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
P31109 UniProt NPD GO	SNC1_YEAST	Synaptobrevin homolog 1	0.07	-	nuc	1	Intracytoplasmic membrane; single-pass type IV membrane protein. Post-Golgi vesicle membrane (Probab ...	transport vesicle [IDA]			117
Q5RF94 UniProt NPD GO	SYBL1_PONPY	Synaptobrevin-like protein 1	0.07	-	cyt	1	Membrane; single-pass type IV membrane protein (Probable)				219
P51809 UniProt NPD GO	SYBL1_HUMAN	Synaptobrevin-like protein 1 (Tetanus insensitive VAMP) (Ti-VAMP) (Ti-VAMP/VAMP7)	0.07	-	cyt	1	Membrane; single-pass type IV membrane protein (Probable)	integral to membrane [NAS]	300053		219
O95473 UniProt NPD GO	SNG4_HUMAN	Synaptogyrin-4	0.07	-	end	3 *	Membrane; multi-pass membrane protein				234
P31431 UniProt NPD GO	SDC4_HUMAN	Syndecan-4 precursor (SYND4) (Amphiglycan) (Ryudocan core protein)	0.07	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	600017	1YBO	198
O35988 UniProt NPD GO	SDC4_MOUSE	Syndecan-4 precursor (SYND4) (Ryudocan core protein)	0.07	-	end	1	Membrane; single-pass type I membrane protein	cell surface [IDA]			198
O08992 UniProt NPD GO	SDCB1_MOUSE	Syntenin-1 (Syndecan-binding protein 1) (Scaffold protein Pbp1)	0.07	-	cyt	1	Membrane; peripheral membrane protein (By similarity)	adherens junction [ISS] cytoskeleton [ISS] interleukin-5 receptor complex [IMP] membrane [ISS] nucleus [ISS]			299
Q99624 UniProt NPD GO	S38A3_HUMAN	System N amino acid transporter 1 (SN1) (N-system amino acid transporter 1) (Solute carrier family 3 ...	0.07	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [ISS]	604437		504
P01735 UniProt NPD GO	TVB2_MOUSE	T-cell receptor beta chain V region 86T1 precursor	0.07	-	mit	0					133
Q29422 UniProt NPD GO	CD1B2_SHEEP	T-cell surface glycoprotein CD1b-2 precursor (CD1b-2 antigen) (SCD1B-42) (Antigen IAH-CC14)	0.07	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				333
Q28073 UniProt NPD GO	CD3E_BOVIN	T-cell surface glycoprotein CD3 epsilon chain precursor	0.07	-	end	1	Membrane; single-pass type I membrane protein				192
Q5R1Q1 UniProt NPD GO	CD3E_FELCA	T-cell surface glycoprotein CD3 epsilon chain precursor	0.07	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)				202
P17987 UniProt NPD GO	TCPA_HUMAN	T-complex protein 1 subunit alpha (TCP-1-alpha) (CCT-alpha)	0.07	-	cyt	0	Cytoplasm	cytosol [TAS]	186980		556
Q75A36 UniProt NPD GO	TCPD_ASHGO	T-complex protein 1 subunit delta (TCP-1-delta) (CCT-delta)	0.07	-	cyt	0	Cytoplasm (Potential)				529
Q6CL82 UniProt NPD GO	TCPD_KLULA	T-complex protein 1 subunit delta (TCP-1-delta) (CCT-delta)	0.07	-	cyt	0	Cytoplasm (Potential)				530
P39077 UniProt NPD GO	TCPG_YEAST	T-complex protein 1 subunit gamma (TCP-1-gamma) (CCT-gamma)	0.07	-	nuc	0	Cytoplasm	chaperonin-containing T-complex [IPI] cytoplasm [TAS] cytoskeleton [TAS]			534
Q9Y3F1 UniProt NPD GO	TA6P_HUMAN	TAP2-associated 6.5 kDa polypeptide	0.07	-	cyt	0					56
Q8W0W4 UniProt NPD GO	TBP2_ORYSA	TATA-binding protein 2 (TATA-box factor 2) (TATA-binding factor 2) (TATA sequence-binding protein 2) ...	0.07	-	cyt	0	Nucleus				203
P50158 UniProt NPD GO	TBP1_MAIZE	TATA-box-binding protein 1 (TATA-box factor 1) (TATA-binding factor 1) (TATA sequence-binding protei ...	0.07	-	mit	0	Nucleus				200
Q9H944 UniProt NPD GO	TRFP_HUMAN	TRF-proximal protein homolog	0.07	-	cyt	0	Nucleus (Probable)	Srb-mediator complex [NAS]			212
O97860 UniProt NPD GO	PPA5_RABIT	Tartrate-resistant acid phosphatase type 5 precursor (EC 3.1.3.2) (TR-AP) (Tartrate-resistant acid A ...	0.07	-	mit	0	Lysosome (By similarity)				325
Q925D8 UniProt NPD GO	TS1R3_MOUSE	Taste receptor type 1 member 3 precursor (Sweet taste receptor T1R3) (Saccharin preference protein)	0.07	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			858
Q8MJU6 UniProt NPD GO	TA2R1_CERAE	Taste receptor type 2 member 1 (T2R1)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				299
Q646G7 UniProt NPD GO	TA2R1_GORGO	Taste receptor type 2 member 1 (T2R1)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				299
Q646G6 UniProt NPD GO	TA2R1_PONPY	Taste receptor type 2 member 1 (T2R1)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				299
Q9NYW7 UniProt NPD GO	TA2R1_HUMAN	Taste receptor type 2 member 1 (T2R1) (Taste receptor family B member 7) (TRB7)	0.07	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	604796		299
Q646D8 UniProt NPD GO	T2R13_PANPA	Taste receptor type 2 member 13 (T2R13)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				303
Q646B6 UniProt NPD GO	T2R13_PANTR	Taste receptor type 2 member 13 (T2R13)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				303
Q67ET7 UniProt NPD GO	TA2R3_RAT	Taste receptor type 2 member 3 (T2R3) (T2R11)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				316
Q697L2 UniProt NPD GO	T2R38_HYLKL	Taste receptor type 2 member 38 (T2R38)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				333
Q7TQA6 UniProt NPD GO	T2R38_MOUSE	Taste receptor type 2 member 38 (T2R38) (T2R138) (mT2R31)	0.07	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			331
P59536 UniProt NPD GO	T2R41_HUMAN	Taste receptor type 2 member 41 (T2R41) (T2R59)	0.07	-	end	6 *	Membrane; multi-pass membrane protein				307
Q645T9 UniProt NPD GO	T2R42_MACMU	Taste receptor type 2 member 42 (T2R42) (T2R55)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				314
Q646A0 UniProt NPD GO	T2R49_GORGO	Taste receptor type 2 member 49 (T2R49)	0.07	+	end	7 *	Membrane; multi-pass membrane protein				309
Q646D0 UniProt NPD GO	T2R60_PANPA	Taste receptor type 2 member 60 (T2R60) (T2R56)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				318
Q646A5 UniProt NPD GO	T2R60_PANTR	Taste receptor type 2 member 60 (T2R60) (T2R56)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				318
Q6PN82 UniProt NPD GO	CX54A_CONMR	Tau conotoxin mr5.4a precursor	0.07	-	exc	0	Secreted protein (By similarity)				62
P15242 UniProt NPD GO	TEST2_RAT	Testin 2 precursor (CMB-23) [Contains: Testin 1 (CMB-22)]	0.07	-	vac	0	Secreted protein				333
Q9D2E1 UniProt NPD GO	TSSK3_MOUSE	Testis-specific serine/threonine-protein kinase 3 (EC 2.7.11.1) (TSSK-3) (Testis-specific kinase 3) ...	0.07	-	cyt	0		intracellular [IC]			268
Q9JHJ7 UniProt NPD GO	TEST_MOUSE	Testisin precursor (EC 3.4.21.-) (Tryptase 4)	0.07	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	membrane fraction [IDA]			324
Q2KIS7 UniProt NPD GO	TETN_BOVIN	Tetranectin precursor (TN) (C-type lectin domain family 3 member B)	0.07	-	nuc	0	Secreted protein (By similarity)				202
P05167 UniProt NPD GO	ALEU_HORVU	Thiol protease aleurain precursor (EC 3.4.22.16)	0.07	-	exc	1 *	Vacuole. Vacuole-like subcellular compartment				362
Q9CQU0 UniProt NPD GO	TXD12_MOUSE	Thioredoxin domain-containing protein 12 precursor (EC 1.8.4.2) (Thioredoxin-like protein p19) (Endo ...	0.07	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen				170
O95881 UniProt NPD GO	TXD12_HUMAN	Thioredoxin domain-containing protein 12 precursor (EC 1.8.4.2) (Thioredoxin-like protein p19) (Endo ...	0.07	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen		609448	1SEN	172
Q6C7L4 UniProt NPD GO	TRXB_YARLI	Thioredoxin reductase (EC 1.8.1.9)	0.07	-	cyt	0	Cytoplasm (By similarity)				319
Q9JLT4 UniProt NPD GO	TRXR2_MOUSE	Thioredoxin reductase 2, mitochondrial precursor (EC 1.8.1.9) (TR3)	0.07	-	mit	0	Mitochondrion	mitochondrion [IEP]		1ZKQ	524
Q9Z0J5 UniProt NPD GO	TRXR2_RAT	Thioredoxin reductase 2, mitochondrial precursor (EC 1.8.1.9) (TR3)	0.07	-	mit	0	Mitochondrion	mitochondrion [IEP]			526
O43396 UniProt NPD GO	TXNL1_HUMAN	Thioredoxin-like protein 1 (32 kDa thioredoxin-related protein)	0.07	-	cyt	0	Cytoplasm	cytoplasm [TAS]	603049	1WWY	288
Q8CDN6 UniProt NPD GO	TXNL1_MOUSE	Thioredoxin-like protein 1 (32 kDa thioredoxin-related protein)	0.07	-	cyt	0	Cytoplasm (By similarity)				288
Q920J4 UniProt NPD GO	TXNL1_RAT	Thioredoxin-like protein 1 (Thioredoxin-related protein)	0.07	-	cyt	0	Cytoplasm (By similarity)				288

You are viewing entries 71101 to 71150 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.