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
P69048 UniProt NPD GO	INS_TRASC	Insulin [Contains: Insulin B chain; Insulin A chain]	0.02	-	cyt	0	Secreted protein				51
P01327 UniProt NPD GO	INS_CHIBR	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.02	-	cyt	0	Secreted protein				86
P51463 UniProt NPD GO	INS_SELRF	Insulin precursor [Contains: Insulin B chain; Insulin A chain] (Fragment)	0.02	-	mit	0	Secreted protein				103
P01337 UniProt NPD GO	INS1_BATSP	Insulin-1	0.02	-	cyt	0	Secreted protein				51
P33717 UniProt NPD GO	IGF2_CHICK	Insulin-like growth factor II (IGF-II)	0.02	-	cyt	0	Secreted protein				66
P83628 UniProt NPD GO	IBP2_ONCTS	Insulin-like growth factor-binding protein 2 (IGFBP-2) (IBP-2) (IGF-binding protein 2) (Fragment)	0.02	-		0	Secreted protein	extracellular region [IC]			20
Q5ZII3 UniProt NPD GO	GP175_CHICK	Integral membrane protein GPR175	0.02	-	vac	7	Membrane; multi-pass membrane protein (By similarity)				364
P13164 UniProt NPD GO	IFM1_HUMAN	Interferon-induced transmembrane protein 1 (Interferon-induced protein 17) (Interferon-inducible pro ...	0.02	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)	plasma membrane [TAS]	604456		125
Q9QYY1 UniProt NPD GO	IL1F5_MOUSE	Interleukin-1 family member 5 (IL-1F5) (Interleukin-1 delta) (IL-1 delta) (Interleukin-1-like protei ...	0.02	-	cyt	0	Secreted protein (By similarity)			1MD6	156
Q5I6E4 UniProt NPD GO	IL13_MACTH	Interleukin-13 precursor (IL-13)	0.02	-	end	0	Secreted protein				132
Q95KP3 UniProt NPD GO	IL2_BUBBU	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.02	-	exc	0	Secreted protein				155
P41324 UniProt NPD GO	IL8_CANFA	Interleukin-8 precursor (IL-8) (CXCL8)	0.02	-	exc	1 *	Secreted protein				101
O62812 UniProt NPD GO	IL8_HORSE	Interleukin-8 precursor (IL-8) (CXCL8)	0.02	-	vac	1 *	Secreted protein				101
P12665 UniProt NPD GO	IRBP_CRISP	Interphotoreceptor retinoid-binding protein (IRBP) (Interstitial retinol-binding protein) (Fragment) ...	0.02	-		0	Interphotoreceptor matrix that permeates the space between the retina and the contiguous layer of pi ...				15
Q9EPL6 UniProt NPD GO	MMP1B_MOUSE	Interstitial collagenase B precursor (EC 3.4.24.7) (Matrix metalloproteinase-1b) (MMP-1b) (Mcol-B)	0.02	-	exc	0					463
P15693 UniProt NPD GO	PPBI_RAT	Intestinal alkaline phosphatase 1 precursor (EC 3.1.3.1) (IAP-I)	0.02	-	end	0	Cell membrane; lipid-anchor; GPI-anchor				540
P25687 UniProt NPD GO	VPRA_DENPO	Intestinal toxin 1 (Mamba intestinal toxin 1) (MIT 1) (MIT1) (Venom protein A)	0.02	-	nuc	0	Secreted protein			1IMT	81
P83670 UniProt NPD GO	IBAP_HUMAN	Iron-binding acute phase protein (EC 1.11.-.-) (88 kDa Eales protein) (Fragment)	0.02	-	nuc	0	Secreted protein	extracellular region [IDA]			28
P21399 UniProt NPD GO	IREB1_HUMAN	Iron-responsive element-binding protein 1 (IRE-BP 1) (Iron regulatory protein 1) (IRP1) (Ferritin re ...	0.02	-	cyt	0	Cytoplasm	cytoplasm [NAS]	100880	2B3Y	889
Q01059 UniProt NPD GO	IREB1_RABIT	Iron-responsive element-binding protein 1 (IRE-BP 1) (Iron regulatory protein 1) (IRP1) (Ferritin re ...	0.02	-	cyt	0	Cytoplasm				889
Q8L8C0 UniProt NPD GO	ISAM3_ARATH	Iron-sulfur assembly protein IscA-like 3, mitochondrial precursor	0.02	-	mit	0	Mitochondrion (Potential)				109
Q28934 UniProt NPD GO	IAPP_SAGOE	Islet amyloid polypeptide (Amylin) (Fragment)	0.02	-	nuc	0	Secreted protein				32
Q9XSG3 UniProt NPD GO	IDHC_BOVIN	Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) (Cytosolic NADP-isocitrate dehydrogenase) ...	0.02	-	pox	0	Cytoplasm (By similarity)				414
Q9Z2K9 UniProt NPD GO	IDHC_MICME	Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) (Cytosolic NADP-isocitrate dehydrogenase) ...	0.02	-	pox	0	Cytoplasm				414
Q6XUZ5 UniProt NPD GO	IDHC_SHEEP	Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) (Cytosolic NADP-isocitrate dehydrogenase) ...	0.02	-	pox	0	Cytoplasm (By similarity)				414
O13294 UniProt NPD GO	IDH2_CANTR	Isocitrate dehydrogenase [NADP] peroxisomal (EC 1.1.1.42) (Oxalosuccinate decarboxylase) (IDH) (PS-N ...	0.02	-	cyt	0	Peroxisome				410
P28241 UniProt NPD GO	IDH2_YEAST	Isocitrate dehydrogenase [NAD] subunit 2, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehydroge ...	0.02	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [NAS] mitochondrion [IDA]			369
P54836 UniProt NPD GO	IDH3A_CANFA	Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (EC 1.1.1.41) (Isocitric dehydrogenase) ...	0.02	-		0	Mitochondrion				13
P52577 UniProt NPD GO	IFRH_ARATH	Isoflavone reductase homolog P3 (EC 1.3.1.-)	0.02	-	cyt	0	Cytoplasm (By similarity)				310
O22309 UniProt NPD GO	7OMT9_MEDSA	Isoflavone-7-O-methyltransferase 9 (EC 2.1.1.150) (Isoflavone-O-methyltransferase 9) (7 IOMT-9)	0.02	-	cyt	0					352
O48964 UniProt NPD GO	IDI1_CAMAC	Isopentenyl-diphosphate delta-isomerase I (EC 5.3.3.2) (IPP isomerase I) (Isopentenyl pyrophosphate ...	0.02	-	cyt	0					235
Q5RBD5 UniProt NPD GO	IVD_PONPY	Isovaleryl-CoA dehydrogenase, mitochondrial precursor (EC 1.3.99.10) (IVD)	0.02	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				423
Q8MZR6 UniProt NPD GO	HYEP1_CTEFE	Juvenile hormone epoxide hydrolase 1 (EC 3.3.2.3) (Juvenile hormone epoxide hydrolase I) (Juvenile h ...	0.02	-	mit	1 *	Microsome; microsomal membrane; single-pass membrane protein				463
P81627 UniProt NPD GO	JHBP_BOMMO	Juvenile hormone-binding protein (Fragment)	0.02	-		0	Secreted protein				20
P56254 UniProt NPD GO	KAB1_OLDAF	Kalata-B1 precursor	0.02	-	exc	0				2F2J	124
P58455 UniProt NPD GO	KAB3_OLDAF	Kalata-B3/B6 precursor [Contains: Kalata-B6; Kalata-B3]	0.02	-	exc	0				1WN8	158
P83938 UniProt NPD GO	KAB4_OLDAF	Kalata-B4	0.02	-	cyt	0				1ZNU	29
P58458 UniProt NPD GO	KABS_OLDAF	Kalata-S	0.02	-	nuc	0					29
P36369 UniProt NPD GO	K1B26_MOUSE	Kallikrein 1-related peptidase b26 precursor (EC 3.4.21.35) (Glandular kallikrein K26) (Tissue kalli ...	0.02	-	exc	0					261
Q9JM71 UniProt NPD GO	K1B27_MOUSE	Kallikrein 1-related peptidase b27 precursor (EC 3.4.21.-) (Tissue kallikrein 27) (Glandular kallikr ...	0.02	-	end	0					263
P15949 UniProt NPD GO	K1KB9_MOUSE	Kallikrein 1-related peptidase b9 precursor (EC 3.4.21.35) (Tissue kallikrein-9) (Glandular kallikre ...	0.02	-	end	0					261
P06870 UniProt NPD GO	KLK1_HUMAN	Kallikrein-1 precursor (EC 3.4.21.35) (Tissue kallikrein) (Kidney/pancreas/salivary gland kallikrein ...	0.02	-	exc	0			147910	1SPJ	262
Q07276 UniProt NPD GO	KLK1_MACFA	Kallikrein-1 precursor (EC 3.4.21.35) (Tissue kallikrein) (Kidney/pancreas/salivary gland kallikrein ...	0.02	-	exc	0					257
Q2KIP6 UniProt NPD GO	OPRK_BOVIN	Kappa-type opioid receptor (KOR-1)	0.02	-	end	7	Membrane; multi-pass membrane protein (By similarity)				380
P0C011 UniProt NPD GO	KAS2_KASSE	Kassinatuerin-2	0.02	-		0	Secreted protein				20
Q9P2N7 UniProt NPD GO	KLH13_HUMAN	Kelch-like protein 13 (BTB and kelch domain-containing protein 2)	0.02	-	cyt	0					604
Q3MIV0 UniProt NPD GO	KR221_HUMAN	Keratin-associated protein 22-1	0.02	-	cyt	0					48
O08633 UniProt NPD GO	KRA81_MOUSE	Keratin-associated protein 8-1 (High-glycine/tyrosine protein keratin) (HGT keratin) (HGTp type I F) ...	0.02	-	cyt	1 *					61
P02448 UniProt NPD GO	KRA81_SHEEP	Keratin-associated protein 8-1 (Keratin, high-tyrosine matrix protein) (Component 0.62) (HGT keratin ...	0.02	-	cyt	0					61
P50053 UniProt NPD GO	KHK_HUMAN	Ketohexokinase (EC 2.7.1.3) (Hepatic fructokinase)	0.02	-	cyt	0			229800		298

You are viewing entries 84101 to 84150 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.