GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaD in Stutzerimonas stutzeri A1501

Align glycine oxidase (EC 1.4.3.19) (characterized)
to candidate WP_085988597.1 PST_RS04985 glycine oxidase ThiO

Query= BRENDA::O31616
         (369 letters)



>NCBI__GCF_000013785.1:WP_085988597.1
          Length = 367

 Score =  146 bits (369), Expect = 8e-40
 Identities = 104/347 (29%), Positives = 166/347 (47%), Gaps = 4/347 (1%)

Query: 6   EAVVIGGGIIGSAIAYYLAKENKNTALFESGTMGGRTTSAAAGMLGAHAECEERDAFFDF 65
           +A V+G G +G   AY LA       + E   +G   + A  G++          A    
Sbjct: 2   KAAVVGAGALGLLSAYQLALAGCQVCVLERCRVGREASWAGGGIVSPLYPWRYSPAVTAL 61

Query: 66  AMHSQRLYKGLGEELYALSGVDIRQHNGGMFKLAFSEE-DVLQLRQMDDLDSVSWYSKEE 124
           A  SQ  Y  LG  L   +GVD   H  G++ L   +E + L   +       S  S E 
Sbjct: 62  AHWSQDFYPQLGARLLEETGVDPEVHVTGLYWLDLHDEAEALNWAERYGRPLTS-VSMET 120

Query: 125 VLEKEPYASGDIFGASFIQDDVHVEPYFVCKAYVKAAKML-GAEIFEHTPVLHVERDGEA 183
           V +  P        A +++   ++    + +A  +A + L    + E  PV    RDG  
Sbjct: 121 VRQAVPSLGEGYERAVYMEGVANIRNPRLLRALREALRQLPNVTVIEQCPVEGFLRDGTR 180

Query: 184 LF-IKTPSGDVWANHVVVASGVWSGMFFKQLGLNNAFLPVKGECLSVWNDDIPLTKTLYH 242
           +  ++T  G++ A+ VVVA+G WS      LGL     P+KG+ +     +  L   +  
Sbjct: 181 IVGVQTAQGEMRADQVVVAAGAWSAKLLATLGLEIPVKPMKGQMILFKCAEDFLPSMVLA 240

Query: 243 DHCYIVPRKSGRLVVGATMKPGDWSETPDLGGLESVMKKAKTMLPAIQNMKVDRFWAGLR 302
              Y +PR+ G ++VG+T++   + +TP    LES+   A  +LPA+ + +V + WAGLR
Sbjct: 241 KRRYAIPRRDGHILVGSTLEDVGFDKTPTEDALESLRATAVELLPALADAQVVKHWAGLR 300

Query: 303 PGTKDGKPYIGRHPEDSRILFAAGHFRNGILLAPATGALISDLIMNK 349
           PG+ DG PYIG+      +    GHFRNG++LAPA+  L+ DL++ +
Sbjct: 301 PGSPDGVPYIGQVSGFDGLWLNCGHFRNGLVLAPASCQLLVDLMLGQ 347


Lambda     K      H
   0.320    0.137    0.419 

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: 309
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: 369
Length of database: 367
Length adjustment: 30
Effective length of query: 339
Effective length of database: 337
Effective search space:   114243
Effective search space used:   114243
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: 49 (23.5 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