Align 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized)
to candidate WP_012102152.1 CKL_RS08630 homocitrate synthase
Query= curated2:Q8RCF9 (384 letters) >NCBI__GCF_000016505.1:WP_012102152.1 Length = 269 Score = 233 bits (594), Expect = 5e-66 Identities = 114/243 (46%), Positives = 163/243 (67%), Gaps = 3/243 (1%) Query: 9 VYIVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPTMGGDEKETVAKIAKL 68 V IVDTTLRDGEQ A V EK+ IA++++++GI Q+E GI +MGGDEK ++ KI L Sbjct: 3 VNIVDTTLRDGEQKACVALGIKEKVEIAKIINDMGITQIEAGIASMGGDEKASIKKIVNL 62 Query: 69 GLKASIMAWNRAVVKDVQESLECGVDAVAISISTSDIHIEHKLKKTRQWVLDSMTEAVRF 128 L + I +WNR + D+ S++CGVD + ISI +SD+ I+ KL K R WV++++ + + + Sbjct: 63 NLNSKISSWNRMNIDDINHSIDCGVDIIHISIPSSDLQIKSKLGKDRNWVVNTIKKCIDY 122 Query: 129 AKKEGVYVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCDTVGFLDPFKTYEMVKAIK 188 +G +SV EDASR D+NFL+E Q G +R+R+ DTVG L P K + + ++ Sbjct: 123 TLGKGYEISVGLEDASRADINFLVELCETVFQMGVERVRYADTVGILYPGKIFYHINKLR 182 Query: 189 DAVDIEIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAALEEVVMALKYVY 248 V +E+E+HTHNDFGMA AN+LA V+AGA FV TV G+GERAGN + V K +Y Sbjct: 183 QEVPVEVEVHTHNDFGMALANSLAAVEAGAAFVDCTVTGIGERAGNC---DFVKFAKVLY 239 Query: 249 KMD 251 ++ Sbjct: 240 MLE 242 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: 273 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: 269 Length adjustment: 28 Effective length of query: 356 Effective length of database: 241 Effective search space: 85796 Effective search space used: 85796 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: 48 (23.1 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