Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_057508628.1 ABB28_RS10765 NAD(P)-dependent oxidoreductase
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_001431535.1:WP_057508628.1 Length = 252 Score = 142 bits (357), Expect = 9e-39 Identities = 89/251 (35%), Positives = 134/251 (53%), Gaps = 12/251 (4%) Query: 3 LKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADL-GSSTEVQGYALD 61 LK K ++TGG G+GLA+A A +GA +++ D+ Q+ ++ L G + G ALD Sbjct: 6 LKGKTAIVTGGVSGIGLAVAEMLAASGAAISVWDLKQEAVDATTEALRGKGVKAIGIALD 65 Query: 62 ITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVN 121 +TDE V A A + + G +++ VNNAGI A ++ D ++ VI+VN Sbjct: 66 VTDEAAVEAAVARTVAELGSVDIAVNNAGI--------AGPAAISGDYPVDGWRKVIDVN 117 Query: 122 LTGTFLCGREAAAAMIESGQAGVIVNISS-LAKAGNVGQSNYAASKAGVAAMSVGWAKEL 180 LT FLC R AM ++G G I+N++S L + G G YAA+K GV ++ A E Sbjct: 118 LTSVFLCQRAQIQAMRDAGNGGSIINMASILGQVGYAGSVAYAAAKHGVVGLTQTAAWEH 177 Query: 181 ARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEN--DY 238 A IR AV PG I+T + M P+ LE + RLG EE+A+ V ++ + + Sbjct: 178 ASDQIRINAVGPGFISTPLLEQMDPKVRATLESRHALKRLGTPEEVAALVAWLASDAASF 237 Query: 239 VNGRVFEVDGG 249 G + +DGG Sbjct: 238 ATGTYYAIDGG 248 Lambda K H 0.317 0.134 0.369 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: 151 Number of extensions: 10 Number of successful extensions: 4 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: 252 Length of database: 252 Length adjustment: 24 Effective length of query: 228 Effective length of database: 228 Effective search space: 51984 Effective search space used: 51984 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 (21.7 bits) S2: 46 (22.3 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