Align 2-keto-isovalerate dehydrogenase component α subunit (EC 1.2.4.4) (characterized)
to candidate WP_011778184.1 MVAN_RS04600 thiamine pyrophosphate-dependent dehydrogenase E1 component subunit alpha
Query= metacyc::MONOMER-11683 (330 letters) >NCBI__GCF_000015305.1:WP_011778184.1 Length = 324 Score = 149 bits (377), Expect = 7e-41 Identities = 112/333 (33%), Positives = 167/333 (50%), Gaps = 23/333 (6%) Query: 11 LTDQEAVDMYRTMLLARKIDERMWLLNRSGKIP-FVIS----------CQGQEAAQVGAA 59 + D +++YRTM L R +E + + K P F I+ C GQE G Sbjct: 1 MDDAVRLELYRTMRLIRTYEEAILREYHADKKPSFDIAKGQIPGEMHLCTGQEPVPAGFG 60 Query: 60 FALDREMDYVLPYYRDMGVVLAFGMTAKDLMMSGFAKAADPNSGGRQMPGH---FGQKKN 116 L R+ D V +R G LA G+ + + F + + G+ GH F Q + Sbjct: 61 PHLRRD-DAVTGPHRPHGWALAKGVDIERMTAEIFGRI---DGLGKGRGGHMHLFDQDAH 116 Query: 117 RIVTGSSPVTTQVPHAVGIALAGRMEKKDIAAFVTFGEGSSNQGDFHEGANFAAVHKLPV 176 +G + +P AVG+ALA + + D A GEG++NQG FHE N AA+ KLPV Sbjct: 117 FSCSGI--IAEGLPTAVGMALAFKKQGSDRVAIAVTGEGAANQGAFHESLNLAALWKLPV 174 Query: 177 IFMCENNKYAISVPYDKQVACENISDRAIGYGMPGVTVNGNDPLEVYQAVKEARERARRG 236 +F+ E+N + +SV + E+ +DRA+ YGMPGV V N +Y EA RAR G Sbjct: 175 VFIVEDNGWGVSVSKAQSTCIESNADRAVAYGMPGVLVKDNAVEAIYAVAGEAISRARAG 234 Query: 237 EGPTLIETISYRLTPHSSDDDDSSYRGREEVEEAKKSDPLLTYQAYLKETGLLSDEIEQT 296 GPTLIE + RL H + D YR +++ DP+ Y+A L+ +LSD+I Sbjct: 235 GGPTLIEAETLRLWGH-FEGDPQLYRA--DLDGVAALDPVPAYEAQLRADSVLSDDIVHE 291 Query: 297 MLDEIMAIVNEATDEAENAPYAAPESALDYVYA 329 + + + V A A+++P P +AL+Y +A Sbjct: 292 VTNWAVERVESAIAFAKSSPEPDPATALNYQFA 324 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: 15 Number of successful extensions: 3 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: 324 Length adjustment: 28 Effective length of query: 302 Effective length of database: 296 Effective search space: 89392 Effective search space used: 89392 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 24 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