Align 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized)
to candidate WP_012568815.1 RC1_RS17665 homocitrate synthase
Query= curated2:Q8RCF9 (384 letters) >NCBI__GCF_000016185.1:WP_012568815.1 Length = 400 Score = 281 bits (720), Expect = 2e-80 Identities = 150/353 (42%), Positives = 206/353 (58%) Query: 9 VYIVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPTMGGDEKETVAKIAKL 68 V + DTTLRDGEQ AGV F EK+ IA+ L G+ ++E GIP G E + + I + Sbjct: 23 VLVHDTTLRDGEQAAGVAFTRAEKLAIAKALAAAGVPEIEAGIPASGPHEIDALRAIVEA 82 Query: 69 GLKASIMAWNRAVVKDVQESLECGVDAVAISISTSDIHIEHKLKKTRQWVLDSMTEAVRF 128 GL ++ AW R + DV+ + GV + +++ SDI + HKL ++R W L + V Sbjct: 83 GLPLTVTAWGRLHLGDVEAAARTGVTRLHLAVPVSDIQLSHKLGRSRDWALAEIGRVVGA 142 Query: 129 AKKEGVYVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCDTVGFLDPFKTYEMVKAIK 188 A G VSV EDASR+D FL++ A+ AGA R R DTVG L+PF T ++ + ++ Sbjct: 143 ATAAGFAVSVGGEDASRSDPAFLLDCIAAAEAAGAVRFRIADTVGALEPFGTLDLFRRLR 202 Query: 189 DAVDIEIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAALEEVVMALKYVY 248 +++E+H H+D G+ATAN LA V GA V TV GLGERAGNA LEEV +AL ++ Sbjct: 203 AGTTLDLEIHAHDDLGLATANTLAAVLGGASHVSTTVVGLGERAGNAPLEEVAVALATLH 262 Query: 249 KMDLGIDTSRFREISEYVALASGRPLPPSKAIVGKNVFAHESGIHVDGALKNPYTYEVFD 308 D G+D + ++ VA ASGRP+P K+IVG F HESGIH DG LK+P TYE Sbjct: 263 GRDTGLDLTALPRLAALVAGASGRPIPAGKSIVGAAAFRHESGIHADGLLKDPRTYEALA 322 Query: 309 PQEVGLERQIVIGKHSGTAALINKFKEYGRVLTEEEANLLLPHVRKMAIQLKR 361 P VG ++ +GKHSG ++ G L A + VR + + KR Sbjct: 323 PALVGRRHELTLGKHSGARSVEAACAGLGLPLDPSRAREVAGMVRAFSAETKR 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: 370 Number of extensions: 19 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: 400 Length adjustment: 31 Effective length of query: 353 Effective length of database: 369 Effective search space: 130257 Effective search space used: 130257 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