Align Putative (R)-citramalate synthase CimA; EC 2.3.3.21 (uncharacterized)
to candidate WP_057509301.1 ABB28_RS14490 2-isopropylmalate synthase
Query= curated2:O26819 (496 letters) >NCBI__GCF_001431535.1:WP_057509301.1 Length = 527 Score = 328 bits (840), Expect = 4e-94 Identities = 202/509 (39%), Positives = 291/509 (57%), Gaps = 25/509 (4%) Query: 2 QVRVLDTTLRDGEQTPGVSLTPEEKLRIALKIDALGADIIEAGSAITSEGEREGIRKITS 61 ++R+ DTTLRDGEQ+PG S++P++KL +A +D LG D+IE G +S+ +RE + I Sbjct: 13 RIRIFDTTLRDGEQSPGCSMSPQQKLVMARALDELGVDVIETGFPASSQSDREAMTMIGR 72 Query: 62 EGLRAEICSFARAVREDIDAAISCDVDS-----VHLVVPTSDLHLEHKLRKTREEVLEQA 116 E R + +R + DI+ ++ +DS +H+ + TS LH EHKLR TRE+VLE Sbjct: 73 EVQRPVLAVLSRCLAADIETSVR-SLDSAAHPRLHVFLSTSPLHREHKLRMTREQVLESV 131 Query: 117 VDCTEYAVDHGILVELSAEDSTRSDMDFLRTIFREGIEAGAERICACDTVGILTPERSYE 176 A + VE SAED+TR+++D+L + R I AGA I DTVG TPE Sbjct: 132 RKHVALARSYIDDVEFSAEDATRTELDYLIEVSRVAIAAGATTINLPDTVGFTTPEEIRA 191 Query: 177 FYR----GLSELGAP----LSVHCHNDFGLAVANSLAGLRAGASEVHATINGIGERAGNA 228 ++ G++++ S HCHND GLAVANSLA + GA +V T+NGIGERAGN Sbjct: 192 MFQQVIAGVADVSGAERVIFSAHCHNDLGLAVANSLAAIEGGARQVECTVNGIGERAGNC 251 Query: 229 ALEEVVVALK---SLYDVDTSINIEMLYETSRMVARMTGVYLQPNKAIVGENAFAHESGI 285 A+EE+ +ALK + YD DT+IN + + TS+++ R+ G+ +Q NKAIVG NAFAHESGI Sbjct: 252 AVEEIAMALKVRQAFYDQDTAINTQRIVSTSQLLQRLVGMPVQRNKAIVGANAFAHESGI 311 Query: 286 HADGVLKKAETYEPITPEMVG-HGRGFVMGKHIGTHALRKRLDELGMKVADDKLMEIFRR 344 H G+L+ TYE + PE VG V+G+H G A+ RL LG + +++L +F + Sbjct: 312 HQHGMLRHRGTYEIMRPEDVGWEDSQMVLGRHSGRAAVEARLRALGFWLEEEELKLVFEQ 371 Query: 345 VKTLGDMGKCVTDVDLQAIAEDVLGVMEDKVVDLQEVTIVS-GNRVTPTASVKLRVDDRE 403 K+L + + VTD DLQ + + G + L +TI G+R + D Sbjct: 372 FKSLCEQQRVVTDSDLQTLMQ---GGASTQGYRLASMTISDVGSRANALVELS-DPDGNR 427 Query: 404 VLEAGTGVGPVDAAIVAIKKSLEDFADITLEEYHVDAITGGTDALIDVVIKLRHGDRIIS 463 V E G GPVDA A+ + + L+ Y V ++ G DA + + +R GD + Sbjct: 428 VAETAQGDGPVDALFGALSSATG--VSLQLDSYQVHSVGIGADARGEANLSVRSGDEVFE 485 Query: 464 ARSTQPDIIMASVEAFLSGVNRLLANEKS 492 T DII AS A+L NRLL ++ Sbjct: 486 GTGTSRDIIEASALAWLDVANRLLRQREA 514 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: 606 Number of extensions: 31 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: 527 Length adjustment: 35 Effective length of query: 461 Effective length of database: 492 Effective search space: 226812 Effective search space used: 226812 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