GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Dyella japonica UNC79MFTsu3.2

Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate N515DRAFT_0465 N515DRAFT_0465 aldehyde dehydrogenase (NAD+)

Query= BRENDA::Q97UA1
         (478 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_0465 N515DRAFT_0465 aldehyde
           dehydrogenase (NAD+)
          Length = 511

 Score =  228 bits (581), Expect = 4e-64
 Identities = 148/462 (32%), Positives = 234/462 (50%), Gaps = 16/462 (3%)

Query: 22  INPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGELMEQEAQE 81
           +NPA  + V+  +   +  D +  + +A   F  W  TPAP+RG  +   GE + +    
Sbjct: 37  VNPATGE-VIGTVHASSAADYETIVKRAQEAFKTWRTTPAPRRGEAVRLCGEALRKHKDA 95

Query: 82  FALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTRIFTVKEPLGV 141
              L+ LE GK   +   EV    ++  F    +  + G T+ S  P  R++    PLG+
Sbjct: 96  LGSLVALEMGKIKPEGDGEVQEMIDIADFAVGQSRMLYGYTMHSERPGHRMYEQYHPLGL 155

Query: 142 VALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKA----GLPEGV 197
           V +I+ +NFP+++  W    A   G+  + KP+ KTPL     +++ ++A    G P+ +
Sbjct: 156 VGIISAFNFPVAVWAWNAFLAAICGDICIWKPSPKTPLSAIATMKICNEALKAGGFPD-I 214

Query: 198 VNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGGKNALY 257
             L    G+++    V D  I  +SFTGST+VG+ + + V    RM R  LELGG NA+ 
Sbjct: 215 FFLFNDAGTDLSQGFVDDKRIPLISFTGSTKVGRMVGERVA--RRMGRSLLELGGNNAII 272

Query: 258 VDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVK--KWRVG-P 314
           +D SADL LA    V G  G  GQ CT T RL +++ +  +   +L+   K  + ++G P
Sbjct: 273 LDASADLKLAIPAIVFGAVGTAGQRCTTTRRLFVHESIVGEVTDKLVAAYKQVEGKIGDP 332

Query: 315 GTEDVDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNIIPG-KGYFLEPTIFEGVTSDM 373
                 MGP+  +   +  L  +E  K  G K++ GG  +   KG F+ PTI  GV +  
Sbjct: 333 TLATTLMGPLNSQDAVQAYLGAVEKAKASGGKVLTGGAALSDRKGNFVLPTIVTGVKNSD 392

Query: 374 RLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRV--EAGVI 431
            + + E F P+L +   K LDEAI L N V  G ++ I   D+KA  +++S    + G+ 
Sbjct: 393 EVVQTETFAPILYIMPFKSLDEAIELQNDVPQGLSSAIFTRDLKAAEQYLSSAGSDCGIA 452

Query: 432 KVNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKT 473
            VN  T G E+   FGG K +G    +E G DA + Y++ +T
Sbjct: 453 NVNIGTSGAEIGGAFGGEKETGG--GRESGSDAWKVYMRRQT 492


Lambda     K      H
   0.316    0.135    0.389 

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: 594
Number of extensions: 35
Number of successful extensions: 5
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: 478
Length of database: 511
Length adjustment: 34
Effective length of query: 444
Effective length of database: 477
Effective search space:   211788
Effective search space used:   211788
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 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