GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Rhodobacter viridis JA737

Align 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase (EC 2.2.1.10) (characterized)
to candidate WP_110805915.1 C8J30_RS10520 3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase

Query= BRENDA::Q57843
         (273 letters)



>NCBI__GCF_003217355.1:WP_110805915.1
          Length = 291

 Score =  130 bits (326), Expect = 4e-35
 Identities = 88/253 (34%), Positives = 137/253 (54%), Gaps = 10/253 (3%)

Query: 15  RLERIFNRESEKTVIVPMDHGVSNGPIKGLIDIRKTVNDVAEGGANAVLLHKGIVRHG-H 73
           RL RIFN ++ +TV++  DHG   GP  GL  +   +  +A+  A+ ++  +G +R    
Sbjct: 39  RLSRIFNPKTGRTVMLAFDHGYFQGPATGLERMDLNILPLADH-ADVLMCTRGALRSTVP 97

Query: 74  RGYGKDVGLIIHLSGGTAISPNPLKKVIVTTVEEAIRMGADAVSIHVNVGSDEDWEAYRD 133
               K V L    SGG +I      + +   +E+AIR+G  A++  V +GS+ + ++  +
Sbjct: 98  PSNTKPVAL--RCSGGNSILTELSNETVAVEIEDAIRLGVCAMAAQVYIGSEYEHKSITN 155

Query: 134 LGMIAETCEYWGMPLIAMMYPRGKHIQNERDPELVAHAARLGAELGADIVKTSYTGDIDS 193
           +  + +T   +G+P +A+    G      RD      A R+ AELGA  VKT +  +   
Sbjct: 156 VLKLIDTGTRYGIPTLAVT---GVGKDMARDARYFGLATRIAAELGAHYVKTYFVEE--G 210

Query: 194 FRDVVKGCPAPVVVAGGPKTNTDEEFLQMIKDAMEAGAAGVAVGRNIFQHDDVVGITRAV 253
           F  V  GCP P+V+AGG K   + E L M   A++ GAAGV +GRNIFQ +  V + +AV
Sbjct: 211 FEKVAAGCPVPLVIAGGKKL-PELEALDMAWKAIDQGAAGVDMGRNIFQSEAPVAMIQAV 269

Query: 254 CKIVHENADVEEA 266
            K+VHEN   +EA
Sbjct: 270 AKVVHENYTAKEA 282


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: 193
Number of extensions: 11
Number of successful extensions: 5
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: 291
Length adjustment: 26
Effective length of query: 247
Effective length of database: 265
Effective search space:    65455
Effective search space used:    65455
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 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