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
O80770 UniProt NPD GO	SPT52_ARATH	Putative transcription elongation factor SPT5 homolog 2	0.38	-	cyt	0	Nucleus (By similarity)				990
Q06247 UniProt NPD GO	YL173_YEAST	Putative uncharacterized protein YLR173W	0.38	-	mit	1	Membrane; single-pass membrane protein (Potential)				608
Q9H2S5 UniProt NPD GO	RNF39_HUMAN	RING finger protein 39 (Protein HZFw)	0.38	-	mit	0	Cytoplasm (By similarity)		607524		420
P38782 UniProt NPD GO	MED6_YEAST	RNA polymerase II mediator complex subunit 6 (RNA polymerase II transcriptional regulation mediator ...	0.38	-	nuc	0	Nucleus	mediator complex [IDA]			295
Q6C7D0 UniProt NPD GO	TFB3_YARLI	RNA polymerase II transcription factor B subunit 3 (RNA polymerase II transcription factor B p38 sub ...	0.38	-	nuc	0	Nucleus (By similarity)				346
Q9CPR1 UniProt NPD GO	RWDD4_MOUSE	RWD domain-containing protein 4A	0.38	+	nuc	0					188
P20936 UniProt NPD GO	RASA1_HUMAN	Ras GTPase-activating protein 1 (GTPase-activating protein) (GAP) (Ras p21 protein activator) (p120G ...	0.38	-	cyt	0	Cytoplasm	cytoplasm [NAS]	139150	1WQ1	1047
P03967 UniProt NPD GO	RASD_DICDI	Ras-like protein rasD (Transforming protein P23)	0.38	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				187
Q8CIX1 UniProt NPD GO	RIMS4_RAT	Regulating synaptic membrane exocytosis protein 4 (Rab3-interacting molecule 4) (RIM 4) (RIM4 gamma) ...	0.38	-	mit	0					269
Q5XM32 UniProt NPD GO	RXFP2_CANFA	Relaxin receptor 2 (Relaxin family peptide receptor 2) (Leucine-rich repeat-containing G-protein cou ...	0.38	-	end	7	Membrane; multi-pass membrane protein				737
O75677 UniProt NPD GO	RFPL1_HUMAN	Ret finger protein-like 1 (RING finger protein 78)	0.38	-	exc	0			605968		317
Q6H3X3 UniProt NPD GO	RET1G_HUMAN	Retinoic acid early transcript 1G protein precursor	0.38	-	exc	0	Cell membrane; single-pass type I membrane protein	plasma membrane [NAS]			334
P47924 UniProt NPD GO	RIBAB_ARATH	Riboflavin biosynthesis protein ribAB, chloroplast precursor [Includes: GTP cyclohydrolase-2 (EC 3.5 ...	0.38	+	nuc	0	Plastid; chloroplast (Potential)				543
Q38716 UniProt NPD GO	RNS2_ANTHI	Ribonuclease S-2 precursor (EC 3.1.27.1) (Stylar glycoprotein 2) (S2-RNase)	0.38	-	end	1 *	Secreted protein; extracellular space				235
P21672 UniProt NPD GO	RIR3_YEAST	Ribonucleoside-diphosphate reductase large chain 2 (EC 1.17.4.1) (Ribonucleotide reductase large sub ...	0.38	-	cyt	0	Cytoplasm	cytoplasm [IDA] mitochondrion [IDA] ribonucleoside-diphosphate reductase complex [IDA]			869
Q6FTT8 UniProt NPD GO	RRF1_CANGA	Ribosomal recycling factor, mitochondrial precursor	0.38	-	nuc	0	Mitochondrion (By similarity)				233
P04928 UniProt NPD GO	SANT_PLAFN	S-antigen protein precursor	0.38	-	nuc	0	Parasitophorous vacuole				309
P18425 UniProt NPD GO	SCR20_OMMSL	S-crystallin SL20-1 (Major lens polypeptide)	0.38	-	nuc	0					222
O95238 UniProt NPD GO	SPDEF_HUMAN	SAM pointed domain-containing Ets transcription factor (Prostate-derived Ets factor) (Prostate epith ...	0.38	-	nuc	0	Nucleus (Probable)		608144	1YO5	335
P49772 UniProt NPD GO	FLT3L_MOUSE	SL cytokine precursor (Fms-related tyrosine kinase 3 ligand) (Flt3 ligand) (Flt3L)	0.38	-	exc	1	Cell membrane; single-pass type I membrane protein. Isoform 3/E6, isoform 4/E6Delta16: Secreted prot ...				232
Q9ET39 UniProt NPD GO	SLAF6_MOUSE	SLAM family member 6 precursor (Lymphocyte antigen 108)	0.38	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				351
P13432 UniProt NPD GO	SMR1_RAT	SMR1 protein precursor (VCS-alpha 1) [Contains: SMR1-related undecapeptide; SMR1-related hexapeptide ...	0.38	-	nuc	0	Secreted protein. Found in blood. Secreted from the salivary compartment into the blood circulation, ...				146
O74843 UniProt NPD GO	SIF1_SCHPO	Sad1-interacting factor 1	0.38	+	nuc	2	Membrane; multi-pass membrane protein				257
P02840 UniProt NPD GO	SGS3_DROME	Salivary glue protein Sgs-3 precursor	0.38	-	exc	0	Secreted protein				307
Q2VL90 UniProt NPD GO	C163A_PIG	Scavenger receptor cysteine-rich type 1 protein M130 precursor (CD163 antigen) [Contains: Soluble CD ...	0.38	-	end	2 *	Cell membrane; single-pass type I membrane protein (By similarity). Soluble CD163: Secreted protein ...				1115
Q711S8 UniProt NPD GO	SPP24_PIG	Secreted phosphoprotein 24 precursor (Spp-24) (Secreted phosphoprotein 2)	0.38	-	exc	0	Secreted protein				204
O14828 UniProt NPD GO	SCAM3_HUMAN	Secretory carrier-associated membrane protein 3 (Secretory carrier membrane protein 3)	0.38	-	end	4	Membrane; multi-pass membrane protein		606913		347
Q9JHW4 UniProt NPD GO	SELB_MOUSE	Selenocysteine-specific elongation factor (Elongation factor sec) (Eukaryotic elongation factor, sel ...	0.38	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				583
O75326 UniProt NPD GO	SEM7A_HUMAN	Semaphorin-7A precursor (Semaphorin L) (Sema L) (Semaphorin K1) (Sema K1) (John-Milton-Hargen human ...	0.38	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor		607961		666
Q09116 UniProt NPD GO	SPN2_SCHPO	Septin homolog spn2	0.38	-	cyt	0		septin complex [IDA] septin ring (sensu Fungi) [IDA]			331
P42208 UniProt NPD GO	SEPT2_MOUSE	Septin-2 (Protein NEDD5) (Neural precursor cell expressed developmentally down-regulated protein 5)	0.38	-	cyt	0	Accumulates near the contractile ring from anaphase through telophase, and finally condenses into th ...	contractile ring [NAS] synaptosome [IDA]			361
P28661 UniProt NPD GO	SEPT4_MOUSE	Septin-4 (Peanut-like protein 2) (Brain protein H5)	0.38	-	nuc	0		flagellum (sensu Eukaryota) [IMP]			478
Q9SV41 UniProt NPD GO	2A5E_ARATH	Serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' epsilon isoform (PP2A, B' subun ...	0.38	-	nuc	0					497
O35280 UniProt NPD GO	CHK1_MOUSE	Serine/threonine-protein kinase Chk1 (EC 2.7.11.1)	0.38	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Nuclear export is mediated at least in part by X ...	nucleus [IDA] replication fork [IDA]			476
Q13177 UniProt NPD GO	PAK2_HUMAN	Serine/threonine-protein kinase PAK 2 (EC 2.7.11.1) (p21-activated kinase 2) (PAK-2) (PAK65) (Gamma- ...	0.38	-	nuc	0			605022		524
P23287 UniProt NPD GO	PP2B1_YEAST	Serine/threonine-protein phosphatase 2B catalytic subunit A1 (EC 3.1.3.16) (Calcineurin A1) (Calmodu ...	0.38	-	nuc	0		calcineurin complex [IPI] cytoplasm [TAS]			553
P13681 UniProt NPD GO	PP11_SCHPO	Serine/threonine-protein phosphatase PP1-1 (EC 3.1.3.16)	0.38	-	cyt	0	Nucleus				327
Q9D7D2 UniProt NPD GO	SPA9_MOUSE	Serpin A9 precursor	0.38	-	mit	0	Secreted protein (Potential)				418
P14872 UniProt NPD GO	ALBUB_XENLA	Serum albumin B precursor (74 kDa serum albumin)	0.38	-	exc	0	Secreted protein				607
O81983 UniProt NPD GO	SYS_HELAN	Seryl-tRNA synthetase (EC 6.1.1.11) (Serine--tRNA ligase) (SerRS)	0.38	-	cyt	0					438
Q96287 UniProt NPD GO	KSG8_ARATH	Shaggy-related protein kinase theta (EC 2.7.11.1) (ASK-theta)	0.38	-	mit	0					472
P14613 UniProt NPD GO	CBT1_NAJKA	Short neurotoxin 1 (Toxin C-6)	0.38	-	nuc	0	Secreted protein				62
O15821 UniProt NPD GO	SRP54_ENTHI	Signal recognition particle 54 kDa protein (SRP54)	0.38	-	mit	0	Cytoplasm				487
Q8R0L1 UniProt NPD GO	STAP2_MOUSE	Signal-transducing adaptor protein 2 (STAP-2)	0.38	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. The translocation to the membranes occurs in respo ...	plasma membrane [IDA]			411
Q5E9C3 UniProt NPD GO	SSNA1_BOVIN	Sjoegren syndrome nuclear autoantigen 1 homolog	0.38	-	nuc	0	Nucleus (By similarity). Centrosome (By similarity)				119
Q9JJ94 UniProt NPD GO	SSNA1_MOUSE	Sjoegren syndrome nuclear autoantigen 1 homolog	0.38	-	nuc	0	Nucleus (By similarity). Centrosome (By similarity)				119
Q9EQR3 UniProt NPD GO	KCNN1_MOUSE	Small conductance calcium-activated potassium channel protein 1 (SK1)	0.38	+	end	5	Membrane; multi-pass membrane protein				580
Q68A93 UniProt NPD GO	CCL25_CANFA	Small inducible cytokine A25 precursor (CCL25)	0.38	-	exc	0	Secreted protein (By similarity)				151
Q9Y258 UniProt NPD GO	CCL26_HUMAN	Small inducible cytokine A26 precursor (CCL26) (Eotaxin-3) (Macrophage inflammatory protein 4-alpha) ...	0.38	-	nuc	0	Secreted protein		604697	1G2T	94
Q8CGN8 UniProt NPD GO	SPRR4_MOUSE	Small proline-rich protein 4	0.38	-	nuc	0	Cytoplasm (By similarity). Cytoplasm; cell cortex (By similarity). Translocates to the cell peripher ...				76

You are viewing entries 33751 to 33800 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.