Align 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized)
to candidate WP_005812386.1 DHAF_RS07595 homocitrate synthase
Query= curated2:Q8RCF9 (384 letters) >NCBI__GCF_000021925.1:WP_005812386.1 Length = 387 Score = 525 bits (1351), Expect = e-153 Identities = 256/372 (68%), Positives = 314/372 (84%), Gaps = 1/372 (0%) Query: 5 KDKPVYIVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPTMGGDEKETVAK 64 +++ + IVDTTLRDGEQTAGVVF+N EK+ IA+MLD++G+ Q+E G+P MGGDE++ + Sbjct: 2 EERKLTIVDTTLRDGEQTAGVVFSNQEKLMIARMLDDLGVHQIEAGVPVMGGDEQKAIRD 61 Query: 65 IAKLGLKASIMAWNRAVVKDVQESLECGVDAVAISISTSDIHIEHKLKKTRQWVLDSMTE 124 I K+GLKASIM WNRAV+ D+++S+ECG DAVAISISTSDIHIEHKL TR+ VL M + Sbjct: 62 IVKMGLKASIMGWNRAVIADIEKSIECGCDAVAISISTSDIHIEHKLMTTREDVLARMVK 121 Query: 125 AVRFAKKEGVYVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCDTVGFLDPFKTYEMV 184 A FAK+ G+Y+SVNAEDASR+D++FL+EFAR AK+AGADRLR+CDTVG L+PF T+E + Sbjct: 122 AAEFAKRNGLYISVNAEDASRSDLDFLLEFARQAKEAGADRLRYCDTVGILEPFTTFERI 181 Query: 185 KAIKDAVDIEIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAALEEVVMAL 244 +K+ +DI++EMHTHNDFGMATANALAGVKAGA +GVTVNGLGERAGNAALEE+VMAL Sbjct: 182 TKLKETIDIDVEMHTHNDFGMATANALAGVKAGASHIGVTVNGLGERAGNAALEEIVMAL 241 Query: 245 KYVYKMDLGIDTSRFREISEYVALASGRPLPPSKAIVGKNVFAHESGIHVDGALKNPYTY 304 KY+ +DL T RF E+SE+VA ASGR +P KAIVG N+FAHESGIH DGALKNP TY Sbjct: 242 KYLAGVDLKFATERFVEVSEFVARASGRSVPAWKAIVGSNMFAHESGIHADGALKNPLTY 301 Query: 305 EVFDPQEVGLERQIVIGKHSGTAALINKFK-EYGRVLTEEEANLLLPHVRKMAIQLKRPL 363 EVF P+EVGLERQIVIGKHSGTAA+ KF+ EYG+ ++EEEAN LL VR A+ +KR L Sbjct: 302 EVFKPEEVGLERQIVIGKHSGTAAIKAKFRNEYGKEISEEEANELLARVRAFAVDMKRSL 361 Query: 364 FDKELMYLYEDV 375 FDKELMY+YED+ Sbjct: 362 FDKELMYIYEDL 373 Lambda K H 0.318 0.135 0.379 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: 483 Number of extensions: 15 Number of successful extensions: 2 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: 384 Length of database: 387 Length adjustment: 30 Effective length of query: 354 Effective length of database: 357 Effective search space: 126378 Effective search space used: 126378 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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