Align 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized)
to candidate WP_011764286.1 AZO_RS02775 homocitrate synthase
Query= curated2:Q8RCF9 (384 letters) >NCBI__GCF_000061505.1:WP_011764286.1 Length = 396 Score = 300 bits (767), Expect = 6e-86 Identities = 166/372 (44%), Positives = 223/372 (59%), Gaps = 4/372 (1%) Query: 8 PVYIVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPTMGGDEKETVAKIAK 67 PV I DTTLRDGEQ+AGV F EK IA++L EIG+ +LE+GIP MG +E + IA Sbjct: 4 PVTIDDTTLRDGEQSAGVAFTRAEKCGIARILAEIGVPELEIGIPAMGSEECGDIRAIAD 63 Query: 68 L----GLKASIMAWNRAVVKDVQESLECGVDAVAISISTSDIHIEHKLKKTRQWVLDSMT 123 G ++ W R D+ V + +S+ SD I HKL TR VL + Sbjct: 64 TLADGGHDTRLIVWGRLTSADIDACRSLPVQMLELSVPVSDQQIRHKLGATRDEVLARIA 123 Query: 124 EAVRFAKKEGVYVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCDTVGFLDPFKTYEM 183 V A++ G V V EDASR D FL E + A+ AGA R RF DT+G LDPF T+E Sbjct: 124 RWVPVAREAGFDVGVGGEDASRADPAFLAEVIQAAEAAGARRFRFADTLGILDPFATFEA 183 Query: 184 VKAIKDAVDIEIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAALEEVVMA 243 ++A++ A +EIEMH H+D G+ATAN LA V+AGA V TVNGLGERAGNAALEEV + Sbjct: 184 IRALRAASKLEIEMHAHDDLGLATANTLAAVRAGASHVNTTVNGLGERAGNAALEEVALG 243 Query: 244 LKYVYKMDLGIDTSRFREISEYVALASGRPLPPSKAIVGKNVFAHESGIHVDGALKNPYT 303 L+ + M ID +R + SE VA ASGRP+ K++VG+ VF HE+GIHVDG LK+P Sbjct: 244 LRQFHGMGEIIDFTRLLDTSEAVARASGRPVGWHKSVVGEGVFTHEAGIHVDGLLKDPAN 303 Query: 304 YEVFDPQEVGLERQIVIGKHSGTAALINKFKEYGRVLTEEEANLLLPHVRKMAIQLKRPL 363 Y+ DP +G ++++GKHSG + + G L LL +R+ + KR Sbjct: 304 YQGIDPALLGRSHRMLLGKHSGGRGVAAAYAGLGIELDAARTACLLARIREFTSRTKRTP 363 Query: 364 FDKELMYLYEDV 375 ++L+ +E++ Sbjct: 364 QREDLLAFWEEL 375 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: 378 Number of extensions: 14 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: 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 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