Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_012277579.1 SHAL_RS12975 citrate synthase
Query= reanno::pseudo6_N2E2:Pf6N2E2_6062 (375 letters) >NCBI__GCF_000019185.1:WP_012277579.1 Length = 429 Score = 192 bits (487), Expect = 2e-53 Identities = 128/381 (33%), Positives = 197/381 (51%), Gaps = 30/381 (7%) Query: 19 QTALSTVGQSGAGLTYRGYDVRDLAADAQFEEVAYLLLYGELPTQAQLDAYTGKLRQLRD 78 ++A++ + L +RGY + LA ++ + ++ YLLLYGELP +A+ + + ++ Sbjct: 54 ESAITYIDGEQGVLLHRGYPIDQLAVESDYLDLCYLLLYGELPNKAEYENFVYTVKTHTM 113 Query: 79 LPQALKEVLERIPADAHPMDVMRTGCSFLGNLEP-EQDFSQQHDKTDRLLAAFP------ 131 + + L DAHPM ++ C G L QD +D+ R +AA+ Sbjct: 114 VNEQLASFFRGFRRDAHPMAML---CGVTGALSAFYQDSLDVNDERHREIAAYRLVSKMP 170 Query: 132 --AIMCYWYRFSHQGQRIECVTDEVSIGGHFLHLLHGKKPSELHV-----KVMNVSLILY 184 A MCY Y GQ +E+S G+FL ++ G E V + M+ IL+ Sbjct: 171 TIAAMCYKYSI---GQPFVYPRNELSYAGNFLSMMFGVPCEEYKVNPIVERAMDRIFILH 227 Query: 185 AEHEFNASTFTARVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSSPQEAIE 244 A+HE NAST T R+ S+ ++ F+CI A I SL GP HGGANEA + M+E S E Sbjct: 228 ADHEQNASTSTVRLAGSSGANPFACIAAGIASLWGPAHGGANEACLNMLEEIGSVDRIPE 287 Query: 245 GTLGMLARKD--KIMGFGHAIYKDNDPRNEVIKGWSKKLADE--VGDTVLFPVSE----A 296 ++D ++MGFGH +YK+ DPR +V++ ++ E V D +L E A Sbjct: 288 FIARAKDKEDPFRLMGFGHRVYKNFDPRAKVMRETCHEVLAELKVNDPLLDVAMELERIA 347 Query: 297 IDKTMWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFE--QRANNRI 354 ++ + KKL+PN DFY +GIPT +FT +F +R GW AH E + ++I Sbjct: 348 LEDEYFVSKKLYPNVDFYSGIIMKAIGIPTSMFTVLFALARTVGWIAHWKEMLDQPGHKI 407 Query: 355 IRPSAEYTGVEQRKFVPIEQR 375 RP YTG +R F+ ++R Sbjct: 408 SRPRQLYTGDPKRDFIDKDKR 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: 358 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: 429 Length adjustment: 31 Effective length of query: 344 Effective length of database: 398 Effective search space: 136912 Effective search space used: 136912 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 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