Align Probable 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (uncharacterized)
to candidate N515DRAFT_2996 N515DRAFT_2996 3-hydroxyisobutyrate dehydrogenase
Query= curated2:P63936 (294 letters) >FitnessBrowser__Dyella79:N515DRAFT_2996 Length = 286 Score = 133 bits (335), Expect = 4e-36 Identities = 94/289 (32%), Positives = 137/289 (47%), Gaps = 10/289 (3%) Query: 5 AFLGLGNMGAPMSANLVGAGHVVRGFDPAPTAASGAAAHGVAVFRSAPEAVAEADVVITM 64 AF+GLG MGAPM+ +L G ++ A + A A + V E +A VI + Sbjct: 6 AFVGLGAMGAPMAGHLKSKG-LLHAVANRTQAKADALARELGVVAPPLEQLAAQCEVIAL 64 Query: 65 LPTGEV-VRRCYTDVLAAARPATLFIDSSTISVTDAREVHALAESHGMLQLDAPVSGGVK 123 T + V +L + + +D ST++ A+ A + G+ LDAPVSGGV+ Sbjct: 65 CVTADADVLATIDTMLPHLKRGAVVVDHSTVAPDTAKRAAARLATAGVDFLDAPVSGGVE 124 Query: 124 GAAAATLAFMVGGDESTLRRARPVLEPMAGKIIHCGAAGAGQAAKVCNNMVLAVQQIAIA 183 GA L+ MVGGD + L RARPVLE A ++ H G GAGQA K N +++A A+ Sbjct: 125 GAKNGKLSVMVGGDAAVLERARPVLEAYALRVTHLGDVGAGQATKAVNQVLVAGIAQAVC 184 Query: 184 EAFVLAEKLGLSAQSLFDVITGATGNCWAVHTNCPVPGPVPTSPANNDFKPGFSTALMNK 243 E L E LGL A+ L + W + + ++F GF AL++K Sbjct: 185 EGLALGEALGLEAERLLPTLGAGAAGSWFLEKR-------GATMLRDEFSVGFKLALLHK 237 Query: 244 DLGLAMDAVAATGATAPLGSHAADIYAKFAAD-HADLDFSAVIHTLRAR 291 DLG+ G + + YA+ + + D D SA+I R R Sbjct: 238 DLGIVKRIAEGAGTDRTVIEKSLADYAELMSQGYGDDDISALIRLKRKR 286 Lambda K H 0.319 0.131 0.382 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: 196 Number of extensions: 6 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: 294 Length of database: 286 Length adjustment: 26 Effective length of query: 268 Effective length of database: 260 Effective search space: 69680 Effective search space used: 69680 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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