Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_015798931.1 AFER_RS07915 2-isopropylmalate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_000023265.1:WP_015798931.1 Length = 516 Score = 360 bits (924), Expect = e-104 Identities = 213/499 (42%), Positives = 285/499 (57%), Gaps = 14/499 (2%) Query: 12 DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71 + +RIFDTTLRDGEQ PG++L P EKL IA +L +GVD IEAGF AS+G+ A+R+IA Sbjct: 8 ERIRIFDTTLRDGEQAPGISLDPLEKLEIAEQLARLGVDIIEAGFPVASQGDFDAVRQIA 67 Query: 72 REELDAEVCSMARMVKGDVDAAVEAEADA----VHIVVPTSEVHVKKKLRMDREEVLERA 127 R+ +C ++R D++ EA DA +H+ + TS H++ LRM ++V+E Sbjct: 68 RQVHGPVICGLSRTHVADIERCYEAVRDAEHHRIHVFISTSPSHLEHMLRMSEDQVVEAV 127 Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187 R + AR+ VE S +D TRT L +LY V ++ GA L DTVG P Sbjct: 128 RRAIARARELVDDVEFSPQDATRTPLPFLYRVLQVAVDEGASTLNIPDTVGYGIPWDFAR 187 Query: 188 AVKKLRERVGEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALEEV 247 V+ +R V ++S HCH+D G+ATAN++AAV AGARQV +NGIGERAGNAALEEV Sbjct: 188 MVESVRREVAGSYVISCHCHNDLGLATANSLAAVAAGARQVECCINGIGERAGNAALEEV 247 Query: 248 VVVL----EELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADG 303 V+ L + + V TGI T L S+LV RLTG V NKAVVG NAF HESGIH G Sbjct: 248 VMGLAIRSDVIGDVTTGIDTRELARTSRLVSRLTGYPVQYNKAVVGRNAFAHESGIHQHG 307 Query: 304 ILKDESTYEPIPPEKVGHE-RRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKRL 362 +L D STYE I VG E + VLGKH G ++ L +MG+ ++ + L +R K L Sbjct: 308 VLTDRSTYEVIDAASVGQEAAQIVLGKHSGRHAFQEALARMGIALEGDALNATFQRFKEL 367 Query: 363 GDRGKRITEADLRAIAEDVLGRPAERDIEVEDFTTVTGKRTIPTASIVVKIDGTRKEAAS 422 DR ++EADL AI + LG E+ F G AS V +DGT EA++ Sbjct: 368 ADRKVELSEADLEAIVAEELGTTLADRFELVSFRVEAGTGREAVASATVLVDGTPVEASA 427 Query: 423 TGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGDIVHSG 482 +G G VDA + L A ++ L + ++TGG DA+ V V + G V Sbjct: 428 SGNGMVDALGRVLAEA---TALEARLTGFSVTSVTGGADALGSVAVTV--DVGGHEVSGR 482 Query: 483 SSREDIVVASLEAFIDGIN 501 DIV AS A ++ +N Sbjct: 483 GVSTDIVEASARALLNALN 501 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: 635 Number of extensions: 39 Number of successful extensions: 4 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: 516 Length adjustment: 35 Effective length of query: 474 Effective length of database: 481 Effective search space: 227994 Effective search space used: 227994 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