GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligK in Cupriavidus basilensis 4G11

Align 4-hydroxy-4-methyl-2-oxoglutarate aldolase; HMG aldolase; Oxaloacetate decarboxylase; OAA decarboxylase; Regulator of ribonuclease activity homolog; EC 4.1.3.17; EC 4.1.1.112 (characterized)
to candidate RR42_RS12215 RR42_RS12215 ribonuclease

Query= SwissProt::Q5SIP7
         (164 letters)



>FitnessBrowser__Cup4G11:RR42_RS12215
          Length = 165

 Score =  138 bits (348), Expect = 4e-38
 Identities = 78/158 (49%), Positives = 102/158 (64%), Gaps = 6/158 (3%)

Query: 1   MEARTTDLSDLYPEGEA------LPMVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEE 54
           M   TTDL D      A      L  VF+ FG RA F+G   TL+VFEDN+LVR+ +E  
Sbjct: 1   MSFATTDLCDANEARLADGSLRVLSPVFQHFGKRAAFSGPAATLKVFEDNSLVRETVESP 60

Query: 55  GAGQVLFVDGGGSLRTALLGGNLARLAWEKGWAGVVVHGAVRDTEELREVPIGLLALAAT 114
           G G+VL VDGGGSLR AL+GGNL  LA + GW G++V+G VRD+ EL    IG+ ALA  
Sbjct: 61  GNGRVLVVDGGGSLRCALVGGNLGVLAEKNGWVGILVNGCVRDSGELAVCDIGVRALALH 120

Query: 115 PKKSAKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLL 152
           P+KS K   GE +V +++ G  V PG+++ AD DG+L+
Sbjct: 121 PQKSQKRNVGEREVTVQMPGAVVRPGNWIYADADGVLV 158


Lambda     K      H
   0.317    0.140    0.403 

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: 93
Number of extensions: 4
Number of successful extensions: 1
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: 164
Length of database: 165
Length adjustment: 18
Effective length of query: 146
Effective length of database: 147
Effective search space:    21462
Effective search space used:    21462
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 (21.6 bits)
S2: 43 (21.2 bits)

This GapMind analysis is from Sep 17 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