YRC Public Data Repository - Protein Structure Prediction

Protein:	XERD_LISMO
Organism:	Listeria monocytogenes
Length:	297 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for XERD_LISMO.

Description	E-value	Query Range	Subject Range
gi\|153167810, gi... - gi\|153167810\|ref\|ZP_01927895.1\| tyrosine recombinase XerD [Listeria monocytogenes FSL N1-017], gi\|13... gi\|254992940 - gi\|254992940\|ref\|ZP_05275130.1\| integrase/recombinase [Listeria monocytogenes FSL J2-064] gi\|153202948, gi... - gi\|254931873\|ref\|ZP_05265232.1\| integrase/recombinase [Listeria monocytogenes HPB2262], gi\|153202948... gi\|254877926 - gi\|254877926\|ref\|ZP_05250636.1\| integrase/recombinase [Listeria monocytogenes FSL J2-071] gi\|255520096 - gi\|255520096\|ref\|ZP_05387333.1\| integrase/recombinase [Listeria monocytogenes FSL J1-175] XERD_LISMF - Tyrosine recombinase XerD OS=Listeria monocytogenes serotype 4b (strain F2365) GN=xerD PE=3 SV=1 gi\|47093384, gi\|... - gi\|47093384\|ref\|ZP_00231151.1\| integrase/recombinase XerD [Listeria monocytogenes str. 4b H7858], gi... gi\|226224560, gi... - gi\|226224560\|ref\|YP_002758667.1\| integrase/recombinase [Listeria monocytogenes Clip81459], gi\|225877... gi\|254852857 - gi\|254852857\|ref\|ZP_05242205.1\| integrase/recombinase [Listeria monocytogenes FSL R2-503] gi\|254825549 - gi\|254825549\|ref\|ZP_05230550.1\| integrase/recombinase [Listeria monocytogenes FSL J1-194]	254.0	[0..1]	[297..1]
XERD_LISIN - Tyrosine recombinase xerD OS=Listeria innocua GN=xerD PE=3 SV=1 XERD_LISIN - Tyrosine recombinase XerD OS=Listeria innocua serovar 6a (strain CLIP 11262) GN=xerD PE=3 SV=1	251.0	[0..1]	[297..1]
XERC_OCEIH - Tyrosine recombinase XerC OS=Oceanobacillus iheyensis (strain DSM 14371 / JCM 11309 / KCTC 3954 / HT... XERC_OCEIH - Tyrosine recombinase xerC OS=Oceanobacillus iheyensis GN=xerC PE=3 SV=1	247.0	[0..1]	[297..4]
gi\|89086178, gi\|... - gi\|89099048\|ref\|ZP_01171927.1\| tyrosine recombinase [Bacillus sp. NRRL B-14911], gi\|89086178\|gb\|EAR6...	243.0	[0..1]	[297..1]
gi\|77545197, gi\|... - gi\|77919114\|ref\|YP_356929.1\| site-specific recombinase [Pelobacter carbinolicus DSM 2380], gi\|775451...	242.0	[0..1]	[296..1]
gi\|98662087 - gi\|98662087\|dbj\|GAA00976.1\| unnamed protein product [Pelotomaculum thermopropionicum SI]	242.0	[0..1]	[297..47]
gi\|74488552, gi\|... - gi\|75763959\|ref\|ZP_00743586.1\| Integrase/recombinase (XerD/RipX family) [Bacillus thuringiensis sero...	242.0	[0..1]	[297..6]
gi\|89152781, gi\|... - gi\|89209284\|ref\|ZP_01187725.1\| Tyrosine recombinase XerC [Bacillus weihenstephanensis KBAB4], gi\|891... gi\|229134638, gi... - gi\|229134638\|ref\|ZP_04263448.1\| Tyrosine recombinase xerC [Bacillus cereus BDRD-ST196], gi\|228648899... gi\|228748268, gi... - gi\|229013014\|ref\|ZP_04170179.1\| Tyrosine recombinase xerC [Bacillus mycoides DSM 2048], gi\|228748268... gi\|228614976, gi... - gi\|229168570\|ref\|ZP_04296293.1\| Tyrosine recombinase xerC [Bacillus cereus AH621], gi\|228614976\|gb\|E...	241.0	[0..1]	[297..5]
XERD_STAEP - (Q7ZAJ2) Tyrosine recombinase xerD gi\|251805594, gi... - gi\|251810914\|ref\|ZP_04825387.1\| integrase/recombinase XerD [Staphylococcus epidermidis BCM-HMP0060],... XERD_STAES - Tyrosine recombinase XerD OS=Staphylococcus epidermidis (strain ATCC 12228) GN=xerD PE=3 SV=1	240.0	[0..1]	[297..1]
XERD_STAHJ - Tyrosine recombinase XerD OS=Staphylococcus haemolyticus (strain JCSC1435) GN=xerD PE=3 SV=1	240.0	[0..1]	[297..1]

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Predicted Domain #1

Region A:
Residues: [1-297]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNDLIEDFLH FLIVERGLSA NTIKAYERDL HYFVSYMDVT KELTDPNTLE RSDIVGFMAF  60
   61 ARQEGKSPRS VARYIASLRS FFHYLMHDGK MSHDPMIQIE TPKQAQGLPK VLNLDDVEKL 120
  121 LSSSDTSTPL GLRDQAMMEI LYATGLRVTE LVSLKMDDLH LHMGFIQTIG KGDKERIIPL 180
  181 GKTATTVLEK YLEEARPKLR RPKYRNDFVF LNHHGQGLTR QGFWKILKGI AKESGIEKPI 240
  241 TPHTLRHSFA THLLENGADL RSVQELLGHA DISTTQIYTH VTKLRLKDVY KQFHPRA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	53.154902
Match:	1a0pA
Description:	SITE-SPECIFIC RECOMBINASE, XERD
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
site-specific recombinase activity	4.99325011803106	bayes_pls_golite062009
integrase activity	3.60695091575172	bayes_pls_golite062009
catalytic activity	2.22520758916604	bayes_pls_golite062009
structure-specific DNA binding	0.11292854906722	bayes_pls_golite062009
DNA binding	0.10970863758177	bayes_pls_golite062009
nucleic acid binding	0.06580979261817	bayes_pls_golite062009

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions: