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
Q5VYX0 UniProt NPD GO	RENAL_HUMAN	Renalase precursor (EC 1.4.-.-)	0.29	-	nuc	0	Secreted protein		609360		342
P40937 UniProt NPD GO	RFC5_HUMAN	Replication factor C subunit 5 (Replication factor C 36 kDa subunit) (RF-C 36 kDa subunit) (RFC36) ( ...	0.29	-	cyt	0	Nucleus (Probable)	DNA replication factor C complex [NAS]	600407	1LFS	340
Q23697 UniProt NPD GO	RFA2_CRIFA	Replication protein A 28 kDa subunit (RP-A) (RF-A) (Replication factor-A protein 2)	0.29	-	cyt	0	Nucleus. Also present in PML nuclear bodies. Redistributes to discrete nuclear foci upon DNA damage ...				258
Q5FW17 UniProt NPD GO	RFA1_XENTR	Replication protein A 70 kDa DNA-binding subunit (RP-A) (RF-A) (Replication factor-A protein 1) (p70 ...	0.29	-	nuc	0	Nucleus (By similarity)				609
Q91ZQ5 UniProt NPD GO	RPE65_MOUSE	Retinal pigment epithelium-specific 65 kDa protein	0.29	+	cyt	0	Cytoplasm (By similarity). Cell membrane; lipid-anchor (By similarity). Attached to the membrane by ...				532
Q28175 UniProt NPD GO	RPE65_BOVIN	Retinal pigment epithelium-specific 65 kDa protein (Membrane receptor p63)	0.29	+	mit	0	Cytoplasm. Cell membrane; lipid-anchor. Attached to the membrane by a lipid anchor when palmitoylate ...				532
Q03277 UniProt NPD GO	PO11_SCICO	Retrovirus-related Pol polyprotein from type-1 retrotransposable element R1 (Retrovirus-related Pol ...	0.29	-	mit	0					1004
O46532 UniProt NPD GO	RNAS6_GORGO	Ribonuclease K6 precursor (EC 3.1.27.-) (RNase K6)	0.29	-	nuc	1 *	Secreted protein				150
O80323 UniProt NPD GO	RNS3_PYRPY	Ribonuclease S-3 precursor (EC 3.1.27.1) (S3-RNase)	0.29	-	exc	1 *				1IQQ	222
P93460 UniProt NPD GO	RNS5_PYRPY	Ribonuclease S-5 precursor (EC 3.1.27.1) (S5-RNase)	0.29	-	exc	1 *					227
P04060 UniProt NPD GO	RNAS1_HYSCR	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.29	-	nuc	0	Secreted protein				128
Q8VD84 UniProt NPD GO	RNS1B_RATTI	Ribonuclease pancreatic beta-type precursor (EC 3.1.27.5) (RNase 1 gamma)	0.29	-	exc	0	Secreted protein (By similarity)				152
Q8SQ11 UniProt NPD GO	RNAS1_HYLLE	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.29	-	nuc	1 *	Secreted protein (By similarity)				156
Q9QYX2 UniProt NPD GO	RNAS1_MUSSA	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.29	-	exc	0	Secreted protein				149
Q8SQ08 UniProt NPD GO	RNAS1_SAISC	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.29	-	nuc	1 *	Secreted protein (By similarity)				156
P32385 UniProt NPD GO	RNP1_YEAST	Ribonucleoprotein 1	0.29	-	nuc	0		cytoplasm [IDA]			249
P42521 UniProt NPD GO	RIR2_DICDI	Ribonucleoside-diphosphate reductase small chain (EC 1.17.4.1) (Ribonucleotide reductase small subun ...	0.29	-	cyt	0					338
Q6CHA2 UniProt NPD GO	RRF1_YARLI	Ribosomal recycling factor, mitochondrial precursor	0.29	-	mit	0	Mitochondrion (By similarity)				264
P25458 UniProt NPD GO	RBS_ANTSP	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) (RuBisCO small subunit)	0.29	-	nuc	0	Plastid; chloroplast				138
Q5KND8 UniProt NPD GO	RUVB2_CRYNE	RuvB-like helicase 2 (EC 3.6.1.-)	0.29	-	cyt	0	Nucleus (By similarity)				463
Q873C7 UniProt NPD GO	RUVB2_NEUCR	RuvB-like helicase 2 (EC 3.6.1.-)	0.29	-	cyt	0	Nucleus (By similarity)				481
Q10585 UniProt NPD GO	SPD1_SCHPO	S-phase delaying protein 1 (Protein p14)	0.29	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			124
Q9JID9 UniProt NPD GO	APS_MOUSE	SH2 and PH domain-containing adapter protein APS (Adapter protein with pleckstrin homology and Src h ...	0.29	-	nuc	0	Cytoplasm (By similarity). Cell membrane (By similarity). Cytoplasmic before PDGF stimulation. After ...	actin filament [IDA] cytoplasm [ISS] plasma membrane [ISS] ruffle [IDA] stress fiber [IDA]		1V5M	621
Q8BZ71 UniProt NPD GO	STAC3_MOUSE	SH3 and cysteine-rich domain-containing protein 3	0.29	-	nuc	0					360
Q06707 UniProt NPD GO	SWC7_YEAST	SWR1-complex protein 7	0.29	-	mit	0	Nucleus	nucleus [IDA] SWR1 complex [IPI]			132
O19116 UniProt NPD GO	SFRP1_BOVIN	Secreted frizzled-related protein 1 precursor (sFRP-1) (Frizzled in aorta protein) (FrzA protein)	0.29	-	exc	0	Secreted protein. Cell membrane or extracellular matrix-associated. Released by heparin-binding				308
Q62178 UniProt NPD GO	SEM4A_MOUSE	Semaphorin-4A precursor (Semaphorin B) (Sema B)	0.29	-	nuc	1	Membrane; single-pass type I membrane protein				760
Q9H3T3 UniProt NPD GO	SEM6B_HUMAN	Semaphorin-6B precursor (Semaphorin Z) (Sema Z)	0.29	+	end	1	Membrane; single-pass type I membrane protein		608873		888
O70141 UniProt NPD GO	SEM6B_RAT	Semaphorin-6B precursor (Semaphorin Z) (Sema Z)	0.29	+	end	1	Membrane; single-pass type I membrane protein				887
P29233 UniProt NPD GO	SENA_APLCA	Sensorin A precursor [Contains: Peptide B; Sensorin A]	0.29	-	mit	1 *	Throughout the neuronal cells (cell body, axon and presynaptic terminals)				113
Q38821 UniProt NPD GO	2ABA_ARATH	Serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform (PP2A, subunit B, ...	0.29	-	nuc	0					513
Q8RW96 UniProt NPD GO	2A5G_ARATH	Serine/threonine protein phosphatase 2A 59 kDa regulatory subunit B' gamma isoform (PP2A, B' subunit ...	0.29	-	mit	0					522
Q8IY84 UniProt NPD GO	NIM1_HUMAN	Serine/threonine-protein kinase NIM1 (EC 2.7.11.1)	0.29	-	nuc	0					436
Q9ES70 UniProt NPD GO	NEK6_MOUSE	Serine/threonine-protein kinase Nek6 (EC 2.7.11.1) (NimA-related protein kinase 6)	0.29	-	cyt	0	Cytoplasm				313
Q99MQ3 UniProt NPD GO	PINK1_MOUSE	Serine/threonine-protein kinase PINK1, mitochondrial precursor (EC 2.7.11.1) (PTEN-induced putative ...	0.29	-	cyt	0	Mitochondrion (By similarity)	mitochondrion [ISS]			580
Q7XQP4 UniProt NPD GO	SAPK7_ORYSA	Serine/threonine-protein kinase SAPK7 (EC 2.7.11.1) (Osmotic stress/abscisic acid-activated protein ...	0.29	-	cyt	0					359
Q7TQP6 UniProt NPD GO	TNI3K_RAT	Serine/threonine-protein kinase TNNI3K (EC 2.7.11.1) (TNNI3-interacting kinase) (Cardiac ankyrin rep ...	0.29	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Expressed at lower levels in the cytoplasm (By s ...				834
Q9XTG7 UniProt NPD GO	AKT2_CAEEL	Serine/threonine-protein kinase akt-2 (EC 2.7.11.1) (Protein kinase B akt-2) (PKB akt-2)	0.29	-	cyt	0		intracellular [IDA]			528
P80203 UniProt NPD GO	ACVL1_RAT	Serine/threonine-protein kinase receptor R3 precursor (EC 2.7.11.30) (SKR3) (TGF-B superfamily recep ...	0.29	-	end	1	Membrane; single-pass type I membrane protein				504
P48480 UniProt NPD GO	PP11_ACECL	Serine/threonine-protein phosphatase PP1 isozyme 1 (EC 3.1.3.16)	0.29	-	cyt	0					319
P30366 UniProt NPD GO	PP11_ARATH	Serine/threonine-protein phosphatase PP1 isozyme 1 (EC 3.1.3.16)	0.29	-	cyt	0					318
P48482 UniProt NPD GO	PP12_ARATH	Serine/threonine-protein phosphatase PP1 isozyme 2 (EC 3.1.3.16)	0.29	-	cyt	0					312
Q19473 UniProt NPD GO	SRD51_CAEEL	Serpentine receptor class delta-51 (Protein srd-51)	0.29	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				336
P91275 UniProt NPD GO	SRG14_CAEEL	Serpentine receptor class gamma-14 (Protein srg-14)	0.29	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				326
O16974 UniProt NPD GO	SRG53_CAEEL	Serpentine receptor class gamma-53 (Protein srg-53)	0.29	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				295
Q9FVS6 UniProt NPD GO	KSG4_ARATH	Shaggy-related protein kinase delta (EC 2.7.11.1) (ASK-delta)	0.29	-	cyt	0					420
Q925N1 UniProt NPD GO	SFXN4_MOUSE	Sideroflexin-4	0.29	-	end	1	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				313
Q9P372 UniProt NPD GO	SRP14_SCHPO	Signal recognition particle subunit srp14 (Signal recognition particle 14 kDa protein homolog)	0.29	+	nuc	0	Cytoplasm (By similarity)				106
Q12118 UniProt NPD GO	SGT2_YEAST	Small glutamine-rich tetratricopeptide repeat-containing protein 2 (Viral protein U-binding protein) ...	0.29	-	nuc	0	Cytoplasm	cytoplasm [IDA]			346
P15390 UniProt NPD GO	SCN4A_RAT	Sodium channel protein type 4 subunit alpha (Sodium channel protein type IV subunit alpha) (Voltage- ...	0.29	-	end	20	Membrane; multi-pass membrane protein				1840

You are viewing entries 41751 to 41800 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.