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
Q5E9U9 UniProt NPD GO	TUSC4_BOVIN	Tumor suppressor candidate 4	0.31	-	cyt	0					380
Q640W2 UniProt NPD GO	TWF2B_XENLA	Twinfilin-2-B	0.31	-	cyt	0	Cytoplasm (By similarity). Cytoplasm; perinuclear region (By similarity). Perinuclear and G-actin-ri ...				349
P08579 UniProt NPD GO	RU2B_HUMAN	U2 small nuclear ribonucleoprotein B''	0.31	-	nuc	0	Nucleus	snRNP U2 [TAS] spliceosome complex [IDA]	603520	1A9N	225
Q5XGE2 UniProt NPD GO	UTP15_XENTR	U3 small nucleolar RNA-associated protein 15 homolog	0.31	-	cyt	0	Nucleus; nucleolus (By similarity)				515
Q8C7V3 UniProt NPD GO	UTP15_MOUSE	U3 small nucleolar RNA-associated protein 15 homolog (Src-associated protein SAW)	0.31	-	cyt	0	Nucleus; nucleolus (By similarity)				528
Q4WNB5 UniProt NPD GO	ALG14_ASPFU	UDP-N-acetylglucosamine transferase subunit alg14 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.31	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				228
Q9VYF8 UniProt NPD GO	COQ5_DROME	Ubiquinone biosynthesis methyltransferase COQ5, mitochondrial precursor (EC 2.1.1.-)	0.31	-	mit	0	Mitochondrion (By similarity)	mitochondrion [ISS]			301
Q4G064 UniProt NPD GO	COQ5_RAT	Ubiquinone biosynthesis methyltransferase COQ5, mitochondrial precursor (EC 2.1.1.-)	0.31	-	mit	0	Mitochondrion (By similarity)				327
Q8MKN0 UniProt NPD GO	COQ9_DROME	Ubiquinone biosynthesis protein COQ9, mitochondrial precursor	0.31	-	mit	0	Mitochondrion (By similarity)	mitochondrial inner membrane [ISS]			326
Q05779 UniProt NPD GO	COQ9_YEAST	Ubiquinone biosynthesis protein COQ9, mitochondrial precursor	0.31	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side	mitochondrial inner membrane [IDA] mitochondrion [IDA]			260
Q8WY64 UniProt NPD GO	MYLIP_HUMAN	Ubiquitin ligase MYLIP (EC 6.3.2.-) (Myosin regulatory light chain-interacting protein) (MIR)	0.31	-	cyt	0	Cytoplasm (Probable)	intracellular [IDA]			445
Q06985 UniProt NPD GO	SIA1B_MOUSE	Ubiquitin ligase SIAH1B (EC 6.3.2.-) (Seven in absentia homolog 1b) (Siah1b) (Siah-1b)	0.31	-	mit	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). Partially (By similarity)				282
Q95044 UniProt NPD GO	UBE2C_SPISO	Ubiquitin-conjugating enzyme E2 C (EC 6.3.2.19) (Ubiquitin-protein ligase C) (Ubiquitin carrier prot ...	0.31	-	nuc	0				2E2C	177
Q7TSS2 UniProt NPD GO	UB2Q1_MOUSE	Ubiquitin-conjugating enzyme E2 Q1 (EC 6.3.2.19) (Ubiquitin-protein ligase Q1) (Ubiquitin carrier pr ...	0.31	-	nuc	0					422
Q7Z7E8 UniProt NPD GO	UB2Q1_HUMAN	Ubiquitin-conjugating enzyme E2 Q1 (EC 6.3.2.19) (Ubiquitin-protein ligase Q1) (Ubiquitin carrier pr ...	0.31	-	nuc	0					422
Q32L27 UniProt NPD GO	UB2Q2_BOVIN	Ubiquitin-conjugating enzyme E2 Q2 (EC 6.3.2.19) (Ubiquitin-protein ligase Q2) (Ubiquitin carrier pr ...	0.31	-	nuc	0	Cytoplasm (By similarity)				342
O59735 UniProt NPD GO	YHXF_SCHPO	Uncharacterized TLC domain-containing protein C3E17.15c	0.31	-	end	7	Membrane; multi-pass membrane protein (Potential)				384
Q04613 UniProt NPD GO	MI25_ARATH	Uncharacterized mitochondrial 22 kDa protein AtMg00640 (ORF 25)	0.31	-	end	1 *	Mitochondrion				192
Q9NXV8 UniProt NPD GO	CN113_HUMAN	Uncharacterized protein C14orf113	0.31	-	nuc	0					159
Q8N9W8 UniProt NPD GO	CN054_HUMAN	Uncharacterized protein C14orf54	0.31	-	nuc	0					422
Q95K27 UniProt NPD GO	CN054_MACFA	Uncharacterized protein C14orf54 homolog (Fragment)	0.31	-	nuc	0					346
Q4KKZ1 UniProt NPD GO	CA158_MOUSE	Uncharacterized protein C1orf158 homolog	0.31	-	nuc	0					194
Q8C5K5 UniProt NPD GO	CX038_MOUSE	Uncharacterized protein CXorf38 homolog	0.31	-	mit	0					320
P43615 UniProt NPD GO	YFL3_YEAST	Uncharacterized protein YFR043C	0.31	-	cyt	0					237
P46984 UniProt NPD GO	YJS4_YEAST	Uncharacterized protein YJL184W	0.31	-	nuc	0					123
P34231 UniProt NPD GO	YKS7_YEAST	Uncharacterized protein YKL187C	0.31	-	end	4 *		mitochondrion [IDA]			750
P28273 UniProt NPD GO	YKV5_YEAST	Uncharacterized protein YKL215C	0.31	-	cyt	0		cytoplasm [IDA]			1286
P40168 UniProt NPD GO	YNT5_YEAST	Uncharacterized protein YNL195C	0.31	-	nuc	0	Mitochondrion	mitochondrion [IDA]			261
Q02786 UniProt NPD GO	YP056_YEAST	Uncharacterized protein YPL056C precursor	0.31	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				101
Q02754 UniProt NPD GO	YP067_YEAST	Uncharacterized protein YPL067C	0.31	-	cyt	0	Cytoplasm	cytoplasm [IDA]			198
P38227 UniProt NPD GO	YBP3_YEAST	Uncharacterized transporter YBR043C	0.31	-	end	12	Membrane; multi-pass membrane protein (Potential)	plasma membrane [IDA]			689
P38767 UniProt NPD GO	YHJ2_YEAST	Uncharacterized transporter YHR032W	0.31	-	end	8	Membrane; multi-pass membrane protein (Potential)				581
Q05588 UniProt NPD GO	UPAR_BOVIN	Urokinase plasminogen activator surface receptor precursor (uPAR) (U-PAR) (CD87 antigen)	0.31	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				330
Q9QZQ3 UniProt NPD GO	UTS2_MOUSE	Urotensin-2 precursor (Urotensin-II) (U-II) (UII)	0.31	-	exc	0	Secreted protein				123
Q9V3J1 UniProt NPD GO	VATH_DROME	Vacuolar ATP synthase subunit H (EC 3.6.3.14) (V-ATPase H subunit) (Vacuolar proton pump subunit H) ...	0.31	-	cyt	0					468
Q68F29 UniProt NPD GO	V26BA_XENLA	Vacuolar protein sorting 26B-A (Vesicle protein sorting 26B-A)	0.31	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Does not localize to endosomes (By similarity)				337
P47075 UniProt NPD GO	VTC4_YEAST	Vacuolar transporter chaperone 4 (Phosphate metabolism protein 3)	0.31	-	end	3	Vacuole; vacuolar membrane; multi-pass membrane protein	intrinsic to vacuolar membrane [IDA]			721
Q00314 UniProt NPD GO	VAN1_CANAL	Vanadate resistance protein	0.31	+	cyt	0					442
P19320 UniProt NPD GO	VCAM1_HUMAN	Vascular cell adhesion protein 1 precursor (V-CAM 1) (CD106 antigen) (INCAM-100)	0.31	-	mit	1	Membrane; single-pass type I membrane protein		192225	1VSC	739
Q9CZT5 UniProt NPD GO	VASN_MOUSE	Vasorin precursor (Protein Slit-like 2)	0.31	-	end	1	Membrane; single-pass type I membrane protein (Probable)				673
Q9FPQ6 UniProt NPD GO	GP1_CHLRE	Vegetative cell wall protein gp1 precursor (Hydroxyproline-rich glycoprotein 1)	0.31	-	mit	1 *					555
P38309 UniProt NPD GO	YB56_YEAST	Very hypothetical protein YBR206W	0.31	-	nuc	0					107
P18759 UniProt NPD GO	SEC18_YEAST	Vesicular-fusion protein SEC18	0.31	-	cyt	0	Cytoplasm	cytoplasm [IDA] extrinsic to plasma membrane [IDA]		1CR5	758
Q27955 UniProt NPD GO	KCAB2_BOVIN	Voltage-gated potassium channel subunit beta-2 (K(+) channel subunit beta-2) (Kv-beta-2)	0.31	-	nuc	0	Cytoplasm (Potential)				367
Q9EP93 UniProt NPD GO	VN1B3_MOUSE	Vomeronasal type-1 receptor B3 (Vomeronasal receptor 5) (Pheromone receptor VN5)	0.31	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				310
Q8JG33 UniProt NPD GO	WFDC1_CHICK	WAP four-disulfide core domain protein 1 precursor (ps20 protein)	0.31	-	mit	1 *	Secreted protein (Potential)				222
Q8JZX3 UniProt NPD GO	WD51A_MOUSE	WD repeat protein 51A	0.31	-	nuc	0					405
Q8VC51 UniProt NPD GO	WDR79_MOUSE	WD repeat protein 79	0.31	-	nuc	0					532
Q9ZUU9 UniProt NPD GO	WBC3_ARATH	White-brown complex homolog protein 3	0.31	-	end	5	Membrane; multi-pass membrane protein (By similarity)				705
Q9BDK6 UniProt NPD GO	AT1B4_PIG	X/potassium-transporting ATPase subunit beta-m (X,K-ATPase beta-m subunit)	0.31	-	nuc	1	Membrane; single-pass type II membrane protein (Potential)	nuclear envelope [IDA]			355

You are viewing entries 39951 to 40000 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.