Align 2-keto-isovalerate dehydrogenase component α subunit (EC 1.2.4.4) (characterized)
to candidate AO353_25160 AO353_25160 ABC transporter substrate-binding protein
Query= metacyc::MONOMER-11683 (330 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25160 Length = 325 Score = 150 bits (379), Expect = 4e-41 Identities = 106/321 (33%), Positives = 164/321 (51%), Gaps = 7/321 (2%) Query: 11 LTDQEAVDMYRTMLLARKIDERMWLLNRSGKIP-FVISCQGQEAAQVGAAFALDREMDYV 69 LT + + Y+ M R +ER+ + +G+IP FV G+EA+ G L R+ D + Sbjct: 5 LTADQLLHAYQVMRTIRVFEERLHVEFATGEIPGFVHLYAGEEASAAGVMAHL-RDDDCI 63 Query: 70 LPYYRDMGVVLAFGMTAKDLMMSGFAKAADPNSG-GRQMPGHFGQKKNRIVTGSSPVTTQ 128 +R G +A G+ +M + K G G M H + ++ + V Sbjct: 64 ASNHRGHGHCIAKGVDVDGMMAEIYGKKTGVCQGKGGSM--HIADFEKGMLGANGIVGAG 121 Query: 129 VPHAVGIALAGRMEKKDIAAFVTFGEGSSNQGDFHEGANFAAVHKLPVIFMCENNKYAIS 188 P VG ALA +++ D A V FG+G SN+G E N A+V LP +F+ ENN YA + Sbjct: 122 APLVVGAALAAKLKGTDSVAVVFFGDGGSNEGAVFEAMNMASVWNLPCLFIAENNGYAEA 181 Query: 189 VPYDKQVACENISDRAIGYGMPGVTVNGNDPLEVYQAVKEARERARRGEGPTLIETISYR 248 + VAC++I+DRA G+GMPGVTV+G D V++A A ERAR GEGP+LIE R Sbjct: 182 TASNWSVACDHIADRAAGFGMPGVTVDGFDFFAVHEAAGAAVERARAGEGPSLIEVKLTR 241 Query: 249 LTPHSSDDDDSSYRGREEVEEAKK-SDPLLTYQAYLKETGLLSDEIEQTMLDEIMAIVNE 307 H + D +YR +EV+ ++ +D L+ ++ + G + E+ ++ Sbjct: 242 YYGH-FEGDAQTYRAPDEVKHFREHNDCLMQFRERIIRAGRAQASQLDQIDSEVELLIEN 300 Query: 308 ATDEAENAPYAAPESALDYVY 328 A +A++AP + L VY Sbjct: 301 AVLKAKSAPKPSAADLLSDVY 321 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: 238 Number of extensions: 9 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: 325 Length adjustment: 28 Effective length of query: 302 Effective length of database: 297 Effective search space: 89694 Effective search space used: 89694 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: 48 (23.1 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