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
P30757 UniProt NPD GO	H2B_SIPNU	Histone H2B	0.76	+	nuc	0	Nucleus				122
P02290 UniProt NPD GO	H2BS1_PARAN	Histone H2B.1, sperm	0.76	+	nuc	0	Nucleus				144
P06145 UniProt NPD GO	H2BS1_STRPU	Histone H2B.1, sperm	0.76	+	nuc	0	Nucleus				139
Q6FPH9 UniProt NPD GO	ESA1_CANGA	Histone acetyltransferase ESA1 (EC 2.3.1.48)	0.76	+	cyt	0	Nucleus (By similarity)				446
P43687 UniProt NPD GO	HMX2_MOUSE	Homeobox protein HMX2 (Homeobox protein Nkx-5.2)	0.76	+	nuc	0	Nucleus (Probable)				273
Q00056 UniProt NPD GO	HXA4_HUMAN	Homeobox protein Hox-A4 (Hox-1D) (Hox-1.4)	0.76	+	nuc	0	Nucleus		142953		320
P50209 UniProt NPD GO	HXA9_AMBME	Homeobox protein Hox-A9 (Fragment)	0.76	+	nuc	0	Nucleus				143
P23681 UniProt NPD GO	HXB8_CHICK	Homeobox protein Hox-B8 (Chox-2.4) (Fragment)	0.76	-	nuc	0	Nucleus				74
P31257 UniProt NPD GO	HXC10_MOUSE	Homeobox protein Hox-C10 (Hox-3.6)	0.76	+	nuc	0	Nucleus				342
Q9PVQ9 UniProt NPD GO	HXC9_ORYLA	Homeobox protein Hox-C9	0.76	+	nuc	0	Nucleus (By similarity)				262
P13378 UniProt NPD GO	HXD8_HUMAN	Homeobox protein Hox-D8 (Hox-4E) (Hox-5.4)	0.76	+	nuc	0	Nucleus	nucleus [NAS]	142985		290
P42582 UniProt NPD GO	NKX25_MOUSE	Homeobox protein Nkx-2.5 (Homeobox protein NK-2 homolog E) (Cardiac-specific homeobox) (Homeobox pro ...	0.76	+	nuc	0	Nucleus (Probable)	transcription factor complex [IDA]			318
Q4LAL6 UniProt NPD GO	ALX4_BOVIN	Homeobox protein aristaless-like 4	0.76	+	nuc	0	Nucleus (By similarity)				397
P41779 UniProt NPD GO	HM20_CAEEL	Homeobox protein ceh-20	0.76	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			338
Q94166 UniProt NPD GO	HM33_CAEEL	Homeobox protein ceh-33	0.76	-	nuc	0	Nucleus (Probable)				261
Q05925 UniProt NPD GO	HME1_HUMAN	Homeobox protein engrailed-1 (Hu-En-1)	0.76	+	nuc	0	Nucleus		131290		392
Q05917 UniProt NPD GO	HME2_CHICK	Homeobox protein engrailed-2 (Gg-En-2)	0.76	+	nuc	0	Nucleus				288
O76971 UniProt NPD GO	OTP_PARLI	Homeobox protein orthopedia-related (PLOTP)	0.76	+	nuc	0	Nucleus (By similarity)				364
P22807 UniProt NPD GO	SLOU_DROME	Homeobox protein slou (S59/2) (Protein slouch) (Homeobox protein NK-1)	0.76	+	nuc	0	Nucleus (Probable)	nucleus [NAS]			659
P20912 UniProt NPD GO	HM16_XENLA	Homeotic protein NRL-16 (NRL-21) (Fragment)	0.76	+	nuc	0	Nucleus				111
O75330 UniProt NPD GO	HMMR_HUMAN	Hyaluronan mediated motility receptor (Intracellular hyaluronic acid-binding protein) (Receptor for ...	0.76	-	nuc	0	Cell surface. Cytoplasm (By similarity)		600936		724
P40536 UniProt NPD GO	YID2_YEAST	Hypothetical 13.8 kDa protein in REG1-SMT4 intergenic region	0.76	+	nuc	0					118
P31920 UniProt NPD GO	YCX7_EUGGR	Hypothetical 35.4 kDa protein in rbcL-atpE intergenic region (ORF295)	0.76	-	nuc	0	Plastid; chloroplast				295
P34239 UniProt NPD GO	YKR6_YEAST	Hypothetical 93.4 kDa protein in STE3-GIN10 intergenic region	0.76	-	mit	0		vesicle coat [IDA]			828
Q10190 UniProt NPD GO	YAWG_SCHPO	Hypothetical GTP-binding protein C3F10.16c in chromosome I	0.76	-	nuc	0					616
Q10122 UniProt NPD GO	YSM1_CAEEL	Hypothetical WD repeat protein F52C9.1	0.76	-	nuc	0					1336
Q8LE98 UniProt NPD GO	Y1714_ARATH	Hypothetical protein At1g17140	0.76	-	nuc	0					344
Q9Y808 UniProt NPD GO	YN91_SCHPO	Hypothetical protein C146.01 in chromosome II	0.76	-	mit	0					1063
Q9Y7Q3 UniProt NPD GO	YQ6A_SCHPO	Hypothetical protein C191.10 in chromosome III	0.76	-	nuc	0					149
Q09776 UniProt NPD GO	YA8B_SCHPO	Hypothetical protein C22F3.11c in chromosome I	0.76	+	nuc	0					151
Q09698 UniProt NPD GO	YA27_SCHPO	Hypothetical protein C2F7.07c in chromosome I	0.76	+	nuc	0					607
Q09261 UniProt NPD GO	YQC2_CAEEL	Hypothetical protein C32A3.2	0.76	-	nuc	1 *					346
Q93364 UniProt NPD GO	YE3O_CAEEL	Hypothetical protein C41G7.7	0.76	+	nuc	0					156
Q9VM75 UniProt NPD GO	HEAT1_DROME	Hypothetical protein CG10805	0.76	-	end	0	Nucleus; nucleolus (By similarity)				2096
P34495 UniProt NPD GO	YMQ4_CAEEL	Hypothetical protein K02D10.4	0.76	-	nuc	0					227
Q10044 UniProt NPD GO	YRT1_CAEEL	Hypothetical protein T07A5.1	0.76	-	nuc	0					622
P34594 UniProt NPD GO	YOD2_CAEEL	Hypothetical protein ZC262.2	0.76	+	nuc	0					233
Q23314 UniProt NPD GO	YHC4_CAEEL	Hypothetical protein ZC434.4	0.76	-	nuc	0					270
Q09624 UniProt NPD GO	YS89_CAEEL	Hypothetical protein ZK945.9	0.76	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				3178
P11487 UniProt NPD GO	FGF3_HUMAN	INT-2 proto-oncogene protein precursor (Fibroblast growth factor 3) (FGF-3) (HBGF-3)	0.76	+	nuc	0		extracellular region [TAS]	164950		239
Q6P7D3 UniProt NPD GO	IER2_RAT	Immediate early response gene 2 protein	0.76	+	nuc	0					221
Q75A73 UniProt NPD GO	TIM50_ASHGO	Import inner membrane translocase subunit TIM50, mitochondrial precursor	0.76	-	mit	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				476
Q22560 UniProt NPD GO	IMA1_CAEEL	Importin alpha-1 subunit (Karyopherin alpha-1 subunit)	0.76	-	nuc	0	Cytoplasm	cytoplasm [IEP] nuclear pore [IMP]			524
P83953 UniProt NPD GO	IMA1_RAT	Importin alpha-1 subunit (Karyopherin alpha-1 subunit) (Importin alpha 5)	0.76	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				538
P52294 UniProt NPD GO	IMA1_HUMAN	Importin alpha-1 subunit (Karyopherin alpha-1 subunit) (SRP1-beta) (RAG cohort protein 2) (Nucleopro ...	0.76	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [TAS] nuclear pore [TAS]	600686		538
O60684 UniProt NPD GO	IMA7_HUMAN	Importin alpha-7 subunit (Karyopherin alpha-6)	0.76	-	nuc	0					536
O13375 UniProt NPD GO	OXA1_SACSE	Inner membrane protein OXA1, mitochondrial precursor (Oxidase assembly protein 1) (Cytochrome oxidas ...	0.76	+	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				371
P29994 UniProt NPD GO	ITPR1_RAT	Inositol 1,4,5-trisphosphate receptor type 1 (Type 1 inositol 1,4,5-trisphosphate receptor) (Type 1 ...	0.76	-	end	6	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				2750
Q14643 UniProt NPD GO	ITPR1_HUMAN	Inositol 1,4,5-trisphosphate receptor type 1 (Type 1 inositol 1,4,5-trisphosphate receptor) (Type 1 ...	0.76	-	end	6	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [NAS] endoplasmic reticulum membrane [NAS] integral to plasma membrane [TAS]	147265		2758
P11881 UniProt NPD GO	ITPR1_MOUSE	Inositol 1,4,5-trisphosphate receptor type 1 (Type 1 inositol 1,4,5-trisphosphate receptor) (Type 1 ...	0.76	-	end	6	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [TAS] endoplasmic reticulum membrane [ISS]		1XZZ	2749

You are viewing entries 10851 to 10900 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.