Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_014027225.1 PYRFU_RS08315 2-isopropylmalate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_000223395.1:WP_014027225.1 Length = 396 Score = 372 bits (956), Expect = e-107 Identities = 192/375 (51%), Positives = 258/375 (68%) Query: 14 VRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIARE 73 +R+FDTTLRDGEQ GV L+ ++K+ IA+ LDE+ VD IEAGF A+S+ + K++ ARE Sbjct: 19 IRVFDTTLRDGEQMAGVELSLDDKIEIAKALDELRVDLIEAGFPASSDIDFKSVLFTARE 78 Query: 74 ELDAEVCSMARMVKGDVDAAVEAEADAVHIVVPTSEVHVKKKLRMDREEVLERAREVVEY 133 A+V +AR K D+D A EAEA +H+ + TS++H+K KLRM REEVL+RA E VEY Sbjct: 79 VSHAKVVGLARANKRDIDMAAEAEAHVIHVFIATSDIHMKYKLRMTREEVLQRAVEAVEY 138 Query: 134 ARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFLAVKKLR 193 A+ +G+ V S ED TR++ E+L +V+ A +EAGA+ + DTVGVM P M V+ +R Sbjct: 139 AKSYGVEVLFSAEDATRSDREFLAQVYRAVIEAGAKYINIPDTVGVMLPWEMEDLVRYIR 198 Query: 194 ERVGEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALEEVVVVLEE 253 ++ +V + VHCH+DFGMATANT+AAVR GA V VTVNG GERAGNAALEEVV L Sbjct: 199 SKLPPNVNIDVHCHNDFGMATANTIAAVRGGANGVQVTVNGFGERAGNAALEEVVATLHF 258 Query: 254 LYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADGILKDESTYEP 313 G+ T IR E+L E+S+LV G+++PPNK +VG+NAF HE+GIH G+L + TYEP Sbjct: 259 KMGLKTNIRLEKLYEVSRLVAAKFGIKLPPNKPIVGDNAFAHEAGIHVHGVLSNPLTYEP 318 Query: 314 IPPEKVGHERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKRLGDRGKRITEAD 373 IPPE VG +RR VLG+H G + LK +G D + + +LRR+K + KR+TE Sbjct: 319 IPPEAVGAKRRIVLGRHSGKHAVEYVLKHLGYDPTPDLVDYVLRRVKEVAPYAKRVTEDL 378 Query: 374 LRAIAEDVLGRPAER 388 +R I E+ L R Sbjct: 379 VRKIVEEFLAERTTR 393 Lambda K H 0.315 0.134 0.367 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: 518 Number of extensions: 17 Number of successful extensions: 1 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: 509 Length of database: 396 Length adjustment: 33 Effective length of query: 476 Effective length of database: 363 Effective search space: 172788 Effective search space used: 172788 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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