GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tdh in Pseudomonas fluorescens FW300-N2C3

Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate AO356_28020 AO356_28020 alcohol dehydrogenase

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



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28020 AO356_28020 alcohol
           dehydrogenase
          Length = 392

 Score =  261 bits (667), Expect = 2e-74
 Identities = 141/377 (37%), Positives = 211/377 (55%)

Query: 7   FIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYD 66
           F+    + GA    +  N    +G  + LIVTD  +   G   DV+ +L+ + I   IY 
Sbjct: 16  FVSPEIMFGAGCRHNVGNYAKTFGARKVLIVTDPGVIAAGWVADVEASLQAQGIDYCIYS 75

Query: 67  GTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVDRS 126
              PNP  E V  G  L +EN+CD ++++GGGSP DC KGI +V A+G  I ++EGVD  
Sbjct: 76  AVSPNPRVEEVMLGADLYRENHCDVIVAVGGGSPMDCGKGIGIVVAHGRSILEFEGVDTL 135

Query: 127 AKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKS 186
             P  P+I I TTAGT++++++F II+++   +K +IV K   P +S+ D    + M   
Sbjct: 136 NVPSPPLILIPTTAGTSADVSQFVIISNQQERMKFSIVSKAAVPDVSLIDPETTLSMDPF 195

Query: 187 LTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAYA 246
           L+A TG+DAL HAIEA+VS    P+TD  AL+A+ +I  NL   + + ++   RE +   
Sbjct: 196 LSACTGIDALVHAIEAFVSTGHGPLTDPHALEAMRLINGNLVQMIANPADIALREKIMLG 255

Query: 247 QFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAAA 306
              AG+AF+NA LG VHAM+H LGGF +LPHG+CNAVL+ HV  FN   A  R +  A  
Sbjct: 256 SMQAGLAFSNAILGAVHAMSHSLGGFLDLPHGLCNAVLVEHVVAFNYNSAPERFKVIAET 315

Query: 307 MGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACGFTN 366
           +G++  G N  E     +  +  L   +     L    V   D   L+ +A+ D C  TN
Sbjct: 316 LGIDCRGLNHREIRTRLVEHLIALKHTIGFHETLGLHGVSTSDIPFLSQHAMHDPCILTN 375

Query: 367 PIQATHEEIVAIYRAAM 383
           P +++  ++  +Y  A+
Sbjct: 376 PRESSQRDVEVVYGEAL 392


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: 372
Number of extensions: 21
Number of successful extensions: 2
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: 392
Length adjustment: 30
Effective length of query: 353
Effective length of database: 362
Effective search space:   127786
Effective search space used:   127786
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 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