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
Q5DRD4 UniProt NPD GO	PCDBH_PANTR	Protocadherin beta 17 precursor (PCDH-beta17)	0.14	-	cyt	2 *	Membrane; single-pass type I membrane protein (By similarity)				788
Q5DRB5 UniProt NPD GO	PCDG5_PANTR	Protocadherin gamma A5 precursor (PCDH-gamma-A5)	0.14	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				931
Q42850 UniProt NPD GO	PORB_HORVU	Protochlorophyllide reductase B, chloroplast precursor (EC 1.3.1.33) (PCR B) (NADPH-protochlorophyll ...	0.14	-	mit	0	Plastid; chloroplast				395
P80359 UniProt NPD GO	HEVP_HEVBR	Pseudo-hevein (Minor hevein)	0.14	-	nuc	0					45
P42556 UniProt NPD GO	PTR1_LEITA	Pteridine reductase 1 (EC 1.5.1.33) (H region methotrexate resistance protein)	0.14	-	cyt	0				1P33	289
P33432 UniProt NPD GO	PUIA_WHEAT	Puroindoline-A precursor	0.14	-	exc	0					148
Q7SA04 UniProt NPD GO	SEM1_NEUCR	Putative 26 proteasome complex subunit sem1	0.14	-	nuc	0					91
P38746 UniProt NPD GO	YLF2_YEAST	Putative GTP-binding protein YLF2	0.14	-	mit	0		mitochondrion [IDA]			405
O81755 UniProt NPD GO	PER48_ARATH	Putative Peroxidase 48 (EC 1.11.1.7) (Atperox P48)	0.14	-	cyt	0					316
Q67UX0 UniProt NPD GO	ADO2_ORYSA	Putative adagio-like protein 2	0.14	-	cyt	0	Nucleus (By similarity)				635
Q9SSG5 UniProt NPD GO	BORL3_ARATH	Putative boron transporter-like protein 3	0.14	-	end	8 *	Membrane; multi-pass membrane protein (By similarity)				683
Q9SZW4 UniProt NPD GO	AHM3_ARATH	Putative cadmium/zinc-transporting ATPase 3 (EC 3.6.3.3) (EC 3.6.3.5)	0.14	-	end	6	Membrane; multi-pass membrane protein				951
P42169 UniProt NPD GO	YKL2_CAEEL	Putative casein kinase I C03C10.2 (EC 2.7.11.1)	0.14	-	cyt	0					363
P56350 UniProt NPD GO	MINE_CHLVU	Putative cell division topological specificity factor	0.14	-	nuc	0	Plastid; chloroplast				127
Q6JAH0 UniProt NPD GO	CZOG_SORBI	Putative cis-zeatin O-glucosyltransferase (EC 2.4.1.215)	0.14	-	mit	0					466
Q9U6Z5 UniProt NPD GO	CX51_CONIM	Putative conotoxin Im5.1 precursor	0.14	-	nuc	0	Secreted protein				62
Q9VN93 UniProt NPD GO	CPR1_DROME	Putative cysteine proteinase CG12163 precursor (EC 3.4.22.-)	0.14	-	exc	0					614
Q27518 UniProt NPD GO	C13A2_CAEEL	Putative cytochrome P450 CYP13A2 (EC 1.14.-.-)	0.14	-	nuc	1 *					515
O74885 UniProt NPD GO	YQE1_SCHPO	Putative dioxygenase C576.01c (EC 1.-.-.-)	0.14	-	cyt	0					413
Q03574 UniProt NPD GO	ELO4_CAEEL	Putative fatty acid elongation protein 4	0.14	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				291
Q9VJF2 UniProt NPD GO	GR36B_DROME	Putative gustatory receptor 36b	0.14	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			391
P38988 UniProt NPD GO	YHM1_YEAST	Putative mitochondrial carrier protein YHM1/SHM1	0.14	-	end	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				300
Q6YUU5 UniProt NPD GO	MDR_ORYSA	Putative multidrug resistance protein (P-glycoprotein)	0.14	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				1245
Q6CUI0 UniProt NPD GO	NNT1_KLULA	Putative nicotinamide N-methyltransferase (EC 2.1.1.1)	0.14	-	cyt	0	Cytoplasm (By similarity)				270
P81911 UniProt NPD GO	OR22C_DROME	Putative odorant receptor 22c	0.14	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			402
O80739 UniProt NPD GO	POT12_ARATH	Putative potassium transporter 12 (AtPOT12)	0.14	-	end	13	Cell membrane; multi-pass membrane protein (Potential)				827
O49423 UniProt NPD GO	POT9_ARATH	Putative potassium transporter 9 (AtPOT9)	0.14	-	end	14	Cell membrane; multi-pass membrane protein (Potential)				807
P34429 UniProt NPD GO	RFC5_CAEEL	Putative replication factor C subunit 5 (Replication factor C 36 kDa subunit) (RF-C 36 kDa subunit) ...	0.14	-	cyt	0	Nucleus (Probable)				368
Q9ZUU4 UniProt NPD GO	ROC1_ARATH	Putative ribonucleoprotein At2g37220, chloroplast precursor	0.14	-	mit	0	Plastid; chloroplast (Potential)				289
Q9VDT6 UniProt NPD GO	RRMJ3_DROME	Putative ribosomal RNA methyltransferase CG11447 (EC 2.1.1.-) (rRNA (uridine-2'-O-)-methyltransferas ...	0.14	-	cyt	0					250
Q8N7Q2 UniProt NPD GO	CJ031_HUMAN	Putative uncharacterized protein C10orf31 precursor	0.14	-	exc	0	Secreted protein (Potential)				173
P38775 UniProt NPD GO	YHK5_YEAST	Putative uncharacterized protein YHR045W	0.14	+	cyt	1 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			560
Q9JMA2 UniProt NPD GO	TGT_MOUSE	Queuine tRNA-ribosyltransferase (EC 2.4.2.29) (tRNA-guanine transglycosylase) (Guanine insertion enz ...	0.14	-	cyt	0					387
Q9ZUC1 UniProt NPD GO	QORL_ARATH	Quinone oxidoreductase-like protein At1g23740, chloroplast precursor (EC 1.-.-.-)	0.14	-	mit	0	Plastid; chloroplast (Potential)				386
Q9GPR2 UniProt NPD GO	RACI_DICDI	RAS-related protein racI	0.14	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				205
O43567 UniProt NPD GO	RNF13_HUMAN	RING finger protein 13	0.14	+	nuc	1	Nucleus (By similarity)				381
O13959 UniProt NPD GO	RBX1_SCHPO	RING-box protein pip1 (Pop-interacting protein 1) (RING-box protein 1)	0.14	-	cyt	0	Cytoplasm. Nucleus	Cul4B-RING ubiquitin ligase complex [TAS] cytoplasm [IDA] nucleus [IDA]			107
P87310 UniProt NPD GO	MED10_SCHPO	RNA polymerase II mediator complex subunit 10	0.14	-	cyt	0	Nucleus (Probable)	mediator complex [IDA]			138
Q8X0V0 UniProt NPD GO	TFB5_NEUCR	RNA polymerase II transcription factor B subunit 5 (General transcription and DNA repair factor IIH ...	0.14	-	cyt	0	Nucleus (By similarity)				72
Q9YGP5 UniProt NPD GO	RBPMS_XENLA	RNA-binding protein with multiple splicing homolog (RBP-MS) (HEart, RRM Expressed Sequence) (Hermes) ...	0.14	-	nuc	0					196
O13066 UniProt NPD GO	RGP1_XENLA	Ran GTPase-activating protein 1	0.14	-	cyt	0	Cytoplasm (Probable)				580
Q04173 UniProt NPD GO	GDS1_BOVIN	Rap1 GTPase-GDP dissociation stimulator 1 (SMG P21 stimulatory GDP/GTP exchange protein) (SMG GDS pr ...	0.14	-	nuc	0					558
O74650 UniProt NPD GO	RAS_CRYNE	Ras-like protein	0.14	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				216
P10301 UniProt NPD GO	RRAS_HUMAN	Ras-related protein R-Ras (p23)	0.14	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Inner surface of plasma membrane poss ...		165090	2FN4	218
P35292 UniProt NPD GO	RAB17_MOUSE	Ras-related protein Rab-17	0.14	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				214
P51159 UniProt NPD GO	RB27A_HUMAN	Ras-related protein Rab-27A (Rab-27) (GTP-binding protein Ram)	0.14	-	cyt	0	Membrane; lipid-anchor		607624		221
P11023 UniProt NPD GO	RAB3A_BOVIN	Ras-related protein Rab-3A (SMG P25A)	0.14	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				219
Q2TBH7 UniProt NPD GO	RAB4A_BOVIN	Ras-related protein Rab-4A	0.14	-	cyt	0	Membrane; peripheral membrane protein (By similarity). Generally associated with membranes. Cytoplas ...				213
P35278 UniProt NPD GO	RAB5C_MOUSE	Ras-related protein Rab-5C	0.14	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Endosome; early endosome; early endos ...	endocytic vesicle [IDA]		1Z0D	216
P51148 UniProt NPD GO	RAB5C_HUMAN	Ras-related protein Rab-5C (RAB5L) (L1880)	0.14	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Endosome; early endosome; early endos ...		604037		216

You are viewing entries 58951 to 59000 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.