Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate GFF1554 HP15_1516 type II citrate synthase
Query= BRENDA::Q9I5E3 (375 letters) >FitnessBrowser__Marino:GFF1554 Length = 424 Score = 196 bits (499), Expect = 8e-55 Identities = 122/381 (32%), Positives = 204/381 (53%), Gaps = 26/381 (6%) Query: 11 GLRGQVAGQTALSTVGQEGAGLTYRGYDVRDLAAAAIFEEVAYLLLYGELPNKQQLDAYL 70 G A ++A++ + L +RGY + LA + + EV YLLL+GELP+ ++ + Sbjct: 45 GFVSTAACESAITYIDGANGVLLHRGYPIEQLAEHSDYLEVCYLLLHGELPSAEENQKFH 104 Query: 71 KKLQGQRDLPQALKEVLERIPKDAHPMDVMRTGASVLGTL------EPELSFDQQRDV-A 123 ++ L ++ + +DAHPM +M V+G L E +++ +QR++ A Sbjct: 105 DTIKNHTMLHDQMRNFFQGFRRDAHPMAIM---CGVVGALSAFYHGEMDVASQEQREITA 161 Query: 124 DRLLAAFPAIMTYWYRFTHEGQRIDCNSDEPTIGGHFLALLHGK-----KPSELHVKVMN 178 RL+A P I + Y++ GQ ++ + +FL ++ G KP+ + K M+ Sbjct: 162 HRLIAKMPTIAAWCYKYAI-GQPFIYPRNDLSYSENFLQMMFGVPCEEYKPNPILAKAMD 220 Query: 179 VSLILYAEHEFNASTFTARVCASTLSDLYSCVTGAIGSLRGPLHGGANEAAMELIERFSS 238 IL+A+HE NAST T R+ ST ++ Y+C+ I +L GP HGGANEA ++++ Sbjct: 221 KIFILHADHEQNASTSTVRLAGSTGANPYACIASGIAALWGPAHGGANEAVLDMLAEIGD 280 Query: 239 PQEATAELLKMLERKD--KIMGFGHAIYKDSDPRNEVIKGWSKQLADEVG--DKVLFAVS 294 + K ++ D ++MGFGH +YK+ DPR +V+ + ++ E+G + L ++ Sbjct: 281 ESNIEKFIAKAKDKDDPFRLMGFGHRVYKNFDPRAKVMAETAHEVLTELGLENDPLLKIA 340 Query: 295 EAIDKTMWE-----QKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRTSGWTAHVFEQR 349 + ++K E ++KL+PN DFY +GIPT +FT IF SRT GW +H E Sbjct: 341 QRLEKIALEDEYFVKRKLYPNVDFYSGLILKAIGIPTSMFTVIFALSRTIGWFSHWNEMV 400 Query: 350 ANN-RIIRPSAEYTGVEQRAF 369 + + RI RP YTG + R + Sbjct: 401 SGDYRIGRPRQLYTGSDSRDY 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: 379 Number of extensions: 23 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: 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 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