Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_013840144.1 DESRU_RS00330 2-isopropylmalate synthase
Query= BRENDA::Q58787 (491 letters) >NCBI__GCF_000215085.1:WP_013840144.1 Length = 501 Score = 340 bits (872), Expect = 7e-98 Identities = 204/498 (40%), Positives = 301/498 (60%), Gaps = 19/498 (3%) Query: 5 IFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLITKEGL 64 IFDTTLRDGEQ+ G++L ++KLEIA++L LGVDVIEAG +S G+ +K I +E Sbjct: 6 IFDTTLRDGEQSLGITLNTHEKLEIARQLVRLGVDVIEAGFPASSPGDMNSVKTIAREIK 65 Query: 65 NAEICSFVRALPVDIDAALECDVDS----VHLVVPTSPIHMKYKLRKTEDEVLETALKAV 120 A IC RA+ DIDA E D+ +H + SP+HM+ KLR + ++V+E A+ AV Sbjct: 66 GAVICGLTRAVAKDIDACAEALRDAEQPRIHTGIAVSPVHMEKKLRLSPEQVVEAAVAAV 125 Query: 121 EYAKEHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRVCVCDTVGVLTPQKSQELFKK 180 ++AK++ VE AEDA+RS+ FL K+ + + GA V + DTVG +TP + EL Sbjct: 126 KHAKKYVSDVEFYAEDASRSEPAFLAKILEKVIEAGATVVNIPDTVGYVTPWQYGELISF 185 Query: 181 ITENV----NLPVSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEVVA 236 +T+NV + +S HCHND GMATANT +AV GA Q T+NGIGERAGN +LEEV+ Sbjct: 186 LTKNVKNIDSAIISTHCHNDLGMATANTLAAVKAGASQVEGTINGIGERAGNTALEEVMM 245 Query: 237 AL---KILYGYDTKIKMEKLYEVSRIVSRLMKLPVPPNKAIVGDNAFAHEAGIHVDGLIK 293 A+ LYG + +K +++ SR+VS + +PVP +KAIVG NAF H +GIH DG++K Sbjct: 246 AVYSQPSLYGVELGVKTKEIAATSRLVSGITGVPVPSHKAIVGANAFMHASGIHQDGVLK 305 Query: 294 NTETYEPIKPEMVG-NRRRIILGKHSGRKALKYKLDLMGINVSDEQLNKIYERVKEFGDL 352 TYE I PE VG R +I+L SGR ALK++L+ +G + + +Y+ + D Sbjct: 306 EKRTYEIIDPETVGILRNKIVLSARSGRHALKHRLEELGYSPEQYDVETVYKEFLQLADQ 365 Query: 353 GKYISDADLLAIVREVTGKLVEEKIKLDELTVVSGNKITPIASVKLHYKGEDITLIETAY 412 K + D DL A++ + I + ++V + T A+V L D L + AY Sbjct: 366 KKEVFDEDLHALMGYTEKE--RNSISIKNISVATNGAATATATVSLAM--NDQILTDAAY 421 Query: 413 GVGPVDAAINAVRKAISGVADIKLVEYRVEAIGGGTDALIEVVVKLRKG-TEIVEVRKSD 471 G GPVDA A+ + I+G+ +KL +Y + ++ G++AL +VK+R G + +V R Sbjct: 422 GNGPVDAVFKAIER-ITGIT-VKLEDYNLSSVSRGSEALGNAIVKVRYGESGLVIGRGVS 479 Query: 472 ADIIRASVDAVMEGINML 489 D+I A+ A + ++ + Sbjct: 480 PDVIEATAKAYVNALSKI 497 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: 596 Number of extensions: 34 Number of successful extensions: 8 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: 501 Length adjustment: 34 Effective length of query: 457 Effective length of database: 467 Effective search space: 213419 Effective search space used: 213419 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 25 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