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
O35550 UniProt NPD GO	RABE1_RAT	Rab GTPase-binding effector protein 1 (Rabaptin-5) (Rabaptin-5alpha)	0.76	-	nuc	0	Cytoplasm (By similarity). Endosome; early endosome (By similarity). Endosome; recycling endosome (B ...				862
Q07292 UniProt NPD GO	KRAF1_CAEEL	Raf homolog serine/threonine-protein kinase (EC 2.7.11.1) (Abnormal cell lineage protein 45)	0.76	-	nuc	0					813
Q61193 UniProt NPD GO	RGL2_MOUSE	Ral guanine nucleotide dissociation stimulator-like 2 (RalGDS-like factor) (RAS-associated protein R ...	0.76	+	nuc	0				1RLF	778
Q96D71 UniProt NPD GO	REPS1_HUMAN	RalBP1-associated Eps domain-containing protein 1 (RalBP1-interacting protein 1)	0.76	-	nuc	0					744
P49792 UniProt NPD GO	RBP2_HUMAN	Ran-binding protein 2 (RanBP2) (Nuclear pore complex protein Nup358) (Nucleoporin Nup358) (358 kDa n ...	0.76	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex. Cytoplasmic filaments	nuclear pore [TAS]	601181	1Z5S	3224
Q865S0 UniProt NPD GO	RCAS1_CANFA	Receptor-binding cancer antigen expressed on SiSo cells (Cancer-associated surface antigen RCAS1) (E ...	0.76	-	mit	0	Golgi apparatus; Golgi membrane; single-pass type III membrane protein. Predominantly located in the ...				213
O00559 UniProt NPD GO	RCAS1_HUMAN	Receptor-binding cancer antigen expressed on SiSo cells (Cancer-associated surface antigen RCAS1) (E ...	0.76	-	mit	0	Golgi apparatus; Golgi membrane; single-pass type III membrane protein. According to Ref.1, it also ...	integral to membrane [NAS] soluble fraction [NAS]	605772		213
O08773 UniProt NPD GO	RGS14_RAT	Regulator of G-protein signaling 14 (RGS14)	0.76	+	nuc	0				1KJY	544
P35600 UniProt NPD GO	RFC1_DROME	Replication factor C subunit 1 (Replication factor C large subunit) (Activator 1 140 kDa subunit) (G ...	0.76	+	nuc	0	Nucleus (Potential)	DNA replication factor C complex [NAS] nucleus [IDA]			986
P18516 UniProt NPD GO	RARG_NOTVI	Retinoic acid receptor gamma (RAR-gamma) (Retinoic acid receptor delta) (RAR-delta)	0.76	+	nuc	0	Nucleus				505
P98171 UniProt NPD GO	RHG04_HUMAN	Rho-GTPase-activating protein 4 (Rho-GAP hematopoietic protein C1) (p115)	0.76	-	nuc	0	Cytoplasm. Just below the plasma membrane	cytoplasm [TAS]	300023		946
Q9BST9 UniProt NPD GO	RTKN_HUMAN	Rhotekin	0.76	-	mit	0			602288		563
Q6IQU6 UniProt NPD GO	RPF1_BRARE	Ribosome production factor 1 (Ribosome biogenesis protein RPF1) (Brix domain-containing protein 5)	0.76	+	nuc	0	Nucleus; nucleolus (By similarity)	nucleolus [ISS]			330
P30957 UniProt NPD GO	RYR2_RABIT	Ryanodine receptor 2 (Cardiac muscle-type ryanodine receptor) (RyR2) (RYR-2) (Cardiac muscle ryanodi ...	0.76	+	end	6	Membrane; multi-pass membrane protein (Probable)				4969
P57725 UniProt NPD GO	SAMN1_MOUSE	SAM domain-containing protein SAMSN-1 (SAM domain, SH3 domain and nuclear localization signals prote ...	0.76	-	nuc	0				1V38	372
Q8C110 UniProt NPD GO	SLIK6_MOUSE	SLIT and NTRK-like protein 6 precursor	0.76	-	exc	1	Membrane; single-pass membrane protein (Potential)				840
Q60898 UniProt NPD GO	SLAP1_MOUSE	SRC-like-adapter (Src-like-adapter protein 1) (mSLAP)	0.76	-	nuc	0	Cytoplasm. Endosome. Colocalizes with endosomes				280
Q9UH36 UniProt NPD GO	SRR1L_HUMAN	SRR1-like protein	0.76	+	mit	0					339
Q5ZK40 UniProt NPD GO	SNF5_CHICK	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1	0.76	-	nuc	0	Nucleus (By similarity)				386
Q12824 UniProt NPD GO	SNF5_HUMAN	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (Integ ...	0.76	-	nuc	0	Nucleus	nucleoplasm [TAS] nucleus [IDA] SWI/SNF complex [IDA]	609322		385
Q9Z0H3 UniProt NPD GO	SNF5_MOUSE	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (Integ ...	0.76	-	nuc	0	Nucleus				385
Q6C9M6 UniProt NPD GO	SWC4_YARLI	SWR1-complex protein 4	0.76	-	nuc	0	Nucleus (By similarity)				504
Q6VYA3 UniProt NPD GO	SOSD1_CHICK	Sclerostin domain-containing protein 1 precursor (Wnt-signaling modulator)	0.76	-	exc	0	Secreted protein				206
O14641 UniProt NPD GO	DVL2_HUMAN	Segment polarity protein dishevelled homolog DVL-2 (Dishevelled-2) (DSH homolog 2)	0.76	+	nuc	0	Cytoplasm	cytoplasm [TAS]	602151		736
Q5R8W9 UniProt NPD GO	SEPP1_PONPY	Selenoprotein P precursor (SeP)	0.76	-	exc	0	Secreted protein (By similarity)				381
Q9W6G6 UniProt NPD GO	SEM3D_BRARE	Semaphorin-3D precursor (Semaphorin-2) (Semaphorin Z2) (Sema-Z2)	0.76	-	nuc	0	Secreted protein (By similarity)				764
P60330 UniProt NPD GO	ESPL1_MOUSE	Separin (EC 3.4.22.49) (Separase) (Caspase-like protein ESPL1) (Extra spindle poles-like 1 protein)	0.76	-	end	0	Cytoplasm (By similarity). Nucleus (By similarity)				2118
O60187 UniProt NPD GO	SID4_SCHPO	Septation initiation protein sid4	0.76	-	nuc	0	Spindle pole body	spindle pole body [IDA]			660
Q92599 UniProt NPD GO	SEPT8_HUMAN	Septin-8	0.76	-	cyt	0			608418		482
Q6C7U0 UniProt NPD GO	ATG1_YARLI	Serine/threonine-protein kinase ATG1 (EC 2.7.11.1) (Autophagy-related protein 1)	0.76	-	nuc	0	Cytoplasm (By similarity)				710
Q07002 UniProt NPD GO	PCTK3_HUMAN	Serine/threonine-protein kinase PCTAIRE-3 (EC 2.7.11.22) (PCTAIRE-motif protein kinase 3)	0.76	-	nuc	0			169190		472
O35832 UniProt NPD GO	PCTK3_RAT	Serine/threonine-protein kinase PCTAIRE-3 (EC 2.7.11.22) (PCTAIRE-motif protein kinase 3)	0.76	-	mit	0					451
Q9IA88 UniProt NPD GO	SN1L2_CHICK	Serine/threonine-protein kinase SNF1-like kinase 2 (EC 2.7.11.1) (Qin-induced kinase)	0.76	-	nuc	0	Cytoplasm	cytoplasm [IDA]			798
P38679 UniProt NPD GO	COT1_NEUCR	Serine/threonine-protein kinase cot-1 (EC 2.7.11.1) (Colonial temperature-sensitive 1)	0.76	-	nuc	0					598
P18168 UniProt NPD GO	SERR_DROME	Serrate protein precursor (Protein beaded)	0.76	-	mit	1	Membrane; single-pass type I membrane protein	integral to membrane [NAS]			1404
Q6TC40 UniProt NPD GO	SRY_HYDLE	Sex-determining region Y protein (Testis-determining factor)	0.76	+	nuc	0	Nucleus				221
P36396 UniProt NPD GO	SRY_URSAR	Sex-determining region Y protein (Testis-determining factor)	0.76	+	nuc	0	Nucleus				232
O00585 UniProt NPD GO	CCL21_HUMAN	Small inducible cytokine A21 precursor (CCL21) (Beta chemokine exodus-2) (6Ckine) (Secondary lymphoi ...	0.76	-	exc	0	Secreted protein		602737		134
O61370 UniProt NPD GO	NACH_DROAN	Sodium channel protein Nach	0.76	-	end	2	Membrane; multi-pass membrane protein	integral to membrane [ISS]			516
O60107 UniProt NPD GO	SNX41_SCHPO	Sorting nexin-41	0.76	-	nuc	0	Endosome; endosomal membrane; peripheral membrane protein (By similarity). Intracellular membrane; p ...				586
Q04053 UniProt NPD GO	SNX41_YEAST	Sorting nexin-41	0.76	-	nuc	0	Perivacuolar punctate structures and endosome	endosome [IDA]			625
Q5IBH6 UniProt NPD GO	SPDYB_MOUSE	Speedy protein B (Rapid inducer of G2/M progression in oocytes B) (RINGO B) (mSpy/Ringo B)	0.76	+	cyt	0	Nucleus (By similarity)	nucleus [ISS]			268
Q9DAC9 UniProt NPD GO	SPRM1_MOUSE	Sperm 1 POU-domain transcription factor (SPRM-1)	0.76	+	nuc	0	Nucleus (By similarity)				329
Q8WNZ4 UniProt NPD GO	HSP1_NATMI	Sperm protamine P1	0.76	+	nuc	0	Nucleus (By similarity)				49
Q8WNZ1 UniProt NPD GO	HSP1_PLEAU	Sperm protamine P1	0.76	+	nuc	0	Nucleus (By similarity)				49
P67833 UniProt NPD GO	HSP1_CAPHI	Sperm protamine P1 (Cysteine-rich protamine)	0.76	+	nuc	0	Nucleus				50
P24713 UniProt NPD GO	HSP1_ORCOR	Sperm protamine P1 (Cysteine-rich protamine)	0.76	+	mit	0	Nucleus				46
P10119 UniProt NPD GO	HSP1_RABIT	Sperm protamine P1 (Cysteine-rich protamine)	0.76	+	nuc	0	Nucleus				49
P68038 UniProt NPD GO	HSP1_SHEEP	Sperm protamine P1 (Cysteine-rich protamine)	0.76	+	nuc	0	Nucleus				50
P15341 UniProt NPD GO	HSP1_HORSE	Sperm protamine P1 (Cysteine-rich protamine) (Protamine ST1)	0.76	+	mit	0	Nucleus				49

You are viewing entries 11051 to 11100 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.