Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_011813495.1 HHAL_RS03550 2-isopropylmalate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_000015585.1:WP_011813495.1 Length = 516 Score = 360 bits (925), Expect = e-104 Identities = 206/506 (40%), Positives = 304/506 (60%), Gaps = 18/506 (3%) Query: 12 DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71 D + IFDTTLRDGEQ+PG ++T EEK+RIA+ L+ + VD +EAGF AAS G+ +++R +A Sbjct: 5 DHLYIFDTTLRDGEQSPGASMTREEKVRIAKGLERMRVDVLEAGFPAASTGDFESVRAVA 64 Query: 72 REELDAEVCSMARMVKGDVDAA----VEAEADAVHIVVPTSEVHVKKKLRMDREEVLERA 127 ++ VC++AR D+ AA +AEA +H + TS +H++ KL M ++V++ A Sbjct: 65 EAIKESRVCALARARDPDIHAAGEALAQAEAGRIHTFIATSPIHMQNKLHMTPDQVVDAA 124 Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187 V AR VE S ED R+E ++L + +A ++AGA + DTVG PE Sbjct: 125 VHAVSLARQLCDDVEFSPEDAGRSEHDFLCRIIEAAIDAGARTINIPDTVGYNLPEQFGG 184 Query: 188 AVKKLRERV--GEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALE 245 ++ LRER+ + + SVHCH+D G+A AN++AAV+AGARQV T+NG+GERAGNAALE Sbjct: 185 LIRTLRERIPNSDKAVFSVHCHNDLGVAVANSLAAVQAGARQVECTINGLGERAGNAALE 244 Query: 246 EVVVVL---EELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHAD 302 EVV+ + ++++ T I + SKLV +TG V PNKA+VG NAF HESGIH D Sbjct: 245 EVVMAVKTRQDVFSCSTRINAREIVPTSKLVANITGFHVQPNKAIVGVNAFAHESGIHQD 304 Query: 303 GILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVD-DEQLLEILRRLK 360 G+LK TYE + E VG H R VLGKH G + R +L+++ + +D +EQL E R K Sbjct: 305 GVLKHRETYEIMRAEDVGWHTNRMVLGKHSGRNAFRSRLEELDIHLDSEEQLNEAFARFK 364 Query: 361 RLGDRGKRITEADLRAIAEDVLGRPAERDIEVEDFTTVTGKRTIPTASIVVKIDGTRKEA 420 L D+ I + DL+A+ + I + + P A++ + IDG ++A Sbjct: 365 TLADKKHEIFDEDLQALVTEAGAALENERIRLLALHVCSETGEQPEATVSLLIDGEERQA 424 Query: 421 ASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGDIVH 480 + G G VDA A++ ++ EL+ Y +T GTD+ V V+L E G V Sbjct: 425 VAPGSGAVDAAFMAVDSLVQS---GTELLLYSVNNITSGTDSQGEVTVRL---ERGGRVA 478 Query: 481 SGSSRE-DIVVASLEAFIDGINSLMA 505 +G + DIV+AS +A+I+ +N ++A Sbjct: 479 NGQGADVDIVIASAKAYINALNKILA 504 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: 685 Number of extensions: 43 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: 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