Align 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized)
to candidate WP_015943174.1 DHAF_RS05305 pyruvate carboxyltransferase
Query= curated2:Q8RCF9 (384 letters) >NCBI__GCF_000021925.1:WP_015943174.1 Length = 377 Score = 302 bits (774), Expect = 9e-87 Identities = 158/363 (43%), Positives = 221/363 (60%) Query: 9 VYIVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPTMGGDEKETVAKIAKL 68 V++ DTTLRDGEQT G+ F EK RIA L E GID++EVG+P++G DE E + + L Sbjct: 5 VWLCDTTLRDGEQTPGIAFRFKEKARIATCLAEAGIDEIEVGVPSVGADEMEIIKGLVDL 64 Query: 69 GLKASIMAWNRAVVKDVQESLECGVDAVAISISTSDIHIEHKLKKTRQWVLDSMTEAVRF 128 L + WNR +D++ S GV AV+I I SD HIE KL+K+R W +DSM EAV Sbjct: 65 RLPVRLATWNRTSKEDLEASFRTGVGAVSICIPVSDQHIERKLRKSRTWAMDSMGEAVEL 124 Query: 129 AKKEGVYVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCDTVGFLDPFKTYEMVKAIK 188 AKKEG YV V EDASR D++F+I+ A+ A+ ADR+R DT+G LDP + + Sbjct: 125 AKKEGKYVCVGFEDASRADVDFMIKMAKVAEGLRADRIRLADTLGILDPLELARRFAPLP 184 Query: 189 DAVDIEIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAALEEVVMALKYVY 248 + +E H HND GMATANAL ++ G K V VTV GLGERAGNA LEE+ +A+ ++ Sbjct: 185 QRTALPLEFHAHNDLGMATANALTALRIGFKAVSVTVGGLGERAGNAPLEEISVAIHHIL 244 Query: 249 KMDLGIDTSRFREISEYVALASGRPLPPSKAIVGKNVFAHESGIHVDGALKNPYTYEVFD 308 + D + +IS V+ + R +P SK +VG +VF H S +H+DG K+ Y+ F Sbjct: 245 QRPTAFDIQKVNDISLLVSDITQREVPRSKPVVGSDVFTHTSAVHLDGIRKDVENYQPFP 304 Query: 309 PQEVGLERQIVIGKHSGTAALINKFKEYGRVLTEEEANLLLPHVRKMAIQLKRPLFDKEL 368 P+ + + +V GK+SG L+ +E T+E+ LL VR + K PL +++ Sbjct: 305 PESISRKHSMVFGKYSGIKELVRLLEEERVPYTQEQLTELLIRVRLHSSIKKIPLQAEDV 364 Query: 369 MYL 371 + L Sbjct: 365 LSL 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: 343 Number of extensions: 11 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: 377 Length adjustment: 30 Effective length of query: 354 Effective length of database: 347 Effective search space: 122838 Effective search space used: 122838 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 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