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
Q12377 UniProt NPD GO	RPN6_YEAST	26S proteasome regulatory subunit RPN6 (Proteasome non-ATPase subunit 4)	0.56	-	nuc	0		proteasome regulatory particle, lid subcomp... [IPI]			433
P14127 UniProt NPD GO	RS17B_YEAST	40S ribosomal protein S17-B (RP51B)	0.56	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			136
Q6CFK6 UniProt NPD GO	RT09_YARLI	40S ribosomal protein S9, mitochondrial precursor	0.56	-	mit	0	Mitochondrion (Potential)				319
Q60484 UniProt NPD GO	5HT1D_CAVPO	5-hydroxytryptamine 1D receptor (5-HT-1D) (Serotonin receptor 1D)	0.56	-	end	7 *	Membrane; multi-pass membrane protein				376
P28221 UniProt NPD GO	5HT1D_HUMAN	5-hydroxytryptamine 1D receptor (5-HT-1D) (Serotonin receptor 1D) (5-HT-1D-alpha)	0.56	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	182133		377
P28566 UniProt NPD GO	5HT1E_HUMAN	5-hydroxytryptamine 1E receptor (5-HT-1E) (Serotonin receptor 1E) (5-HT1E) (S31)	0.56	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	182132		365
Q9N2B6 UniProt NPD GO	5HT1E_PANTR	5-hydroxytryptamine 1E receptor (5-HT-1E) (Serotonin receptor 1E) (Fragment)	0.56	-	end	7 *	Membrane; multi-pass membrane protein				363
P11892 UniProt NPD GO	RK25_PEA	50S ribosomal protein CL25, chloroplast precursor	0.56	-	nuc	0	Plastid; chloroplast				104
Q9Z2F2 UniProt NPD GO	OASL2_MOUSE	54 kDa 2'-5'-oligoadenylate synthetase-like protein 2 (EC 2.7.7.-) (p54 OASL) (p54OASL) (M1204)	0.56	-	cyt	0					473
P41127 UniProt NPD GO	RL131_ARATH	60S ribosomal protein L13-1 (Protein BBC1 homolog)	0.56	-	mit	0	Cytoplasm				206
Q7T3P1 UniProt NPD GO	RL15_ANGJA	60S ribosomal protein L15	0.56	-	nuc	0					203
Q7T3N9 UniProt NPD GO	RL15_CARAU	60S ribosomal protein L15	0.56	-	nuc	0					203
Q7T3N7 UniProt NPD GO	RL15_CYPCA	60S ribosomal protein L15	0.56	-	nuc	0					203
P61367 UniProt NPD GO	RL15_EPICO	60S ribosomal protein L15	0.56	-	nuc	0					203
P61368 UniProt NPD GO	RL15_HYDAT	60S ribosomal protein L15	0.56	-	nuc	0					203
Q90YV2 UniProt NPD GO	RL15_ICTPU	60S ribosomal protein L15	0.56	-	nuc	0					203
Q7T3N3 UniProt NPD GO	RL15_PARDA	60S ribosomal protein L15	0.56	-	nuc	0					203
P41961 UniProt NPD GO	RL15_BRUPA	60S ribosomal protein L15 (Fragment)	0.56	-	nuc	0					70
Q6BM53 UniProt NPD GO	RL17_DEBHA	60S ribosomal protein L17	0.56	-	mit	0					185
Q93VI3 UniProt NPD GO	RL171_ARATH	60S ribosomal protein L17-1	0.56	-	nuc	0					176
Q3SZQ6 UniProt NPD GO	RL32_BOVIN	60S ribosomal protein L32	0.56	-	nuc	0					134
Q8SS18 UniProt NPD GO	RL32_ENCCU	60S ribosomal protein L32	0.56	-	nuc	0					139
P62910 UniProt NPD GO	RL32_HUMAN	60S ribosomal protein L32	0.56	-	nuc	0					134
Q76KA3 UniProt NPD GO	RL32_MACFA	60S ribosomal protein L32	0.56	-	nuc	0					134
P62911 UniProt NPD GO	RL32_MOUSE	60S ribosomal protein L32	0.56	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [IDA]			134
Q6QAT0 UniProt NPD GO	RL32_PIG	60S ribosomal protein L32	0.56	-	nuc	0					134
P62912 UniProt NPD GO	RL32_RAT	60S ribosomal protein L32	0.56	-	nuc	0					134
P45842 UniProt NPD GO	RL34_AEDAL	60S ribosomal protein L34 (L31)	0.56	-	mit	0					129
Q90YT4 UniProt NPD GO	RL35_ICTPU	60S ribosomal protein L35	0.56	-	nuc	0					122
Q6PBC1 UniProt NPD GO	RL35_XENTR	60S ribosomal protein L35	0.56	-	nuc	0					122
Q3T171 UniProt NPD GO	RL36_BOVIN	60S ribosomal protein L36	0.56	-	nuc	0					104
Q96W55 UniProt NPD GO	RL39_CANAL	60S ribosomal protein L39 (L46)	0.56	-	mit	0					51
P33190 UniProt NPD GO	RL40_TETPY	60S ribosomal protein L40 (CEP52) (CEP53)	0.56	+	nuc	0					53
Q58DW5 UniProt NPD GO	RL5_BOVIN	60S ribosomal protein L5	0.56	-	mit	0	Cytoplasm. Nucleus; nucleolus (By similarity)				296
P46777 UniProt NPD GO	RL5_HUMAN	60S ribosomal protein L5	0.56	-	mit	0	Cytoplasm. Nucleus; nucleolus	cytosolic large ribosomal subunit (sensu Eu... [TAS]	603634		296
Q4R5M0 UniProt NPD GO	RL5_MACFA	60S ribosomal protein L5	0.56	-	nuc	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)				296
Q8L4L4 UniProt NPD GO	RL52_ORYSA	60S ribosomal protein L5-2	0.56	-	mit	0					304
Q58DQ3 UniProt NPD GO	RL6_BOVIN	60S ribosomal protein L6	0.56	+	nuc	0					286
Q2YGT9 UniProt NPD GO	RL6_PIG	60S ribosomal protein L6	0.56	+	nuc	0					283
Q7SBD5 UniProt NPD GO	RL7_NEUCR	60S ribosomal protein L7	0.56	+	cyt	0					248
Q90YW2 UniProt NPD GO	RL7A_ICTPU	60S ribosomal protein L7a	0.56	-	nuc	0					265
O57592 UniProt NPD GO	RL7A_FUGRU	60S ribosomal protein L7a (Surfeit locus protein 3)	0.56	-	nuc	0					265
P46936 UniProt NPD GO	YAP1_CHICK	65 kDa Yes-associated protein (YAP65)	0.56	-	nuc	0					448
P14056 UniProt NPD GO	ARAF_RAT	A-Raf proto-oncogene serine/threonine-protein kinase (EC 2.7.11.1)	0.56	-	cyt	0		cytosol [IDA] insoluble fraction [IDA]			604
Q9QYV0 UniProt NPD GO	ADA15_RAT	ADAM 15 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 15) (Metalloproteinase-l ...	0.56	-	exc	1	Membrane; single-pass type I membrane protein				816
Q5RFQ8 UniProt NPD GO	ATS4_PONPY	ADAMTS-4 precursor (EC 3.4.24.82) (A disintegrin and metalloproteinase with thrombospondin motifs 4) ...	0.56	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix (By similarity)				837
Q9TT93 UniProt NPD GO	ATS4_BOVIN	ADAMTS-4 precursor (EC 3.4.24.82) (A disintegrin and metalloproteinase with thrombospondin motifs 4) ...	0.56	+	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				839
P35197 UniProt NPD GO	GCS1_YEAST	ADP-ribosylation factor GTPase-activating protein GCS1	0.56	-	nuc	0	Cytoplasm. Mitochondrion. Cytoplasm; perinuclear region. Found also in the mitochondria and in the p ...	cytoskeleton [IMP] ER-Golgi intermediate compartment [IPI]			352
Q9UJY5 UniProt NPD GO	GGA1_HUMAN	ADP-ribosylation factor-binding protein GGA1 (Golgi-localized, gamma ear-containing, ARF-binding pro ...	0.56	-	nuc	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein. End ...	Golgi apparatus [TAS]	606004	1X79	639
O80452 UniProt NPD GO	AMPD_ARATH	AMP deaminase (EC 3.5.4.6) (AtAMPD) (Protein EMBRYONIC FACTOR 1)	0.56	-	nuc	1 *	Membrane; single-pass membrane protein. Might be associated with the inner mitochondrial membrane (B ...			2A3L	839

You are viewing entries 21151 to 21200 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.