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
P53942 UniProt NPD GO	RNHL_YEAST	Ribonuclease HI 35 large subunit (EC 3.1.26.4) (RNase HI large subunit) (RNase H(35))	0.59	-	nuc	0		nucleus [IDA]			307
Q5M882 UniProt NPD GO	RPP29_RAT	Ribonuclease P protein subunit p29 (EC 3.1.26.5)	0.59	-	nuc	0	Nucleus; nucleolus (By similarity)				221
Q6FP42 UniProt NPD GO	RNY1_CANGA	Ribonuclease T2-like precursor (EC 3.1.27.1) (RNase T2-like)	0.59	-	nuc	0	Secreted protein (By similarity)				433
Q8VD85 UniProt NPD GO	RNS1D_RATTI	Ribonuclease pancreatic delta-type precursor (EC 3.1.27.5) (RNase 1 delta)	0.59	-	nuc	0	Secreted protein (By similarity)				150
O61065 UniProt NPD GO	RIR1_CRYPV	Ribonucleoside-diphosphate reductase large chain (EC 1.17.4.1) (Ribonucleotide reductase R1 subunit) ...	0.59	-	nuc	0					803
P67999 UniProt NPD GO	KS6B1_RAT	Ribosomal protein S6 kinase beta-1 (EC 2.7.11.1) (Ribosomal protein S6 kinase I) (S6K) (p70-S6K)	0.59	+	mit	0	Cytoplasm. Synaptosome. Also found in the soluble synaptosomal fractions				525
Q04652 UniProt NPD GO	KELC_DROME	Ring canal kelch protein [Contains: Kelch short protein]	0.59	-	nuc	0	Inner surface of cytoplasmic bridges or ring canals present in egg chambers. Subcortically in imagin ...	ring canal inner rim [TAS]			1477
Q6FSF1 UniProt NPD GO	RUVB2_CANGA	RuvB-like helicase 2 (EC 3.6.1.-)	0.59	-	cyt	0	Nucleus (By similarity)				476
Q6BSB8 UniProt NPD GO	RUVB2_DEBHA	RuvB-like helicase 2 (EC 3.6.1.-)	0.59	-	cyt	0	Nucleus (By similarity)				480
Q8CG65 UniProt NPD GO	SSPO_MOUSE	SCO-spondin precursor	0.59	-	exc	0	Secreted protein; extracellular space (By similarity)	cytoplasm [IC]			4998
Q14140 UniProt NPD GO	SRTD2_HUMAN	SERTA domain-containing protein 2 (Transcriptional regulator interacting with the PHD-bromodomain 2) ...	0.59	-	nuc	0					314
Q9JJG5 UniProt NPD GO	SRTD2_MOUSE	SERTA domain-containing protein 2 (Transcriptional regulator interacting with the PHD-bromodomain 2) ...	0.59	-	nuc	0					309
Q39490 UniProt NPD GO	SFAS_CHLEU	SF-assemblin	0.59	-	nuc	0					269
P29353 UniProt NPD GO	SHC1_HUMAN	SHC-transforming protein 1 (SH2 domain protein C1) (Src homology 2 domain-containing-transforming pr ...	0.59	-	nuc	0	Cytoplasm. Isoform p46Shc: Mitochondrion; mitochondrial matrix. Isoform p46Shc is localized to the m ...	plasma membrane [IDA]	600560	1QG1	583
Q8BLY1 UniProt NPD GO	SMOC1_MOUSE	SPARC-related modular calcium-binding protein 1 precursor (Secreted modular calcium-binding protein ...	0.59	-	exc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane (By similarity). In o ...				463
Q8BRF7 UniProt NPD GO	SCFD1_MOUSE	Sec1 family domain-containing protein 1 (Syntaxin-binding protein 1-like 2)	0.59	-	nuc	0	Cytoplasm (By similarity). Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membran ...				639
Q9WU66 UniProt NPD GO	SFRP5_MOUSE	Secreted frizzled-related protein 5 precursor (sFRP-5)	0.59	-	exc	0	Secreted protein (By similarity)				314
Q2MHE4 UniProt NPD GO	HT1_ARATH	Serine/threonine-protein kinase HT1 (EC 2.7.11.1) (High leaf temperature protein 1)	0.59	-	nuc	0					390
Q9LSF1 UniProt NPD GO	OXI1_ARATH	Serine/threonine-protein kinase OXI1 (EC 2.7.11.1) (Protein OXIDATIVE SIGNAL-INDUCIBLE1)	0.59	-	cyt	0					421
Q8BN21 UniProt NPD GO	VRK2_MOUSE	Serine/threonine-protein kinase VRK2 (EC 2.7.11.1) (Vaccinia-related kinase 2)	0.59	-	nuc	1 *	Membrane; single-pass type IV membrane protein (Potential)	endoplasmic reticulum [IDA] membrane fraction [IDA]			503
O59790 UniProt NPD GO	ARK1_SCHPO	Serine/threonine-protein kinase ark1 (EC 2.7.11.1) (Aurora-related kinase 1)	0.59	-	nuc	0		condensed chromosome kinetochore [IDA] spindle midzone [IDA]			355
P48456 UniProt NPD GO	PP2B1_DROME	Serine/threonine-protein phosphatase 2B catalytic subunit 1 (EC 3.1.3.16) (Calmodulin-dependent calc ...	0.59	-	mit	0		synaptic vesicle [NAS]			622
Q9TUN9 UniProt NPD GO	TRPC1_RABIT	Short transient receptor potential channel 1 (TrpC1) (Calcium influx channel TRPC1A)	0.59	-	end	7	Membrane; multi-pass membrane protein (Probable)				759
P42231 UniProt NPD GO	STA5A_SHEEP	Signal transducer and activator of transcription 5A (Mammary gland factor)	0.59	-	cyt	0	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation				794
Q61045 UniProt NPD GO	SIM1_MOUSE	Single-minded homolog 1 (mSIM1)	0.59	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			765
P84102 UniProt NPD GO	SERF2_MOUSE	Small EDRK-rich factor 2 (4F5rel)	0.59	-	nuc	0					59
P84101 UniProt NPD GO	SERF2_HUMAN	Small EDRK-rich factor 2 (4F5rel) (h4F5rel) (Gastric cancer-related protein VRG107)	0.59	-	nuc	0			605054		59
P84444 UniProt NPD GO	CC21B_MOUSE	Small inducible cytokine A21b precursor (CCL21) (Beta chemokine exodus-2) (6Ckine) (Thymus-derived c ...	0.59	-	exc	0	Secreted protein				133
P40018 UniProt NPD GO	RSMB_YEAST	Small nuclear ribonucleoprotein-associated protein B (snRNP-B) (Sm protein B) (Sm-B) (SmB)	0.59	-	nuc	0	Nucleus	snRNP U1 [IDA] snRNP U5 [IPI] U4/U6 x U5 tri-snRNP complex [IDA]			196
P04774 UniProt NPD GO	SCN1A_RAT	Sodium channel protein type 1 subunit alpha (Sodium channel protein type I subunit alpha) (Voltage-g ...	0.59	+	end	19	Membrane; multi-pass membrane protein				2009
Q9UBY0 UniProt NPD GO	SL9A2_HUMAN	Sodium/hydrogen exchanger 2 (Na(+)/H(+) exchanger 2) (NHE-2) (Solute carrier family 9 member 2)	0.59	-	end	13 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]	600530		812
Q9Y5W7 UniProt NPD GO	SNX14_HUMAN	Sorting nexin-14	0.59	-	end	1 *					886
Q7TME2 UniProt NPD GO	SPAG5_MOUSE	Sperm-associated antigen 5 (Mastrin) (Mitotic spindle-associated protein p126) (MAP126)	0.59	-	nuc	0	Cytoplasm (By similarity). In a punctate pattern in interphase cells. During mitosis, detected at sp ...	spindle microtubule [IDA]			1165
Q9Y705 UniProt NPD GO	ALP4_SCHPO	Spindle pole body component alp4 (Altered polarity protein 4)	0.59	-	cyt	0	Spindle pole body. And the microtubule organizing center (MTOC)	equatorial microtubule organizing center [IDA] gamma-tubulin complex [TAS] spindle pole body [IDA]			784
Q13243 UniProt NPD GO	SFRS5_HUMAN	Splicing factor, arginine/serine-rich 5 (Pre-mRNA-splicing factor SRP40) (Delayed-early protein HRS) ...	0.59	+	nuc	0	Nucleus		600914		272
O18776 UniProt NPD GO	SFRS6_RABIT	Splicing factor, arginine/serine-rich 6 (Pre-mRNA-splicing factor SRP55) (Fragment)	0.59	+	mit	0	Nucleus				81
O43815 UniProt NPD GO	STRN_HUMAN	Striatin	0.59	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				780
Q9FJP9 UniProt NPD GO	DHSB3_ARATH	Succinate dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial precursor (EC 1.3.5.1) (IP ...	0.59	-	nuc	0	Mitochondrion; mitochondrial inner membrane (By similarity)				309
Q43876 UniProt NPD GO	SPS_VICFA	Sucrose-phosphate synthase (EC 2.4.1.14) (UDP-glucose-fructose-phosphate glucosyltransferase)	0.59	-	nuc	0					1059
O35716 UniProt NPD GO	SOCS1_MOUSE	Suppressor of cytokine signaling 1 (SOCS-1) (JAK-binding protein) (JAB) (STAT-induced STAT inhibitor ...	0.59	+	nuc	0					212
O14544 UniProt NPD GO	SOCS6_HUMAN	Suppressor of cytokine signaling 6 (SOCS-6) (Suppressor of cytokine signaling 4) (SOCS-4) (Cytokine- ...	0.59	-	nuc	0		cytoplasm [TAS]	605118		535
Q9BQS2 UniProt NPD GO	SYT15_HUMAN	Synaptotagmin-15 (Synaptotagmin XV) (SytXV) (Chr10Syt)	0.59	-	mit	1 *	Isoform 1, isoform 2, isoform 4: Cell membrane; single-pass type III membrane protein (By similarity ...		608081		421
P47861 UniProt NPD GO	SYT5_RAT	Synaptotagmin-5 (Synaptotagmin V) (SytV) (Synaptotagmin IX)	0.59	-	nuc	1 *	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein. Endosome; recycling endoso ...				386
O94531 UniProt NPD GO	UFE1_SCHPO	Syntaxin ufe1	0.59	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein (By simi ...				319
P61266 UniProt NPD GO	STX1C_HUMAN	Syntaxin-1B2	0.59	-	gol	1	Membrane; single-pass type IV membrane protein (Potential)				288
P61264 UniProt NPD GO	STX1C_MOUSE	Syntaxin-1B2 (Syntaxin 1B)	0.59	-	gol	1	Membrane; single-pass type IV membrane protein (Potential)				288
P61268 UniProt NPD GO	STX1C_SHEEP	Syntaxin-1B2 (Syntaxin 1B)	0.59	-	gol	1	Membrane; single-pass type IV membrane protein (Potential)				288
P61265 UniProt NPD GO	STX1C_RAT	Syntaxin-1B2 (Syntaxin 1B) (P35B)	0.59	-	gol	1	Membrane; single-pass type IV membrane protein (Potential)				288
P61267 UniProt NPD GO	STX1C_BOVIN	Syntaxin-1B2 (Syntaxin 1B) (Synaptocanalin I)	0.59	-	gol	1	Membrane; single-pass type IV membrane protein (Potential)				288
P32856 UniProt NPD GO	STX2_HUMAN	Syntaxin-2 (Epimorphin)	0.59	-	gol	1	Membrane; single-pass type IV membrane protein	microsome [TAS] soluble fraction [TAS]	132350		288

You are viewing entries 19851 to 19900 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.