GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Dechlorosoma suillum PS

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



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

 Score =  309 bits (792), Expect = 1e-88
 Identities = 184/471 (39%), Positives = 270/471 (57%), Gaps = 9/471 (1%)

Query: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69
           YI GQ+V   G+A+IDV NPATE VI+R+P+G A DA +A  AA  A P W AL   ER 
Sbjct: 8   YIGGQWVAPDGNAFIDVENPATETVIARVPEGTATDADRAARAAAAAFPAWAALSGAERG 67

Query: 70  SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129
           ++L+KI+ G++ R  E+  LI  E G   +LA   V        + A    R   E    
Sbjct: 68  AFLQKIADGLKARQDELGRLIASEVGMPVKLA-TRVQAGNPIFTFAA--CARIAAEGFAE 124

Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189
           +R G++++L K   G    I PWNFP   IA K+  AL  G T+V+KPSE  P NA   A
Sbjct: 125 ERIGQSLVL-KVPTGPVACITPWNFPLHQIAAKVGAALAAGCTVVLKPSEVAPLNAFLLA 183

Query: 190 KIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVC 249
           ++++  GLP GVFNLV G G  VG+ LA +P +A VS TGS +AG+++ A AA  + +V 
Sbjct: 184 EVIEAAGLPAGVFNLVTGYGPVVGEALAAHPALAAVSFTGSTAAGKRVAAVAAATVKRVS 243

Query: 250 LELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAM 309
           LELGGK+ ++V+ DADL  AVK  V    +NSGQ C+   R+ V +  Y +      +A 
Sbjct: 244 LELGGKSASVVLPDADLAAAVKGTVAGCFLNSGQACSALTRLLVPQERYAEAAALAVQAA 303

Query: 310 QAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAV-EG--KGYYYP 366
            A   G+P       +GPL++    +RV   + +AV +GA +  GG A  EG   GYY  
Sbjct: 304 AAYTLGDPLAEGS-RLGPLVSGLQRQRVRAMIEQAVADGAELLCGGSAAPEGLPTGYYVR 362

Query: 367 PTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKA 426
           PT+   VR + ++  EE FGPVL ++ +    +A ++AN +DYGL +++++     A+  
Sbjct: 363 PTVFGRVRPDAALAREEVFGPVLAILTYRDEAEAEAIANGTDYGLAAAVWSAEEARALAF 422

Query: 427 IKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477
            + L+ G+  IN   F  +  F  G+++SG G   G+HG+ ++L+TQ + L
Sbjct: 423 ARRLRAGQVDINGAFFNLLAPF-GGFKQSGYGRELGRHGVEDFLETQSIQL 472


Lambda     K      H
   0.318    0.135    0.392 

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: 531
Number of extensions: 19
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: 479
Length of database: 476
Length adjustment: 34
Effective length of query: 445
Effective length of database: 442
Effective search space:   196690
Effective search space used:   196690
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: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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