Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate Dsui_3259 Dsui_3259 dehydrogenase of unknown specificity, short-chain alcohol dehydrogenase like protein
Query= uniprot:Q8EGC1 (252 letters) >FitnessBrowser__PS:Dsui_3259 Length = 256 Score = 125 bits (314), Expect = 8e-34 Identities = 92/261 (35%), Positives = 137/261 (52%), Gaps = 25/261 (9%) Query: 6 KVVVITGGAGGLGLAMAHNFAQAGAKL---------ALIDVDQDKLERACADLG-SSTEV 55 K ++ITGG+ G+G A A+AG + A + + + D G + Sbjct: 3 KTLLITGGSRGIGAATVRLAARAGYAVCFSYRQDAAAAQQLVAEVTRESSRDSGREGAPI 62 Query: 56 QGYALDITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQ 115 + DI+ EE++ A FA + FG I LVNNAGIL V+ DG D+ Q Sbjct: 63 LAFQADISREEEIRALFAAAEQRFGPITALVNNAGILELQTRVEDMDG--------DRLQ 114 Query: 116 SVINVNLTGTFLCGREAAAAMI--ESGQAGVIVNISS-LAKAGNVGQS-NYAASKAGVAA 171 + N+ GTFLC REA + G G IVN+SS A+ G G+ +YAASKA + Sbjct: 115 RIFATNVIGTFLCCREAVRRLSTRHGGHGGAIVNLSSRAARLGAAGEYVDYAASKAAIDT 174 Query: 172 MSVGWAKELARYNIRSAAVAPGVIATEMTAA-MKPEALERLEKLVPVGRLGHAEEIASTV 230 +++G A+E+A IR AVAPG+I T++ A+ +P +ERL +P+ R G EE+A + Sbjct: 175 LTLGLAREVAAEGIRVNAVAPGLIDTDIHASGGEPGRVERLRTGIPMQRGGTPEEVAKAI 234 Query: 231 RFIIEND--YVNGRVFEVDGG 249 +++ D Y G + +V GG Sbjct: 235 LWLLSEDASYTTGAILDVAGG 255 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: 151 Number of extensions: 6 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: 256 Length adjustment: 24 Effective length of query: 228 Effective length of database: 232 Effective search space: 52896 Effective search space used: 52896 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 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