Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_012045924.1 BBTA_RS28270 2-isopropylmalate synthase
Query= curated2:O26819 (496 letters) >NCBI__GCF_000015165.1:WP_012045924.1 Length = 523 Score = 361 bits (926), Expect = e-104 Identities = 210/505 (41%), Positives = 300/505 (59%), Gaps = 16/505 (3%) Query: 2 QVRVLDTTLRDGEQTPGVSLTPEEKLRIALKIDALGADIIEAGSAITSEGEREGIRKITS 61 +V + DTTLRDGEQ PG ++T EEKL IA +D +G D+IEAG I S+G+ E + +I Sbjct: 11 RVVIFDTTLRDGEQCPGATMTFEEKLNIAAMLDGMGVDVIEAGFPIASDGDFEAVNEIAK 70 Query: 62 EGLRAEICSFARAVREDID----AAISCDVDSVHLVVPTSDLHLEHKLRKTREEVLEQAV 117 A +C +RA +DID A +H + TS +H+++KL+ + V E V Sbjct: 71 RTQNAVVCGLSRAGAKDIDRCAEAIRPAKRGRIHTFLSTSPVHMKYKLQMEPQAVFELVV 130 Query: 118 DCTEYAVDHGILVELSAEDSTRSDMDFLRTIFREGIEAGAERICACDTVGILTPERSYEF 177 A +H VE S+ED TR++ DFL I+AGA I DTVG PE Y+ Sbjct: 131 SSVTRARNHTDDVEWSSEDGTRTEFDFLCRCVEAAIKAGATTINIPDTVGYAVPEEYYDL 190 Query: 178 YRGLSEL-----GAPLSVHCHNDFGLAVANSLAGLRAGASEVHATINGIGERAGNAALEE 232 ++ + E A SVHCHND G+AVANS+AG+RAGA ++ TINGIGERAGNAALEE Sbjct: 191 FKRVRETVPNSDKAVFSVHCHNDLGMAVANSMAGIRAGARQIECTINGIGERAGNAALEE 250 Query: 233 VVVALKSLYD---VDTSINIEMLYETSRMVARMTGVYLQPNKAIVGENAFAHESGIHADG 289 VV+A++ D I+ L S++V+ T +Q NKAIVG NAFAHESGIH DG Sbjct: 251 VVMAMRVRNDKLPFWNKIDTTQLTHASKVVSAATSFPVQYNKAIVGRNAFAHESGIHQDG 310 Query: 290 VLKKAETYEPITPEMVG-HGRGFVMGKHIGTHALRKRLDELGMKVADDKLMEIFRRVKTL 348 +LK A+TYE + PE VG VMGKH G HA +L+E+G K+A +++ + F R K L Sbjct: 311 MLKNAQTYEIMLPETVGVKQTSLVMGKHSGRHAFIHKLEEMGHKLAGNQVEDAFVRFKAL 370 Query: 349 GDMGKCVTDVDLQAIAEDVLGVMEDKVVDLQEVTIVSGNRVTPTASVKLRVDDREVLEAG 408 D K + D D++A+ ++ + D+ + L +++++G R A++KL VD +E Sbjct: 371 ADRKKHIYDEDIEALIDEGMVSAHDR-IKLLSLSVIAGTRGPQRATMKLDVDGVTKIEES 429 Query: 409 TGVGPVDAAIVAIKKSLEDFADITLEEYHVDAITGGTDALIDVVIKLRHGDRIISARSTQ 468 G GPVDA IK + + LE Y V A+T GTDA +V ++L R ++AR+ Sbjct: 430 EGNGPVDAVFNCIKSLVPH--EAKLELYQVHAVTEGTDAQAEVSVRLSQDGRSMTARAAD 487 Query: 469 PDIIMASVEAFLSGVNRLLANEKSE 493 PD ++AS +A+L +N+L+ + + Sbjct: 488 PDTLVASAKAYLGALNKLVMKRQRD 512 Lambda K H 0.317 0.135 0.373 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: 34 Number of successful extensions: 7 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: 496 Length of database: 523 Length adjustment: 34 Effective length of query: 462 Effective length of database: 489 Effective search space: 225918 Effective search space used: 225918 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 (21.7 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