GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Amantichitinum ursilacus IGB-41

Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized)
to candidate WP_053937509.1 WG78_RS09155 3-oxoacyl-ACP reductase FabG

Query= SwissProt::Q1NEI6
         (249 letters)



>NCBI__GCF_001294205.1:WP_053937509.1
          Length = 247

 Score =  127 bits (320), Expect = 2e-34
 Identities = 73/240 (30%), Positives = 126/240 (52%), Gaps = 5/240 (2%)

Query: 10  GRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDAT----HVVALDVS 65
           G+ A+VTG + G+G+ +A  +   G  V     + +   A  A + A     H + L V+
Sbjct: 5   GKVALVTGASRGIGQAIALELGRLGATVVGTATSQEGADAITAYLQAAGLKGHGLRLQVT 64

Query: 66  DHAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNRE 125
           +  A  A         G + +L+ +AGIT   + +     D +  ++  NL  ++  ++ 
Sbjct: 65  EDGACEALVSQIEKDSGAIAVLVNNAGITRDNL-LMRMKDDEWDAIMATNLKPVYQLSKA 123

Query: 126 VVPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALT 185
           V+  M++  +GRIVN+ASV G  GNP  + YSA+KA + GFTKSL +E+  +G+  NA+ 
Sbjct: 124 VIRGMMKARWGRIVNIASVVGATGNPGQTNYSAAKAALFGFTKSLAREIGSRGITVNAVA 183

Query: 186 PATFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTSGG 245
           P   ++ +   LP  Q   +   I +GRLG  ++ A  V F++S++  + T +T   +GG
Sbjct: 184 PGFIDTDMTRGLPDEQKAKLVESIALGRLGAAQDIADAVAFLSSDKAGYITGNTLHVNGG 243


Lambda     K      H
   0.318    0.132    0.381 

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: 136
Number of extensions: 5
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: 249
Length of database: 247
Length adjustment: 24
Effective length of query: 225
Effective length of database: 223
Effective search space:    50175
Effective search space used:    50175
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 24 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