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
Q96S59 UniProt NPD GO	RANB9_HUMAN	Ran-binding protein 9 (RanBP9) (RanBP7) (Ran-binding protein M) (RanBPM) (BPM90) (BPM-L)	0.48	-	nuc	0	Nucleus. Cytoplasm. A phosphorylated form is associated with the plasma membrane	nucleus [IDA]	603854		729
Q9H2L5 UniProt NPD GO	RASF4_HUMAN	Ras association domain-containing protein 4	0.48	-	nuc	0					321
Q566C5 UniProt NPD GO	RASF4_RAT	Ras association domain-containing protein 4	0.48	-	nuc	0					322
Q758G1 UniProt NPD GO	ERFD_ASHGO	Ras modification protein ERF4	0.48	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)				225
P11233 UniProt NPD GO	RALA_HUMAN	Ras-related protein Ral-A	0.48	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		179550	2BOV	206
P63321 UniProt NPD GO	RALA_MOUSE	Ras-related protein Ral-A	0.48	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				206
P63322 UniProt NPD GO	RALA_RAT	Ras-related protein Ral-A	0.48	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				206
P63320 UniProt NPD GO	RALA_SAGOE	Ras-related protein Ral-A	0.48	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)			1U90	206
Q15303 UniProt NPD GO	ERBB4_HUMAN	Receptor tyrosine-protein kinase erbB-4 precursor (EC 2.7.10.1) (p180erbB4) (Tyrosine kinase-type ce ...	0.48	-	exc	2	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	600543	2AHX	1308
Q64455 UniProt NPD GO	PTPRJ_MOUSE	Receptor-type tyrosine-protein phosphatase eta precursor (EC 3.1.3.48) (Protein-tyrosine phosphatase ...	0.48	-	nuc	1	Membrane; single-pass type I membrane protein				1238
Q9FJR0 UniProt NPD GO	RENT1_ARATH	Regulator of nonsense transcripts 1 homolog (EC 3.6.1.-) (ATP-dependent helicase UPF1)	0.48	-	nuc	0	Cytoplasm (Potential)				1254
Q8K4Q0 UniProt NPD GO	RPTOR_MOUSE	Regulatory-associated protein of mTOR (Raptor) (P150 target of rapamycin (TOR)-scaffold protein)	0.48	-	nuc	0					1335
Q92372 UniProt NPD GO	RFA1_SCHPO	Replication factor-A protein 1 (Single-stranded DNA-binding protein p68 subunit)	0.48	-	mit	0	Nucleus	DNA replication factor A complex [IDA]			609
O60858 UniProt NPD GO	RFP2_HUMAN	Ret finger protein 2 (Leukemia-associated protein 5) (B-cell chronic lymphocytic leukemia tumor supp ...	0.48	-	mit	1			605661		407
Q9BSG5 UniProt NPD GO	RTBDN_HUMAN	Retbindin precursor	0.48	-	exc	0	Secreted protein (Potential)		609553		229
P28705 UniProt NPD GO	RXRG_MOUSE	Retinoic acid receptor RXR-gamma (Retinoid X receptor gamma)	0.48	+	nuc	0	Nucleus				463
Q9CTN4 UniProt NPD GO	RHBT3_MOUSE	Rho-related BTB domain-containing protein 3	0.48	-	cyt	0					611
Q9H633 UniProt NPD GO	RPP21_HUMAN	Ribonuclease P protein subunit p21 (EC 3.1.26.5) (RNaseP protein p21) (Ribonucleoprotein V)	0.48	-	nuc	0	Nucleus; nucleolus				154
O59678 UniProt NPD GO	RRS1_SCHPO	Ribosome biogenesis regulatory protein homolog	0.48	-	nuc	0	Nucleus; nucleolus				166
Q9UTE3 UniProt NPD GO	SEB1_SCHPO	Rpb7-binding protein seb1	0.48	-	nuc	0	Nucleus				620
Q9WTM5 UniProt NPD GO	RUVB2_MOUSE	RuvB-like 2 (EC 3.6.1.-) (p47 protein)	0.48	-	nuc	0	Nucleus (By similarity)				462
P27013 UniProt NPD GO	SCRY1_OCTVU	S-crystallin 1	0.48	-	nuc	0					214
P27012 UniProt NPD GO	SCRY4_OCTDO	S-crystallin 4 (OL4)	0.48	-	nuc	0					215
Q8R3Q2 UniProt NPD GO	SAPS2_MOUSE	SAPS domain family member 2	0.48	-	nuc	0					923
Q9JK48 UniProt NPD GO	SHLB1_MOUSE	SH3 domain GRB2-like protein B1 (EC 2.3.1.-) (Endophilin B1)	0.48	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Associated with internal membranes	endoplasmic reticulum [IC] membrane [IDA] microsome [IDA]		1X43	365
Q8TE82 UniProt NPD GO	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats-containing protein 1	0.48	-	cyt	0					1336
O35179 UniProt NPD GO	SH3G2_RAT	SH3-containing GRB2-like protein 2 (EC 2.3.1.-) (SH3 domain protein 2A) (Endophilin 1) (SH3p4) (Frag ...	0.48	+	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Concentrated in presynaptic nerve terminals in neu ...			2C08	248
Q5RAC4 UniProt NPD GO	SLIK1_PONPY	SLIT and NTRK-like protein 1 precursor	0.48	-	end	1	Membrane; single-pass membrane protein (Potential)				696
Q62247 UniProt NPD GO	SOX16_MOUSE	SOX-16 protein (Fragment)	0.48	-	nuc	0	Nucleus (Potential)				57
Q96HF1 UniProt NPD GO	SFRP2_HUMAN	Secreted frizzled-related protein 2 precursor (sFRP-2) (Secreted apoptosis-related protein 1) (SARP- ...	0.48	-	exc	0	Secreted protein (By similarity)		604157		295
P11384 UniProt NPD GO	SECR_RAT	Secretin precursor	0.48	-	nuc	0	Secreted protein				134
Q9BYH1 UniProt NPD GO	SEZ6L_HUMAN	Seizure 6-like protein precursor	0.48	-	nuc	1	Membrane; single-pass type I membrane protein (Probable)		607021		1024
Q9Z123 UniProt NPD GO	SEM4F_MOUSE	Semaphorin-4F precursor (Semaphorin W) (Sema W)	0.48	-	end	1	Membrane; single-pass type I membrane protein	plasma membrane [IDA]			777
Q9Z143 UniProt NPD GO	SEM4F_RAT	Semaphorin-4F precursor (Semaphorin W) (Sema W)	0.48	-	end	1	Membrane; single-pass type I membrane protein	integral to membrane [IDA] integral to membrane of membrane fraction [IDA] postsynaptic membrane [IDA] synapse [IDA] synaptosome [IDA]			776
Q9H3T2 UniProt NPD GO	SEM6C_HUMAN	Semaphorin-6C precursor (Semaphorin Y) (Sema Y)	0.48	-	exc	0	Membrane; single-pass type I membrane protein				930
O64483 UniProt NPD GO	SIRK_ARATH	Senescence-induced receptor-like serine/threonine-protein kinase precursor (FLG22-induced receptor-l ...	0.48	-	end	2 *	Membrane; single-pass type I membrane protein				876
O94364 UniProt NPD GO	YHOH_SCHPO	Serine-rich protein C428.17c in chromosome II	0.48	-	nuc	0	Nucleus	nucleus [IDA]			602
Q9LU89 UniProt NPD GO	2A5N_ARATH	Serine/threonine protein phosphatase 2A 59 kDa regulatory subunit B' eta isoform (PP2A, B' subunit, ...	0.48	-	nuc	0					510
Q6BNW4 UniProt NPD GO	PTPA1_DEBHA	Serine/threonine-protein phosphatase 2A activator 1 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.48	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				441
Q7TPA5 UniProt NPD GO	SPA11_RAT	Serpin A11 precursor (Liver regeneration-related protein LRRG023)	0.48	-	cyt	0	Secreted protein (Potential)				462
Q95175 UniProt NPD GO	SRY_CROSU	Sex-determining region Y protein (Testis-determining factor) (Fragment)	0.48	-	nuc	0	Nucleus				52
Q95202 UniProt NPD GO	SRY_NEOAN	Sex-determining region Y protein (Testis-determining factor) (Fragment)	0.48	-	nuc	0	Nucleus				52
O35750 UniProt NPD GO	SHOX2_RAT	Short stature homeobox protein 2 (Paired family homeodomain protein Prx3) (Fragment)	0.48	+	nuc	0	Nucleus				237
Q61AP6 UniProt NPD GO	STAT1_CAEBR	Signal transducer and activator of transcription 1	0.48	-	nuc	0	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation (By similarity)				713
O93436 UniProt NPD GO	STAM2_CHICK	Signal transducing adapter molecule 2 (STAM-2) (Epidermal growth factor receptor-associated protein ...	0.48	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein				468
P90953 UniProt NPD GO	SIM_CAEEL	Single-minded homolog	0.48	-	nuc	0	Nucleus (Potential)	nucleus [ISS]			322
O43805 UniProt NPD GO	SSNA1_HUMAN	Sjoegren syndrome nuclear autoantigen 1 (Nuclear autoantigen of 14 kDa)	0.48	-	nuc	0	Nucleus. Centrosome	nucleus [TAS]			119
O43765 UniProt NPD GO	SGTA_HUMAN	Small glutamine-rich tetratricopeptide repeat-containing protein A (Vpu-binding protein) (UBP)	0.48	-	nuc	0			603419		313
Q5ZI43 UniProt NPD GO	SPN1_CHICK	Snurportin-1 (RNA U transporter 1)	0.48	-	mit	0	Nucleus (By similarity). Cytoplasm (By similarity). Nucleoplasmic shuttling protein (By similarity)				365
Q5EA77 UniProt NPD GO	SNX17_BOVIN	Sorting nexin-17	0.48	-	cyt	0	Cytoplasm (By similarity). Endosome; early endosome (By similarity). Associated with early endosomes ...				470

You are viewing entries 26551 to 26600 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.