Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_012170577.1 AZC_RS10620 NAD(P)-dependent oxidoreductase
Query= uniprot:Q8EGC1 (252 letters) >NCBI__GCF_000010525.1:WP_012170577.1 Length = 261 Score = 140 bits (354), Expect = 2e-38 Identities = 89/249 (35%), Positives = 130/249 (52%), Gaps = 14/249 (5%) Query: 5 DKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGYALDITD 64 DKV ++TG A G+GLA A F G ++ L+D+D L A+LG D++ Sbjct: 6 DKVALVTGAARGIGLAAARRFLDEGWRVGLLDIDGPALRAVVAELGEDHRTLAIECDVSG 65 Query: 65 EEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVNLTG 124 V A ++ FG+I+ LVNNAG+ L++ D D+++ V+ VNLTG Sbjct: 66 RAGVAAAMEELVAKFGRIDALVNNAGVAVFKPLLETAD---------DEWERVLAVNLTG 116 Query: 125 TFLCGREAAAAMIESGQAGVIVNISSLA-KAGNVGQSNYAASKAGVAAMSVGWAKELARY 183 FLC AA M G G IVNI+S++ + +S Y SKAG+A ++ A EL Sbjct: 117 PFLCTTAAAPIMAREG-GGAIVNITSISGLRASTLRSAYGTSKAGLAHLTKQLAVELGEM 175 Query: 184 NIRSAAVAPGVIATEMTAAMKPEALER-LEKLVPVGRLGHAEEIASTVRFII--ENDYVN 240 IR AVAPG + T M A+ A+ +P+ R G EE+A + F+ ++ Y+ Sbjct: 176 GIRVNAVAPGPVDTAMAKAVHSPAIRADYHDAIPLNRYGREEELAEAIYFLCSDKSSYIT 235 Query: 241 GRVFEVDGG 249 G+V VDGG Sbjct: 236 GQVLAVDGG 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: 163 Number of extensions: 19 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: 261 Length adjustment: 24 Effective length of query: 228 Effective length of database: 237 Effective search space: 54036 Effective search space used: 54036 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: 47 (22.7 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