Align 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized)
to candidate WP_041314050.1 HM1_RS13635 homocitrate synthase
Query= curated2:Q8RCF9 (384 letters) >NCBI__GCF_000019165.1:WP_041314050.1 Length = 378 Score = 523 bits (1347), Expect = e-153 Identities = 255/370 (68%), Positives = 315/370 (85%) Query: 6 DKPVYIVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPTMGGDEKETVAKI 65 ++ + IVDTTLRDGEQTAGVVFAN EKIRIA+MLDEIG+ Q+E GIP MGGDEKET+AKI Sbjct: 3 NRQITIVDTTLRDGEQTAGVVFANKEKIRIAKMLDEIGVHQIEAGIPVMGGDEKETIAKI 62 Query: 66 AKLGLKASIMAWNRAVVKDVQESLECGVDAVAISISTSDIHIEHKLKKTRQWVLDSMTEA 125 K+GLKASIM WNRAV+ D+Q S++CG DAVAISISTSDIHI+HKL+ +R+WVL+SM +A Sbjct: 63 CKMGLKASIMGWNRAVISDIQHSIDCGCDAVAISISTSDIHIQHKLRTSREWVLESMMKA 122 Query: 126 VRFAKKEGVYVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCDTVGFLDPFKTYEMVK 185 V FAK +G+YVS+NAEDASR+D+ FLI+FA AK+ GA+RLR+CDTVG ++PF YE +K Sbjct: 123 VDFAKSQGLYVSINAEDASRSDIEFLIQFATEAKKLGANRLRYCDTVGIMEPFTIYEHIK 182 Query: 186 AIKDAVDIEIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAALEEVVMALK 245 +++AVDI+IEMHTH+DFGMATANA+AGV+AGA +GVTVNGLGERAGNAALEEVVMALK Sbjct: 183 RLREAVDIDIEMHTHDDFGMATANAIAGVRAGATHIGVTVNGLGERAGNAALEEVVMALK 242 Query: 246 YVYKMDLGIDTSRFREISEYVALASGRPLPPSKAIVGKNVFAHESGIHVDGALKNPYTYE 305 Y +DLG + +FRE+ EYV+ ASGR LP K+IVG N+FAHESGIH DG LKNP TYE Sbjct: 243 YCDNIDLGFKSEKFRELCEYVSKASGRFLPTWKSIVGSNMFAHESGIHGDGVLKNPKTYE 302 Query: 306 VFDPQEVGLERQIVIGKHSGTAALINKFKEYGRVLTEEEANLLLPHVRKMAIQLKRPLFD 365 V P+EVGL RQIVIGKHSGTA++ KF+E+ +TE +A +L VR+ A++LKRPLFD Sbjct: 303 VISPEEVGLTRQIVIGKHSGTASIKAKFREFEIDMTEVQAAEVLARVRETAVELKRPLFD 362 Query: 366 KELMYLYEDV 375 KELM++YE++ Sbjct: 363 KELMFIYEEL 372 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: 466 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: 378 Length adjustment: 30 Effective length of query: 354 Effective length of database: 348 Effective search space: 123192 Effective search space used: 123192 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