GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Sphingomonas koreensis DSMZ 15582

Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate Ga0059261_1894 Ga0059261_1894 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

Query= reanno::BFirm:BPHYT_RS16920
         (266 letters)



>FitnessBrowser__Korea:Ga0059261_1894
          Length = 259

 Score =  229 bits (584), Expect = 4e-65
 Identities = 121/254 (47%), Positives = 155/254 (61%), Gaps = 1/254 (0%)

Query: 12  ADSAFARYPSLVDRTVLITGGATGIGASFVEHFAAQGARVAFFDIDASAGEALADELGDS 71
           A SA A YPSL  + VL+TGG +GIGA  VE FA QGA V FFDI  +  + L + L   
Sbjct: 6   AASAAAVYPSLKGKRVLVTGGGSGIGAGIVEGFARQGADVTFFDIAGAESQLLVERLSAD 65

Query: 72  KHKPLFLSCDLTDIDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAV 131
            HK  F   DLTD+ +LQ  IA +    G   +LVNNAAND RH I E+T   +D  ++V
Sbjct: 66  GHKACFERVDLTDVASLQAVIARLIKGAGGFDILVNNAANDDRHAIDEITEAYWDERLSV 125

Query: 132 NIRHQFFAAQAVMEDMKAANSGSIINLGSISWMLKNGGYPVYVMSKSAVQGLTRGLARDL 191
           N++H FF AQAV+  M+A   G+I+NLGSISW L      +Y   K+A++GLTR LARDL
Sbjct: 126 NLKHIFFCAQAVVPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDL 185

Query: 192 GHFNIRVNTLVPGWVMTEKQKRLWLDDAGRRSIKEGQCIDAELEPADLARMALFLAADDS 251
           G   IR   ++PG V T +Q + W    G   I   QC+D  L P D+A M LFLA+DD+
Sbjct: 186 GRDGIRATCVIPGNVRTPRQLK-WYSPEGEAEIVAAQCLDGRLAPEDVAAMVLFLASDDA 244

Query: 252 RMITAQDIVVDGGW 265
           R++T     VD GW
Sbjct: 245 RLVTGHSYFVDAGW 258


Lambda     K      H
   0.320    0.134    0.388 

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: 201
Number of extensions: 4
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: 266
Length of database: 259
Length adjustment: 25
Effective length of query: 241
Effective length of database: 234
Effective search space:    56394
Effective search space used:    56394
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 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 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