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
Q5RD01 UniProt NPD GO	PCTK3_PONPY	Serine/threonine-protein kinase PCTAIRE-3 (EC 2.7.11.22) (PCTAIRE-motif protein kinase 3)	0.77	-	nuc	0					472
Q62673 UniProt NPD GO	PLK1_RAT	Serine/threonine-protein kinase PLK1 (EC 2.7.11.21) (Polo-like kinase 1) (PLK-1)	0.77	-	nuc	0	Nucleus (By similarity)				603
Q70PP2 UniProt NPD GO	SMG1_DROME	Serine/threonine-protein kinase Smg1 (EC 2.7.11.1)	0.77	-	nuc	0	Cytoplasm	cytoplasm [ISS] nucleus [ISS]			3218
Q5BBL3 UniProt NPD GO	STE20_EMENI	Serine/threonine-protein kinase ste20 (EC 2.7.11.1)	0.77	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				848
Q4WVM7 UniProt NPD GO	ATM_ASPFU	Serine/threonine-protein kinase tel1 (EC 2.7.11.1) (DNA-damage checkpoint kinase tel1) (Telomere len ...	0.77	-	end	0	Nucleus. Localizes to nuclear DNA repair foci with other DNA repair proteins in response to DNA doub ...				2796
Q767K9 UniProt NPD GO	PP1RA_PIG	Serine/threonine-protein phosphatase 1 regulatory subunit 10 (MHC class I region proline-rich protei ...	0.77	+	nuc	0	Nucleus. Found in discrete nucleoplasmic bodies and within nucleoli (By similarity)				925
O55000 UniProt NPD GO	PP1RA_RAT	Serine/threonine-protein phosphatase 1 regulatory subunit 10 (Phosphatase 1 nuclear targeting subuni ...	0.77	+	nuc	0	Nucleus. Found in discrete nucleoplasmic bodies and within nucleoli (By similarity)	nuclear chromatin [IDA]			872
Q6CPD5 UniProt NPD GO	PP4R2_KLULA	Serine/threonine-protein phosphatase 4 regulatory subunit 2 (PP4R2)	0.77	-	nuc	0	Nucleus (By similarity)				402
Q764M5 UniProt NPD GO	STAT1_PIG	Signal transducer and activator of transcription 1	0.77	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Translocated into the nucleus in response to pho ...				757
O75093 UniProt NPD GO	SLIT1_HUMAN	Slit homolog 1 protein precursor (Slit-1) (Multiple epidermal growth factor-like domains 4)	0.77	-	nuc	0	Secreted protein (By similarity)	extracellular space [TAS]	603742		1534
O14120 UniProt NPD GO	MVP1_SCHPO	Sorting nexin mvp1	0.77	-	nuc	0	Cytoplasm (By similarity)				664
Q9GJU4 UniProt NPD GO	HSP1_MACMU	Sperm protamine P1	0.77	+	nuc	0	Nucleus (By similarity)	nucleoplasm [ISS]			50
Q7JIX8 UniProt NPD GO	HSP1_PAPCY	Sperm protamine P1	0.77	+	nuc	0	Nucleus (By similarity)	nucleoplasm [ISS]			50
Q8WNZ9 UniProt NPD GO	HSP1_PTEHP	Sperm protamine P1	0.77	+	nuc	0	Nucleus (By similarity)				48
Q9GKQ1 UniProt NPD GO	HSP1_SAISC	Sperm protamine P1	0.77	+	nuc	0	Nucleus (By similarity)				49
P83215 UniProt NPD GO	HSP3_OCTVU	Sperm protamine P3 (Po3) (Fragment)	0.77	+	nuc	0	Nucleus	nucleosome [NAS] nucleus [NAS]			24
P83265 UniProt NPD GO	PRT2_SCOSC	Sperm protamine alpha isoform 2 (Scombrine alpha-2)	0.77	+	nuc	0	Nucleus	nucleosome [TAS] nucleus [TAS]			34
P26369 UniProt NPD GO	U2AF2_MOUSE	Splicing factor U2AF 65 kDa subunit (U2 auxiliary factor 65 kDa subunit) (U2 snRNP auxiliary factor ...	0.77	+	nuc	0	Nucleus				475
P26368 UniProt NPD GO	U2AF2_HUMAN	Splicing factor U2AF 65 kDa subunit (U2 auxiliary factor 65 kDa subunit) (U2 snRNP auxiliary factor ...	0.77	+	nuc	0	Nucleus	spliceosome complex [IDA]	191318	2U2F	475
Q13247 UniProt NPD GO	SFRS6_HUMAN	Splicing factor, arginine/serine-rich 6 (Pre-mRNA-splicing factor SRP55)	0.77	+	nuc	0	Nucleus		601944		344
Q700W2 UniProt NPD GO	SPL9_ARATH	Squamosa promoter-binding-like protein 9	0.77	-	nuc	0	Nucleus (Probable)				375
Q90987 UniProt NPD GO	STMN2_CHICK	Stathmin-2 (SCG10 protein) (Superior cervical ganglion-10 protein)	0.77	-	nuc	0	Cytoplasm (By similarity). Cytoplasm; perinuclear region (By similarity). Associated with punctate s ...				179
P21818 UniProt NPD GO	STMN2_RAT	Stathmin-2 (SCG10 protein) (Superior cervical ganglion-10 protein)	0.77	-	nuc	0	Cytoplasm. Cytoplasm; perinuclear region. Associated with punctate structures in the perinuclear cyt ...				179
P52957 UniProt NPD GO	AFLR_EMENI	Sterigmatocystin biosynthesis regulatory protein	0.77	-	nuc	0	Nucleus (By similarity)				433
Q61539 UniProt NPD GO	ERR2_MOUSE	Steroid hormone receptor ERR2 (Estrogen-related receptor, beta) (ERR-beta) (Estrogen receptor-like 2 ...	0.77	-	nuc	0	Nucleus (Potential)				433
Q9Y6Q2 UniProt NPD GO	STON1_HUMAN	Stonin-1 (Stoned B-like factor)	0.77	-	nuc	0	Cytoplasm. Membrane. Some fraction is membrane-associated		605357		735
Q01846 UniProt NPD GO	MDM1_YEAST	Structural protein MDM1	0.77	-	end	1 *	Cytoplasm	cytoplasm [TAS] intermediate filament [TAS]			1127
Q8CHC4 UniProt NPD GO	SYNJ1_MOUSE	Synaptojanin-1 (EC 3.1.3.36) (Synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1)	0.77	-	nuc	0	Cytoplasm (By similarity)	clathrin coat [TAS]			1574
Q5R4L2 UniProt NPD GO	STX1A_PONPY	Syntaxin-1A	0.77	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				288
Q16623 UniProt NPD GO	STX1A_HUMAN	Syntaxin-1A (Neuron-specific antigen HPC-1)	0.77	-	gol	1	Cell membrane; single-pass type IV membrane protein. Isoform 2: Secreted protein (Probable)		186590		288
Q5T5C0 UniProt NPD GO	STXB5_HUMAN	Syntaxin-binding protein 5 (Tomosyn-1) (Lethal(2) giant larvae protein homolog 3)	0.77	-	mit	0	Cytoplasm (By similarity). Cell membrane; peripheral membrane protein (By similarity). Membrane; per ...		604586		1151
Q60707 UniProt NPD GO	TBX2_MOUSE	T-box transcription factor TBX2 (T-box protein 2)	0.77	-	nuc	0	Nucleus (Potential)	nucleus [IDA] transcription factor complex [IDA]			701
Q8TDR4 UniProt NPD GO	TCP1L_HUMAN	T-complex protein 10A homolog 2 (T-complex protein 10A-2) (TCP10A-2) (TCP10-like)	0.77	-	nuc	0					215
P82094 UniProt NPD GO	TMF1_HUMAN	TATA element modulatory factor (TMF)	0.77	-	nuc	0			601126		1093
Q5ZMV3 UniProt NPD GO	TBAP_CHICK	TATA-binding protein-associated phosphoprotein (Down-regulator of transcription 1)	0.77	-	nuc	0	Nucleus (By similarity)				176
Q01658 UniProt NPD GO	TBAP_HUMAN	TATA-binding protein-associated phosphoprotein (Down-regulator of transcription 1) (Dr1 protein) (Ne ...	0.77	-	nuc	0	Nucleus		601482	1JFI	176
Q91WV0 UniProt NPD GO	TBAP_MOUSE	TATA-binding protein-associated phosphoprotein (Down-regulator of transcription 1) (Negative cofacto ...	0.77	-	nuc	0	Nucleus (By similarity)				176
Q5XI68 UniProt NPD GO	TBAP_RAT	TATA-binding protein-associated phosphoprotein (Down-regulator of transcription 1) (Negative cofacto ...	0.77	-	nuc	0	Nucleus (By similarity)				176
Q8BYH7 UniProt NPD GO	TBC17_MOUSE	TBC1 domain family member 17	0.77	-	cyt	0					645
Q40392 UniProt NPD GO	TMVRN_NICGU	TMV resistance protein N	0.77	-	nuc	0	Cytoplasm (Probable)				1144
Q60803 UniProt NPD GO	TRAF3_MOUSE	TNF receptor-associated factor 3 (CD40 receptor-associated factor 1) (CRAF1) (TRAFAMN)	0.77	-	nuc	0					567
Q9Y4G6 UniProt NPD GO	TLN2_HUMAN	Talin-2	0.77	-	nuc	0	Cell membrane; cell-matrix junction; focal adhesion. Synapse. Focal adhesion plaques and synapses	actin cytoskeleton [NAS] intercellular junction [IC] synapse [NAS]	607349		2542
O88746 UniProt NPD GO	TOM1_MOUSE	Target of Myb protein 1	0.77	-	nuc	0	Cytoplasm (Probable)	cytosol [ISS] early endosome [ISS] membrane [ISS]			492
Q6IQ55 UniProt NPD GO	TTBK2_HUMAN	Tau-tubulin kinase 2 (EC 2.7.11.1)	0.77	-	nuc	0					1244
Q8N6V9 UniProt NPD GO	TEX9_HUMAN	Testis-expressed sequence 9 protein	0.77	-	nuc	0					391
O94900 UniProt NPD GO	TOX_HUMAN	Thymus high mobility group box protein TOX	0.77	+	nuc	0	Nucleus (By similarity)		606863		526
Q5JTD0 UniProt NPD GO	TJAP1_HUMAN	Tight junction-associated protein 1 (Tight junction protein 4) (Protein incorporated later into tigh ...	0.77	-	nuc	0	Golgi apparatus (By similarity). Cell membrane; cell-cell junction; tight junction (By similarity). ...				557
Q9JHE6 UniProt NPD GO	HES6_MOUSE	Transcription cofactor HES-6 (Hairy and enhancer of split 6)	0.77	-	nuc	0	Nucleus (Probable)	transcription factor complex [IDA]			224
Q39081 UniProt NPD GO	CAL_ARATH	Transcription factor CAULIFLOWER (Agamous-like MADS-box protein AGL10)	0.77	-	nuc	0	Nucleus				253
Q9Y5Q3 UniProt NPD GO	MAFB_HUMAN	Transcription factor MafB (V-maf musculoaponeurotic fibrosarcoma oncogene homolog B)	0.77	-	nuc	0	Nucleus (By similarity)	nucleus [TAS]	608968		323

You are viewing entries 10601 to 10650 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.