GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Lacinutrix algicola AKS293

Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate WP_055437269.1 ASC41_RS13975 3-oxoacyl-[acyl-carrier-protein] reductase

Query= SwissProt::Q92RN6
         (256 letters)



>NCBI__GCF_001418085.1:WP_055437269.1
          Length = 248

 Score =  144 bits (364), Expect = 1e-39
 Identities = 87/245 (35%), Positives = 134/245 (54%), Gaps = 2/245 (0%)

Query: 11  LRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFIQA 70
           L  +  ++TG   GIG  + E FA+QGA VAF   ++  +    EK     G      ++
Sbjct: 4   LEGKTAIITGASRGIGKGIAEVFAQQGANVAFTYSSSVEAANALEKELNALGVKAKGYKS 63

Query: 71  DLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFFMC 130
           +  N +  +  A++ +A+ GS+ +L+NNA       L  + E  +D+ + VNL+ +F M 
Sbjct: 64  NAANFDESQKLAEDVLAEFGSIDILINNAGITKDNLLMRMGEADFDKVIEVNLKSVFNMT 123

Query: 131 QAVAPHMQRQGGGSIVNFSSIAFLLNMPEIPAYSTAKAGIIGLTKSLAGKLGPDNIRVNA 190
           +AV   M +Q  GSI+N SS+  +        Y+ +KAGIIG +KS+A +LG  NIR N 
Sbjct: 124 KAVQRTMLKQRKGSIINMSSVVGVKGNAGQTNYAASKAGIIGFSKSVALELGSRNIRSNV 183

Query: 191 ILPGMIVTERQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAMTAQAMI 250
           I PG I TE   +  L EE++   +    LKR    +D+   C+FLASD SA +T Q + 
Sbjct: 184 IAPGFIETEMTAK--LDEETVKSWRNAIPLKRGGTPEDIANVCVFLASDMSAYVTGQTIN 241

Query: 251 IDGGV 255
           +DGG+
Sbjct: 242 VDGGM 246


Lambda     K      H
   0.321    0.133    0.377 

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: 121
Number of extensions: 6
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: 256
Length of database: 248
Length adjustment: 24
Effective length of query: 232
Effective length of database: 224
Effective search space:    51968
Effective search space used:    51968
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 (21.9 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