GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__PS:Dsui_0105
          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 (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