Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_015738274.1 ADEG_RS01145 2-isopropylmalate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_000024605.1:WP_015738274.1 Length = 525 Score = 409 bits (1051), Expect = e-118 Identities = 233/504 (46%), Positives = 312/504 (61%), Gaps = 14/504 (2%) Query: 12 DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71 + V IFDTTLRDGEQ+PGV+L +EK+ AR+L +GVD IEAGF AS G+ A R IA Sbjct: 12 ERVYIFDTTLRDGEQSPGVSLNVKEKVEAARQLARLGVDVIEAGFPVASPGDFNACREIA 71 Query: 72 REELDAEVCSMARMVKGDVD----AAVEAEADAVHIVVPTSEVHVKKKLRMDREEVLERA 127 R VC++AR D+D A EAE+ +H + TS++H++ KLRM RE+VLE A Sbjct: 72 RAVRGVTVCALARARFADIDRAWEAIKEAESPRIHTFIATSDIHLQYKLRMTREQVLEAA 131 Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187 RE V YA+ + VE S ED +R++ ++L V + AGA + DTVG PE Sbjct: 132 REAVAYAKRYTSDVEFSAEDASRSDPDFLCRVLAEAIAAGATVVNIPDTVGYAVPEEFGE 191 Query: 188 AVKKLRERVG--EDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALE 245 ++ ++E+ E V++S HCH+D G+A ANT+AA+R G RQV VTVNGIGERAGNAALE Sbjct: 192 LIRTIKEKTPGIEKVVISCHCHNDLGLAVANTLAAIRNGVRQVEVTVNGIGERAGNAALE 251 Query: 246 EVVVVL---EELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHAD 302 EVV+ L Y V TGIRTE + SKL+ LTG+ V PNKA+VG+NAF HESGIH D Sbjct: 252 EVVMALYARRAFYQVTTGIRTEEIYRTSKLISSLTGMPVQPNKAIVGKNAFAHESGIHQD 311 Query: 303 GILKDESTYEPIPPEKVGHER-RFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKR 361 G+LK+ +TYE I P +G R R VLGKH G R +L+++G ++ +E+L +R K Sbjct: 312 GVLKERTTYEIIDPAVIGVPRSRLVLGKHSGRHAFRVRLRELGYELSEEELNAAFQRFKE 371 Query: 362 LGDRGKRITEADLRAIAEDVLGRPAERDIEVEDFTTVTGKRTIPTASIVVKIDGTRKEAA 421 L DR K IT+ DL A+ E+ +G+ E+ F +G +PTA++ +KI KE A Sbjct: 372 LCDRKKEITDDDLLALVEEEIGQ-VPPTYELRYFHISSGTTVVPTATVALKIGEEVKEEA 430 Query: 422 STGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGDIVHS 481 + G GPVDA KA++ K G L Y EA+T G DAI V V++ D E G Sbjct: 431 ACGNGPVDAIYKAID---KLTGRHLRLDSYSIEAVTEGKDAIGSVTVRVTDEERGKTYLG 487 Query: 482 GSSREDIVVASLEAFIDGINSLMA 505 D++ AS A+ID +N L A Sbjct: 488 RGISTDVLEASARAYIDALNKLAA 511 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: 660 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: 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 Apr 10 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