Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_013460368.1 SULKU_RS07600 homocitrate synthase
Query= curated2:O26819 (496 letters) >NCBI__GCF_000183725.1:WP_013460368.1 Length = 371 Score = 266 bits (679), Expect = 1e-75 Identities = 141/364 (38%), Positives = 223/364 (61%), Gaps = 2/364 (0%) Query: 7 DTTLRDGEQTPGVSLTPEEKLRIALKIDALGADIIEAGSAITSEGEREGIRKITSEGLRA 66 DTTLRDGEQ P V+ EEKLRIA +DA GAD +E G A ERE I+++ + GL+A Sbjct: 6 DTTLRDGEQAPYVAFNTEEKLRIATLLDACGADELEIGIAAMGAKEREDIKELLNLGLKA 65 Query: 67 EICSFARAVREDIDAAISCDVDSVHLVVPTSDLHLEHKLRKTREEVLEQAVDCTEYAVDH 126 + ++ R ED+DA++SC V +V L +P SDL + K ++ +VL + A Sbjct: 66 RMMTWNRMKLEDLDASLSCGVQAVDLSIPISDLLIGVKFGGSKIKVLNELERVVTAATRE 125 Query: 127 GILVELSAEDSTRSDMDFLRTIFREGIEAGAERICACDTVGILTPERSYEFYRGLSELG- 185 G+ V + EDS+R ++ F+R + G E GA R CDT+G++TP ++Y+ + L +L Sbjct: 126 GLFVCIGGEDSSRGELSFMRDVMELGRECGAGRFRYCDTIGVMTPTQTYQAVKELCDLNL 185 Query: 186 APLSVHCHNDFGLAVANSLAGLRAGASEVHATINGIGERAGNAALEEVVVALKSLYDVDT 245 P+ +H HNDFGLA AN+L+G+ AGA ++ T+ G+GERAGNA+ E+++++LK LY Sbjct: 186 LPIEMHTHNDFGLANANALSGIDAGAISMNTTVIGLGERAGNASFEQILMSLKHLYGESR 245 Query: 246 SINIEMLYETSRMVARMTGVYLQPNKAIVGENAFAHESGIHADGVLKKAETYEPITPEMV 305 +++ +L + VA + L N I+GE FAHESGIHADG++K + YEP + V Sbjct: 246 AVDPLLLRSLVQSVADAANINLSANAPIIGERIFAHESGIHADGMMKDSHAYEPYEAKEV 305 Query: 306 GHGRGFVMGKHIGTHALRKRLDELGMKVADDKLMEIFRRVKTLGDMGKCVTDV-DLQAIA 364 G F +GKH G+ +R L +G+ + L ++ +++ + K V ++ +L+++ Sbjct: 306 GLTSSFPIGKHSGSATIRYHLARMGISADNSILGDLLPKIREIVTSRKRVLEIGELKSLY 365 Query: 365 EDVL 368 +D + Sbjct: 366 QDAV 369 Lambda K H 0.317 0.135 0.373 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: 452 Number of extensions: 21 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: 496 Length of database: 371 Length adjustment: 32 Effective length of query: 464 Effective length of database: 339 Effective search space: 157296 Effective search space used: 157296 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 (21.7 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