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
Q18801 UniProt NPD GO	GMD1_CAEEL	Probable GDP-mannose 4,6 dehydratase 1 (EC 4.2.1.47) (GDP-D-mannose dehydratase) (GMD)	0.03	-	cyt	0					399
Q8NKC0 UniProt NPD GO	ASPG3_SCHPO	Probable L-asparaginase 3 precursor (EC 3.5.1.1) (L-asparagine amidohydrolase 3)	0.03	-	exc	0	Cell wall (By similarity)				360
Q9HDW9 UniProt NPD GO	PIGL_SCHPO	Probable N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase (EC 3.5.1.89)	0.03	-	mit	0					248
Q9ZU75 UniProt NPD GO	UB12L_ARATH	Probable NEDD8-conjugating enzyme Ubc12-like (EC 6.3.2.-) (RUB1-conjugating enzyme 2) (RUB1-protein ...	0.03	-	nuc	0					185
Q7SYR1 UniProt NPD GO	GCP_XENLA	Probable O-sialoglycoprotein endopeptidase (EC 3.4.24.57)	0.03	-	cyt	0					335
Q27522 UniProt NPD GO	METN_CAEEL	Probable S-adenosylmethionine synthetase T13A10.11 (EC 2.5.1.6) (Methionine adenosyltransferase) (Ad ...	0.03	-	cyt	0					404
Q10147 UniProt NPD GO	TCPB_SCHPO	Probable T-complex protein 1 subunit beta (TCP-1-beta) (CCT-beta)	0.03	-	cyt	0	Cytoplasm (Potential)				527
P78921 UniProt NPD GO	TCPQ_SCHPO	Probable T-complex protein 1 subunit theta (TCP-1-theta) (CCT-theta)	0.03	-	cyt	0	Cytoplasm (By similarity)				546
O64765 UniProt NPD GO	UAP1_ARATH	Probable UDP-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23)	0.03	-	cyt	0	Cytoplasm (By similarity)				502
Q6YZI0 UniProt NPD GO	SPY_ORYSA	Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY (EC 2.4.1.-)	0.03	-	cyt	0	Nucleus (By similarity)				927
P38709 UniProt NPD GO	UGPA2_YEAST	Probable UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (UDP-glucose pyrophosphorylase) ( ...	0.03	-	cyt	0					493
O45687 UniProt NPD GO	ADH2_CAEEL	Probable alcohol dehydrogenase K12G11.4 (EC 1.1.1.1)	0.03	-	cyt	0					351
O60170 UniProt NPD GO	MEU22_SCHPO	Probable amino-acid permease meu22 (Meiotic expression up-regulated protein 22)	0.03	-	end	12	Membrane; multi-pass membrane protein (Potential)				574
P25794 UniProt NPD GO	PIP2_PEA	Probable aquaporin PIP-type 7a (Turgor-responsive protein 7a) (Turgor-responsive protein 31)	0.03	-	end	5	Cell membrane; multi-pass membrane protein (By similarity)				289
Q39196 UniProt NPD GO	PIP14_ARATH	Probable aquaporin PIP1.4 (Plasma membrane intrinsic protein 1.4) (Transmembrane protein C) (TMP-C)	0.03	-	end	6	Cell membrane; multi-pass membrane protein (By similarity)				287
Q8LAA6 UniProt NPD GO	PIP15_ARATH	Probable aquaporin PIP1.5 (Plasma membrane intrinsic protein 1d) (PIP1d)	0.03	-	end	6	Cell membrane; multi-pass membrane protein (By similarity)				287
Q8H5N9 UniProt NPD GO	PIP21_ORYSA	Probable aquaporin PIP2.1 (Plasma membrane intrinsic protein 2a) (PIP2a) (OsPIP2.1)	0.03	-	end	6 *	Cell membrane; multi-pass membrane protein (By similarity)				290
Q6K215 UniProt NPD GO	PIP22_ORYSA	Probable aquaporin PIP2.2 (Plasma membrane intrinsic protein 2.2) (OsPIP2.2)	0.03	-	end	6 *	Cell membrane; multi-pass membrane protein (By similarity)				288
Q7XUA6 UniProt NPD GO	PIP23_ORYSA	Probable aquaporin PIP2.3 (Plasma membrane intrinsic protein 2.3) (OsPIP2.3)	0.03	-	end	6 *	Cell membrane; multi-pass membrane protein (By similarity)				290
Q9FF53 UniProt NPD GO	PIP24_ARATH	Probable aquaporin PIP2.4 (Plasma membrane intrinsic protein 2.4)	0.03	-	end	6 *	Cell membrane; multi-pass membrane protein (By similarity)				291
Q7XLR1 UniProt NPD GO	PIP26_ORYSA	Probable aquaporin PIP2.6 (Plasma membrane intrinsic protein 2.6) (OsPIP2.6)	0.03	-	end	6 *	Cell membrane; multi-pass membrane protein (By similarity)				282
Q9ZV07 UniProt NPD GO	PIP26_ARATH	Probable aquaporin PIP2.6 (Plasma membrane intrinsic protein 2e) (PIP2e)	0.03	-	end	6 *	Cell membrane; multi-pass membrane protein (By similarity)				289
P23958 UniProt NPD GO	TIPA_PHAVU	Probable aquaporin TIP-type alpha (Tonoplast intrinsic protein alpha) (Alpha TIP)	0.03	-	end	6 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				256
Q9C9W4 UniProt NPD GO	CAMT2_ARATH	Probable caffeoyl-CoA O-methyltransferase At1g67990 (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltra ...	0.03	-	cyt	0					232
Q9LXW3 UniProt NPD GO	CPR2_ARATH	Probable cysteine proteinase At3g43960 precursor (EC 3.4.22.-)	0.03	-	exc	1 *		anchored to membrane [TAS]			376
O81769 UniProt NPD GO	DPH5_ARATH	Probable diphthine synthase (EC 2.1.1.98) (Diphthamide biosynthesis methyltransferase)	0.03	-	cyt	0					277
Q9H2P9 UniProt NPD GO	DPH5_HUMAN	Probable diphthine synthase (EC 2.1.1.98) (Diphthamide biosynthesis methyltransferase)	0.03	-	cyt	0					285
Q12480 UniProt NPD GO	ETFA_YEAST	Probable electron transfer flavoprotein subunit alpha, mitochondrial precursor (Alpha-ETF)	0.03	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			344
P87111 UniProt NPD GO	ETFD_SCHPO	Probable electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (EC 1.5.5 ...	0.03	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				632
P34460 UniProt NPD GO	EF1B1_CAEEL	Probable elongation factor 1-beta/1-delta 1 (EF-1-beta/delta 1)	0.03	-	end	0					213
Q9U2H9 UniProt NPD GO	EF1B2_CAEEL	Probable elongation factor 1-beta/1-delta 2 (EF-1-beta/delta 2)	0.03	-	cyt	0					262
Q9LYC1 UniProt NPD GO	GI1L2_ARATH	Probable gibberellin receptor GID1L2 (EC 3.-.-.-) (GID1-like protein 2)	0.03	-	cyt	0	Nucleus (By similarity)				358
Q09596 UniProt NPD GO	GST5_CAEEL	Probable glutathione S-transferase 5 (EC 2.5.1.18) (GST class-sigma)	0.03	-	cyt	0				1ZL9	207
O65857 UniProt NPD GO	GSTH1_ORYSA	Probable glutathione S-transferase GSTF1 (EC 2.5.1.18) (GST-I)	0.03	-	cyt	0					219
P50471 UniProt NPD GO	GSTX1_NICPL	Probable glutathione S-transferase MSR-1 (EC 2.5.1.18) (Auxin-regulated protein MSR-1)	0.03	-	mit	0					219
P25317 UniProt NPD GO	GSTXA_TOBAC	Probable glutathione S-transferase parA (EC 2.5.1.18) (Auxin-regulated protein parA) (STR246C protei ...	0.03	-	mit	0					220
P49332 UniProt NPD GO	GSTXC_TOBAC	Probable glutathione S-transferase parC (EC 2.5.1.18) (Auxin-regulated protein parC)	0.03	-	cyt	0					221
Q08959 UniProt NPD GO	YP206_YEAST	Probable glycerophosphodiester phosphodiesterase YPL206C (EC 3.1.4.46)	0.03	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein (Potenti ...	cytoplasm [IDA] endoplasmic reticulum [IDA] mitochondrion [IDA]			321
Q9LQL0 UniProt NPD GO	GCSH2_ARATH	Probable glycine cleavage system H protein 2, mitochondrial precursor	0.03	-	mit	0	Mitochondrion				166
Q18680 UniProt NPD GO	IPYR_CAEEL	Probable inorganic pyrophosphatase 1 (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.03	-	mit	0					407
Q09628 UniProt NPD GO	ILB3_CAEEL	Probable insulin-like peptide beta-type 3 precursor	0.03	-	vac	1 *	Secreted protein (Potential)				107
Q5RDZ1 UniProt NPD GO	MAWBP_PONPY	Probable isomerase MAWBP (EC 5.1.-.-)	0.03	-	cyt	0					288
Q18026 UniProt NPD GO	KYNU_CAEEL	Probable kynureninase (EC 3.7.1.3) (L-kynurenine hydrolase)	0.03	-	cyt	0	Cytoplasm (By similarity)				478
Q9CPU9 UniProt NPD GO	COPT2_MOUSE	Probable low-affinity copper uptake protein 2 (CTR2) (Copper transporter 2) (Solute carrier family 3 ...	0.03	-	end	3 *	Membrane; multi-pass membrane protein (Probable)				143
O02640 UniProt NPD GO	MDHM_CAEEL	Probable malate dehydrogenase, mitochondrial precursor (EC 1.1.1.37)	0.03	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)				341
P53868 UniProt NPD GO	ALG9_YEAST	Probable mannosyltransferase ALG9 (EC 2.4.1.-)	0.03	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum [IMP]			555
Q75HE6 UniProt NPD GO	MTHR_ORYSA	Probable methylenetetrahydrofolate reductase (EC 1.5.1.20)	0.03	-	cyt	0					594
P52713 UniProt NPD GO	MMSA_CAEEL	Probable methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (EC 1.2.1.27 ...	0.03	-	mit	0	Mitochondrion (By similarity)	mitochondrion [ISS]			523
Q9LFA3 UniProt NPD GO	MDAR3_ARATH	Probable monodehydroascorbate reductase, cytoplasmic isoform 3 (EC 1.6.5.4) (MDAR 3)	0.03	-	cyt	0	Cytoplasm (Potential)	peroxisomal matrix [IDA]			434
P83902 UniProt NPD GO	TX23_PHOKE	Probable neurotoxin PKTx23C3	0.03	-	nuc	0	Secreted protein				58

You are viewing entries 81201 to 81250 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.