Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate GFF1023 Psest_1056 2-isopropylmalate synthase, bacterial type
Query= curated2:Q8TYM1 (509 letters) >FitnessBrowser__psRCH2:GFF1023 Length = 514 Score = 392 bits (1007), Expect = e-113 Identities = 216/500 (43%), Positives = 310/500 (62%), Gaps = 15/500 (3%) Query: 12 DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71 D V IFDTTLRDGEQ+PG ++T EEKLRIAR L+ + VD IEAGFA AS G+ A++ +A Sbjct: 5 DRVIIFDTTLRDGEQSPGASMTAEEKLRIARALERLKVDVIEAGFAIASPGDFAAVKLVA 64 Query: 72 REELDAEVCSMARMVKGDVDAAVEAEADA----VHIVVPTSEVHVKKKLRMDREEVLERA 127 D+ VCS+AR V D++ A EA A A +H + TS +H++ KLRM ++V+E+A Sbjct: 65 DNIKDSTVCSLARAVDADIERAAEALAGANSGRIHTFIATSPIHMQYKLRMQPDQVVEQA 124 Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187 V+ AR VE S ED R+E+++L + A ++AGA + DTVG P Sbjct: 125 VRAVKKARSLCADVEFSCEDAGRSEIDFLCRIIKAAIDAGARTINIPDTVGYAIPHQYAD 184 Query: 188 AVKKLRERV--GEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALE 245 +++L ER+ + + SVHCH+D G+A AN++AAV AGARQV T+NG+GERAGNAALE Sbjct: 185 TIRQLLERIPNADKAVFSVHCHNDLGLAVANSLAAVVAGARQVECTINGLGERAGNAALE 244 Query: 246 EVVVVL---EELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHAD 302 E+V+ + ++L V T I TE + S+LV +TG V PNKA+VG NAF HESGIH D Sbjct: 245 EIVMAIKTRQDLINVHTRIETEHILAASRLVSGITGFPVQPNKAIVGANAFAHESGIHQD 304 Query: 303 GILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKR 361 G+LK TYE + + VG + + V+GKH G + R +L ++G+ ++ ++L R K Sbjct: 305 GVLKHRETYEIMSAQSVGWNANKMVMGKHSGRAAFRSRLDELGIVLEGDELNAAFARFKE 364 Query: 362 LGDRGKRITEADLRAIAEDVLGRPAERDIEVEDFTTVTGKRTIPTASIVVKIDGTRKEAA 421 L D+ I + DL+A+ D L A ++ + TIP A +V+ +DG + A Sbjct: 365 LADKKHEIFDEDLQALVSDTLADEAPEHFKLASLEVASKTGTIPEAKLVISVDGAERSAQ 424 Query: 422 STGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGDIVHS 481 + G GPVDAT KA+E A+ + G +L Y A+T GTD+ V V+L + G IV+ Sbjct: 425 AQGSGPVDATFKAIE-AVAESGATLQL--YSVNAITQGTDSQGEVTVRLE--KGGRIVNG 479 Query: 482 GSSREDIVVASLEAFIDGIN 501 + DIVVAS +A+++ +N Sbjct: 480 NGADTDIVVASAKAYLNALN 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: 611 Number of extensions: 34 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 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