GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Dyella japonica UNC79MFTsu3.2

Align 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)
to candidate N515DRAFT_0944 N515DRAFT_0944 3-oxoacyl-[acyl-carrier protein] reductase

Query= SwissProt::O18404
         (255 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0944
          Length = 242

 Score = 76.6 bits (187), Expect = 4e-19
 Identities = 80/252 (31%), Positives = 117/252 (46%), Gaps = 24/252 (9%)

Query: 8   LVTGGASGLGRATAERLAKQGASVILADLPSSKGNEVAKE----LGDKVVFVPVDVTSEK 63
           LVTG + G+GRA A RLA+ G  ++L         E  +     LG +   +  D+    
Sbjct: 6   LVTGSSRGIGRAIALRLAQAGYDLVLHCRSRRDEAEAVQAAIQALGRQARVLQFDIADRA 65

Query: 64  DVSAALQTAKDKFGRLDLTVNCAGTATAVKTFNFNKNVAHRLEDFQRVININTVGTFNVI 123
             +AAL+      G     V C    T    F      A   ED+ +V+  N  G +NV+
Sbjct: 66  ACAAALEADLAAHGAY-YGVVCNAGLTRDGAFP-----ALTDEDWDQVLRTNLDGFYNVL 119

Query: 124 R-LSAGLMGANEPNQDGQRGVIVNTASVAAFDGQIGQAAYSASKAAVVGMTLPIARDLST 182
             L   ++    P      G IV   SV+   G  GQ  YSASKA V+G    +A +L+ 
Sbjct: 120 HPLVMPMIRRRAP------GRIVCITSVSGLIGNRGQVNYSASKAGVIGAAKALALELAK 173

Query: 183 QGIRICTIAPGLFNTPML-AALPEKVRTFLAKSIPFPQRLGEPSEYAHLVQAIY--ENPL 239
           + I +  +APGL +T M+ A LP  +   LA +IP  QR+G P E A  VQ +   E   
Sbjct: 174 RRITVNCVAPGLIDTDMVDAGLP--LDEILA-AIPM-QRMGTPDEVAAAVQFLLSPEAGY 229

Query: 240 LNGEVIRIDGAL 251
           +  +V+ ++G L
Sbjct: 230 ITRQVLAVNGGL 241


Lambda     K      H
   0.317    0.133    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: 149
Number of extensions: 8
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: 255
Length of database: 242
Length adjustment: 24
Effective length of query: 231
Effective length of database: 218
Effective search space:    50358
Effective search space used:    50358
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.

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