GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__PS:Dsui_0105
          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.

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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