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
P28769 UniProt NPD GO	TCPA_ARATH	T-complex protein 1 subunit alpha (TCP-1-alpha) (CCT-alpha)	0.09	-	cyt	0	Cytoplasm				545
Q9NB32 UniProt NPD GO	TCPD_AEDTR	T-complex protein 1 subunit delta (TCP-1-delta) (CCT-delta)	0.09	-	nuc	0	Cytoplasm				533
Q6FQT2 UniProt NPD GO	TCPD_CANGA	T-complex protein 1 subunit delta (TCP-1-delta) (CCT-delta)	0.09	-	cyt	0	Cytoplasm (Potential)				529
P01048 UniProt NPD GO	KNT1_RAT	T-kininogen 1 precursor (T-kininogen I) (Major acute phase protein) (Alpha-1-MAP) (Thiostatin) [Cont ...	0.09	-	exc	0	Secreted protein; extracellular space				430
Q9W6Z2 UniProt NPD GO	TBLP1_XENLA	TATA box-binding protein-like protein 1 (TBP-like protein 1) (TBP-like factor)	0.09	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				186
Q9D8Z2 UniProt NPD GO	TRIA1_MOUSE	TP53-regulated inhibitor of apoptosis 1 (p53-inducible cell-survival factor) (p53CSV) (Protein 15E1. ...	0.09	-	nuc	0	Cytoplasm; perinuclear region (By similarity)	mitochondrion [ISS]			76
Q6X9T7 UniProt NPD GO	TYOBP_RAT	TYRO protein tyrosine kinase-binding protein precursor (DNAX-activation protein 12)	0.09	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				114
Q99PG6 UniProt NPD GO	TS1R1_MOUSE	Taste receptor type 1 member 1 precursor (G-protein coupled receptor 70)	0.09	-	end	7	Membrane; multi-pass membrane protein				842
Q645Z4 UniProt NPD GO	T2R10_GORGO	Taste receptor type 2 member 10 (T2R10)	0.09	-	end	7 *	Membrane; multi-pass membrane protein				307
Q67ES7 UniProt NPD GO	TR134_RAT	Taste receptor type 2 member 134 (T2R134) (T2R34) (Taste receptor type 2 member 23) (T2R23)	0.09	-	end	6 *	Membrane; multi-pass membrane protein				329
Q7TQB0 UniProt NPD GO	TR134_MOUSE	Taste receptor type 2 member 134 (T2R134) (Taste receptor type 2 member 34) (T2R34)	0.09	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			298
Q697L4 UniProt NPD GO	T2R38_GORGO	Taste receptor type 2 member 38 (T2R38)	0.09	-	end	7 *	Membrane; multi-pass membrane protein				333
Q6PN85 UniProt NPD GO	CX51B_CONMR	Tau conotoxin mr5.1b precursor	0.09	-	exc	0	Secreted protein (By similarity)				65
Q6PN84 UniProt NPD GO	CX52_CONMR	Tau conotoxin mr5.2 precursor (Gla-MrIII)	0.09	-	exc	0	Secreted protein (By similarity)				66
Q9BXU2 UniProt NPD GO	TX13B_HUMAN	Testis-expressed sequence 13B protein	0.09	-	cyt	0			300313		312
Q9Y6I9 UniProt NPD GO	TX264_HUMAN	Testis-expressed sequence 264 protein precursor (Secreted protein ZSIG11)	0.09	-	mit	1 *	Secreted protein (Potential)				313
Q9Y6M0 UniProt NPD GO	TEST_HUMAN	Testisin precursor (EC 3.4.21.-) (Eosinophil serine protease 1) (ESP-1)	0.09	-	end	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)	cytoplasm [TAS] membrane fraction [TAS] plasma membrane [TAS]	608159		314
P83747 UniProt NPD GO	TX3_THEBL	Theraphotoxin-3 (TlTx3)	0.09	-	nuc	0	Secreted protein				35
P41835 UniProt NPD GO	THI6_YEAST	Thiamine biosynthetic bifunctional enzyme [Includes: Thiamine-phosphate pyrophosphorylase (EC 2.5.1. ...	0.09	-	cyt	0		cytoplasm [IDA]			540
Q3BCR4 UniProt NPD GO	TPMT_CERAE	Thiopurine S-methyltransferase (EC 2.1.1.67) (Thiopurine methyltransferase)	0.09	-	cyt	0	Cytoplasm				245
Q9MT28 UniProt NPD GO	THRC_SOLTU	Threonine synthase, chloroplast precursor (EC 4.2.3.1) (TS)	0.09	-	pox	0	Plastid; chloroplast (By similarity)				519
Q866G7 UniProt NPD GO	TSCOT_CANFA	Thymic stromal cotransporter homolog (CE11)	0.09	-	end	10	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membranes o ...				481
Q8SRG2 UniProt NPD GO	TYS3_ENCCU	Thymidylate synthase 3 (EC 2.1.1.45) (TS 3) (TSase 3)	0.09	-	cyt	0					294
P20065 UniProt NPD GO	TYB4_MOUSE	Thymosin beta-4 (T beta 4) [Contains: Hematopoietic system regulatory peptide (Seraspenide)]	0.09	-	nuc	0	Cytoplasm	cytosol [IDA] nucleus [IDA]		1T44	50
Q92748 UniProt NPD GO	THRSP_HUMAN	Thyroid hormone-inducible hepatic protein (Spot 14 protein) (SPOT14) (S14 protein)	0.09	-	cyt	0	Nucleus		601926		146
P04143 UniProt NPD GO	THRSP_RAT	Thyroid hormone-inducible hepatic protein (Spot 14 protein) (SPOT14) (S14 protein)	0.09	-	mit	0	Nucleus				150
Q9ZSK1 UniProt NPD GO	GTOMC_ARATH	Tocopherol O-methyltransferase, chloroplast precursor (EC 2.1.1.95) (Gamma-tocopherol methyltransfer ...	0.09	-	mit	0	Plastid; chloroplast (By similarity)				348
P60977 UniProt NPD GO	CALB_CALS5	Toxic peptide B	0.09	-	nuc	0	Secreted protein				39
P60978 UniProt NPD GO	CALC_CALS5	Toxic peptide C	0.09	-	nuc	0	Secreted protein				39
Q5QD21 UniProt NPD GO	TAA7C_RAT	Trace amine-associated receptor 7c	0.09	-	end	7 *	Membrane; multi-pass membrane protein				358
Q29593 UniProt NPD GO	TALDO_PIG	Transaldolase (EC 2.2.1.2) (Fragment)	0.09	-	nuc	0	Cytoplasm (Probable)				61
Q7S743 UniProt NPD GO	SPT4_NEUCR	Transcription elongation factor spt-4 (Chromatin elongation factor spt-4)	0.09	-	mit	0	Nucleus. Centromere and heterochromatin (By similarity)				120
Q15582 UniProt NPD GO	BGH3_HUMAN	Transforming growth factor-beta-induced protein ig-h3 precursor (Beta ig-h3) (Kerato-epithelin) (RGD ...	0.09	-	exc	1 *	Secreted protein; extracellular space. May be associated both with microfibrils and with the cell su ...	extracellular space [TAS]	121900	1X3B	683
P50137 UniProt NPD GO	TKT_RAT	Transketolase (EC 2.2.1.1) (TK)	0.09	-	cyt	0					623
Q14232 UniProt NPD GO	EI2BA_HUMAN	Translation initiation factor eIF-2B subunit alpha (eIF-2B GDP-GTP exchange factor subunit alpha)	0.09	-	cyt	0			606686		305
Q4R4V8 UniProt NPD GO	EI2BA_MACFA	Translation initiation factor eIF-2B subunit alpha (eIF-2B GDP-GTP exchange factor subunit alpha)	0.09	-	cyt	0					305
Q9USP0 UniProt NPD GO	EI2BA_SCHPO	Translation initiation factor eIF-2B subunit alpha (eIF-2B GDP-GTP exchange factor subunit alpha)	0.09	-	mit	0					341
Q962A2 UniProt NPD GO	TCTP_WUCBA	Translationally-controlled tumor protein homolog (TCTP)	0.09	-	cyt	0	Cytoplasm (By similarity)				181
P90697 UniProt NPD GO	TCTP_BRUMA	Translationally-controlled tumor protein homolog (TCTP) (TPH-1)	0.09	-	cyt	0	Cytoplasm (By similarity)				181
P43308 UniProt NPD GO	SSRB_HUMAN	Translocon-associated protein subunit beta precursor (TRAP-beta) (Signal sequence receptor subunit b ...	0.09	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	endoplasmic reticulum [TAS] integral to membrane [TAS]	600867		183
Q9CPW5 UniProt NPD GO	SSRB_MOUSE	Translocon-associated protein subunit beta precursor (TRAP-beta) (Signal sequence receptor subunit b ...	0.09	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				183
O14894 UniProt NPD GO	T4S5_HUMAN	Transmembrane 4 L6 family member 5 (Tetraspan transmembrane protein L6H)	0.09	-	end	4 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	604657		197
Q9BZD6 UniProt NPD GO	TMG4_HUMAN	Transmembrane gamma-carboxyglutamic acid protein 4 precursor (Proline-rich Gla protein 4) (Proline-r ...	0.09	-	end	1	Membrane; single-pass type I membrane protein	integral to membrane [NAS]			226
Q9H3S3 UniProt NPD GO	TMPS5_HUMAN	Transmembrane protease, serine 5 (EC 3.4.21.-) (Spinesin)	0.09	-	gol	1 *	Membrane; single-pass type II membrane protein (Potential)		606751		457
Q569C0 UniProt NPD GO	TM100_RAT	Transmembrane protein 100	0.09	-	end	2	Membrane; multi-pass membrane protein (Potential)				134
Q8TBE7 UniProt NPD GO	TMM22_HUMAN	Transmembrane protein 22	0.09	-	end	10	Membrane; multi-pass membrane protein (Potential)				412
Q6IP19 UniProt NPD GO	TMM47_XENLA	Transmembrane protein 47 (Transmembrane 4 superfamily member 10)	0.09	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				179
P40416 UniProt NPD GO	ATM1_YEAST	Transporter ATM1, mitochondrial precursor	0.09	-	mit	5	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA]			690
Q03403 UniProt NPD GO	TFF2_HUMAN	Trefoil factor 2 precursor (Spasmolytic polypeptide) (SP) (Spasmolysin)	0.09	-	exc	0	Secreted protein		182590		129
P01370 UniProt NPD GO	TA13_TREME	Tremerogen A-13	0.09	-		0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				13

You are viewing entries 67151 to 67200 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.