GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Nocardiopsis gilva YIM 90087

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_017617176.1 CDO52_RS11130 3-oxoacyl-ACP reductase

Query= BRENDA::Q99714
         (261 letters)



>NCBI__GCF_002263495.1:WP_017617176.1
          Length = 254

 Score =  127 bits (319), Expect = 2e-34
 Identities = 96/256 (37%), Positives = 133/256 (51%), Gaps = 21/256 (8%)

Query: 9   KGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSE 68
           +G VAVITG  SG+G ATA RL  +G + V +DL    GEA AK+ G   ++  ADVT E
Sbjct: 5   EGRVAVITGAGSGIGKATALRLASEGGTVVAVDLDRDAGEAVAKETGG--LYIAADVTDE 62

Query: 69  KDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNV 128
           + V+ A A  K  +GRVDVA N AGI+       L  G    +E +++V +VNL   +  
Sbjct: 63  EAVKAAFAEVKEVYGRVDVAFNNAGISPPDDDSILDTG----IEAWRKVQEVNLTSVYLC 118

Query: 129 IRLVAGEMGQNEPDQGGQRGVIINTAS-VAAFEGQVGQAAYSASKGGIVGMTLPIARDLA 187
            +     M     +QG  +G I+NTAS VA       Q +Y+ASKGG++ M+  +    A
Sbjct: 119 CKYALPYM----REQG--KGAIVNTASFVATMGAATSQISYTASKGGVLAMSRELGVQFA 172

Query: 188 PIGIRVMTIAPGLFGTPLLTSL----PEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIEN 243
             G+RV  ++PG   TPLL  L    PE+    L   VPF  R  +P E A  V  +  +
Sbjct: 173 RDGVRVNALSPGPVNTPLLKELFAKDPERAQRRLV-HVPF-GRFAEPEEIASAVAFLASD 230

Query: 244 --PFLNGEVIRLDGAI 257
              F+      +DG I
Sbjct: 231 DASFITASNFLVDGGI 246


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: 173
Number of extensions: 11
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.

Links

Downloads

Related tools

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