Align 2-keto-isovalerate dehydrogenase component α subunit (EC 1.2.4.4) (characterized)
to candidate 349840 BT0312 2-oxoisovalerate dehydrogenase beta subunit (NCBI ptt file)
Query= metacyc::MONOMER-11683 (330 letters) >FitnessBrowser__Btheta:349840 Length = 678 Score = 160 bits (404), Expect = 1e-43 Identities = 107/325 (32%), Positives = 167/325 (51%), Gaps = 15/325 (4%) Query: 12 TDQEAVDM-YRTMLLARKIDER-----MWLLNRSGKIPFVISCQGQEAAQ--VGAAFALD 63 TD E + Y M L R +DE+ + L S P+ G + Q VG F L Sbjct: 10 TDVETLKKWYHLMTLGRALDEKAPSYQLQSLGWSYHAPYA----GHDGIQLAVGQVFTLG 65 Query: 64 REMDYVLPYYRDMGVVLAFGMTAKDLMMSGFAKAADPNSGGRQMPGHFGQKKNRIVTGSS 123 D++ PYYRDM VL+ GMTA++++++G +KA DP SGGR M HF + + I SS Sbjct: 66 E--DFLFPYYRDMLTVLSAGMTAEEIILNGISKATDPGSGGRHMSNHFAKPEWHIENISS 123 Query: 124 PVTTQVPHAVGIALAGRMEKKDIAAFVTFGEGSSNQGDFHEGANFAAVHKLPVIFMCENN 183 T HA G+A A A + GE ++++G +E N A++ +LPVIF+ ++N Sbjct: 124 ATGTHDLHAAGVARAMVYYGHKGVAITSHGESATSEGFVYEAINGASLERLPVIFVIQDN 183 Query: 184 KYAISVPYDKQVACENISDRAIGY-GMPGVTVNGNDPLEVYQAVKEARERARRGEGPTLI 242 Y ISVP +Q A +++ G+ + + NG D + A+ EARE A P ++ Sbjct: 184 GYGISVPKSEQTANRKVAENFSGFKNLKIIYCNGKDVFDSMNAMTEAREYAISTRNPVIV 243 Query: 243 ETISYRLTPHSSDDDDSSYRGREEVEEAKKSDPLLTYQAYLKETGLLSDEIEQTMLDEIM 302 + R+ HS+ D + YR E+E K++DPL+ ++ L L++E + E Sbjct: 244 QANCVRIGSHSNSDKHTLYRDENELEYVKEADPLMKFRRMLLRYKRLTEEELLQIEAESK 303 Query: 303 AIVNEATDEAENAPYAAPESALDYV 327 ++ A +A AP P+S D+V Sbjct: 304 KELSAANRKALAAPEPDPKSIYDFV 328 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: 472 Number of extensions: 18 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: 678 Length adjustment: 33 Effective length of query: 297 Effective length of database: 645 Effective search space: 191565 Effective search space used: 191565 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: 51 (24.3 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