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
P79108 UniProt NPD GO	GHR_BOSIN	Growth hormone receptor precursor (GH receptor) (Somatotropin receptor) [Contains: Growth hormone-bi ...	0.24	-	nuc	1	Cell membrane; single-pass type I membrane protein. On growth hormone binding, GHR is ubiquitinated, ...				634
O46600 UniProt NPD GO	GHR_BOVIN	Growth hormone receptor precursor (GH receptor) (Somatotropin receptor) [Contains: Growth hormone-bi ...	0.24	-	nuc	1	Cell membrane; single-pass type I membrane protein. On growth hormone binding, GHR is ubiquitinated, ...				634
Q9P5U4 UniProt NPD GO	GRPE_NEUCR	GrpE protein homolog, mitochondrial precursor	0.24	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				238
Q5E9F0 UniProt NPD GO	GBG11_BOVIN	Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-11 subunit precursor	0.24	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				73
P79959 UniProt NPD GO	GBB1_XENLA	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta 1 (Transducin beta chain 1) (XGbeta1) ...	0.24	-	cyt	0					340
P38404 UniProt NPD GO	GNAO_LOCMI	Guanine nucleotide-binding protein G(o) subunit alpha	0.24	-	cyt	0					354
P09471 UniProt NPD GO	GNAO1_HUMAN	Guanine nucleotide-binding protein G(o) subunit alpha 1	0.24	-	cyt	0			139311		353
P08239 UniProt NPD GO	GNAO1_BOVIN	Guanine nucleotide-binding protein G(o) subunit alpha 1 (GTP-binding protein G39)	0.24	-	cyt	0					353
O14775 UniProt NPD GO	GBB5_HUMAN	Guanine nucleotide-binding protein subunit beta 5 (Transducin beta chain 5) (Gbeta5)	0.24	-	cyt	0		heterotrimeric G-protein complex [NAS]	604447		395
P33617 UniProt NPD GO	HLAF_MACMU	HLA class I histocompatibility antigen, alpha chain F precursor (HLA F antigen) (Leukocyte antigen F ...	0.24	-	end	1	Membrane; single-pass type I membrane protein				348
P22954 UniProt NPD GO	HSP72_ARATH	Heat shock cognate 70 kDa protein 2 (Hsc70.2)	0.24	-	cyt	0	Cytoplasm (Probable)				653
Q90473 UniProt NPD GO	HSP7C_BRARE	Heat shock cognate 71 kDa protein (Heat shock 70 kDa protein 8)	0.24	-	cyt	0					649
P11142 UniProt NPD GO	HSP7C_HUMAN	Heat shock cognate 71 kDa protein (Heat shock 70 kDa protein 8)	0.24	-	cyt	0	Cytoplasm. Translocates rapidly from the cytoplasm to the nuclei, and especially to the nucleoli, up ...	cell surface [IEP] intracellular [NAS]	600816		646
Q71U34 UniProt NPD GO	HSP7C_SAGOE	Heat shock cognate 71 kDa protein (Heat shock 70 kDa protein 8) (Intracellular vitamin D-binding pro ...	0.24	-	cyt	0	Cytoplasm (By similarity). Translocates rapidly from the cytoplasm to the nuclei, and especially to ...				646
O75031 UniProt NPD GO	HSF2B_HUMAN	Heat shock factor 2-binding protein	0.24	-	nuc	0			604554		334
Q9CQZ1 UniProt NPD GO	HSBP1_MOUSE	Heat shock factor-binding protein 1	0.24	-	nuc	0	Nucleus (By similarity)				76
Q8K3X8 UniProt NPD GO	HSBP1_RAT	Heat shock factor-binding protein 1	0.24	-	nuc	0	Nucleus (By similarity)	cytoskeleton [IDA]			76
P10592 UniProt NPD GO	HSP72_YEAST	Heat shock protein SSA2	0.24	-	cyt	0	Cytoplasm. Cell wall	cell wall (sensu Fungi) [IDA] chaperonin-containing T-complex [IPI] cytoplasm [IDA] vacuolar membrane (sensu Fungi) [IDA]			638
Q707X3 UniProt NPD GO	HSP75_ZYGRO	Heat shock protein SSB	0.24	-	cyt	0	Cytoplasm. Associated with translating ribosomes; may bind directly to the nascent polypeptide				612
P11484 UniProt NPD GO	HSP75_YEAST	Heat shock protein SSB1 (Cold-inducible protein YG101)	0.24	-	cyt	0	Cytoplasm. Associated with translating ribosomes; may bind directly to the nascent polypeptide	polysome [IDA] soluble fraction [IDA]			612
P12031 UniProt NPD GO	HCYB_HELPO	Hemocyanin, beta-C chain unit D (Fragment)	0.24	-	cyt	0					410
P20164 UniProt NPD GO	HR1B_TRIFL	Hemorrhagic metalloproteinase HR1b precursor (EC 3.4.24.52) (Trimerelysin-1) (Trimerelysin I) [Conta ...	0.24	-	nuc	0	Secreted protein				614
O35310 UniProt NPD GO	OST1_MOUSE	Heparan sulfate glucosamine 3-O-sulfotransferase 1 precursor (EC 2.8.2.23) (Heparan sulfate D-glucos ...	0.24	-	mit	0	Golgi apparatus; Golgi lumen (Probable)			1VKJ	311
Q9FF10 UniProt NPD GO	HPSE1_ARATH	Heparanase-like protein 1 precursor (EC 3.2.-.-)	0.24	-	end	0	Lysosome; lysosomal membrane; peripheral membrane protein (By similarity). Secreted protein (By simi ...				543
P61516 UniProt NPD GO	HEPC1_BRARE	Hepcidin precursor 1	0.24	-	exc	1 *	Secreted protein				91
Q86YV9 UniProt NPD GO	HPS6_HUMAN	Hermansky-Pudlak syndrome 6 protein (Ruby-eye protein homolog) (Ru)	0.24	-	mit	0			607522		775
P31943 UniProt NPD GO	HNRH1_HUMAN	Heterogeneous nuclear ribonucleoprotein H (hnRNP H)	0.24	-	cyt	0	Nucleus; nucleoplasm	heterogeneous nuclear ribonucleoprotein com... [TAS] nucleus [TAS]	601035		448
O35737 UniProt NPD GO	HNRH1_MOUSE	Heterogeneous nuclear ribonucleoprotein H (hnRNP H)	0.24	-	cyt	0	Nucleus; nucleoplasm (By similarity)				448
P50505 UniProt NPD GO	HAK1_DEBOC	High affinity potassium transporter	0.24	-	end	10	Membrane; multi-pass membrane protein				821
P33433 UniProt NPD GO	HRG_BOVIN	Histidine-rich glycoprotein (Histidine-proline-rich glycoprotein) (HPRG) (Fragments)	0.24	-	nuc	0	Secreted protein				396
P12305 UniProt NPD GO	H1_TETPY	Histone H1	0.24	+	nuc	0	Nucleus. Macronuclei				165
P27806 UniProt NPD GO	H1_WHEAT	Histone H1	0.24	-	nuc	0	Nucleus				238
P15864 UniProt NPD GO	H12_MOUSE	Histone H1.2 (H1 VAR.1) (H1c)	0.24	+	nuc	0	Nucleus				211
P40279 UniProt NPD GO	H2A_EUGGR	Histone H2A	0.24	-	nuc	0	Nucleus				136
Q6CK59 UniProt NPD GO	H2A_KLULA	Histone H2A	0.24	-	nuc	0	Nucleus (By similarity)				129
Q96QV6 UniProt NPD GO	H2A1A_HUMAN	Histone H2A type 1-A	0.24	-	nuc	0	Nucleus				130
Q00728 UniProt NPD GO	H2A4_RAT	Histone H2A type 4 (Histone H2A, testis) (TH2A)	0.24	-	nuc	0	Nucleus				129
Q6FWM7 UniProt NPD GO	H2A1_CANGA	Histone H2A.1	0.24	-	nuc	0	Nucleus				130
P16868 UniProt NPD GO	H2B4_VOLCA	Histone H2B.4 (H2B-IV)	0.24	-	nuc	0	Nucleus				154
Q9ZUS0 UniProt NPD GO	H2B4_ARATH	Histone H2B.4 (HTB5)	0.24	-	nuc	0	Nucleus (By similarity)				137
O13298 UniProt NPD GO	PHD1_SCHPO	Histone deacetylase phd1	0.24	-	cyt	0	Nucleus (Potential)	cytoplasm [IDA]			434
P55813 UniProt NPD GO	HBX4_ECHGR	Homeobox protein EgHBX4 (Fragment)	0.24	-	nuc	0	Nucleus (Probable)				60
Q9S9E3 UniProt NPD GO	IBB_DOLBI	Horsegram inhibitor 1 (Horsegram inhibitor I) (Bowman-Birk type proteinase inhibitor HGI-I) [Contain ...	0.24	-	nuc	0					76
Q6L711 UniProt NPD GO	HABP2_RAT	Hyaluronan-binding protein 2 precursor (EC 3.4.21.-) (Plasma hyaluronan-binding protein) [Contains: ...	0.24	-	exc	1 *	Secreted protein (By similarity). Secreted as an inactive single-chain precursor and is then activat ...				558
Q07523 UniProt NPD GO	HAOX2_RAT	Hydroxyacid oxidase 2 (EC 1.1.3.15) (HAOX2) ((S)-2-hydroxy-acid oxidase, peroxisomal) (Long chain al ...	0.24	-	cyt	0	Peroxisome			1TB3	352
P22370 UniProt NPD GO	YPC5_CLAPU	Hypothetical 11.8 kDa protein (ORF5)	0.24	-	mit	0					104
P53182 UniProt NPD GO	YGE1_YEAST	Hypothetical 12.0 kDa protein in DST1-HEM2 intergenic region	0.24	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)				104
P46986 UniProt NPD GO	YJS2_YEAST	Hypothetical 12.5 kDa protein in SWE1-ATP12 intergenic region	0.24	-	nuc	2 *					105
P43576 UniProt NPD GO	YFB9_YEAST	Hypothetical 13.7 kDa protein in PAU5-LPD1 intergenic region	0.24	-	cyt	0					117
P47081 UniProt NPD GO	YJA3_YEAST	Hypothetical 14.1 kDa protein in CYR1-OST1 intergenic region	0.24	-	mit	1 *		mitochondrial inner membrane [IDA]			118

You are viewing entries 46351 to 46400 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.