Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate Ga0059261_0941 Ga0059261_0941 citrate synthase (EC 2.3.3.1)
Query= BRENDA::Q8NSH7 (381 letters) >FitnessBrowser__Korea:Ga0059261_0941 Length = 424 Score = 196 bits (498), Expect = 1e-54 Identities = 122/383 (31%), Positives = 190/383 (49%), Gaps = 11/383 (2%) Query: 9 GLNGVISDYTSISKVMPESNSLTYRGYAVEDLVENCSFEEVIYLLWFGELPTTEQLRTFN 68 G S + ++ + + +L +RGY + L E+ SF EV YLL GELP+ ++L TF+ Sbjct: 42 GFTSTASCESGLTYIDGDEGTLLHRGYPIGQLAEHSSFMEVAYLLLNGELPSKDELGTFS 101 Query: 69 TTGRSYRSLDAGLISLIHSLPNTCHPMDVLRTAVSYMGTFDPDPFTRDADHIRSIG-HNL 127 T + + L + HPM V+ V + F D + R + H L Sbjct: 102 NTITRHTMVHEQLATFYRGFRRDAHPMAVMCGVVGALSAFYHDSTDISDPYQRMVASHRL 161 Query: 128 LAQLPMVVAMDIRRRSGEEIIAPDHNKGIASNFLSMVFGNDDGSVANSADDIRDFERSLI 187 +A++P + AM + G+ + PD+N NFL M FG + R +R I Sbjct: 162 IAKMPTIAAMAYKYTVGQPFLYPDNNLSYTGNFLRMTFGVPAEEYVVNPVVERALDRIFI 221 Query: 188 LYAEHSFNASTFSARVISSTRSDTYSAITGAIGALKGPLHGGANEFVMHTMLDIDDPNNA 247 L+A+H NAST + R+ S+ ++ ++ I I L GP HGGANE ++ + +I P Sbjct: 222 LHADHEQNASTSTVRLAGSSGANPFACIAAGIACLWGPAHGGANEAALNMLREIGRPERI 281 Query: 248 ADWMGKALDRKE--RIMGFGHRVYKNGDSRVPSMEKSMRS-LAARHRGQKWVHMYESMQE 304 +++ +A D+ + R+MGFGHRVYKN D R M+K++R L+A + + ++E Sbjct: 282 PEYIARAKDKNDPFRLMGFGHRVYKNYDPRATVMQKTVREVLSALNVSDPLFDVALQLEE 341 Query: 305 V-----MEARTGIKPNLDFPAGPAYYMLGFPVDFFTPLFVLARVSGWTAHIVEQFE--NN 357 + + PN+DF +G +GFP FT LF LAR GW A E + Sbjct: 342 MALKDEYFVEKKLFPNVDFYSGVILSAIGFPTTMFTVLFALARTVGWVAQWNEMISDPDQ 401 Query: 358 ALIRPLSAYNGVEEREVVPISER 380 + RP Y G ER+ VP+ +R Sbjct: 402 KIGRPRQLYTGPTERDYVPLDKR 424 Lambda K H 0.319 0.134 0.398 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: 390 Number of extensions: 22 Number of successful extensions: 6 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: 381 Length of database: 424 Length adjustment: 31 Effective length of query: 350 Effective length of database: 393 Effective search space: 137550 Effective search space used: 137550 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