Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate CCNA_01747 CCNA_01747 3-oxoacyl-(acyl-carrier protein) reductase
Query= uniprot:Q8EGC1 (252 letters) >FitnessBrowser__Caulo:CCNA_01747 Length = 246 Score = 129 bits (323), Expect = 7e-35 Identities = 86/255 (33%), Positives = 133/255 (52%), Gaps = 16/255 (6%) Query: 2 DLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGYALD 61 DL K ++TG GG+G A+A GA + L + L A+LG + Sbjct: 3 DLTGKTALVTGATGGIGGAIARALHAQGAHVVLSGTRESALAELKAELGERAST--VVAN 60 Query: 62 ITDEEDVVAGFAYILEDFGK-INVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINV 120 ++D E V A E G +++++ NAG+ RDG++V+ KD + + +VI V Sbjct: 61 LSDAEQVDGLVAKAEEAAGAPLDIVIANAGVTRDGLIVRMKD---------EDWDTVIKV 111 Query: 121 NLTGTFLCGREAAAAMIESGQAGVIVNISSLAKA-GNVGQSNYAASKAGVAAMSVGWAKE 179 NL G F R AA M++ +AG I+ I+S+ GN GQ+NYAASKAG+ S A+E Sbjct: 112 NLEGYFRLSRAAAKGMMKR-RAGRIIGITSIVGVTGNPGQTNYAASKAGMIGFSKALAQE 170 Query: 180 LARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEND-- 237 LA + VAPG IA+ MT A+ + + +P G+LG +IA+ ++ + Sbjct: 171 LASRGVTVNCVAPGFIASPMTDALNEQQKAGILSTIPAGKLGEGADIAAACVYLASDQAG 230 Query: 238 YVNGRVFEVDGGIRL 252 YV G+ V+GG+ + Sbjct: 231 YVTGQTLHVNGGMAM 245 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: 163 Number of extensions: 10 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: 246 Length adjustment: 24 Effective length of query: 228 Effective length of database: 222 Effective search space: 50616 Effective search space used: 50616 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