GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lhgD in Limnohabitans curvus MWH-C5

Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate WP_108358527.1 B9Z44_RS13415 NAD(P)/FAD-dependent oxidoreductase

Query= SwissProt::Q9LES4
         (483 letters)



>NCBI__GCF_003063475.1:WP_108358527.1
          Length = 369

 Score =  342 bits (877), Expect = 1e-98
 Identities = 192/404 (47%), Positives = 252/404 (62%), Gaps = 45/404 (11%)

Query: 78  ERVDTVVIGAGVVGLAVARELSLRG----REVLILDAASSFGTVTSSRNSEVVHAGIYYP 133
           ++VD VVIGAGVVGLA AR L        RE L+L+AA + GT TSSRNSEV+HAGIYYP
Sbjct: 2   DKVDGVVIGAGVVGLATARALIQAAPETAREWLVLEAADAIGTGTSSRNSEVIHAGIYYP 61

Query: 134 PNSLKAKFCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGL 193
             SLKAK CV+GR+ LY Y +E  + H++ GKLIVAT + ++P LD L+     N V+ +
Sbjct: 62  QGSLKAKLCVQGRDRLYAYATERGVSHQRCGKLIVATHADQLPALDALLQKAHANGVTDV 121

Query: 194 RMLEGFEAMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEA 253
            ML   +A  MEP L CV AL SP +GI+D+H  MLS                  LQG+ 
Sbjct: 122 VMLSAEQAQVMEPSLSCVAALHSPSTGIVDSHGLMLS------------------LQGDF 163

Query: 254 QNNHATFSYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQA 313
           +N     + N+ V +    +  + + +AD              EL+   VVN+AGL A  
Sbjct: 164 ENAGGIVALNSPVASAVCRDDGIVVRMADGS------------ELLAQTVVNAAGLTAPW 211

Query: 314 LAKRLHGLDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEGGLGVHVTVDLNGLVK 373
           LAK   GL  + VP +++A+G YFTLSG    PF+ L+YP+PE  GLGVH+T+DL G  K
Sbjct: 212 LAKHFEGLAAQHVPQAYFAKGNYFTLSG--KSPFSHLIYPVPEAAGLGVHLTLDLGGQAK 269

Query: 374 FGPDVEWIECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKL 433
           FGPDV+W++  D         D  V+ +  + FY E+RKY+P L DG+L+ GY+GIRPK+
Sbjct: 270 FGPDVQWVDRPD---------DLLVSAEHEQVFYNEVRKYWPALGDGALQAGYAGIRPKI 320

Query: 434 SGPKQSPADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHI 477
           SGP ++ ADF IQG   HGV GLVNLFGIESPGLTS+LAI + +
Sbjct: 321 SGPHEAAADFCIQGPAVHGVKGLVNLFGIESPGLTSALAIGDAV 364


Lambda     K      H
   0.318    0.136    0.401 

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: 480
Number of extensions: 17
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: 483
Length of database: 369
Length adjustment: 32
Effective length of query: 451
Effective length of database: 337
Effective search space:   151987
Effective search space used:   151987
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 (21.7 bits)
S2: 50 (23.9 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