GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Pseudomonas simiae WCS417

Align 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)
to candidate GFF2717 PS417_13860 3-hydroxy-2-methylbutyryl-CoA dehydrogenase

Query= SwissProt::O18404
         (255 letters)



>FitnessBrowser__WCS417:GFF2717
          Length = 255

 Score =  253 bits (646), Expect = 3e-72
 Identities = 134/252 (53%), Positives = 171/252 (67%), Gaps = 2/252 (0%)

Query: 2   IKNAVSLVTGGASGLGRATAERLAKQGASVILADLPSSKGNEVAKELGDKVVFVPVDVTS 61
           I+N + LV+GGASGLG ATAE L   GA V+L DL +      A++LG        D++ 
Sbjct: 3   IENKIFLVSGGASGLGAATAEMLVAAGAKVMLVDLNADAVAAKAQQLGGNARSAVADISQ 62

Query: 62  EKDVSAALQTAKDKFGRLDLTVNCAGTATAVKTFNFNKNVAHRLEDFQRVININTVGTFN 121
           E    AA+Q     FG L   VNCAG     K     K+  H L  F +VIN+N +G+FN
Sbjct: 63  EAAAEAAVQATVAAFGGLHGLVNCAGVVRGEKILG--KDGPHGLASFAQVINVNLIGSFN 120

Query: 122 VIRLSAGLMGANEPNQDGQRGVIVNTASVAAFDGQIGQAAYSASKAAVVGMTLPIARDLS 181
           ++RL+A  +   E N DG+RGVI+NTASVAAFDGQIGQAAY+ASK A+  +TLP AR+L+
Sbjct: 121 LLRLAAAAIAETEANADGERGVIINTASVAAFDGQIGQAAYAASKGAIASLTLPAARELA 180

Query: 182 TQGIRICTIAPGLFNTPMLAALPEKVRTFLAKSIPFPQRLGEPSEYAHLVQAIYENPLLN 241
             GIR+ TIAPG+F TPM+A + E+VR  LA  +PFP RLG+P+EYA LV+ I EN +LN
Sbjct: 181 RFGIRVMTIAPGIFETPMMAGMTEQVRESLAAGVPFPPRLGKPAEYAALVRHIIENSMLN 240

Query: 242 GEVIRIDGALRM 253
           GEVIR+DGALRM
Sbjct: 241 GEVIRLDGALRM 252


Lambda     K      H
   0.317    0.133    0.369 

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: 215
Number of extensions: 8
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: 255
Length of database: 255
Length adjustment: 24
Effective length of query: 231
Effective length of database: 231
Effective search space:    53361
Effective search space used:    53361
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 17 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