GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoD in Pseudomonas fluorescens GW456-L13

Align Probable 6-oxopurine nucleoside phosphorylase; EC 2.4.2.1; Purine nucleoside phosphorylase; PNP (uncharacterized)
to candidate PfGW456L13_4030 5'-methylthioadenosine phosphorylase (EC 2.4.2.28)

Query= curated2:O66839
         (277 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4030
          Length = 245

 Score =  204 bits (520), Expect = 1e-57
 Identities = 107/255 (41%), Positives = 148/255 (58%), Gaps = 16/255 (6%)

Query: 4   IIGGSGLYNLPGIKVKEEVQVKTPFGEPSSPVVIAEVEGKKVAFLARHGRGHEYPPHLVP 63
           IIGG+GL  L G+ +++ + V TP+G PS+ V I E  GK+V FLARHG  H +PPH V 
Sbjct: 6   IIGGTGLTQLEGLSIRQSLAVDTPYGAPSADVQIGEYAGKEVLFLARHGHPHRFPPHQVN 65

Query: 64  YRANLWALREVGVKRVLGISAVGGINELLMPGDFVVIHDYLDFTKTRRSTYYEGKFSVKV 123
           YRANLWAL++ G + +L ++AVGGI+  +  G F V H  +D+T  R  TY+        
Sbjct: 66  YRANLWALKQAGAEAILAVNAVGGIHAAMGAGHFCVPHQLIDYTSGREHTYFADDLE--- 122

Query: 124 EGEDKVAKLLREGKVVHVDMSEAYCPEMRKVLIQILKEKNFRFHPKGVYACTEGPRFETP 183
                         V H+D S  Y   +R+ LI  L  +   +   GVYACT+GPR ET 
Sbjct: 123 -------------HVTHIDFSYPYSEPLRQQLIAALAAEGVGYSSHGVYACTQGPRLETV 169

Query: 184 SEIKMLKLLGADVVGMTGYPEVALARELTMCYASLCVVANPAAGIAGYRLTSNEVIQLMK 243
           +EI  L+  G D+VGMTG PE ALAREL + YA L +V NPAAG +   +T  E+ Q + 
Sbjct: 170 AEIARLERDGCDIVGMTGMPEAALARELELDYACLALVVNPAAGKSTAVITMAEIEQALH 229

Query: 244 RKEEEIKEVVLKFIK 258
               ++K  + + +K
Sbjct: 230 DGMGKVKSTLARVLK 244


Lambda     K      H
   0.319    0.139    0.406 

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: 216
Number of extensions: 9
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: 277
Length of database: 245
Length adjustment: 24
Effective length of query: 253
Effective length of database: 221
Effective search space:    55913
Effective search space used:    55913
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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