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
Q96C55 UniProt NPD GO	ZN524_HUMAN	Zinc finger protein 524	0.70	+	nuc	0	Nucleus (Probable)				264
O00488 UniProt NPD GO	ZN593_HUMAN	Zinc finger protein 593 (Zinc finger protein T86)	0.70	-	nuc	0	Nucleus; nucleolus			1ZR9	116
P55878 UniProt NPD GO	GLI1_CHICK	Zinc finger protein GLI1 (GLI) (Fragment)	0.70	-	nuc	0	Nucleus				556
Q62158 UniProt NPD GO	TRI27_MOUSE	Zinc finger protein RFP (Ret finger protein) (Tripartite motif-containing protein 27)	0.70	-	nuc	0	Or: Nucleus (By similarity). Or: Cytoplasm (By similarity). Nuclear or cytoplasmic depending on the ...	cytoplasm [IDA]			513
Q9DB43 UniProt NPD GO	ZFPL1_MOUSE	Zinc finger protein-like 1	0.70	-	nuc	1					310
P55114 UniProt NPD GO	NAS33_CAEEL	Zinc metalloproteinase nas-33 precursor (EC 3.4.24.21) (Nematode astacin 33)	0.70	-	nuc	0	Secreted protein (Potential)				551
Q93243 UniProt NPD GO	NAS37_CAEEL	Zinc metalloproteinase nas-37 precursor (EC 3.4.24.21) (Nematode astacin 37)	0.70	-	exc	1 *	Secreted protein	extracellular region [IDA]			765
O88799 UniProt NPD GO	ZAN_MOUSE	Zonadhesin precursor	0.70	+	end	1	Cell membrane; single-pass type I membrane protein. Exclusively on the apical region of the sperm he ...				5376
Q80SU3 UniProt NPD GO	ZAR1_MOUSE	Zygote arrest 1 (Oocyte-specific maternal effect factor)	0.70	-	nuc	0	Cytoplasm				361
O76074 UniProt NPD GO	PDE5A_HUMAN	cGMP-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.35) (CGB-PDE) (cGMP-binding cGMP-specific pho ...	0.70	-	cyt	0			603310	2H44	875
Q51MB1 UniProt NPD GO	PALI_MAGGR	pH-response regulator protein palI/RIM9	0.70	-	end	4 *	Cell membrane; multi-pass membrane protein (By similarity)				736
Q12400 UniProt NPD GO	TRM10_YEAST	tRNA (guanine-N(1)-)-methyltransferase TRM10 (EC 2.1.1.31) (tRNA methyltransferase 10)	0.70	+	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			293
Q9NX74 UniProt NPD GO	DUS2L_HUMAN	tRNA-dihydrouridine synthase 2-like (EC 1.-.-.-) (hDUS2) (Up-regulated in lung cancer) (URLC8)	0.70	-	cyt	0	Cytoplasm. Endoplasmic reticulum. Mainly at the endoplasmic reticulum		609707		493
P36612 UniProt NPD GO	PRS4_SCHPO	26S protease regulatory subunit 4 homolog (Protein mts2)	0.69	-	nuc	0	Cytoplasm (Potential). Nucleus (Potential)				448
Q9NAP9 UniProt NPD GO	RT15_CAEEL	28S ribosomal protein S15, mitochondrial precursor (MRS-S15)	0.69	-	mit	0	Mitochondrion (By similarity)				330
O59865 UniProt NPD GO	RS24B_SCHPO	40S ribosomal protein S24-B	0.69	+	nuc	0					133
Q6FJH3 UniProt NPD GO	RS6_CANGA	40S ribosomal protein S6	0.69	-	nuc	0					236
P25626 UniProt NPD GO	IMG1_YEAST	60S ribosomal protein IMG1, mitochondrial precursor (PetCR46)	0.69	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			169
Q90YV5 UniProt NPD GO	RL13_ICTPU	60S ribosomal protein L13	0.69	-	nuc	0					210
Q9LUQ6 UniProt NPD GO	RL192_ARATH	60S ribosomal protein L19-2	0.69	-	nuc	0					209
P49630 UniProt NPD GO	RL36_DROME	60S ribosomal protein L36 (Protein minute(1)1B)	0.69	+	nuc	0					115
Q28346 UniProt NPD GO	RL4_CANFA	60S ribosomal protein L4 (L1)	0.69	+	nuc	0					420
P49636 UniProt NPD GO	RL40_NICSY	60S ribosomal protein L40 (CEP52)	0.69	-	nuc	0					52
O49224 UniProt NPD GO	RL41_SOYBN	60S ribosomal protein L41	0.69	+	nuc	0					25
Q9WUQ1 UniProt NPD GO	ATS1_RAT	ADAMTS-1 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 1) ...	0.69	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				967
Q9UHI8 UniProt NPD GO	ATS1_HUMAN	ADAMTS-1 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 1) ...	0.69	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		605174		967
Q8TE56 UniProt NPD GO	ATS17_HUMAN	ADAMTS-17 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 17 ...	0.69	+	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		607511		1095
O95450 UniProt NPD GO	ATS2_HUMAN	ADAMTS-2 precursor (EC 3.4.24.14) (A disintegrin and metalloproteinase with thrombospondin motifs 2) ...	0.69	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)		604539		1211
P38749 UniProt NPD GO	YAP3_YEAST	AP-1-like transcription factor YAP3	0.69	-	nuc	0	Cytoplasm. Nucleus	nucleus [IPI]			330
Q2KJA2 UniProt NPD GO	ABCF2_BOVIN	ATP-binding cassette sub-family F member 2	0.69	-	nuc	0					625
Q5APT8 UniProt NPD GO	DBP3_CANAL	ATP-dependent RNA helicase DBP3 (EC 3.6.1.-)	0.69	+	nuc	0	Nucleus; nucleolus (By similarity)				564
Q5BGX6 UniProt NPD GO	DBP7_EMENI	ATP-dependent RNA helicase dbp7 (EC 3.6.1.-)	0.69	-	nuc	0	Nucleus; nucleolus (By similarity)				778
P33736 UniProt NPD GO	MS2A_DROSE	Accessory gland-specific peptide 26Aa precursor (Male accessory gland secretory protein 355A)	0.69	-	exc	0	Secreted protein; extracellular space				255
P19360 UniProt NPD GO	ASCL2_RAT	Achaete-scute homolog 2 (Mash2)	0.69	+	nuc	0	Nucleus (By similarity)	nucleus [IDA]			260
Q8BL65 UniProt NPD GO	ABLM2_MOUSE	Actin-binding LIM protein 2 (Actin-binding LIM protein family member 2) (abLIM-2)	0.69	-	nuc	0	Cytoplasm (Probable)				612
Q6KC51 UniProt NPD GO	ABLM2_RAT	Actin-binding LIM protein 2 (Actin-binding LIM protein family member 2) (abLIM-2)	0.69	-	nuc	0	Cytoplasm (Probable)				612
Q8K4K7 UniProt NPD GO	ABRA_RAT	Actin-binding Rho-activating protein (Striated muscle activator of Rho-dependent signaling) (STARS) ...	0.69	+	nuc	0	Localized to the I-band of the sarcomere and to a lesser extent to the sarcomeric structure between ...	actin cytoskeleton [ISS] sarcomere [IDA]			375
P53999 UniProt NPD GO	TCP4_HUMAN	Activated RNA polymerase II transcriptional coactivator p15 (SUB1 homolog) (Positive cofactor 4) (PC ...	0.69	+	nuc	0	Nucleus	transcription factor complex [IDA]	600503	2C62	126
Q8J1X7 UniProt NPD GO	FUSC3_FUSCU	Allergen Fus c 3	0.69	+	nuc	0					450
Q7TPR4 UniProt NPD GO	ACTN1_MOUSE	Alpha-actinin-1 (Alpha-actinin cytoskeletal isoform) (Non-muscle alpha-actinin-1) (F-actin cross lin ...	0.69	-	nuc	0	Cytoplasm. Colocalizes with MYOZ2 and PPP3CA at the Z-line of heart and skeletal muscle	Z disc [IDA]			892
P35611 UniProt NPD GO	ADDA_HUMAN	Alpha-adducin (Erythrocyte adducin subunit alpha)	0.69	+	nuc	0			102680		737
P35220 UniProt NPD GO	CTNA_DROME	Alpha-catenin	0.69	-	nuc	0	Cell membrane; cell-cell junction. Found only at cell-cell boundaries	adherens junction [NAS] zonula adherens [NAS]			917
Q9DBR4 UniProt NPD GO	APBB2_MOUSE	Amyloid beta A4 precursor protein-binding family B member 2	0.69	-	nuc	0		cytoplasm [IDA] nucleus [IDA]		1WGU	760
P38042 UniProt NPD GO	CDC27_YEAST	Anaphase-promoting complex subunit CDC27 (Cell division control protein 27) (Anaphase-promoting comp ...	0.69	-	nuc	0	Cytoplasm. Nucleus	anaphase-promoting complex [TAS]			758
Q8N6S4 UniProt NPD GO	AN13C_HUMAN	Ankyrin repeat domain-containing protein 13C	0.69	-	nuc	0					541
Q05753 UniProt NPD GO	AKR_ARATH	Ankyrin repeat protein, chloroplast precursor (AKRP)	0.69	+	mit	0	Plastid; chloroplast (Potential)				435
P10419 UniProt NPD GO	FMR1_ANTEL	Antho-RFamide neuropeptides type 1 precursor [Contains: Antho-RFamide]	0.69	-	vac	0	Secreted protein				435
P92964 UniProt NPD GO	RSP31_ARATH	Arginine/serine-rich-splicing factor RSP31	0.69	-	nuc	0	Nucleus (Potential)				264
O43918 UniProt NPD GO	AIRE_HUMAN	Autoimmune regulator (Autoimmune polyendocrinopathy candidiasis ectodermal dystrophy protein) (APECE ...	0.69	-	nuc	0	Nucleus. Cytoplasm. Associated with tubular structures and in discrete nuclear dots resembling ND10 ...	nucleus [NAS]	240300	1XWH	545
Q6CFR0 UniProt NPD GO	ATG11_YARLI	Autophagy-related protein 11	0.69	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Vacuolar and perivacuolar p ...				924

You are viewing entries 14101 to 14150 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.