Align Putative (R)-citramalate synthase CimA; EC 2.3.1.182 (uncharacterized)
to candidate 14220 b0074 2-isopropylmalate synthase (NCBI)
Query= curated2:Q8TYM1 (509 letters) >FitnessBrowser__Keio:14220 Length = 523 Score = 305 bits (780), Expect = 3e-87 Identities = 186/503 (36%), Positives = 286/503 (56%), Gaps = 19/503 (3%) Query: 13 EVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIAR 72 +V IFDTTLRDGEQ +L+ +EKL+IA L+ +GVD +E GF +S G+ ++++ IAR Sbjct: 4 QVIIFDTTLRDGEQALQASLSVKEKLQIALALERMGVDVMEVGFPVSSPGDFESVQTIAR 63 Query: 73 EELDAEVCSMARMVKGDVDAAVE----AEADAVHIVVPTSEVHVKKKLRMDREEVLERAR 128 + ++ VC++AR V+ D+D A E AEA +H + TS +H+ KLR +EV+ERA Sbjct: 64 QVKNSRVCALARCVEKDIDVAAESLKVAEAFRIHTFIATSPMHIATKLRSTLDEVIERAI 123 Query: 129 EVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFLA 188 +V+ AR++ VE S ED RT + L V +A + AGA + DTVG P Sbjct: 124 YMVKRARNYTDDVEFSCEDAGRTPIADLARVVEAAINAGATTINIPDTVGYTMPFEFAGI 183 Query: 189 VKKLRERVG--EDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALEE 246 + L ERV + I+SVH HDD G+A N++AAV AGARQV +NGIGERAGN +LEE Sbjct: 184 ISGLYERVPNIDKAIISVHTHDDLGLAVGNSLAAVHAGARQVEGAMNGIGERAGNCSLEE 243 Query: 247 VVV---VLEELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADG 303 V++ V +++ V T I + + S+LV ++ + +P NKA+VG AF H SGIH DG Sbjct: 244 VIMAIKVRKDILNVHTAINHQEIWRTSQLVSQICNMPIPANKAIVGSGAFAHSSGIHQDG 303 Query: 304 ILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKRL 362 +LK+ YE + PE +G ++ + L G + ++ ++ +MG + L + +L Sbjct: 304 VLKNRENYEIMTPESIGLNQIQLNLTSRSGRAAVKHRMDEMGYKESEYNLDNLYDAFLKL 363 Query: 363 GDRGKRITEADLRAIAEDVLGRPAE--RDIEVEDFTTVTGKRTIPTASIVVKIDGTRKEA 420 D+ ++ + DL A+A +G+ E ++ F+ +G I TA++ + K Sbjct: 364 ADKKGQVFDYDLEALA--FIGKQQEEPEHFRLDYFSVQSGSNDIATAAVKLACGEEVKAE 421 Query: 421 ASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGDIVH 480 A+ G GPVDA +A+ R + + ELV+Y A G DA+ VD+ G H Sbjct: 422 AANGNGPVDAVYQAINRITE---YNVELVKYSLTAKGHGKDALGQVDIVAN--YNGRRFH 476 Query: 481 SGSSREDIVVASLEAFIDGINSL 503 DIV +S +A + +N++ Sbjct: 477 GVGLATDIVESSAKAMVHVLNNI 499 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: 550 Number of extensions: 31 Number of successful extensions: 5 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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