Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_011320730.1 AVA_RS20495 homocitrate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_000204075.1:WP_011320730.1 Length = 372 Score = 296 bits (759), Expect = 6e-85 Identities = 156/355 (43%), Positives = 222/355 (62%), Gaps = 2/355 (0%) Query: 14 VRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIARE 73 + I DTTLRDGEQ G+A EEK+ IA LD IGV +E G A E ++I RIA+ Sbjct: 6 IHINDTTLRDGEQAAGIAFNVEEKIAIASLLDSIGVHELEVGIPAMGHEEAESITRIAKL 65 Query: 74 ELDAEVCSMARMVKGDVDAAVEAEADAVHIVVPTSEVHVKKKLRMDREEVLERAREVVEY 133 L+A++ R D+ A+++ D VH+ VP S++ + K + R+ VL++ R+ + + Sbjct: 66 GLNAKLLGWNRANLSDIQASIDCGLDRVHVSVPVSDIQIAAKFKGQRQLVLDKLRDAINF 125 Query: 134 ARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFLAVKKLR 193 A D GL+V + ED +R + +L EV + E GA R + DTVG++ P + V L Sbjct: 126 ACDRGLSVSVGGEDSSRADESFLLEVAQSAQEWGAFRFRFCDTVGILDPTTTYKKVSHLV 185 Query: 194 ERVGEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALEEVVVVLEE 253 + +++ +H HDDFGMA ANT+A V+AGA V+ TVNGIGERAGNA LEEVV+ L+ Sbjct: 186 SHLS--IVIEMHTHDDFGMALANTLAGVKAGAISVNTTVNGIGERAGNAPLEEVVMGLKY 243 Query: 254 LYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADGILKDESTYEP 313 LY + TGI T+RL E+S+LV + T V P KA+VGEN F HESGIHA G+L++ TYEP Sbjct: 244 LYDIPTGIDTKRLVEVSRLVSKATNFPVLPWKAIVGENTFAHESGIHAHGVLQNPITYEP 303 Query: 314 IPPEKVGHERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKRLGDRGKR 368 PE VG ERR V+GKH G ++ L+Q G+ + ++ +L ++ + KR Sbjct: 304 FAPEDVGWERRLVVGKHSGRHLLLSVLEQHGITLGQAEIQSVLDAVRHQSVKTKR 358 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: 419 Number of extensions: 19 Number of successful extensions: 2 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: 372 Length adjustment: 32 Effective length of query: 477 Effective length of database: 340 Effective search space: 162180 Effective search space used: 162180 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 Jul 25 2024. The underlying query database was built on Jul 25 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