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
Q96T68 UniProt NPD GO	SETB2_HUMAN	Probable histone-lysine N-methyltransferase, H3 lysine-9 specific (EC 2.1.1.43) (Histone H3-K9 methy ...	0.91	-	nuc	0	Nucleus (Potential)		607865		719
O94823 UniProt NPD GO	AT10B_HUMAN	Probable phospholipid-transporting ATPase VB (EC 3.6.3.1)	0.91	-	end	9	Membrane; multi-pass membrane protein				1461
P34498 UniProt NPD GO	MOG1_CAEEL	Probable pre-mRNA-splicing factor ATP-dependent RNA helicase mog-1 (EC 3.6.1.-) (Sex determination p ...	0.91	+	cyt	0	Nucleus (By similarity)				1131
O74908 UniProt NPD GO	SEN54_SCHPO	Probable tRNA-splicing endonuclease subunit sen54 (tRNA-intron endonuclease sen54)	0.91	-	cyt	0					384
Q03631 UniProt NPD GO	YMH6_YEAST	Probable transcriptional regulatory protein YML076C	0.91	-	end	0	Nucleus (Probable)	mitochondrion [IDA] nucleus [IDA]			944
P56698 UniProt NPD GO	CAC1B_DISOM	Probable voltage-dependent N-type calcium channel subunit alpha-1B (Voltage-gated calcium channel su ...	0.91	-	end	19	Membrane; multi-pass membrane protein (By similarity)				2326
P48193 UniProt NPD GO	41_MOUSE	Protein 4.1 (Band 4.1) (P4.1) (4.1R)	0.91	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				858
Q9QYW0 UniProt NPD GO	AATF_RAT	Protein AATF (Apoptosis-antagonizing transcription factor)	0.91	-	nuc	0	Nucleus				523
Q12433 UniProt NPD GO	AHC1_YEAST	Protein AHC1 (ADA HAT complex component 1)	0.91	+	nuc	0	Cytoplasm. Nucleus	Ada2/Gcn5/Ada3 transcription activator complex [IPI]			566
P40507 UniProt NPD GO	AIR1_YEAST	Protein AIR1 (Arginine methyltransferase-interacting RING finger protein 1)	0.91	-	nuc	0	Cytoplasm. Nucleus	nucleolus [IDA] nucleus [IPI] TRAMP complex [IDA]			360
Q6CQB7 UniProt NPD GO	LIC4_KLULA	Protein ATC1/LIC4	0.91	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				283
Q6BXX1 UniProt NPD GO	BFR2_DEBHA	Protein BFR2	0.91	-	nuc	0	Nucleus; nucleolus (By similarity)				514
O42914 UniProt NPD GO	YBI8_SCHPO	Protein C16A3.08c in chromosome II	0.91	-	nuc	0	Cytoplasm				284
Q86VQ0 UniProt NPD GO	CF152_HUMAN	Protein C6orf152	0.91	-	nuc	0					697
Q8N9R8 UniProt NPD GO	CI126_HUMAN	Protein C9orf126	0.91	-	mit	0	Membrane; single-pass membrane protein (Potential)				606
Q8C8N2 UniProt NPD GO	CI126_MOUSE	Protein C9orf126 homolog	0.91	+	mit	0	Membrane; single-pass membrane protein (Potential)				606
Q8TAL5 UniProt NPD GO	CI043_HUMAN	Protein C9orf43	0.91	-	nuc	0					461
Q9UBU7 UniProt NPD GO	DBF4_HUMAN	Protein DBF4 homolog (Activator of S phase Kinase)	0.91	+	nuc	0	Nucleus		604281		674
Q5JSJ4 UniProt NPD GO	DX26B_HUMAN	Protein DDX26B	0.91	-	nuc	0					861
Q5RDC1 UniProt NPD GO	FA21C_PONPY	Protein FAM21C	0.91	-	nuc	0					1340
Q5ZM71 UniProt NPD GO	FA48A_CHICK	Protein FAM48A	0.91	-	nuc	0					687
Q66HC7 UniProt NPD GO	FA48A_RAT	Protein FAM48A	0.91	-	nuc	0					530
Q14320 UniProt NPD GO	FA50A_HUMAN	Protein FAM50A (XAP-5 protein) (HXC-26 protein)	0.91	+	nuc	0	Nucleus (Potential)	nucleus [TAS]	300453		339
Q06179 UniProt NPD GO	FMP27_YEAST	Protein FMP27, mitochondrial precursor (Found in mitochondrial proteome protein 27)	0.91	-	nuc	0	Mitochondrion	mitochondrion [IDA]			2628
Q07653 UniProt NPD GO	HBT1_YEAST	Protein HBT1 (HUB1 target protein 1)	0.91	-	nuc	0	Cytoplasm	mating projection [IDA]			1046
Q8BQZ4 UniProt NPD GO	K1219_MOUSE	Protein KIAA1219	0.91	-	nuc	0					1484
Q3UWM4 UniProt NPD GO	K1718_MOUSE	Protein KIAA1718	0.91	-	nuc	0					940
Q6NYC8 UniProt NPD GO	K1949_HUMAN	Protein KIAA1949	0.91	-	nuc	0					613
P10962 UniProt NPD GO	MAK16_YEAST	Protein MAK16 (Maintenance of killer protein 16)	0.91	-	nuc	0	Nucleus	nucleolus [IDA]			306
P40578 UniProt NPD GO	MGA2_YEAST	Protein MGA2	0.91	+	nuc	1		endoplasmic reticulum membrane [IDA]			1113
P22148 UniProt NPD GO	MSN1_YEAST	Protein MSN1 (Multicopy suppressor of SNF1 protein 1)	0.91	-	nuc	0	Nucleus	nucleus [IDA]			382
Q99373 UniProt NPD GO	PET20_YEAST	Protein PET20, mitochondrial precursor (Petite colonies protein 20)	0.91	-	mit	0	Mitochondrion				253
Q9VD28 UniProt NPD GO	PTDSR_DROME	Protein PSR	0.91	+	nuc	0	Nucleus (By similarity)	nucleus [ISS]			408
Q6GND3 UniProt NPD GO	PTSRA_XENLA	Protein PTDSR-A	0.91	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			403
Q6AWX6 UniProt NPD GO	SCAR1_ARATH	Protein SCAR1 (AtSCAR1) (Protein WAVE1)	0.91	-	nuc	0					821
Q9LP46 UniProt NPD GO	SCAR3_ARATH	Protein SCAR3 (AtSCAR3) (Protein WAVE2)	0.91	-	nuc	0					1020
Q02794 UniProt NPD GO	STD1_YEAST	Protein STD1 (Glucose repression modulator MSN3) (Suppressor of fluoride sensitivity 3)	0.91	-	nuc	0		nucleus [IDA] plasma membrane [IDA]			444
P14083 UniProt NPD GO	TKR_DROME	Protein TKR (dTKR)	0.91	-	nuc	0	Nucleus (Potential)				1046
Q6R2W3 UniProt NPD GO	ZN452_HUMAN	Protein ZNF452	0.91	-	nuc	0					1325
Q568E2 UniProt NPD GO	ZN750_BRARE	Protein ZNF750	0.91	+	nuc	0					607
Q9W0K4 UniProt NPD GO	BAB2_DROME	Protein bric-a-brac 2	0.91	+	nuc	0	Nucleus	nucleus [TAS]			1067
Q96RK0 UniProt NPD GO	CIC_HUMAN	Protein capicua homolog	0.91	+	nuc	0					1608
Q9QXP4 UniProt NPD GO	DONS_MOUSE	Protein downstream neighbor of Son (Protein 3SG)	0.91	-	nuc	0	Nucleus (By similarity)				560
Q09260 UniProt NPD GO	LAG3_CAEEL	Protein lag-3 (Abnormal germ line proliferation protein 3) (Abnormal cell lineage protein 3)	0.91	-	nuc	0	Nucleus			2FO1	490
Q09330 UniProt NPD GO	MLO3_SCHPO	Protein mlo3	0.91	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			199
Q99MR9 UniProt NPD GO	PPR3A_MOUSE	Protein phosphatase 1 regulatory subunit 3A (Protein phosphatase 1 glycogen-associated regulatory su ...	0.91	+	nuc	1	Membrane; single-pass membrane protein (By similarity)				1089
Q8T0D4 UniProt NPD GO	TAN_DROME	Protein tantalus	0.91	-	nuc	0	Nucleus. Cytoplasm. In embryos, it is predominantly cytoplasmic. In third instar larvae, it is predo ...	cytoplasm [IEP] nucleus [IEP]			299
P49021 UniProt NPD GO	TIM_DROME	Protein timeless	0.91	-	nuc	0	Nucleus. Cytoplasm; perinuclear region. Nuclear at specific periods of the day. First accumulates in ...	cytoplasm [TAS] nucleus [TAS]			1421
O44431 UniProt NPD GO	TIM_DROHY	Protein timeless (Fragment)	0.91	-	nuc	0	Nucleus. Cytoplasm; perinuclear region. Nuclear at specific periods of the day. First accumulates in ...				676
Q24119 UniProt NPD GO	TRH_DROME	Protein trachealess	0.91	-	nuc	0	Nucleus	nucleus [ISS]			958

You are viewing entries 3851 to 3900 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.