GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Pseudomonas simiae WCS417

Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate GFF2362 PS417_12045 iditol 2-dehydrogenase

Query= BRENDA::O58389
         (348 letters)



>FitnessBrowser__WCS417:GFF2362
          Length = 371

 Score =  174 bits (440), Expect = 4e-48
 Identities = 120/340 (35%), Positives = 176/340 (51%), Gaps = 18/340 (5%)

Query: 19  LVEVDVPKPGPGEVLIKVLATSICGTDLHIYE-----WNEWAQSR-IKPPQIMGHEVAGE 72
           L  VDVP PGP E+L KV    IC  D+  Y      W +  Q R +KPP I GHE    
Sbjct: 33  LETVDVPVPGPDEILTKVELCGICMGDIKTYRGAPSFWGDAEQPRYVKPPMIPGHEFVCR 92

Query: 73  VVEIGPGVE--GIEVGDYVSVETHIVCGKCYACRRGQYHVCQNTKIFGVDTD--GVFAEY 128
           VV +GPG E  G++VGD V  E  + C  C  C  GQY +CQ   ++G   +  G  A+Y
Sbjct: 93  VVALGPGAEKRGVKVGDRVISEQIVPCWGCRFCNHGQYWMCQKHDLYGFQNNVQGAMAQY 152

Query: 129 AVVPAQNI-WKNPKSIPPEYATLQEPLGNAVDTVLAGPISGKSVLIT-GAGPLGLLGIAV 186
            +   + I  K P SI P+ A L EPL  ++       +    V++  GAG LGL  I  
Sbjct: 153 MIFTKEGIIHKVPDSIAPDEAILIEPLACSLHAAERANVDFDDVVVVAGAGTLGLGIIGA 212

Query: 187 AKASGAYPVIVSEPSDFRRELAKKVGADYVINPFEEDVVKEVMDITDGNGVDVFLEFSGA 246
            +      +IV +    R  LA ++GAD V NP EEDV+ ++ +ITDG G D+++E +G 
Sbjct: 213 VRMRNPKKLIVLDMKPERAALALRMGADEVWNPAEEDVLAKIREITDGYGCDIYIEATGH 272

Query: 247 PKALEQGLQAVTPAGRVSLLGLYPGKVTIDFNNLIIFKALTIYGITGRHLWETWY-TVSR 305
            KA+ QGL  +   GR     ++  + T+D++ +   K L    + G HL    Y     
Sbjct: 273 HKAVNQGLAMLRKLGRFVEFSVFNDEATVDWSIIGDRKEL---DVLGSHLGPYMYPRAID 329

Query: 306 LLQSGKLNLDPIITHKYKGFDKYEEAFELMRAG-KTGKVV 344
            + + K+++  ++TH +   D ++EAF +M  G K+ KVV
Sbjct: 330 FIGNRKIDMRDVVTHTFALAD-FKEAFAVMERGDKSLKVV 368


Lambda     K      H
   0.318    0.139    0.418 

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: 333
Number of extensions: 30
Number of successful extensions: 5
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: 348
Length of database: 371
Length adjustment: 29
Effective length of query: 319
Effective length of database: 342
Effective search space:   109098
Effective search space used:   109098
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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