Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate BPHYT_RS30150 BPHYT_RS30150 methylcitrate synthase
Query= BRENDA::Q2Z1A8 (398 letters) >FitnessBrowser__BFirm:BPHYT_RS30150 Length = 389 Score = 670 bits (1728), Expect = 0.0 Identities = 324/390 (83%), Positives = 357/390 (91%), Gaps = 5/390 (1%) Query: 8 APDAAPDATASEPAAPRVKKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEF 67 A ++ P+A A +P KKSVALSGVTAGNTALCTVG+TGNDLHYRGYDILDIA CEF Sbjct: 4 ADNSTPNAGAFKP-----KKSVALSGVTAGNTALCTVGKTGNDLHYRGYDILDIASACEF 58 Query: 68 EEIAHLLVHGKLPTKSELAAYKAKLKSLRGLPANVKAALEWVPASAHPMDVMRTGVSVLG 127 EEIA+LLVH KLPT++EL AYK KLK+LRGLPANVKAALEW+PA+AHPMDVMRTGVSVLG Sbjct: 59 EEIAYLLVHEKLPTQAELTAYKTKLKALRGLPANVKAALEWIPAAAHPMDVMRTGVSVLG 118 Query: 128 TVLPEKEDHNTPGARDIADRLMASLGSMLLYWYHYSHNGRRIEVETDDDSIGGHFLHLLH 187 TVLPEK+DHN PGARDIAD+LMASLGSMLLYWYHYSHNG+RIEVETDDDSIGGHFLHLLH Sbjct: 119 TVLPEKDDHNLPGARDIADKLMASLGSMLLYWYHYSHNGKRIEVETDDDSIGGHFLHLLH 178 Query: 188 GEKPSALWERAMHTSLNLYAEHEFNASTFTARVIAGTGSDMYSSISGAIGALRGPKHGGA 247 G +PS W AMH SLNLYAEHEFNASTFT RVIAGTGSD+YS+I+GAIGALRGPKHGGA Sbjct: 179 GVEPSKAWVDAMHVSLNLYAEHEFNASTFTGRVIAGTGSDIYSAITGAIGALRGPKHGGA 238 Query: 248 NEVAFEIQKRYDNPDEAQADITRRVGNKEVVIGFGHPVYTTGDPRNQVIKEVAKKLSKDA 307 NEVAFEIQ RY PDEA+ADI +RV NKEVVIGFGHPVYT DPRN+VIKE+A+KLSK+A Sbjct: 239 NEVAFEIQSRYQTPDEAEADIRKRVENKEVVIGFGHPVYTISDPRNKVIKEIARKLSKEA 298 Query: 308 GSMKMFDIAERLETVMWDIKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHI 367 G+ K+F+IAERLE+VMWD KKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIART+GW+AHI Sbjct: 299 GNSKLFNIAERLESVMWDAKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTAGWSAHI 358 Query: 368 IEQRIDNKIIRPSANYTGPENLKFVPIGKR 397 IEQRIDNKIIRPSANYTGP++L FVP+ KR Sbjct: 359 IEQRIDNKIIRPSANYTGPDDLPFVPLAKR 388 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: 623 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: 398 Length of database: 389 Length adjustment: 31 Effective length of query: 367 Effective length of database: 358 Effective search space: 131386 Effective search space used: 131386 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