Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate 5211056 Shew_3472 2-isopropylmalate synthase (RefSeq)
Query= curated2:Q8TYM1 (509 letters) >FitnessBrowser__PV4:5211056 Length = 523 Score = 315 bits (807), Expect = 3e-90 Identities = 188/506 (37%), Positives = 289/506 (57%), Gaps = 26/506 (5%) Query: 12 DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71 + V IFDTTLRDGEQ +LT +EKL+IA L+ +GVD +E GF +S G+ ++++ IA Sbjct: 3 NRVIIFDTTLRDGEQALAASLTVKEKLQIALSLERLGVDVMEVGFPVSSPGDFESVQTIA 62 Query: 72 REELDAEVCSMARMVKGDVDAAVE----AEADAVHIVVPTSEVHVKKKLRMDREEVLERA 127 R ++ VC++AR ++ D+DAA + AE +H + TS +HV+ KL+ ++VL+ A Sbjct: 63 RTIKNSRVCALARALEKDIDAAAQSLSVAEQFRIHTFISTSTIHVESKLKRSFDQVLDMA 122 Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187 V+YAR VE S ED RT ++ L + +A ++AGA+ + DTVG P Sbjct: 123 VGAVKYARRFTDDVEFSCEDAGRTPIDNLCRMVEAAIKAGAKTINIPDTVGYTVPSEFGG 182 Query: 188 AVKKLRERVG--EDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALE 245 ++ L +RV + ++SVHCHDD G++ AN++ AV+ GARQ+ TVNGIGERAGN +LE Sbjct: 183 IIQNLFDRVPNIDQAVISVHCHDDLGLSVANSITAVQHGARQIECTVNGIGERAGNCSLE 242 Query: 246 EVVVVL---EELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHAD 302 E+ +++ + G++TGI + + S LV +L + V NKA+VG NAFTH SGIH D Sbjct: 243 EIAMIIATRKASLGLETGINAKEIHRTSNLVSQLCNMPVQANKAIVGANAFTHSSGIHQD 302 Query: 303 GILKDESTYEPIPPEKVGHERRFV-LGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKR 361 G+LK ++TYE + PE +G R + + G VI+ ++++MG D + + + Sbjct: 303 GVLKSQNTYEIMTPESIGLNRNNLNMTSRSGRHVIKHRMEEMGYGEQDYDMDTLYEAFLK 362 Query: 362 LGDRGKRITEADLRAI------AEDVLGRPAERDIEVEDFTTVTGKRTIPTASIVVKIDG 415 L D+ ++ + DL A+ AED ++ + D T + TA++ + IDG Sbjct: 363 LADKKGQVFDYDLEALVYVEAQAEDENHYGLQQLVVHSDST-----QGQATATVTLSIDG 417 Query: 416 TRKEAASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPET 475 A+TG GPVDA KA+ RA G + + Y+ A G DA+ VD+ + + Sbjct: 418 KAVTEAATGNGPVDAAYKAIARA---SGCEINISSYQLSAKGQGQDALGQVDITAKYHDQ 474 Query: 476 GDIVHSGSSREDIVVASLEAFIDGIN 501 H D+V AS A I +N Sbjct: 475 S--FHGVGLATDVVEASAAALIHVMN 498 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: 565 Number of extensions: 30 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: 523 Length adjustment: 35 Effective length of query: 474 Effective length of database: 488 Effective search space: 231312 Effective search space used: 231312 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