GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Geotalea uraniireducens Rf4

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 WP_011939652.1 GURA_RS14275 NAD(P)-dependent oxidoreductase

Query= BRENDA::Q9LSV0
         (289 letters)



>NCBI__GCF_000016745.1:WP_011939652.1
          Length = 288

 Score =  170 bits (431), Expect = 3e-47
 Identities = 89/284 (31%), Positives = 160/284 (56%)

Query: 2   EVGFLGLGIMGKAMSMNLLKNGFKVTVWNRTLSKCDELVEHGASVCESPAEVIKKCKYTI 61
           ++GF+GLG +G+ M+ NL K+ + +TV++      ++LV+ GA    +P+E  K     I
Sbjct: 4   KIGFIGLGTVGRHMAANLTKSDYDLTVYDDDAEPLNDLVKLGAKAAATPSEAAKGKDMVI 63

Query: 62  AMLSDPCAALSVVFDKGGVLEQICEGKGYIDMSTVDAETSLKINEAITGKGGRFVEGPVS 121
            +L +     + VF K GVLE +  G   +DM T   ET+LK+ +    +   F+E PV 
Sbjct: 64  VILPESHGLETFVFGKDGVLEGLDPGTILVDMGTHSLETTLKLADEAIKRRVMFLEAPVW 123

Query: 122 GSKKPAEDGQLIILAAGDKALFEESIPAFDVLGKRSFYLGQVGNGAKMKLIVNMIMGSMM 181
           G+K+ A +G + ILA GD +L      AF   G    ++G++G+  KMK IVN++   +M
Sbjct: 124 GTKEHAANGLVTILAGGDPSLLGRCREAFSYFGLNIIHIGKIGDATKMKFIVNLVQAELM 183

Query: 182 NAFSEGLVLADKSGLSSDTLLDILDLGAMTNPMFKGKGPSMNKSSYPPAFPLKHQQKDMR 241
            + +EG+V  +K G ++D +L++LD G + +P+F  KG S+ +  +     LK+  + + 
Sbjct: 184 QSLAEGIVFGEKLGFNADKILEVLDSGGVASPLFHSKGRSIARGDFSRNLALKYVHEQLL 243

Query: 242 LALALGDENAVSMPVAAAANEAFKKARSLGLGDLDFSAVIEAVK 285
           L +    +  + +P    A + +++A   G G+ D+SAV++ ++
Sbjct: 244 LVMDAAKKVNLDLPGVEVACKLYEQAVKDGRGEEDYSAVVKVLR 287


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: 179
Number of extensions: 9
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: 289
Length of database: 288
Length adjustment: 26
Effective length of query: 263
Effective length of database: 262
Effective search space:    68906
Effective search space used:    68906
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 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