Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_011766887.1 AZO_RS15865 2-isopropylmalate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_000061505.1:WP_011766887.1 Length = 511 Score = 380 bits (976), Expect = e-110 Identities = 216/505 (42%), Positives = 316/505 (62%), Gaps = 20/505 (3%) Query: 12 DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71 D + IFDTTLRDGEQ+PG ++T +EKLRIAR+L+ + VD IEAGFAAAS G+ +++R IA Sbjct: 3 DALIIFDTTLRDGEQSPGASMTRDEKLRIARQLERMRVDVIEAGFAAASNGDFESVRSIA 62 Query: 72 REELDAEVCSMARMVKGDVDAAVEAEADA----VHIVVPTSEVHVKKKLRMDREEVLERA 127 ++ VCS+AR + D+ A EA A +H + TS +H++KKLRM ++V+E+A Sbjct: 63 EAIKESTVCSLARANENDIRRAGEAIRPAARGRIHTFIATSPIHMEKKLRMTPDQVVEQA 122 Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187 + + +AR++ +E S ED R+E+++L +FDA ++AGA+ + DTVG PE Sbjct: 123 VKAIGWAREYTDDIEFSAEDAGRSEIDFLCRIFDAVIKAGAKTINVPDTVGYNVPEQYAA 182 Query: 188 AVKKLRERV--GEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALE 245 ++ L ERV + VI SVHCH+D G+A +N++AAV AGARQV T+NG+GERAGNA+LE Sbjct: 183 TLRTLIERVPNADKVIWSVHCHNDLGLAVSNSLAAVMAGARQVECTINGLGERAGNASLE 242 Query: 246 EVVVVLE---ELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHAD 302 E+V+ + +++ V T I T ++ SKLV ++TG V PNKA+VG NAF HESGIH D Sbjct: 243 EIVMAVRTRADVFPVSTNIDTTQIVPASKLVSQITGYPVQPNKAIVGANAFAHESGIHQD 302 Query: 303 GILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDV-DDEQLLEILRRLK 360 G+LK TYE + E VG + VLGKH G + R +L+++G+++ +EQL R K Sbjct: 303 GVLKHRETYEIMRAEDVGWGANKLVLGKHSGRNAFRARLQELGIEIGSEEQLNHAFARFK 362 Query: 361 RLGDRGKRITEADLRAIAEDVLGRPAERDIEV--EDFTTVTGKRTIPTASIVVKIDGTRK 418 L D+ I + DL A+ D P + + F + TG+ P A + + I G Sbjct: 363 ELADKKHEIFDEDLHALMSDEAVTPEQEHFRLVATRFHSETGE--TPRAEVTLAIGGQET 420 Query: 419 EAASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGDI 478 + + G GPVDA KA+E G EL+ Y A+T GTDA V V+L + G + Sbjct: 421 RSQAEGSGPVDAAFKAIESV---AGSGSELLLYSVNAITTGTDAQGEVTVRL--AKDGRV 475 Query: 479 VHSGSSREDIVVASLEAFIDGINSL 503 V+ + DI+VAS +A+++ +N L Sbjct: 476 VNGQGADTDIIVASAKAYLNALNKL 500 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: 628 Number of extensions: 32 Number of successful extensions: 8 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: 511 Length adjustment: 34 Effective length of query: 475 Effective length of database: 477 Effective search space: 226575 Effective search space used: 226575 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 Jul 25 2024. The underlying query database was built on Jul 25 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