Align Putative (R)-citramalate synthase CimA; EC 2.3.1.182 (uncharacterized)
to candidate H281DRAFT_04556 H281DRAFT_04556 2-isopropylmalate synthase
Query= curated2:Q8TYM1 (509 letters) >FitnessBrowser__Burk376:H281DRAFT_04556 Length = 515 Score = 349 bits (896), Expect = e-100 Identities = 211/508 (41%), Positives = 309/508 (60%), Gaps = 24/508 (4%) Query: 12 DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71 D++ IFDTTLRDGEQ+PG ++T EEK+RIA++L+ + VD IEAGFAA+S G+ +I+ IA Sbjct: 3 DKLIIFDTTLRDGEQSPGASMTKEEKIRIAKQLERMKVDVIEAGFAASSNGDFDSIQTIA 62 Query: 72 REELDAEVCSMARMVKGDV----DAAVEAEADAVHIVVPTSEVHVKKKLRMDREEVLERA 127 ++ VCS+AR D+ DA AE +H + TS +H++KKLRM ++V E+A Sbjct: 63 GLIKESMVCSLARANDKDIQRAADALKPAERFRIHTFIATSPLHMEKKLRMTPDQVFEQA 122 Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187 + V +AR VE S EDG+R+++++L V +A + GA + DTVG PE Sbjct: 123 KLAVRFARKFTDDVEFSPEDGSRSDMDFLCRVLEAVIAEGATTINIADTVGYGVPELYGN 182 Query: 188 AVKKLRERV--GEDVILSVHCHDDFGMATANTVAAVR-AGARQVHVTVNGIGERAGNAAL 244 VK LRER+ + SVHCH+D GMA AN++A V+ GARQV T+NG+GERAGN +L Sbjct: 183 LVKTLRERIPNSHKAVFSVHCHNDLGMAVANSLAGVQIGGARQVECTINGLGERAGNTSL 242 Query: 245 EEVVVVL---EELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHA 301 EE+V+ + ++ +G++ G+ T ++ SKLV ++TG V PNKAVVG NAF H SGIH Sbjct: 243 EEIVMAVKTRKDYFGLELGLDTTQIVPASKLVSQITGFVVQPNKAVVGANAFAHASGIHQ 302 Query: 302 DGILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDE-QLLEILRRL 359 DG+LK TYE + E VG + VLGK G + +++L+++G+ +D E +L R Sbjct: 303 DGVLKARDTYEIMRAEDVGWSANKIVLGKLSGRNAFKQRLQELGIALDSEAELNTAFARF 362 Query: 360 KRLGDRGKRITEADLRAIAEDVLGRPAERD----IEVEDFTTVTGKRTIPTASIVVKIDG 415 K L DR I + D+ AI + +++ + + + TG++ P A IV +DG Sbjct: 363 KELADRKAEIFDEDIIAIVTEESAEAQQKEHYKFLSLSQHSE-TGEQ--PHAKIVFAMDG 419 Query: 416 TRKEAASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPET 475 + G GPVDAT+ A+E + G EL+ Y A+T GT A V V+L ++ Sbjct: 420 KEITGEARGNGPVDATLNAIE---TEVGSGSELLLYSVNAITTGTQAQGEVTVRL--SKS 474 Query: 476 GDIVHSGSSREDIVVASLEAFIDGINSL 503 G IV+ + DIV AS +A+I +N L Sbjct: 475 GRIVNGVGTDPDIVAASAKAYISALNKL 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: 598 Number of extensions: 28 Number of successful extensions: 9 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: 515 Length adjustment: 35 Effective length of query: 474 Effective length of database: 480 Effective search space: 227520 Effective search space used: 227520 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