GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Shewanella sp. ANA-3

Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate 7025403 Shewana3_2558 3-oxoacyl-[acyl-carrier-protein] reductase (RefSeq)

Query= uniprot:Q8EGC1
         (252 letters)



>FitnessBrowser__ANA3:7025403
          Length = 248

 Score =  135 bits (340), Expect = 8e-37
 Identities = 87/255 (34%), Positives = 137/255 (53%), Gaps = 19/255 (7%)

Query: 1   MDLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGYAL 60
           + L  KV ++TG + G+G A+A    +AGA    I V     E+  A +      +G+ L
Sbjct: 5   LSLAGKVALVTGASRGIGRAIAETLVEAGA----IVVGTATSEKGAAAIQEYLGDKGFGL 60

Query: 61  --DITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVI 118
             ++TD + V   F  I E  G +++LVNNAGI RD +L++ KD         D++  +I
Sbjct: 61  VLNVTDSQSVTDLFDSIKEKAGDVDILVNNAGITRDNLLMRMKD---------DEWNDII 111

Query: 119 NVNLTGTFLCGREAAAAMIESGQAGVIVNISSLAKA-GNVGQSNYAASKAGVAAMSVGWA 177
           + NLT  F   +     M++  + G I+NI S+    GN GQ NY+A+KAG+   +   A
Sbjct: 112 DTNLTSLFRLSKPVMRTMMKK-RFGRIINIGSVVGTMGNAGQVNYSAAKAGLIGFTKSLA 170

Query: 178 KELARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEND 237
           +E+A   I   A+APG I T+MT  +  +  + +   VP+ RLG A+EIA+ V F+  + 
Sbjct: 171 REVASRQITVNAIAPGFIQTDMTDELTEDQQKAIMSQVPMERLGQAQEIANAVLFLASDS 230

Query: 238 --YVNGRVFEVDGGI 250
             Y+ G    V+GG+
Sbjct: 231 AAYITGETLHVNGGM 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: 168
Number of extensions: 7
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: 248
Length adjustment: 24
Effective length of query: 228
Effective length of database: 224
Effective search space:    51072
Effective search space used:    51072
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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