Align Putative (R)-citramalate synthase CimA; EC 2.3.1.182 (uncharacterized)
to candidate 3607175 Dshi_0596 2-isopropylmalate synthase (RefSeq)
Query= curated2:Q8TYM1 (509 letters) >FitnessBrowser__Dino:3607175 Length = 525 Score = 357 bits (915), Expect = e-103 Identities = 212/511 (41%), Positives = 301/511 (58%), Gaps = 16/511 (3%) Query: 7 DADPPDEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKA 66 D D V IFDTTLRDGEQ+PG +T +EKL IA LDE+GVD IEAGF AS+G+ A Sbjct: 3 DKTDQDRVLIFDTTLRDGEQSPGATMTHDEKLEIAALLDEMGVDIIEAGFPIASDGDFAA 62 Query: 67 IRRIAREELDAEVCSMARMVKGDVDAAVEAEADA----VHIVVPTSEVHVKKKLRMDREE 122 + IA+ +++ +C +AR D+D EA A +H + TS +H + + +E Sbjct: 63 VSEIAKNSVNSVICGLARANFKDIDRCWEAVRHARQPRIHTFIGTSPLH-RAIPNLTMDE 121 Query: 123 VLERAREVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAP 182 + +R + V +AR+ V+ S D TRTE +YL V + ++AGA + DTVG AP Sbjct: 122 MADRIHDTVTHARNLCDNVQWSPMDATRTEYDYLCRVIEIAIKAGATTINIPDTVGYTAP 181 Query: 183 -EGMFLAVKKLRERVG-EDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAG 240 E L + + + G EDV + HCH+D GMATAN +AAV AGARQV T+NG+GERAG Sbjct: 182 RESADLIARLIADVPGAEDVTFATHCHNDLGMATANALAAVDAGARQVECTINGLGERAG 241 Query: 241 NAALEEVVVVL---EELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHES 297 N ALEEVV+ L ++ T I T ++ +S+ V ++G V NKA+VG+NAF HES Sbjct: 242 NTALEEVVMALRVRNDIMPYQTRIDTRKIMNISRRVAAVSGFAVQFNKAIVGKNAFAHES 301 Query: 298 GIHADGILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEIL 356 GIH DG+LK+ T+E + PE +G E V+GKH G + +R KLK +G ++ D QL ++ Sbjct: 302 GIHQDGMLKNAETFEIMRPEDIGLSETNLVMGKHSGRAALRAKLKDLGYELADNQLKDVF 361 Query: 357 RRLKRLGDRGKRITEADLRAIAEDVLGRPAERDIEVEDFTTVTGKRTIPTASIVVKIDGT 416 R K L DR K I + DL A+ + PA + V+ + G +A + + IDG Sbjct: 362 VRFKALADRKKEIYDEDLVALMSESSSDPARERLSVKFLRVICGTEAPQSADLTLSIDGV 421 Query: 417 RKEAASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETG 476 K+ + G GPVDAT A+ +AL +L Y+ A+T GTDA V V++ E G Sbjct: 422 DKQVTAQGDGPVDATFNAV-KALFPHTARLQL--YQVHAVTEGTDAQATVTVRME--EDG 476 Query: 477 DIVHSGSSREDIVVASLEAFIDGINSLMARK 507 IV ++ D VVAS +A++ +N L+ R+ Sbjct: 477 RIVSGQAADTDTVVASAKAYVAALNRLILRR 507 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: 622 Number of extensions: 32 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: 525 Length adjustment: 35 Effective length of query: 474 Effective length of database: 490 Effective search space: 232260 Effective search space used: 232260 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