Align 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized)
to candidate BWI76_RS18860 BWI76_RS18860 homocitrate synthase
Query= curated2:Q8RCF9 (384 letters) >FitnessBrowser__Koxy:BWI76_RS18860 Length = 380 Score = 270 bits (689), Expect = 6e-77 Identities = 152/375 (40%), Positives = 217/375 (57%) Query: 9 VYIVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPTMGGDEKETVAKIAKL 68 V I DTTLRDGEQ+ GV F +EK+ IA+ L GI +EVG P MG +E + + + Sbjct: 4 VLINDTTLRDGEQSPGVAFRTSEKVAIAEALYAAGITAMEVGTPAMGDEEIARIQLVRRQ 63 Query: 69 GLKASIMAWNRAVVKDVQESLECGVDAVAISISTSDIHIEHKLKKTRQWVLDSMTEAVRF 128 A++M W R ++++S + G+D V ISI SD ++KL++ +L+ + + Sbjct: 64 LPDATLMTWCRMNALEIRQSADLGIDWVDISIPASDKLRQYKLREPLAVLLERLAMFIHL 123 Query: 129 AKKEGVYVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCDTVGFLDPFKTYEMVKAIK 188 A G+ V + EDASR L A A+Q A RLR+ DTVG LDPF T + A++ Sbjct: 124 AHTLGLKVCIGCEDASRASGQTLRAIAEVAQQCAAARLRYADTVGLLDPFTTAAQISALR 183 Query: 189 DAVDIEIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAALEEVVMALKYVY 248 D EIEMH HND GMATAN LA V AGA V TV GLGERAGNAALE V + L+ Sbjct: 184 DVWSGEIEMHAHNDLGMATANTLAAVSAGATSVNTTVLGLGERAGNAALETVALGLERCL 243 Query: 249 KMDLGIDTSRFREISEYVALASGRPLPPSKAIVGKNVFAHESGIHVDGALKNPYTYEVFD 308 ++ G+ S + + VA A+ R + P + +VG+ VF HESG+HV L++ +Y+ Sbjct: 244 GVETGVHFSALPALCQRVAEAAQRAIDPQQPLVGELVFTHESGVHVAALLRDSESYQSIA 303 Query: 309 PQEVGLERQIVIGKHSGTAALINKFKEYGRVLTEEEANLLLPHVRKMAIQLKRPLFDKEL 368 P +G ++V+GKHSG A+ F + G L + N LLP +R+ A KR D EL Sbjct: 304 PSLMGRSYRLVLGKHSGRQAVNGVFDQMGYHLNAAQINQLLPAIRRFAENWKRSPKDYEL 363 Query: 369 MYLYEDVIVKGKAKA 383 + +Y+++ + +A Sbjct: 364 VAIYDELCGESALRA 378 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: 333 Number of extensions: 10 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