GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Bacillus safensis FO-36b

Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate WP_034279790.1 BA81_RS01220 lactonase family protein

Query= uniprot:Q9HWH7
         (388 letters)



>NCBI__GCF_000691165.1:WP_034279790.1
          Length = 347

 Score =  161 bits (407), Expect = 3e-44
 Identities = 106/356 (29%), Positives = 178/356 (50%), Gaps = 19/356 (5%)

Query: 32  VGTYTEGSSEGIQVYRFDGADGSVKGPLRVAHTSNPSYLTFAPDQRTLFVVNENGRGGKG 91
           +GTYT+G S+G+  +  +     ++     A   NP+YLT + DQ+ ++ V + G     
Sbjct: 8   IGTYTKGDSKGVYTFTLNTDKQQIEQVEVAAELENPTYLTVSEDQKFVYAVVKKG----- 62

Query: 92  DTVGRATSYRFDPISGRLQQISQVQTLADHPTYSSLSHDGRYLFVANYSVQPEGSVAVLP 151
            + G   +Y+ D  +GRL  I+Q       P + S+    +  + ANY    +G+  +  
Sbjct: 63  -SQGGLAAYQIDSTTGRLHFINQELADGASPCHVSVDSQTKTAYTANYH---KGTAEMYE 118

Query: 152 VRAD-GSLAPVVQVESHQASKVHP-RQVSGHVHSVVSSPDGQYLFAPDLGADKVFVYRYA 209
           + A+ GS+   +    H+ +  +  RQ   H H +  +PD Q+  A DLG D ++ Y+  
Sbjct: 119 IDAENGSVIRTLSQAQHEGTGPNEDRQEKPHTHFMGLTPDEQFAVAVDLGTDGIYTYK-- 176

Query: 210 PEQAERPLQAADPAFVPTPPGSGPRHLIFSADGRFAYLTLELSGQVMVFAHEGNGRLRQL 269
             + +  L+ A      T PGSGPRH+ F      AY+  ELS +V+V  +  +G   ++
Sbjct: 177 --KEDGKLELAHT--FETKPGSGPRHITFHPTKPVAYVMTELSSEVIVLRYFEDGHFEEI 232

Query: 270 QTHDLAPAGFQGKVGAGALHLSADGRFLGVLNRGDDNQLVTFAVDPASGQLRFVERRSVE 329
           QT    P+ F       A+H+S+DG+F+   NRG D+  +  A D   GQL  VE  S E
Sbjct: 233 QTIATIPSDFTENNQGSAIHVSSDGQFVYAGNRGHDSIAIFKADD--DGQLSLVEIASSE 290

Query: 330 GTEPREFAFSPGGRFVLVANQNSDQLRVFARDPQSGQVGKTLQSVEVGSPSDLRFV 385
           G  PR+F   P   F++ +NQ S  L ++ RD ++G++      + V  P  ++F+
Sbjct: 291 GNWPRDFVLDPTEEFLVGSNQESSNLVLYKRDKETGRLTVLQSDITVPHPVCVKFL 346


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: 431
Number of extensions: 34
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 388
Length of database: 347
Length adjustment: 30
Effective length of query: 358
Effective length of database: 317
Effective search space:   113486
Effective search space used:   113486
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.

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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