Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_011020307.1 MA_RS01330 citrate (Si)-synthase
Query= BRENDA::Q9I5E3 (375 letters) >NCBI__GCF_000007345.1:WP_011020307.1 Length = 355 Score = 228 bits (582), Expect = 1e-64 Identities = 129/345 (37%), Positives = 196/345 (56%), Gaps = 16/345 (4%) Query: 26 GQEGAGLTYRGYDVRDLAAAAIFEEVAYLLLYGELPNKQQLDAYLKKLQGQRDLPQALKE 85 G EG L YR D+ +L ++ V+YLL+ G LP +Q+L Y +L +R + + + + Sbjct: 10 GLEGV-LKYREVDINELVKLP-YDAVSYLLIRGRLPGEQELAEYSARLHAERRINKEVID 67 Query: 86 VLERIPKDAHPMDVMRTGASVLGTLEPEL---SFDQQRDVADRLLAAFPAIMTYWYRFTH 142 V+ + M +RT S + +P+L S + A RL+A P I+ +YR + Sbjct: 68 VIRMCNFNIDAMAALRTVISFISQFDPDLNDSSPEGNMRKAIRLIAIVPTIVATYYRMAN 127 Query: 143 EGQRIDCNSDEPTI--GGHFLALLHGKKPSELHVKVMNVSLILYAEHEFNASTFTARVCA 200 + + +P++ G +FL ++ G KP L +VM IL AEHE NASTF++RV A Sbjct: 128 GKEPLP---PDPSLSHGANFLYMIKGSKPDPLDAEVMEKDFILSAEHELNASTFSSRVTA 184 Query: 201 STLSDLYSCVTGAIGSLRGPLHGGANEAAMELIERFSSPQEATAELLKMLERKDKIMGFG 260 ST+SDLYS V + +L+GPLHGGA M +++ +SP+ A +L+ + +++KIMGFG Sbjct: 185 STMSDLYSAVVSGLCTLKGPLHGGARAEVMTMLDEVASPENAEKFVLEKISQREKIMGFG 244 Query: 261 HAIYKDSDPRNEVIKGWSKQLADEVGDKVLFAVSEAIDKTMWEQ------KKLFPNADFY 314 H +YK DPR + K SK+LA+ GD + +EA++ + + K ++PN DFY Sbjct: 245 HRVYKTYDPRGVIFKQLSKKLAESKGDMHWYTTAEAVENVVVRELVEKRGKPIYPNVDFY 304 Query: 315 HASAYHFMGIPTKLFTPIFVCSRTSGWTAHVFEQRANNRIIRPSA 359 Y +M IP +L T IF R SGW AH F+Q +IIRP A Sbjct: 305 SGVIYKYMEIPPQLATSIFAIGRVSGWIAHCFDQYERKKIIRPRA 349 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: 327 Number of extensions: 16 Number of successful extensions: 3 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: 355 Length adjustment: 30 Effective length of query: 345 Effective length of database: 325 Effective search space: 112125 Effective search space used: 112125 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: 49 (23.5 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