Align 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized)
to candidate AZOBR_RS05495 AZOBR_RS05495 homocitrate synthase
Query= curated2:Q8RCF9 (384 letters) >FitnessBrowser__azobra:AZOBR_RS05495 Length = 381 Score = 353 bits (905), Expect = e-102 Identities = 183/364 (50%), Positives = 245/364 (67%) Query: 11 IVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPTMGGDEKETVAKIAKLGL 70 I DTTLRDGEQTAGV F +EKI IA+ LDE G+ +LE+GIP MG +E+E + +A LGL Sbjct: 9 INDTTLRDGEQTAGVAFTLDEKIAIARALDEAGVPELEIGIPAMGPEEREGIRAVAALGL 68 Query: 71 KASIMAWNRAVVKDVQESLECGVDAVAISISTSDIHIEHKLKKTRQWVLDSMTEAVRFAK 130 KA +M W R D++ +L+C V V +S+ SDIHI KLK++R W L + V+ A+ Sbjct: 69 KARLMVWCRMHDTDLKAALDCKVGTVNLSMPVSDIHITKKLKRSRAWALAEIERKVKTAR 128 Query: 131 KEGVYVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCDTVGFLDPFKTYEMVKAIKDA 190 G+ VS+ ED+SR DM+FLI A A++AGA R RF DT+G LDPF+T ++ ++ A Sbjct: 129 DHGLEVSLGGEDSSRADMDFLIAAATVAQEAGARRFRFADTLGVLDPFQTRACIERLRRA 188 Query: 191 VDIEIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAALEEVVMALKYVYKM 250 D+EIE+H H+D G+A AN+LA V GA V TVNGLGERAGNA LEEVV++LK +Y Sbjct: 189 TDLEIEIHAHDDLGLANANSLAAVLGGATHVNTTVNGLGERAGNAPLEEVVVSLKVLYGQ 248 Query: 251 DLGIDTSRFREISEYVALASGRPLPPSKAIVGKNVFAHESGIHVDGALKNPYTYEVFDPQ 310 D G+DT IS+ V AS RP+ +K+IVG VF HE+GIHVDG L++ TY+ FDP Sbjct: 249 DCGVDTRALGAISDLVERASNRPVAVNKSIVGDAVFTHEAGIHVDGLLRDRATYQNFDPA 308 Query: 311 EVGLERQIVIGKHSGTAALINKFKEYGRVLTEEEANLLLPHVRKMAIQLKRPLFDKELMY 370 EVG E +IV+GKHSGTA + + + G + A +LP VR +A + KR +EL Sbjct: 309 EVGREHRIVLGKHSGTAGVKMAYGQLGIPCDDATAQAVLPRVRALATRAKRAPTAEELRA 368 Query: 371 LYED 374 ++D Sbjct: 369 FHDD 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: 385 Number of extensions: 12 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: 381 Length adjustment: 30 Effective length of query: 354 Effective length of database: 351 Effective search space: 124254 Effective search space used: 124254 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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