Align 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized)
to candidate WP_011801696.1 PNAP_RS11555 homocitrate synthase
Query= curated2:Q8RCF9 (384 letters) >NCBI__GCF_000015505.1:WP_011801696.1 Length = 395 Score = 337 bits (864), Expect = 3e-97 Identities = 174/365 (47%), Positives = 237/365 (64%), Gaps = 1/365 (0%) Query: 11 IVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPTMGGDEKETVAKIAKLGL 70 I DTTLRDGEQTAGV F +EK IA L G+ ++E+GIP MG +E + + IA L L Sbjct: 7 INDTTLRDGEQTAGVAFTVDEKCAIACALAAAGVPEMEIGIPAMGEEEIDCINTIAALEL 66 Query: 71 KASIMAWNRAVVKDVQESLECGVDAVAISISTSDIHIEHKLKKTRQWVLDSMTEAVRFAK 130 A++M W R D+ +L C D + +SI SDIH+ HKL+++R+WVL +T + A Sbjct: 67 PAALMIWGRLTDADLASALRCQADIIHLSIPVSDIHLRHKLRQSREWVLAQVTRVIEKAV 126 Query: 131 KEGVYVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCDTVGFLDPFKTYEMVKAIKDA 190 G +S+ AEDASR D FL + AR A+ GA R+RF DT+G LDPF TYE + +++A Sbjct: 127 ASGRKISLGAEDASRADAGFLSQVARRAQDCGASRIRFADTLGVLDPFTTYEAITRLREA 186 Query: 191 VDIEIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAALEEVVMALKYVYKM 250 V ++IE+H HND G+ATAN LA ++AGA TVNGLGERAGNAALEEVVM +++++ Sbjct: 187 VHLDIEIHAHNDLGLATANTLAALRAGATHANTTVNGLGERAGNAALEEVVMGVRHLHHA 246 Query: 251 DLGIDTSRFREISEYVALASGRPLPPSKAIVGKNVFAHESGIHVDGALKNPYTYEVFDPQ 310 G+ T IS VA ASGR + +K+IVG+ VF HESGIH+DG LKN TYE FDP Sbjct: 247 QTGVSTQALVSISRLVARASGRQVAFNKSIVGEAVFTHESGIHIDGLLKNASTYESFDPS 306 Query: 311 EVGLERQIVIGKHSGTAALINKFKEYGRVLTEEE-ANLLLPHVRKMAIQLKRPLFDKELM 369 E+G ER+ V+GKHSG+ ++ + G VL ++ +L +R A+++K+ EL Sbjct: 307 ELGRERRTVLGKHSGSQSVRQAYGAMGVVLDDDALTGRVLARIRDHAMRVKQEATPDELR 366 Query: 370 YLYED 374 D Sbjct: 367 GFLRD 371 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: 372 Number of extensions: 6 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: 395 Length adjustment: 30 Effective length of query: 354 Effective length of database: 365 Effective search space: 129210 Effective search space used: 129210 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