GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Pseudomonas putida KT2440

Align Sorbitol-6-phosphate 2-dehydrogenase; EC 1.1.1.140; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized)
to candidate PP_2214 PP_2214 3-hydroxyacyl-CoA dehydrogenase type-2

Query= curated2:P37079
         (267 letters)



>FitnessBrowser__Putida:PP_2214
          Length = 255

 Score =  111 bits (277), Expect = 2e-29
 Identities = 67/200 (33%), Positives = 107/200 (53%), Gaps = 15/200 (7%)

Query: 5   LNLKDNVIIVTGGASGIGLAIVDELLSQGAHVQMIDIHG----GDRHHNGDNYHFWSTDI 60
           +++ +   IV+G ASG+G A    L+  GA V ++D++           GDN  F   DI
Sbjct: 1   MHIANKHFIVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVEAKARELGDNARFAVADI 60

Query: 61  SSATEVQQTIDAIIQRWSRIDGLVNNAGVNFPRLLVDEKAPAGRYELNEAAFEKMVNINQ 120
           S     Q  +DA +  +  + GLVN AG+     ++ ++ P G      A+F K++N+N 
Sbjct: 61  SDEQAAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGL-----ASFAKVINVNL 115

Query: 121 KGVFFMSQAVARQMVKQRA------GVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSW 174
            G F + +  A  M +  A      GVI+N +S +  +G  GQ+ YAA+K A+ S T   
Sbjct: 116 IGSFNLLRLAAAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPA 175

Query: 175 SKELGKYGIRVVGVAPGILE 194
           ++EL ++GIRV+ +APGI E
Sbjct: 176 ARELARFGIRVMTIAPGIFE 195


Lambda     K      H
   0.316    0.133    0.386 

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: 134
Number of extensions: 11
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: 267
Length of database: 255
Length adjustment: 25
Effective length of query: 242
Effective length of database: 230
Effective search space:    55660
Effective search space used:    55660
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 (21.6 bits)
S2: 47 (22.7 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