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
Q13153 UniProt NPD GO	PAK1_HUMAN	Serine/threonine-protein kinase PAK 1 (EC 2.7.11.1) (p21-activated kinase 1) (PAK-1) (P65-PAK) (Alph ...	0.65	+	nuc	0	Cytoplasm. Cell membrane; cell-matrix junction; focal adhesion. Recruited to focal adhesions upon ac ...		602590	1ZSG	545
P35465 UniProt NPD GO	PAK1_RAT	Serine/threonine-protein kinase PAK 1 (EC 2.7.11.1) (p21-activated kinase 1) (PAK-1) (P68-PAK) (Alph ...	0.65	+	nuc	0		cytosol [IDA]		1E0A	544
Q9R011 UniProt NPD GO	PLK3_RAT	Serine/threonine-protein kinase PLK3 (EC 2.7.11.21) (Polo-like kinase 3) (PLK-3) (Cytokine-inducible ...	0.65	-	nuc	0	When induced, it translocates into the dendrites of activated neurons	dendrite [IDA]			615
Q9R1U5 UniProt NPD GO	SN1L1_RAT	Serine/threonine-protein kinase SNF1-like kinase 1 (EC 2.7.11.1) (Serine/threonine-protein kinase SN ...	0.65	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). May translocate to the nucleus on activation (By ...	cytoplasm [ISS]			776
Q99986 UniProt NPD GO	VRK1_HUMAN	Serine/threonine-protein kinase VRK1 (EC 2.7.11.1) (Vaccinia-related kinase 1)	0.65	+	nuc	0	Nucleus. Dispersed throughout the cell but not located on mitotic spindle or chromatids during mitos ...		602168		396
Q8IV63 UniProt NPD GO	VRK3_HUMAN	Serine/threonine-protein kinase VRK3 (EC 2.7.11.1) (Vaccinia-related kinase 3)	0.65	-	nuc	0					474
P23647 UniProt NPD GO	FUSED_DROME	Serine/threonine-protein kinase fused (EC 2.7.11.1)	0.65	-	nuc	0		Hedgehog signaling complex [IPI] membrane [IDA]			805
Q09205 UniProt NPD GO	SRA3_CAEEL	Serpentine receptor class alpha-3 (Protein sra-3)	0.65	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				329
Q9NYZ4 UniProt NPD GO	SIGL8_HUMAN	Sialic acid-binding Ig-like lectin 8 precursor (Siglec-8) (Sialoadhesin family member 2) (SAF-2) (CD ...	0.65	+	end	1	Membrane; single-pass type I membrane protein	integral to membrane [TAS]	605639		499
Q9TUM3 UniProt NPD GO	STA5B_BOVIN	Signal transducer and activator of transcription 5B	0.65	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Translocated into the nucleus in response to pho ...				787
P51692 UniProt NPD GO	STA5B_HUMAN	Signal transducer and activator of transcription 5B	0.65	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Translocated into the nucleus in response to pho ...		604260		787
P42232 UniProt NPD GO	STA5B_MOUSE	Signal transducer and activator of transcription 5B	0.65	-	nuc	0	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation	cytoplasm [IDA] nucleus [IDA]			786
Q86C56 UniProt NPD GO	GCY31_CAEEL	Soluble guanylate cyclase gcy-31 (EC 4.6.1.2)	0.65	-	cyt	0	Cytoplasm (By similarity)				702
Q5RID7 UniProt NPD GO	SNX17_BRARE	Sorting nexin-17	0.65	-	nuc	0	Cytoplasm (By similarity). Endosome; early endosome (By similarity). Associated with early endosomes ...				473
Q9CY18 UniProt NPD GO	SNX7_MOUSE	Sorting nexin-7	0.65	-	cyt	0					387
Q9Y4P9 UniProt NPD GO	SPEF1_HUMAN	Sperm flagellar protein 1	0.65	+	nuc	0	Cytoplasm. Present in the tails of developing and epididymal sperm, internal to the fibrous sheath a ...				208
P54217 UniProt NPD GO	SPE11_CAEEL	Spermatocyte protein spe-11	0.65	-	nuc	0	Cytoplasm; perinuclear region. Localized to the perinuclear region of sperm				299
Q5ZMV2 UniProt NPD GO	SAS6_CHICK	Spindle assembly abnormal protein 6 homolog	0.65	-	nuc	0	Centrosome. Component of the centrosome (By similarity)				640
Q6CWQ4 UniProt NPD GO	ICL1_KLULA	Spindle assembly checkpoint kinase (EC 2.7.11.1) (Aurora kinase)	0.65	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and on elongated and disassembling spin ...				361
O75533 UniProt NPD GO	SF3B1_HUMAN	Splicing factor 3B subunit 1 (Spliceosome-associated protein 155) (SAP 155) (SF3b155) (Pre-mRNA-spli ...	0.65	-	end	0	Nucleus; nucleoplasm; nuclear speckle. During mitosis, transiently dispersed from the nuclear speckl ...	spliceosome complex [NAS]	605590	2F9J	1304
P50569 UniProt NPD GO	STF1_RAT	Steroidogenic factor 1 (STF-1) (SF-1) (Adrenal 4-binding protein) (Steroid hormone receptor Ad4BP) ( ...	0.65	+	nuc	0	Nucleus				462
O55106 UniProt NPD GO	STRN_MOUSE	Striatin	0.65	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein				780
Q8NFX7 UniProt NPD GO	STXB6_HUMAN	Syntaxin-binding protein 6 (Amisyn)	0.65	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein		607958		210
O75529 UniProt NPD GO	TAF5L_HUMAN	TAF5-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 5L (PCAF-ass ...	0.65	-	nuc	0	Nucleus				589
O14981 UniProt NPD GO	BTAF1_HUMAN	TATA-binding protein-associated factor 172 (EC 3.6.1.-) (ATP-dependent helicase BTAF1) (TBP-associat ...	0.65	-	end	0	Nucleus	nucleus [NAS]	605191		1849
Q9BWF2 UniProt NPD GO	TRAIP_HUMAN	TRAF-interacting protein	0.65	-	nuc	0	Cytoplasm. Cytoplasm; perinuclear region		605958		469
O35144 UniProt NPD GO	TERF2_MOUSE	Telomeric repeat-binding factor 2 (TTAGGG repeat-binding factor 2) (Telomeric DNA-binding protein)	0.65	-	nuc	0	Nucleus (By similarity). Colocalizes with telomeric DNA in interphase cells and is located at chromo ...				495
Q99LB0 UniProt NPD GO	TDIF1_MOUSE	Terminal deoxynucleotidyltransferase-interacting factor 1 (TdT-interacting factor 1) (TdIF1)	0.65	+	nuc	0	Nucleus (By similarity)				328
Q96AE7 UniProt NPD GO	TTC17_HUMAN	Tetratricopeptide repeat protein 17 (TPR repeat protein 17)	0.65	-	cyt	0					1141
Q9Z0U1 UniProt NPD GO	ZO2_MOUSE	Tight junction protein ZO-2 (Zonula occludens 2 protein) (Zona occludens 2 protein) (Tight junction ...	0.65	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side (By similarity). Nucleus (By similarity ...	plasma membrane [IDA]		2CSJ	1167
P79065 UniProt NPD GO	TIP1_SCHPO	Tip elongation protein 1 (Protein noc1)	0.65	-	nuc	0	Cytoplasm. Located at the microtubule tips	cell cortex of cell tip [IDA]			461
Q95M53 UniProt NPD GO	TLR2_MACFA	Toll-like receptor 2 precursor (CD282 antigen)	0.65	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				784
Q8MQI6 UniProt NPD GO	ELOF1_DROME	Transcription elongation factor 1 homolog	0.65	+	nuc	0	Nucleus (By similarity)				82
Q91ZW1 UniProt NPD GO	TFAM_RAT	Transcription factor A, mitochondrial precursor (mtTFA)	0.65	-	nuc	0	Nucleus. Mitochondrion	mitochondrion [IDA]			244
Q4V860 UniProt NPD GO	TFCP2_XENLA	Transcription factor CP2	0.65	-	nuc	0	Nucleus (By similarity)				506
Q5RB16 UniProt NPD GO	TF2L1_PONPY	Transcription factor CP2-like protein 1	0.65	-	nuc	0	Nucleus				457
Q3ZBG4 UniProt NPD GO	HES1_BOVIN	Transcription factor HES-1 (Hairy and enhancer of split 1)	0.65	-	nuc	0	Nucleus (By similarity)				280
P49866 UniProt NPD GO	HNF4_DROME	Transcription factor HNF-4 homolog (dHNF4)	0.65	-	nuc	0	Nucleus				666
Q69IL4 UniProt NPD GO	RF2A_ORYSA	Transcription factor RF2a	0.65	-	nuc	0	Nucleus				380
Q39127 UniProt NPD GO	TINY_ARATH	Transcriptional factor TINY	0.65	-	nuc	0	Nucleus (Probable)				218
Q7TN60 UniProt NPD GO	TMC6_MOUSE	Transmembrane channel-like protein 6	0.65	+	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				810
P35072 UniProt NPD GO	TCB1_CAEBR	Transposable element Tcb1 transposase (Transposable element Barney transposase)	0.65	-	nuc	0	Nucleus				273
Q9WUH5 UniProt NPD GO	TRI10_MOUSE	Tripartite motif-containing protein 10 (RING finger protein 9) (Hematopoietic RING finger 1)	0.65	-	cyt	0		cytoplasm [IDA]			489
Q9XUN9 UniProt NPD GO	TNNI3_CAEEL	Troponin I 3 (TnI 3)	0.65	+	nuc	0					260
Q6X1E1 UniProt NPD GO	DMAW_BALOB	Tryptophan dimethylallyltransferase (EC 2.5.1.34) (DMATS) (All-trans-hexaprenyl-diphosphate synthase ...	0.65	-	nuc	0					465
Q9SEA4 UniProt NPD GO	TBGN_GUITH	Tubulin gamma chain, nucleomorph (Nucleomorph gamma tubulin)	0.65	-	nuc	0					424
Q9Y6Q6 UniProt NPD GO	TNR11_HUMAN	Tumor necrosis factor receptor superfamily member 11A precursor (Receptor activator of NF-KB) (Osteo ...	0.65	-	end	1	Membrane; single-pass type I membrane protein (Potential)		603499		616
O94399 UniProt NPD GO	TWF1_SCHPO	Twinfilin	0.65	-	nuc	0					328
Q11094 UniProt NPD GO	TWIST_CAEEL	Twist-related protein (CeTwist) (Helix-loop-helix protein 8)	0.65	-	nuc	0	Nucleus (By similarity)	nucleus [IC]			178
P32019 UniProt NPD GO	I5P2_HUMAN	Type II inositol-1,4,5-trisphosphate 5-phosphatase precursor (EC 3.1.3.36) (Phosphoinositide 5-phosp ...	0.65	-	nuc	0		integral to membrane [NAS]	147264		993

You are viewing entries 16601 to 16650 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.