Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate 201087 SO1926 citrate synthase (NCBI ptt file)
Query= reanno::pseudo6_N2E2:Pf6N2E2_6062 (375 letters) >FitnessBrowser__MR1:201087 Length = 428 Score = 192 bits (487), Expect = 2e-53 Identities = 129/387 (33%), Positives = 197/387 (50%), Gaps = 26/387 (6%) Query: 11 GLRGQVAGQTALSTVGQSGAGLTYRGYDVRDLAADAQFEEVAYLLLYGELPTQAQLDAYT 70 G + ++A++ + L +RGY + LA D+ + ++ YLLLYGELPT+ Q + Sbjct: 46 GFLATASCESAITYIDGDQGILLHRGYPIEQLAVDSDYLDLCYLLLYGELPTKEQYAEFV 105 Query: 71 GKLRQLRDLPQALKEVLERIPADAHPMDVMRTGCSFLGNLEP-EQDFSQQHDKTDRLLAA 129 ++ + + + DAHPM ++ C G L QD +D R +AA Sbjct: 106 HTVKTHTMVHEQIAFFFRGFRRDAHPMAML---CGVTGALSAFYQDSLDVNDPRHREIAA 162 Query: 130 F------PAIMCYWYRFSHQGQRIECVTDEVSIGGHFLHLLHGKKPSELHV-----KVMN 178 + P I Y++S GQ +++S G+FL ++ E V + M+ Sbjct: 163 YRLVSKMPTIAAMCYKYS-SGQPFVYPRNDLSYAGNFLSMMFAVPCEEYKVNPIVERAMD 221 Query: 179 VSLILYAEHEFNASTFTARVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSS 238 IL+A+HE NAST T R+ S+ ++ F+CI A I SL GP HGGANEA ++M+E S Sbjct: 222 RIFILHADHEQNASTSTVRLAGSSGANPFACIAAGIASLWGPAHGGANEACLQMLEEIGS 281 Query: 239 PQEAIEGTLGMLARKD--KIMGFGHAIYKDNDPRNEVIKGWSKKLADE--VGDTVLFPVS 294 E + D ++MGFGH +YK+ DPR +V++ ++ E V D +L Sbjct: 282 VDRIPEFIARAKDKNDPFRLMGFGHRVYKNFDPRAKVMRETCHEVLKELKVQDPLLDVAM 341 Query: 295 E----AIDKTMWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFE--Q 348 E A++ + KKL+PN DFY +GIPT +FT +F SR GW AH E Sbjct: 342 ELERIALEDEYFISKKLYPNVDFYSGIIMKAIGIPTSMFTVLFALSRTVGWIAHWKEMLD 401 Query: 349 RANNRIIRPSAEYTGVEQRKFVPIEQR 375 + ++I RP YTG R FV +++R Sbjct: 402 QPGHKISRPRQLYTGETARDFVDLDKR 428 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: 366 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: 428 Length adjustment: 31 Effective length of query: 344 Effective length of database: 397 Effective search space: 136568 Effective search space used: 136568 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