Align 2-methylcitrate synthase; 2-MCS; MCS; Citrate synthase; EC 2.3.3.5; EC 2.3.3.16 (characterized)
to candidate H281DRAFT_06634 H281DRAFT_06634 2-methylcitrate synthase (EC 2.3.3.5)
Query= SwissProt::Q937N9 (385 letters) >FitnessBrowser__Burk376:H281DRAFT_06634 Length = 287 Score = 489 bits (1260), Expect = e-143 Identities = 236/273 (86%), Positives = 254/273 (93%) Query: 11 KPKKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEFEEIAHLLVHGKLPTKS 70 KPKKSVALSGVTAGNTALCTVG+TGNDLHYRGYDILDIA CEFEEIA+LLVH KLPT++ Sbjct: 15 KPKKSVALSGVTAGNTALCTVGKTGNDLHYRGYDILDIAGNCEFEEIAYLLVHEKLPTQA 74 Query: 71 ELAAYKAKLKSLRGLPANVKAALEWVPASAHPMDVMRTGVSVLGTVLPEKEDHNTPGARD 130 EL AYK KLK+LRGLPANVKAALEW+PA+AHPMDVMRTGVSVLGTVLPEK+DHN PGARD Sbjct: 75 ELTAYKTKLKALRGLPANVKAALEWIPAAAHPMDVMRTGVSVLGTVLPEKDDHNLPGARD 134 Query: 131 IADRLMASLGSMLLYWYHYSHNGRRIEVETDDDSIGGHFLHLLHGEKPSALWERAMNTSL 190 IAD+LMASLGSMLLYWYHYSHNG+RIEVETDDDSIGGHFLHLLHG +PS W AM+ SL Sbjct: 135 IADKLMASLGSMLLYWYHYSHNGKRIEVETDDDSIGGHFLHLLHGVEPSKSWVDAMHVSL 194 Query: 191 NLYAEHEFNASTFTARVIAGTGSDMYSSISGAIGALRGPKHGGANEVAFEIQKRYDNPDE 250 NLYAEHEFNASTFT RVIAGTGSD+YS+I+GAIGALRGPKHGGANEVAFEIQ RY PDE Sbjct: 195 NLYAEHEFNASTFTGRVIAGTGSDIYSAITGAIGALRGPKHGGANEVAFEIQSRYQTPDE 254 Query: 251 AQADITRRVENKEVVIGFGHPVYTTGDPRNQVI 283 A++DI RRVENKEVVIGFGHPVYT DPRN+VI Sbjct: 255 AESDIRRRVENKEVVIGFGHPVYTISDPRNKVI 287 Lambda K H 0.317 0.133 0.394 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: 457 Number of extensions: 8 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: 385 Length of database: 287 Length adjustment: 28 Effective length of query: 357 Effective length of database: 259 Effective search space: 92463 Effective search space used: 92463 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: 49 (23.5 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