GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Pseudomonas fluorescens FW300-N2E3

Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate AO353_22415 AO353_22415 alcohol dehydrogenase

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



>FitnessBrowser__pseudo3_N2E3:AO353_22415
          Length = 387

 Score =  257 bits (657), Expect = 3e-73
 Identities = 137/377 (36%), Positives = 211/377 (55%)

Query: 7   FIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYD 66
           F+    + GA    +  N    +G  + L+V+D  +   G   DV+ +L+   I   +Y 
Sbjct: 11  FVSPEIIFGAGCRHNVGNYAKTFGARKVLVVSDPGVIAAGWVADVEASLQALGIDYCLYS 70

Query: 67  GTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVDRS 126
              PNP  E V  G ++ +EN+CD ++++GGGSP DC KGI +V A+G  I ++EGVD  
Sbjct: 71  AVSPNPRVEEVMLGAEIYRENHCDVIVAVGGGSPMDCGKGIGIVVAHGRSILEFEGVDMI 130

Query: 127 AKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKS 186
             P  P+I I TTAGT++++++F II+++   +K +IV K V P +S+ D    + M   
Sbjct: 131 RVPSPPLILIPTTAGTSADVSQFVIISNQQERMKFSIVSKAVVPDVSLIDPETTLSMDPF 190

Query: 187 LTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAYA 246
           L+A TG+DAL HAIEA+VS    P+TD  AL+A+ +I  NL   + + ++   RE +   
Sbjct: 191 LSACTGIDALVHAIEAFVSTGHGPLTDPHALEAMRLINGNLVQMIANPTDIALREKIMLG 250

Query: 247 QFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAAA 306
              AG+AF+NA LG VHAM+H LGGF +LPHG+CNAVL+ HV  FN   A  R +  A  
Sbjct: 251 SMQAGLAFSNAILGAVHAMSHSLGGFLDLPHGLCNAVLVEHVVAFNYSSAPERFKVIAET 310

Query: 307 MGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACGFTN 366
            G++  G N  +     +  +  L   +     L    V   D   L+ +A+ D C  TN
Sbjct: 311 FGIDCRGLNHRQICGRLVEHLIALKHAIGFHETLGLHGVGTSDIPFLSQHAMDDPCILTN 370

Query: 367 PIQATHEEIVAIYRAAM 383
           P +++  ++  +Y  A+
Sbjct: 371 PRESSQRDVEVVYGEAL 387


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: 344
Number of extensions: 15
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: 387
Length adjustment: 30
Effective length of query: 353
Effective length of database: 357
Effective search space:   126021
Effective search space used:   126021
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