Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_010532009.1 ON01_RS15965 2-isopropylmalate synthase
Query= BRENDA::Q58787 (491 letters) >NCBI__GCF_000224785.1:WP_010532009.1 Length = 515 Score = 353 bits (907), Expect = e-102 Identities = 206/499 (41%), Positives = 305/499 (61%), Gaps = 18/499 (3%) Query: 3 VRIFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLITKE 62 ++IFDTTLRDGEQ+PGV+L +KLEIAK+L+++G+D +EAG +SKG+ E +K I K Sbjct: 4 IKIFDTTLRDGEQSPGVNLNKPEKLEIAKQLEKMGIDRMEAGFPASSKGDFEAVKEIAKT 63 Query: 63 GLNAEICSFVRALPVDIDAALE----CDVDSVHLVVPTSPIHMKYKLRKTEDEVLETALK 118 N + R + DID A E + +HL V TSPIHM YKL+++ ++V+E A+ Sbjct: 64 IKNTSVTGLARTVKSDIDTAWEALKYAEEPRLHLFVATSPIHMTYKLKQSPEQVIENAVS 123 Query: 119 AVEYAKEHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRVCVCDTVGVLTPQKSQELF 178 V YA E VE SAEDA+RSD+ FL ++ + GA + + DTVG TP + +F Sbjct: 124 MVSYASEKFPQVEWSAEDASRSDLTFLAQIIEKVIDAGATVINLPDTVGYTTPAEYGAMF 183 Query: 179 KKITENV----NLPVSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEV 234 + I ENV + +S HCHND G+A AN+ +AV G Q T+NGIGERAGNASLEEV Sbjct: 184 RYIRENVPNIDKVELSCHCHNDLGLAVANSIAAVENGVTQVEGTINGIGERAGNASLEEV 243 Query: 235 VAALKI---LYGYDTKIKMEKLYEVSRIVSRLMKLPVPPNKAIVGDNAFAHEAGIHVDGL 291 AL++ Y Y T++K+++ S ++++L + V NKAIVG NAF HEAGIH DG+ Sbjct: 244 AVALRVRSDYYPYTTRLKLDETKRTSDLIAKLSGMYVQANKAIVGRNAFQHEAGIHQDGV 303 Query: 292 IKNTETYEPIKPEMVGNRR-RIILGKHSGRKALKYKLDLMGINVSDEQLNKIYERVKEFG 350 +KN ETYE + PEMVG + + LGKHSGR A K +++ +G+ +S+++L + + K+ Sbjct: 304 LKNKETYEIMTPEMVGVKADTLFLGKHSGRHAFKDRVNELGVQLSEDKLKEAFTMFKQLT 363 Query: 351 DLGKYISDADLLAIVREV-TGKLVEEKIKLDELTVVSGNKITPIASVKLHYKGEDITLIE 409 D + ++D DL I+ E+ T K +L+ V G P A+V L D ++ Sbjct: 364 DRKREVTDDDLYTILMEIQTDTSAVNKYQLEMFQVQYGTSNIPTATVSL--TAPDGKTVQ 421 Query: 410 TAY-GVGPVDAAINAVRKAISGVADIKLVEYRVEAIGGGTDALIEVVVKLRKGTEIVEVR 468 TA G G V+A + I +++L +Y++ ++G G DAL E V+L E + R Sbjct: 422 TAQTGQGSVEALYKTLDALIK--EELQLTDYQLNSVGRGKDALAESHVQLIVNGETMNGR 479 Query: 469 KSDADIIRASVDAVMEGIN 487 + D+++ASV+A + +N Sbjct: 480 GTAQDVLQASVNAFLNAVN 498 Lambda K H 0.316 0.136 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: 577 Number of extensions: 22 Number of successful extensions: 6 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: 491 Length of database: 515 Length adjustment: 34 Effective length of query: 457 Effective length of database: 481 Effective search space: 219817 Effective search space used: 219817 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 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