GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoD in Dechlorosoma suillum PS

Align purine-nucleoside phosphorylase (EC 2.4.2.1) (characterized)
to candidate Dsui_2698 Dsui_2698 purine nucleoside phosphorylase

Query= BRENDA::Q8U2I1
         (265 letters)



>FitnessBrowser__PS:Dsui_2698
          Length = 250

 Score =  188 bits (477), Expect = 1e-52
 Identities = 97/215 (45%), Positives = 134/215 (62%), Gaps = 8/215 (3%)

Query: 4   IAIVGGSGVYDFP-AENKREETVKTPYGEVK--ITVGVVGDEEVAFLARHGKGHSIPPHK 60
           +AI+GGSG+      +    E V+TPYGE    +T G +  +   F+ARHG GH+IPPH+
Sbjct: 2   LAIIGGSGLTQLANLDISHREIVRTPYGEPSGPVTFGNICGQPAMFVARHGYGHTIPPHE 61

Query: 61  INYRANIWALYELGVERIIATSAVGSMNPEMKPGDFVILDQIIDFTVSRPRTFYDGEESP 120
           +NYRAN+WAL+      I++ ++VG +  ++ PGD V+  QIID+T  R  TF++G+   
Sbjct: 62  VNYRANLWALWSKKATAIVSVASVGGIRGDLAPGDIVVPHQIIDYTWGRRSTFHEGDGCT 121

Query: 121 HERKFVAHVDFTEPYCPEIRKALITAARNLGLPYHPRGTYVCTEGPRFETAAEIRAYRIL 180
                V HVDFT PY   +R  ++TAA  +G      G Y  T+GPR ETAAEI      
Sbjct: 122 -----VTHVDFTHPYDELLRNQILTAASMIGEEVRMGGVYAATQGPRLETAAEINRMERD 176

Query: 181 GGDVVGMTQCPEAILARELEMCYATVAIVTNYAAG 215
           G D+VGMT  PEA+LAREL++ YA + +V NYAAG
Sbjct: 177 GADLVGMTGMPEAVLARELDLPYAAINVVANYAAG 211


Lambda     K      H
   0.320    0.138    0.412 

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: 242
Number of extensions: 13
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: 265
Length of database: 250
Length adjustment: 24
Effective length of query: 241
Effective length of database: 226
Effective search space:    54466
Effective search space used:    54466
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 (21.8 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