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
Q96PI1 UniProt NPD GO	SPRR4_HUMAN	Small proline-rich protein 4	0.37	-	nuc	0	Cytoplasm. Cytoplasm; cell cortex. Translocates to the cell periphery of keratinocytes and is integr ...				79
Q28362 UniProt NPD GO	SL9A3_DIDMA	Sodium/hydrogen exchanger 3 (Na(+)/H(+) exchanger 3) (NHE-3) (Solute carrier family 9 member 3)	0.37	+	end	13 *	Membrane; multi-pass membrane protein				839
Q9Z0X2 UniProt NPD GO	SL9A5_RAT	Sodium/hydrogen exchanger 5 (Na(+)/H(+) exchanger 5) (NHE-5) (Solute carrier family 9 member 5)	0.37	-	end	10 *	Membrane; multi-pass membrane protein				898
Q9LKW9 UniProt NPD GO	NHX7_ARATH	Sodium/hydrogen exchanger 7 (Na(+)/H(+) exchanger 7) (NHE-7) (Protein SALT OVERLY SENSITIVE 1)	0.37	-	end	9 *	Cell membrane; multi-pass membrane protein				1146
P16043 UniProt NPD GO	SLIB_MOUSE	Somatoliberin precursor (Growth hormone-releasing factor) (GRF) (Growth hormone-releasing hormone) ( ...	0.37	-	nuc	0	Secreted protein				103
P30936 UniProt NPD GO	SSR3_RAT	Somatostatin receptor type 3 (SS3R) (SSR-28)	0.37	-	end	7 *	Membrane; multi-pass membrane protein. Internalized into endoplasmic vesicles upon somatostatin-stim ...				428
O73848 UniProt NPD GO	SOMA_PROAN	Somatotropin precursor (Growth hormone)	0.37	-	exc	0	Secreted protein				206
P45643 UniProt NPD GO	SOMA_SOLSE	Somatotropin precursor (Growth hormone)	0.37	-	mit	0	Secreted protein				203
Q6C2S9 UniProt NPD GO	SNX3_YARLI	Sorting nexin-3	0.37	-	nuc	0	Cytoplasm (By similarity)				152
Q9DA32 UniProt NPD GO	SPA4L_MOUSE	Sperm-associated antigen 4-like protein	0.37	-	mit	0					348
O88452 UniProt NPD GO	STC2_MOUSE	Stanniocalcin-2 precursor (STC-2)	0.37	-	exc	0	Secreted protein (Potential)				296
P79245 UniProt NPD GO	STAR_SHEEP	Steroidogenic acute regulatory protein, mitochondrial precursor (StAR) (StARD1)	0.37	-	mit	0	Mitochondrion				285
Q5ZM98 UniProt NPD GO	GRP75_CHICK	Stress-70 protein, mitochondrial precursor (75 kDa glucose-regulated protein) (GRP 75)	0.37	-	mit	0	Mitochondrion				675
Q5F413 UniProt NPD GO	SMP1L_CHICK	Stromal membrane-associated protein 1-like	0.37	-	nuc	0					428
O00161 UniProt NPD GO	SNP23_HUMAN	Synaptosomal-associated protein 23 (SNAP-23) (Vesicle-membrane fusion protein SNAP-23)	0.37	-	nuc	0	Cell membrane; peripheral membrane protein. Mainly localized to the plasma membrane	plasma membrane [TAS]	602534	1NHL	211
O09044 UniProt NPD GO	SNP23_MOUSE	Synaptosomal-associated protein 23 (SNAP-23) (Vesicle-membrane fusion protein SNAP-23) (Syndet)	0.37	-	nuc	0	Cell membrane; peripheral membrane protein. Mainly localized to the plasma membrane	microsome [IDA]			210
P21521 UniProt NPD GO	SY65_DROME	Synaptotagmin (p65)	0.37	+	nuc	1	Synaptic vesicles in neurons	integral to synaptic vesicle membrane [NAS]			474
Q94KK5 UniProt NPD GO	SYP73_ARATH	Syntaxin-73 (AtSYP73)	0.37	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)				263
Q63493 UniProt NPD GO	CD1D_RAT	T-cell surface glycoprotein CD1d precursor (CD1d antigen)	0.37	+	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS]			336
Q9TUF8 UniProt NPD GO	CD3Z_RABIT	T-cell surface glycoprotein CD3 zeta chain precursor (T-cell receptor T3 zeta chain)	0.37	-	nuc	2 *	Membrane; single-pass type I membrane protein				165
P18074 UniProt NPD GO	ERCC2_HUMAN	TFIIH basal transcription factor complex helicase subunit (EC 3.6.1.-) (DNA-repair protein complemen ...	0.37	-	cyt	0	Nucleus	nucleus [NAS] transcription factor TFIIH complex [TAS]	601675		760
Q09917 UniProt NPD GO	PKD2_SCHPO	TRP-like ion channel pkd2 precursor (Polycystic kidney disease-related ion channel 2)	0.37	-	end	9	Cell membrane; multi-pass membrane protein. Golgi apparatus; Golgi membrane; multi-pass membrane pro ...	integral to Golgi membrane [IDA] integral to plasma membrane [IDA]			710
O15273 UniProt NPD GO	TELT_HUMAN	Telethonin (Titin cap protein)	0.37	-	nuc	0	Sarcomeric		601954	2F8V	167
Q6T8D8 UniProt NPD GO	TELT_BOVIN	Telethonin (Titin-cap protein)	0.37	-	nuc	0	Sarcomeric (By similarity)				166
Q91Y53 UniProt NPD GO	TDIF1_RAT	Terminal deoxynucleotidyltransferase-interacting factor 1 (TdT-interacting factor 1) (TdIF1)	0.37	-	nuc	0	Nucleus (By similarity)				327
Q9H3N1 UniProt NPD GO	TXND1_HUMAN	Thioredoxin domain-containing protein 1 precursor (Transmembrane Trx-related protein) (Thioredoxin-r ...	0.37	-	end	3 *	Membrane; single-pass type I membrane protein (Potential). Predominantly found in the endoplasmic re ...	endoplasmic reticulum membrane [IDA] membrane fraction [IDA]		1X5E	280
Q03350 UniProt NPD GO	TSP2_MOUSE	Thrombospondin-2 precursor	0.37	-	nuc	0					1172
Q2KIG5 UniProt NPD GO	THAS_BOVIN	Thromboxane-A synthase (EC 5.3.99.5) (TXA synthase) (TXS) (Cytochrome P450 5A1)	0.37	-	end	0	Membrane; multi-pass membrane protein				533
P13775 UniProt NPD GO	REP1_KLULA	Trans-acting factor B (REP1)	0.37	-	cyt	0					415
Q9UH73 UniProt NPD GO	COE1_HUMAN	Transcription factor COE1 (OE-1) (O/E-1) (Early B-cell factor)	0.37	-	nuc	0	Nucleus (Potential)		164343		591
Q07802 UniProt NPD GO	COE1_MOUSE	Transcription factor COE1 (OE-1) (O/E-1) (Early B-cell factor)	0.37	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			591
Q9BQW3 UniProt NPD GO	COE4_HUMAN	Transcription factor COE4 (Early B-cell factor 4) (EBF-4) (Olf-1/EBF-like 4) (OE-4) (O/E-4)	0.37	-	mit	0	Nucleus (Potential)		609935		644
P38915 UniProt NPD GO	SPT8_YEAST	Transcription factor SPT8	0.37	-	nuc	0	Nucleus (Probable)	nucleus [IDA] SAGA complex [IDA]			602
P52655 UniProt NPD GO	TF2AA_HUMAN	Transcription initiation factor IIA subunit 1 (General transcription factor IIA1) (TFIIA-42) (TFIIAL ...	0.37	-	nuc	0	Nucleus		600520	1NVP	376
Q5RCU0 UniProt NPD GO	TF2AA_PONPY	Transcription initiation factor IIA subunit 1 (General transcription factor IIA1) [Contains: Transcr ...	0.37	-	cyt	0	Nucleus (By similarity)				376
O08949 UniProt NPD GO	TF2AA_RAT	Transcription initiation factor IIA subunit 1 (General transcription factor IIA1) [Contains: Transcr ...	0.37	-	nuc	0	Nucleus (By similarity)				377
Q5R886 UniProt NPD GO	TF2B_PONPY	Transcription initiation factor IIB (General transcription factor TFIIB)	0.37	-	nuc	0	Nucleus (By similarity)				316
P29054 UniProt NPD GO	TF2B_XENLA	Transcription initiation factor IIB (General transcription factor TFIIB)	0.37	-	nuc	0	Nucleus				316
Q00403 UniProt NPD GO	TF2B_HUMAN	Transcription initiation factor IIB (General transcription factor TFIIB) (S300-II)	0.37	-	nuc	0	Nucleus		189963	1VOL	316
O08629 UniProt NPD GO	TIF1B_RAT	Transcription intermediary factor 1-beta (TIF1-beta) (Tripartite motif-containing protein 28) (Nucle ...	0.37	-	nuc	0	Nucleus	nucleolus [IDA]			86
P36611 UniProt NPD GO	HAP3_SCHPO	Transcriptional activator hap3	0.37	-	nuc	0	Nucleus				116
Q90511 UniProt NPD GO	EI2BB_FUGRU	Translation initiation factor eIF-2B subunit beta (eIF-2B GDP-GTP exchange factor subunit beta) (S20 ...	0.37	-	cyt	0					355
P21825 UniProt NPD GO	SEC62_YEAST	Translocation protein SEC62 (Sec62/63 complex 30 kDa subunit)	0.37	-	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [TAS] Sec62/Sec63 complex [IPI]			274
Q8IWA4 UniProt NPD GO	MFN1_HUMAN	Transmembrane GTPase MFN1 (EC 3.6.5.-) (Mitofusin-1) (Fzo homolog)	0.37	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (Probable). Isoform 2: Cyto ...	integral to membrane [NAS]	608506		741
Q23424 UniProt NPD GO	FZO1_CAEEL	Transmembrane GTPase fzo-1 (EC 3.6.5.-)	0.37	-	nuc	2	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				774
Q3T0N3 UniProt NPD GO	TMCO1_BOVIN	Transmembrane and coiled-coil domain-containing protein 1	0.37	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				188
Q921L3 UniProt NPD GO	TMCO1_MOUSE	Transmembrane and coiled-coil domain-containing protein 1	0.37	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				188
Q5R9B0 UniProt NPD GO	TMCO1_PONPY	Transmembrane and coiled-coil domain-containing protein 1	0.37	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				188
Q9UM00 UniProt NPD GO	TMCO1_HUMAN	Transmembrane and coiled-coil domain-containing protein 1 (Xenogeneic cross-immune protein PCIA3)	0.37	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...				188
Q5I0H4 UniProt NPD GO	TMCO1_RAT	Transmembrane and coiled-coil domains protein 1 (Meg-2-like protein)	0.37	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				188

You are viewing entries 34551 to 34600 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.