GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dopDH in Pedobacter sp. GW460-11-11-14-LB5

Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate CA265_RS19780 CA265_RS19780 aldehyde dehydrogenase family protein

Query= BRENDA::Q97UA1
         (478 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS19780 CA265_RS19780 aldehyde
           dehydrogenase family protein
          Length = 513

 Score =  249 bits (636), Expect = 2e-70
 Identities = 151/455 (33%), Positives = 246/455 (54%), Gaps = 17/455 (3%)

Query: 30  VLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGELMEQEAQEFALLMTLE 89
           ++A  ++ T DD    + KA   F  W   PAPKRG I+ + G+ + +       L++ E
Sbjct: 46  LIASAKIATADDYDAVVLKAQEAFTAWRSVPAPKRGEIVRQFGDALRENKDALGTLVSYE 105

Query: 90  EGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTRIFTVKEPLGVVALITPWN 149
            GK+L++   EV    ++  F   L+ ++ G T+ S  P+ R++    PLG+V +I+ +N
Sbjct: 106 MGKSLQEGFGEVQEMIDICDFAVGLSRQLYGLTMHSERPSHRMYEQWHPLGIVGIISAFN 165

Query: 150 FPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKA----GLPEGVVNLVVGKG 205
           FP+++  W  A AL  GN  + KP+ KTPL       +++K      + EGV NL++G  
Sbjct: 166 FPVAVWSWNTALALVCGNVCIWKPSEKTPLTAIACQHIIAKVFKDNDIAEGVCNLILG-D 224

Query: 206 SEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGGKNALYVDKSADLT 265
            EVG+ + +D  I  +S TGST +GK +   VG   R+ +  LELGG NA+ + + ADL 
Sbjct: 225 REVGERMTNDGRIPLISATGSTRMGKAVGAAVG--ARLGKSLLELGGNNAIIISEHADLD 282

Query: 266 LAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWRVG-PGTEDVDMGPV 324
           ++   AV G  G  GQ CT+T RLII++ VY  F  +L++   + R+G P  ++  +GP+
Sbjct: 283 MSLIGAVFGAVGTAGQRCTSTRRLIIHESVYDAFTAKLVKAYGQLRIGDPLDQNNHVGPL 342

Query: 325 VDEGQFKKDLEYIEYGKNVGAKLIYGGNIIPGKGY----FLEPTIFEGVTSDMRLFKEEI 380
           +D       L+ I   K  G   +  G ++ G  Y    +++P I E V +D ++ + E 
Sbjct: 343 IDTDAVAAYLDSIAKCKAEGGNFVVEGGVLSGDAYTSGCYVKPCIAE-VQNDFKIVQHET 401

Query: 381 FGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSR--VEAGVIKVNKPTV 438
           F P+L + + K LDEAI L N V  G ++ I+  +++   +F+S    + G+  VN  T 
Sbjct: 402 FAPILYLIKYKTLDEAIALQNGVPQGLSSAIMTLNLREAEQFLSAKGSDCGIANVNIGTS 461

Query: 439 GLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKT 473
           G E+   FGG K +G    +E G DA   Y++ +T
Sbjct: 462 GAEIGGAFGGEKETGG--GRESGSDAWRAYMRRQT 494


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: 602
Number of extensions: 33
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: 478
Length of database: 513
Length adjustment: 34
Effective length of query: 444
Effective length of database: 479
Effective search space:   212676
Effective search space used:   212676
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