GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoD in Sulfuritalea hydrogenivorans sk43H DSM 22779

Align Probable 6-oxopurine nucleoside phosphorylase; EC 2.4.2.1; Purine nucleoside phosphorylase; PNP (uncharacterized)
to candidate WP_041098386.1 SUTH_RS08025 S-methyl-5'-thioinosine phosphorylase

Query= curated2:O66839
         (277 letters)



>NCBI__GCF_000828635.1:WP_041098386.1
          Length = 245

 Score =  194 bits (493), Expect = 2e-54
 Identities = 105/232 (45%), Positives = 138/232 (59%), Gaps = 16/232 (6%)

Query: 1   MLGIIGGSGLYNLPGIKVKEEVQVKTPFGEPSSPVVIAEVEGKKVAFLARHGRGHEYPPH 60
           MLGIIGGSGL  L  + V     V+TP+GEPS P+    + G  V F+ARHG GH  PPH
Sbjct: 1   MLGIIGGSGLTQLANLDVSHREVVRTPYGEPSGPLTFGRINGHDVVFIARHGYGHTIPPH 60

Query: 61  LVPYRANLWALREVGVKRVLGISAVGGINELLMPGDFVVIHDYLDFTKTRRSTYYEGKFS 120
           LV YRAN+ AL   GV +++ +++VGGI   L PG  VV H  +D+T  R  T+  G   
Sbjct: 61  LVNYRANIHALETSGVTQIVSVASVGGIRGDLGPGALVVPHQIIDYTWGREMTFQSG--- 117

Query: 121 VKVEGEDKVAKLLREGKVVHVDMSEAYCPEMRKVLIQILKEKNFRFHPKGVYACTEGPRF 180
                         +G V+HVD ++ Y  E+R++L+ + +          VYA T+GPR 
Sbjct: 118 -------------GDGPVIHVDFTDPYDAEVRQLLLDVSRRIGEPVIDGAVYATTQGPRL 164

Query: 181 ETPSEIKMLKLLGADVVGMTGYPEVALARELTMCYASLCVVANPAAGIAGYR 232
           ET +EI  ++  GAD+VGMTG PE  LAREL + YA+LCVVAN AAG A  R
Sbjct: 165 ETAAEINRMEDDGADIVGMTGMPEAGLARELELPYAALCVVANWAAGRADSR 216


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: 217
Number of extensions: 7
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 Apr 09 2024. 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