GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Chromobacterium vaccinii MWU205

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_046158881.1 VL52_RS21015 3-hydroxybutyryl-CoA dehydrogenase

Query= BRENDA::Q0KEY8
         (284 letters)



>NCBI__GCF_000971335.1:WP_046158881.1
          Length = 282

 Score =  308 bits (789), Expect = 9e-89
 Identities = 153/278 (55%), Positives = 205/278 (73%)

Query: 6   VGIVGAGTMGNGIAQACAVVGLNVVMVDISDAAVQKGVATVASSLDRLIKKEKLTEADKA 65
           +G+VGAGTMGNGIAQ  A+ G +VV+ D+SDAA+ KGVA +  SL R+ KKE + EA+  
Sbjct: 5   IGVVGAGTMGNGIAQVFAMKGFDVVLADVSDAALVKGVANINISLQRMAKKELIAEANIP 64

Query: 66  SALARIKGSTSYDDLKATDIVIEAATENYDLKVKILKQIDGIVGENVIIASNTSSISITK 125
             +A I+ +T   DL   D+V+EAATEN ++K +I +++D  VGE  ++ASNTSSIS+T+
Sbjct: 65  GIVAHIRATTQLADLAGCDVVVEAATENAEIKERIFRELDAAVGEKCVLASNTSSISLTR 124

Query: 126 LAAVTSRADRFIGMHFFNPVPVMALVELIRGLQTSDTTHAAVEALSKQLGKYPITVKNSP 185
           +A+  S  +R +GMHF NPVP+M LVE+IR LQT D  +  V  LS+ LGK P+TVK+  
Sbjct: 125 IASWVSHPERVVGMHFMNPVPLMELVEIIRALQTGDEAYHTVFHLSQALGKTPVTVKDGA 184

Query: 186 GFVVNRILCPMINEAFCVLGEGLASPEEIDEGMKLGCNHPIGPLALADMIGLDTMLAVME 245
           GFV NR+L PMINEA   L E LA+ E+ID  MKLG NHPIGPLALAD+IGLDT L++M+
Sbjct: 185 GFVSNRVLMPMINEAAFALYENLATAEDIDTVMKLGMNHPIGPLALADLIGLDTCLSIMD 244

Query: 246 VLYTEFADPKYRPAMLMREMVAAGYLGRKTGRGVYVYS 283
           +L+ EF D KYR   L+ ++V AG+LGRK+G+G Y Y+
Sbjct: 245 ILHREFRDSKYRACPLLVQLVQAGHLGRKSGKGFYSYN 282


Lambda     K      H
   0.319    0.134    0.373 

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: 221
Number of extensions: 4
Number of successful extensions: 1
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: 284
Length of database: 282
Length adjustment: 26
Effective length of query: 258
Effective length of database: 256
Effective search space:    66048
Effective search space used:    66048
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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.

Links

Downloads

Related tools

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