Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_101589879.1 BJEO58_RS12875 citrate synthase
Query= reanno::pseudo6_N2E2:Pf6N2E2_6062 (375 letters) >NCBI__GCF_900169175.1:WP_101589879.1 Length = 428 Score = 206 bits (524), Expect = 1e-57 Identities = 127/386 (32%), Positives = 208/386 (53%), Gaps = 23/386 (5%) Query: 11 GLRGQVAGQTALSTVGQSGAGLTYRGYDVRDLAADAQFEEVAYLLLYGELPTQAQLDAYT 70 G + +A++ + L YRGYD+ DL + F EV+YLL+YGELPT QL + Sbjct: 45 GFANTASLSSAITYIDGDEGILRYRGYDIADLTEKSTFVEVSYLLIYGELPTPEQLADFD 104 Query: 71 GKLRQLRDLPQALKEVLERIPADAHPMDVMRTGCSFLGNLEPEQ----DFSQQHDKTDRL 126 G+LR+ L + ++ + P DAHPM ++ + + + + D +Q T RL Sbjct: 105 GRLREHTLLHEDMRRFFQAFPYDAHPMPMVSSAIAAMSTFYQDSLSITDEAQIDISTARL 164 Query: 127 LAAFPAIMCYWYRFSHQGQRIECVTDEVSIGGHFLHLLHGKKPSE------LHVKVMNVS 180 LA P I + +R + +G + + + + +FL + G PSE L +K ++ Sbjct: 165 LAKMPTIAAFAHRHA-EGVPVVFPDNNLGLVENFLRVNFG-FPSEDYEVDPLALKALDQL 222 Query: 181 LILYAEHEFNASTFTARVCASTLSDLFSCITAAIGSLRGPLHGGANEAAMEMIERFSSPQ 240 IL+A+HE N ST T R+ S+ ++L+ I+A I +L GPLHGGAN A +EM+E + Sbjct: 223 FILHADHEQNCSTSTVRLVGSSQANLYQSISAGIHALAGPLHGGANSAVLEMLEEIQASD 282 Query: 241 EAIEGTLGMLARKD---KIMGFGHAIYKDNDPRNEVIKGWSKKLADEVG--DTVLFPVSE 295 + + + + K+ ++MGFGH +YK+ DPR +IK + ++ +++G D +L + Sbjct: 283 DGPKKFMERVKNKEDGVRLMGFGHRVYKNYDPRATIIKKTADEVLEKLGGNDEMLQLAKD 342 Query: 296 ----AIDKTMWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRLTGWAAHVFE--QR 349 A+ + ++KL+PN DFY Y +G PT +FT +F RL GW A E + Sbjct: 343 LEEIALADDYFVERKLYPNVDFYTGLIYKALGFPTNMFTVLFAVGRLPGWIAQWREAAKD 402 Query: 350 ANNRIIRPSAEYTGVEQRKFVPIEQR 375 + +I RP YTG +R + P++ R Sbjct: 403 SETKIGRPRQIYTGAPKRLYTPVDDR 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: 370 Number of extensions: 21 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 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