GapMind for catabolism of small carbon sources

 

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

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate N515DRAFT_0465 N515DRAFT_0465 aldehyde dehydrogenase (NAD+)

Query= BRENDA::Q1XGK8
         (486 letters)



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

 Score =  189 bits (481), Expect = 1e-52
 Identities = 142/480 (29%), Positives = 222/480 (46%), Gaps = 28/480 (5%)

Query: 10  GAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALKGPWGKLSVAERAEI 69
           G +  ++     + +NP+ G+VIG VH +  A+ +  VK A+ A K  W       R E 
Sbjct: 23  GEWSRTSDAGALQPVNPATGEVIGTVHASSAADYETIVKRAQEAFK-TWRTTPAPRRGEA 81

Query: 70  LHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKNVANEAFEM- 128
           +    + +    D       L+ GK K        P G    +   D+      ++  + 
Sbjct: 82  VRLCGEALRKHKDALGSLVALEMGKIK--------PEGDGEVQEMIDIADFAVGQSRMLY 133

Query: 129 ---ATPDGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEETPL 185
                 +  G   Y    P G++G+IS +N P+ +  W    A  CG+  + KPS +TPL
Sbjct: 134 GYTMHSERPGHRMYEQYHPLGLVGIISAFNFPVAVWAWNAFLAAICGDICIWKPSPKTPL 193

Query: 186 TAT----LLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIM 241
           +A     +  E ++A G P  ++ + +  G D +  F+ +   +   +FTG T  G ++ 
Sbjct: 194 SAIATMKICNEALKAGGFP-DIFFLFNDAGTDLSQGFVDDKR-IPLISFTGSTKVGRMVG 251

Query: 242 RAAAKGVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIF 301
              A+ + +  LELGG NA I+ A  D+  AI   +  A    GQ C  T R++V   I 
Sbjct: 252 ERVARRMGRSLLELGGNNAIILDASADLKLAIPAIVFGAVGTAGQRCTTTRRLFVHESIV 311

Query: 302 DEFVARLKAGAESL--MIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGV 359
            E   +L A  + +   IG P  A++  GPL S    +  L   ++A   GG V+TGG  
Sbjct: 312 GEVTDKLVAAYKQVEGKIGDPTLATTLMGPLNSQDAVQAYLGAVEKAKASGGKVLTGGAA 371

Query: 360 PDMPAHLAGGAWVQPTIWTGLSDDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLA 419
                    G +V PTI TG+ +   VV  E F P  +I PF + +EAIEL N +P GL+
Sbjct: 372 LSDRK----GNFVLPTIVTGVKNSDEVVQTETFAPILYIMPFKSLDEAIELQNDVPQGLS 427

Query: 420 SAIWTENGSRAHRVAGQI--EAGIVWVN-SWFLRDLRTAFGGSKQSGIGREGGVHSLEFY 476
           SAI+T +   A +       + GI  VN      ++  AFGG K++G GRE G  + + Y
Sbjct: 428 SAIFTRDLKAAEQYLSSAGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKVY 487


Lambda     K      H
   0.318    0.136    0.411 

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: 649
Number of extensions: 38
Number of successful extensions: 6
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: 486
Length of database: 511
Length adjustment: 34
Effective length of query: 452
Effective length of database: 477
Effective search space:   215604
Effective search space used:   215604
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 (21.7 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