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
Q921F4 UniProt NPD GO	HNRLL_MOUSE	Heterogeneous nuclear ribonucleoprotein L-like	0.17	-	nuc	0				1WEX	591
P62748 UniProt NPD GO	HPCL1_MOUSE	Hippocalcin-like protein 1 (Visinin-like protein 3) (VILIP-3) (Neural visinin-like protein 3) (NVL-3 ...	0.17	-	nuc	0					192
P62749 UniProt NPD GO	HPCL1_RAT	Hippocalcin-like protein 1 (Visinin-like protein 3) (VILIP-3) (Neural visinin-like protein 3) (NVL-3 ...	0.17	-	nuc	0					192
P45353 UniProt NPD GO	HIS2_PICPA	Histidine biosynthesis trifunctional protein [Includes: Phosphoribosyl-AMP cyclohydrolase (EC 3.5.4. ...	0.17	-	cyt	0					842
P00815 UniProt NPD GO	HIS2_YEAST	Histidine biosynthesis trifunctional protein [Includes: Phosphoribosyl-AMP cyclohydrolase (EC 3.5.4. ...	0.17	-	cyt	0		intracellular [TAS]			799
P07263 UniProt NPD GO	SYH_YEAST	Histidyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.21) (Histidine--tRNA ligase) (HisRS)	0.17	+	mit	0	Mitochondrion. Cytoplasm	cytoplasm [IMP] mitochondrion [IMP]			546
P40265 UniProt NPD GO	H13_GLYBA	Histone H1-III	0.17	+	nuc	0	Nucleus				228
P40276 UniProt NPD GO	H1B_CHITE	Histone H1B	0.17	+	nuc	0	Nucleus				232
Q4HTT1 UniProt NPD GO	H2A_GIBZE	Histone H2A	0.17	-	nuc	0	Nucleus (By similarity)				133
Q8IUE6 UniProt NPD GO	H2A2B_HUMAN	Histone H2A type 2-B	0.17	-	nuc	0	Nucleus				129
Q64522 UniProt NPD GO	H2A2B_MOUSE	Histone H2A type 2-B (H2a-613A)	0.17	-	nuc	0	Nucleus				129
Q7ZUY3 UniProt NPD GO	H2AX_BRARE	Histone H2A.x (H2a/x)	0.17	-	nuc	0	Nucleus (By similarity)				141
P80553 UniProt NPD GO	H3_NARPS	Histone H3 (Fragment)	0.17	-		0	Nucleus (By similarity)				19
O17695 UniProt NPD GO	HDA1_CAEEL	Histone deacetylase 1	0.17	-	cyt	0	Nucleus. Except in the germ line where it is also cytoplasmic. Cytoplasm	cytoplasm [IDA] female germ cell nucleus [IDA] nucleus [IDA] NuRD complex [IPI]			461
Q96DB2 UniProt NPD GO	HDA11_HUMAN	Histone deacetylase 11 (HD11)	0.17	-	cyt	0	Nucleus. Predominantly	histone deacetylase complex [IDA] nucleus [IDA]	607226		347
Q20296 UniProt NPD GO	HDA6_CAEEL	Histone deacetylase 6	0.17	+	cyt	0	Nucleus (Probable)				955
Q9GZV7 UniProt NPD GO	HPLN2_HUMAN	Hyaluronan and proteoglycan link protein 2 precursor (Brain link protein 1)	0.17	-	vac	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				340
Q6RHW4 UniProt NPD GO	HYAL1_PIG	Hyaluronidase-1 precursor (EC 3.2.1.35) (Hyal-1) (Hyaluronoglucosaminidase-1)	0.17	-	exc	0	Secreted protein (By similarity). Lysosome (By similarity)				435
Q76HN1 UniProt NPD GO	HYAL1_RAT	Hyaluronidase-1 precursor (EC 3.2.1.35) (Hyal-1) (Hyaluronoglucosaminidase-1)	0.17	-	mit	0	Secreted protein (By similarity). Lysosome (By similarity)				449
Q12794 UniProt NPD GO	HYAL1_HUMAN	Hyaluronidase-1 precursor (EC 3.2.1.35) (Hyal-1) (Hyaluronoglucosaminidase-1) (LUCA-1)	0.17	-	end	0	Secreted protein. Lysosome	extracellular space [TAS]	607071		435
Q9Z2Q3 UniProt NPD GO	HYAL2_RAT	Hyaluronidase-2 precursor (EC 3.2.1.35) (Hyal-2) (Hyaluronoglucosaminidase-2) (LUCA-2)	0.17	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				473
Q93WP8 UniProt NPD GO	HSYA_TOBAC	Hydroxyproline-rich systemin A precursor [Contains: HypSysA I (TobHypSysA I); HypSysA II (TobHypSysA ...	0.17	-	exc	0		intracellular [NAS]			165
P05678 UniProt NPD GO	Y109_EMENI	Hypothetical 10.9 kDa protein in spoC1 gene cluster region	0.17	-	mit	0					97
P32858 UniProt NPD GO	YKD7_YEAST	Hypothetical 12.9 kDa protein in PTM1-IXR1 intergenic region	0.17	-	mit	3 *					118
P53231 UniProt NPD GO	YG1X_YEAST	Hypothetical 13.5 kDa protein in SCM4-MUP1 intergenic region	0.17	-	mit	0					118
P53717 UniProt NPD GO	YN82_YEAST	Hypothetical 14.7 kDa protein in RPC34-VPS27 intergenic region	0.17	-	cyt	1					134
P53902 UniProt NPD GO	YNP0_YEAST	Hypothetical 14.8 kDa protein in RPC8-MFA2 intergenic region	0.17	-	nuc	0					135
P34245 UniProt NPD GO	YKJ7_YEAST	Hypothetical 15.4 kDa protein in APE1/LAP4-CWP1 intergenic region	0.17	-	cyt	0					136
P47076 UniProt NPD GO	YJB1_YEAST	Hypothetical 18.6 kDa protein in CCT3-CCT8 intergenic region	0.17	-	nuc	0		DNA-directed RNA polymerase III complex [IDA]			161
P53117 UniProt NPD GO	YGO6_YEAST	Hypothetical 34.7 kDa protein in RPL9A-TIP20 intergenic region	0.17	-	end	1	Membrane; multi-pass membrane protein (Potential)	membrane [NAS]			311
P47140 UniProt NPD GO	YJ70_YEAST	Hypothetical 37.5 kDa protein in YUH1-URA8 intergenic region	0.17	-	mit	0					327
P53934 UniProt NPD GO	YNJ2_YEAST	Hypothetical 45.5 kDa protein in YPT53-RHO2 intergenic region	0.17	-	cyt	0					400
P15563 UniProt NPD GO	YMN3_PODAN	Hypothetical 49.1 kDa protein in ND3 intron	0.17	-	mit	1 *					433
Q9SVC5 UniProt NPD GO	DOF35_ARATH	Hypothetical Dof zinc finger protein DOF3.5 (AtDOF3.5)	0.17	-	nuc	0	Nucleus (Probable)				247
Q02857 UniProt NPD GO	YCF24_ANTSP	Hypothetical UPF0051 protein in atpA 3'region (ORF 3) (Fragment)	0.17	-	nuc	0	Plastid; chloroplast				297
P93287 UniProt NPD GO	M200_ARATH	Hypothetical mitochondrial protein AtMg00200 (ORF107B)	0.17	-	nuc	0	Mitochondrion (Potential)				107
P92534 UniProt NPD GO	M1000_ARATH	Hypothetical mitochondrial protein AtMg01000 (ORF114)	0.17	-	mit	0	Mitochondrion (Potential)				114
P92550 UniProt NPD GO	M1200_ARATH	Hypothetical mitochondrial protein AtMg01200 (ORF294)	0.17	-	end	3 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				294
Q09224 UniProt NPD GO	YP78_CAEEL	Hypothetical protein B0228.8	0.17	-	end	0					211
P46553 UniProt NPD GO	YKG3_CAEEL	Hypothetical protein B0285.3	0.17	-	nuc	0					166
P34310 UniProt NPD GO	YKR4_CAEEL	Hypothetical protein C06G4.4	0.17	-	nuc	1					129
Q09454 UniProt NPD GO	YQ32_CAEEL	Hypothetical protein C09G5.2 in chromosome II	0.17	+	cyt	0					476
O13727 UniProt NPD GO	YDO7_SCHPO	Hypothetical protein C15A10.07 in chromosome I	0.17	-	cyt	0					190
O13815 UniProt NPD GO	YE0I_SCHPO	Hypothetical protein C17H9.18c in chromosome I	0.17	-	mit	0					105
O13861 UniProt NPD GO	YEXA_SCHPO	Hypothetical protein C1A6.10 in chromosome I	0.17	-	nuc	2 *					485
Q09764 UniProt NPD GO	YA7B_SCHPO	Hypothetical protein C24H6.11c in chromosome I	0.17	-	end	8	Membrane; multi-pass membrane protein (Potential)				958
Q09246 UniProt NPD GO	YP98_CAEEL	Hypothetical protein C28H8.8	0.17	-	mit	0					297
P34348 UniProt NPD GO	YK82_CAEEL	Hypothetical protein C30A5.2	0.17	-	cyt	0					245
Q8STG4 UniProt NPD GO	Y5G6_ENCCU	Hypothetical protein ECU05_1660/ECU11_0070	0.17	-	end	6 *					239
Q8STE6 UniProt NPD GO	Y705_ENCCU	Hypothetical protein ECU07_0050/ECU09_2020	0.17	-	nuc	0					216

You are viewing entries 54401 to 54450 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.