Align 4-hydroxy-2-oxovalerate aldolase; HOA; EC 4.1.3.39; 4-hydroxy-2-keto-pentanoic acid aldolase; 4-hydroxy-2-oxopentanoate aldolase (uncharacterized)
to candidate CCNA_01610 CCNA_01610 2-isopropylmalate synthase
Query= curated2:B1VRH5 (340 letters) >FitnessBrowser__Caulo:CCNA_01610 Length = 524 Score = 67.8 bits (164), Expect = 6e-16 Identities = 82/283 (28%), Positives = 118/283 (41%), Gaps = 61/283 (21%) Query: 4 VVIHDPTLRDGQHAVHHRLGLTELRRYAEAADAARVPVVEVGH---GNG----------L 50 VV+ D T+RDG+ + + L E A+ + V V+E G NG L Sbjct: 15 VVVFDTTMRDGEQSPGASMSLEEKLELAKILEEMGVDVIEAGFPIASNGDFEAVRQIAEL 74 Query: 51 GASSLQVGLAAATD---DAMLSTVREALRHSRLGTFM------------LPGWGTSDDLR 95 S GLA A D VR A R R+ TF+ + + + Sbjct: 75 ITESTVCGLARAAAGDIDRCAEAVRRAKR-GRIHTFISTSPVHMKYKLQMEPDAVLEAIT 133 Query: 96 RAISHGVD-VFRVGVHATEASLAEHHLGFLRDAGAEAHCVLMMSHMASPGELAEQAARAV 154 R++SH + V V A +A+ E FL+ CV E A +A Sbjct: 134 RSVSHARNLVGDVEWSAEDATRTERD--FLK------RCV-------------EAAIKA- 171 Query: 155 GYGAQAVGIMDSAGHFLPPDVTARIGAIVEAV-GTVPVIF--HGHNNLGMAVANSVAAAE 211 GA + + D+ G+ P + ++ +V G IF H HN+LG+AVANS+AA E Sbjct: 172 --GATTINLPDTVGYSYPSEYGELFRDVITSVPGADKAIFSAHCHNDLGLAVANSIAAIE 229 Query: 212 AGARIIDGCARGFGAGAGNTQLEVLVPVLERSG----FATGID 250 GAR ++ G G AGN LE +V L G + T +D Sbjct: 230 GGARQVEVAINGIGERAGNAALEEIVMALRVRGDHLPYGTSVD 272 Lambda K H 0.320 0.135 0.393 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: 380 Number of extensions: 16 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 340 Length of database: 524 Length adjustment: 32 Effective length of query: 308 Effective length of database: 492 Effective search space: 151536 Effective search space used: 151536 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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