GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Geotalea uraniireducens Rf4

Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate WP_011938770.1 GURA_RS09505 3-oxoacyl-[acyl-carrier-protein] reductase

Query= BRENDA::B8H1Z0
         (248 letters)



>NCBI__GCF_000016745.1:WP_011938770.1
          Length = 246

 Score =  106 bits (265), Expect = 4e-28
 Identities = 75/243 (30%), Positives = 119/243 (48%), Gaps = 5/243 (2%)

Query: 8   SLKGKRVVITGGGSGIGAGLTAGFARQGAEVIFLDIADEDSRALEAELAGSPIPPVYKRC 67
           SL G+  VITG   GIG  +    A +GA+++    + E +R    E+       +  + 
Sbjct: 2   SLNGRVAVITGASRGIGKAVALKLAAEGADLVVTATSLEAARMTADEIIQLGGKALALKV 61

Query: 68  DLMNLEAIKAVF----AEIGDVDVLVNNAGNDDRHKLADVTGAYWDERINVNLRHMLFCT 123
           D+   E ++++F     E G VD+L+NNAG      L  +  A WD  ++VNL+    CT
Sbjct: 62  DVSITEEVESLFHKTIEEFGRVDILINNAGITRDGLLLRMKEADWDAVLDVNLKGAFNCT 121

Query: 124 QAVAPGMKKRGGGAVINFGSISWHLGLEDLVLYETAKAGIEGMTRALARELGPDDIRVTC 183
           +  A  M K   G ++N  S+   +G    V Y  +KAG+ G+T+A AREL   +I V  
Sbjct: 122 REAAKYMTKARYGRIVNISSVVGEIGNAGQVNYCASKAGMFGLTKATARELAKRNITVNA 181

Query: 184 VVPGNVKTKRQEKWYTPEGEAQIVAAQCLKGRIVPENVAALVLFLASDDASLCTGHEYWI 243
           V PG ++T       + +    ++    L+    PE++AA V FL S  +   TGH   +
Sbjct: 182 VSPGFIETD-MTGVLSEKVRENLLQQIPLERLGQPEDIAAAVYFLVSAQSGYITGHVLSV 240

Query: 244 DAG 246
           + G
Sbjct: 241 NGG 243


Lambda     K      H
   0.319    0.137    0.416 

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: 135
Number of extensions: 5
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: 248
Length of database: 246
Length adjustment: 24
Effective length of query: 224
Effective length of database: 222
Effective search space:    49728
Effective search space used:    49728
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: 46 (22.3 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