Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_028949923.1 Q385_RS0101285 2-isopropylmalate synthase
Query= BRENDA::Q58787 (491 letters) >NCBI__GCF_000619805.1:WP_028949923.1 Length = 516 Score = 384 bits (987), Expect = e-111 Identities = 227/501 (45%), Positives = 323/501 (64%), Gaps = 25/501 (4%) Query: 5 IFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLITKEGL 64 IFDTTLRDGEQ PG S+T +K+++A +L++LGVDVIEAG A S+G+ E +K + +E Sbjct: 6 IFDTTLRDGEQAPGFSMTVEEKVKMALQLEKLGVDVIEAGFAAASEGDFEAVKRVAEEIK 65 Query: 65 NAEICSFVRALPVDIDAALE----CDVDSVHLVVPTSPIHMKYKLRKTEDEVLETALKAV 120 NA++CS RAL DID A E + +H + TSPIHM+YKL+ + DEV+E A+ AV Sbjct: 66 NAKVCSLARALQSDIDKAGEALTPAENRRIHTFIATSPIHMQYKLKMSPDEVVERAIAAV 125 Query: 121 EYAKEHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRVCVCDTVGVLTPQKSQELFKK 180 +YA ++ VE SAEDA RS+ FL ++F K GA + V DTVG P++ +L Sbjct: 126 KYALKYTDDVEFSAEDAFRSEREFLYRVFEAVIKAGAKTINVPDTVGYAIPEEFGQLIAD 185 Query: 181 ITENV----NLPVSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEVVA 236 I NV +SVHCHND G+A AN+ SAV GA Q H TVNGIGERAGNA++EEVV Sbjct: 186 IKNNVPNIDKAVISVHCHNDLGLAVANSLSAVKNGARQVHATVNGIGERAGNAAVEEVVM 245 Query: 237 ALKILYGY----DTKIKMEKLYEVSRIVSRLMKLPVPPNKAIVGDNAFAHEAGIHVDGLI 292 A+K+ + Y T + +++Y+ SR++ R+ V PNKAIVGDNAFAHEAGIH G++ Sbjct: 246 AIKVRHDYFKGIYTTVNTKEIYKTSRLLCRITGSFVQPNKAIVGDNAFAHEAGIHQHGIL 305 Query: 293 KNTETYEPIKPEMVG-NRRRIILGKHSGRKALKYKLDLMG-INVSDEQLNKIYERVKEFG 350 + ETYE ++ E VG + +I+LGKHSGR A K +L +G N++D +++ ++ + K+ Sbjct: 306 AHRETYEIMRAEDVGVPKSKIVLGKHSGRHAFKTRLQELGYTNLTDAEIDSLFIKFKKLA 365 Query: 351 DLGKYISDADLLAIVREVTGKLVEEKIKLDELTVVSGNKITPIASVKLHYKGEDITLIET 410 D K + D D+ A++ E E K+K++ VVSG+ + P A+VK+ GE+I + T Sbjct: 366 DKKKEVFDEDIEALILE-EFSFFENKVKVNYFHVVSGDNVIPSATVKIEKDGEEI--VST 422 Query: 411 AYGVGPVDAAINAVRKAISGVADI--KLVEYRVEAIGGGTDALIEVVVKLR-KGTEIVEV 467 A G GP+D+ INAV KA+ DI KL++Y + ++ G DA+ EV V +R T+ V Sbjct: 423 ASGDGPIDSVINAVEKAL----DIKGKLLDYTIRSLSSGKDAMGEVRVLVRFDDTDYVAS 478 Query: 468 RK-SDADIIRASVDAVMEGIN 487 K + DII AS+ A ++ N Sbjct: 479 GKGTSTDIIEASLKAYVDAYN 499 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: 619 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: 491 Length of database: 516 Length adjustment: 34 Effective length of query: 457 Effective length of database: 482 Effective search space: 220274 Effective search space used: 220274 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