Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_012974876.1 AZL_RS12310 beta-ketoacyl-ACP reductase
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_000010725.1:WP_012974876.1 Length = 240 Score = 147 bits (371), Expect = 2e-40 Identities = 92/247 (37%), Positives = 136/247 (55%), Gaps = 16/247 (6%) Query: 6 KVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGYALDITDE 65 +V V+TGG G+G A+A AG K+A D+ A + + T + Y D+ D Sbjct: 3 RVAVVTGGTRGIGEAVAIALKNAGYKVAANYAGNDQ---AAEEFTARTGIPTYKFDVADF 59 Query: 66 EDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVNLTGT 125 + G A I D G ++VL+NNAGI RDG++ RM++ Q+++VI+ NL+ Sbjct: 60 DACKKGIAAIESDLGPVDVLINNAGITRDGVM---------HRMTYQQWEAVIHTNLSSC 110 Query: 126 FLCGREAAAAMIESGQAGVIVNISSL-AKAGNVGQSNYAASKAGVAAMSVGWAKELARYN 184 F R M E G G IVNI S+ +AG GQ NYAA+K+G+ + A+E A Sbjct: 111 FNMCRNVIDGMRERG-FGRIVNIGSINGQAGQYGQVNYAAAKSGIHGFTKALAQESAAKG 169 Query: 185 IRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFII--ENDYVNGR 242 I A+APG I T+M A+ LE++ +PVGRLG A EIA+ V F++ +N ++ G Sbjct: 170 ITVNAIAPGYIDTDMVRAVPANVLEKIVARIPVGRLGRASEIANAVLFLVNDDNGFMTGS 229 Query: 243 VFEVDGG 249 ++GG Sbjct: 230 TLSINGG 236 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: 168 Number of extensions: 3 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: 252 Length of database: 240 Length adjustment: 24 Effective length of query: 228 Effective length of database: 216 Effective search space: 49248 Effective search space used: 49248 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