Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate 7023089 Shewana3_0327 3-ketoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= uniprot:Q8EGC1 (252 letters) >FitnessBrowser__ANA3:7023089 Length = 241 Score = 107 bits (267), Expect = 2e-28 Identities = 79/248 (31%), Positives = 128/248 (51%), Gaps = 17/248 (6%) Query: 8 VVITGGAGGLGLAMAHNFAQAGAKLAL-IDVDQDKLERACADLGS-STEVQGYALDITDE 65 V++TG + G+G A+A A AG +AL +Q + + A+L + V D+ D Sbjct: 5 VLVTGSSRGIGKAIALKLAAAGYDIALHYHSNQAAADASAAELSALGVNVSLLKFDVADR 64 Query: 66 EDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVNLTGT 125 V A +E G ++ NAGI RD MS ++ SVI+ NL G Sbjct: 65 AAVKAAIEADIEANGAYYGVILNAGINRDNAF---------PAMSEAEWDSVIHTNLDGF 115 Query: 126 FLCGREAAAAMIESGQAGVIVNISSLAK-AGNVGQSNYAASKAGVAAMSVGWAKELARYN 184 + M++ + G I+ ++S++ AGN GQ NY+ASKAG+ + + ELA+ Sbjct: 116 YNVIHPCVMPMVQGRKGGRIITLASVSGIAGNRGQVNYSASKAGLIGATKALSLELAKRK 175 Query: 185 IRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEND--YVNGR 242 I +APG+I T+M A + + +E+LVP+ R+G EIA+ F++ +D Y+ + Sbjct: 176 ITVNCIAPGLIETDMVADIPK---DMVEQLVPMRRMGKPNEIAALAAFLMSDDAAYITRQ 232 Query: 243 VFEVDGGI 250 V V+GG+ Sbjct: 233 VISVNGGM 240 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: 133 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: 252 Length of database: 241 Length adjustment: 24 Effective length of query: 228 Effective length of database: 217 Effective search space: 49476 Effective search space used: 49476 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 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