GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Streptococcus oralis 7747

Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate WP_000665611.1 HK29_RS05400 lactonase family protein

Query= uniprot:Q9HWH7
         (388 letters)



>NCBI__GCF_000382825.1:WP_000665611.1
          Length = 337

 Score =  142 bits (357), Expect = 2e-38
 Identities = 104/337 (30%), Positives = 157/337 (46%), Gaps = 24/337 (7%)

Query: 33  GTYTEGSSEGIQVYRFDGADGSVKGPLRVAHTSNPSYLTFAPDQRTLFVVNENGRGGKGD 92
           GTYT  SS+GI    FD   G +      A   +P+YL F   Q    V +++G GG   
Sbjct: 8   GTYTRRSSKGIYKADFDTETGQLANLELFAAEPSPTYLAFDQQQHLYTVGSQDGLGG--- 64

Query: 93  TVGRATSYRFDPISGRLQQISQVQTLADHPTYSSLSHDGRYLFVANYSVQPEGSVAVLPV 152
                 +Y+ D   G L     V+  A H  Y ++      ++ ANY    +G + V   
Sbjct: 65  ----IAAYKTD---GTLLN-HVVEEGAPH-CYVAVDEKRSLVYGANYH---KGQILVYQR 112

Query: 153 RADGSLAPVVQVESHQASKVHPRQVSGHVHSVVSSPDGQYLFAPDLGADKVFVYRYAPEQ 212
           + DGSL     ++ H     H  Q S HVH    +PD QYL   DLG D+V  Y  +PE 
Sbjct: 113 QTDGSLIQT-DLDQHSGQGPHENQTSPHVHFTDLTPD-QYLVTCDLGTDEVTTYDVSPEG 170

Query: 213 AERPLQAADPAFVPTPPGSGPRHLIFSADGRFAYLTLELSGQVMVFAHEGNGRLRQLQTH 272
               L         + PG+G RH++F    + AYL  EL+  + V  ++G G   ++Q  
Sbjct: 171 KLSKLHTYH-----SQPGAGARHIVFHHHYKIAYLICELNSTIEVLIYDGVGEFERMQVI 225

Query: 273 DLAPAGFQGKVGAGALHLSADGRFLGVLNRGDDNQLVTFAVDPASGQLRFVERRSVEGTE 332
              P  ++      A+ LS DG++L   NRG D+  V   +  A G L  +E     G  
Sbjct: 226 STLPDRYEDFNATAAIRLSKDGKYLYASNRGHDSIAVYTIL--ADGSLELLEIVPTHGQN 283

Query: 333 PREFAFSPGGRFVLVANQNSDQLRVFARDPQSGQVGK 369
           PR+F  +P   F++  +Q+SD   VF R+P++G++ +
Sbjct: 284 PRDFDLTPDQEFLIAVHQDSDNATVFKRNPETGRLAE 320


Lambda     K      H
   0.318    0.135    0.395 

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: 406
Number of extensions: 38
Number of successful extensions: 9
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: 388
Length of database: 337
Length adjustment: 29
Effective length of query: 359
Effective length of database: 308
Effective search space:   110572
Effective search space used:   110572
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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