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
Q8I0Y4 UniProt NPD GO	H4_OIKDI	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)				102
P62797 UniProt NPD GO	H4_ONCMY	Histone H4	0.29	-	cyt	0	Nucleus	nucleosome [ISS]			102
P62796 UniProt NPD GO	H4_ORENI	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
P62780 UniProt NPD GO	H4_PARLI	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)				102
P62802 UniProt NPD GO	H4_PIG	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
P62777 UniProt NPD GO	H4_PISBR	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)				102
P62778 UniProt NPD GO	H4_PISOC	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)				102
P62795 UniProt NPD GO	H4_PLADU	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
P62781 UniProt NPD GO	H4_PSAMI	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)				102
P62779 UniProt NPD GO	H4_PYCHE	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)				102
P84050 UniProt NPD GO	H4_RHYAM	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
P62783 UniProt NPD GO	H4_STRPU	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)				102
Q27765 UniProt NPD GO	H4_STYPL	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)				102
P84045 UniProt NPD GO	H4_TIGCA	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [NAS]			102
P62794 UniProt NPD GO	H4_URECA	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
P62798 UniProt NPD GO	H4_XENBO	Histone H4	0.29	-	cyt	0	Nucleus (By similarity)	nucleosome [ISS]			102
P62799 UniProt NPD GO	H4_XENLA	Histone H4	0.29	-	cyt	0	Nucleus	nucleosome [ISS]		2F8N	102
P62803 UniProt NPD GO	H4_BOVIN	Histone H4 (H4.1)	0.29	-	cyt	0	Nucleus	nucleosome [ISS]			102
P62804 UniProt NPD GO	H4_RAT	Histone H4 [Contains: Osteogenic growth peptide (OGP)]	0.29	-	cyt	0	Nucleus. Osteogenic growth peptide is secreted by a mechanism independent from a hydrophobic signal ...	nucleosome [ISS]			102
P70081 UniProt NPD GO	H48_CHICK	Histone H4 type VIII	0.29	-	cyt	0	Nucleus (By similarity)				102
Q4P553 UniProt NPD GO	HAT2_USTMA	Histone acetyltransferase type B subunit 2 (EC 2.3.1.48)	0.29	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				485
Q9M4U4 UniProt NPD GO	HD2C_MAIZE	Histone deacetylase 2c (HD2c) (Zm-HD2c)	0.29	-	nuc	0	Nucleus; nucleolus (By similarity)				300
Q8SVD3 UniProt NPD GO	HD3_ENCCU	Homeobox protein HD-3 (EcHD-3)	0.29	-	nuc	0	Nucleus				107
Q8STR8 UniProt NPD GO	HD4_ENCCU	Homeobox protein HD-4 (EcHD-4)	0.29	-	nuc	0	Nucleus				132
P51610 UniProt NPD GO	HCFC1_HUMAN	Host cell factor (HCF) (HCF-1) (C1 factor) (VP16 accessory protein) (VCAF) (CFF) [Contains: HCF N-te ...	0.29	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]	300019		2035
P48794 UniProt NPD GO	HYALP_MOUSE	Hyaluronidase PH-20 precursor (EC 3.2.1.35) (Hyal-PH20) (Sperm surface protein PH-20) (Sperm adhesio ...	0.29	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor	acrosome [IDA] plasma membrane [IDA]			512
P43539 UniProt NPD GO	YFG5_YEAST	Hypothetical 11.8 kDa protein in COS4 5'region	0.29	-	mit	0					102
P53103 UniProt NPD GO	YGT2_YEAST	Hypothetical 12.2 kDa protein in COX4-GTS1 intergenic region	0.29	-	nuc	0					107
P25561 UniProt NPD GO	YCC1_YEAST	Hypothetical 13.6 kDa protein in AGP1-LEU2 intergenic region	0.29	-	nuc	0					117
P38357 UniProt NPD GO	YB8F_YEAST	Hypothetical 14.4 kDa protein in CTP1-SUL2 intergenic region	0.29	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				123
O20142 UniProt NPD GO	YCX5_CHLVU	Hypothetical 15.7 kDa protein in ycf4-trnK intergenic region (ORF131)	0.29	-	nuc	1	Plastid; chloroplast				131
P51235 UniProt NPD GO	YCXC_PORPU	Hypothetical 17.2 kDa protein in cemA-psbI intergenic region (ORF149)	0.29	-	nuc	0	Plastid; chloroplast				149
P36133 UniProt NPD GO	YK20_YEAST	Hypothetical 19.2 kDa protein in GAP1-NAP1 intergenic region	0.29	+	end	4 *					167
P38892 UniProt NPD GO	YH09_YEAST	Hypothetical 33.8 kDa protein in TWT1-FLO5 intergenic region	0.29	-	cyt	0					291
O78472 UniProt NPD GO	YCF39_GUITH	Hypothetical 35.9 kDa protein ycf39	0.29	-	cyt	0	Plastid; chloroplast				314
P15612 UniProt NPD GO	YM11_PARTE	Hypothetical 43.7 kDa protein (ORF11)	0.29	-	cyt	2 *					367
P15615 UniProt NPD GO	YM14_PARTE	Hypothetical 47.2 kDa protein (ORF14)	0.29	-	end	8 *					387
P16424 UniProt NPD GO	Y1R1_DROME	Hypothetical 50 kDa protein in type I retrotransposable element R1DM (ORF 1)	0.29	-	nuc	0					471
P47018 UniProt NPD GO	YJM3_YEAST	Hypothetical 53.5 kDa protein in GCD14-POS18 intergenic region	0.29	-	nuc	0		cytoplasm [IDA] Golgi apparatus [IDA]			478
P93278 UniProt NPD GO	M040_ARATH	Hypothetical ATP synthase C chain-like protein (ORF315)	0.29	-	end	3 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				315
Q9LXB4 UniProt NPD GO	U247_ARATH	Hypothetical UPF0247 protein At5g10620	0.29	-	cyt	0					193
O13709 UniProt NPD GO	YDZ1_SCHPO	Hypothetical protein C14C4.01c in chromosome I	0.29	-	nuc	0					244
Q09254 UniProt NPD GO	YQ5B_CAEEL	Hypothetical protein C16C10.11	0.29	-	mit	0					154
O60154 UniProt NPD GO	YHY5_SCHPO	Hypothetical protein C19C7.05 in chromosome II	0.29	-	nuc	1 *					150
P34352 UniProt NPD GO	YK86_CAEEL	Hypothetical protein C30A5.6	0.29	-	end	4					362
Q94175 UniProt NPD GO	YCEL_CAEEL	Hypothetical protein C43G2.4 in chromosome IV	0.29	-	nuc	4 *					399
O13621 UniProt NPD GO	YNG5_SCHPO	Hypothetical protein C691.05c in chromosome II	0.29	-	end	9	Membrane; multi-pass membrane protein (Potential)				668
P34378 UniProt NPD GO	YLM4_CAEEL	Hypothetical protein D2007.4	0.29	-	nuc	0					170
Q3BAI2 UniProt NPD GO	YCX91_PHAAO	Hypothetical protein ORF91	0.29	-	exc	0	Plastid; chloroplast				91
Q03607 UniProt NPD GO	YN03_CAEEL	Hypothetical protein T23G5.3	0.29	-	nuc	0					262

You are viewing entries 41351 to 41400 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.