GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA 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)



>FitnessBrowser__Pedo557:CA265_RS19780
          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.

Links

Downloads

Related tools

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