GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Methanobacterium lacus AL-21

Align 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase (EC 2.2.1.10) (characterized)
to candidate WP_013644952.1 METBO_RS06790 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase

Query= BRENDA::Q57843
         (273 letters)



>NCBI__GCF_000191585.1:WP_013644952.1
          Length = 266

 Score =  332 bits (850), Expect = 7e-96
 Identities = 153/259 (59%), Positives = 208/259 (80%)

Query: 10  LGKLVRLERIFNRESEKTVIVPMDHGVSNGPIKGLIDIRKTVNDVAEGGANAVLLHKGIV 69
           +GK +R+ERI NR++ + VIVPMDHG+S GP+ G+ID+ +T+++VA GGANAV+ HKG+V
Sbjct: 2   IGKRIRIERILNRKTGRCVIVPMDHGMSIGPVDGIIDMAETIDEVASGGANAVIEHKGMV 61

Query: 70  RHGHRGYGKDVGLIIHLSGGTAISPNPLKKVIVTTVEEAIRMGADAVSIHVNVGSDEDWE 129
             GHRGYG D+GLIIHLS  T++ P+P  KV+VT+VE+A+++GADAVS+HVN+GS+++ E
Sbjct: 62  GKGHRGYGNDIGLIIHLSASTSVGPDPDHKVLVTSVEKALKLGADAVSVHVNIGSEKEPE 121

Query: 130 AYRDLGMIAETCEYWGMPLIAMMYPRGKHIQNERDPELVAHAARLGAELGADIVKTSYTG 189
               +G IAETC+ WGMPLIAMMYPRGK I+NE   ++V  AAR GAELGADI+KT+YTG
Sbjct: 122 MLVQMGTIAETCDEWGMPLIAMMYPRGKKIENEHSVDVVKLAARAGAELGADIIKTNYTG 181

Query: 190 DIDSFRDVVKGCPAPVVVAGGPKTNTDEEFLQMIKDAMEAGAAGVAVGRNIFQHDDVVGI 249
           D  +F++VV GCP PVV+AGGP   TD++ L+M+K++++ G AGVA+GRNIFQ       
Sbjct: 182 DPQTFKEVVDGCPVPVVIAGGPMVETDKQLLEMVKNSVDVGGAGVAIGRNIFQAKSPSKT 241

Query: 250 TRAVCKIVHENADVEEALK 268
           TRA+ +IVH N +VE+ALK
Sbjct: 242 TRAIAEIVHNNMEVEDALK 260


Lambda     K      H
   0.318    0.138    0.401 

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: 285
Number of extensions: 12
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: 273
Length of database: 266
Length adjustment: 25
Effective length of query: 248
Effective length of database: 241
Effective search space:    59768
Effective search space used:    59768
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: 47 (22.7 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