GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Marinobacter adhaerens HP15

Align glyoxylate reductase (EC 1.1.1.26); 4-hydroxybutyrate dehydrogenase (EC 1.1.1.61); glyoxylate reductase (NADP+) (EC 1.1.1.79) (characterized)
to candidate GFF1376 HP15_1343 2-hydroxy-3-oxopropionate reductase

Query= BRENDA::Q9LSV0
         (289 letters)



>FitnessBrowser__Marino:GFF1376
          Length = 290

 Score =  155 bits (393), Expect = 8e-43
 Identities = 89/281 (31%), Positives = 142/281 (50%), Gaps = 1/281 (0%)

Query: 3   VGFLGLGIMGKAMSMNLLKNG-FKVTVWNRTLSKCDELVEHGASVCESPAEVIKKCKYTI 61
           + F+GLGIMG  M+ NLL  G   + V+NR+      L + GA V +S A+ +++     
Sbjct: 5   LAFIGLGIMGSRMAANLLDKGDVNLIVFNRSTEAEKSLKDKGAKVADSAADAVRQADVVF 64

Query: 62  AMLSDPCAALSVVFDKGGVLEQICEGKGYIDMSTVDAETSLKINEAITGKGGRFVEGPVS 121
           +ML+ P     +   + G +  + E   ++D STV+   +    E    +G RF++ PV+
Sbjct: 65  SMLASPPVVQDMALGEDGFVSAMAENALWVDCSTVNPSFTEYAGEVARAQGIRFMDAPVA 124

Query: 122 GSKKPAEDGQLIILAAGDKALFEESIPAFDVLGKRSFYLGQVGNGAKMKLIVNMIMGSMM 181
           G+++PA  G+L  L   D   F+   P    +GK+  ++GQVG G   K++VN ++   M
Sbjct: 125 GTREPAASGELTFLVGADDEDFQSVEPLLQTMGKKIVHVGQVGRGTAFKMLVNAMLAQSM 184

Query: 182 NAFSEGLVLADKSGLSSDTLLDILDLGAMTNPMFKGKGPSMNKSSYPPAFPLKHQQKDMR 241
            AF+E  +L +K G S D L+D L    +T P   GK   +    +   FPL+   KD+ 
Sbjct: 185 LAFAETTLLGEKLGFSRDFLMDTLPNLPVTPPFIGGKAELIRNGDFDAQFPLELMHKDLH 244

Query: 242 LALALGDENAVSMPVAAAANEAFKKARSLGLGDLDFSAVIE 282
           L      E    + +A  A E +  A S G G  DF++V E
Sbjct: 245 LLEQTAYEVGQPLYLANLAKEVYGSASSSGWGRKDFASVFE 285


Lambda     K      H
   0.317    0.134    0.379 

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: 187
Number of extensions: 6
Number of successful extensions: 2
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: 289
Length of database: 290
Length adjustment: 26
Effective length of query: 263
Effective length of database: 264
Effective search space:    69432
Effective search space used:    69432
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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