Align 2-keto-isovalerate dehydrogenase component α subunit (EC 1.2.4.4) (characterized)
to candidate WP_011384713.1 AMB_RS11705 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= metacyc::MONOMER-11683 (330 letters) >NCBI__GCF_000009985.1:WP_011384713.1 Length = 332 Score = 153 bits (387), Expect = 5e-42 Identities = 108/313 (34%), Positives = 156/313 (49%), Gaps = 9/313 (2%) Query: 12 TDQEAVDMYRTMLLARKIDERMWLLNRSGKIP-FVISCQGQEAAQVGAAFALDREMDYVL 70 T QE + YR MLL R+ +E+ L G I F GQEA VG A+ D + Sbjct: 14 TPQELIRYYREMLLIRRFEEKAGQLYGMGLINGFCHLYIGQEAVVVGMQ-AVAGAADSCI 72 Query: 71 PYYRDMGVVLAFGMTAKDLM--MSGFAKAADPNSGGRQMPGHFGQKKNRIVTGSSPVTTQ 128 YRD G +L GM K +M ++G A GG H ++ R G V Q Sbjct: 73 TSYRDHGHMLVCGMDPKGVMAELTGRAGGYSRGKGGSM---HMFSREKRFYGGHGIVGAQ 129 Query: 129 VPHAVGIALAGRMEKKDIAAFVTFGEGSSNQGDFHEGANFAAVHKLPVIFMCENNKYAIS 188 VP G+ A + K + A V G+G+ NQG +E N AA+ KLPV+F+ ENNKYA+ Sbjct: 130 VPLGTGLGFAHKYSKDNGVAHVYCGDGAVNQGQVYEAFNMAALWKLPVVFVIENNKYAMG 189 Query: 189 VPYDKQVACENISDRAIGYGMPGVTVNGNDPLEVYQAVKEARERARRGEGPTLIETISYR 248 + A + + R YG+PG VNG + + V A A E AR G GP ++E +YR Sbjct: 190 TSTVRHAAGQELYMRGAAYGIPGEPVNGMNIIAVRDAAARALEHARSGNGPYILEMNTYR 249 Query: 249 LTPHSSDDDDSSYRGREEVEEAKKS-DPLLTYQAYLKETGLLSDEIEQTMLDEIMAIVNE 307 HS D + YR +EEV + ++ DP+ + L GL+ + + + E+ IV E Sbjct: 250 YRGHSM-SDPAKYRSKEEVTKMREQHDPIDQLKEKLLAEGLIDEAGLKEIDREVKVIVTE 308 Query: 308 ATDEAENAPYAAP 320 A + ++++P P Sbjct: 309 AAEFSQSSPEPDP 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: 261 Number of extensions: 17 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: 332 Length adjustment: 28 Effective length of query: 302 Effective length of database: 304 Effective search space: 91808 Effective search space used: 91808 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