YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24348362, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	369 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 gi|24348362, gi|....

Description	E-value	Query Range	Subject Range
gi\|194683350, gi... - gi\|197285863\|ref\|YP_002151735.1\| tyrosine recombinase [Proteus mirabilis HI4320], gi\|194683350\|emb\|C... gi\|227163474, gi... - gi\|227356364\|ref\|ZP_03840752.1\| tyrosine recombinase [Proteus mirabilis ATCC 29906], gi\|227163474\|gb... XERD_PROMI - Tyrosine recombinase XerD OS=Proteus mirabilis GN=xerD PE=1 SV=1	194.0	[0..34]	[369..9]
gi\|116095121, gi... - gi\|116629539\|ref\|YP_814711.1\| integrase [Lactobacillus gasseri ATCC 33323], gi\|116095121\|gb\|ABJ60273... gi\|238834835, gi... - gi\|238852689\|ref\|ZP_04643099.1\| tyrosine recombinase XerD [Lactobacillus gasseri 202-4], gi\|23883483...	194.0	[0..40]	[368..3]
gi\|254912513, gi... - gi\|254912513\|ref\|ZP_05262525.1\| hypothetical protein LmonJ2_06931 [Listeria monocytogenes J2818], gi... gi\|133729635, gi... - gi\|254827160\|ref\|ZP_05231847.1\| hypothetical protein LmonocytogeFSL_01770 [Listeria monocytogenes FS... XERD_LISMO - Tyrosine recombinase xerD OS=Listeria monocytogenes GN=xerD PE=3 SV=1 gi\|254936840 - gi\|254936840\|ref\|ZP_05268537.1\| hypothetical protein LmonF6_06921 [Listeria monocytogenes F6900] gi\|47097098, gi\|... - gi\|47097098\|ref\|ZP_00234668.1\| integrase/recombinase XerD [Listeria monocytogenes str. 1/2a F6854], ... gi\|255028942 - gi\|255028942\|ref\|ZP_05300893.1\| hypothetical protein LmonL_06711 [Listeria monocytogenes LO28] XERD_LISMO - Tyrosine recombinase XerD OS=Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) GN=xe... gi\|224498595 - gi\|224498595\|ref\|ZP_03666944.1\| hypothetical protein LmonF1_02414 [Listeria monocytogenes Finland 19... gi\|224501245 - gi\|224501245\|ref\|ZP_03669552.1\| hypothetical protein LmonFR_01770 [Listeria monocytogenes FSL R2-561... gi\|254899348, gi... - gi\|254899348\|ref\|ZP_05259272.1\| hypothetical protein LmonJ_06029 [Listeria monocytogenes J0161], gi\|...	193.0	[0..47]	[367..4]
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]	193.0	[0..47]	[367..4]
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	192.0	[0..47]	[367..4]
gi\|41583295, gi\|... - gi\|42519008\|ref\|NP_964938.1\| integrase/recombinase XerD [Lactobacillus johnsonii NCC 533], gi\|415832...	192.0	[0..48]	[368..5]
gi\|116097246, gi... - gi\|116618399\|ref\|YP_818770.1\| tyrosine recombinase XerD subunit [Leuconostoc mesenteroides subsp. me...	192.0	[0..42]	[367..2]
XERC_BACHD - Tyrosine recombinase XerC OS=Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM ... XERC_BACHD - Tyrosine recombinase xerC OS=Bacillus halodurans GN=xerC PE=3 SV=1	191.0	[0..50]	[369..11]

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Predicted Domain #1

Region A:
Residues: [1-369]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSKSIQIYTA DDSHSHQAVG ISANLTKPFT QGDKTFFEES SLPQSVHADF YNAASETEYE  60
   61 ISNNTRRVYR ISFSFFEQYC LEHNLQSLPA DPRSIISFIG HQKELLQAST GMQLSKQTLT 120
  121 TRIAAIRFYH IQAGFPTPTE HPQVIRVMRG LSRNHHRLVQ DYDQQPIMYD EVELLIQAVD 180
  181 QQPHPLLRLR DKAIIQLGLQ GGFRRSELAN LKVHYLSFMR DKLKVRLPFS KSNQQGLREW 240
  241 KSLPDSEPFA AYHAVKSWLN ESQITDGHLF RSISRDGKTL RPYHVNDNSK PKSTFSRNSG 300
  301 FLNGDDIYRI IKQYCLKAGL PAQYYGAHSL RSGCVTQLHE NNKDILYIMA RTGHTDPRSL 360
  361 RHYLKPKED

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	45.154902
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: