Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate PP_2335 PP_2335 methylcitrate synthase
Query= BRENDA::Q9I5E3 (375 letters) >FitnessBrowser__Putida:PP_2335 Length = 375 Score = 673 bits (1737), Expect = 0.0 Identities = 332/375 (88%), Positives = 348/375 (92%) Query: 1 MAEAKVLSGAGLRGQVAGQTALSTVGQEGAGLTYRGYDVRDLAAAAIFEEVAYLLLYGEL 60 MAEAKVLSGAGLRGQVAGQTALSTVGQ GAGLTYRGYDVRDLAA A FEEVAYLLLYGEL Sbjct: 1 MAEAKVLSGAGLRGQVAGQTALSTVGQAGAGLTYRGYDVRDLAAGAEFEEVAYLLLYGEL 60 Query: 61 PNKQQLDAYLKKLQGQRDLPQALKEVLERIPKDAHPMDVMRTGASVLGTLEPELSFDQQR 120 P + +L Y +KL+G RDLPQALKEVLERIP+DAHPMDVMRTG SVLGTLEPEL+F+ QR Sbjct: 61 PTQAELADYKRKLKGLRDLPQALKEVLERIPRDAHPMDVMRTGCSVLGTLEPELTFEAQR 120 Query: 121 DVADRLLAAFPAIMTYWYRFTHEGQRIDCNSDEPTIGGHFLALLHGKKPSELHVKVMNVS 180 D DRLLA FPA+M YWYRFTH G RIDC +DE T+GGHFL LLHGKKPSELHVKVMNVS Sbjct: 121 DKTDRLLALFPAVMCYWYRFTHHGVRIDCTTDEDTLGGHFLHLLHGKKPSELHVKVMNVS 180 Query: 181 LILYAEHEFNASTFTARVCASTLSDLYSCVTGAIGSLRGPLHGGANEAAMELIERFSSPQ 240 LILYAEHEFNASTFTARVCASTLSDLYSCVT AIGSLRGPLHGGANEAAMELIERF SPQ Sbjct: 181 LILYAEHEFNASTFTARVCASTLSDLYSCVTAAIGSLRGPLHGGANEAAMELIERFQSPQ 240 Query: 241 EATAELLKMLERKDKIMGFGHAIYKDSDPRNEVIKGWSKQLADEVGDKVLFAVSEAIDKT 300 EATAELL+MLERKDKIMGFGHAIYK+SDPRNEVIKGWSKQLADEVGDKVL+ VSEAIDKT Sbjct: 241 EATAELLRMLERKDKIMGFGHAIYKESDPRNEVIKGWSKQLADEVGDKVLYPVSEAIDKT 300 Query: 301 MWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRTSGWTAHVFEQRANNRIIRPSAE 360 MWEQK+LFPNADFYHASAYHFMGIPTKLFTPIFVCSR +GW AHVFEQRANNRIIRPSAE Sbjct: 301 MWEQKRLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFEQRANNRIIRPSAE 360 Query: 361 YTGVEQRAFVPLEQR 375 Y GVEQR FVP+EQR Sbjct: 361 YVGVEQRQFVPIEQR 375 Lambda K H 0.319 0.134 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: 580 Number of extensions: 12 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: 375 Length adjustment: 30 Effective length of query: 345 Effective length of database: 345 Effective search space: 119025 Effective search space used: 119025 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 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