GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Dechlorosoma suillum PS

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase

Query= BRENDA::Q8VWZ1
         (503 letters)



>FitnessBrowser__PS:Dsui_0105
          Length = 476

 Score =  335 bits (860), Expect = 2e-96
 Identities = 200/479 (41%), Positives = 275/479 (57%), Gaps = 16/479 (3%)

Query: 9   QLFIDGEWRVPILNKRIPNINPSTENIIGDIPAATKEDVDLAVDAAKRAISRKNGRDWSA 68
           + +I G+W  P  N  I   NP+TE +I  +P  T  D D A  AA  A        W+A
Sbjct: 6   RFYIGGQWVAPDGNAFIDVENPATETVIARVPEGTATDADRAARAAAAAFPA-----WAA 60

Query: 69  ASGSLRARYLRAIAAKIKEKKDELGKLESIDCGKPLEEAL-ADLDDVVACFEYYAGLAEE 127
            SG+ R  +L+ IA  +K ++DELG+L + + G P++ A      + +  F   A +A E
Sbjct: 61  LSGAERGAFLQKIADGLKARQDELGRLIASEVGMPVKLATRVQAGNPIFTFAACARIAAE 120

Query: 128 LDSKQKAPISLPMDTFKSYILKEPIGVVALITPWNYPFLMATWKIAPALAAGCAAILKPS 187
             ++++   SL        +LK P G VA ITPWN+P      K+  ALAAGC  +LKPS
Sbjct: 121 GFAEERIGQSL--------VLKVPTGPVACITPWNFPLHQIAAKVGAALAAGCTVVLKPS 172

Query: 188 ELASVTCLELGEICKEVGLPRGVLNIVTGLGHEAGASLASHPDVDKISFTGSSATGSKIM 247
           E+A +    L E+ +  GLP GV N+VTG G   G +LA+HP +  +SFTGS+A G ++ 
Sbjct: 173 EVAPLNAFLLAEVIEAAGLPAGVFNLVTGYGPVVGEALAAHPALAAVSFTGSTAAGKRVA 232

Query: 248 TTAAQLVKPVSLELGGKSPIVVFEDVDLDKVAEWTVFGCFFTNGQICSATSRLIVHESIA 307
             AA  VK VSLELGGKS  VV  D DL    + TV GCF  +GQ CSA +RL+V +   
Sbjct: 233 AVAAATVKRVSLELGGKSASVVLPDADLAAAVKGTVAGCFLNSGQACSALTRLLVPQERY 292

Query: 308 VEFVDKLVKWAENIKISDPLEEGCRLGPIVSEAQYKKVLNCISSAKSEGATILTGG-RRP 366
            E     V+ A    + DPL EG RLGP+VS  Q ++V   I  A ++GA +L GG   P
Sbjct: 293 AEAAALAVQAAAAYTLGDPLAEGSRLGPLVSGLQRQRVRAMIEQAVADGAELLCGGSAAP 352

Query: 367 EHLKKGYFVEPTIITDVTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTHYGLGSAVM 426
           E L  GY+V PT+   V     + REEVFGPVLA+ T+  E EA  +AN T YGL +AV 
Sbjct: 353 EGLPTGYYVRPTVFGRVRPDAALAREEVFGPVLAILTYRDEAEAEAIANGTDYGLAAAVW 412

Query: 427 SNDLERCERLSKALQAGIVWINCAQPSFIQAPWGGIKRSGFGRELGEWGLENYLSVKQV 485
           S +  R    ++ L+AG V IN A  + + AP+GG K+SG+GRELG  G+E++L  + +
Sbjct: 413 SAEEARALAFARRLRAGQVDINGAFFNLL-APFGGFKQSGYGRELGRHGVEDFLETQSI 470


Lambda     K      H
   0.317    0.134    0.402 

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: 503
Number of extensions: 23
Number of successful extensions: 5
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: 503
Length of database: 476
Length adjustment: 34
Effective length of query: 469
Effective length of database: 442
Effective search space:   207298
Effective search space used:   207298
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.

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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