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
Q24151 UniProt NPD GO	STAT_DROME	Signal transducer and transcription activator (Protein marelle) (d-STAT)	0.36	-	nuc	0	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation (By similarity)	cytoplasm [IDA] nucleus [IDA]			761
O73847 UniProt NPD GO	SOML_PROAN	Somatolactin precursor (SL)	0.36	-	end	1 *	Secreted protein				232
P30935 UniProt NPD GO	SSR3_MOUSE	Somatostatin receptor type 3 (SS3R) (SSR-28)	0.36	-	end	7 *	Membrane; multi-pass membrane protein. Internalized into endoplasmic vesicles upon somatostatin-stim ...				428
P69158 UniProt NPD GO	SOMA_CTEID	Somatotropin precursor (Growth hormone)	0.36	-	exc	0	Secreted protein				210
P69159 UniProt NPD GO	SOMA_HYPMO	Somatotropin precursor (Growth hormone)	0.36	-	exc	0	Secreted protein				210
P69160 UniProt NPD GO	SOMA_HYPNO	Somatotropin precursor (Growth hormone)	0.36	-	exc	0	Secreted protein				210
Q9W6J7 UniProt NPD GO	SOMA_LABRO	Somatotropin precursor (Growth hormone)	0.36	-	exc	0	Secreted protein				207
P06880 UniProt NPD GO	SOMA_MOUSE	Somatotropin precursor (Growth hormone)	0.36	-	exc	0	Secreted protein				216
P50110 UniProt NPD GO	SAM37_YEAST	Sorting assembly machinery 37 kDa subunit (Mitochondrial 37 kDa outer membrane protein) (MAS37 prote ...	0.36	-	nuc	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein	mitochondrial sorting and assembly machiner... [IDA]			327
Q758Y7 UniProt NPD GO	SNX3_ASHGO	Sorting nexin-3	0.36	-	cyt	0	Cytoplasm (By similarity)				163
O95219 UniProt NPD GO	SNX4_HUMAN	Sorting nexin-4	0.36	-	cyt	0			605931		450
Q6P8X1 UniProt NPD GO	SNX6_MOUSE	Sorting nexin-6	0.36	-	cyt	0					406
Q9NY87 UniProt NPD GO	SPNXC_HUMAN	Sperm protein associated with the nucleus on the X chromosome C (Nuclear-associated protein SPAN-Xc) ...	0.36	-	nuc	0	Cytoplasm. Nucleus. Associated with nuclear craters	nucleus [TAS]	300330		97
Q9JJF2 UniProt NPD GO	SPAG4_MOUSE	Sperm-associated antigen 4 protein (Outer dense fiber-associated protein SPAG4)	0.36	-	mit	2	Membrane; multi-pass membrane protein (Potential). Isoform 1: Axoneme (By similarity). In spermatids ...				443
P34890 UniProt NPD GO	SPE17_CAEEL	Spermatogenesis-defective protein spe-17	0.36	-	nuc	0					142
Q12230 UniProt NPD GO	LSP1_YEAST	Sphingolipid long chain base-responsive protein LSP1	0.36	-	nuc	0	Cytoplasm. Punctate intracellular structures	cytoplasm [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA]			341
P83985 UniProt NPD GO	IGWS_GINCI	Splenic IgW, short secretory form (Fragment)	0.36	-	nuc	0	Secreted protein				195
Q15393 UniProt NPD GO	SF3B3_HUMAN	Splicing factor 3B subunit 3 (Spliceosome-associated protein 130) (SAP 130) (SF3b130) (Pre-mRNA-spli ...	0.36	-	end	0	Nucleus	small nuclear ribonucleoprotein complex [TAS] spliceosome complex [TAS]	605592		1217
P15269 UniProt NPD GO	SP70_DICDI	Spore coat protein SP70 precursor (Beejin protein)	0.36	-	exc	0					537
Q9UL01 UniProt NPD GO	SART2_HUMAN	Squamous cell carcinoma antigen recognized by T-cells 2 precursor (SART-2)	0.36	-	end	3 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [TAS]	605942		958
Q01406 UniProt NPD GO	SRC8_CHICK	Src substrate protein p85 (p80) (Cortactin)	0.36	-	exc	0	Cell membrane. Endoplasmic reticulum. In normal cells, probably in association with the plasma membr ...				563
Q9R0K8 UniProt NPD GO	STC2_RAT	Stanniocalcin-2 precursor (STC-2)	0.36	-	exc	0	Secreted protein (Potential)				296
Q28918 UniProt NPD GO	STAR_BOVIN	Steroidogenic acute regulatory protein, mitochondrial precursor (StAR) (StARD1)	0.36	-	mit	0	Mitochondrion				285
O46689 UniProt NPD GO	STAR_HORSE	Steroidogenic acute regulatory protein, mitochondrial precursor (StAR) (StARD1)	0.36	-	mit	0	Mitochondrion				285
P58405 UniProt NPD GO	STRN3_RAT	Striatin-3 (Cell-cycle autoantigen SG2NA) (S/G2 antigen) (Fragment)	0.36	-	mit	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				461
P49040 UniProt NPD GO	SUS1_ARATH	Sucrose synthase (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase)	0.36	-	nuc	0					806
O00204 UniProt NPD GO	ST2B1_HUMAN	Sulfotransferase family cytosolic 2B member 1 (EC 2.8.2.2) (Sulfotransferase 2B1) (Alcohol sulfotran ...	0.36	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [TAS]	604125	1Q22	365
Q9UMX1 UniProt NPD GO	SUFU_HUMAN	Suppressor of fused homolog (SUFUH)	0.36	-	mit	0	Cytoplasm. Nucleus	cytoplasm [TAS] nucleus [TAS]	155255	1M1L	484
O70377 UniProt NPD GO	SNP23_RAT	Synaptosomal-associated protein 23 (SNAP-23) (Vesicle-membrane fusion protein SNAP-23)	0.36	-	nuc	0	Cell membrane; peripheral membrane protein. Mainly localized to the plasma membrane (By similarity)				210
Q8N9I0 UniProt NPD GO	SYT2_HUMAN	Synaptotagmin-2 (Synaptotagmin II) (SytII)	0.36	+	nuc	1	Synaptic vesicles and chromaffin granules (By similarity)		600104		419
P46097 UniProt NPD GO	SYT2_MOUSE	Synaptotagmin-2 (Synaptotagmin II) (SytII)	0.36	+	nuc	1	Synaptic vesicles and chromaffin granules	plasma membrane [IDA] vesicular fraction [IDA]			422
P29101 UniProt NPD GO	SYT2_RAT	Synaptotagmin-2 (Synaptotagmin II) (SytII)	0.36	+	nuc	1	Synaptic vesicles and chromaffin granules	synaptic vesicle membrane [TAS]			422
Q925B4 UniProt NPD GO	SYT8_RAT	Synaptotagmin-8 (Synaptotagmin VIII) (SytVIII)	0.36	-	nuc	1 *	Cell membrane; single-pass type III membrane protein (By similarity). Acrosome (By similarity)				395
Q9ZSD4 UniProt NPD GO	SY121_ARATH	Syntaxin-121 (AtSYP121) (Syntaxin-related protein At-Syr1)	0.36	-	nuc	1	Cell membrane; single-pass type IV membrane protein (By similarity)				346
Q9ES03 UniProt NPD GO	TBX20_MOUSE	T-box transcription factor TBX20 (T-box protein 20)	0.36	-	nuc	0	Nucleus (Potential)				297
P04435 UniProt NPD GO	TVB2_HUMAN	T-cell receptor beta chain V region CTL-L17 precursor	0.36	-	exc	0		plasma membrane [NAS]			133
P41688 UniProt NPD GO	CD8A_FELCA	T-cell surface glycoprotein CD8 alpha chain precursor (CD8a antigen)	0.36	-	exc	2 *	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			239
Q92804 UniProt NPD GO	RBP56_HUMAN	TATA-binding protein-associated factor 2N (RNA-binding protein 56) (TAFII68) (TAF(II)68)	0.36	+	nuc	0	Nucleus (Potential)		601574		592
Q9H2K2 UniProt NPD GO	TNKS2_HUMAN	Tankyrase-2 (EC 2.4.2.30) (TANK2) (Tankyrase II) (TNKS-2) (TRF1-interacting ankyrin-related ADP-ribo ...	0.36	-	nuc	0	Cytoplasm. Golgi apparatus; Golgi membrane; peripheral membrane protein. Nucleus. Associated with th ...		607128		1166
Q2QLF4 UniProt NPD GO	TES_PANTR	Testin	0.36	-	nuc	0					421
Q9UGI8 UniProt NPD GO	TES_HUMAN	Testin (TESS)	0.36	-	nuc	0			606085		421
Q9BXU3 UniProt NPD GO	TX13A_HUMAN	Testis-expressed sequence 13A protein	0.36	-	nuc	0			300312		409
O88852 UniProt NPD GO	TSYL1_MOUSE	Testis-specific Y-encoded-like protein 1 (TSPY-like 1)	0.36	+	cyt	0	Nucleus; nucleolus (By similarity)				379
P47787 UniProt NPD GO	THAS_PIG	Thromboxane-A synthase (EC 5.3.99.5) (TXA synthase) (TXS) (Cytochrome P450 5A1)	0.36	-	vac	2 *	Membrane; multi-pass membrane protein				534
Q2YDF2 UniProt NPD GO	TR25_BOVIN	Thyroid hormone receptor-associated protein 6 (Thyroid hormone receptor-associated protein complex 2 ...	0.36	-	nuc	0	Nucleus (Potential)				193
P20352 UniProt NPD GO	TF_MOUSE	Tissue factor precursor (TF) (Coagulation factor III) (CD142 antigen)	0.36	-	end	2 *	Membrane; single-pass type I membrane protein				294
P00750 UniProt NPD GO	TPA_HUMAN	Tissue-type plasminogen activator precursor (EC 3.4.21.68) (tPA) (t-PA) (t-plasminogen activator) (A ...	0.36	-	exc	0	Secreted protein; extracellular space		173370	1TPN	562
Q9EPW9 UniProt NPD GO	TLR6_MOUSE	Toll-like receptor 6 precursor	0.36	-	end	2 *	Cell membrane; single-pass type I membrane protein. Phagosome; phagosomal membrane; single-pass type ...	membrane [ISS] phagocytic vesicle [ISS]			795
Q6P752 UniProt NPD GO	TOIP2_RAT	Torsin-1A-interacting protein 2	0.36	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				578
Q5M936 UniProt NPD GO	TOR3A_RAT	Torsin-3A precursor (Torsin family 3 member A)	0.36	-	exc	0	Cytoplasm. Endoplasmic reticulum (By similarity)				395

You are viewing entries 35401 to 35450 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.