Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_007152345.1 MDG893_RS03515 citrate (Si)-synthase
Query= BRENDA::Q9I5E3 (375 letters) >NCBI__GCF_000170835.1:WP_007152345.1 Length = 424 Score = 194 bits (494), Expect = 3e-54 Identities = 121/360 (33%), Positives = 197/360 (54%), Gaps = 26/360 (7%) Query: 32 LTYRGYDVRDLAAAAIFEEVAYLLLYGELPNKQQLDAYLKKLQGQRDLPQALKEVLERIP 91 L +RGY + +LA + + EV YLLL GELP ++ + ++ L ++ + Sbjct: 66 LLHRGYPIEELAENSDYLEVCYLLLNGELPTAEENKRFHDTIKNHTMLHDQMRNFFQGFR 125 Query: 92 KDAHPMDVMRTGASVLGTL------EPELSFDQQRDV-ADRLLAAFPAIMTYWYRFTHEG 144 +DAHPM +M V+G L + +++ +QR++ A RL+A P I + Y+++ G Sbjct: 126 RDAHPMAIM---CGVVGALSAFYHDQMDVTNIEQREITAHRLVAKMPTIAAWCYKYSI-G 181 Query: 145 QRIDCNSDEPTIGGHFLALLHGK-----KPSELHVKVMNVSLILYAEHEFNASTFTARVC 199 Q ++ T +FL ++ G KP+ + K M+ IL+A+HE NAST T R+ Sbjct: 182 QPFMYPRNDLTYSENFLQMMFGVPCEEYKPNPILAKAMDKIFILHADHEQNASTSTVRLA 241 Query: 200 ASTLSDLYSCVTGAIGSLRGPLHGGANEAAMELIERFSSPQEATAELLKMLERKD--KIM 257 ST ++ Y+C+ I +L GP HGGANEA ++++ + K ++ D ++M Sbjct: 242 GSTGANPYACIASGIAALWGPAHGGANEAVLDMLAEIGDESNIEKFIAKAKDKDDPFRLM 301 Query: 258 GFGHAIYKDSDPRNEVIKGWSKQLADEVG--DKVLFAVSEAIDKTMWE-----QKKLFPN 310 GFGH +YK+ DPR +V+ + ++ E+G + L +++ ++K E Q+KL+PN Sbjct: 302 GFGHRVYKNFDPRAKVMAETAHEVLTELGLENDPLLKIAQRLEKIALEDEYFVQRKLYPN 361 Query: 311 ADFYHASAYHFMGIPTKLFTPIFVCSRTSGWTAHVFEQRANN-RIIRPSAEYTGVEQRAF 369 DFY +GIPT +FT IF SRT GW +H E + + RI RP YTG E R++ Sbjct: 362 VDFYSGLILKAIGIPTSMFTVIFALSRTIGWFSHWNEMVSGDYRIGRPRQLYTGSEARSY 421 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: 368 Number of extensions: 23 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: 375 Length of database: 424 Length adjustment: 31 Effective length of query: 344 Effective length of database: 393 Effective search space: 135192 Effective search space used: 135192 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 24 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