Align 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate BPHYT_RS02790 BPHYT_RS02790 hypothetical protein
Query= curated2:C3K1K7 (559 letters) >FitnessBrowser__BFirm:BPHYT_RS02790 Length = 348 Score = 454 bits (1167), Expect = e-132 Identities = 210/339 (61%), Positives = 268/339 (79%) Query: 3 MLKDPSSKYRAFPTIDIPDRTWPSKTITEAPIWCSSDLRDGNQSLIEPMDAVKKLRFWKT 62 ML++P+ KYR FP + + R WPS+TI + P+W S+DLRDGNQ+LIEPM+A +KL F++ Sbjct: 1 MLQNPAEKYRPFPAVRLTGRKWPSRTIDQTPVWMSTDLRDGNQALIEPMNAAQKLEFFEM 60 Query: 63 LVAVGVKEIEASFPAASQTDFDFVRTLIEDNHIPEDTTIQVLTQGREDLIARTFESLRGA 122 LVA+G KEIE +P+ASQ DFDFVR LIE+ IP+D TI+V R +LIARTFE+L GA Sbjct: 61 LVAIGFKEIEVGYPSASQMDFDFVRKLIEEKRIPDDVTIEVFMPSRAELIARTFEALEGA 120 Query: 123 KKAIVHLYNATSPSFRRIVFNQDKEGIKAIAVNAAKLFVKYAAQQPETQWTFEYSPETFS 182 +AIVHLYNA PSFRRIVFNQ K IKA+AV+ ++ ++A +P T WTF+YSPETF+ Sbjct: 121 PRAIVHLYNAICPSFRRIVFNQTKAEIKALAVHGTQIIKEHAQARPGTHWTFQYSPETFN 180 Query: 183 ATELEFAKEVCDAVIEVWNPTPEHKMILNLPATVECATPNIYADQIEWFGRHINRRDSVI 242 ATEL FA+EVCDAV + W PT +HKMI+NLPA+VE ATPN++ADQIEW R++ RDS++ Sbjct: 181 ATELPFAREVCDAVAQTWRPTRDHKMIVNLPASVEAATPNVFADQIEWMHRNLGYRDSIV 240 Query: 243 ISLHTHNDRGTGVAATELGLMAGADRVEGCLFGNGERTGNVDLVTVALNMYTQGLDPQLD 302 +S+H HNDRGT VAA EL L+AGADRVEGCLFGNGERTGNVDLV +A+N+ QG+D LD Sbjct: 241 LSVHPHNDRGTAVAAAELALLAGADRVEGCLFGNGERTGNVDLVALAMNLAAQGVDTGLD 300 Query: 303 FSDIDGVRKVVEECNQIQVHPRHPYVGDLVHTAFSGSHQ 341 FS+++ VR+VVE CNQ+ VHPRHPY G+ + A + Q Sbjct: 301 FSNMEAVRRVVERCNQLPVHPRHPYAGEAMMRAKNAERQ 339 Lambda K H 0.317 0.133 0.391 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: 543 Number of extensions: 18 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: 559 Length of database: 348 Length adjustment: 32 Effective length of query: 527 Effective length of database: 316 Effective search space: 166532 Effective search space used: 166532 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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