GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Pseudomonas putida KT2440

Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate PP_0552 PP_0552 2,3-butanediol dehydrogenase

Query= SwissProt::Q8U259
         (348 letters)



>FitnessBrowser__Putida:PP_0552
          Length = 362

 Score =  165 bits (417), Expect = 2e-45
 Identities = 104/307 (33%), Positives = 154/307 (50%), Gaps = 22/307 (7%)

Query: 27  PGPGEVLIKILATSICGTDLHIYEWNE--------WAQTRIRPPQIMGHEVAGEVVEVGP 78
           P PG V IK+    ICG+DLH Y               T I+   I+GHE  G + ++G 
Sbjct: 31  PAPGWVQIKVDWCGICGSDLHEYVAGPVFIPVEAPHPLTGIQGQCILGHEFCGHIAKLGE 90

Query: 79  GVEGIEVGDYVSVETHIVCGKCYACKRGQYHVCQNTKIFGVDTDGVFAEYAVVPAQNVWK 138
           GVEG  VGD V+ +    CG CY C  G Y++C+     G+  +G FAE   VPA  +++
Sbjct: 91  GVEGYAVGDPVAADACQHCGTCYYCTHGLYNICERLAFTGLMNNGAFAELVNVPANLLYR 150

Query: 139 NPKNIPPEYATLQEPLGNAVDTV-LAGPIAGKSVLITGAGPLGLLGIAVAKASGAYPVIV 197
            P+  P E   L EPL   +  V  AG + G++V++ GAG +GL  I  AKA+GA  VI 
Sbjct: 151 LPQGFPAEAGALIEPLAVGMHAVKKAGSLLGQTVVVVGAGTIGLCTIMCAKAAGAAQVIA 210

Query: 198 SEPSEFRRNLAKKVGADYVINPFEEDVVKEVMDITDGNGVDVFLEFSGAPKALEQGLQAV 257
            E S  R+  AK+ GA+ V++P + D + E+  +T G G DV  E  G     +  +  +
Sbjct: 211 LEMSSARKAKAKEAGANVVLDPSQCDALAEIRALTAGLGADVSFECIGNKHTAKLAIDTI 270

Query: 258 TPAGRVSLLGLFPGKVSIDFNNLI-----IFKALTVYGITGRHLWETWYTVSRLLQSGKL 312
             AG+  L+G+F      +F  L+     +  AL   G         +  V   +  G+L
Sbjct: 271 RKAGKCVLVGIFEEPSEFNFFELVSTEKQVLGALAYNG--------EFADVIAFIADGRL 322

Query: 313 NIDPIIT 319
           +I P++T
Sbjct: 323 DIRPLVT 329


Lambda     K      H
   0.318    0.138    0.417 

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: 323
Number of extensions: 22
Number of successful extensions: 3
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: 362
Length adjustment: 29
Effective length of query: 319
Effective length of database: 333
Effective search space:   106227
Effective search space used:   106227
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.

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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