Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate GFF1974 HP15_1931 2-methylcitrate synthase/citrate synthase II
Query= reanno::pseudo6_N2E2:Pf6N2E2_6062 (375 letters) >FitnessBrowser__Marino:GFF1974 Length = 376 Score = 583 bits (1504), Expect = e-171 Identities = 283/375 (75%), Positives = 324/375 (86%) Query: 1 MAEAKVLSGAGLRGQVAGQTALSTVGQSGAGLTYRGYDVRDLAADAQFEEVAYLLLYGEL 60 MAEAK LSGAGLRGQVAG+TAL TVG+SGAGLTYRGYD+ DLA AQFEE+AYLLL G+L Sbjct: 1 MAEAKQLSGAGLRGQVAGETALCTVGKSGAGLTYRGYDIADLAEKAQFEEIAYLLLRGKL 60 Query: 61 PTQAQLDAYTGKLRQLRDLPQALKEVLERIPADAHPMDVMRTGCSFLGNLEPEQDFSQQH 120 P + +LDAY KL+ LR LP ALK VLE+IP DAHPMDVMRTGCS LGNLE E+DFS+Q Sbjct: 61 PNRQELDAYKKKLQSLRGLPAALKTVLEQIPKDAHPMDVMRTGCSMLGNLETEEDFSEQD 120 Query: 121 DKTDRLLAAFPAIMCYWYRFSHQGQRIECVTDEVSIGGHFLHLLHGKKPSELHVKVMNVS 180 DK DR+LA FP+I+ YWYRF+H+G RIE +D SIGGHFL LLHGKKPSELH +VMNVS Sbjct: 121 DKIDRMLAVFPSIITYWYRFAHEGVRIETESDVDSIGGHFLELLHGKKPSELHERVMNVS 180 Query: 181 LILYAEHEFNASTFTARVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSSPQ 240 LILYAEHEFNASTFTARVCASTLSD+ SC+T AIGSLRGPLHGGANEAAM +I++F +P+ Sbjct: 181 LILYAEHEFNASTFTARVCASTLSDIHSCVTGAIGSLRGPLHGGANEAAMALIQKFKTPE 240 Query: 241 EAIEGTLGMLARKDKIMGFGHAIYKDNDPRNEVIKGWSKKLADEVGDTVLFPVSEAIDKT 300 EA EG +GML RK+KIMGFGHAIYK++DPRN +IK WSKKLA+EVGDTVL+PVSE + Sbjct: 241 EAEEGLMGMLERKEKIMGFGHAIYKESDPRNAIIKQWSKKLAEEVGDTVLYPVSERCEAV 300 Query: 301 MWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFEQRANNRIIRPSAE 360 MW +KKLF NADF+HASAYHFMGIPT+LFTPIFV SR++GW AHV EQR NNRIIRPSA+ Sbjct: 301 MWREKKLFCNADFFHASAYHFMGIPTELFTPIFVMSRVSGWTAHVKEQRENNRIIRPSAD 360 Query: 361 YTGVEQRKFVPIEQR 375 YTG K+VPIE+R Sbjct: 361 YTGPADAKWVPIEER 375 Lambda K H 0.321 0.135 0.406 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: 473 Number of extensions: 9 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: 376 Length adjustment: 30 Effective length of query: 345 Effective length of database: 346 Effective search space: 119370 Effective search space used: 119370 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 (21.9 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