Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_011320648.1 AVA_RS20055 homocitrate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_000204075.1:WP_011320648.1 Length = 377 Score = 289 bits (739), Expect = 1e-82 Identities = 163/370 (44%), Positives = 225/370 (60%), Gaps = 4/370 (1%) Query: 12 DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71 ++V I DTTLRDGEQ GV T EEK+ IA+ LD IGV +E G A E E++AI I+ Sbjct: 2 NKVLINDTTLRDGEQAAGVVFTLEEKVAIAKFLDTIGVPELEVGIPAMGEEEMRAICAIS 61 Query: 72 REELDAEVCSMARMVKGDVDAAVEAEADAVHIVVPTSEVHVKKKLRMDREEVLERAREVV 131 L A + + R V D+ A+V + VHI +P S + + K L+R ++ + Sbjct: 62 NLGLKANLLAWNRAVISDIKASVACGMERVHIAIPVSGIQIAAKFHGQWRVSLQRLKDCI 121 Query: 132 EYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFLAVKK 191 +A D GL V + ED +R + +L +V E GA R + DTVGV+ P + VK Sbjct: 122 SFAVDQGLWVAVGGEDSSRADENFLLDVALYAQEWGASRFRFCDTVGVLDPFTTYGKVKL 181 Query: 192 LRERVGEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALEEVVVVL 251 L + + + VH H+DFGMATAN +A ++AGA V+ TV G+GERAGNAALEEVV+ + Sbjct: 182 LVSAL--TIPVEVHTHNDFGMATANALAGIKAGAASVNTTVIGLGERAGNAALEEVVMAI 239 Query: 252 EELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADGILKDESTY 311 + +YGVD GI T RL ELS+LV +G VPP KA+VGEN F HESGIHA G+L++ TY Sbjct: 240 KRIYGVDMGIDTPRLLELSQLVAAASGANVPPWKAIVGENTFAHESGIHAHGVLQNPDTY 299 Query: 312 EPIPPEKVGHERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKRLGDRGKR--I 369 EP PE+VG ERR V+GKH G + L+Q G+ ++ E+ +L +++ + KR Sbjct: 300 EPFAPEEVGWERRLVVGKHSGRHSVSNLLEQHGIFLNPEETQSVLDAVRQQSVKKKRSLT 359 Query: 370 TEADLRAIAE 379 TE L + E Sbjct: 360 TEELLNLVKE 369 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: 444 Number of extensions: 16 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: 377 Length adjustment: 32 Effective length of query: 477 Effective length of database: 345 Effective search space: 164565 Effective search space used: 164565 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