Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_073040916.1 BUB04_RS14925 2-isopropylmalate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_900129305.1:WP_073040916.1 Length = 520 Score = 306 bits (785), Expect = 9e-88 Identities = 194/502 (38%), Positives = 288/502 (57%), Gaps = 19/502 (3%) Query: 14 VRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIARE 73 +RIFDTTLRDGE++PG L+ EEKLR+AR+L +GVD +EAGF AASE + +A+RRIA E Sbjct: 4 IRIFDTTLRDGEKSPGTVLSVEEKLRLARQLARLGVDVLEAGFPAASERQFEAVRRIAEE 63 Query: 74 ELDAEVCSMARMVKG-DVDAAVEAEADA----VHIVVPTSEVHVKKKLRMDREEVLERAR 128 + ++AR D AA +A A A +H VP S + + L+MD E L A Sbjct: 64 VQGPVIAALARPTHPRDFQAAADALAGAARRRIHTFVPVSPSYRRHFLQMDLGEALGLAA 123 Query: 129 EVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAP---EGM 185 + VE AR+ VE S D R L+ + + A EAGA + DTVG P E + Sbjct: 124 KGVELAREKVEDVEFSLVDALRAPLDDVTAMARAAAEAGARIINIADTVGYATPSEVERL 183 Query: 186 FLAVKKLRERVGEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALE 245 AV K+ + +DV LS+HCH+D G+A AN++AAVRAGARQ+H TVNGIGERAGNAALE Sbjct: 184 VEAVAKVLDSF-DDVHLSIHCHNDLGLAVANSLAAVRAGARQIHCTVNGIGERAGNAALE 242 Query: 246 EVVVVLE---ELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHAD 302 EV +L+ + +G +TGI +++ +LV+R+TG+ + +K +VG NAF +E + Sbjct: 243 EVAAILKARRDHFGCETGIHLDQIGPTCRLVKRITGIGIQAHKPIVGTNAFFYEISVPQI 302 Query: 303 GILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKR 361 +++ Y+ + PE++G + + +H+ + K++G +D + L + Sbjct: 303 ADAEEQPPYQIVSPEELGLLDHGGEIPRHITRDQFAELAKRLGYVLDGDCLDRCWAAFRN 362 Query: 362 LGDRGKRITEADLRAIAEDVLGRPAERDIEVEDFTTVTGKRTIPTASIVVKIDGTRKEAA 421 L DR + + E DL I ++ P R + G ++P A++ +++DG + A Sbjct: 363 LLDRKENVYETDLETILDEHAMAPEGR-YRLLYLNVSAGSISVPNATVQMEVDGEVIQDA 421 Query: 422 STGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGDIVHS 481 G GPVDAT K + + ++ +LV Y A+T GTDA+ V V+L E G +V Sbjct: 422 GFGQGPVDATFKTICKIVRRFP---KLVRYEVSAVTSGTDALGEVSVRLE--EDGQLVQG 476 Query: 482 GSSREDIVVASLEAFIDGINSL 503 DIV+AS +A ID +N L Sbjct: 477 RGVAADIVMASAKALIDAMNKL 498 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: 659 Number of extensions: 42 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: 520 Length adjustment: 35 Effective length of query: 474 Effective length of database: 485 Effective search space: 229890 Effective search space used: 229890 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