GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Pseudomonas fluorescens GW456-L13

Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate PfGW456L13_2105 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)

Query= uniprot:Q8EGC1
         (252 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2105
          Length = 246

 Score =  140 bits (354), Expect = 2e-38
 Identities = 91/254 (35%), Positives = 137/254 (53%), Gaps = 14/254 (5%)

Query: 1   MDLKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSS-TEVQGYA 59
           M L+ KV ++TG + G+G A+A    + GA +          ER  A L  +  +  G  
Sbjct: 1   MSLQGKVALVTGASRGIGQAIALELGRQGAVVVGTATSASGAERIAATLKENGIQGTGLE 60

Query: 60  LDITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVIN 119
           L++T +E V +  A I E FG   +LVNNAGI RD ++++ KD         D++  V++
Sbjct: 61  LNVTSDESVASVLASIQEQFGAPAILVNNAGITRDNLMMRMKD---------DEWHDVVD 111

Query: 120 VNLTGTFLCGREAAAAMIESGQAGVIVNISSLAKA-GNVGQSNYAASKAGVAAMSVGWAK 178
            NL   F   +     M ++ + G I++I S+  A GN GQ NYAA+KAG+   S   A+
Sbjct: 112 TNLNSLFRLSKGVLRGMTKA-RWGRIISIGSVVGAMGNAGQVNYAAAKAGLEGFSRALAR 170

Query: 179 ELARYNIRSAAVAPGVIATEMTAAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEND- 237
           E+   +I   +VAPG I T+MT  +     E L+  +P+GRLG A+EIAS V F+  +  
Sbjct: 171 EVGSRSITVNSVAPGFIDTDMTRELPEAQREALQTQIPLGRLGQAQEIASVVAFLASDGA 230

Query: 238 -YVNGRVFEVDGGI 250
            YV G    V+GG+
Sbjct: 231 AYVTGATIPVNGGM 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: 152
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: 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 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