Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_013843393.1 DESRU_RS17390 homocitrate synthase
Query= curated2:Q8TJJ1 (483 letters) >NCBI__GCF_000215085.1:WP_013843393.1 Length = 288 Score = 166 bits (420), Expect = 1e-45 Identities = 96/263 (36%), Positives = 143/263 (54%) Query: 1 MRDGEQTPGVALTREKKLLIARALDEMRINVIEAGSAITSAGERESIKAVANAGLDAEIC 60 +RDGEQ+ GVA + ++K+ IA LD + + IEAG E E+I ++ L A+I Sbjct: 11 LRDGEQSVGVAFSAKEKVHIAGLLDAVGVYQIEAGIPAMGQLEMEAIYSILALNLKAKIS 70 Query: 61 SYCRIVKMDVDHALECDVDSIHLVAPVSDLHIKTKIKKDRDTVRQIAAEVTEYAKDHGLI 120 ++ R D+ +L+C ++H+ APVSD+HI+ K+ + R+ V YA+D G Sbjct: 71 TWNRTNLDDIKASLDCGARNLHISAPVSDIHIRYKLNRSREWVLDCMKRAVAYARDAGAT 130 Query: 121 VELSGEDASRADPEFLKAIYSDGIDAGADRLCFCDTVGLLVPEKTTEIFRDLSSSLKAPI 180 V + EDASRAD EFL + GA L F DT+G++ P T + + Sbjct: 131 VTVGAEDASRADMEFLLQFAREAKKEGAVYLRFADTLGVMDPFTTRNRVEQIIRRTGIDV 190 Query: 181 SIHCHNDFGLATANTVAALAAGAKQSHVTINGLGERAGNASLEEVVMSLEWLYKYDTGIK 240 +H HNDFG+ATAN++AA AGA+ T+ G+GERAGN+ EEVV L ++ + Sbjct: 191 EMHGHNDFGMATANSLAAYKAGARYLSTTVLGMGERAGNSPYEEVVEMLRYVEGIPLPVN 250 Query: 241 HEQIYRTSRLVSRLTGIPVSPNK 263 ++ R V+ PV P K Sbjct: 251 ETKLEELIRFVAGAANWPVKPLK 273 Lambda K H 0.316 0.132 0.366 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: 317 Number of extensions: 8 Number of successful extensions: 1 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: 483 Length of database: 288 Length adjustment: 30 Effective length of query: 453 Effective length of database: 258 Effective search space: 116874 Effective search space used: 116874 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: 49 (23.5 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