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
Q9STT8 UniProt NPD GO	ATH3_ARATH	Putative ABC2 homolog 3	0.17	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				895
Q7SGY1 UniProt NPD GO	ALO_NEUCR	Putative D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) (ALO) (L-galactono-gamma-lactone oxidase)	0.17	-	nuc	0	Mitochondrion; mitochondrial membrane (By similarity). Membrane-embedded (By similarity)				556
Q84L30 UniProt NPD GO	RD23D_ARATH	Putative DNA repair protein RAD23-4 (RAD23-like protein 4) (AtRAD23-4)	0.17	-	cyt	0	Nucleus (Probable)				378
Q8T4E1 UniProt NPD GO	GPI8_DROME	Putative GPI-anchor transamidase precursor (EC 3.-.-.-) (GPI transamidase)	0.17	-	exc	0		GPI-anchor transamidase complex [ISS]			355
Q8VZT0 UniProt NPD GO	NLAL1_ARATH	Putative H/ACA ribonucleoprotein complex subunit 1-like protein 1	0.17	+	mit	0	Nucleus; nucleolus (By similarity)	thylakoid membrane (sensu Viridiplantae) [IDA]			202
Q9M9L7 UniProt NPD GO	LONH4_ARATH	Putative Lon protease homolog 4, mitochondrial precursor (EC 3.4.21.-)	0.17	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				942
Q9SUU1 UniProt NPD GO	BORL4_ARATH	Putative boron transporter-like protein 4	0.17	+	end	12 *	Membrane; multi-pass membrane protein (By similarity)				710
Q9M2L4 UniProt NPD GO	ACA11_ARATH	Putative calcium-transporting ATPase 11, plasma membrane-type (EC 3.6.3.8) (Ca(2+)-ATPase isoform 11 ...	0.17	-	end	10	Membrane; multi-pass membrane protein				1025
Q18932 UniProt NPD GO	CAH2_CAEEL	Putative carbonic anhydrase-like protein 2 precursor	0.17	-	nuc	0	Secreted protein (Potential)				337
Q07505 UniProt NPD GO	DLHH_YEAST	Putative carboxymethylenebutenolidase (EC 3.1.1.45) (Dienelactone hydrolase) (DLH)	0.17	-	cyt	0		cytoplasm [IDA] mitochondrion [IDA]			273
Q9FKQ2 UniProt NPD GO	CAP18_ARATH	Putative clathrin assembly protein At5g65370	0.17	-	mit	0					295
Q9U6Z8 UniProt NPD GO	CX52_CONGL	Putative conotoxin Gm5.2 precursor	0.17	-	exc	0	Secreted protein				62
O64790 UniProt NPD GO	DRL17_ARATH	Putative disease resistance protein At1g61300	0.17	-	cyt	0					766
P46238 UniProt NPD GO	GUXC_FUSOX	Putative exoglucanase type C precursor (EC 3.2.1.91) (Exocellobiohydrolase I) (1,4-beta-cellobiohydr ...	0.17	-	exc	0					514
Q17533 UniProt NPD GO	EXOS4_CAEEL	Putative exosome complex exonuclease RRP41 (EC 3.1.13.-) (Ribosomal RNA-processing protein 41)	0.17	-	nuc	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)				240
Q9VSH2 UniProt NPD GO	GR66A_DROME	Putative gustatory receptor 66a	0.17	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			530
Q9VD76 UniProt NPD GO	GR93A_DROME	Putative gustatory receptor 93a	0.17	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			419
Q09834 UniProt NPD GO	YAD8_SCHPO	Putative mitochondrial carrier C4G8.08	0.17	-	nuc	4 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				271
Q9SU40 UniProt NPD GO	SKU5_ARATH	Putative monocopper oxidase precursor (Skewed roots)	0.17	-	exc	0	Cell wall; lipid-anchor; GPI-anchor. Partially soluble and located in the cell wall	anchored to membrane [TAS]			587
O45870 UniProt NPD GO	NSMA_CAEEL	Putative neutral sphingomyelinase (EC 3.1.4.12)	0.17	-	end	2	Membrane; multi-pass membrane protein (Potential)				434
P91148 UniProt NPD GO	NDX7_CAEEL	Putative nudix hydrolase 7 (EC 3.6.1.-)	0.17	-	mit	0					295
P82982 UniProt NPD GO	OR65A_DROME	Putative odorant receptor 65a	0.17	-	end	6	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			417
Q10130 UniProt NPD GO	DHS5_CAEEL	Putative oxidoreductase dhs-5 (EC 1.-.-.-)	0.17	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				378
P34453 UniProt NPD GO	PEX19_CAEEL	Putative peroxisomal biogenesis factor 19 (Peroxin-19)	0.17	-	nuc	0	Peroxisome (Potential)				282
Q8VXB5 UniProt NPD GO	HAK8_ORYSA	Putative potassium transporter 8 (OsHAK8)	0.17	-	end	12 *	Membrane; multi-pass membrane protein (By similarity)				793
P52715 UniProt NPD GO	YUA6_CAEEL	Putative serine carboxypeptidase F13S12.6 precursor (EC 3.4.16.-)	0.17	+	end	1 *					454
Q00710 UniProt NPD GO	STCO_EMENI	Putative sterigmatocystin biosynthesis protein stcO	0.17	-	end	1					297
Q9HDX4 UniProt NPD GO	YKN1_SCHPO	Putative transporter B1A11.01	0.17	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				495
P53838 UniProt NPD GO	YN15_YEAST	Putative transporter YNL275W	0.17	-	end	10	Membrane; multi-pass membrane protein (Potential)	membrane fraction [IDA] plasma membrane [IDA]			576
P25596 UniProt NPD GO	YCH0_YEAST	Putative uncharacterized protein YCL073C	0.17	-	end	12	Membrane; multi-pass membrane protein (Potential)				615
P38729 UniProt NPD GO	YHE2_YEAST	Putative uncharacterized protein YHL042W precursor	0.17	-	mit	1 *					150
Q9NVS9 UniProt NPD GO	PNPO_HUMAN	Pyridoxine-5'-phosphate oxidase (EC 1.4.3.5) (Pyridoxamine-phosphate oxidase)	0.17	-	mit	0			603287	1NRG	261
Q91XF0 UniProt NPD GO	PNPO_MOUSE	Pyridoxine-5'-phosphate oxidase (EC 1.4.3.5) (Pyridoxamine-phosphate oxidase)	0.17	-	cyt	0					261
P37213 UniProt NPD GO	PPDK_ENTHI	Pyruvate, phosphate dikinase (EC 2.7.9.1) (Pyruvate, orthophosphate dikinase)	0.17	-	cyt	0					885
Q01314 UniProt NPD GO	AKT1_BOVIN	RAC-alpha serine/threonine-protein kinase (EC 2.7.11.1) (RAC-PK-alpha) (Protein kinase B) (PKB)	0.17	-	cyt	0	Cytoplasm. Nucleus. Nucleus after activation by integrin-linked protein kinase 1 (ILK1)				480
Q60823 UniProt NPD GO	AKT2_MOUSE	RAC-beta serine/threonine-protein kinase (EC 2.7.11.1) (RAC-PK-beta) (Protein kinase Akt-2) (Protein ...	0.17	-	cyt	0		lamellipodium [IDA]			481
P47197 UniProt NPD GO	AKT2_RAT	RAC-beta serine/threonine-protein kinase (EC 2.7.11.1) (RAC-PK-beta) (Protein kinase Akt-2) (Protein ...	0.17	-	cyt	0					481
P34144 UniProt NPD GO	RAC1A_DICDI	RAS-related protein rac1A	0.17	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				194
Q90972 UniProt NPD GO	RNF13_CHICK	RING finger protein 13 (C-RZF)	0.17	+	nuc	1	Nucleus				381
Q5R7K8 UniProt NPD GO	RN141_PONPY	RING finger protein 141	0.17	-	nuc	0					230
Q8WVD5 UniProt NPD GO	RN141_HUMAN	RING finger protein 141 (Zinc finger protein 230)	0.17	-	nuc	0					230
Q9SG96 UniProt NPD GO	ATL3C_ARATH	RING-H2 finger protein ATL3C	0.17	-	nuc	1 *					181
P32570 UniProt NPD GO	MED22_YEAST	RNA polymerase II mediator complex subunit 22 (Suppressor of RNA polymerase B 6)	0.17	-	cyt	0	Nucleus	mediator complex [IDA]			121
Q9USH1 UniProt NPD GO	MED31_SCHPO	RNA polymerase II mediator complex subunit 31 (Cell separation protein sep10) (Soh1 homolog)	0.17	-	cyt	0	Nucleus (Potential)	mediator complex [IGI]			139
Q64012 UniProt NPD GO	RALY_MOUSE	RNA-binding protein Raly (hnRNP associated with lethal yellow protein) (Maternally expressed hnRNP C ...	0.17	-	nuc	0	Nucleus (Probable)				312
Q9WVB0 UniProt NPD GO	RBPMS_MOUSE	RNA-binding protein with multiple splicing (RBP-MS) (HEart, RRM Expressed Sequence) (Hermes)	0.17	-	nuc	0					197
Q5M782 UniProt NPD GO	RIPB_XENLA	RPA-interacting protein B	0.17	-	cyt	0	Nucleus (By similarity)				220
Q9UBK7 UniProt NPD GO	RBL2A_HUMAN	Rab-like protein 2A	0.17	-	cyt	0			605412		228
Q9SBJ6 UniProt NPD GO	RAC6_ARATH	Rac-like GTP-binding protein ARAC6 (GTPase protein ROP5)	0.17	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Associated with th ...				197
P41391 UniProt NPD GO	RNA1_SCHPO	Ran GTPase-activating protein 1 (Protein rna1)	0.17	-	mit	0	Cytoplasm. Cytoplasm; perinuclear region (Probable). Possibly enriched in the nuclear periphery	cytoplasm [IDA] nuclear membrane [IDA]		2CA6	386

You are viewing entries 54851 to 54900 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.