Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate GFF2275 Psest_2320 2-methylcitrate synthase/citrate synthase II
Query= BRENDA::Q9I5E3 (375 letters) >FitnessBrowser__psRCH2:GFF2275 Length = 375 Score = 628 bits (1620), Expect = 0.0 Identities = 308/375 (82%), Positives = 338/375 (90%) Query: 1 MAEAKVLSGAGLRGQVAGQTALSTVGQEGAGLTYRGYDVRDLAAAAIFEEVAYLLLYGEL 60 MAEAKVLSGAGLRGQ+AGQTAL TVG+ GAGLTYRGYDVRDLAA FEEVAYLL YGEL Sbjct: 1 MAEAKVLSGAGLRGQIAGQTALCTVGKTGAGLTYRGYDVRDLAAECDFEEVAYLLFYGEL 60 Query: 61 PNKQQLDAYLKKLQGQRDLPQALKEVLERIPKDAHPMDVMRTGASVLGTLEPELSFDQQR 120 P QQL Y +L+ RDLPQALKEVLERIP +AHPMDVMRTG+SVLGTLEPE+SF+QQR Sbjct: 61 PTAQQLADYKNRLKTMRDLPQALKEVLERIPANAHPMDVMRTGSSVLGTLEPEVSFEQQR 120 Query: 121 DVADRLLAAFPAIMTYWYRFTHEGQRIDCNSDEPTIGGHFLALLHGKKPSELHVKVMNVS 180 DVA+RL+AAFPAIM YWYRFTH+G RI+C SDE T+GGHFLALLH KKPS+LHVKVMNVS Sbjct: 121 DVAERLMAAFPAIMCYWYRFTHDGVRINCTSDEDTLGGHFLALLHDKKPSDLHVKVMNVS 180 Query: 181 LILYAEHEFNASTFTARVCASTLSDLYSCVTGAIGSLRGPLHGGANEAAMELIERFSSPQ 240 LILYAEHEFNASTFTARVCASTLSDLYSCVTGAIGSLRGPLHGGANEAAM++IE+++SP+ Sbjct: 181 LILYAEHEFNASTFTARVCASTLSDLYSCVTGAIGSLRGPLHGGANEAAMDMIEQWTSPE 240 Query: 241 EATAELLKMLERKDKIMGFGHAIYKDSDPRNEVIKGWSKQLADEVGDKVLFAVSEAIDKT 300 EA +L MLERKDKIMGFGHAIY SDPRNEVIK W+K+LADEVGD VL+ VS A+D+T Sbjct: 241 EAREAILGMLERKDKIMGFGHAIYSVSDPRNEVIKVWAKKLADEVGDTVLYPVSVAVDET 300 Query: 301 MWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRTSGWTAHVFEQRANNRIIRPSAE 360 MWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSR +GW +HVFEQR+NNRIIRPSAE Sbjct: 301 MWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRVTGWASHVFEQRSNNRIIRPSAE 360 Query: 361 YTGVEQRAFVPLEQR 375 Y G EQR VP+ QR Sbjct: 361 YIGPEQRKVVPIAQR 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: 554 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: 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