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
P02707 UniProt NPD GO	LECH_CHICK	Hepatic lectin	0.20	-	cyt	1 *	Membrane; single-pass type II membrane protein				207
Q9R098 UniProt NPD GO	HGFA_MOUSE	Hepatocyte growth factor activator precursor (EC 3.4.21.-) (HGF activator) (HGFA) [Contains: Hepatoc ...	0.20	-	exc	0	Secreted protein (By similarity). Secreted as an inactive single-chain precursor and is then activat ...				653
P27680 UniProt NPD GO	COQ3_YEAST	Hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (EC 2.1.1.114) (Dihydroxyhexa ...	0.20	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side	extrinsic to membrane [IDA] mitochondrial inner membrane [IDA] mitochondrion [IDA]			312
P31581 UniProt NPD GO	HCE21_ORYLA	High choriolytic enzyme 2 precursor (EC 3.4.24.67) (Hatching enzyme zinc-protease HCE 2 subunit) (Ch ...	0.20	-	exc	0	Stored as proenzymes in the zymogen granules				279
Q58DV7 UniProt NPD GO	HNMT_BOVIN	Histamine N-methyltransferase (EC 2.1.1.8) (HMT)	0.20	-	nuc	0	Cytoplasm (By similarity)				292
P34084 UniProt NPD GO	HIS1_MACFA	Histatin-1	0.20	-	nuc	0					38
Q5R4R2 UniProt NPD GO	SYH_PONPY	Histidyl-tRNA synthetase (EC 6.1.1.21) (Histidine--tRNA ligase) (HisRS)	0.20	-	nuc	0					509
P54671 UniProt NPD GO	H1_DICDI	Histone H1	0.20	-	nuc	0	Nucleus				179
P02253 UniProt NPD GO	H11_BOVIN	Histone H1.1 (Fragment)	0.20	-	nuc	0	Nucleus				104
P13912 UniProt NPD GO	H2A_CAIMO	Histone H2A	0.20	-	nuc	0	Nucleus				128
P40280 UniProt NPD GO	H2A_MAIZE	Histone H2A	0.20	-	cyt	0	Nucleus				159
Q8X132 UniProt NPD GO	H2A_NEUCR	Histone H2A	0.20	-	nuc	0	Nucleus				133
Q4PEF9 UniProt NPD GO	H2A_USTMA	Histone H2A	0.20	-	nuc	0	Nucleus (By similarity)				135
Q93077 UniProt NPD GO	H2A1C_HUMAN	Histone H2A type 1-C	0.20	-	nuc	0	Nucleus	nucleosome [NAS]	602794		129
P0C169 UniProt NPD GO	H2A1C_RAT	Histone H2A type 1-C	0.20	-	nuc	0	Nucleus				129
P0C170 UniProt NPD GO	H2A1E_RAT	Histone H2A type 1-E	0.20	-	nuc	0	Nucleus				129
P35062 UniProt NPD GO	H2A3_CHICK	Histone H2A-III	0.20	-	nuc	0	Nucleus				128
P02263 UniProt NPD GO	H2A4_CHICK	Histone H2A-IV	0.20	-	nuc	0	Nucleus			2HIO	128
Q74ZL4 UniProt NPD GO	H2A1_ASHGO	Histone H2A.1	0.20	-	nuc	0	Nucleus				130
Q6BKW8 UniProt NPD GO	H2A1_DEBHA	Histone H2A.1	0.20	-	nuc	0	Nucleus (By similarity)				129
Q757L4 UniProt NPD GO	H2A2_ASHGO	Histone H2A.2	0.20	-	nuc	0	Nucleus				130
Q6GM86 UniProt NPD GO	H2AX_XENLA	Histone H2A.x (H2a/x)	0.20	-	nuc	0	Nucleus (By similarity)				138
P54346 UniProt NPD GO	H2B3_CHLRE	Histone H2B.3 (H2B-III)	0.20	-	nuc	0	Nucleus				152
Q43217 UniProt NPD GO	H2B3_WHEAT	Histone H2B.3 (wcH2B-8)	0.20	+	nuc	0	Nucleus (By similarity)				137
P31256 UniProt NPD GO	HXB6_XENLA	Homeobox protein Hox-B6 (XlHox-2.2) (Fragment)	0.20	+	nuc	0	Nucleus				48
Q8K0D2 UniProt NPD GO	HABP2_MOUSE	Hyaluronan-binding protein 2 precursor (EC 3.4.21.-) (Plasma hyaluronan-binding protein) [Contains: ...	0.20	-	mit	1 *	Secreted protein. Secreted as an inactive single-chain precursor and is then activated to a heterodi ...				558
P46591 UniProt NPD GO	HYR1_CANAL	Hyphally-regulated protein precursor	0.20	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				937
P47004 UniProt NPD GO	YJP0_YEAST	Hypothetical 11.9 kDa protein in INO1-IDS2 intergenic region	0.20	-	mit	1 *					100
P43566 UniProt NPD GO	YFD2_YEAST	Hypothetical 12.4 kDa protein in RIM15-HAC1 intergenic region	0.20	-	mit	2 *	Membrane; multi-pass membrane protein (Potential)				106
P39532 UniProt NPD GO	YJU2_YEAST	Hypothetical 12.9 kDa protein in PRP21-UBP12 intergenic region	0.20	-	nuc	2 *					115
P47034 UniProt NPD GO	YJH7_YEAST	Hypothetical 14.8 kDa protein in SCP160-SMC3 intergenic region	0.20	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				131
P40102 UniProt NPD GO	YE17_YEAST	Hypothetical 15.4 kDa protein in ISC10 3'region	0.20	-	cyt	0					141
Q04814 UniProt NPD GO	YM86_YEAST	Hypothetical 15.6 kDa protein in HOR7-COX7 intergenic region	0.20	-	mit	0		mitochondrion [IDA]			134
P53132 UniProt NPD GO	YGL8_YEAST	Hypothetical 16.9 kDa protein in ABC1-CDC20 intergenic region	0.20	-	cyt	0					145
P43536 UniProt NPD GO	YFG8_YEAST	Hypothetical 18.6 kDa protein in COS4 5'region	0.20	-	end	1	Membrane; multi-pass membrane protein (Potential)				160
P36067 UniProt NPD GO	YKN1_YEAST	Hypothetical 19.8 kDa protein in APL2-MYO3 intergenic region	0.20	-	nuc	0					173
P39971 UniProt NPD GO	YEI6_YEAST	Hypothetical 24.5 kDa protein in DLD3 5'region	0.20	-	nuc	0					216
O78431 UniProt NPD GO	YCX3_GUITH	Hypothetical 30.1 kDa protein (ORF252)	0.20	-	end	0	Plastid; chloroplast				252
P53265 UniProt NPD GO	YG2W_YEAST	Hypothetical 46.7 kDa protein in CLB6-SHY1 intergenic region	0.20	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			400
Q03648 UniProt NPD GO	YM59_YEAST	Hypothetical 52.2 kDa protein in RAR1-SCJ1 intergenic region	0.20	-	nuc	1 *	Membrane; multi-pass membrane protein (Potential)				457
P56809 UniProt NPD GO	YCF15_ARATH	Hypothetical 9.0 kDa protein ycf15 (ORF77)	0.20	-	nuc	0	Plastid; chloroplast				77
O78473 UniProt NPD GO	YCF24_GUITH	Hypothetical UPF0051 protein ycf24	0.20	-	cyt	0	Plastid; chloroplast				483
P92540 UniProt NPD GO	M1060_ARATH	Hypothetical mitochondrial protein AtMg01060 (ORF107g)	0.20	-	nuc	0	Mitochondrion (Potential)				107
P92554 UniProt NPD GO	M1240_ARATH	Hypothetical mitochondrial protein AtMg01240 (ORF100c)	0.20	-	nuc	0	Mitochondrion (Potential)				100
Q10926 UniProt NPD GO	YWR2_CAEEL	Hypothetical protein B0302.2	0.20	-	nuc	0					79
Q11071 UniProt NPD GO	YT43_CAEEL	Hypothetical protein B0416.3	0.20	-	end	4	Membrane; multi-pass membrane protein (Potential)				210
Q10196 UniProt NPD GO	YBY5_SCHPO	Hypothetical protein C11C11.05 precursor	0.20	-	exc	2 *	Membrane; multi-pass membrane protein (Potential)				284
O13995 UniProt NPD GO	YL81_SCHPO	Hypothetical protein C25B8.01 in chromosome I	0.20	-	nuc	1 *					166
Q8ST42 UniProt NPD GO	Y5G1_ENCCU	Hypothetical protein ECU05_1610/ECU11_0120	0.20	-	end	5 *					266
P34671 UniProt NPD GO	YO21_CAEEL	Hypothetical protein ZK688.1	0.20	-	exc	0					192

You are viewing entries 50701 to 50750 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.