Align 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized)
to candidate WP_012282226.1 HM1_RS05075 homocitrate synthase
Query= curated2:Q8RCF9 (384 letters) >NCBI__GCF_000019165.1:WP_012282226.1 Length = 380 Score = 327 bits (837), Expect = 4e-94 Identities = 167/363 (46%), Positives = 233/363 (64%) Query: 9 VYIVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPTMGGDEKETVAKIAKL 68 V+++DTTLRDGEQT GV F EK +A+ L E G+ ++E G+P MG DE+ET+A+I KL Sbjct: 5 VWLMDTTLRDGEQTPGVAFCPQEKALLARRLAEAGVHEIETGVPAMGEDEQETIARIVKL 64 Query: 69 GLKASIMAWNRAVVKDVQESLECGVDAVAISISTSDIHIEHKLKKTRQWVLDSMTEAVRF 128 L + WNRAV+ D++ SL CGV +VAI + +SD I KL+++RQWVLD M VR Sbjct: 65 NLPTRVTTWNRAVISDLEASLNCGVRSVAICLPSSDQQITQKLRQSRQWVLDQMGACVRR 124 Query: 129 AKKEGVYVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCDTVGFLDPFKTYEMVKAIK 188 AK EG+YV + EDASR D FLI+ A++ +RLR DT+G LDP +T+ + + Sbjct: 125 AKAEGLYVVIGLEDASRADPQFLIQLGLEAERLKVNRLRISDTLGILDPIRTFNLFDRLT 184 Query: 189 DAVDIEIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAALEEVVMALKYVY 248 ++ I +E+H HND GMATAN ++ ++AGAK VTV GLGERAGNA LEEV +AL+ Sbjct: 185 SSLSIPLEIHAHNDLGMATANTVSAIQAGAKAASVTVCGLGERAGNAPLEEVALALRQCC 244 Query: 249 KMDLGIDTSRFREISEYVALASGRPLPPSKAIVGKNVFAHESGIHVDGALKNPYTYEVFD 308 D I+ + + V+ ++ RP+P SK +VG++ F H S IHVDG K+ YE + Sbjct: 245 AADTRINLALLPALCRLVSWSTRRPIPFSKPVVGRDAFTHASSIHVDGLNKDRSNYEAYP 304 Query: 309 PQEVGLERQIVIGKHSGTAALINKFKEYGRVLTEEEANLLLPHVRKMAIQLKRPLFDKEL 368 P+ VG +I GK+SG L K G L +EE LL +VR+++ LKRPL ++ Sbjct: 305 PEYVGRRHRIAFGKYSGRKLLAELLKAQGHDLDQEEMTQLLLNVRQLSQVLKRPLRQHDI 364 Query: 369 MYL 371 + L Sbjct: 365 VDL 367 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: 322 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: 380 Length adjustment: 30 Effective length of query: 354 Effective length of database: 350 Effective search space: 123900 Effective search space used: 123900 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