Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_020177082.1 A3OQ_RS0119280 homocitrate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_000385335.1:WP_020177082.1 Length = 399 Score = 287 bits (735), Expect = 4e-82 Identities = 160/376 (42%), Positives = 213/376 (56%), Gaps = 4/376 (1%) Query: 1 MREANADADPPDEVRIF--DTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAA 58 M NA A +F DTTLRDGEQ PGVA T +EK+ IA L GV IEAG A Sbjct: 1 MSSGNASARSGLRTPVFLNDTTLRDGEQAPGVAFTIDEKVAIAEALATAGVPEIEAGTPA 60 Query: 59 ASEGELKAIRRIAREELDAEVCSMARMVKGDVDAAVEAEADAVHIVVPTSEVHVKKKLRM 118 E+ AI I + L + RM++ D+DAAV V+ VP S++ +K K Sbjct: 61 MGAEEIAAINAIVGQNLPLTPIAWCRMLRADIDAAVATGVRMVNASVPVSDIQLKAKFGA 120 Query: 119 DREEVLERAREVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVG 178 R L VV YARD GL V + ED +R + +L EV DA AGA R + DT+G Sbjct: 121 GRAHALALIENVVPYARDCGLEVAVGGEDASRADPGFLAEVLDAVARAGARRFRFADTLG 180 Query: 179 VMAPEGMFLAVKKLRERVGEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGER 238 V+ P + V+ LR D+ + +H HDD G+ATANT+AA+RAGA VTV G+GER Sbjct: 181 VLDPFATYAMVEHLRRH--SDLEIEIHAHDDLGLATANTLAALRAGASHASVTVVGLGER 238 Query: 239 AGNAALEEVVVVLEELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESG 298 AGNA LEEV V + LYG++TGI L+ +++ V + G +P KA+VG+ FTHESG Sbjct: 239 AGNAPLEEVAVAVSALYGLETGIDLRSLSAVAQTVMKAAGRAIPEAKAIVGDAVFTHESG 298 Query: 299 IHADGILKDESTYEPIPPEKVGHERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRR 358 IH DG+LKD YE + P +G R VLGKH G + K++G+DV ++ IL Sbjct: 299 IHVDGLLKDRKCYEALDPAVLGRTHRLVLGKHSGLGAVVNAFKELGIDVQSDEAKAILAL 358 Query: 359 LKRLGDRGKRITEADL 374 ++ +R K A + Sbjct: 359 VRAYAERTKAAVPASM 374 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: 480 Number of extensions: 28 Number of successful extensions: 3 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: 399 Length adjustment: 33 Effective length of query: 476 Effective length of database: 366 Effective search space: 174216 Effective search space used: 174216 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