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
Q646H0 UniProt NPD GO	TA2R1_PANTR	Taste receptor type 2 member 1 (T2R1)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				299
Q67ES3 UniProt NPD GO	TR143_RAT	Taste receptor type 2 member 143 (T2R143) (Taste receptor type 2 member 27) (T2R27)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				294
Q9JKT2 UniProt NPD GO	T2R19_MOUSE	Taste receptor type 2 member 19 (T2R19)	0.06	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			335
Q646F3 UniProt NPD GO	T2R41_PAPHA	Taste receptor type 2 member 41 (T2R41)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				307
Q646F9 UniProt NPD GO	T2R44_PAPHA	Taste receptor type 2 member 44 (T2R44)	0.06	-	end	6 *	Membrane; multi-pass membrane protein				309
Q646E1 UniProt NPD GO	T2R46_PANPA	Taste receptor type 2 member 46 (T2R46)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				309
Q646C0 UniProt NPD GO	T2R46_PANTR	Taste receptor type 2 member 46 (T2R46)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				309
P59541 UniProt NPD GO	T2R47_HUMAN	Taste receptor type 2 member 47 (T2R47)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				319
Q646C1 UniProt NPD GO	T2R47_PANTR	Taste receptor type 2 member 47 (T2R47)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				319
Q646E3 UniProt NPD GO	T2R49_PANPA	Taste receptor type 2 member 49 (T2R49)	0.06	+	end	7 *	Membrane; multi-pass membrane protein				309
Q646C2 UniProt NPD GO	T2R49_PANTR	Taste receptor type 2 member 49 (T2R49)	0.06	+	end	7 *	Membrane; multi-pass membrane protein				309
Q646G1 UniProt NPD GO	T2R49_PAPHA	Taste receptor type 2 member 49 (T2R49)	0.06	+	end	7 *	Membrane; multi-pass membrane protein				309
Q645V6 UniProt NPD GO	T2R49_PONPY	Taste receptor type 2 member 49 (T2R49)	0.06	+	end	7 *	Membrane; multi-pass membrane protein				309
P59543 UniProt NPD GO	T2R49_HUMAN	Taste receptor type 2 member 49 (T2R49) (T2R56)	0.06	+	end	7 *	Membrane; multi-pass membrane protein				309
Q645Z1 UniProt NPD GO	TA2R5_GORGO	Taste receptor type 2 member 5 (T2R5)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				299
Q9NYW4 UniProt NPD GO	TA2R5_HUMAN	Taste receptor type 2 member 5 (T2R5)	0.06	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IC]	605062		299
Q646D5 UniProt NPD GO	TA2R5_PANPA	Taste receptor type 2 member 5 (T2R5)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				299
Q646A4 UniProt NPD GO	TA2R5_PANTR	Taste receptor type 2 member 5 (T2R5)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				299
Q645U0 UniProt NPD GO	TA2R5_PONPY	Taste receptor type 2 member 5 (T2R5)	0.06	-	end	7 *	Membrane; multi-pass membrane protein				299
Q8S9G6 UniProt NPD GO	T5AT_TAXCH	Taxadien-5-alpha-ol O-acetyltransferase (EC 2.3.1.162) (Taxa-4(20),11(12)-dien-5alpha-ol-O-acetyltra ...	0.06	-	cyt	0					439
Q9M6F0 UniProt NPD GO	T5AT_TAXCU	Taxadien-5-alpha-ol O-acetyltransferase (EC 2.3.1.162) (Taxa-4(20),11(12)-dien-5alpha-ol-O-acetyltra ...	0.06	-	cyt	0					439
Q9US52 UniProt NPD GO	BQT2_SCHPO	Telomere bouquet protein 2 (Meiotic chromosome segregation protein bqt2) (Meiotically up-regulated p ...	0.06	-	cyt	0	Nucleus. Spindle pole body. Colocalizes with the telomere cluster during the 'horsetail' stage and t ...				118
Q27270 UniProt NPD GO	TEN3_TENMO	Tenecin-3 precursor	0.06	-	vac	0	Secreted protein				96
Q9H2S6 UniProt NPD GO	TNMD_HUMAN	Tenomodulin (TeM) (hTeM) (Chondromodulin-I-like protein) (ChM1L) (hChM1L) (Myodulin) (Tendin)	0.06	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)		300459		317
Q96PN8 UniProt NPD GO	TSSK3_HUMAN	Testis-specific serine/threonine-protein kinase 3 (EC 2.7.11.1) (TSSK-3) (Testis-specific kinase 3) ...	0.06	-	cyt	0		intracellular [ISS]	607660		268
O60637 UniProt NPD GO	TSN3_HUMAN	Tetraspanin-3 (Tspan-3) (Transmembrane 4 superfamily member 8) (Tetraspanin TM4-A)	0.06	-	end	4 *	Membrane; multi-pass membrane protein (Probable)	integral to membrane [TAS]			253
Q9QY33 UniProt NPD GO	TSN3_MOUSE	Tetraspanin-3 (Tspan-3) (Transmembrane 4 superfamily member 8) (Tetraspanin TM4-A) (OSP-associated p ...	0.06	-	end	4 *	Membrane; multi-pass membrane protein (Probable)				253
Q9SMH2 UniProt NPD GO	TLP1_CASSA	Thaumatin-like protein 1 precursor	0.06	-	nuc	0	Secreted protein (Potential)				243
P27357 UniProt NPD GO	TLP_WHEAT	Thaumatin-like protein PWIR2 precursor	0.06	-	exc	0					173
P50694 UniProt NPD GO	TLP_PRUAV	Thaumatin-like protein precursor	0.06	-	exc	1 *	Secreted protein (Potential)				245
Q07471 UniProt NPD GO	THI3_YEAST	Thiamine metabolism regulatory protein THI3 (EC 4.1.1.-) (Keto isocaproate decarboxylase KID1)	0.06	-	cyt	0	Nucleus	nucleus [IDA]			609
Q9BZV2 UniProt NPD GO	S19A3_HUMAN	Thiamine transporter 2 (ThTr-2) (ThTr2) (Solute carrier family 19 member 3)	0.06	-	end	12 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]	607483		496
Q4R877 UniProt NPD GO	S19A3_MACFA	Thiamine transporter 2 (ThTr-2) (ThTr2) (Solute carrier family 19 member 3)	0.06	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				496
P51361 UniProt NPD GO	THIG_PORPU	Thiazole biosynthesis protein thiG	0.06	-	cyt	0	Plastid; chloroplast				277
P20108 UniProt NPD GO	PRDX3_MOUSE	Thioredoxin-dependent peroxide reductase, mitochondrial precursor (EC 1.11.1.15) (Perioredoxin-3) (P ...	0.06	-	mit	0	Mitochondrion (By similarity)	mitochondrion [IDA]			257
Q9NX01 UniProt NPD GO	TXN4B_HUMAN	Thioredoxin-like protein 4B (Dim1-like protein)	0.06	-	nuc	0	Nucleus			1XBS	149
Q42598 UniProt NPD GO	THRC_SCHPO	Threonine synthase (EC 4.2.3.1) (TS)	0.06	-	cyt	0					514
P56486 UniProt NPD GO	TA2R_CERAE	Thromboxane A2 receptor (TXA2-R) (Prostanoid TP receptor)	0.06	-	end	6 *	Membrane; multi-pass membrane protein				343
Q8CA03 UniProt NPD GO	TSCOT_MOUSE	Thymic stromal cotransporter protein	0.06	-	end	11	Cell membrane; multi-pass membrane protein (Probable)	cell surface [IDA]			479
P00572 UniProt NPD GO	KTHY_YEAST	Thymidylate kinase (EC 2.7.4.9) (dTMP kinase)	0.06	-	cyt	0		cytoplasm [IDA] nucleus [IDA]		3TMK	216
P12461 UniProt NPD GO	TYSY_CANAL	Thymidylate synthase (EC 2.1.1.45) (TS) (TSase)	0.06	-	cyt	0					314
P26352 UniProt NPD GO	TYB12_ONCMY	Thymosin beta-12	0.06	-	nuc	0	Cytoplasm				42
P34981 UniProt NPD GO	TRFR_HUMAN	Thyrotropin-releasing hormone receptor (TRH-R) (Thyroliberin receptor)	0.06	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	188545		398
P05543 UniProt NPD GO	THBG_HUMAN	Thyroxine-binding globulin precursor (T4-binding globulin) (Serpin A7)	0.06	-	end	0	Secreted protein	extracellular region [NAS] extracellular space [TAS]	314200		415
P61640 UniProt NPD GO	THBG_PANTR	Thyroxine-binding globulin precursor (T4-binding globulin) (Serpin A7)	0.06	-	end	0	Secreted protein				415
Q9ERA9 UniProt NPD GO	TOR1A_CRICR	Torsin A (Torsin family 1 member A) (Dystonia 1 protein) (Fragment)	0.06	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				273
O14656 UniProt NPD GO	TOR1A_HUMAN	Torsin A precursor (Torsin family 1 member A) (Dystonia 1 protein)	0.06	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen. Mainly. Nucleus; nuclear membrane. Also found as ...	cytoplasm [TAS] endoplasmic reticulum [TAS]	605204		332
Q60HG2 UniProt NPD GO	TOR1A_MACFA	Torsin A precursor (Torsin family 1 member A) (Dystonia 1 protein)	0.06	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				332
O14657 UniProt NPD GO	TOR1B_HUMAN	Torsin B precursor (Torsin family 1 member B)	0.06	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)		608050		336
P60272 UniProt NPD GO	TXMO_HADIN	Toxin ACTX-Hi:OB4219	0.06	-	nuc	0	Secreted protein			1KQI	38

You are viewing entries 73301 to 73350 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.