Align 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized)
to candidate WP_043879531.1 AZC_RS17440 homocitrate synthase
Query= curated2:Q8RCF9 (384 letters) >NCBI__GCF_000010525.1:WP_043879531.1 Length = 399 Score = 311 bits (796), Expect = 3e-89 Identities = 164/368 (44%), Positives = 218/368 (59%) Query: 7 KPVYIVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPTMGGDEKETVAKIA 66 + ++ DTTLRDGEQ GV F EKI IA L G+ ++E G P MG +E ET+ I Sbjct: 14 RTAFLNDTTLRDGEQAPGVAFTRKEKIEIAAALAAAGVPEIEAGTPAMGDEEVETIRSIV 73 Query: 67 KLGLKASIMAWNRAVVKDVQESLECGVDAVAISISTSDIHIEHKLKKTRQWVLDSMTEAV 126 L L +MAW R D+ ++ GV V +SI TSD + KL K R W L + E V Sbjct: 74 SLNLPTRVMAWCRMSEDDLMAAVAAGVKIVNVSIPTSDRQLAGKLGKDRAWALGRVAEVV 133 Query: 127 RFAKKEGVYVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCDTVGFLDPFKTYEMVKA 186 A++ G V+V ED+SR D +FL A AK AGA RLR DT+G LDPF TY +V+ Sbjct: 134 TLARRLGFEVAVGGEDSSRADPDFLCRLAETAKAAGAFRLRLADTLGVLDPFGTYALVRR 193 Query: 187 IKDAVDIEIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAALEEVVMALKY 246 + DIE+E H H+D G+ATAN LA V GA+ VTV GLGERAGNAALEEV +AL+ Sbjct: 194 VAATTDIELEFHAHDDLGLATANTLAAVMGGARHASVTVAGLGERAGNAALEEVAIALRQ 253 Query: 247 VYKMDLGIDTSRFREISEYVALASGRPLPPSKAIVGKNVFAHESGIHVDGALKNPYTYEV 306 + + GI + + ++E V A+ RP+P KAIVG +VF HESGIHV G LK+ TYE Sbjct: 254 TARAETGIAPAALKPLAELVCGAAARPVPRGKAIVGADVFTHESGIHVSGLLKDRATYEA 313 Query: 307 FDPQEVGLERQIVIGKHSGTAALINKFKEYGRVLTEEEANLLLPHVRKMAIQLKRPLFDK 366 +P+ G +V+GKHSG AA+ + G + +L VR A++ K + + Sbjct: 314 LNPELFGRGHTVVLGKHSGLAAVEKALADEGITVDAVRGRAILDRVRAFAVRTKENVSRE 373 Query: 367 ELMYLYED 374 L+ Y+D Sbjct: 374 TLLRFYQD 381 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: 355 Number of extensions: 12 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: 399 Length adjustment: 31 Effective length of query: 353 Effective length of database: 368 Effective search space: 129904 Effective search space used: 129904 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 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