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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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