Align 2-keto-isovalerate dehydrogenase component α subunit (EC 1.2.4.4) (characterized)
to candidate RR42_RS21725 RR42_RS21725 ABC transporter substrate-binding protein
Query= metacyc::MONOMER-11683 (330 letters) >FitnessBrowser__Cup4G11:RR42_RS21725 Length = 334 Score = 148 bits (374), Expect = 2e-40 Identities = 106/323 (32%), Positives = 160/323 (49%), Gaps = 7/323 (2%) Query: 9 LGLTDQEAVDMYRTMLLARKIDERMWLLNRSGKIP-FVISCQGQEAAQVGAAFALDREMD 67 L L QE + +YR M R +ER+ + G IP FV G+EAA VG L + D Sbjct: 13 LPLDKQELLAVYRRMRTIRDFEERLHVDFGRGDIPGFVHLYAGEEAAGVGILHHLG-DGD 71 Query: 68 YVLPYYRDMGVVLAFGMTAKDLMMSGFA-KAADPNSGGRQMPGHFGQKKNRIVTGSSPVT 126 + +R G +A G+ +M + K N G M H ++ + + Sbjct: 72 RIASTHRGHGHCIAKGVDPVAMMKEIYGRKGGSCNGKGGSM--HIADLSKGMMGANGILG 129 Query: 127 TQVPHAVGIALAGRMEKKDIAAFVTFGEGSSNQGDFHEGANFAAVHKLPVIFMCENNKYA 186 P G ALA + K G+G+SNQG F E N AAV LPVIF+ ENN YA Sbjct: 130 AGAPLVCGAALAAKFRGKGEIGITFAGDGASNQGTFLESLNLAAVWNLPVIFVIENNGYA 189 Query: 187 ISVPYDKQVACENISDRAIGYGMPGVTVNGNDPLEVYQAVKEARERARRGEGPTLIETIS 246 S D A ++ DRA G+G+PGVTV+G D V++A E +RAR G GP L+E Sbjct: 190 ESTARDYGTAVDSYVDRAAGFGIPGVTVDGTDFFAVHEAAGEVIKRAREGGGPALLECKM 249 Query: 247 YRLTPHSSDDDDSSYRGREEVEEAK-KSDPLLTYQAYLKETGLLSDEIEQTMLDEIMAIV 305 R H + D +YR E+++ + D L + A + + G+++ + + + +++ A++ Sbjct: 250 VRFYGH-FEGDAQTYRASGELDDIRANKDCLKKFTATVTQAGVIALDELKAIDEQVAALI 308 Query: 306 NEATDEAENAPYAAPESALDYVY 328 +A +A+ AP+ P L VY Sbjct: 309 EDAVQQAKAAPFPTPADLLTDVY 331 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: 260 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: 334 Length adjustment: 28 Effective length of query: 302 Effective length of database: 306 Effective search space: 92412 Effective search space used: 92412 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