Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_028583428.1 G494_RS0103555 3-oxoacyl-ACP reductase FabG
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_000429965.1:WP_028583428.1 Length = 246 Score = 122 bits (307), Expect = 5e-33 Identities = 80/255 (31%), Positives = 131/255 (51%), Gaps = 17/255 (6%) Query: 2 DLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERA----CADLGSSTEVQG 57 + K V++G G+G A++ GA + + + R+ C++ G ++ Sbjct: 3 EFSGKKAVVSGATRGIGRAISEALLAGGATVIGVYGGNREAARSFQESCSEYGERLVLE- 61 Query: 58 YALDITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSV 117 LD++D V A FA + E + I++L+NNAGI RD +L K+ ++++ V Sbjct: 62 -QLDVSDLAAVSAFFARVEERYDTIDILINNAGIRRDAVLALMKE---------EEWRQV 111 Query: 118 INVNLTGTFLCGREAAAAMIESGQAGVIVNISSLAKAGNVGQSNYAASKAGVAAMSVGWA 177 I+VNLTG + R M++ +I S + + G GQSNYAASKAG + A Sbjct: 112 IDVNLTGGYGMCRHGVGLMLKQRYGRIIFITSPMGRMGFSGQSNYAASKAGQVGLMKSLA 171 Query: 178 KELARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEN- 236 +E+A+ NI V+PG I+T+ + ++ K+VP R G +E+A V F+ + Sbjct: 172 QEVAKRNITVNCVSPGFISTDFIDDLSEAQVKSYRKMVPQRRFGTPQEVADAVLFLAGDR 231 Query: 237 -DYVNGRVFEVDGGI 250 Y+NG V EV GG+ Sbjct: 232 AAYINGAVLEVTGGL 246 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: 7 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: 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 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