Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_011160139.1 TX73_RS23540 homocitrate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_000195775.1:WP_011160139.1 Length = 397 Score = 276 bits (705), Expect = 1e-78 Identities = 155/344 (45%), Positives = 200/344 (58%), Gaps = 2/344 (0%) Query: 18 DTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIAREELDA 77 DTTLRDGEQ PGVA + EK+ IAR L GV IEAG A E+ AIR I L Sbjct: 26 DTTLRDGEQAPGVAFSTAEKVAIARALARAGVPEIEAGTPAMGVDEIAAIRAIVEAGLPL 85 Query: 78 EVCSMARMVKGDVDAAVEAEADAVHIVVPTSEVHVKKKLRMDREEVLERAREVVEYARDH 137 + RM DVDAA++A V++ VP S+V + KL R +E + VV YARD Sbjct: 86 TTIAWCRMRTEDVDAALKAGVAMVNVSVPVSDVQIAAKLGGKRSNAIETVKRVVGYARDR 145 Query: 138 GLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFLAVKKLRERVG 197 GL V + ED +R + E+L EV +GA R DT+ V+ P + LR Sbjct: 146 GLDVAVGGEDSSRADPEFLAEVIATAKASGARRFRIADTLSVLDPFSSHALLATLR--AS 203 Query: 198 EDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALEEVVVVLEELYGV 257 D+ L H HDD G+ATANT+AA+RAGA VTV G+GERAGNA LEEV V L++LYG Sbjct: 204 TDLELEFHGHDDLGLATANTLAALRAGASHASVTVIGLGERAGNAPLEEVAVALKQLYGR 263 Query: 258 DTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADGILKDESTYEPIPPE 317 DTGI L ++ LV +P NKA+VGE+ FTHESGIH DG+LKD+ TY+ + P Sbjct: 264 DTGIVLSELGNVADLVATAAARTIPLNKAIVGEHVFTHESGIHVDGLLKDQRTYQSLDPN 323 Query: 318 KVGHERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKR 361 G R V+GKH G S I L ++ + ++ IL +++R Sbjct: 324 LFGRSNRIVIGKHSGLSAITSSLAKLDLPATADEAQGILAKVRR 367 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: 474 Number of extensions: 29 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: 397 Length adjustment: 33 Effective length of query: 476 Effective length of database: 364 Effective search space: 173264 Effective search space used: 173264 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