GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Halococcus hamelinensis 100A6

Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized)
to candidate WP_007690719.1 C447_RS02885 SDR family oxidoreductase

Query= SwissProt::Q1NEI6
         (249 letters)



>NCBI__GCF_000336675.1:WP_007690719.1
          Length = 258

 Score =  140 bits (352), Expect = 3e-38
 Identities = 92/247 (37%), Positives = 127/247 (51%), Gaps = 10/247 (4%)

Query: 10  GRCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDATHV----VALDVS 65
           G+ A+VTG   GLG  +A      G  VA+ D++ +       EI    V    V  DVS
Sbjct: 11  GQRAVVTGAGRGLGNVMATAYAEAGADVAIVDVDAETAEQAADEIAELGVETTSVTADVS 70

Query: 66  DHAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNRE 125
           D A V A  +     LG +DIL+ +AGI   T P  E PVD +Q  +D+NL G+F C++ 
Sbjct: 71  DEAEVEAMTETVVDRLGGIDILLNNAGIVSNT-PAEEMPVDEWQATMDVNLTGVFLCSKH 129

Query: 126 VVPFMLENGYGRIVNLASVAGKEGN-PNAS-AYSASKAGVIGFTKSLGKELAGKGVIANA 183
           V   MLE G G IVN++S++G   N P    AY+ASKAGVI  T+SL  E   +GV  N+
Sbjct: 130 VGRHMLERGSGTIVNISSMSGLVANHPQPQIAYNASKAGVIMVTRSLASEWGDRGVRVNS 189

Query: 184 LTPATFESPILDQLPQ---SQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTF 240
           + P    + +++ + +      +  R   PMGRLG   E   +  F+ASE  SF      
Sbjct: 190 IAPGYMRTDLVEDVLEEDPEMAETWREYTPMGRLGKPTELGPVAVFLASEASSFMNGEIV 249

Query: 241 DTSGGRT 247
              GG T
Sbjct: 250 SFDGGYT 256


Lambda     K      H
   0.318    0.132    0.381 

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: 152
Number of extensions: 9
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: 249
Length of database: 258
Length adjustment: 24
Effective length of query: 225
Effective length of database: 234
Effective search space:    52650
Effective search space used:    52650
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