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
P01686 UniProt NPD GO	KV05_RABIT	Ig kappa chain V region BS-1	0.03	-	cyt	0					108
P01687 UniProt NPD GO	KV06_RABIT	Ig kappa chain V region BS-5	0.03	-	cyt	0					108
P01724 UniProt NPD GO	LV1B_MOUSE	Ig lambda-1 chain V regions MOPC 104E/RPC20/J558/S104 precursor	0.03	-	vac	0				1A6W	129
Q9HEG3 UniProt NPD GO	HIS7_NEUCR	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.03	-	cyt	0					229
Q9UVE1 UniProt NPD GO	HIS7_ZYGRO	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.03	-	cyt	0					226
Q9V8F5 UniProt NPD GO	IM23_DROME	Immune-induced peptide 23 precursor (DIM-23)	0.03	-	exc	0	Secreted protein	extracellular region [IDA]			117
P82705 UniProt NPD GO	IM04_DROME	Immune-induced peptide 4 precursor (DIM-4)	0.03	-	exc	0	Secreted protein	extracellular region [IDA]			42
P81906 UniProt NPD GO	ISPI2_GALME	Inducible serine protease inhibitor 2 (ISPI-2) (Fragment)	0.03	-	cyt	0					52
Q9VRX6 UniProt NPD GO	INX4_DROME	Innexin inx4 (Innexin-4) (Protein zero population growth)	0.03	-	end	4 *	Integral membrane protein; concentrated at the interface between germline and somatic support cells ...	gap junction [IEP] integral to membrane [NAS]			367
O62136 UniProt NPD GO	INX14_CAEEL	Innexin-14	0.03	+	end	4 *	Membrane; multi-pass membrane protein				434
Q19746 UniProt NPD GO	INX3_CAEEL	Innexin-3	0.03	-	end	4 *	Membrane; multi-pass membrane protein				420
Q8VYM2 UniProt NPD GO	PHT11_ARATH	Inorganic phosphate transporter 1-1 (AtPht1;1) (H(+)/Pi cotransporter)	0.03	-	end	11 *	Cell membrane; multi-pass membrane protein				524
O48639 UniProt NPD GO	PHT13_ARATH	Inorganic phosphate transporter 1-3 (AtPht1;3) (H(+)/Pi cotransporter)	0.03	-	end	11 *	Membrane; multi-pass membrane protein (By similarity)				521
Q15181 UniProt NPD GO	IPYR_HUMAN	Inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.03	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [TAS]	179030		289
O13505 UniProt NPD GO	IPYR_PICPA	Inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.03	-	cyt	0	Cytoplasm				284
Q9C0T9 UniProt NPD GO	IPYR_ZYGBA	Inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase)	0.03	-	cyt	0	Cytoplasm (By similarity)				287
P42800 UniProt NPD GO	INO1_CANAL	Inositol-3-phosphate synthase (EC 5.5.1.4) (Myo-inositol-1-phosphate synthase) (MI-1-P synthase) (IP ...	0.03	-	nuc	0	Cytoplasm				520
Q9SSV4 UniProt NPD GO	INO1_NICPA	Inositol-3-phosphate synthase (EC 5.5.1.4) (Myo-inositol-1-phosphate synthase) (MI-1-P synthase) (IP ...	0.03	-	cyt	0	Cytoplasm (By similarity)				510
P11986 UniProt NPD GO	INO1_YEAST	Inositol-3-phosphate synthase (EC 5.5.1.4) (Myo-inositol-1-phosphate synthase) (MI-1-P synthase) (IP ...	0.03	-	nuc	0	Cytoplasm	cytoplasm [IDA]		1P1K	533
P55902 UniProt NPD GO	SIX1_BUTOC	Insect toxin 1 (BotIT1)	0.03	-	nuc	0	Secreted protein				65
P59863 UniProt NPD GO	SIX2_BUTOC	Insect toxin 2 (Bot IT2) (BotIT2)	0.03	-	cyt	0	Secreted protein				60
P15221 UniProt NPD GO	SCX2_BUTEU	Insectotoxin I2 (BeI2)	0.03	-	nuc	0	Secreted protein				62
P12703 UniProt NPD GO	INS_ALLMI	Insulin [Contains: Insulin B chain; Insulin A chain]	0.03	-	cyt	0	Secreted protein				51
P68245 UniProt NPD GO	INS_ANSAN	Insulin [Contains: Insulin B chain; Insulin A chain]	0.03	-	cyt	0	Secreted protein				51
P68243 UniProt NPD GO	INS_CAIMO	Insulin [Contains: Insulin B chain; Insulin A chain]	0.03	-	cyt	0	Secreted protein				51
P68991 UniProt NPD GO	INS_CHIMO	Insulin [Contains: Insulin B chain; Insulin A chain]	0.03	-	cyt	0	Secreted protein				59
P01336 UniProt NPD GO	INS_GADCA	Insulin [Contains: Insulin B chain; Insulin A chain]	0.03	-	cyt	0	Secreted protein				51
P68992 UniProt NPD GO	INS_HYDCO	Insulin [Contains: Insulin B chain; Insulin A chain]	0.03	-	cyt	0	Secreted protein				59
P68988 UniProt NPD GO	INS_LAMFL	Insulin [Contains: Insulin B chain; Insulin A chain]	0.03	-	cyt	0	Secreted protein				57
P68987 UniProt NPD GO	INS_PETMA	Insulin [Contains: Insulin B chain; Insulin A chain]	0.03	-	cyt	0	Secreted protein				57
P12708 UniProt NPD GO	INS_ZAODH	Insulin [Contains: Insulin B chain; Insulin A chain]	0.03	-	nuc	0	Secreted protein				51
P01333 UniProt NPD GO	INS_ANAPL	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.03	-	cyt	0	Secreted protein				81
P01321 UniProt NPD GO	INS_CANFA	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.03	-	exc	0	Secreted protein				110
P69045 UniProt NPD GO	INS_LOPAM	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.03	-	exc	0	Secreted protein				116
P04667 UniProt NPD GO	INS_ONCKE	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.03	-	exc	0	Secreted protein				105
P01318 UniProt NPD GO	INS_SHEEP	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.03	-	vac	0	Secreted protein				105
Q60HC1 UniProt NPD GO	ITM2B_MACFA	Integral membrane protein 2B	0.03	-	mit	1	Membrane; single-pass type II membrane protein (Potential)				266
Q5R876 UniProt NPD GO	ITM2B_PONPY	Integral membrane protein 2B	0.03	-	mit	1	Membrane; single-pass type II membrane protein (Potential)				266
Q9Y287 UniProt NPD GO	ITM2B_HUMAN	Integral membrane protein 2B (Transmembrane protein BRI) [Contains: ABri/ADan amyloid peptide]	0.03	-	mit	1	Membrane; single-pass type II membrane protein (Potential)		603904		266
Q86W33 UniProt NPD GO	GP175_HUMAN	Integral membrane protein GPR175	0.03	-	end	7 *	Membrane; multi-pass membrane protein				373
Q8WWA0 UniProt NPD GO	ITLN1_HUMAN	Intelectin-1 precursor (Intestinal lactoferrin receptor) (Galactofuranose-binding lectin) (Endotheli ...	0.03	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. Secreted protein		609873		313
Q8R460 UniProt NPD GO	IL1F9_MOUSE	Interleukin-1 family member 9 (IL-1F9)	0.03	-	cyt	0	Secreted protein (By similarity)				164
Q61730 UniProt NPD GO	IL1AP_MOUSE	Interleukin-1 receptor accessory protein precursor (IL-1 receptor accessory protein) (IL-1RAcP)	0.03	-	mit	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein				570
P26952 UniProt NPD GO	IL3RA_MOUSE	Interleukin-3 receptor class 2 alpha chain precursor (Interleukin-3 receptor class II alpha chain) ( ...	0.03	-	end	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Intracellular membrane; si ...				396
P79255 UniProt NPD GO	IL8_BOVIN	Interleukin-8 precursor (IL-8) (CXCL8)	0.03	-	exc	1 *	Secreted protein	extracellular region [NAS] extracellular space [ISS]			101
Q03020 UniProt NPD GO	ISU1_YEAST	Iron sulfur cluster assembly protein 1, mitochondrial precursor (Iron sulfur cluster scaffold protei ...	0.03	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA] mitochondrion [IDA]			165
P38993 UniProt NPD GO	FET3_YEAST	Iron transport multicopper oxidase FET3 precursor (EC 1.-.-.-)	0.03	-	end	1	Cell membrane; single-pass type I membrane protein; extracellular side	plasma membrane [IDA]		1ZPU	636
Q38924 UniProt NPD GO	PPAF_ARATH	Iron(III)-zinc(II) purple acid phosphatase precursor (EC 3.1.3.2) (PAP)	0.03	+	exc	1 *	Secreted protein				469
Q90875 UniProt NPD GO	IREB1_CHICK	Iron-responsive element-binding protein (IRE-BP) (Iron regulatory protein) (IRP) (Ferritin repressor ...	0.03	-	cyt	0	Cytoplasm (By similarity)				889
P28271 UniProt NPD GO	IREB1_MOUSE	Iron-responsive element-binding protein 1 (IRE-BP 1) (Iron regulatory protein 1) (IRP1) (Ferritin re ...	0.03	-	cyt	0	Cytoplasm	cytoplasm [IDA]			889

You are viewing entries 80351 to 80400 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.