GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Dechlorosoma suillum PS

Align Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized)
to candidate Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase

Query= curated2:Q49Z69
         (475 letters)



>lcl|FitnessBrowser__PS:Dsui_0105 Dsui_0105 NAD-dependent aldehyde
           dehydrogenase
          Length = 476

 Score =  349 bits (895), Expect = e-100
 Identities = 195/471 (41%), Positives = 271/471 (57%), Gaps = 2/471 (0%)

Query: 1   MRNFTKQYINGEWVESTSGETLEVINPATEEVAGTIAKGNKEDVEKAVEAADNVYLEFRH 60
           M+  ++ YI G+WV       ++V NPATE V   + +G   D ++A  AA   +  +  
Sbjct: 1   MQQHSRFYIGGQWVAPDGNAFIDVENPATETVIARVPEGTATDADRAARAAAAAFPAWAA 60

Query: 61  TSVKERQDLLDQIVQEYKNRKEDLIQAITDELGAPLSVAENVHYQMGLDHFEA-ARDALN 119
            S  ER   L +I    K R+++L + I  E+G P+ +A  V     +  F A AR A  
Sbjct: 61  LSGAERGAFLQKIADGLKARQDELGRLIASEVGMPVKLATRVQAGNPIFTFAACARIAAE 120

Query: 120 DFQFEERRGDDLVVKEAIGVSGLITPWNFPTNQTSLKLAAAFAAGSPVVFKPSEETPFAA 179
            F  EER G  LV+K   G    ITPWNFP +Q + K+ AA AAG  VV KPSE  P  A
Sbjct: 121 GFA-EERIGQSLVLKVPTGPVACITPWNFPLHQIAAKVGAALAAGCTVVLKPSEVAPLNA 179

Query: 180 IILAEIFDKVGVPKGVFNLVNGDGQGVGNPLSEHPKVRMMSFTGSGPTGSSIMKKAAEDF 239
            +LAE+ +  G+P GVFNLV G G  VG  L+ HP +  +SFTGS   G  +   AA   
Sbjct: 180 FLLAEVIEAAGLPAGVFNLVTGYGPVVGEALAAHPALAAVSFTGSTAAGKRVAAVAAATV 239

Query: 240 KKVSLELGGKSPYIILDDADIDGAASAAANKVVFNTGQVCTAGTRTIVPASIKEDFLTAV 299
           K+VSLELGGKS  ++L DAD+  A          N+GQ C+A TR +VP     +     
Sbjct: 240 KRVSLELGGKSASVVLPDADLAAAVKGTVAGCFLNSGQACSALTRLLVPQERYAEAAALA 299

Query: 300 KEKFSQVKVGNPREEGTQVGPIISKKQFDQVQAYIDKGIEEGAELLYGGPGKPEGLDKGY 359
            +  +   +G+P  EG+++GP++S  Q  +V+A I++ + +GAELL GG   PEGL  GY
Sbjct: 300 VQAAAAYTLGDPLAEGSRLGPLVSGLQRQRVRAMIEQAVADGAELLCGGSAAPEGLPTGY 359

Query: 360 FARPTIFNNVDNSMTIAQEEIFGPVMSVITYNDLDEAIKIANDTKYGLAGYVYGSDKDTL 419
           + RPT+F  V     +A+EE+FGPV++++TY D  EA  IAN T YGLA  V+ +++   
Sbjct: 360 YVRPTVFGRVRPDAALAREEVFGPVLAILTYRDEAEAEAIANGTDYGLAAAVWSAEEARA 419

Query: 420 HKVARSIEAGTVEINEAGRKPDLPFGGYKQSGLGREWGDYGIEEFLEVKSI 470
              AR + AG V+IN A      PFGG+KQSG GRE G +G+E+FLE +SI
Sbjct: 420 LAFARRLRAGQVDINGAFFNLLAPFGGFKQSGYGRELGRHGVEDFLETQSI 470


Lambda     K      H
   0.313    0.134    0.380 

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: 539
Number of extensions: 16
Number of successful extensions: 1
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: 475
Length of database: 476
Length adjustment: 33
Effective length of query: 442
Effective length of database: 443
Effective search space:   195806
Effective search space used:   195806
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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