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
Q8SQ27 UniProt NPD GO	RBM12_MACMU	RNA-binding protein 12 (RNA-binding motif protein 12) (SH3/WW domain anchor protein in the nucleus) ...	0.45	+	nuc	0	Nucleus (By similarity)				932
P09851 UniProt NPD GO	RASA1_BOVIN	Ras GTPase-activating protein 1 (GTPase-activating protein) (GAP) (Ras p21 protein activator) (p120G ...	0.45	-	cyt	0	Cytoplasm	cytoplasm [ISS]			1044
Q9NS23 UniProt NPD GO	RASF1_HUMAN	Ras association domain-containing protein 1	0.45	-	nuc	0	Isoform A: Cytoskeleton. Centrosome. Spindle. Isoform A localizes to cytoplasmic microtubules during ...	microtubule cytoskeleton [IEP] nucleus [IEP]	605082		344
P04626 UniProt NPD GO	ERBB2_HUMAN	Receptor tyrosine-protein kinase erbB-2 precursor (EC 2.7.10.1) (p185erbB2) (C-erbB-2) (NEU proto-on ...	0.45	-	end	2	Membrane; single-pass type I membrane protein	integral to membrane [NAS] plasma membrane [NAS]	164870	2A91	1255
P23467 UniProt NPD GO	PTPRB_HUMAN	Receptor-type tyrosine-protein phosphatase beta precursor (EC 3.1.3.48) (Protein-tyrosine phosphatas ...	0.45	-	end	0	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	176882	2HC2	1997
P49446 UniProt NPD GO	PTPRE_MOUSE	Receptor-type tyrosine-protein phosphatase epsilon precursor (EC 3.1.3.48) (Protein-tyrosine phospha ...	0.45	-	nuc	1 *	Membrane; single-pass type I membrane protein				699
Q12913 UniProt NPD GO	PTPRJ_HUMAN	Receptor-type tyrosine-protein phosphatase eta precursor (EC 3.1.3.48) (Protein-tyrosine phosphatase ...	0.45	+	mit	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	600925	2CFV	1337
P03870 UniProt NPD GO	FLP_YEAST	Recombinase Flp protein (Protein Able)	0.45	-	nuc	0				1P4E	423
O43665 UniProt NPD GO	RGS10_HUMAN	Regulator of G-protein signaling 10 (RGS10)	0.45	-	nuc	0			602856		173
P34295 UniProt NPD GO	RGS1_CAEEL	Regulator of G-protein signaling rgs-1	0.45	-	nuc	0					201
O75678 UniProt NPD GO	RFPL2_HUMAN	Ret finger protein-like 2 (RING finger protein 79)	0.45	-	nuc	0			605969		378
Q16799 UniProt NPD GO	RTN1_HUMAN	Reticulon-1 (Neuroendocrine-specific protein)	0.45	-	nuc	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	integral to endoplasmic reticulum membrane [TAS]	600865		776
Q9BZR6 UniProt NPD GO	RTN4R_HUMAN	Reticulon-4 receptor precursor (Nogo receptor) (NgR) (Nogo-66 receptor)	0.45	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	membrane [NAS]	605566	1P8T	473
Q99M75 UniProt NPD GO	RTN4R_RAT	Reticulon-4 receptor precursor (Nogo receptor) (NgR) (Nogo-66 receptor)	0.45	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				473
Q8K0S5 UniProt NPD GO	R4RL1_MOUSE	Reticulon-4 receptor-like 1 precursor (Nogo-66 receptor homolog 2) (Nogo-66 receptor-related protein ...	0.45	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential). Localized to the surface of neurons, including ...	anchored to plasma membrane [ISS]			445
Q9W6R5 UniProt NPD GO	XLRS1_FUGRU	Retinoschisin precursor (X-linked juvenile retinoschisis protein homolog)	0.45	-	end	0	Secreted protein (By similarity)				280
Q05118 UniProt NPD GO	PO23_POPJA	Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 (Retrovirus-related Pol ...	0.45	-	cyt	0					606
Q863J7 UniProt NPD GO	RNAS9_MACAS	Ribonuclease-like protein 9 precursor	0.45	-	exc	0	Secreted protein (Probable)				203
P50647 UniProt NPD GO	RIR1_PLAFG	Ribonucleoside-diphosphate reductase large chain (EC 1.17.4.1) (Ribonucleotide reductase R1 subunit) ...	0.45	-	nuc	0					804
Q8WZ73 UniProt NPD GO	RFFL_HUMAN	Rififylin (RING finger and FYVE-like domain-containing protein 1) (FYVE-RING finger protein Sakura) ...	0.45	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein		609735	1Y02	363
Q9FMF5 UniProt NPD GO	RPT3_ARATH	Root phototropism protein 3 (Non-phototropic hypocotyl protein 3)	0.45	+	nuc	0	Cell membrane; peripheral membrane protein				745
Q6C3X6 UniProt NPD GO	RUVB2_YARLI	RuvB-like helicase 2 (EC 3.6.1.-)	0.45	-	cyt	0	Nucleus (By similarity)				424
Q9H7B4 UniProt NPD GO	SMYD3_HUMAN	SET and MYND domain-containing protein 3 (EC 2.1.1.43) (Zinc finger MYND domain-containing protein 1 ...	0.45	-	cyt	0	Cytoplasm. Mainly cytoplasmic when cells are arrested at G0/G1. Nucleus. Accumulates in the nucleus ...		608783		428
Q8BTK5 UniProt NPD GO	SMYD4_MOUSE	SET and MYND domain-containing protein 4	0.45	-	nuc	0					799
P40651 UniProt NPD GO	MG42_TARMA	SRY-related protein MG42 (Fragment)	0.45	-	nuc	0	Nucleus (Potential)				72
Q62280 UniProt NPD GO	SSXT_MOUSE	SSXT protein (SYT protein) (Synovial sarcoma-associated Ss18-alpha)	0.45	-	nuc	0					418
Q15532 UniProt NPD GO	SSXT_HUMAN	SSXT protein (Synovial sarcoma, translocated to X chromosome) (SYT protein)	0.45	-	nuc	0		nucleus [TAS]	600192		418
Q754T8 UniProt NPD GO	SWC5_ASHGO	SWR1-complex protein 5	0.45	-	nuc	0	Nucleus (By similarity)				286
P25236 UniProt NPD GO	SEPP1_RAT	Selenoprotein P precursor (SeP) [Contains: Selenoprotein Se-P10; Selenoprotein Se-P6; Selenoprotein ...	0.45	-	end	0	Secreted protein				385
Q62177 UniProt NPD GO	SEM3B_MOUSE	Semaphorin-3B precursor (Semaphorin A) (Sema A)	0.45	-	mit	0	Secreted protein (By similarity)				748
Q9NPR2 UniProt NPD GO	SEM4B_HUMAN	Semaphorin-4B precursor	0.45	-	end	1	Membrane; single-pass type I membrane protein				832
Q9JHN8 UniProt NPD GO	STK19_MOUSE	Serine/threonine-protein kinase 19 (EC 2.7.11.1) (RP1 protein)	0.45	+	mit	0	Nucleus (By similarity)				254
Q69ZM6 UniProt NPD GO	STK36_MOUSE	Serine/threonine-protein kinase 36 (EC 2.7.11.1) (Fused homolog)	0.45	-	end	0	Cytoplasm (By similarity). Low level: Nucleus (By similarity). Low levels also present in the nucleu ...	cytoplasm [ISS] nucleus [ISS]			1268
Q12505 UniProt NPD GO	SKS1_YEAST	Serine/threonine-protein kinase SKS1 (EC 2.7.11.1) (Suppressor kinase of SNF3)	0.45	-	nuc	0		cytoplasm [IDA]			502
Q9NLA1 UniProt NPD GO	FLR4_CAEEL	Serine/threonine-protein kinase flr-4 (EC 2.7.11.1) (Fluoride-resistant protein 4)	0.45	-	end	3	Membrane; multi-pass membrane protein (Probable)				570
Q15173 UniProt NPD GO	2A5B_HUMAN	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform (PP2A, B subunit, B' ...	0.45	-	cyt	0	Cytoplasm	cytoplasm [TAS]	601644		497
Q8CIE0 UniProt NPD GO	SPA11_MOUSE	Serpin A11 precursor	0.45	-	mit	0	Secreted protein (Potential)				424
P26638 UniProt NPD GO	SYS_MOUSE	Seryl-tRNA synthetase (EC 6.1.1.11) (Serine--tRNA ligase) (SerRS)	0.45	-	cyt	0					511
O43017 UniProt NPD GO	SWD3_SCHPO	Set1 complex component swd3 (Set1C component swd3) (COMPASS component swd3) (Complex proteins associ ...	0.45	-	nuc	0	Nucleus (Probable)	COMPASS complex [IDA]			380
Q64JA4 UniProt NPD GO	SIG13_PANTR	Sialic acid-binding Ig-like lectin 13 precursor (Siglec-13)	0.45	-	end	1	Membrane; single-pass type I membrane protein				387
Q9ULV8 UniProt NPD GO	CBLC_HUMAN	Signal transduction protein CBL-C (SH3-binding protein CBL-C) (CBL-3) (RING finger protein 57)	0.45	-	nuc	0	Nucleus (Potential)		608453		474
P56873 UniProt NPD GO	SSA27_MOUSE	Sjoegren syndrome/scleroderma autoantigen 1 homolog (Autoantigen p27 homolog) (Protein C184L)	0.45	-	nuc	0					199
P70606 UniProt NPD GO	KCNN1_RAT	Small conductance calcium-activated potassium channel protein 1 (SK1)	0.45	+	end	5	Membrane; multi-pass membrane protein				536
Q8BSU2 UniProt NPD GO	SCYBG_MOUSE	Small inducible cytokine B16 precursor (Transmembrane chemokine CXCL16) (SR-PSOX) (Scavenger recepto ...	0.45	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				246
Q9Y5Y9 UniProt NPD GO	SC10A_HUMAN	Sodium channel protein type 10 subunit alpha (Sodium channel protein type X subunit alpha) (Voltage- ...	0.45	-	end	20	Membrane; multi-pass membrane protein (By similarity). It can be translocated to the extracellular m ...		604427		1956
Q9U6A0 UniProt NPD GO	NCKX_DROME	Sodium/potassium/calcium exchanger (Na(+)/K(+)/Ca(2+)-exchange protein)	0.45	-	end	9	Membrane; multi-pass membrane protein				856
P14693 UniProt NPD GO	SAM35_YEAST	Sorting assembly machinery 35 kDa subunit (TOB complex 38 kDa subunit) (Mitochondrial 38 kDa outer m ...	0.45	-	cyt	0	Mitochondrion; mitochondrial outer membrane	extrinsic to membrane [IDA] mitochondrial sorting and assembly machiner... [IDA]			329
P57768 UniProt NPD GO	SNX16_HUMAN	Sorting nexin-16	0.45	-	mit	0					343
Q4WQI6 UniProt NPD GO	SNX4_ASPFU	Sorting nexin-4 (Autophagy-related protein 24)	0.45	+	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Endosome; endosoma ...				497
Q8CFD4 UniProt NPD GO	SNX8_MOUSE	Sorting nexin-8	0.45	-	cyt	0					459

You are viewing entries 28601 to 28650 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.