NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
P06407 UniProt NPD GO	PSAB_TOBAC	Photosystem I P700 chlorophyll a apoprotein A2 (PsaB) (PSI-B)	0.03	-	end	11 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				734
Q8M9X4 UniProt NPD GO	YCF4_CHAGL	Photosystem I assembly protein ycf4	0.03	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				184
P49179 UniProt NPD GO	YCF4_SOYBN	Photosystem I assembly protein ycf4	0.03	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				203
O96804 UniProt NPD GO	PSAC_SKECO	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.03	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
Q9TLR2 UniProt NPD GO	PSAD_CYACA	Photosystem I reaction center subunit II (Photosystem I 16 kDa polypeptide) (PSI-D)	0.03	-	cyt	0	Plastid; chloroplast				140
P49482 UniProt NPD GO	PSAE_ODOSI	Photosystem I reaction center subunit IV (PSI-E)	0.03	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				71
Q41229 UniProt NPD GO	PSAEB_NICSY	Photosystem I reaction center subunit IV B, chloroplast precursor (PSI-E B) [Contains: Photosystem I ...	0.03	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				143
P49486 UniProt NPD GO	PSAL_ODOSI	Photosystem I reaction center subunit XI (PSI-L) (PSI subunit V)	0.03	-	end	3 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				150
P31590 UniProt NPD GO	PSAM_MARPO	Photosystem I reaction center subunit XII (PSI-M)	0.03	-	nuc	1 *	Plastid; chloroplast				32
P31567 UniProt NPD GO	PSAK_GALSU	Photosystem I reaction center subunit psaK (Photosystem I subunit X) (PSI-K)	0.03	-	nuc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				69
O78444 UniProt NPD GO	PSAK_GUITH	Photosystem I reaction center subunit psaK (Photosystem I subunit X) (PSI-K)	0.03	-	nuc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				87
Q9XF91 UniProt NPD GO	PSBS_ARATH	Photosystem II 22 kDa protein, chloroplast precursor (CP22)	0.03	-	end	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				265
Q9FPP4 UniProt NPD GO	PSBS_SOLSG	Photosystem II 22 kDa protein, chloroplast precursor (CP22)	0.03	-	end	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				276
Q02060 UniProt NPD GO	PSBS_SPIOL	Photosystem II 22 kDa protein, chloroplast precursor (CP22)	0.03	-	end	0	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Extreme lateral l ...				274
Q85AU0 UniProt NPD GO	PSBC_ANTFO	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.03	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
P06414 UniProt NPD GO	PSBC_MARPO	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.03	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
Q9XPS4 UniProt NPD GO	PSBC_WHEAT	Photosystem II 44 kDa reaction center protein (P6 protein) (CP43)	0.03	-	end	7 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				473
P48103 UniProt NPD GO	PSBB_CYAPA	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.03	-	end	5 *	Plastid; cyanelle; cyanelle thylakoid membrane; multi-pass membrane protein (By similarity)				509
P41624 UniProt NPD GO	PSBB_PINTH	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.03	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
O78433 UniProt NPD GO	PSBY_GUITH	Photosystem II protein Y	0.03	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				37
O19925 UniProt NPD GO	PSBH_CYACA	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.03	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				67
Q9BBQ7 UniProt NPD GO	PSBH_LOTJA	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.03	-	gol	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				72
Q9XQR3 UniProt NPD GO	PSBH_PEA	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.03	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				72
O19882 UniProt NPD GO	PSBI_CYACA	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.03	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P56326 UniProt NPD GO	PSBN_CHLVU	Photosystem II reaction center N protein	0.03	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (Probable)				44
Q9TLZ2 UniProt NPD GO	PSBW_CYACA	Photosystem II reaction center W protein	0.03	-	cyt	0	Plastid; chloroplast				115
Q9AW48 UniProt NPD GO	P2SAF_GUITH	Photosystem II stability/assembly factor HCF136, chloroplast precursor	0.03	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				395
P80093 UniProt NPD GO	CRTI_CAPAN	Phytoene dehydrogenase, chloroplast precursor (EC 1.14.99.-) (Phytoene desaturase)	0.03	-	cyt	0	Plastid; chloroplast. Plastid; chromoplast				582
Q9AR88 UniProt NPD GO	PSK4_ORYSA	Phytosulfokines 4 precursor [Contains: Phytosulfokine-alpha (PSK-alpha) (Phytosulfokine-a); Phytosul ...	0.03	-	gol	1 *	Secreted protein (By similarity)				83
P91963 UniProt NPD GO	PDH1_PENVA	Pigment-dispersing hormone type 1 precursor [Contains: PDH precursor-related peptide (PPRD); Pigment ...	0.03	-	exc	1 *	Secreted protein (By similarity)				79
Q26464 UniProt NPD GO	MYR2_MYRPI	Pilosulin-2 precursor (Allergen Myr p 2) (Myr p II)	0.03	-	exc	1 *	Secreted protein				75
P51476 UniProt NPD GO	OPSP_COLLI	Pinopsin (Pineal opsin) (P-opsin) (Pineal gland-specific opsin)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				349
P0C006 UniProt NPD GO	PISC3_MORCS	Piscidin-3	0.03	-	mit	0	Secreted protein				22
Q9Y547 UniProt NPD GO	PP25_HUMAN	Placental protein 25 (PP25)	0.03	-	cyt	0				1XPW	144
Q99KR8 UniProt NPD GO	FUCO2_MOUSE	Plasma alpha-L-fucosidase precursor (EC 3.2.1.51) (Alpha-L-fucosidase 2) (Alpha-L-fucoside fucohydro ...	0.03	-	end	0	Secreted protein (Probable)				461
P24774 UniProt NPD GO	RETB1_ONCMY	Plasma retinol-binding protein I (PRBP-I)	0.03	-	cyt	0					176
P24775 UniProt NPD GO	RETB2_ONCMY	Plasma retinol-binding protein II (PRBP-II)	0.03	-	cyt	0					176
Q61233 UniProt NPD GO	PLSL_MOUSE	Plastin-2 (L-plastin) (Lymphocyte cytosolic protein 1) (LCP-1) (65 kDa macrophage protein) (pp65)	0.03	-	cyt	0	Cytoplasm	actin filament [IDA] cytoplasm [IDA] phagocytic cup [IDA] ruffle [IDA]			626
P13796 UniProt NPD GO	PLSL_HUMAN	Plastin-2 (L-plastin) (Lymphocyte cytosolic protein 1) (LCP-1) (LC64P)	0.03	-	cyt	0	Cytoplasm	cytoplasm [NAS] cytosol [IDA]	153430		626
P08248 UniProt NPD GO	PLAS_HORVU	Plastocyanin, chloroplast precursor	0.03	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				155
P06765 UniProt NPD GO	PLF4_RAT	Platelet factor 4 precursor (PF-4) (CXCL4)	0.03	-	nuc	0	Secreted protein	extracellular region [ISS]			105
P26201 UniProt NPD GO	CD36_BOVIN	Platelet glycoprotein 4 (Platelet glycoprotein IV) (GPIV) (GPIIIB) (CD36 antigen) (PAS IV) (PAS-4 pr ...	0.03	-	end	2 *	Membrane; multi-pass membrane protein				471
Q8VDG7 UniProt NPD GO	PAFA2_MOUSE	Platelet-activating factor acetylhydrolase 2, cytoplasmic (EC 3.1.1.47) (Serine-dependent phospholip ...	0.03	-	cyt	0	Cytoplasm (By similarity)				390
Q9GL51 UniProt NPD GO	LIS1_PIG	Platelet-activating factor acetylhydrolase IB alpha subunit (PAF acetylhydrolase 45 kDa subunit) (PA ...	0.03	-	cyt	0	Cytoplasm (By similarity). Centrosome (By similarity). Localizes to the plus end of microtubules and ...				409
Q5REG7 UniProt NPD GO	LIS1_PONPY	Platelet-activating factor acetylhydrolase IB alpha subunit (PAF acetylhydrolase 45 kDa subunit) (PA ...	0.03	-	cyt	0	Cytoplasm (By similarity). Centrosome (By similarity). Localizes to the plus end of microtubules and ...				409
P63004 UniProt NPD GO	LIS1_RAT	Platelet-activating factor acetylhydrolase IB alpha subunit (PAF acetylhydrolase 45 kDa subunit) (PA ...	0.03	-	cyt	0	Localizes to the plus end of microtubules and to the centrosome. May localize to the nuclear membran ...				409
P43033 UniProt NPD GO	LIS1_BOVIN	Platelet-activating factor acetylhydrolase IB subunit alpha (PAF acetylhydrolase 45 kDa subunit) (PA ...	0.03	-	cyt	0	Localizes to the plus end of microtubules and to the centrosome. Redistributes to axons during neuro ...				409
P43034 UniProt NPD GO	LIS1_HUMAN	Platelet-activating factor acetylhydrolase IB subunit alpha (PAF acetylhydrolase 45 kDa subunit) (PA ...	0.03	-	cyt	0	Redistributes to axons during neuronal development. Also localizes to the microtubules of the manche ...	astral microtubule [IDA] cell cortex [IDA] kinetochore [IDA] microtubule associated complex [IDA] nuclear envelope [IDA]	607432		409
Q8HXX0 UniProt NPD GO	LIS1_MACFA	Platelet-activating factor acetylhydrolase IB subunit alpha (PAF acetylhydrolase 45 kDa subunit) (PA ...	0.03	-	cyt	0	Cytoplasm (By similarity). Centrosome (By similarity). Localizes to the plus end of microtubules and ...				409
P63005 UniProt NPD GO	LIS1_MOUSE	Platelet-activating factor acetylhydrolase IB subunit alpha (PAF acetylhydrolase 45 kDa subunit) (PA ...	0.03	-	cyt	0	Nucleus; nuclear membrane (By similarity). May localize to the nuclear membrane (By similarity). Cyt ...	centrosome [IDA] cytoplasm [IDA] microtubule associated complex [IDA]		1VYH	409

You are viewing entries 81101 to 81150 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.