GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lhgD in Acidovorax sp. GW101-3H11

Align L-2-hydroxyglutarate dehydrogenase, mitochondrial; EC 1.1.99.2 (characterized)
to candidate Ac3H11_4104 Aminobutyraldehyde dehydrogenase (EC 1.2.1.19)

Query= SwissProt::Q9LES4
         (483 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4104
          Length = 365

 Score =  379 bits (973), Expect = e-110
 Identities = 198/401 (49%), Positives = 264/401 (65%), Gaps = 41/401 (10%)

Query: 78  ERVDTVVIGAGVVGLAVARELSLRGREVLILDAASSFGTVTSSRNSEVVHAGIYYPPNSL 137
           + VD VV+GAGVVGLAVAR L+L+GREV++L+AA + GT  SSRNSEV+HAG+YYP  S+
Sbjct: 3   DAVDCVVVGAGVVGLAVARALALQGREVMVLEAADAIGTGISSRNSEVIHAGLYYPTGSI 62

Query: 138 KAKFCVRGRELLYKYCSEYEIPHKKIGKLIVATGSSEIPKLDLLMHLGTQNRVSGLRMLE 197
           KA+ CVRG+ELLY YC+E  +PH++ GKL+VAT ++++  ++ +      N V  L+ L 
Sbjct: 63  KAQLCVRGKELLYAYCAERGVPHRRCGKLLVATSAAQLASVESIQARAQANGVLDLQWLS 122

Query: 198 GFEAMRMEPQLRCVKALLSPESGILDTHSFMLSLVEKSFDFMVYRDNNNLRLQGEAQNNH 257
             EA+ +EP L CV AL SP +GI+D+H+ ML+                  LQG+ +N  
Sbjct: 123 RDEALALEPALECVGALYSPSTGIVDSHALMLA------------------LQGDLENAG 164

Query: 258 ATFSYNTVVLNGRVEEKKMHLYVADTRFSESRCEAEAQLELIPNLVVNSAGLGAQALAKR 317
              + N+ +    + E  ++L  +D    ++R             VVN+AGL A ALA R
Sbjct: 165 GLVAVNSPLARAHIAEGAINLEASDGTRLQAR------------TVVNAAGLYAPALAAR 212

Query: 318 LHGLDHRFVPSSHYARGCYFTLSGIKAPPFNKLVYPIPEEGGLGVHVTVDLNGLVKFGPD 377
             GLD   VP++H+A+G YFTL+G    PF+ L+YP+PE  GLGVH+T+DL G  KFGPD
Sbjct: 213 FVGLDPAHVPTAHFAKGSYFTLTG--KAPFSHLIYPVPEAAGLGVHLTLDLGGQAKFGPD 270

Query: 378 VEWIECTDDTSSFLNKFDYRVNPQRSEKFYPEIRKYYPDLKDGSLEPGYSGIRPKLSGPK 437
           V+W+   D         D  V+P R + FY E+RKY+P L+DG+L PGY+GIRPK+ G  
Sbjct: 271 VQWVTSAD---------DLLVDPARGDAFYAEVRKYWPGLRDGALAPGYAGIRPKIHGAS 321

Query: 438 QSPADFVIQGEETHGVPGLVNLFGIESPGLTSSLAIAEHIA 478
           Q  ADFVIQG   HGVPGLVNLFGIESPGLTSSLAIAEH+A
Sbjct: 322 QPAADFVIQGPAVHGVPGLVNLFGIESPGLTSSLAIAEHVA 362


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: 481
Number of extensions: 16
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: 365
Length adjustment: 32
Effective length of query: 451
Effective length of database: 333
Effective search space:   150183
Effective search space used:   150183
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 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