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
Q28427 UniProt NPD GO	RHLD_GORGO	RH-like protein ID (Rhesus-like protein ID)	0.00	-	end	10 *	Membrane; multi-pass membrane protein				416
P38204 UniProt NPD GO	RRN10_YEAST	RNA polymerase I-specific transcription initiation factor RRN10	0.00	-	cyt	0	Nucleus; nucleolus	RNA polymerase I upstream activating factor... [TAS]			145
P18110 UniProt NPD GO	HTF1_ROMMI	RO-1 (RO I) (Hypertrehalosaemic factor)	0.00	-		0	Secreted protein				10
P22287 UniProt NPD GO	AVR9_CLAFU	Race-specific elicitor A9 precursor	0.00	-	mit	1 *					63
P22689 UniProt NPD GO	TKNB_RANCA	Ranatachykinin-B (RTK B)	0.00	-		0	Secreted protein				10
P82742 UniProt NPD GO	RAN2_RANCA	Ranatuerin-2	0.00	-	cyt	0	Secreted protein				31
P84114 UniProt NPD GO	RA2BA_RANBO	Ranatuerin-2BYa	0.00	-	cyt	0	Secreted protein				32
P82878 UniProt NPD GO	RN2CA_RANCL	Ranatuerin-2Ca	0.00	-	cyt	0	Secreted protein				31
P82879 UniProt NPD GO	RN2CB_RANCL	Ranatuerin-2Cb	0.00	-	cyt	0	Secreted protein				27
P82828 UniProt NPD GO	RN2LA_RANLU	Ranatuerin-2La	0.00	-	cyt	0	Secreted protein				32
P82829 UniProt NPD GO	RN2LB_RANLU	Ranatuerin-2Lb	0.00	-	cyt	0	Secreted protein				32
P82819 UniProt NPD GO	RAN4_RANCA	Ranatuerin-4	0.00	-	mit	0	Secreted protein				24
P82820 UniProt NPD GO	RAN5_RANCA	Ranatuerin-5	0.00	-		0	Secreted protein				12
P82823 UniProt NPD GO	RAN8_RANCA	Ranatuerin-8	0.00	-		0	Secreted protein				13
P82824 UniProt NPD GO	RAN9_RANCA	Ranatuerin-9	0.00	-		0	Secreted protein				14
P60763 UniProt NPD GO	RAC3_HUMAN	Ras-related C3 botulinum toxin substrate 3 (p21-Rac3)	0.00	-	cyt	0	Cytoplasm. Membrane-associated when activated. Intracytoplasmic membrane. Co-localizes with NRBP to ...	endomembrane system [IDA]	602050	2C2H	192
P60764 UniProt NPD GO	RAC3_MOUSE	Ras-related C3 botulinum toxin substrate 3 (p21-Rac3)	0.00	-	cyt	0	Cytoplasm (By similarity). Membrane-associated when activated. Intracytoplasmic membrane (By similar ...	endomembrane system [ISS]			192
P49103 UniProt NPD GO	RAB2A_MAIZE	Ras-related protein Rab-2-A	0.00	-	cyt	0	Endoplasmic reticulum-Golgi intermediate compartment; endoplasmic reticulum-Golgi intermediate compa ...				209
P46629 UniProt NPD GO	RAB25_RABIT	Ras-related protein Rab-25	0.00	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				213
Q13636 UniProt NPD GO	RAB31_HUMAN	Ras-related protein Rab-31 (Rab-22B)	0.00	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		605694	2FG5	194
O95716 UniProt NPD GO	RAB3D_HUMAN	Ras-related protein Rab-3D	0.00	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		604350	2GF9	219
P07560 UniProt NPD GO	SEC4_YEAST	Ras-related protein SEC4 (Suppressor of RHO3 protein 6)	0.00	-	cyt	0	Secretory vesicle; secretory vesicle membrane; lipid-anchor; cytoplasmic side. Cell membrane; lipid- ...	actin cap [IDA] incipient bud site [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA] transport vesicle [TAS]		1G17	215
Q9WUP1 UniProt NPD GO	RAMP3_MOUSE	Receptor activity-modifying protein 3 precursor	0.00	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)				147
Q96HR9 UniProt NPD GO	REEP6_HUMAN	Receptor expression-enhancing protein 6 (Polyposis locus protein 1-like 1)	0.00	-	mit	2 *	Membrane; multi-pass membrane protein (By similarity)		609346		184
P08939 UniProt NPD GO	RPCH_PANBO	Red pigment-concentrating hormone (RPCH)	0.00	-		0	Secreted protein				8
P32824 UniProt NPD GO	KLKR_PRANA	Renal glandular kallikrein precursor (EC 3.4.21.35) (Tissue kallikrein)	0.00	-	exc	0					263
P35244 UniProt NPD GO	RFA3_HUMAN	Replication protein A 14 kDa subunit (RP-A) (RF-A) (Replication factor-A protein 3) (p14)	0.00	-	cyt	0	Nucleus	DNA replication factor A complex [TAS]	179837	1QUQ	121
Q8WWV3 UniProt NPD GO	RT4I1_HUMAN	Reticulon-4-interacting protein 1, mitochondrial precursor (NOGO-interacting mitochondrial protein)	0.00	-	mit	0	Mitochondrion				396
O88851 UniProt NPD GO	RBBP9_MOUSE	Retinoblastoma-binding protein 9 (RBBP-9) (B5T overexpressed gene protein) (Bog protein)	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				186
O75884 UniProt NPD GO	RBBP9_HUMAN	Retinoblastoma-binding protein 9 (RBBP-9) (Retinoblastoma-binding protein 10) (RBBP-10) (B5T overexp ...	0.00	-	cyt	0	Cytoplasm. Nucleus		602908		186
Q8CEE7 UniProt NPD GO	RDH13_MOUSE	Retinol dehydrogenase 13 (EC 1.1.1.-)	0.00	-	mit	0					334
P02694 UniProt NPD GO	RET1_BOVIN	Retinol-binding protein I, cellular (Cellular retinol-binding protein) (CRBP)	0.00	-	cyt	0	Cytoplasm				134
Q9S8P4 UniProt NPD GO	RHRE_PEA	Rhicadhesin receptor precursor (Germin-like protein)	0.00	-	vac	0	Cell wall				217
P49261 UniProt NPD GO	CROB_LEPLU	Rho beta-crystallin (Fragments)	0.00	-	cyt	0					89
P52202 UniProt NPD GO	OPSD_ALLMI	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				352
Q90245 UniProt NPD GO	OPSD_AMBTI	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				354
P41591 UniProt NPD GO	OPSD_ANOCA	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				352
Q9YGZ1 UniProt NPD GO	OPSD_ATHBO	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				354
P02699 UniProt NPD GO	OPSD_BOVIN	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein			1VQX	348
P35359 UniProt NPD GO	OPSD_BRARE	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]			354
P56515 UniProt NPD GO	OPSD_BUFMA	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				354
Q6W3E1 UniProt NPD GO	OPSD_CALPD	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				348
P32308 UniProt NPD GO	OPSD_CANFA	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				348
P32309 UniProt NPD GO	OPSD_CARAU	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				354
Q9YGZ8 UniProt NPD GO	OPSD_CHELB	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				353
P51488 UniProt NPD GO	OPSD_CYPCA	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				354
Q9YGZ4 UniProt NPD GO	OPSD_DICLA	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				353
Q9YH05 UniProt NPD GO	OPSD_DIPAN	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				353
Q9YH04 UniProt NPD GO	OPSD_DIPVU	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				353
Q95KU1 UniProt NPD GO	OPSD_FELCA	Rhodopsin	0.00	-	end	7 *	Membrane; multi-pass membrane protein				348

You are viewing entries 97551 to 97600 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.