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
P05201 UniProt NPD GO	AATC_MOUSE	Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1) (Transaminase A) (Glutamate oxaloacetate transa ...	0.02	-	cyt	0	Cytoplasm				412
P00506 UniProt NPD GO	AATM_PIG	Aspartate aminotransferase, mitochondrial precursor (EC 2.6.1.1) (Transaminase A) (Glutamate oxaloac ...	0.02	-	nuc	0	Mitochondrion; mitochondrial matrix				430
Q43086 UniProt NPD GO	PYRB1_PEA	Aspartate carbamoyltransferase 1, chloroplast precursor (EC 2.1.3.2) (Aspartate transcarbamylase 1) ...	0.02	-	mit	0	Plastid; chloroplast				386
Q03197 UniProt NPD GO	API10_SOLTU	Aspartic protease inhibitor 10 precursor (Wound-induced aspartate proteinase CDI inhibitor)	0.02	-	exc	0					219
P16348 UniProt NPD GO	API11_SOLTU	Aspartic protease inhibitor 11 (Cathepsin D inhibitor PDI) (Allergen Sola t 2)	0.02	-	cyt	0	Vacuole (By similarity)				188
P58518 UniProt NPD GO	API3_SOLTU	Aspartic protease inhibitor 3 (API-3) (Fragment)	0.02	-	cyt	0	Vacuole (By similarity)				169
P58520 UniProt NPD GO	API6_SOLTU	Aspartic protease inhibitor 6 (API-6) (Fragment)	0.02	-	cyt	0	Vacuole (By similarity)				169
P17979 UniProt NPD GO	API8_SOLTU	Aspartic protease inhibitor 8 precursor (pi8) (PI-8) (API) (API-8) (Cathepsin D inhibitor)	0.02	-	exc	1 *	Vacuole (By similarity)				220
P58521 UniProt NPD GO	API9_SOLTU	Aspartic protease inhibitor 9 (Novel inhibitor of cathepsin D) (NID)	0.02	-	cyt	0	Vacuole (By similarity)				187
P01512 UniProt NPD GO	ATTB_HYACE	Attacin-B precursor (Immune protein P5)	0.02	-	exc	0	Secreted protein				233
Q6C4Q6 UniProt NPD GO	ATG5_YARLI	Autophagy protein 5	0.02	-	mit	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				255
Q751W1 UniProt NPD GO	ATG22_ASHGO	Autophagy-related protein 22	0.02	-	end	11 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Vacuole and punctate struct ...				507
Q5AVT9 UniProt NPD GO	AT222_EMENI	Autophagy-related protein 22-2	0.02	-	end	12 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Vacuole and punctate struct ...				593
Q96247 UniProt NPD GO	AUX1_ARATH	Auxin transporter protein 1 (Auxin influx carrier protein 1) (Polar auxin transport inhibitor-resist ...	0.02	-	end	10	Cell membrane; multi-pass membrane protein. In S2 columella cells, a dynamic cytoplasmic to membrane ...				485
Q5N892 UniProt NPD GO	LAX1_ORYSA	Auxin transporter-like protein 1	0.02	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				492
Q688J2 UniProt NPD GO	LAX2_ORYSA	Auxin transporter-like protein 2	0.02	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				482
Q9FEL7 UniProt NPD GO	LAX2_MEDTR	Auxin transporter-like protein 2 (AUX1-like protein 2) (MtLAX2)	0.02	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				484
Q8L884 UniProt NPD GO	LAX4_MEDTR	Auxin transporter-like protein 4 (AUX1-like protein 4) (MtLAX4)	0.02	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				482
Q94BT2 UniProt NPD GO	AIR12_ARATH	Auxin-induced in root cultures protein 12 precursor	0.02	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				252
P33082 UniProt NPD GO	AXX15_SOYBN	Auxin-induced protein X15	0.02	-	cyt	0					82
O24410 UniProt NPD GO	IAA20_ARATH	Auxin-responsive protein IAA20 (Indoleacetic acid-induced protein 20)	0.02	-	mit	0	Nucleus (By similarity)				175
P56732 UniProt NPD GO	AVR2_CHICK	Avidin-related protein 2 precursor	0.02	-	exc	0				1WBI	150
P56734 UniProt NPD GO	AVR4_CHICK	Avidin-related protein 4/5 precursor	0.02	-	exc	0				2FHN	150
Q13072 UniProt NPD GO	BAGE1_HUMAN	B melanoma antigen 1 precursor (B melanoma antigen) (Antigen MZ2-BA)	0.02	-	exc	0			605167		43
Q27017 UniProt NPD GO	B1_TENMO	B1 protein precursor (Fragment)	0.02	-	cyt	0	Secreted protein (Potential)				130
Q8WY22 UniProt NPD GO	BRI3B_HUMAN	BRI3-binding protein (I3-binding protein) (Cervical cancer 1 proto-oncogene-binding protein KG19) (H ...	0.02	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				251
P34324 UniProt NPD GO	BAT15_CAEEL	BTB and MATH domain-containing protein 15 (Fragment)	0.02	-	cyt	0					273
Q9NXS3 UniProt NPD GO	BTBD5_HUMAN	BTB/POZ domain-containing protein 5	0.02	-	cyt	0					571
Q8BU51 UniProt NPD GO	BPIL3_MOUSE	Bactericidal/permeability-increasing protein-like 3 precursor	0.02	-	end	0	Secreted protein (By similarity)				449
Q41159 UniProt NPD GO	LCB1_ROBPS	Bark agglutinin I, polypeptide A precursor (RPbAI) (LECRPA1)	0.02	-	exc	1 *				1FNZ	285
P61283 UniProt NPD GO	BAF_BOVIN	Barrier-to-autointegration factor	0.02	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Significantly enriched at the nuclear inner memb ...				89
Q5RBU9 UniProt NPD GO	BAF_PONPY	Barrier-to-autointegration factor	0.02	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Significantly enriched at the nuclear inner memb ...				89
O75531 UniProt NPD GO	BAF_HUMAN	Barrier-to-autointegration factor (Breakpoint cluster region protein 1)	0.02	-	cyt	0	Nucleus. Cytoplasm. Significantly enriched at the nuclear inner membrane; diffusely throughout the n ...			2EZZ	89
O54962 UniProt NPD GO	BAF_MOUSE	Barrier-to-autointegration factor (Breakpoint cluster region protein 1) (LAP2-binding protein 1)	0.02	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Significantly enriched at the nuclear inner memb ...				89
Q9H503 UniProt NPD GO	BAFL_HUMAN	Barrier-to-autointegration factor-like protein (BAF-L)	0.02	-	cyt	0	Nucleus. Cytoplasm				90
P82107 UniProt NPD GO	BDEL_HIRME	Bdellastasin (Bdellin A)	0.02	-	nuc	0	Secreted protein			1EJA	59
P09865 UniProt NPD GO	IBD3_HIRME	Bdellin B-3 (Fragment)	0.02	-	cyt	0					56
P28873 UniProt NPD GO	BMRP_CANAL	Benomyl/methotrexate resistance protein	0.02	-	end	12	Membrane; multi-pass membrane protein				564
Q9BYV7 UniProt NPD GO	BCDO2_HUMAN	Beta,beta-carotene 9',10'-dioxygenase (EC 1.14.99.-) (Beta-carotene dioxygenase 2) (B-diox-II)	0.02	-	cyt	0		intracellular [ISS]			556
Q8HXG8 UniProt NPD GO	BCDO2_MACFA	Beta,beta-carotene 9',10'-dioxygenase (EC 1.14.99.-) (Beta-carotene dioxygenase 2) (B-diox-II)	0.02	-	cyt	0		intracellular [ISS]			556
O42574 UniProt NPD GO	ADRB1_XENLA	Beta-1 adrenergic receptor (Beta-1 adrenoceptor) (Beta-1 adrenoreceptor) (X-BETA1AR)	0.02	-	end	7 *	Membrane; multi-pass membrane protein				385
Q9NJ98 UniProt NPD GO	BGBP1_MANSE	Beta-1,3-glucan-binding protein 1 precursor (BGBP-1) (Beta-1,3-glucan recognition protein 1) (BetaGR ...	0.02	-	exc	0	Secreted protein	extracellular region [IDA]			487
Q76DI2 UniProt NPD GO	BGBP_TENMO	Beta-1,3-glucan-binding protein precursor (BGBP) (Beta-1,3-glucan recognition protein) (BetaGRP)	0.02	-	exc	0	Secreted protein	extracellular region [IDA]			481
P01886 UniProt NPD GO	B2MG_CAVPO	Beta-2-microglobulin	0.02	-	cyt	0	Secreted protein				99
P19341 UniProt NPD GO	B2MG_CANFA	Beta-2-microglobulin (Fragment)	0.02	-	cyt	1 *	Secreted protein				42
Q03422 UniProt NPD GO	B2MG_CYPCA	Beta-2-microglobulin precursor	0.02	-	nuc	0	Secreted protein				116
Q5MGS7 UniProt NPD GO	B2MG_FELCA	Beta-2-microglobulin precursor	0.02	-	exc	0	Secreted protein				118
O42197 UniProt NPD GO	B2MG_ICTPU	Beta-2-microglobulin precursor	0.02	-	exc	0	Secreted protein				116
O77534 UniProt NPD GO	B2MG_SAIBB	Beta-2-microglobulin precursor	0.02	-	exc	0	Secreted protein				119
Q71UN6 UniProt NPD GO	B2MG_SAISC	Beta-2-microglobulin precursor	0.02	-	exc	0	Secreted protein				119

You are viewing entries 82551 to 82600 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.