Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_011021246.1 MA_RS06370 homocitrate synthase
Query= curated2:Q8TJJ1 (483 letters) >NCBI__GCF_000007345.1:WP_011021246.1 Length = 289 Score = 179 bits (455), Expect = 8e-50 Identities = 101/267 (37%), Positives = 150/267 (56%) Query: 1 MRDGEQTPGVALTREKKLLIARALDEMRINVIEAGSAITSAGERESIKAVANAGLDAEIC 60 +RDGEQ+ GV + E+++ I ALD+ + IEAG E E++ + + + + Sbjct: 14 LRDGEQSAGVVFSIEERVNIISALDKANVKWIEAGIPAMGKQECEALSLMLELPIKSNLI 73 Query: 61 SYCRIVKMDVDHALECDVDSIHLVAPVSDLHIKTKIKKDRDTVRQIAAEVTEYAKDHGLI 120 ++ R D+ ++EC +H+ PVSDLHI+ K++K R V EY K+ G+ Sbjct: 74 AWNRANLKDLKASIECGFKFVHVSLPVSDLHIEYKLQKSRAWVLDQLKTCLEYLKNSGIT 133 Query: 121 VELSGEDASRADPEFLKAIYSDGIDAGADRLCFCDTVGLLVPEKTTEIFRDLSSSLKAPI 180 + + EDASRADP+F GA R+ + DTVG L T + + P+ Sbjct: 134 IIVGAEDASRADPDFFLQYADVAASYGAIRIRYSDTVGCLDHFTTYNKIESIVNRSPLPV 193 Query: 181 SIHCHNDFGLATANTVAALAAGAKQSHVTINGLGERAGNASLEEVVMSLEWLYKYDTGIK 240 IH HNDFGLA ANT+AA AGAK + VTI G+GERAGNAS+EE +SL+ Y YD GI+ Sbjct: 194 EIHAHNDFGLALANTLAAYRAGAKFASVTITGIGERAGNASMEETAVSLKHFYNYDCGIE 253 Query: 241 HEQIYRTSRLVSRLTGIPVSPNKALVG 267 + + +V++ + + P K +VG Sbjct: 254 LKALPSLVEMVAKASERTLFPYKPVVG 280 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: 320 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: 289 Length adjustment: 30 Effective length of query: 453 Effective length of database: 259 Effective search space: 117327 Effective search space used: 117327 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: 50 (23.9 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