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
P01408 UniProt NPD GO	TS931_DENAN	Synergistic-type venom protein C9S3, chain 1	0.00	-	nuc	0	Secreted protein				63
P01409 UniProt NPD GO	TS932_DENAN	Synergistic-type venom protein C9S3, chain 2	0.00	-	nuc	0	Secreted protein				63
P80697 UniProt NPD GO	SNSP_HUMAN	Synovial stimulatory protein p205 (Fragments)	0.00	-	cyt	0		extracellular region [NAS]			79
P84845 UniProt NPD GO	CXT5A_CONSP	T-1-conotoxin sr5a	0.00	-		0	Secreted protein	extracellular region [IDA]			13
P01738 UniProt NPD GO	TVA1_MOUSE	T-cell receptor alpha chain V region PHDS58 precursor	0.00	-	mit	0				1TCR	130
Q28565 UniProt NPD GO	CD1B1_SHEEP	T-cell surface glycoprotein CD1b-1 precursor (CD1b-1 antigen) (SCD1A25)	0.00	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				333
Q9QZZ0 UniProt NPD GO	CD1B3_CAVPO	T-cell surface glycoprotein CD1b3 precursor (CD1-b3 antigen)	0.00	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				332
Q9QZY9 UniProt NPD GO	CD1B4_CAVPO	T-cell surface glycoprotein CD1b4 precursor (CD1-b4 antigen)	0.00	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				330
P05542 UniProt NPD GO	CD4_SHEEP	T-cell surface glycoprotein CD4 (T-cell surface antigen T4/Leu-3) (Fragment)	0.00	-		0	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			20
Q29068 UniProt NPD GO	TCPG_PIG	T-complex protein 1 subunit gamma (TCP-1-gamma) (CCT-gamma) (Matricin) (Fragment)	0.00	-	cyt	0	Cytoplasm				82
P81753 UniProt NPD GO	TRPA_LEUMA	Tachykinin-related peptide 10 (LemTRP 10)	0.00	-		0	Secreted protein				15
Q9JKA3 UniProt NPD GO	TR103_MOUSE	Taste receptor type 2 member 103 (T2R103) (Taste receptor type 2 member 10) (T2R10) (Taste receptor ...	0.00	-	end	7 *	Membrane; multi-pass membrane protein				312
Q67ET5 UniProt NPD GO	TR103_RAT	Taste receptor type 2 member 103 (T2R103) (Taste receptor type 2 member 15) (T2R15)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				312
Q645S2 UniProt NPD GO	T2R60_MACMU	Taste receptor type 2 member 60 (T2R60) (T2R56)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				318
P84116 UniProt NPD GO	TE1BA_RANBO	Temporin-1BYa	0.00	-		0	Secreted protein				13
P82880 UniProt NPD GO	TE1CA_RANCL	Temporin-1Ca	0.00	-		0	Secreted protein				13
P82881 UniProt NPD GO	TE1CB_RANCL	Temporin-1Cb	0.00	-		0	Secreted protein				13
P83307 UniProt NPD GO	TE1JA_RANJA	Temporin-1Ja	0.00	-		0	Secreted protein				13
P82831 UniProt NPD GO	TE1LB_RANLU	Temporin-1Lb	0.00	-		0	Secreted protein				14
P82848 UniProt NPD GO	TEM1P_RANPI	Temporin-1P	0.00	-		0	Secreted protein				13
P56917 UniProt NPD GO	TEMA_RANTE	Temporin-A	0.00	-		0	Secreted protein				13
P56918 UniProt NPD GO	TEMC_RANTE	Temporin-C	0.00	-		0	Secreted protein				13
P56919 UniProt NPD GO	TEMD_RANTE	Temporin-D	0.00	-		0	Secreted protein				13
P56920 UniProt NPD GO	TEME_RANTE	Temporin-E	0.00	-		0	Secreted protein				13
P56921 UniProt NPD GO	TEMF_RANTE	Temporin-F	0.00	-		0	Secreted protein				13
P57104 UniProt NPD GO	TEML_RANTE	Temporin-L	0.00	-		0	Secreted protein				13
P30833 UniProt NPD GO	ACTPA_ACTTE	Tenebrosin-A (Fragment)	0.00	-		0	Secreted protein. Found in nematocyst				20
P30834 UniProt NPD GO	ACTPB_ACTTE	Tenebrosin-B (Fragment)	0.00	-		0	Secreted protein. Found in nematocyst				20
P80936 UniProt NPD GO	ECD1_LYMDI	Testis ecdysiotropin peptide 1 (TE)	0.00	-	cyt	0					21
P80938 UniProt NPD GO	ECDA_LYMDI	Testis ecdysiotropin peptide A (TE)	0.00	-		0					15
P80939 UniProt NPD GO	ECDB_LYMDI	Testis ecdysiotropin peptide B (TE)	0.00	-	cyt	0					23
P80940 UniProt NPD GO	ECDC_LYMDI	Testis ecdysiotropin peptide C (TE)	0.00	-		0					14
Q12634 UniProt NPD GO	T4HR_MAGGR	Tetrahydroxynaphthalene reductase (EC 1.1.1.252) (T4HN reductase) (THNR)	0.00	-	cyt	0				1YBV	282
Q3T0S3 UniProt NPD GO	TSN1_BOVIN	Tetraspanin-1 (Tspan-1)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Probable)				241
Q5RC27 UniProt NPD GO	TSN1_PONPY	Tetraspanin-1 (Tspan-1)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				241
O60635 UniProt NPD GO	TSN1_HUMAN	Tetraspanin-1 (Tspan-1) (Tetraspan NET-1) (Tetraspanin TM4-C)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Probable)	integral to membrane [TAS]			241
O95859 UniProt NPD GO	TSN12_HUMAN	Tetraspanin-12 (Tspan-12) (Transmembrane 4 superfamily member 12) (Tetraspan NET-2)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Probable)	integral to membrane [TAS] membrane fraction [TAS]			305
Q9D8C2 UniProt NPD GO	TSN13_MOUSE	Tetraspanin-13 (Tspan-13) (Transmembrane 4 superfamily member 13)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Probable)				204
Q5FVL6 UniProt NPD GO	TSN13_RAT	Tetraspanin-13 (Tspan-13) (Transmembrane 4 superfamily member 13)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Probable)				204
O95857 UniProt NPD GO	TSN13_HUMAN	Tetraspanin-13 (Tspan-13) (Transmembrane 4 superfamily member 13) (Tetraspan NET-6)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [TAS] membrane fraction [TAS]			204
Q8QZY6 UniProt NPD GO	TSN14_MOUSE	Tetraspanin-14 (Tspan-14) (Transmembrane 4 superfamily member 14)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Probable)				270
Q8NG11 UniProt NPD GO	TSN14_HUMAN	Tetraspanin-14 (Tspan-14) (Transmembrane 4 superfamily member 14) (DC-TM4F2)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Probable)				270
O95858 UniProt NPD GO	TSN15_HUMAN	Tetraspanin-15 (Tspan-15) (Transmembrane 4 superfamily member 15) (Tetraspan NET-7)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [TAS] membrane fraction [TAS]			294
Q9UKR8 UniProt NPD GO	TSN16_HUMAN	Tetraspanin-16 (Tspan-16) (Transmembrane 4 superfamily member 16) (Tetraspanin TM4-B)	0.00	-	end	3 *	Membrane; multi-pass membrane protein (Probable)	integral to membrane [TAS]			245
Q58CY8 UniProt NPD GO	TSN18_BOVIN	Tetraspanin-18 (Tspan-18)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				249
Q96SJ8 UniProt NPD GO	TSN18_HUMAN	Tetraspanin-18 (Tspan-18)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				248
O60636 UniProt NPD GO	TSN2_HUMAN	Tetraspanin-2 (Tspan-2)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Probable)	integral to membrane [TAS]			221
Q922J6 UniProt NPD GO	TSN2_MOUSE	Tetraspanin-2 (Tspan-2)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Probable)				221
Q9JJW1 UniProt NPD GO	TSN2_RAT	Tetraspanin-2 (Tspan-2)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Probable)				221
Q7ZUB3 UniProt NPD GO	TSN31_BRARE	Tetraspanin-31 (Tspan-31) (Sarcoma amplified sequence homolog)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				212

You are viewing entries 98201 to 98250 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.