Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate BWI76_RS23705 BWI76_RS23705 3-oxoacyl-ACP reductase
Query= uniprot:Q8EGC1 (252 letters) >FitnessBrowser__Koxy:BWI76_RS23705 Length = 244 Score = 154 bits (390), Expect = 1e-42 Identities = 94/254 (37%), Positives = 140/254 (55%), Gaps = 12/254 (4%) Query: 1 MDLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGYAL 60 M L K ++TG A G+G +A A+ GA++ + D D A + S + + Sbjct: 1 MKLASKTAIVTGAARGIGFGIAQVLAREGARVIIADRDAHGEAAAASLRESGAQALFISC 60 Query: 61 DITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINV 120 +I D+ V A F+ E FG ++++VNNAGI RD ML K + + +VI+V Sbjct: 61 NIGDKAQVEALFSQAEEAFGAVDIVVNNAGINRDAMLHKLSEA---------DWDTVIDV 111 Query: 121 NLTGTFLCGREAAAAMIESGQAGVIVNISSLAKAGNVGQSNYAASKAGVAAMSVGWAKEL 180 NL GTFLC ++AA M E G AG I+NI+S + GNVGQ+NY+ASKAGV M+ +EL Sbjct: 112 NLKGTFLCMQQAAIRMRERG-AGRIINIASASWLGNVGQTNYSASKAGVVGMTKTACREL 170 Query: 181 ARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEND--Y 238 A+ + A+ PG I T+MT + + + +P G G A+++ V F+ + Y Sbjct: 171 AKKGVTVNAICPGFIDTDMTRGVPENVWQIMINKIPAGYAGEAKDVGECVAFLASDGARY 230 Query: 239 VNGRVFEVDGGIRL 252 +NG V V GG+ L Sbjct: 231 INGEVINVGGGMVL 244 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: 175 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: 244 Length adjustment: 24 Effective length of query: 228 Effective length of database: 220 Effective search space: 50160 Effective search space used: 50160 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