Align 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized)
to candidate WP_012333360.1 M446_RS17125 homocitrate synthase
Query= curated2:Q8RCF9 (384 letters) >NCBI__GCF_000019365.1:WP_012333360.1 Length = 403 Score = 306 bits (784), Expect = 7e-88 Identities = 169/374 (45%), Positives = 227/374 (60%) Query: 7 KPVYIVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPTMGGDEKETVAKIA 66 + V++ DTTLRDGEQ GV F EKI IA+ L G+ ++E G P MG DE ET+ I Sbjct: 20 RTVFLNDTTLRDGEQAPGVAFTRREKIEIAEALAAAGVPEIEAGTPAMGEDEIETIRSIV 79 Query: 67 KLGLKASIMAWNRAVVKDVQESLECGVDAVAISISTSDIHIEHKLKKTRQWVLDSMTEAV 126 L L ++AW R D+ ++ GV AV SI SD + KL + R + LD++ V Sbjct: 80 SLRLPLRVIAWCRMREDDLLAAVAAGVPAVNHSIPVSDAQLRGKLGRDRAFALDAVAATV 139 Query: 127 RFAKKEGVYVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCDTVGFLDPFKTYEMVKA 186 A++ G+ V+V AEDASR D +FL A A+ AGA+RLR DT+G LDPF +V+ Sbjct: 140 ARARRLGLAVAVGAEDASRADPDFLCRVAEAARAAGAERLRLADTLGVLDPFAADALVRR 199 Query: 187 IKDAVDIEIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAALEEVVMALKY 246 + A D+ +E H H+ G+ATAN LA ++AGA+ VTV GLGERAGNAALEEV +AL Sbjct: 200 LAAATDLALEFHAHDYLGLATANTLAALRAGARHASVTVTGLGERAGNAALEEVAVALAR 259 Query: 247 VYKMDLGIDTSRFREISEYVALASGRPLPPSKAIVGKNVFAHESGIHVDGALKNPYTYEV 306 + GID R ++ VA A+ RPLP KAIVG+++F HESGIHV G L++ TYE Sbjct: 260 FGQGPTGIDLRALRPLAAAVAAAAERPLPRGKAIVGEDIFTHESGIHVAGLLRDRATYEA 319 Query: 307 FDPQEVGLERQIVIGKHSGTAALINKFKEYGRVLTEEEANLLLPHVRKMAIQLKRPLFDK 366 DP +G +IVIGKHSG AAL + GR L E A LL VR A++ K + Sbjct: 320 LDPGMLGRSHRIVIGKHSGVAALASALAAQGRSLDAEVARDLLERVRAAAVRTKAAVPPG 379 Query: 367 ELMYLYEDVIVKGK 380 L L+++ ++ + Sbjct: 380 LLRRLHDECLMSAR 393 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: 311 Number of extensions: 8 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: 403 Length adjustment: 31 Effective length of query: 353 Effective length of database: 372 Effective search space: 131316 Effective search space used: 131316 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 09 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