GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Paucidesulfovibrio gracilis DSM 16080

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_078715956.1 B5D49_RS01965 3-oxoacyl-[acyl-carrier-protein] reductase

Query= SwissProt::Q1NEI6
         (249 letters)



>NCBI__GCF_900167125.1:WP_078715956.1
          Length = 247

 Score =  140 bits (354), Expect = 2e-38
 Identities = 87/238 (36%), Positives = 127/238 (53%), Gaps = 6/238 (2%)

Query: 13  AIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDA-----THVVALDVSDH 67
           A+VTGG+ G+G+  A R+ A+G  V L  ++    A T  +  A        V LD SD 
Sbjct: 8   ALVTGGSRGIGRACAERLAADGFEVWLTYVSKPEAAETVVQTIADAGGTARAVQLDSSDR 67

Query: 68  AAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNREVV 127
            AVA+  KD       +  L+ +AGIT   + +   P D +  V+DINL G F C +E  
Sbjct: 68  EAVASFFKDEIKGKVHLAALVNNAGITRDGLLIRMKPED-WDSVLDINLTGAFSCLQEAA 126

Query: 128 PFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALTPA 187
             M     G I+N++SV G+ GN   + Y A+KAG+IG TK+  +ELAG+GV  NA+ P 
Sbjct: 127 KIMARQRGGSIINISSVVGQMGNAGQANYVAAKAGLIGLTKAAARELAGRGVRVNAVAPG 186

Query: 188 TFESPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTSGG 245
             E+ +   LP+  V+ M++ IP+ RLG   + AA V F+A     + T      +GG
Sbjct: 187 FIETDMTKDLPEKTVESMKTMIPLSRLGSPGDIAAAVSFLAGNGAGYITGQVLAVNGG 244


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: 154
Number of extensions: 7
Number of successful extensions: 3
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 Apr 09 2024. 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