GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Pandoraea thiooxydans ATSB16

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_047214213.1 PATSB16_RS11230 glucose 1-dehydrogenase

Query= BRENDA::Q99714
         (261 letters)



>NCBI__GCF_001931675.1:WP_047214213.1
          Length = 255

 Score = 96.7 bits (239), Expect = 4e-25
 Identities = 81/255 (31%), Positives = 126/255 (49%), Gaps = 22/255 (8%)

Query: 12  VAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGE----AQAKKLGNNCVFAPADVTS 67
           VA++TG A G+G A A RL  +GA  V+ D  ++       AQ +  G++      +V S
Sbjct: 7   VALVTGSAQGIGRAIAVRLAQEGAKIVVEDRQDADAAEQTLAQVRAAGSDGCVIAGNVGS 66

Query: 68  EKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFN 127
             D +  +  A  K GR+DV VN AG+   +    + +       D+  VLDVNL G F 
Sbjct: 67  VHDARGVVDAAVAKLGRIDVLVNNAGVERNAPFLEVSEA------DYDLVLDVNLKGAFF 120

Query: 128 VIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLA 187
           + + V   +   +  +GG+   I+N +SV          +Y ASKGG+  M   +A +LA
Sbjct: 121 MTQAVVRHL--RDSHRGGR---IVNISSVHEELPFPHFTSYCASKGGMKMMVRNLAIELA 175

Query: 188 PIGIRVMTIAPGLFGTPLLTSL---PEKVCNFLASQVPFPSRLGDPAEYAH--LVQAIIE 242
           P+GI V  +APG  GT +   L   P ++   LA+ +P   RLG   + A+  L  A  E
Sbjct: 176 PLGITVNNVAPGAVGTAINNKLLHDPAELSALLAN-IPL-KRLGKVEDVANAVLFLASDE 233

Query: 243 NPFLNGEVIRLDGAI 257
             ++ G  + +DG +
Sbjct: 234 ASYVTGTTVYVDGGL 248


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: 148
Number of extensions: 6
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: 255
Length adjustment: 24
Effective length of query: 237
Effective length of database: 231
Effective search space:    54747
Effective search space used:    54747
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