Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_043745065.1 AMB_RS17765 2-isopropylmalate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_000009985.1:WP_043745065.1 Length = 514 Score = 384 bits (986), Expect = e-111 Identities = 215/508 (42%), Positives = 311/508 (61%), Gaps = 17/508 (3%) Query: 12 DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71 + V IFDTTLRDGEQ+PG ++ EEK+RIA L+E+GVD IEAGF AS G+ +A+ +A Sbjct: 4 NRVIIFDTTLRDGEQSPGASMNLEEKVRIALVLEEMGVDVIEAGFPIASNGDFEAVEAVA 63 Query: 72 REELDAEVCSMARMVKGDVDAAVEAEADA----VHIVVPTSEVHVKKKLRMDREEVLERA 127 + + +C +AR KGD++ EA A +H + TS +H+K KL+M+ E+VLE+ Sbjct: 64 KAVKTSVICGLARATKGDIERCAEAIRPAARGRIHTFLSTSPLHMKYKLQMEPEKVLEKV 123 Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187 E V YAR VE S EDG+RTE ++L +A + AGA + DTVG P+ Sbjct: 124 AESVAYARKLTDDVEWSAEDGSRTEHDFLCRCVEAAIAAGARTINIPDTVGYAVPDEYAA 183 Query: 188 AVKKLRERVG--EDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALE 245 + L RV + +LSVHCH+D G+A AN++AAV GARQ+ TVNG+GERAGNAA+E Sbjct: 184 LIAMLINRVPNIDKAVLSVHCHNDLGLAVANSLAAVGKGARQIECTVNGLGERAGNAAME 243 Query: 246 EVVVVLE---ELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHAD 302 E+V+ L +L TGI+TE +T S+LV +TG V PNKA+VG+NAF HESGIH D Sbjct: 244 EIVMALRTRPDLLPFKTGIKTENITRASRLVSTITGFVVQPNKAIVGKNAFAHESGIHQD 303 Query: 303 GILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKR 361 G+LK TYE + PE VG H V+GKH G + + KLK++G ++ D + + R K Sbjct: 304 GVLKHAQTYEIMTPESVGLHRSNLVMGKHSGRAAFKAKLKELGYELGDNAIEDAFTRFKD 363 Query: 362 LGDRGKRITEADLRAIAEDVLGRPAERDIEVEDFTTVTG-KRTIPTASIVVKIDGTRKEA 420 L DR K + + D+ A+ +D + R +R +++ + G K P+A++ + +DG K Sbjct: 364 LADRKKDVFDEDIVALVDDAVVRGNDR-VKLVSLEVLCGTKHQPPSATLELSVDGEVKGV 422 Query: 421 ASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGDIVH 480 +TG GPVDAT A++ + L Y+ A+T GTDA V V+L E G V+ Sbjct: 423 RATGDGPVDATFNAIKALFPHEA---RLQLYQVSAVTQGTDAQAEVTVRLE--EDGKTVN 477 Query: 481 SGSSREDIVVASLEAFIDGINSLMARKR 508 + D +VAS A+++ +N L+ +++ Sbjct: 478 GQGAETDTLVASARAYVNALNKLLVKRQ 505 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: 614 Number of extensions: 26 Number of successful extensions: 6 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: 514 Length adjustment: 35 Effective length of query: 474 Effective length of database: 479 Effective search space: 227046 Effective search space used: 227046 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 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