Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate N515DRAFT_2064 N515DRAFT_2064 citrate synthase
Query= BRENDA::Q9I5E3 (375 letters) >FitnessBrowser__Dyella79:N515DRAFT_2064 Length = 431 Score = 188 bits (477), Expect = 3e-52 Identities = 120/385 (31%), Positives = 199/385 (51%), Gaps = 22/385 (5%) Query: 11 GLRGQVAGQTALSTVGQEGAGLTYRGYDVRDLAAAAIFEEVAYLLLYGELPNKQQLDAYL 70 G + ++A++ + + L YRGY + LA + F E AYLLL GELP+K + + Sbjct: 49 GYGSTASTKSAITYIDGDQGVLLYRGYPIEQLAEKSSFLETAYLLLNGELPSKSEFVKFE 108 Query: 71 KKLQGQRDLPQALKEVLERIPKDAHPMDVMRTG-ASVLGTLEPELSFDQQRD---VADRL 126 + + ++LK+ + DAHPM ++ AS+ ++ D D A RL Sbjct: 109 DDITHHTMMHESLKDFFKGFHHDAHPMAMLAASVASLSAFYHDDIDVDDAEDRKLAAIRL 168 Query: 127 LAAFPAIMTYWYRFTHEGQRIDCNSDEPTIGGHFLALLHGKKPSE------LHVKVMNVS 180 +A P I +R++ G + FL ++ + PSE + K +++ Sbjct: 169 IAKMPTIAAACFRYSI-GWPFRYPRNNLEYVDRFLHMMF-EVPSEPLTLSPVAAKALDLL 226 Query: 181 LILYAEHEFNASTFTARVCASTLSDLYSCVTGAIGSLRGPLHGGANEAAMELIERFSSPQ 240 IL+A+HE NAST T R+ ST ++ Y+ + I +L GP HGGANEA ++++E + Sbjct: 227 FILHADHEQNASTSTVRLVGSTGANPYASIAAGITALWGPAHGGANEAVLKMLEEIGTAD 286 Query: 241 EATAELLKMLERKD--KIMGFGHAIYKDSDPRNEVIKGWSKQLADEVG------DKVLFA 292 + + + ++ D ++MGFGH +YK+ DPR ++I+ + ++ E+G + L Sbjct: 287 KVETAVKRAKDKNDNFRLMGFGHRVYKNFDPRAKIIREMTHKVLGELGVNDPLLEVALKL 346 Query: 293 VSEAIDKTMWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRTSGWTAHVFEQR--A 350 A+ + ++KL+PN DFY Y + IPT++FT +F +RT+GW AH EQ Sbjct: 347 EEAALKDDYFVERKLYPNVDFYSGIIYKALNIPTEMFTVMFAIARTAGWIAHWIEQHETP 406 Query: 351 NNRIIRPSAEYTGVEQRAFVPLEQR 375 RI RP YTG R +V ++R Sbjct: 407 GARIGRPRQIYTGANVRDYVSADKR 431 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: 400 Number of extensions: 22 Number of successful extensions: 5 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: 431 Length adjustment: 31 Effective length of query: 344 Effective length of database: 400 Effective search space: 137600 Effective search space used: 137600 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