Align 2-keto-isovalerate dehydrogenase component α subunit (EC 1.2.4.4) (characterized)
to candidate 3607112 Dshi_0534 dehydrogenase E1 component (RefSeq)
Query= metacyc::MONOMER-11683 (330 letters) >FitnessBrowser__Dino:3607112 Length = 339 Score = 113 bits (282), Expect = 8e-30 Identities = 90/287 (31%), Positives = 133/287 (46%), Gaps = 7/287 (2%) Query: 19 MYRTMLLARKIDERMWLLNRSGKIP--FVISCQGQEAAQVGAAFALDREMDYVLPYYRDM 76 +Y M R +ER+ L GK + G+E+A VG + R+ D ++R Sbjct: 9 LYEDMRRVRTFEERVGELFVRGKSAGSMLHLSIGEESAAVGVCAHM-RDGDTFTTHHRGH 67 Query: 77 GVVLAFGMTAKDLMMSGFAKAADPNSGGRQMPGHFGQKKNRIVTGSSPVTTQVPHAVGIA 136 G+ LA G D MM+ A G+ H + ++ V +P VG Sbjct: 68 GIFLARGADP-DRMMAEIAGKESGYCHGKGGSMHIADMGLGHLGANAIVGGGIPSVVGAG 126 Query: 137 LAGRMEKKDIAAFVTFGEGSSNQGDFHEGANFAAVHKLPVIFMCENNKYAISVPYDKQVA 196 L+ R +K + FG+G++ QG +E N AA+ KLPVIF+C NN+Y + D+ A Sbjct: 127 LSARHKKSGAISVAFFGDGATGQGILYESMNMAALWKLPVIFVCINNQYGMGTRIDQATA 186 Query: 197 CENISDRAIGYGMPGVTVNGNDPLEVYQAVKEARERARRGEGPTLIETISYRLTPHSSDD 256 N+ +RA +G+ TV+G D +V A + AR G P + YR H+ Sbjct: 187 NPNLHERAAAFGLAARTVDGLDVEDVADAAADLIAGAREGR-PAFLSIDCYRFFGHAR-K 244 Query: 257 DDSSYRGREEVEEAKKSDPLLTYQAYLKETGLLSDEIEQTMLDEIMA 303 D S YR E E +K DP+L + L GL+S E E LD +A Sbjct: 245 DKSPYRDEAEEAEGRKKDPVLRARDKLISDGLMS-EAELDALDTRVA 290 Lambda K H 0.316 0.132 0.377 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: 246 Number of extensions: 12 Number of successful extensions: 2 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: 330 Length of database: 339 Length adjustment: 28 Effective length of query: 302 Effective length of database: 311 Effective search space: 93922 Effective search space used: 93922 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: 49 (23.5 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