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
Q5R8U3 UniProt NPD GO	SEP11_PONPY	Septin-11	0.56	-	cyt	0					424
O77201 UniProt NPD GO	SRYA_DROVI	Serendipity locus protein alpha	0.56	-	cyt	0	Cytoplasm (By similarity). Cell membrane; peripheral membrane protein; cytoplasmic side (By similari ...				537
P49842 UniProt NPD GO	STK19_HUMAN	Serine/threonine-protein kinase 19 (EC 2.7.11.1) (Protein RP1) (Protein G11)	0.56	-	cyt	0	Nucleus	nucleus [TAS]	604977		368
Q06098 UniProt NPD GO	ISR1_YEAST	Serine/threonine-protein kinase ISR1 (EC 2.7.11.1) (Inhibition of staurosporine resistance protein 1 ...	0.56	-	nuc	0					443
P50873 UniProt NPD GO	MRK1_YEAST	Serine/threonine-protein kinase MRK1 (EC 2.7.11.1)	0.56	+	nuc	0					501
Q9R0A5 UniProt NPD GO	NEK3_MOUSE	Serine/threonine-protein kinase Nek3 (EC 2.7.11.1) (NimA-related protein kinase 3)	0.56	-	nuc	0					511
P36002 UniProt NPD GO	PTK1_YEAST	Serine/threonine-protein kinase PTK1/STK1 (EC 2.7.11.1)	0.56	-	nuc	0					649
Q12705 UniProt NPD GO	PP2B_SCHPO	Serine/threonine-protein phosphatase 2B catalytic subunit (EC 3.1.3.16)	0.56	-	cyt	0					554
O14829 UniProt NPD GO	PPE1_HUMAN	Serine/threonine-protein phosphatase with EF-hands 1 (EC 3.1.3.16) (PPEF-1) (Protein phosphatase wit ...	0.56	-	mit	0			300109		653
Q91274 UniProt NPD GO	ALBU_PETMA	Serum albumin SDS-1 precursor	0.56	-	nuc	0	Secreted protein				1423
Q39230 UniProt NPD GO	SYS_ARATH	Seryl-tRNA synthetase (EC 6.1.1.11) (Serine--tRNA ligase) (SerRS)	0.56	-	cyt	0					451
P36392 UniProt NPD GO	SRY_MELME	Sex-determining region Y protein (Testis-determining factor) (Fragment)	0.56	-	nuc	0	Nucleus				55
Q91Y57 UniProt NPD GO	SIG12_MOUSE	Sialic acid-binding Ig-like lectin 12 precursor (Siglec-12) (Sialic acid-binding Ig-like lectin-like ...	0.56	-	exc	1	Membrane; single-pass type I membrane protein				467
Q9UQ49 UniProt NPD GO	NEUR3_HUMAN	Sialidase-3 (EC 3.2.1.18) (Membrane sialidase) (Ganglioside sialidase) (N-acetyl-alpha-neuraminidase ...	0.56	-	cyt	0	Membrane; peripheral membrane protein	integral to plasma membrane [TAS] plasma membrane [IDA]	604617		428
P0C0A9 UniProt NPD GO	SVIP_RAT	Small VCP/p97-interacting protein	0.56	-	nuc	0	Endoplasmic reticulum; smooth endoplasmic reticulum; smooth endoplasmic reticulum membrane; peripher ...				76
O70593 UniProt NPD GO	SGTA_RAT	Small glutamine-rich tetratricopeptide repeat-containing protein A	0.56	-	exc	0					314
Q5KSV9 UniProt NPD GO	SCYBA_CANFA	Small inducible cytokine B10 precursor (CXCL10)	0.56	-	exc	1 *	Secreted protein (By similarity)				98
Q9NY46 UniProt NPD GO	SCN3A_HUMAN	Sodium channel protein type 3 subunit alpha (Sodium channel protein type III subunit alpha) (Voltage ...	0.56	+	end	20	Membrane; multi-pass membrane protein	voltage-gated sodium channel complex [NAS]	182391		2000
Q8BHY8 UniProt NPD GO	SNX14_MOUSE	Sorting nexin-14	0.56	-	end	2 *					937
Q91WE1 UniProt NPD GO	SNX15_MOUSE	Sorting nexin-15	0.56	-	nuc	0					337
Q5A748 UniProt NPD GO	SNX3_CANAL	Sorting nexin-3	0.56	-	nuc	0	Cytoplasm (By similarity)				157
O42772 UniProt NPD GO	DHSB_MYCGR	Succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (EC 1.3.5.1) (IP)	0.56	-	mit	0	Mitochondrion; mitochondrial inner membrane				297
Q04672 UniProt NPD GO	SBP_SOYBN	Sucrose-binding protein precursor (SBP)	0.56	-	exc	1 *	Membrane; peripheral membrane protein				524
Q9JLY0 UniProt NPD GO	SOCS6_MOUSE	Suppressor of cytokine signaling 6 (SOCS-6) (Suppressor of cytokine signaling 4) (SOCS-4) (Cytokine- ...	0.56	-	nuc	0					533
P17599 UniProt NPD GO	SYN1_BOVIN	Synapsin-1 (Synapsin I)	0.56	-	mit	0	Synapse			1AUX	706
Q3TIR3 UniProt NPD GO	RIC8A_MOUSE	Synembryn-A (Protein Ric-8A)	0.56	-	nuc	0	Cytoplasm (By similarity)				530
Q64704 UniProt NPD GO	STX3_MOUSE	Syntaxin-3	0.56	-	cyt	1	Membrane; single-pass type IV membrane protein (Potential)				289
P20963 UniProt NPD GO	CD3Z_HUMAN	T-cell surface glycoprotein CD3 zeta chain precursor (T-cell receptor T3 zeta chain) (CD237 antigen) ...	0.56	-	nuc	1 *	Membrane; single-pass type I membrane protein	cytoplasm [IDA] plasma membrane [IDA] T cell receptor complex [IDA]	186780	1TCE	164
P20227 UniProt NPD GO	TBP_DROME	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (Tr ...	0.56	-	nuc	0	Nucleus	DNA-directed RNA polymerase III complex [IC] transcription factor TFIIIB complex [IPI]			353
P14232 UniProt NPD GO	TGA1A_TOBAC	TGACG-sequence-specific DNA-binding protein TGA-1A (TGA1a) (ASF-1 protein)	0.56	-	cyt	0	Nucleus				359
Q8NA92 UniProt NPD GO	THAP8_HUMAN	THAP domain-containing protein 8	0.56	-	nuc	0					274
Q5EDF9 UniProt NPD GO	TRH_BRARE	Thyroliberin precursor [Contains: Prothyroliberin; Thyroliberin (Thyrotropin-releasing hormone) (TRH ...	0.56	-	exc	0	Secreted protein				199
Q5KT11 UniProt NPD GO	TRH_CYPCA	Thyroliberin precursor [Contains: Prothyroliberin; Thyroliberin (Thyrotropin-releasing hormone) (TRH ...	0.56	-	exc	0	Secreted protein				187
Q96HZ4 UniProt NPD GO	HES6_HUMAN	Transcription cofactor HES-6 (Hairy and enhancer of split 6) (C-HAIRY1)	0.56	-	nuc	0	Nucleus (Probable)	transcription factor complex [ISS]			224
Q5ALX3 UniProt NPD GO	SPT5_CANAL	Transcription elongation factor SPT5 (Chromatin elongation factor SPT5)	0.56	+	cyt	0	Nucleus (By similarity)				956
Q60420 UniProt NPD GO	HTF4_MESAU	Transcription factor 12 (Transcription factor HTF-4) (E-box-binding protein) (DNA-binding protein HT ...	0.56	-	nuc	0	Nucleus				437
P54843 UniProt NPD GO	MAF_MOUSE	Transcription factor Maf (Proto-oncogene c-maf)	0.56	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			370
P54844 UniProt NPD GO	MAF_RAT	Transcription factor Maf (Proto-oncogene c-maf)	0.56	-	nuc	0	Nucleus				369
Q90WR8 UniProt NPD GO	SP3_CHICK	Transcription factor Sp3	0.56	-	nuc	0	Nucleus (By similarity)				771
Q04226 UniProt NPD GO	TAF11_YEAST	Transcription initiation factor TFIID subunit 11 (TBP-associated factor 11) (TBP-associated factor 4 ...	0.56	-	nuc	0	Nucleus	transcription factor TFIID complex [IDA]			346
P82798 UniProt NPD GO	ATRX_MACEU	Transcriptional regulator ATRX (EC 3.6.1.-) (ATP-dependent helicase ATRX) (X-linked nuclear protein) ...	0.56	-	vac	4	Nucleus (By similarity)				497
Q07141 UniProt NPD GO	TLE4_RAT	Transducin-like enhancer protein 4 (Protein ESP2)	0.56	-	nuc	0	Nucleus	nucleus [IDA]			741
P13474 UniProt NPD GO	ETS1A_CHICK	Transforming protein p54/c-ets-1	0.56	+	nuc	0		soluble fraction [IDA]			441
P55072 UniProt NPD GO	TERA_HUMAN	Transitional endoplasmic reticulum ATPase (TER ATPase) (15S Mg(2+)-ATPase p97 subunit) (Valosin-cont ...	0.56	+	cyt	0	Cytoplasm. Nucleus	cytosol [IDA] endoplasmic reticulum [IDA] microsome [ISS] nucleus [IDA]	601023		805
Q01853 UniProt NPD GO	TERA_MOUSE	Transitional endoplasmic reticulum ATPase (TER ATPase) (15S Mg(2+)-ATPase p97 subunit) (Valosin-cont ...	0.56	+	cyt	0	Cytoplasm. Nucleus	cytosol [ISS] endoplasmic reticulum [ISS] microsome [IDA]		1YQI	805
P46462 UniProt NPD GO	TERA_RAT	Transitional endoplasmic reticulum ATPase (TER ATPase) (15S Mg(2+)-ATPase p97 subunit) (Valosin-cont ...	0.56	+	cyt	0					805
Q8R310 UniProt NPD GO	TMCC3_MOUSE	Transmembrane and coiled-coil domains protein 3	0.56	-	end	1					446
Q9UPQ4 UniProt NPD GO	TRI35_HUMAN	Tripartite motif-containing protein 35 (Hemopoietic lineage switch protein 5)	0.56	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Found predominantly in cytoplasm with a granular ...				493
Q6P9F5 UniProt NPD GO	TRI40_HUMAN	Tripartite motif-containing protein 40 (RING finger protein 35)	0.56	-	nuc	0					258
Q5PQN5 UniProt NPD GO	TRI55_RAT	Tripartite motif-containing protein 55 (Muscle-specific RING finger protein 2) (MuRF2) (MURF-2) (RIN ...	0.56	-	nuc	0	Cytoplasm. Nucleus. Nuclear under atrophic conditions and upon mechanical signals. Localizes to the ...				545

You are viewing entries 21651 to 21700 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.