVIAGTGSDMYSSISGAIGALRGPKHGGANEVAFEIQKRYDNPDEAQ 265 YAEHEFNASTFT RVIAGTGSDMYS+I+GAIGALRGPKHGGANEVAFEIQKRYDNPDEA+ Sbjct: 192 YAEHEFNASTFTGRVIAGTGSDMYSAITGAIGALRGPKHGGANEVAFEIQKRYDNPDEAE 251 Query: 266 ADITRRVGNKEVVIGFGHPVYTTGDPRNQVIKEVAKKLSKDAGSMKMFDIAERLETVMWD 325 ADI RRV NKEVVIGFGHPVYT DPRN+VIKEVA+KLSK+AGS KMFDIAERLETVMWD Sbjct: 252 ADIRRRVENKEVVIGFGHPVYTISDPRNKVIKEVARKLSKEAGSTKMFDIAERLETVMWD 311 Query: 326 IKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNKIIRPSANYTG 385 IKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNKIIRPSANY G Sbjct: 312 IKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNKIIRPSANYVG 371 Query: 386 PENLKFVPIGKRK 398 PE+LKFVPIGKRK Sbjct: 372 PEDLKFVPIGKRK 384 Lambda K H 0.317 0.133 0.396 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: 635 Number of extensions: 13 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: 398 Length of database: 384 Length adjustment: 31 Effective length of query: 367 Effective length of database: 353 Effective search space: 129551 Effective search space used: 129551 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 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