Alignments for a candidate for adh in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Dyella japonica UNC79MFTsu3.2

Align Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized)
to candidate N515DRAFT_0379 N515DRAFT_0379 Acyl-CoA reductase

Query= SwissProt::Q8S528
         (534 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0379
          Length = 476

 Score =  225 bits (574), Expect = 3e-63
 Identities = 154/462 (33%), Positives = 238/462 (51%), Gaps = 23/462 (4%)

Query: 74  LDPRNGEVIAQVSEGDAEDVNRAVAAARKAFDEGPWPKMTAYERSKILFRFADLIEKHND 133
           LD  +G+V  +V+  DA+   +A+AAA KA +  P  +   +ER  +L        +  D
Sbjct: 24  LDKYSGKVATRVAVPDAKATEQAIAAAVKAAE--PMRQFKPWERQAVLQHCVQRFTERRD 81

Query: 134 EIAALETWDNGKPYEQSAQIEVPMLARVFRYYAGWADKIHGMTMPGD-----GPHHVQTL 188
           E+A     + GKP + SA  EV  L   F   A  A + +G T+  +       +H  T 
Sbjct: 82  ELAYALCVEAGKPIKDSAG-EVTRLIETFGIAAEEAVRTNGETINLEIAKRLNGYHGYTR 140

Query: 189 HEPIGVAGQIIPWNFPLLMLSWKLGPALACGNTVVLKTAEQTPLSALLVGKLLHEAGLPD 248
             P+G    I P+NFPL +++ K+ PA+A G   VLK AE+TP+ AL++G++L E  LP 
Sbjct: 141 RVPLGPVSFITPFNFPLNLVAHKVAPAIAAGCPFVLKPAERTPIGALIIGEVLAETDLPK 200

Query: 249 GVVNIVSGFGATAGAAIASHMDVDKVAFTGSTDVGKIILELASKSNLKAVTLELGGKSPF 308
           G  +I++  G  A + +        ++FTGS    +I  +L +++  K VTLELGG +  
Sbjct: 201 GAFSILNLDGKHA-SPLVEDPRFKLLSFTGS----QIGWDLKTRAGHKKVTLELGGNAAC 255

Query: 309 IVCEDAD----VDQAVELAHFALFFNQGQCCCAGSRTFVHERVYDEFVEKAKARALKRNV 364
           IV  DAD    +D  +E   F  F+  GQ C +  R + HE +YDE  ++  A       
Sbjct: 256 IV--DADQLPRLDHVIERLVFGAFYQSGQSCISVQRIYAHESLYDELKKRLVAAVKGLKA 313

Query: 365 GDPFKSGIEQGPQVDSEQFNKILKYIKHGVEAGATLQAGGDRLGSKGYYIQPTVFSDVKD 424
           GDP K     GP +D     ++  +I+   + G  +  GG R   KG  ++ T+  +V+ 
Sbjct: 314 GDPKKKETFLGPMIDEAAAERLHGWIEEARKGGGKVLCGGKR---KGPMLEATLMENVRG 370

Query: 425 DMLIATDEIFGPVQTILKFKDLDEVIARANNSRYGLAAGVFTQNLDTAHRLMRALRVGTV 484
           D  +   E+FGP   +  FK LDE IA  N+S YGL AG+FT +L  A R    L  G V
Sbjct: 371 DAKVNRQEVFGPFALLAPFKSLDEAIAMTNDSDYGLQAGIFTDSLANAMRAWNELEQGGV 430

Query: 485 WINCFDVLDA-SIPFGGYKMSGIGREKGIYSLNNYLQVKAVV 525
            +N        ++P+GG K+SG GRE   Y++ +  +++ +V
Sbjct: 431 IVNDVPSFRVDNMPYGGVKLSGAGREGVRYAIEDMTEIRLMV 472


Lambda     K      H
   0.319    0.135    0.401 

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: 612
Number of extensions: 31
Number of successful extensions: 7
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: 534
Length of database: 476
Length adjustment: 34
Effective length of query: 500
Effective length of database: 442
Effective search space:   221000
Effective search space used:   221000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources