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
Q8HZQ0 UniProt NPD GO	RNAS4_PANTR	Ribonuclease 4 precursor (EC 3.1.27.-) (RNase 4)	0.55	-	exc	1 *	Secreted protein (By similarity)				147
P15468 UniProt NPD GO	RNAS4_PIG	Ribonuclease 4 precursor (EC 3.1.27.-) (RNase 4) (Ribonuclease PL3)	0.55	-	exc	1 *	Secreted protein				147
Q6FPU0 UniProt NPD GO	RLP24_CANGA	Ribosome biogenesis protein RLP24	0.55	-	nuc	0	Nucleus; nucleolus (By similarity)				197
P27016 UniProt NPD GO	SCR18_OMMSL	S-crystallin SL18	0.55	-	nuc	0					308
Q92503 UniProt NPD GO	S14L1_HUMAN	SEC14-like protein 1	0.55	-	mit	0		Golgi apparatus [TAS] membrane [TAS]	601504		715
Q91Z67 UniProt NPD GO	FNBP2_MOUSE	SLIT-ROBO Rho GTPase-activating protein 2 (srGAP2) (Formin-binding protein 2) (Formin-binding protei ...	0.55	-	nuc	0		mitochondrial inner membrane [IDA]			405
Q8R424 UniProt NPD GO	STABP_RAT	STAM-binding protein (EC 3.1.2.15) (Associated molecule with the SH3 domain of STAM)	0.55	-	nuc	0	Nucleus (By similarity). Membrane; peripheral membrane protein (By similarity). Cytoplasm (By simila ...				424
Q6TH47 UniProt NPD GO	STABP_BRARE	STAM-binding protein-like (EC 3.1.2.15)	0.55	-	nuc	0					418
Q9XSC1 UniProt NPD GO	SFRP5_BOVIN	Secreted frizzled-related protein 5 precursor (sFRP-5)	0.55	-	exc	0	Secreted protein (Probable)				315
Q70I47 UniProt NPD GO	SPP24_ONCMY	Secreted phosphoprotein 24 precursor (Spp-24) (Secreted phosphoprotein 2)	0.55	-	exc	0	Secreted protein (By similarity)				192
Q9NZV5 UniProt NPD GO	SEPN1_HUMAN	Selenoprotein N precursor	0.55	+	mit	0	Isoform 2: Endoplasmic reticulum. Probably membrane-associated	extracellular region [NAS]	606210		590
Q14563 UniProt NPD GO	SEM3A_HUMAN	Semaphorin-3A precursor (Semaphorin III) (Sema III)	0.55	+	mit	0	Secreted protein (By similarity)	extracellular region [TAS]	603961		771
P07665 UniProt NPD GO	SRYB_DROME	Serendipity locus protein beta	0.55	-	nuc	0	Nucleus	nucleus [IDA] polytene chromosome interband [IDA]			356
Q96GD4 UniProt NPD GO	AURKB_HUMAN	Serine/threonine-protein kinase 12 (EC 2.7.11.1) (Aurora- and Ipl1-like midbody-associated protein 1 ...	0.55	-	nuc	0	Nucleus. Localizes on chromosome arms and inner centromeres from prophase through metaphase and then ...		604970		344
Q9BYT3 UniProt NPD GO	STK33_HUMAN	Serine/threonine-protein kinase 33 (EC 2.7.11.1)	0.55	-	nuc	0			607670		514
O08874 UniProt NPD GO	PKN2_RAT	Serine/threonine-protein kinase N2 (EC 2.7.11.13) (Protein kinase C-like 2) (Protein-kinase C-relate ...	0.55	-	nuc	0	Cytoplasm				842
P23790 UniProt NPD GO	SRF_XENLA	Serum response factor (SRF)	0.55	-	nuc	0	Nucleus				448
Q61143 UniProt NPD GO	TRPC6_MOUSE	Short transient receptor potential channel 6 (TrpC6) (Calcium entry channel)	0.55	-	end	7	Membrane; multi-pass membrane protein (Probable)				930
Q9U5L1 UniProt NPD GO	SRPR_DROME	Signal recognition particle receptor subunit alpha homolog (SR-alpha) (Docking protein alpha) (DP-al ...	0.55	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)	endoplasmic reticulum membrane [IDA]			614
Q5M869 UniProt NPD GO	SIT1_RAT	Signaling threshold-regulating transmembrane adapter 1 (Suppression-inducing transmembrane adapter 1 ...	0.55	-	nuc	1 *	Cell membrane; single-pass type III membrane protein (By similarity)				178
P31170 UniProt NPD GO	HS21C_ARATH	Small heat shock protein, chloroplast precursor	0.55	-	mit	0	Plastid; chloroplast				227
Q68A91 UniProt NPD GO	CCL28_CANFA	Small inducible cytokine A28 precursor (CCL28)	0.55	-	exc	0	Secreted protein (By similarity)				128
Q8INF0 UniProt NPD GO	GCY8E_DROME	Soluble guanylate cyclase 88E (EC 4.6.1.2)	0.55	-	nuc	0	Cytoplasm (By similarity)	guanylate cyclase complex, soluble [IC]			947
Q5B797 UniProt NPD GO	SNX4_EMENI	Sorting nexin-4 (Autophagy-related protein 24)	0.55	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Endosome; endosoma ...				487
Q6CTQ0 UniProt NPD GO	SNX4_KLULA	Sorting nexin-4 (Autophagy-related protein 24)	0.55	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Endosome; endosoma ...				400
Q60P76 UniProt NPD GO	SAS6_CAEBR	Spindle assembly abnormal protein 6	0.55	-	nuc	0	Cytoplasm (By similarity). Centriole (By similarity). Localizes to centrioles (By similarity)				497
Q6C3J2 UniProt NPD GO	IPL1_YARLI	Spindle assembly checkpoint kinase (EC 2.7.11.1) (Aurora kinase)	0.55	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and on elongated and disassembling spin ...				371
Q95L87 UniProt NPD GO	STF1_MACEU	Steroidogenic factor 1 (STF-1) (SF-1)	0.55	+	nuc	0	Nucleus (By similarity)				463
Q6CUV2 UniProt NPD GO	ATG26_KLULA	Sterol 3-beta-glucosyltransferase (EC 2.4.1.173) (Autophagy-related protein 26)	0.55	-	nuc	0	Membrane; peripheral membrane protein (Potential)				1209
Q8IYB5 UniProt NPD GO	SMAP1_HUMAN	Stromal membrane-associated protein 1	0.55	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side (By similarity)			2CRR	467
Q91VZ6 UniProt NPD GO	SMAP1_MOUSE	Stromal membrane-associated protein 1	0.55	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side (Probable)				440
O62653 UniProt NPD GO	SUIS_SUNMU	Sucrase-isomaltase, intestinal [Contains: Sucrase (EC 3.2.1.48); Isomaltase (EC 3.2.1.10)]	0.55	-	mit	1 *	Cell membrane; single-pass type II membrane protein. Brush border				1812
P32583 UniProt NPD GO	SRP40_YEAST	Suppressor protein SRP40	0.55	-	nuc	0		nucleolus [IDA]			406
P97801 UniProt NPD GO	SMN_MOUSE	Survival motor neuron protein	0.55	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Localized in subnuclear structures next to coile ...	cytoplasm [IDA] nucleus [IDA]			288
Q9CQQ4 UniProt NPD GO	GEMI2_MOUSE	Survival of motor neuron protein-interacting protein 1 (SMN-interacting protein 1) (Component of gem ...	0.55	-	nuc	0	Nucleus; gem (By similarity). Localized in subnuclear structures next to coiled bodies, called gems, ...	cytoplasm [IDA] nucleus [IDA]			269
Q9QZP1 UniProt NPD GO	GEMI2_RAT	Survival of motor neuron protein-interacting protein 1 (SMN-interacting protein 1) (Component of gem ...	0.55	-	nuc	0	Nucleus; gem (By similarity). Localized in subnuclear structures next to coiled bodies, called gems, ...				269
O88935 UniProt NPD GO	SYN1_MOUSE	Synapsin-1 (Synapsin I)	0.55	-	mit	0	Synapse	synapse [IDA] synaptic vesicle membrane [IDA]			706
P09951 UniProt NPD GO	SYN1_RAT	Synapsin-1 (Synapsin I)	0.55	-	nuc	0	Synapse	synaptic vesicle [IDA]		1PX2	704
P17600 UniProt NPD GO	SYN1_HUMAN	Synapsin-1 (Synapsin I) (Brain protein 4.1)	0.55	-	nuc	0	Synapse		313440		705
Q92777 UniProt NPD GO	SYN2_HUMAN	Synapsin-2 (Synapsin II)	0.55	-	nuc	0	Synapse		600755		582
P57077 UniProt NPD GO	TAK1L_HUMAN	TAK1-like protein	0.55	-	nuc	0					242
Q9D9I4 UniProt NPD GO	TBC20_MOUSE	TBC1 domain family member 20	0.55	-	end	2	Membrane; multi-pass membrane protein (Potential)				402
Q95KI1 UniProt NPD GO	TB22A_MACFA	TBC1 domain family member 22A (Fragment)	0.55	-	cyt	0					497
P70191 UniProt NPD GO	TRAF5_MOUSE	TNF receptor-associated factor 5	0.55	-	nuc	0	Cytoplasm (Probable)				558
Q923U0 UniProt NPD GO	TM1L1_MOUSE	TOM1-like 1 protein (Target of myb-like 1 protein) (Src-activating and signaling molecule protein)	0.55	-	nuc	0	Golgi apparatus; Golgi stack. Endosome; endosomal membrane (Potential)				474
O95271 UniProt NPD GO	TNKS1_HUMAN	Tankyrase-1 (EC 2.4.2.30) (TANK1) (Tankyrase I) (TNKS-1) (TRF1-interacting ankyrin-related ADP-ribos ...	0.55	-	mit	0	Cytoplasm. Golgi apparatus; Golgi membrane; peripheral membrane protein. Nucleus; nuclear envelope; ...	chromosome, telomeric region [IDA]	603303		1327
Q8VD63 UniProt NPD GO	TSYL4_MOUSE	Testis-specific Y-encoded-like protein 4 (TSPY-like 4)	0.55	-	nuc	0					406
Q8VD72 UniProt NPD GO	TTC8_MOUSE	Tetratricopeptide repeat protein 8 (TPR repeat protein 8) (Bardet-Biedl syndrome 8 protein homolog)	0.55	-	cyt	0	Centrosome (By similarity)				515
O15455 UniProt NPD GO	TLR3_HUMAN	Toll-like receptor 3 precursor (CD283 antigen)	0.55	-	mit	1	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [TAS] membrane [NAS]	603029	2A0Z	904
Q9NR96 UniProt NPD GO	TLR9_HUMAN	Toll-like receptor 9 precursor (CD289 antigen)	0.55	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)	extracellular region [NAS]	605474		1032

You are viewing entries 22201 to 22250 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.