GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacB in Magnetospirillum magneticum AMB-1

Align Galactose-6-phosphate isomerase subunit LacB; EC 5.3.1.26 (characterized)
to candidate WP_043744338.1 AMB_RS11810 ribose 5-phosphate isomerase B

Query= SwissProt::P23495
         (171 letters)



>NCBI__GCF_000009985.1:WP_043744338.1
          Length = 149

 Score = 97.4 bits (241), Expect = 9e-26
 Identities = 49/127 (38%), Positives = 77/127 (60%)

Query: 3   IAIGCDHIVTDVKMAVSEFLKSKGYEVLDFGTYDHVRTHYPIYGKKVGEAVVSGQADLGV 62
           +AI CDH   ++K  +++ L + G+ VLD GT       YP +   + +A+ SG+A+ GV
Sbjct: 6   MAIACDHGGIELKELLAKDLAASGWSVLDLGTNGPESVDYPDFAVTLADALKSGKAERGV 65

Query: 63  CICGTGVGINNAVNKVPGVRSALVRDMTSALYAKEELNANVIGFGGMITGGLLMNDIIEA 122
            +CGTG+GI+ A N+ P VR+ALV D   A   ++  +ANV+  GG  TG  +  D ++ 
Sbjct: 66  LLCGTGIGISIAANRFPHVRAALVHDAFGARMCRQHNDANVLVMGGRTTGPEVARDCLKI 125

Query: 123 FIEAEYK 129
           FIE E++
Sbjct: 126 FIETEFE 132


Lambda     K      H
   0.318    0.137    0.405 

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: 77
Number of extensions: 5
Number of successful extensions: 1
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: 171
Length of database: 149
Length adjustment: 17
Effective length of query: 154
Effective length of database: 132
Effective search space:    20328
Effective search space used:    20328
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 (21.7 bits)
S2: 43 (21.2 bits)

This GapMind analysis is from Sep 17 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