Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_011383972.1 AMB_RS07875 homocitrate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_000009985.1:WP_011383972.1 Length = 381 Score = 283 bits (724), Expect = 8e-81 Identities = 157/356 (44%), Positives = 217/356 (60%), Gaps = 2/356 (0%) Query: 18 DTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIAREELDA 77 DTTLRDGEQT GVA +EKL IAR LD GV IE G A E AIR++A L A Sbjct: 11 DTTLRDGEQTAGVAFRLDEKLDIARTLDIAGVPEIEVGIPAMGAEEQAAIRKVAGLGLKA 70 Query: 78 EVCSMARMVKGDVDAAVEAEADAVHIVVPTSEVHVKKKLRMDREEVLERAREVVEYARDH 137 + + RM++ D++AA + V++ +P S++ + K+ DR LE R +V AR Sbjct: 71 RLIAWCRMMEDDLEAAALCDVATVNLSIPVSDLQLAAKMGRDRAWALEHIRVMVGKARAM 130 Query: 138 GLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFLAVKKLRERVG 197 G V + ED +R + +L +V AC AGA+R + DT+G+M P + A + LR Sbjct: 131 GFDVLVGGEDSSRADPAFLADVVRACEAAGAQRFRFADTMGIMDPFAVHDAFRALRAATS 190 Query: 198 EDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALEEVVVVLEELYGV 257 + L +H HDD G+ATAN++AAVR GA V TVNG+GERAGNA LEEVVV L LYG Sbjct: 191 ME--LEIHAHDDLGLATANSLAAVRGGATHVSTTVNGLGERAGNAPLEEVVVALGHLYGR 248 Query: 258 DTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADGILKDESTYEPIPPE 317 +TGI +L +SKLV +G VP +K++VGEN FTHESGIH G+L+D TY+ + P Sbjct: 249 ETGIDKRQLGRVSKLVAEASGRPVPVDKSIVGENIFTHESGIHVSGLLRDPRTYQALDPA 308 Query: 318 KVGHERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKRLGDRGKRITEAD 373 ++G R VLGKH G + + +++G++VD + +L +++R K I AD Sbjct: 309 ELGRGHRLVLGKHSGLTSVLHACREIGLEVDAAKARAMLAQVRRHASTTKTIPTAD 364 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: 462 Number of extensions: 24 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: 381 Length adjustment: 32 Effective length of query: 477 Effective length of database: 349 Effective search space: 166473 Effective search space used: 166473 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 09 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