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
P22553 UniProt NPD GO	SLSG2_BRAOA	S-locus-specific glycoprotein BS29-2 precursor	0.50	-	exc	1 *					435
P40655 UniProt NPD GO	LG28_EUBMA	SRY-related protein LG28 (Fragment)	0.50	-	nuc	0	Nucleus (Potential)				71
Q9CQ26 UniProt NPD GO	STABP_MOUSE	STAM-binding protein (EC 3.1.2.15) (Associated molecule with the SH3 domain of STAM)	0.50	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Membrane; peripheral membrane protein (By simila ...				424
P70274 UniProt NPD GO	SEPP1_MOUSE	Selenoprotein P precursor (SeP) (Plasma selenoprotein P)	0.50	-	exc	0	Secreted protein	extracellular region [TAS] extracellular space [IDA]			380
Q5EA85 UniProt NPD GO	SEM4A_BOVIN	Semaphorin-4A precursor (Semaphorin B) (Sema B)	0.50	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				762
Q9UTR4 UniProt NPD GO	ETD1_SCHPO	Septation protein etd1	0.50	-	nuc	0		cell cortex of cell tip [IDA] contractile ring (sensu Fungi) [IDA]			391
Q3SZN0 UniProt NPD GO	SEP11_BOVIN	Septin-11	0.50	+	mit	0					427
Q6CLQ5 UniProt NPD GO	GLYM_KLULA	Serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1) (Serine methylase) (Glycine hy ...	0.50	-	mit	0	Mitochondrion				498
Q6Z8B7 UniProt NPD GO	2ABB_ORYSA	Serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform (PP2A, subunit B, b ...	0.50	-	nuc	0					525
O04375 UniProt NPD GO	2A5A_ARATH	Serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' alpha isoform (PP2A, B' subunit ...	0.50	-	nuc	0					495
O04376 UniProt NPD GO	2A5B_ARATH	Serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' beta isoform (PP2A, B' subunit, ...	0.50	-	nuc	0					499
Q6PGN3 UniProt NPD GO	DCAK2_MOUSE	Serine/threonine-protein kinase DCAMKL2 (EC 2.7.11.1) (Doublecortin-like and CAM kinase-like 2)	0.50	+	nuc	0					756
P70268 UniProt NPD GO	PKN1_MOUSE	Serine/threonine-protein kinase N1 (EC 2.7.11.13) (Protein kinase C-like 1) (Protein-kinase C-relate ...	0.50	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [IDA] cytoplasmic membrane-bound vesicle [IDA]			946
P34208 UniProt NPD GO	CHK1_SCHPO	Serine/threonine-protein kinase chk1 (EC 2.7.11.1) (Checkpoint kinase 1)	0.50	-	nuc	0	Nucleus (By similarity)				496
Q9EQY0 UniProt NPD GO	ERN1_MOUSE	Serine/threonine-protein kinase/endoribonuclease IRE1 precursor (Inositol-requiring protein 1) (IRE1 ...	0.50	-	end	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	endoplasmic reticulum membrane [IDA] integral to endoplasmic reticulum membrane [IEP]			977
Q8K3K4 UniProt NPD GO	SPB10_RAT	Serpin B10 (Transforming growth factor beta repressible serpin) (TGF-beta-repressible serine protein ...	0.50	-	cyt	0	Cytoplasm				397
Q05738 UniProt NPD GO	SRY_MOUSE	Sex-determining region Y protein (Testis-determining factor)	0.50	-	nuc	0	Nucleus				395
Q62563 UniProt NPD GO	SRY_MUSSP	Sex-determining region Y protein (Testis-determining factor)	0.50	-	nuc	0	Nucleus				355
O43699 UniProt NPD GO	SIGL6_HUMAN	Sialic acid-binding Ig-like lectin 6 precursor (Siglec-6) (Obesity-binding protein 1) (OB-BP1) (CD33 ...	0.50	-	end	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein	integral to plasma membrane [TAS] membrane fraction [TAS]	604405		442
P36057 UniProt NPD GO	SRPB_YEAST	Signal recognition particle receptor subunit beta (SR-beta)	0.50	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane (Potential)	integral to endoplasmic reticulum membrane [IDA] signal recognition particle receptor complex [TAS]		2GED	244
O35903 UniProt NPD GO	CCL25_MOUSE	Small inducible cytokine A25 precursor (CCL25) (Chemokine TECK) (Thymus expressed chemokine)	0.50	-	exc	0	Secreted protein				144
Q9WTU3 UniProt NPD GO	SCN8A_MOUSE	Sodium channel protein type 8 subunit alpha (Sodium channel protein type VIII subunit alpha) (Voltag ...	0.50	+	end	19	Membrane; multi-pass membrane protein	voltage-gated sodium channel complex [IC]			1978
Q5R4A5 UniProt NPD GO	SNX17_PONPY	Sorting nexin-17	0.50	-	cyt	0	Cytoplasm (By similarity). Endosome; early endosome (By similarity). Associated with early endosomes ...				470
Q6FV07 UniProt NPD GO	IPL1_CANGA	Spindle assembly checkpoint kinase (EC 2.7.11.1) (Aurora kinase)	0.50	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and on elongated and disassembling spin ...				358
P53541 UniProt NPD GO	SPO1_YEAST	Sporulation-specific protein 1	0.50	-	cyt	0		nucleus [IDA]			536
Q99JB2 UniProt NPD GO	STML2_MOUSE	Stomatin-like protein 2 (SLP-2)	0.50	-	mit	0	Membrane; peripheral membrane protein (By similarity). Cytoplasm (By similarity). Associated with th ...	mitochondrial inner membrane [IDA] mitochondrion [IDA]			353
Q13033 UniProt NPD GO	STRN3_HUMAN	Striatin-3 (Cell-cycle autoantigen SG2NA) (S/G2 antigen)	0.50	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)	cytosol [NAS] membrane fraction [NAS] nucleus [IDA]			797
Q8TF42 UniProt NPD GO	STS1_HUMAN	Suppressor of T-cell receptor signaling 1 (Sts-1) (Cbl-interacting protein p70)	0.50	-	mit	0	Cytoplasm (By similarity). Nucleus (Potential)		609201	2CPW	649
Q18240 UniProt NPD GO	SPR2_CAEEL	Suppressor of presenilin 2	0.50	-	cyt	0	Nucleus				312
P33302 UniProt NPD GO	PDR5_YEAST	Suppressor of toxicity of sporidesmin	0.50	-	end	14	Membrane; multi-pass membrane protein	mitochondrion [IDA] plasma membrane [IDA]			1511
P80352 UniProt NPD GO	2SS3_CAPMA	Sweet protein mabinlin-3 (Mabinlin III) (MAB III) [Contains: Sweet protein mabinlin-3 chain A; Sweet ...	0.50	-	mit	0					104
P40748 UniProt NPD GO	SYT3_RAT	Synaptotagmin-3 (Synaptotagmin III) (SytIII)	0.50	+	nuc	1	Synaptic vesicle; synaptic vesicle membrane; single-pass membrane protein	synapse [NAS]		1DQV	588
Q62746 UniProt NPD GO	SYT6_RAT	Synaptotagmin-6 (Synaptotagmin VI) (SytVI)	0.50	-	exc	1	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (By similarity)				511
Q9R0N7 UniProt NPD GO	SYT7_MOUSE	Synaptotagmin-7 (Synaptotagmin VII) (SytVII)	0.50	-	nuc	1 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein (By similarity)	lysosome [IDA]			403
P50279 UniProt NPD GO	STX2_RAT	Syntaxin-2 (Epimorphin)	0.50	-	gol	1	Membrane; single-pass type IV membrane protein	integral to membrane [TAS] midbody [IDA] SNARE complex [TAS]			290
Q13277 UniProt NPD GO	STX3_HUMAN	Syntaxin-3	0.50	-	gol	1	Membrane; single-pass type IV membrane protein (Potential)		600876		289
Q94KK6 UniProt NPD GO	SYP72_ARATH	Syntaxin-72 (AtSYP72)	0.50	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				267
Q29037 UniProt NPD GO	CD4_SAISC	T-cell surface glycoprotein CD4 precursor (T-cell surface antigen T4/Leu-3)	0.50	-	end	1	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			457
Q8R2K4 UniProt NPD GO	TAF6L_MOUSE	TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L (PCAF-ass ...	0.50	-	cyt	0	Nucleus (By similarity)				616
O13270 UniProt NPD GO	TBP_CHICK	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (Tr ...	0.50	+	nuc	0	Nucleus				302
P20226 UniProt NPD GO	TBP_HUMAN	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (Tr ...	0.50	+	nuc	0	Nucleus	transcription factor TFIID complex [IDA]	600075	1TGH	339
P29037 UniProt NPD GO	TBP_MOUSE	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (Tr ...	0.50	+	nuc	0	Nucleus	nucleus [IDA] RNA polymerase I transcription factor complex [TAS]			316
P39429 UniProt NPD GO	TRAF2_MOUSE	TNF receptor-associated factor 2	0.50	-	nuc	0	Cytoplasm				501
P30975 UniProt NPD GO	TLR2_DROME	Tachykinin-like peptides receptor 99D (dTKR)	0.50	-	end	7	Membrane; multi-pass membrane protein				519
Q06184 UniProt NPD GO	TEB_EUPCR	Telomere-binding protein 51 kDa subunit	0.50	-	nuc	0	Nucleus				446
Q29116 UniProt NPD GO	TENA_PIG	Tenascin precursor (TN) (Hexabrachion) (Cytotactin) (Neuronectin) (GMEM) (JI) (Miotendinous antigen) ...	0.50	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				1746
Q8BYI9 UniProt NPD GO	TENR_MOUSE	Tenascin-R precursor (TN-R) (Restrictin) (Janusin) (Neural recognition molecule J1-160/180)	0.50	-	cyt	0	Secreted protein; extracellular space; extracellular matrix	cell surface [IDA] lipid raft [IDA]			1358
O95801 UniProt NPD GO	TTC4_HUMAN	Tetratricopeptide repeat protein 4 (TPR repeat protein 4)	0.50	-	cyt	0			606753		387
Q62361 UniProt NPD GO	TRH_MOUSE	Thyroliberin precursor [Contains: Prothyroliberin; Thyroliberin (Thyrotropin-releasing hormone) (TRH ...	0.50	-	exc	0	Secreted protein				256
Q8WZ42 UniProt NPD GO	TITIN_HUMAN	Titin (EC 2.7.11.1) (Connectin) (Rhabdomyosarcoma antigen MU-RMS-40.14)	0.50	+	nuc	0	Cytoplasm (Probable). Nucleus	condensed nuclear chromosome [TAS] myofibril [TAS] Z disc [IDA]	188840	2F8V	34350

You are viewing entries 25251 to 25300 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.