GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligK in Pseudomonas fluorescens FW300-N2E3

Align Putative 4-hydroxy-4-methyl-2-oxoglutarate aldolase; HMG aldolase; EC 4.1.3.17; Oxaloacetate decarboxylase; OAA decarboxylase; EC 4.1.1.112; Regulator of ribonuclease activity homolog; RraA-like protein (uncharacterized)
to candidate AO353_00850 AO353_00850 ribonuclease activity regulator protein RraA

Query= curated2:Q9S4U0
         (163 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_00850
          Length = 163

 Score =  304 bits (779), Expect = 4e-88
 Identities = 144/163 (88%), Positives = 154/163 (94%)

Query: 1   MIHYVTPDLCDAYPELVQVVEPMFSNFGGRDSFGGEIVTIKCFEDNSLVKEQADQPGAGK 60
           M HY+TPDLCDAYPELVQV+EPMFSNFGGRDSFGGEIVTIKCFEDNSLVKEQ +  G GK
Sbjct: 1   MNHYLTPDLCDAYPELVQVLEPMFSNFGGRDSFGGEIVTIKCFEDNSLVKEQVEHKGNGK 60

Query: 61  VLVVDGGGSLRRALLGDMIAEKAAKNGWEGLVIYGCVRDVDVLAQTDLGVQALAPHPMKT 120
           VLVVDGGGSLRRALLGDMIAEKA KNGWEGLVIYGC+RDVDV+AQTDLGVQALA HPMKT
Sbjct: 61  VLVVDGGGSLRRALLGDMIAEKAVKNGWEGLVIYGCIRDVDVIAQTDLGVQALASHPMKT 120

Query: 121 DKRGIGDLNVVVTFASVTFRPGEYVYADNNGVIVSPSPLKMPE 163
           D+RG+G+LN+ VTFA VTFRPGEY+YADNNGVIVSPSPLKMPE
Sbjct: 121 DRRGVGELNIAVTFAGVTFRPGEYIYADNNGVIVSPSPLKMPE 163


Lambda     K      H
   0.319    0.140    0.418 

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: 197
Number of extensions: 1
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: 163
Length of database: 163
Length adjustment: 18
Effective length of query: 145
Effective length of database: 145
Effective search space:    21025
Effective search space used:    21025
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 43 (21.2 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