GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4104 Aminobutyraldehyde
           dehydrogenase (EC 1.2.1.19)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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