Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_066325976.1 BLR17_RS13745 2-isopropylmalate synthase
Query= curated2:Q8TYM1 (509 letters) >NCBI__GCF_900100165.1:WP_066325976.1 Length = 391 Score = 281 bits (719), Expect = 3e-80 Identities = 156/375 (41%), Positives = 227/375 (60%), Gaps = 9/375 (2%) Query: 12 DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71 D+V+IFDTTLRDGEQ PG L +KL IA +LD +GVD IEAGF +S G+ ++ I+ Sbjct: 4 DKVQIFDTTLRDGEQVPGCKLDTNQKLVIAERLDNMGVDIIEAGFPVSSPGDFLSVTEIS 63 Query: 72 REELDAEVCSMARMVKGDVDAAV----EAEADAVHIVVPTSEVHVKKKLRMDREEVLERA 127 + +A VC + R VK D+D A A+ +H + TSE H+ KL+ RE+++ RA Sbjct: 64 KIVKNATVCGLTRAVKNDIDVAAAALKHAKRPRIHTGIGTSESHILHKLQTTREDIIARA 123 Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187 + V +A+ + VE ED RT+ +L +V + +++GA L DT G PE Sbjct: 124 KAAVAHAKSYVEDVEFYAEDAGRTDNAFLAQVCEEVIKSGATVLNIPDTTGYCLPEEYGA 183 Query: 188 AVKKLRERVG--EDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALE 245 +K L+E V E+V +S HCH+D GMATAN+++ GARQ+ T+NGIGERAGN ALE Sbjct: 184 KIKYLKENVKGIENVTISCHCHNDLGMATANSISGAINGARQIECTINGIGERAGNTALE 243 Query: 246 EVVVVLEELYGVD--TGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADG 303 EVV++ ++ ++ T I T++L E+S+LV G+ V PNKA+VG NAF H SGIH DG Sbjct: 244 EVVMIFKQHPDLNLYTDIDTKQLNEMSRLVSESMGMMVQPNKAIVGANAFAHSSGIHQDG 303 Query: 304 ILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKRL 362 ++K+ +TYE I P VG +E VL G + + + K++G ++ QL + + Sbjct: 304 VIKNRATYEIIDPLDVGVNESSIVLTARSGRAALAYRAKKVGYELTKNQLDVVYVEFLKF 363 Query: 363 GDRGKRITEADLRAI 377 D K I + D+ I Sbjct: 364 ADVKKEILDDDIHLI 378 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: 491 Number of extensions: 32 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: 391 Length adjustment: 32 Effective length of query: 477 Effective length of database: 359 Effective search space: 171243 Effective search space used: 171243 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: 51 (24.3 bits)
This GapMind analysis is from Jul 26 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