Align 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized)
to candidate WP_051955429.1 DL88_RS00795 homocitrate synthase
Query= curated2:Q8RCF9 (384 letters) >NCBI__GCF_000745425.1:WP_051955429.1 Length = 396 Score = 296 bits (758), Expect = 7e-85 Identities = 153/368 (41%), Positives = 223/368 (60%) Query: 7 KPVYIVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPTMGGDEKETVAKIA 66 KP+ + DTTLRDGEQ GV F+ EKI IA+ L G+ ++E G P MG E + + Sbjct: 11 KPIVLNDTTLRDGEQAPGVAFSPEEKIAIAKALAGAGVPEIEAGTPAMGEREIAAIRDVV 70 Query: 67 KLGLKASIMAWNRAVVKDVQESLECGVDAVAISISTSDIHIEHKLKKTRQWVLDSMTEAV 126 L A I+AW R V +D+ ++ GV + +S+ SDI ++ K R + D ++ + Sbjct: 71 AEKLPAKIIAWCRMVRQDIDAAVASGVGMINLSLPVSDIQLKAKFSADRAYARDMISRFI 130 Query: 127 RFAKKEGVYVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCDTVGFLDPFKTYEMVKA 186 +A+ +G+ V++ EDASR D++FL E A G RLRF DT+G LDPF T+ MV+ Sbjct: 131 PYARDKGLEVALGCEDASRADLSFLGELADLGASLGVRRLRFADTLGVLDPFMTFSMVEQ 190 Query: 187 IKDAVDIEIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAALEEVVMALKY 246 ++ D+EIE+H H+D G+ATAN LA ++AGA VTV GLGERAGNA LEEV +A+K Sbjct: 191 LRAGTDLEIEIHAHDDLGLATANTLAALRAGATHASVTVVGLGERAGNAPLEEVAVAVKS 250 Query: 247 VYKMDLGIDTSRFREISEYVALASGRPLPPSKAIVGKNVFAHESGIHVDGALKNPYTYEV 306 +Y + +D + ++ V A+GR +P +KAIVG+ VF HESGIHVDG LK+ Y+ Sbjct: 251 LYGLSTEVDLTALAGVARVVTSAAGRSIPEAKAIVGEVVFTHESGIHVDGLLKDLQCYQA 310 Query: 307 FDPQEVGLERQIVIGKHSGTAALINKFKEYGRVLTEEEANLLLPHVRKMAIQLKRPLFDK 366 DP +G +V+GKHSG A+ N + G ++ +EA +L ++ A Q K + Sbjct: 311 LDPALLGRSHHVVLGKHSGLRAVTNALAQQGLSVSADEAKFVLARIKLYAEQEKASVPGN 370 Query: 367 ELMYLYED 374 L+ Y + Sbjct: 371 ILLDFYRE 378 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: 360 Number of extensions: 10 Number of successful extensions: 1 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: 396 Length adjustment: 31 Effective length of query: 353 Effective length of database: 365 Effective search space: 128845 Effective search space used: 128845 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