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
P83177 UniProt NPD GO	HCY2_CARMA	Hemocyanin subunit 2 (Fragment)	0.05	-	cyt	0	Secreted protein; extracellular space				25
P82308 UniProt NPD GO	HCY6_MAISQ	Hemocyanin subunit 6 (Fragment)	0.05	-	nuc	0	Secreted protein; extracellular space				21
P80946 UniProt NPD GO	HBBA_ANGAN	Hemoglobin anodic subunit beta (Hemoglobin anodic beta chain)	0.05	-	cyt	0					147
P01972 UniProt NPD GO	HBA_ODOVI	Hemoglobin subunit alpha-1/2 (Hemoglobin alpha-1/2 chain) (Alpha-1/2-globin)	0.05	-	cyt	0				1HDS	141
P16417 UniProt NPD GO	HBAD_LIOMI	Hemoglobin subunit alpha-D (Hemoglobin alpha-D chain) (Alpha-D-globin)	0.05	-	cyt	0					141
P07429 UniProt NPD GO	HBB1_XENTR	Hemoglobin subunit beta-1 (Hemoglobin beta-1 chain) (Beta-1-globin)	0.05	-	cyt	0					146
P06467 UniProt NPD GO	HBAZ_MOUSE	Hemoglobin subunit zeta (Hemoglobin zeta chain) (Zeta-globin) (Alpha-like embryonic globin chain x)	0.05	-	cyt	0					141
Q25513 UniProt NPD GO	HGLY_MANSE	Hemolymph glycoprotein precursor	0.05	-	exc	0					233
P83512 UniProt NPD GO	BAP1_BOTAS	Hemorrhagic metalloproteinase BaP1 (EC 3.4.24.-)	0.05	-	nuc	0	Secreted protein			1ND1	203
O64390 UniProt NPD GO	HXK1_SOLTU	Hexokinase-1 (EC 2.7.1.1) (StHK1)	0.05	-	nuc	1 *	Plastid; chloroplast; chloroplast outer membrane; single-pass membrane protein (By similarity)				498
Q2KNB5 UniProt NPD GO	HXK10_ORYSA	Hexokinase-10 (EC 2.7.1.1) (Hexokinase-7)	0.05	-	nuc	1 *	Plastid; chloroplast; chloroplast outer membrane; single-pass membrane protein (By similarity)				504
P30273 UniProt NPD GO	FCERG_HUMAN	High affinity immunoglobulin epsilon receptor gamma-subunit precursor (FceRI gamma) (IgE Fc receptor ...	0.05	-	end	1 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	147139		86
P21109 UniProt NPD GO	CXCR1_RABIT	High affinity interleukin-8 receptor A (IL-8R A) (CXCR-1) (CD181 antigen)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				355
P55920 UniProt NPD GO	CXCR1_PANTR	High affinity interleukin-8 receptor A (IL-8R A) (IL-8 receptor type 1) (CXCR-1) (CD181 antigen)	0.05	-	end	6 *	Membrane; multi-pass membrane protein				350
P25024 UniProt NPD GO	CXCR1_HUMAN	High affinity interleukin-8 receptor A (IL-8R A) (IL-8 receptor type 1) (CXCR-1) (CD181 antigen) (CD ...	0.05	-	vac	6 *	Membrane; multi-pass membrane protein	membrane [TAS]	146929	1ILQ	350
Q28519 UniProt NPD GO	CXCR2_MACMU	High affinity interleukin-8 receptor B (IL-8R B) (CXCR-2) (CD182 antigen) (Fragment)	0.05	-	end	6 *	Membrane; multi-pass membrane protein				353
P35344 UniProt NPD GO	CXCR2_RABIT	High affinity interleukin-8 receptor B (IL-8R B) (CXCR-2) (GRO/MGSA receptor) (CD182 antigen)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				358
P53391 UniProt NPD GO	SUT1_STYHA	High affinity sulfate transporter 1	0.05	-	end	11	Membrane; multi-pass membrane protein (Potential)				667
P53392 UniProt NPD GO	SUT2_STYHA	High affinity sulfate transporter 2	0.05	-	end	10	Membrane; multi-pass membrane protein (Potential)				662
P30825 UniProt NPD GO	CTR1_HUMAN	High-affinity cationic amino acid transporter 1 (CAT-1) (CAT1) (System Y+ basic amino acid transport ...	0.05	-	end	14 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	104615		629
Q09143 UniProt NPD GO	CTR1_MOUSE	High-affinity cationic amino acid transporter 1 (CAT-1) (CAT1) (System Y+ basic amino acid transport ...	0.05	-	end	14 *	Membrane; multi-pass membrane protein				622
P30823 UniProt NPD GO	CTR1_RAT	High-affinity cationic amino acid transporter 1 (CAT-1) (CAT1) (System Y+ basic amino acid transport ...	0.05	-	end	14 *	Membrane; multi-pass membrane protein				624
O74849 UniProt NPD GO	GHT6_SCHPO	High-affinity fructose transporter ght6 (Hexose transporter 6) (Meiotic expression up-regulated prot ...	0.05	-	end	10 *	Membrane; multi-pass membrane protein				535
O74869 UniProt NPD GO	NIC1_SCHPO	High-affinity nickel transport protein nic1	0.05	-	end	7 *	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [TAS]			405
P28506 UniProt NPD GO	ITHF_HIRME	Hirudin IIB	0.05	-	nuc	0	Secreted protein			1RIW	65
P28511 UniProt NPD GO	ITHK_HIRME	Hirudin IIIB'	0.05	-	nuc	0	Secreted protein			1ZGV	65
P80302 UniProt NPD GO	ANTA_HIRME	Hirustasin	0.05	-	nuc	0	Secreted protein			1HIA	55
Q76MS7 UniProt NPD GO	HRH2_GORGO	Histamine H2 receptor (H2R) (Gastric receptor I)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				359
P25021 UniProt NPD GO	HRH2_HUMAN	Histamine H2 receptor (H2R) (Gastric receptor I)	0.05	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	142703		359
P60021 UniProt NPD GO	HRH2_PANTR	Histamine H2 receptor (H2R) (Gastric receptor I)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				359
P61752 UniProt NPD GO	HRH2_PONPY	Histamine H2 receptor (H2R) (Gastric receptor I)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				359
Q8SQ21 UniProt NPD GO	HINT2_BOVIN	Histidine triad nucleotide-binding protein 2 (EC 3.-.-.-) (HINT-2) (HINT-3)	0.05	-	mit	0		mitochondrion [ISS]			163
P04929 UniProt NPD GO	HRPX_PLALO	Histidine-rich glycoprotein precursor	0.05	-	exc	0					351
P36605 UniProt NPD GO	HIS8_SCHPO	Histidinol-phosphate aminotransferase (EC 2.6.1.9) (Imidazole acetol-phosphate transaminase)	0.05	-	cyt	0					384
P84553 UniProt NPD GO	H1A2_CHICK	Histone H1.A2 (Fragment)	0.05	-		0	Nucleus				11
P08992 UniProt NPD GO	H2AV_TETTH	Histone H2A.Z	0.05	-	cyt	0	Nucleus				145
P35063 UniProt NPD GO	H2AX_PICAB	Histone H2AX	0.05	-	nuc	0	Nucleus				138
P39984 UniProt NPD GO	HAT2_YEAST	Histone acetyltransferase type B subunit 2 (EC 2.3.1.48)	0.05	-	cyt	0	Cytoplasm. Nucleus. The nuclear location requires the presence of HAT2	cytoplasm [IDA] histone acetyltransferase complex [IPI] nucleus [IDA]			401
Q6P3H7 UniProt NPD GO	RBBP4_BRARE	Histone-binding protein RBBP4 (Retinoblastoma-binding protein 4) (RBBP-4)	0.05	-	cyt	0	Nucleus (By similarity)				423
Q3SWX8 UniProt NPD GO	RBBP7_BOVIN	Histone-binding protein RBBP7 (Retinoblastoma-binding protein 7) (RBBP-7)	0.05	-	cyt	0	Nucleus (By similarity)				425
Q4R304 UniProt NPD GO	RBBP7_MACFA	Histone-binding protein RBBP7 (Retinoblastoma-binding protein 7) (RBBP-7)	0.05	-	cyt	0	Nucleus (By similarity)				425
Q5R654 UniProt NPD GO	RBBP7_PONPY	Histone-binding protein RBBP7 (Retinoblastoma-binding protein 7) (RBBP-7)	0.05	-	cyt	0	Nucleus (By similarity)				426
Q71UF4 UniProt NPD GO	RBBP7_RAT	Histone-binding protein RBBP7 (Retinoblastoma-binding protein 7) (RBBP-7)	0.05	-	cyt	0	Nucleus (By similarity)				425
Q16576 UniProt NPD GO	RBBP7_HUMAN	Histone-binding protein RBBP7 (Retinoblastoma-binding protein 7) (RBBP-7) (Retinoblastoma-binding pr ...	0.05	-	cyt	0	Nucleus		602922		425
Q60973 UniProt NPD GO	RBBP7_MOUSE	Histone-binding protein RBBP7 (Retinoblastoma-binding protein 7) (RBBP-7) (Retinoblastoma-binding pr ...	0.05	-	cyt	0	Nucleus	nucleus [IDA] NuRD complex [IDA]			425
Q00667 UniProt NPD GO	HGD_EMENI	Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (Homogentisicase) (Homogentisate oxygenase) (Homogentis ...	0.05	-	cyt	0					448
Q80WM4 UniProt NPD GO	HPLN4_MOUSE	Hyaluronan and proteoglycan link protein 4 precursor (Brain link protein 2) (Link protein 4)	0.05	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix (By similarity)				400
O24496 UniProt NPD GO	GLO2C_ARATH	Hydroxyacylglutathione hydrolase cytoplasmic (EC 3.1.2.6) (Glyoxalase II) (Glx II)	0.05	-	cyt	0	Cytoplasm				258
P46597 UniProt NPD GO	HIOM_HUMAN	Hydroxyindole O-methyltransferase (EC 2.1.1.4) (HIOMT) (Acetylserotonin O-methyltransferase) (ASMT)	0.05	-	cyt	0			402500		345
P35915 UniProt NPD GO	HMGCL_CHICK	Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4) (HMG-CoA lyase) (HL) (3-hydroxy-3-methylglutarate-CoA l ...	0.05	-	mit	0	Mitochondrion; mitochondrial matrix				298

You are viewing entries 74601 to 74650 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.