GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Nocardioides daejeonensis MJ31

Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate WP_110207257.1 DNK54_RS12225 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q99714
         (261 letters)



>NCBI__GCF_003194585.1:WP_110207257.1
          Length = 254

 Score =  287 bits (735), Expect = 1e-82
 Identities = 152/250 (60%), Positives = 185/250 (74%), Gaps = 3/250 (1%)

Query: 12  VAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDV 71
           VA++TGGASGLG AT E L+ +G  AV+LDLP   GE  AK+LG+   F PADV SE+DV
Sbjct: 7   VALVTGGASGLGRATVEALLAKGGRAVILDLPGGAGETTAKELGDAVRFVPADVRSEEDV 66

Query: 72  QTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVIRL 131
           + A+A A  + G + V VNCAG   A KT   +  + +  + FQR++++NL+GTFNVIRL
Sbjct: 67  KAAIAAAS-ELGELRVVVNCAGTGDAIKTVG-RGNEPYPYDKFQRIIEINLLGTFNVIRL 124

Query: 132 VAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGI 191
            A  M   +   G +RGVI+NTASVAAF+GQ+GQAAYSASKGG+VGMTLPIARDL+ +GI
Sbjct: 125 TAAHMAGLDL-LGEERGVIVNTASVAAFDGQIGQAAYSASKGGVVGMTLPIARDLSTLGI 183

Query: 192 RVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENPFLNGEVI 251
           RV+TIAPGLF TPLL SLPE+    L  QVP PSRLGDPAEY  L   ++ENP LNGE I
Sbjct: 184 RVVTIAPGLFDTPLLASLPEEARRSLGQQVPHPSRLGDPAEYGALAAHVVENPMLNGETI 243

Query: 252 RLDGAIRMQP 261
           RLDGAIRM P
Sbjct: 244 RLDGAIRMAP 253


Lambda     K      H
   0.318    0.135    0.385 

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: 264
Number of extensions: 9
Number of successful extensions: 3
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: 261
Length of database: 254
Length adjustment: 24
Effective length of query: 237
Effective length of database: 230
Effective search space:    54510
Effective search space used:    54510
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