Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_022947189.1 H035_RS0101200 2-isopropylmalate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_000421465.1:WP_022947189.1 Length = 514 Score = 375 bits (962), Expect = e-108 Identities = 215/506 (42%), Positives = 314/506 (62%), Gaps = 18/506 (3%) Query: 12 DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71 D++ IFDTTLRDGEQ+PG ++ EEK+RIA+ L+ + VD IEAGF AAS G+ A++ ++ Sbjct: 3 DKLIIFDTTLRDGEQSPGASMNREEKIRIAKALERLRVDVIEAGFPAASGGDFDAVKAVS 62 Query: 72 REELDAEVCSMARMVKGDVDAAVEAEADA----VHIVVPTSEVHVKKKLRMDREEVLERA 127 + ++ VC +AR + D+D A EA A A +H + TS +H++ KLRM ++V+ERA Sbjct: 63 QAVGESAVCGLARALDTDIDRAGEALAVARRSRIHTFIATSPIHMEHKLRMTPDQVVERA 122 Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187 V+ AR + VE S ED R+E ++L + +A + AGA + DTVG P Sbjct: 123 VAAVQRARRYTDDVEFSPEDAGRSEEDFLCRIIEAVIAAGATTINIPDTVGYSLPPAFGA 182 Query: 188 AVKKLRERV--GEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALE 245 + +LRER+ + + SVHCH+D G+A AN++AAV +GARQV T+NG+GERAGNAALE Sbjct: 183 MIGRLRERIPNADKAVFSVHCHNDLGLAVANSLAAVMSGARQVECTINGLGERAGNAALE 242 Query: 246 EVVVVL---EELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHAD 302 EVV+ + ++ + DTGI T+ + SKLV +TG V PNKA+VG NAF HESGIH D Sbjct: 243 EVVMAVKTRQDAFPCDTGINTQEIVPCSKLVSSITGFPVQPNKAIVGANAFAHESGIHQD 302 Query: 303 GILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLL-EILRRLK 360 G+LK TYE + E VG R VLGKH G + R +++++G++ + E+ L E R K Sbjct: 303 GVLKSRETYEIMRAEDVGWSANRMVLGKHSGRNAFRTRMRELGIEFEAEEALNEAFARFK 362 Query: 361 RLGDRGKRITEADLRA-IAEDVLGRPAERDIEVEDFTTVTGKRTIPTASIVVKIDGTRKE 419 L D+ I E DL+A I+E + AER +++ + P A +V+K+DG K Sbjct: 363 DLADKKHEIFEEDLQALISEQIYESEAER-VKLIALHVCSDTGETPRAQVVLKVDGEEKT 421 Query: 420 AASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGDIV 479 + S G G VDAT+KA+E L L+ Y ++T GTDA V V+L G IV Sbjct: 422 SESEGSGVVDATLKAIESLL---ATGASLLLYSVNSITTGTDAQGEVTVRLE--RGGRIV 476 Query: 480 HSGSSREDIVVASLEAFIDGINSLMA 505 + + DIV+AS +A+++ ++ L++ Sbjct: 477 NGLGADTDIVIASAKAYLNAVDKLLS 502 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: 655 Number of extensions: 36 Number of successful extensions: 7 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 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