GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Methanobacterium veterum MK4

Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate WP_048081445.1 EJ01_RS05790 3-oxoacyl-ACP reductase FabG

Query= SwissProt::Q92RN6
         (256 letters)



>NCBI__GCF_000745485.1:WP_048081445.1
          Length = 258

 Score =  132 bits (332), Expect = 7e-36
 Identities = 81/250 (32%), Positives = 133/250 (53%), Gaps = 6/250 (2%)

Query: 10  DLRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDIAAESSLALCEKVAAQTGQAPHFIQ 69
           DL+ +  +VTG   G+GA    A+A++GA VA +    E   +L E++ +  G     +Q
Sbjct: 6   DLKGKVAVVTGASGGLGADAARAYAQEGADVALLARRKERLESLAEEIES-AGVKALAVQ 64

Query: 70  ADLRNVEAVRAAADEAVAKLGSVRVLVNNAARDDRQALEAVTEESWDESLSVNLRHLFFM 129
            D+ + E+V  A DE +   G + +L+NNA    R  + +++ E WD+ + VN++ +F +
Sbjct: 65  CDVADEESVENAIDEVIKYFGKIDILLNNAGIAVRGGVHSLSVEDWDKGMDVNVKGIFLV 124

Query: 130 CQAVAPHMQRQGGGSIVNFSSIAFLL----NMPEIPAYSTAKAGIIGLTKSLAGKLGPDN 185
            + V PHM +   G IVN SSI  +      M     Y+ +KA + GLT  +A   G   
Sbjct: 125 SKYVLPHMMKNNYGKIVNTSSINSIAGDKSEMFIRHVYNASKAAVRGLTMGMACSYGKYG 184

Query: 186 IRVNAILPGMIVTE-RQRRLWLTEESIARMQERQCLKRMLVADDLVGPCLFLASDSSAAM 244
           I VNA+ P +  +E     L+ +EE + R      L R     +L GP +FL+S++S+ +
Sbjct: 185 ITVNAVAPALFESEMTSNTLFKSEEFLERYSNVVPLNRPAKKGELNGPIIFLSSEASSYI 244

Query: 245 TAQAMIIDGG 254
           T Q + +DGG
Sbjct: 245 TGQTIFVDGG 254


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: 106
Number of extensions: 8
Number of successful extensions: 4
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: 258
Length adjustment: 24
Effective length of query: 232
Effective length of database: 234
Effective search space:    54288
Effective search space used:    54288
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: 47 (22.7 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