Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate AZOBR_RS24300 AZOBR_RS24300 methylcitrate synthase
Query= BRENDA::Q2Z1A8 (398 letters) >FitnessBrowser__azobra:AZOBR_RS24300 Length = 387 Score = 655 bits (1690), Expect = 0.0 Identities = 322/388 (82%), Positives = 348/388 (89%), Gaps = 2/388 (0%) Query: 11 AAPDATASEPAAPRVKKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEFEEI 70 +AP+ A P P KKSVALSGVTAGNTALCTVG++GNDLHYRGYDILDIAE CEFEE+ Sbjct: 2 SAPETAAPTPFKP--KKSVALSGVTAGNTALCTVGKSGNDLHYRGYDILDIAERCEFEEV 59 Query: 71 AHLLVHGKLPTKSELAAYKAKLKSLRGLPANVKAALEWVPASAHPMDVMRTGVSVLGTVL 130 A+LLVHGKLPT +EL AYKAKL+SLRGLP NV+ ALE +PASAHPMDVMRTGVS LG L Sbjct: 60 AYLLVHGKLPTFAELKAYKAKLQSLRGLPTNVRQALECLPASAHPMDVMRTGVSALGCAL 119 Query: 131 PEKEDHNTPGARDIADRLMASLGSMLLYWYHYSHNGRRIEVETDDDSIGGHFLHLLHGEK 190 PEK+DHN PGARDIADRLMASLGSMLLYWYH+S NGRRIEVETDD+SIG HFLHLLHG K Sbjct: 120 PEKDDHNIPGARDIADRLMASLGSMLLYWYHWSSNGRRIEVETDDESIGAHFLHLLHGRK 179 Query: 191 PSALWERAMHTSLNLYAEHEFNASTFTARVIAGTGSDMYSSISGAIGALRGPKHGGANEV 250 PSALWERAMHTSL LYAEHEFNASTFT RVIAGTGSD+YS+I+GAIGALRGPKHGGANEV Sbjct: 180 PSALWERAMHTSLILYAEHEFNASTFTGRVIAGTGSDLYSAITGAIGALRGPKHGGANEV 239 Query: 251 AFEIQKRYDNPDEAQADITRRVGNKEVVIGFGHPVYTTGDPRNQVIKEVAKKLSKDAGSM 310 AFEIQKRYD PDEA+ADI RRV NKEVVIGFGHPVYT DPRN VI+ VA KLS DAGS Sbjct: 240 AFEIQKRYDTPDEAEADIRRRVENKEVVIGFGHPVYTVSDPRNDVIRGVAHKLSVDAGSA 299 Query: 311 KMFDIAERLETVMWDIKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQ 370 +MFDIA RLE VMW++K+MFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQ Sbjct: 300 RMFDIAARLEAVMWEVKRMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQ 359 Query: 371 RIDNKIIRPSANYTGPENLKFVPIGKRK 398 RIDNKIIRPSANY GP++ FV I +R+ Sbjct: 360 RIDNKIIRPSANYVGPDDRVFVAIDQRQ 387 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: 588 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: 387 Length adjustment: 31 Effective length of query: 367 Effective length of database: 356 Effective search space: 130652 Effective search space used: 130652 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