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
Q99ME6 UniProt NPD GO	AT1B4_MOUSE	X/potassium-transporting ATPase subunit beta-m (X,K-ATPase beta-m subunit)	0.28	-	mit	1	Membrane; single-pass type II membrane protein (Potential)	nucleus [IDA]			356
Q9CR11 UniProt NPD GO	YETS4_MOUSE	YEATS domain-containing protein 4	0.28	-	cyt	0	Nucleus (By similarity)	nucleoplasm [IDA]			227
P08031 UniProt NPD GO	ZEB2_MAIZE	Zein-beta precursor (Zein-2) (16 kDa) (Zein ZC1)	0.28	-	nuc	0	Protein body. Endosperm protein bodies				183
Q6NNI8 UniProt NPD GO	ZF2N1_ARATH	Zinc finger A20 and AN1 domains-containing protein At1g12440	0.28	-	nuc	0				1WFP	168
Q15649 UniProt NPD GO	ZNHI3_HUMAN	Zinc finger HIT domain-containing protein 3 (Thyroid receptor-interacting protein 3) (TRIP-3) (Thyro ...	0.28	-	nuc	0		intracellular [NAS]	604500		155
Q8NB15 UniProt NPD GO	ZN511_HUMAN	Zinc finger protein 511	0.28	-	nuc	0	Nucleus (Potential)				262
P51505 UniProt NPD GO	ZNF80_MACMU	Zinc finger protein 80	0.28	-	nuc	0	Nucleus (Probable)				293
P51504 UniProt NPD GO	ZNF80_HUMAN	Zinc finger protein 80 (ZNFPT17)	0.28	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	194553		273
Q9SK53 UniProt NPD GO	COL3_ARATH	Zinc finger protein CONSTANS-LIKE 3	0.28	-	mit	0	Nucleus (Potential)				294
Q93542 UniProt NPD GO	NAS24_CAEEL	Zinc metalloproteinase nas-24 precursor (EC 3.4.24.21) (Nematode astacin 24)	0.28	-	mit	0	Secreted protein (Potential)				396
Q00193 UniProt NPD GO	ZP4_RABIT	Zona pellucida sperm-binding protein 4 precursor (Zona pellucida sperm-binding protein B) (Zona pell ...	0.28	-	end	2 *	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				540
Q8BFP9 UniProt NPD GO	PDK1_MOUSE	[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (EC 2.7.11.2) (Pyruva ...	0.28	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			434
Q16654 UniProt NPD GO	PDK4_HUMAN	[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 4, mitochondrial precursor (EC 2.7.11.2) (Pyruva ...	0.28	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]	602527		411
P05207 UniProt NPD GO	KAP2_PIG	cAMP-dependent protein kinase type II-alpha regulatory subunit (Fragment)	0.28	-	nuc	0					155
Q9Y606 UniProt NPD GO	TRUA_HUMAN	tRNA pseudouridine synthase A (EC 5.4.99.12) (tRNA-uridine isomerase I) (tRNA pseudouridylate syntha ...	0.28	-	nuc	0	Nucleus (By similarity)	nucleus [NAS]	608109		399
Q07262 UniProt NPD GO	1A1C_TOBAC	1-aminocyclopropane-1-carboxylate synthase (EC 4.4.1.14) (ACC synthase) (S-adenosyl-L-methionine met ...	0.27	-	cyt	0					491
Q9S9U6 UniProt NPD GO	1A111_ARATH	1-aminocyclopropane-1-carboxylate synthase 11 (EC 4.4.1.14) (ACC synthase 11) (S-adenosyl-L-methioni ...	0.27	-	cyt	0					460
P48347 UniProt NPD GO	14310_ARATH	14-3-3-like protein GF14 epsilon (General regulatory factor 10)	0.27	-	nuc	0					254
P49106 UniProt NPD GO	14331_MAIZE	14-3-3-like protein GF14-6	0.27	-	cyt	0					261
Q6EUP4 UniProt NPD GO	14335_ORYSA	14-3-3-like protein GF14-E (G-box factor 14-3-3 homolog E)	0.27	-	nuc	0	Cytoplasm. Nucleus				262
P32478 UniProt NPD GO	HS150_YEAST	150 kDa heat shock glycoprotein precursor (Covalently-linked cell wall protein 7) (Protein with inte ...	0.27	-	exc	0	Cell wall. Covalently attached to the cell wall	cell wall (sensu Fungi) [IDA]			413
Q6B8L5 UniProt NPD GO	GPMI_GRATL	2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.1) (Phosphoglyceromutase) (BPG ...	0.27	-	nuc	0	Plastid; chloroplast				510
P17980 UniProt NPD GO	PRS6A_HUMAN	26S protease regulatory subunit 6A (TAT-binding protein 1) (TBP-1) (Proteasome subunit P50)	0.27	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)	nucleus [TAS] proteasome complex (sensu Eukaryota) [TAS]	186852		439
P33297 UniProt NPD GO	PRS6A_YEAST	26S protease regulatory subunit 6A (TAT-binding protein homolog 1) (TBP-1)	0.27	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)	proteasome regulatory particle, base subcom... [IDA]			433
Q9NVS2 UniProt NPD GO	RT18A_HUMAN	28S ribosomal protein S18a, mitochondrial precursor (MRP-S18-a) (Mrps18a) (MRP-S18-3)	0.27	-	nuc	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]			196
P48022 UniProt NPD GO	HMDH2_LYCES	3-hydroxy-3-methylglutaryl-coenzyme A reductase 2 (EC 1.1.1.34) (HMG-CoA reductase 2)	0.27	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				602
P55811 UniProt NPD GO	LEU2_RHINI	3-isopropylmalate dehydratase (EC 4.2.1.33) (Isopropylmalate isomerase) (Alpha-IPM isomerase) (IPMI) ...	0.27	-	cyt	0					750
O00093 UniProt NPD GO	PHYB_EMENI	3-phytase B precursor (EC 3.1.3.8) (Myo-inositol-hexaphosphate 3-phosphohydrolase B) (3 phytase B) ( ...	0.27	-	exc	0					463
P19752 UniProt NPD GO	HSP30_NEUCR	30 kDa heat shock protein	0.27	-	nuc	0	Cytoplasm. Associated with mitochondria at heat shock temperature, soluble at normal growth temperat ...				228
P47909 UniProt NPD GO	RR31_ORYSA	30S ribosomal protein S31, mitochondrial precursor	0.27	-	mit	0	Plastid; chloroplast				82
P41965 UniProt NPD GO	DEF4_LEIQH	4 kDa defensin (Antibacterial 4 kDa peptide)	0.27	-	mit	0	Secreted protein				38
P17704 UniProt NPD GO	RS17_DROME	40S ribosomal protein S17	0.27	-	mit	0					130
Q8IT98 UniProt NPD GO	RS18_AEQIR	40S ribosomal protein S18	0.27	-	nuc	0	Cytoplasm				152
P35271 UniProt NPD GO	RS18_YEAST	40S ribosomal protein S18	0.27	-	cyt	0	Cytoplasm	cytosolic small ribosomal subunit (sensu Eu... [TAS] mitochondrion [IDA]		1K5X	145
P38701 UniProt NPD GO	RS20_YEAST	40S ribosomal protein S20	0.27	-	nuc	0	Cytoplasm	cytosolic small ribosomal subunit (sensu Eu... [TAS]		1K5X	120
P41959 UniProt NPD GO	RS26_BRUPA	40S ribosomal protein S26 (Fragment)	0.27	-	nuc	0					83
P55833 UniProt NPD GO	RS27_HOMAM	40S ribosomal protein S27	0.27	-	nuc	0					83
Q8WQI3 UniProt NPD GO	RS29_SPOFR	40S ribosomal protein S29	0.27	-	mit	0					56
P08195 UniProt NPD GO	4F2_HUMAN	4F2 cell-surface antigen heavy chain (4F2hc) (Lymphocyte activation antigen 4F2 large subunit) (4F2 ...	0.27	-	nuc	1	Membrane; single-pass type II membrane protein	cell surface [IEP] integral to membrane [NAS]	158070		529
Q6BX71 UniProt NPD GO	HEM1_DEBHA	5-aminolevulinate synthase, mitochondrial precursor (EC 2.3.1.37) (5-aminolevulinic acid synthase) ( ...	0.27	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				575
P08237 UniProt NPD GO	K6PF_HUMAN	6-phosphofructokinase, muscle type (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) (Phosph ...	0.27	-	cyt	0		6-phosphofructokinase complex [IDA]	232800		779
Q963B6 UniProt NPD GO	RL10A_SPOFR	60S ribosomal protein L10a	0.27	+	nuc	0					217
P38061 UniProt NPD GO	RL32_YEAST	60S ribosomal protein L32	0.27	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	130
P46291 UniProt NPD GO	RL38_LYCES	60S ribosomal protein L38	0.27	-	nuc	0					69
O15594 UniProt NPD GO	RL4_ENTHI	60S ribosomal protein L4 (L1) (Fragments)	0.27	-	nuc	1					245
Q9V3G1 UniProt NPD GO	RL8_DROME	60S ribosomal protein L8	0.27	-	mit	0	Cytoplasm				256
Q6RYS3 UniProt NPD GO	RL8_MAMBR	60S ribosomal protein L8	0.27	-	mit	0	Cytoplasm				257
Q95V39 UniProt NPD GO	RL8_SPOFR	60S ribosomal protein L8	0.27	-	mit	0	Cytoplasm				257
Q07502 UniProt NPD GO	SRP_SOYBN	8.4 kDa sulfur-rich protein precursor (SE60 protein) (Probable proteinase inhibitor P322)	0.27	-	exc	1 *					74
P32357 UniProt NPD GO	AAR2_YEAST	A1 cistron-splicing factor AAR2	0.27	-	cyt	0	Cytoplasm. Nucleus. This protein lacks a nuclear localization signal, it may interact in the cytopla ...	snRNP U5 [IDA]			355

You are viewing entries 42851 to 42900 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.