GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Paraburkholderia bryophila 376MFSha3.1

Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate H281DRAFT_05508 H281DRAFT_05508 Alcohol dehydrogenase, class IV

Query= ecocyc::EG12293-MONOMER
         (383 letters)



>FitnessBrowser__Burk376:H281DRAFT_05508
          Length = 383

 Score =  197 bits (502), Expect = 3e-55
 Identities = 118/353 (33%), Positives = 196/353 (55%), Gaps = 4/353 (1%)

Query: 30  GFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGTQPNPTTENVAAGLKLLKENNC 89
           G    L+V+D  +   G+       L    I    +   + +P+   V A  +L + +  
Sbjct: 30  GVNSVLLVSDRGVKNAGLLEAPMAHLRTSGIAVECFFDVEADPSAATVQAAAQLARSSGV 89

Query: 90  DSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVDRSAKPQLPMIAINTTAGTASEMTRF 149
           D V+++GGGSP D AK  AL+A +G D+ D  G+ ++  P+L ++ + TTAGT SE T  
Sbjct: 90  DCVVAIGGGSPMDVAKLAALLAKSGVDLEDIYGIHKTEGPRLRLVLVPTTAGTGSEATPI 149

Query: 150 CIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKSLTAATGMDALTHAIEAYVSIA-A 208
            I+T  A   K  +V   + P ++V D+ L IG+PK ++AATG+DA+ HAIEAY S +  
Sbjct: 150 SIVTTGAGE-KKGVVCPVLLPDIAVLDAELTIGLPKHVSAATGIDAMVHAIEAYTSRSLK 208

Query: 209 TPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAYAQFLAGMAFNNASLGYVHAMAHQ 268
            P++D  A +A+ ++  +L      G + + R+AM     LAGMAF NA +  VHA+A+ 
Sbjct: 209 NPLSDCLAREALRLLGPHLERVCAQGHDVETRQAMLLGANLAGMAFANAPVAAVHALAYP 268

Query: 269 LGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAAAMGVNVTGKNDAEGAEACINAIR 328
           +G  +++PHG+ N+++LP V  FN   A +   + A+ +  N  G  + E   A +  + 
Sbjct: 269 IGARFHVPHGLSNSLMLPAVLRFNMTSAESLYAELASLLVPNAIGSPE-ELTRALLAYLT 327

Query: 329 ELAKKVDIPAGLRDLNVKEEDFAVLATNALKDA-CGFTNPIQATHEEIVAIYR 380
           EL  K+ +P  LRD+ +  ED   LA +A+K +     NP +  +++ +A+Y+
Sbjct: 328 ELPVKLGLPVRLRDVGITAEDLPDLAIDAMKQSRLLVNNPREVGYDDALAMYQ 380


Lambda     K      H
   0.318    0.131    0.373 

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: 361
Number of extensions: 16
Number of successful extensions: 4
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: 383
Length of database: 383
Length adjustment: 30
Effective length of query: 353
Effective length of database: 353
Effective search space:   124609
Effective search space used:   124609
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 (21.8 bits)
S2: 50 (23.9 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