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
Q13907 UniProt NPD GO	IDI1_HUMAN	Isopentenyl-diphosphate delta-isomerase 1 (EC 5.3.3.2) (IPP isomerase 1) (Isopentenyl pyrophosphate ...	0.17	-	cyt	0	Peroxisome	peroxisome [TAS]	604055		227
Q9W729 UniProt NPD GO	NXL6_BUNMU	Kappa-6-bungarotoxin precursor (K-6 bungarotoxin)	0.17	-	nuc	0	Secreted protein				87
Q95149 UniProt NPD GO	CASK_CEREL	Kappa-casein (Fragment)	0.17	-	nuc	0	Secreted protein				122
Q95191 UniProt NPD GO	CASK_MAZAM	Kappa-casein (Fragment)	0.17	-	mit	0	Secreted protein				122
P33618 UniProt NPD GO	CASK_RABIT	Kappa-casein precursor	0.17	-	mit	0	Secreted protein				180
P82187 UniProt NPD GO	CASK_HORSE	Kappa-casein precursor (Kappa-CN)	0.17	-	exc	0	Secreted protein				185
Q58CV6 UniProt NPD GO	KLDC3_BOVIN	Kelch domain-containing protein 3	0.17	-	cyt	0	Cytoplasm. Also found in meiotic chromatin (By similarity)				370
Q6AYI2 UniProt NPD GO	KLDC3_RAT	Kelch domain-containing protein 3	0.17	-	cyt	0	Cytoplasm. Also found in meiotic chromatin (By similarity)				382
Q8VEM9 UniProt NPD GO	KLDC3_MOUSE	Kelch domain-containing protein 3 (Protein Peas) (Testis intracellular mediator protein)	0.17	-	cyt	0	Cytoplasm. Also found in meiotic chromatin	cytoplasm [ISS] nuclear chromatin [ISS]			382
Q9Z2X8 UniProt NPD GO	KEAP1_MOUSE	Kelch-like ECH-associated protein 1 (Cytosolic inhibitor of Nrf2)	0.17	-	cyt	0	Cytoplasm			1X2R	624
Q9C0H6 UniProt NPD GO	KLHL4_HUMAN	Kelch-like protein 4	0.17	-	nuc	0		cytoskeleton [ISS]	300348		718
P05782 UniProt NPD GO	K1C3_XENLA	Keratin, type I cytoskeletal 47 kDa (Fragment)	0.17	-	cyt	0					280
P43631 UniProt NPD GO	KI2S2_HUMAN	Killer cell immunoglobulin-like receptor 2DS2 precursor (MHC class I NK cell receptor) (Natural kill ...	0.17	-	exc	1	Membrane; single-pass type I membrane protein	integral to membrane [NAS]	604953	1M4K	304
P09807 UniProt NPD GO	KTXG_KLULA	Killer toxin subunit gamma precursor (RF3 protein)	0.17	-	exc	0					249
P83856 UniProt NPD GO	KNG_GADMO	Kininogen [Contains: Bradykinin] (Fragments)	0.17	-	nuc	0					123
Q800F1 UniProt NPD GO	KNL1_PHYSA	Kininogen-1 precursor [Contains: [Thr6]-phyllokinin; [Thr6]-bradykinin]	0.17	-	exc	0	Secreted protein				62
P10073 UniProt NPD GO	HKR2_HUMAN	Krueppel-related zinc finger protein 2 (Protein HKR2) (Zinc finger protein 50) (Zinc finger and SCAN ...	0.17	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	165260		106
Q05979 UniProt NPD GO	KYNU_YEAST	Kynureninase (EC 3.7.1.3) (L-kynurenine hydrolase)	0.17	-	mit	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			453
Q08415 UniProt NPD GO	KAT1_RAT	Kynurenine--oxoglutarate transaminase 1, mitochondrial precursor (EC 2.6.1.7) (Kynurenine--oxoglutar ...	0.17	-	mit	0	Isoform 2: Cytoplasm. Isoform 1: Mitochondrion; mitochondrial matrix				457
Q70KY3 UniProt NPD GO	LAC1_MELAO	Laccase-1 precursor (EC 1.10.3.2) (Benzenediol:oxygen oxidoreductase) (Urishiol oxidase) (Ligninolyt ...	0.17	-	exc	0		extraorganismal space [IDA]		1GW0	623
P21956 UniProt NPD GO	MFGM_MOUSE	Lactadherin precursor (Milk fat globule-EGF factor 8) (MFG-E8) (MFGM) (Sperm surface protein SP47) ( ...	0.17	-	exc	0	Membrane; peripheral membrane protein	external side of plasma membrane [IDA] extracellular space [IDA] extrinsic to plasma membrane [IDA]			463
Q9Y2S2 UniProt NPD GO	CRYL1_HUMAN	Lambda-crystallin homolog	0.17	-	cyt	0			609877		318
P19588 UniProt NPD GO	LEC5_DOLBI	Lectin DB58 precursor [Contains: Lectin DB58 subunit alpha; Lectin DB58 subunit beta]	0.17	-	exc	0				1LUL	275
P24527 UniProt NPD GO	LKHA4_MOUSE	Leukotriene A-4 hydrolase (EC 3.3.2.6) (LTA-4 hydrolase) (Leukotriene A(4) hydrolase)	0.17	-	cyt	0	Cytoplasm				610
Q8MA01 UniProt NPD GO	CHLB_CHAGL	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.17	-	cyt	0	Plastid; chloroplast				513
P26238 UniProt NPD GO	CHLB_MARPO	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.17	-	cyt	0	Plastid; chloroplast				513
P38414 UniProt NPD GO	LOX1_LENCU	Lipoxygenase (EC 1.13.11.12)	0.17	-	cyt	0	Cytoplasm				866
P48304 UniProt NPD GO	REG1B_HUMAN	Lithostathine 1 beta precursor (Regenerating protein I beta)	0.17	-	exc	0			167771		166
P01383 UniProt NPD GO	NXL1_NAJME	Long neurotoxin 1 (Neurotoxin 3.9.4)	0.17	-	nuc	0	Secreted protein				71
P01387 UniProt NPD GO	NXL1_OPHHA	Long neurotoxin 1 (Neurotoxin A)	0.17	-	nuc	0	Secreted protein				73
P25674 UniProt NPD GO	NXL1_NAJHH	Long neurotoxin 1 (Toxin CM-5)	0.17	-	nuc	0	Secreted protein				71
Q61114 UniProt NPD GO	LPLC1_MOUSE	Long palate, lung and nasal epithelium carcinoma-associated protein 1 precursor	0.17	-	end	0	Secreted protein (By similarity)				474
P81693 UniProt NPD GO	PPAC_PIG	Low molecular weight phosphotyrosine protein phosphatase (EC 3.1.3.48) (Low molecular weight cytosol ...	0.17	-	nuc	0	Cytoplasm				157
P51885 UniProt NPD GO	LUM_MOUSE	Lumican precursor (Keratan sulfate proteoglycan lumican) (KSPG lumican)	0.17	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)	extracellular matrix (sensu Metazoa) [IDA]			338
Q93ZH0 UniProt NPD GO	LYM1_ARATH	LysM domain GPI-anchored protein 1 precursor	0.17	-	exc	1 *	Isoform 1: Cell membrane; lipid-anchor; GPI-anchor. Isoform 2: Secreted protein (Probable)				416
P05300 UniProt NPD GO	LAMP1_CHICK	Lysosome-associated membrane glycoprotein 1 precursor (LAMP-1) (Lysosome membrane glycoprotein LEP10 ...	0.17	-	end	1	Cell membrane; single-pass type I membrane protein. Endosome; endosomal membrane; single-pass type I ...				414
Q90617 UniProt NPD GO	LAMP2_CHICK	Lysosome-associated membrane glycoprotein 2 precursor (LAMP-2)	0.17	-	end	1 *	Cell membrane; single-pass type I membrane protein (By similarity). Endosome; endosomal membrane; si ...				425
P81711 UniProt NPD GO	LYSC_SYRSO	Lysozyme C (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C) (CPL)	0.17	-	nuc	0					129
P29615 UniProt NPD GO	LYSP_DROME	Lysozyme P precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase P)	0.17	-	nuc	0					141
Q8MJ24 UniProt NPD GO	LOXL4_BOVIN	Lysyl oxidase homolog 4 precursor (EC 1.4.3.-) (Lysyl oxidase-like protein 4)	0.17	-	exc	0	Secreted protein; extracellular space (Potential)				757
Q90ZB9 UniProt NPD GO	MLN64_SALFO	MLN64-like protein (Fragment)	0.17	-	mit	0					294
O22757 UniProt NPD GO	MLO8_ARATH	MLO-like protein 8 (AtMlo8)	0.17	-	end	8 *	Membrane; multi-pass membrane protein (By similarity)				593
Q6PF18 UniProt NPD GO	MORN3_HUMAN	MORN repeat-containing protein 3	0.17	-	cyt	0					240
P19875 UniProt NPD GO	MIP2A_HUMAN	Macrophage inflammatory protein 2-alpha precursor (MIP2-alpha) (CXCL2) (Growth-regulated protein bet ...	0.17	-	mit	0	Secreted protein	extracellular space [TAS] soluble fraction [TAS]	139110	1QNK	107
O74558 UniProt NPD GO	MOB2_SCHPO	Maintenance of ploidy protein mob2	0.17	-	mit	0	Cytoplasm. Cytoplasm; cell cortex. Localizes to the cell periphery and to the division site during s ...	cell cortex [IDA] cytoplasm [IDA]			244
Q01238 UniProt NPD GO	HCC2_CRYCO	Major basic nuclear protein 2 (Protein p14 alpha chain)	0.17	-	nuc	0	Nucleus				102
P49927 UniProt NPD GO	PRIO_PIG	Major prion protein precursor (PrP) (CD230 antigen)	0.17	-	end	3 *	Cell membrane; lipid-anchor; GPI-anchor			1XYQ	257
P13262 UniProt NPD GO	MSP1_ONCVO	Major sperm protein 1 (MSP1)	0.17	-	cyt	0					126
P13263 UniProt NPD GO	MSP2_ONCVO	Major sperm protein 2 (MSP2)	0.17	-	cyt	0					126
Q19832 UniProt NPD GO	MSP3_CAEEL	Major sperm protein 3 (MSP)	0.17	-	cyt	0					126

You are viewing entries 54501 to 54550 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.