GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoD in Dokdonella koreensis DS-123

Align purine-nucleoside phosphorylase (EC 2.4.2.1) (characterized)
to candidate WP_067643618.1 I596_RS02340 S-methyl-5'-thioinosine phosphorylase

Query= BRENDA::Q8U2I1
         (265 letters)



>NCBI__GCF_001632775.1:WP_067643618.1
          Length = 249

 Score =  197 bits (500), Expect = 2e-55
 Identities = 103/215 (47%), Positives = 141/215 (65%), Gaps = 8/215 (3%)

Query: 4   IAIVGGSGVYDFPA-ENKREETVKTPYGEV--KITVGVVGDEEVAFLARHGKGHSIPPHK 60
           +A++GG+G+Y FP  E+  +  V T +G    +I +G VG++ +AFLARHG+GHS+ PH+
Sbjct: 7   LAVIGGTGLYRFPGLEDAEKHVVNTRFGTPSDRIVIGRVGNKRIAFLARHGEGHSVAPHR 66

Query: 61  INYRANIWALYELGVERIIATSAVGSMNPEMKPGDFVILDQIIDFTVSRPRTFYDGEESP 120
           +NYRAN+WAL+ LG  R++A +AVG +  +M P   V+ DQIID+T  R  +F D E + 
Sbjct: 67  VNYRANVWALHHLGARRVVAVNAVGGIREDMGPRAVVVPDQIIDYTHGRLSSFCDVEGAE 126

Query: 121 HERKFVAHVDFTEPYCPEIRKALITAARNLGLPYHPRGTYVCTEGPRFETAAEIRAYRIL 180
                V HVDF+ PY   +R  L+ AAR  G+     G Y  T+GPR ET AEI   R  
Sbjct: 127 -----VRHVDFSHPYSAGLRAELLVAARKAGVAVVNGGCYGATQGPRLETVAEIARLRRD 181

Query: 181 GGDVVGMTQCPEAILARELEMCYATVAIVTNYAAG 215
           G D+VGMT  PEA LARELE+ YA +A+V N+AAG
Sbjct: 182 GCDLVGMTGMPEAALARELELDYACLALVANWAAG 216


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: 237
Number of extensions: 11
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: 265
Length of database: 249
Length adjustment: 24
Effective length of query: 241
Effective length of database: 225
Effective search space:    54225
Effective search space used:    54225
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 24 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