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
Q05620 UniProt NPD GO	CREA_ASPNG	DNA-binding protein creA (Carbon catabolite repressor)	0.82	-	nuc	0	Nucleus				427
O95602 UniProt NPD GO	RPA1_HUMAN	DNA-directed RNA polymerase I largest subunit (EC 2.7.7.6) (RNA polymerase I 194 kDa subunit) (RPA19 ...	0.82	-	nuc	0	Nucleus	DNA-directed RNA polymerase I complex [NAS]			1717
Q85FM7 UniProt NPD GO	RPOB_ADICA	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.82	-	cyt	0	Plastid; chloroplast				1071
Q8WI24 UniProt NPD GO	RPOB_PSINU	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.82	-	cyt	0	Plastid; chloroplast				1066
Q56P11 UniProt NPD GO	RPOC2_LACSA	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.82	-	nuc	0	Plastid; chloroplast				1381
P60290 UniProt NPD GO	RPOC2_PHYPA	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.82	+	nuc	0	Plastid; chloroplast				1330
Q9Z1L3 UniProt NPD GO	DEDD_MOUSE	Death effector domain-containing protein (DEDPro1)	0.82	-	nuc	0	Cytoplasm (By similarity). Translocated to the nucleus during CD95-mediated apoptosis where it is lo ...	cytoplasm [IDA] nucleolus [IDA]			318
O75618 UniProt NPD GO	DEDD_HUMAN	Death effector domain-containing protein (Death effector domain-containing testicular molecule) (DED ...	0.82	-	nuc	0	Cytoplasm. Translocated to the nucleus during CD95-mediated apoptosis where it is localized in the n ...	cytoplasm [ISS] nucleolus [ISS]	606841		318
Q96N67 UniProt NPD GO	DOCK7_HUMAN	Dedicator of cytokinesis protein 7	0.82	-	nuc	0					1542
P40059 UniProt NPD GO	DOT6_YEAST	Disrupter of telomere silencing protein 6	0.82	-	nuc	0	Nucleus (Probable)	cytoplasm [IDA] nucleus [IDA]			670
P22290 UniProt NPD GO	PVDR_PLAVS	Duffy receptor precursor (Erythrocyte-binding protein)	0.82	+	mit	1	Membrane; single-pass type I membrane protein				1070
Q01397 UniProt NPD GO	DYNA_NEUCR	Dynactin, 150 kDa isoform (150 kDa dynein-associated polypeptide) (DP-150) (DAP-150) (p150-glued)	0.82	-	nuc	0	Cytoplasm				1300
P41161 UniProt NPD GO	ETV5_HUMAN	ETS translocation variant 5 (Ets-related protein ERM)	0.82	-	nuc	0	Nucleus		601600		510
P49880 UniProt NPD GO	ECR_AEDAE	Ecdysone receptor (Ecdysteroid receptor) (20-hydroxy-ecdysone receptor) (20E receptor) (EcRH)	0.82	-	nuc	0	Nucleus				675
P12064 UniProt NPD GO	EDN2_CANFA	Endothelin-2 precursor (ET-2) (Preproendothelin-2) (PPET2)	0.82	+	nuc	0	Secreted protein				178
O74423 UniProt NPD GO	ENT1_SCHPO	Epsin-1	0.82	+	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Localizes in a punctate pattern. Colocalizes with ...	actin cortical patch [IDA]			706
Q9YH33 UniProt NPD GO	ESR1_ORENI	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha)	0.82	+	nuc	0	Nucleus				585
P50241 UniProt NPD GO	ESR1_ORYLA	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha)	0.82	-	nuc	0	Nucleus				620
Q91250 UniProt NPD GO	ESR1_POEGU	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha)	0.82	+	nuc	0	Nucleus	chromatin remodeling complex [ISS] membrane [ISS]			587
O13012 UniProt NPD GO	ESR2_ANGJA	Estrogen receptor beta (ER-beta)	0.82	+	nuc	0	Nucleus	nucleus [ISS]			573
Q92731 UniProt NPD GO	ESR2_HUMAN	Estrogen receptor beta (ER-beta)	0.82	+	nuc	0	Nucleus	mitochondrion [IDA] nucleus [TAS]	601663	1ZAF	530
Q19192 UniProt NPD GO	E2AK3_CAEEL	Eukaryotic translation initiation factor 2-alpha kinase precursor (EC 2.7.11.1) (PRKR-like endoplasm ...	0.82	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				1077
Q9NV70 UniProt NPD GO	EXOC1_HUMAN	Exocyst complex component 1 (Exocyst complex component Sec3)	0.82	-	nuc	0		exocyst [NAS]	607879		893
P39112 UniProt NPD GO	MSU1_YEAST	Exoribonuclease II, mitochondrial precursor (EC 3.1.13.1) (Ribonuclease II) (RNase II) (Mitochondria ...	0.82	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA] mitochondrion [IDA]			969
O94769 UniProt NPD GO	ECM2_HUMAN	Extracellular matrix protein 2 precursor (Matrix glycoprotein SC1/ECM2)	0.82	-	nuc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [TAS]	603479		699
Q12830 UniProt NPD GO	FALZ_HUMAN	Fetal Alzheimer antigen (Fetal Alz-50-reactive clone 1)	0.82	-	nuc	0	Cytoplasm. Nucleus. Detected in both the cytoplasm and nucleus of cells in the developing cortex. In ...	cytoplasm [TAS] nucleus [IDA]	601819		810
Q64732 UniProt NPD GO	FOXB1_MOUSE	Forkhead box protein B1 (Transcription factor FKH-5)	0.82	+	nuc	0	Nucleus				325
Q4VYS1 UniProt NPD GO	FOXP2_XENLA	Forkhead box protein P2 (xlFoxP2)	0.82	-	nuc	0	Nucleus (Probable)				706
Q9DBY0 UniProt NPD GO	FOXP4_MOUSE	Forkhead box protein P4 (Fork head-related protein like A) (mFKHLA)	0.82	-	nuc	0	Nucleus (Probable)	nucleus [IC]			795
Q9NZ56 UniProt NPD GO	FMN2_HUMAN	Formin-2 (Fragments)	0.82	-	nuc	0					632
P24866 UniProt NPD GO	CG11_CANAL	G1/S-specific cyclin CLN1	0.82	-	nuc	0					646
P47829 UniProt NPD GO	CG21_CANAL	G2/mitotic-specific cyclin CYB1	0.82	-	nuc	0					492
Q91677 UniProt NPD GO	GATA4_XENLA	GATA-binding factor 4 (Transcription factor xGATA-4)	0.82	-	nuc	0	Nucleus				392
Q91678 UniProt NPD GO	GAT6A_XENLA	GATA-binding factor 6-A (Transcription factor xGATA-6A)	0.82	-	nuc	0	Nucleus				391
Q2UH15 UniProt NPD GO	GPI10_ASPOR	GPI mannosyltransferase 3 (EC 2.4.1.-) (GPI mannosyltransferase III) (GPI-MT-III) (Glycosylphosphati ...	0.82	-	end	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				728
Q13480 UniProt NPD GO	GAB1_HUMAN	GRB2-associated-binding protein 1 (GRB2-associated binder 1)	0.82	-	nuc	0			604439		694
P51599 UniProt NPD GO	GCH1_NEUCR	GTP cyclohydrolase I (EC 3.5.4.16) (GTP-CH-I)	0.82	+	nuc	0					313
Q24352 UniProt NPD GO	GBRAL_DROME	Gamma-aminobutyric-acid receptor alpha-like precursor (GABA(A) receptor alpha-like and glycine recep ...	0.82	-	nuc	5 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]			686
O13186 UniProt NPD GO	GCR_SAIBB	Glucocorticoid receptor (GR)	0.82	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in the absence of ligand; nuclear af ...				777
O46567 UniProt NPD GO	GCR_SAISC	Glucocorticoid receptor (GR)	0.82	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in the absence of ligand; nuclear af ...				778
P02858 UniProt NPD GO	GLYG4_SOYBN	Glycinin G4 precursor [Contains: Glycinin A5 subunit; Glycinin A4 subunit; Glycinin B3 subunit]	0.82	-	exc	0					562
Q01722 UniProt NPD GO	GCR2_YEAST	Glycolytic genes transcriptional activator GCR2	0.82	-	nuc	0	Nucleus (Probable)	nucleus [IC]			534
Q9NZW0 UniProt NPD GO	GOG8A_HUMAN	Golgin subfamily A member 8A/B (Golgi autoantigen golgin-67) (88 kDa Golgi protein) (Gm88 autoantige ...	0.82	-	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein		609619		460
Q64096 UniProt NPD GO	MCF2L_MOUSE	Guanine nucleotide exchange factor DBS (DBL's big sister) (MCF2-transforming sequence-like protein)	0.82	-	nuc	0		lamellipodium [IDA] membrane [IDA]		1LB1	1149
Q9UBP5 UniProt NPD GO	HEY2_HUMAN	Hairy/enhancer-of-split related with YRPW motif 2 (Cardiovascular helix-loop-helix factor 1) (Hairy ...	0.82	-	nuc	0	Nucleus (Probable)		604674		337
Q28555 UniProt NPD GO	HAND1_SHEEP	Heart- and neural crest derivatives-expressed protein 1 (Extraembryonic tissues, heart, autonomic ne ...	0.82	+	nuc	0					204
O81821 UniProt NPD GO	HSF3_ARATH	Heat shock factor protein 3 (HSF 3) (Heat shock transcription factor 3) (HSTF 3)	0.82	-	nuc	0	Nucleus (By similarity)				481
Q9SCW4 UniProt NPD GO	HSF6_ARATH	Heat shock factor protein 6 (HSF 6) (Heat shock transcription factor 6) (HSTF 6)	0.82	-	nuc	0	Nucleus (By similarity)				299
Q9EQ21 UniProt NPD GO	HEPC_MOUSE	Hepcidin precursor	0.82	-	exc	0	Secreted protein				83
O95263 UniProt NPD GO	PDE8B_HUMAN	High-affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8B (EC 3.1.4.17) (HS ...	0.82	-	nuc	0			603390		885

You are viewing entries 7801 to 7850 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.