GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmB in Hafnia paralvei ATCC 29927

Align beta-Phosphoglucomutase (EC 5.4.2.6) (characterized)
to candidate WP_040012372.1 M988_RS10410 hexitol phosphatase HxpB

Query= BRENDA::P71447
         (221 letters)



>NCBI__GCF_001655005.1:WP_040012372.1
          Length = 220

 Score = 81.6 bits (200), Expect = 1e-20
 Identities = 61/196 (31%), Positives = 100/196 (51%), Gaps = 7/196 (3%)

Query: 3   KAVLFDLDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADK 62
           +AV+FD+DG++ D+     +    +   +GI+       E L    R D + K+      
Sbjct: 7   EAVIFDMDGLLIDSEPLWTQGEHDVFSSLGIDVNAADIPETLG--LRIDLVVKLWYQRTP 64

Query: 63  KVSAEEFKELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASKNGPF- 121
              A + +E+ +R     +++++D  P  + PG+   LK  R   +KI LASAS      
Sbjct: 65  WQGASQ-EEVTERIIRRVIELVRDTKP--LLPGVEHALKLCRQQGMKIGLASASPLYMLN 121

Query: 122 -LLEKMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKD 180
            +LE  N++ YFDA+     +  SKP P++++ AAHA+GV P   + LEDS  G+ A K 
Sbjct: 122 DVLEMFNISQYFDAVVSAEALPYSKPHPEVYLNAAHALGVDPLNCVTLEDSFNGMIATKA 181

Query: 181 SGALPIGVGRPEDLGD 196
           +    I V  PE++ D
Sbjct: 182 ARMRSIVVPAPENIND 197


Lambda     K      H
   0.316    0.135    0.377 

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: 121
Number of extensions: 9
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: 221
Length of database: 220
Length adjustment: 22
Effective length of query: 199
Effective length of database: 198
Effective search space:    39402
Effective search space used:    39402
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 (21.6 bits)
S2: 45 (21.9 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