GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_0465
          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.

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