Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_093427735.1 BM272_RS05405 2-isopropylmalate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_900112605.1:WP_093427735.1 Length = 515 Score = 370 bits (950), Expect = e-107 Identities = 206/505 (40%), Positives = 308/505 (60%), Gaps = 16/505 (3%) Query: 12 DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71 + + IFDTTLRDGEQ+PG ++T EEK+RIAR+L+ + VD IEAGF AASEG+ +++R +A Sbjct: 4 EHLTIFDTTLRDGEQSPGASMTREEKIRIARQLERLRVDVIEAGFPAASEGDFESVRAVA 63 Query: 72 REELDAEVCSMARMVKGDVDAAVEAEADA----VHIVVPTSEVHVKKKLRMDREEVLERA 127 ++ VC +AR V+ D++ A EA A A +H + TS VH++ KLRM +EV+ERA Sbjct: 64 ESVKESTVCGLARAVERDIERAGEALAGAAHARIHTFIATSTVHMENKLRMGPDEVVERA 123 Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187 V ARD VE S ED R+E ++LY + +A ++AGA + DTVG PE Sbjct: 124 VAAVRRARDFVDDVEFSAEDAGRSEPDFLYRIVEAAIDAGATTINIPDTVGYAIPEQFGQ 183 Query: 188 AVKKLRERV--GEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALE 245 + +R V + S HCH+D G+A AN++AAV GARQV T+NG+GERAGNAALE Sbjct: 184 LIADIRANVPNSDRATFSSHCHNDLGLAVANSLAAVTNGARQVECTINGLGERAGNAALE 243 Query: 246 EVVVVL---EELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHAD 302 E+V+ L ++++ +T I T ++ SKLV +TG + PNKA+VG NAF HESGIH D Sbjct: 244 EIVMALQVRQDVFPCNTRIDTTQIVPSSKLVASVTGFQPQPNKAIVGANAFAHESGIHQD 303 Query: 303 GILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLL-EILRRLK 360 G+LK TYE + E VG + R VLGKH G + + +L ++G++++ E +L + + K Sbjct: 304 GVLKHRETYEIMRAEDVGWNTNRMVLGKHSGRNAFKSRLAEIGIELESEAILNDAFAKFK 363 Query: 361 RLGDRGKRITEADLRAIAEDVLGRPAERDIEVEDFTTVTGKRTIPTASIVVKIDGTRKEA 420 L D+ I + DL+ + + + +++ + P A++ +++DG ++ Sbjct: 364 ELADKKHEIFDEDLQTLVTEAGVEAENQRVQLVSVHVCSETGETPEATVTLEVDGEERQG 423 Query: 421 ASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGDIVH 480 +TG G VDAT A+E + +L+ Y +T GTDA V V+L G IV+ Sbjct: 424 RATGSGSVDATFSAIEAVMAS---TTQLLLYSVNNITSGTDAQGEVTVRLE--RGGRIVN 478 Query: 481 SGSSREDIVVASLEAFIDGINSLMA 505 + DIV+AS +A+I+ +N +MA Sbjct: 479 GQGADVDIVIASAQAYINALNKIMA 503 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: 675 Number of extensions: 39 Number of successful extensions: 8 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: 515 Length adjustment: 35 Effective length of query: 474 Effective length of database: 480 Effective search space: 227520 Effective search space used: 227520 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 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