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
P30548 UniProt NPD GO	NK1R_MOUSE	Substance-P receptor (SPR) (NK-1 receptor) (NK-1R) (Tachykinin receptor 1)	0.10	-	end	7 *	Membrane; multi-pass membrane protein				407
Q6ZDY8 UniProt NPD GO	DHSA_ORYSA	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1) (FP) ...	0.10	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				630
Q920L2 UniProt NPD GO	DHSA_RAT	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1) (Fp) ...	0.10	-	cyt	0	Mitochondrion; mitochondrial inner membrane (By similarity)				656
P33303 UniProt NPD GO	SFC1_YEAST	Succinate/fumarate mitochondrial transporter (Regulator of acetyl-CoA synthetase activity)	0.10	-	end	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				322
O97580 UniProt NPD GO	SUCB1_PIG	Succinyl-CoA ligase [ADP-forming] beta-chain, mitochondrial precursor (EC 6.2.1.5) (Succinyl-CoA syn ...	0.10	-	cyt	0	Mitochondrion				425
P53400 UniProt NPD GO	SUCA2_TRIVA	Succinyl-CoA ligase [GDP-forming] subunit alpha-2, mitochondrial precursor (EC 6.2.1.4) (Succinyl-Co ...	0.10	-	cyt	0	Hydrogenosome				309
P31925 UniProt NPD GO	SUSY_SACOF	Sucrose synthase (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase) (Fragment)	0.10	-	cyt	0					218
Q41608 UniProt NPD GO	SUS1_TULGE	Sucrose synthase 1 (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase 1)	0.10	-	mit	0					805
P49035 UniProt NPD GO	SUS1_DAUCA	Sucrose synthase isoform I (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase 1) (Susy*Dc1)	0.10	-	cyt	0					808
Q58CP2 UniProt NPD GO	SUMF2_BOVIN	Sulfatase-modifying factor 2 precursor (C-alpha-formyglycine-generating enzyme 2)	0.10	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				301
P56862 UniProt NPD GO	MET3_ASPTE	Sulfate adenylyltransferase (EC 2.7.7.4) (Sulfate adenylate transferase) (SAT) (ATP-sulfurylase)	0.10	-	cyt	0					568
P50443 UniProt NPD GO	S26A2_HUMAN	Sulfate transporter (Diastrophic dysplasia protein) (Solute carrier family 26 member 2)	0.10	-	end	9	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	606718		739
P50226 UniProt NPD GO	ST1A2_HUMAN	Sulfotransferase 1A2 (EC 2.8.2.1) (Aryl sulfotransferase 2) (Phenol sulfotransferase 2) (Phenol-sulf ...	0.10	-	cyt	0	Cytoplasm		601292		295
Q6BK66 UniProt NPD GO	CCS1_DEBHA	Superoxide dismutase 1 copper chaperone	0.10	-	nuc	0	Cytoplasm (By similarity)				250
O13401 UniProt NPD GO	SODM_CANAL	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.10	-	mit	0	Mitochondrion; mitochondrial matrix				234
Q9UQX0 UniProt NPD GO	SODM_SCHPO	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.10	-	mit	0	Mitochondrion; mitochondrial matrix				218
P00447 UniProt NPD GO	SODM_YEAST	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.10	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA] mitochondrion [IDA]			233
Q09885 UniProt NPD GO	SVF1_SCHPO	Survival factor 1	0.10	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				380
O35775 UniProt NPD GO	SYCN_RAT	Syncollin (SIP9)	0.10	-	exc	1 *	Zymogen granule membrane protein				145
P18828 UniProt NPD GO	SDC1_MOUSE	Syndecan-1 precursor (SYND1)	0.10	-	end	1	Membrane; single-pass type I membrane protein	cell surface [IDA]			311
Q42374 UniProt NPD GO	SY111_ARATH	Syntaxin-related protein KNOLLE (Syntaxin-111) (AtSYP111)	0.10	-	nuc	1	Membrane; single-pass type IV membrane protein				310
Q8TB96 UniProt NPD GO	TIP_HUMAN	T-cell immunomodulatory protein precursor (Protein TIP) (Integrin alpha FG-GAP repeat-containing pro ...	0.10	-	end	2 *	Secreted protein (Potential). Membrane; single-pass type I membrane protein (Potential)				612
P56279 UniProt NPD GO	TCL1A_HUMAN	T-cell leukemia/lymphoma protein 1A (P14 TCL1 protein) (TCL1 oncogene) (TCL-1 protein)	0.10	-	cyt	0	Microsome. Microsomal fraction		186960	1JSG	114
P04436 UniProt NPD GO	TVA1_HUMAN	T-cell receptor alpha chain V region HPB-MLT precursor (Fragment)	0.10	-	mit	0		integral to plasma membrane [NAS]			131
P06322 UniProt NPD GO	TVA1_RABIT	T-cell receptor alpha chain V region RL-5 precursor	0.10	-	end	0					134
P06335 UniProt NPD GO	TCC4_MOUSE	T-cell receptor gamma chain C region 5/10-13	0.10	-	nuc	1					190
P03978 UniProt NPD GO	TVC2_MOUSE	T-cell receptor gamma chain V region V108B precursor (Fragment)	0.10	-	cyt	0					115
P29328 UniProt NPD GO	CD3E_SHEEP	T-cell surface glycoprotein CD3 epsilon chain precursor	0.10	-	end	1	Membrane; single-pass type I membrane protein				192
Q9XT06 UniProt NPD GO	TCPA_MONDO	T-complex protein 1 subunit alpha (TCP-1-alpha) (CCT-alpha)	0.10	-	cyt	0	Cytoplasm (By similarity)				557
O15891 UniProt NPD GO	TCPA_TETPY	T-complex protein 1 subunit alpha (TCP-1-alpha) (CCT-alpha)	0.10	-	nuc	0	Cytoplasm				547
Q5ZJK8 UniProt NPD GO	TCPH_CHICK	T-complex protein 1 subunit eta (TCP-1-eta) (CCT-eta)	0.10	-	cyt	0	Cytoplasm (By similarity)				553
P54408 UniProt NPD GO	TCPG_TETPY	T-complex protein 1 subunit gamma (TCP-1-gamma) (CCT-gamma)	0.10	-	cyt	0	Cytoplasm				559
P46550 UniProt NPD GO	TCPZ_CAEEL	T-complex protein 1 subunit zeta (TCP-1-zeta) (CCT-zeta)	0.10	-	mit	0	Cytoplasm (By similarity)				539
P26357 UniProt NPD GO	TBP_SOLTU	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (TB ...	0.10	-	mit	0	Nucleus				200
Q717B4 UniProt NPD GO	TDPZ3_MOUSE	TD and POZ domain-containing protein 3	0.10	-	cyt	0					365
O43715 UniProt NPD GO	TRIA1_HUMAN	TP53-regulated inhibitor of apoptosis 1 (p53-inducible cell-survival factor) (p53CSV) (Protein 15E1. ...	0.10	-	nuc	0	Cytoplasm; perinuclear region	mitochondrion [IDA]			76
Q99576 UniProt NPD GO	T22D3_HUMAN	TSC22 domain family protein 3 (Glucocorticoid-induced leucine zipper protein) (Delta sleep-inducing ...	0.10	-	cyt	0			300506		134
Q9Z2S7 UniProt NPD GO	T22D3_MOUSE	TSC22 domain family protein 3 (Glucocorticoid-induced leucine zipper protein) (TSC22-related-inducib ...	0.10	-	nuc	0					137
P13686 UniProt NPD GO	PPA5_HUMAN	Tartrate-resistant acid phosphatase type 5 precursor (EC 3.1.3.2) (TR-AP) (Tartrate-resistant acid A ...	0.10	-	mit	0	Lysosome	integral to membrane [TAS]	171640	2BQ8	325
Q9JKT5 UniProt NPD GO	TR105_RAT	Taste receptor type 2 member 105 (T2R105) (Taste receptor type 2 member 9) (T2R9)	0.10	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			309
P59533 UniProt NPD GO	T2R38_HUMAN	Taste receptor type 2 member 38 (T2R38) (T2R61) (PTC bitter taste receptor)	0.10	-	end	7 *	Membrane; multi-pass membrane protein		607751		333
Q645Y3 UniProt NPD GO	T2R41_GORGO	Taste receptor type 2 member 41 (T2R41)	0.10	-	end	6 *	Membrane; multi-pass membrane protein				307
Q645U9 UniProt NPD GO	T2R42_PONPY	Taste receptor type 2 member 42 (T2R42) (T2R55)	0.10	-	end	7 *	Membrane; multi-pass membrane protein				314
P83745 UniProt NPD GO	TX1_THEBL	Theraphotoxin-1 (TlTx1)	0.10	-	nuc	0	Secreted protein				35
Q06490 UniProt NPD GO	THI22_YEAST	Thiamine biosynthesis protein THI22 precursor	0.10	-	exc	0	Secreted protein (Potential)				572
Q6B924 UniProt NPD GO	THIG_GRATL	Thiazole biosynthesis protein thiG	0.10	-	nuc	0	Plastid; chloroplast				276
P43156 UniProt NPD GO	CYSP_HEMSP	Thiol protease SEN102 precursor (EC 3.4.22.-)	0.10	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				360
Q3BCR6 UniProt NPD GO	TPMT_HORSE	Thiopurine S-methyltransferase (EC 2.1.1.67) (Thiopurine methyltransferase)	0.10	-	cyt	0	Cytoplasm				245
Q3BCQ8 UniProt NPD GO	TPMT_RABIT	Thiopurine S-methyltransferase (EC 2.1.1.67) (Thiopurine methyltransferase)	0.10	-	cyt	0	Cytoplasm				245
O48737 UniProt NPD GO	TRXM1_ARATH	Thioredoxin M-type 1, chloroplast precursor (TRX-M1)	0.10	-	mit	0	Plastid; chloroplast; chloroplast membrane (Potential)				179

You are viewing entries 65301 to 65350 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.