Align 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized)
to candidate Dsui_0578 Dsui_0578 homocitrate synthase NifV
Query= curated2:Q8RCF9 (384 letters) >FitnessBrowser__PS:Dsui_0578 Length = 384 Score = 351 bits (901), Expect = e-101 Identities = 182/364 (50%), Positives = 238/364 (65%) Query: 9 VYIVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPTMGGDEKETVAKIAKL 68 + I DTTLRDGEQTAGV F EK+ IAQ L G+ ++EVGIP MG E+E + IA L Sbjct: 4 ITINDTTLRDGEQTAGVAFTAAEKLAIAQALAAAGVPEMEVGIPAMGEQEQEVIRAIAGL 63 Query: 69 GLKASIMAWNRAVVKDVQESLECGVDAVAISISTSDIHIEHKLKKTRQWVLDSMTEAVRF 128 GL + +M W R D++ + C V +SI SD I HKL K +WVLDS+ V Sbjct: 64 GLSSRLMVWGRMCAADLEVTRRCNAHIVNLSIPVSDQQIRHKLNKDHRWVLDSIRRFVPE 123 Query: 129 AKKEGVYVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCDTVGFLDPFKTYEMVKAIK 188 A+ G+ V V ED+SR D++FL A+ AGA R RF DT+G LDPF T++ + A++ Sbjct: 124 ARAAGLEVCVGGEDSSRADLDFLHRVMEAAQAAGARRFRFADTLGVLDPFITHQRIAALR 183 Query: 189 DAVDIEIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAALEEVVMALKYVY 248 D+EIE+H H+D G+ATAN LA V AGA + TVNGLGERAGNA LEE V+AL+++Y Sbjct: 184 ARSDLEIEIHAHDDLGLATANTLAAVTAGATHINTTVNGLGERAGNAPLEESVIALRHLY 243 Query: 249 KMDLGIDTSRFREISEYVALASGRPLPPSKAIVGKNVFAHESGIHVDGALKNPYTYEVFD 308 +D G+D + IS+ VA ASGRP+ +K+IVG NVF HE+GIHVDG KNP Y+ FD Sbjct: 244 DIDSGVDPLQLPAISDLVAKASGRPVAVNKSIVGANVFTHEAGIHVDGLAKNPANYQAFD 303 Query: 309 PQEVGLERQIVIGKHSGTAALINKFKEYGRVLTEEEANLLLPHVRKMAIQLKRPLFDKEL 368 P EVG +IV+GKHSG+ A+I+ +K+ G + E A +L VR A+ KRP +EL Sbjct: 304 PAEVGKGHRIVLGKHSGSTAVIHAYKDLGIDIDEGMARRILSRVRSYAMAFKRPPGFREL 363 Query: 369 MYLY 372 M Y Sbjct: 364 MSYY 367 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: 365 Number of extensions: 9 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: 384 Length adjustment: 30 Effective length of query: 354 Effective length of database: 354 Effective search space: 125316 Effective search space used: 125316 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