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
Q40965 UniProt NPD GO	RNS2_PYRPY	Ribonuclease S-2 precursor (EC 3.1.27.1) (S2-RNase)	0.49	-	nuc	0	Secreted protein; extracellular space				221
Q9UW15 UniProt NPD GO	RIR1_NEUCR	Ribonucleoside-diphosphate reductase large chain (EC 1.17.4.1) (Ribonucleotide reductase large subun ...	0.49	-	nuc	0					929
Q15349 UniProt NPD GO	KS6A2_HUMAN	Ribosomal protein S6 kinase alpha-2 (EC 2.7.11.1) (S6K-alpha 2) (90 kDa ribosomal protein S6 kinase ...	0.49	-	mit	0	Nucleus	nucleus [TAS]	601685		733
Q682S0 UniProt NPD GO	RPT2_ARATH	Root phototropism protein 2	0.49	-	end	0					593
Q9Y230 UniProt NPD GO	RUVB2_HUMAN	RuvB-like 2 (EC 3.6.1.-) (48 kDa TATA box-binding protein-interacting protein) (48 kDa TBP-interacti ...	0.49	-	nuc	0	Nucleus; nuclear matrix. Nucleus; nucleoplasm. Mainly localized in the nucleus, associated with nucl ...	cytosol [TAS] nucleus [IDA] TIP60 histone acetyltransferase complex [IDA]	604788	2CQA	462
Q9Y3Z3 UniProt NPD GO	SAMH1_HUMAN	SAM domain and HD domain-containing protein 1 (Dendritic cell-derived IFNG-induced protein) (DCIP) ( ...	0.49	-	nuc	0		intracellular [NAS]	606754		626
Q9UHV2 UniProt NPD GO	SRTD1_HUMAN	SERTA domain-containing protein 1 (Transcriptional regulator interacting with the PHD-bromodomain 1) ...	0.49	-	nuc	0					236
Q9CWR2 UniProt NPD GO	SMYD3_MOUSE	SET and MYND domain-containing protein 3 (EC 2.1.1.43) (Zinc finger MYND domain-containing protein 1 ...	0.49	-	nuc	0	Cytoplasm (By similarity). Mainly cytoplasmic when cells are arrested at G0/G1. Nucleus (By similari ...				428
O95905 UniProt NPD GO	SGT1_HUMAN	SGT1 protein (hSGT1) (Ecdysoneless homolog) (Suppressor of GCR2)	0.49	-	nuc	0					644
Q9CS74 UniProt NPD GO	SGT1_MOUSE	SGT1 protein homolog (Ecdysoneless homolog)	0.49	-	nuc	0					641
O88834 UniProt NPD GO	SHD_MOUSE	SH2 domain-containing adapter protein D	0.49	-	nuc	0					343
P40650 UniProt NPD GO	SOX13_XENLA	SOX-13 protein (xSOX-13) (Fragment)	0.49	-	nuc	0	Nucleus (Potential)				54
P40634 UniProt NPD GO	ADW2_ALLMI	SRY-related protein ADW2 (Fragment)	0.49	-	nuc	0	Nucleus (Potential)				72
P40640 UniProt NPD GO	AES6_ALLMI	SRY-related protein AES6 (Fragment)	0.49	+	nuc	0	Nucleus (Potential)				72
O75177 UniProt NPD GO	S18L1_HUMAN	SS18-like protein 1 (SYT homolog 1)	0.49	-	nuc	0			606472		396
Q91WD9 UniProt NPD GO	SEGN_MOUSE	Secretagogin	0.49	-	mit	0	Cytoplasm (By similarity)				276
Q08535 UniProt NPD GO	SECR_MOUSE	Secretin precursor	0.49	-	nuc	0	Secreted protein				133
Q96G97 UniProt NPD GO	BSCL2_HUMAN	Seipin (Bernardinelli-Seip congenital lipodystrophy type 2 protein)	0.49	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	integral to endoplasmic reticulum membrane [IDA]	606158		400
Q98SV0 UniProt NPD GO	SELPB_BRARE	Selenoprotein Pb precursor (zSelPb)	0.49	-	nuc	0	Secreted protein (By similarity)	extracellular region [NAS]			265
O36023 UniProt NPD GO	SPN1_SCHPO	Septin homolog spn1	0.49	-	nuc	0	Present at the septation site during cell fission	septin complex [IDA] septin ring (sensu Fungi) [IDA]			469
Q8WYJ6 UniProt NPD GO	SEPT1_HUMAN	Septin-1 (LARP) (Serologically defined breast cancer antigen NY-BR-24)	0.49	-	cyt	0					367
Q14141 UniProt NPD GO	SEPT6_HUMAN	Septin-6	0.49	+	cyt	0					433
Q5RBA5 UniProt NPD GO	SQSTM_PONPY	Sequestosome-1 (Ubiquitin-binding protein p62)	0.49	-	nuc	0	Cytoplasm. In cardiac muscles localizes to the sarcomeric band. Localizes to late endosomes. May als ...				440
O88445 UniProt NPD GO	AURKC_MOUSE	Serine/threonine-protein kinase 13 (EC 2.7.11.1) (Aurora/Ipl1/Eg2 protein 1) (Aurora-C)	0.49	-	cyt	0	Spindle (By similarity). Localized to spindle pole from anaphase to cytokinesis (By similarity)	chromosome, pericentric region [IDA]			282
Q9Y6E0 UniProt NPD GO	STK24_HUMAN	Serine/threonine-protein kinase 24 (EC 2.7.11.1) (STE20-like kinase MST3) (MST-3) (Mammalian STE20-l ...	0.49	-	nuc	0	Cytoplasm (By similarity)		604984		443
Q99MW1 UniProt NPD GO	STK31_MOUSE	Serine/threonine-protein kinase 31 (EC 2.7.11.1)	0.49	-	cyt	0					1018
P51566 UniProt NPD GO	AFC1_ARATH	Serine/threonine-protein kinase AFC1 (EC 2.7.12.1)	0.49	+	cyt	0					467
Q9BVS4 UniProt NPD GO	RIOK2_HUMAN	Serine/threonine-protein kinase RIO2 (EC 2.7.11.1) (RIO kinase 2)	0.49	-	nuc	0					552
Q9HBY8 UniProt NPD GO	SGK2_HUMAN	Serine/threonine-protein kinase Sgk2 (EC 2.7.11.1) (Serum/glucocorticoid-regulated kinase 2)	0.49	-	cyt	0			607589		427
Q59H18 UniProt NPD GO	TNI3K_HUMAN	Serine/threonine-protein kinase TNNI3K (EC 2.7.11.1) (TNNI3-interacting kinase) (Cardiac ankyrin rep ...	0.49	-	cyt	0	Nucleus. Cytoplasm. Expressed at lower levels in the cytoplasm				936
P12688 UniProt NPD GO	YPK1_YEAST	Serine/threonine-protein kinase YPK1 (EC 2.7.11.1)	0.49	-	nuc	0		bud neck [IDA] cytosol [IDA] plasma membrane [IDA]			680
Q9P1A2 UniProt NPD GO	PP4RL_HUMAN	Serine/threonine-protein phosphatase 4 regulatory subunit 1-like	0.49	-	cyt	0					438
P58005 UniProt NPD GO	SESN3_HUMAN	Sestrin-3	0.49	-	nuc	0			607768		492
O14415 UniProt NPD GO	SEC65_CANAL	Signal recognition particle SEC65 subunit	0.49	-	nuc	0	Cytoplasm (By similarity)				275
Q62771 UniProt NPD GO	STA5A_RAT	Signal transducer and activator of transcription 5A (Mammary gland factor)	0.49	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Mostly cytoplasmic during pregnancy, whereas it ...	cytoplasm [IDA] nucleus [IDA]			793
Q9NRJ3 UniProt NPD GO	CCL28_HUMAN	Small inducible cytokine A28 precursor (CCL28) (Mucosae-associated epithelial chemokine) (MEC) (Prot ...	0.49	+	exc	0	Secreted protein	extracellular region [TAS]	605240		127
Q62205 UniProt NPD GO	SCN9A_MOUSE	Sodium channel protein type 9 subunit alpha (Sodium channel protein type IX subunit alpha) (Voltage- ...	0.49	-	nuc	1	Membrane; multi-pass membrane protein (By similarity)				309
Q9NRS6 UniProt NPD GO	SNX15_HUMAN	Sorting nexin-15	0.49	-	nuc	0		cytosol [NAS] membrane [NAS]	605964		342
Q8BVL3 UniProt NPD GO	SNX17_MOUSE	Sorting nexin-17	0.49	-	cyt	0	Cytoplasm. Endosome; early endosome. Associated with early endosomes	cytoplasm [IDA] endosome [IPI]			470
Q7SGV1 UniProt NPD GO	SNX4_NEUCR	Sorting nexin-4 (Autophagy-related protein 24)	0.49	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Endosome; endosoma ...				493
P11860 UniProt NPD GO	PHI3_MYTCA	Sperm-specific protein Phi-3 (PL-IV)	0.49	+	nuc	0	Nucleus				45
O43597 UniProt NPD GO	SPY2_HUMAN	Sprouty homolog 2 (Spry-2)	0.49	-	nuc	0	Cytoplasm. Cell membrane. Associated with microtubules in unstimulated cells but is translocated to ...		602466		315
Q9QXV8 UniProt NPD GO	SPY2_MOUSE	Sprouty homolog 2 (Spry-2)	0.49	-	nuc	0	Cytoplasm. Cell membrane. Associated with microtubules in unstimulated cells but is translocated to ...				315
Q2MJR0 UniProt NPD GO	SPRE3_HUMAN	Sprouty-related, EVH1 domain-containing protein 3 (Spred-3)	0.49	-	nuc	0	Membrane; peripheral membrane protein (By similarity)		609293		410
Q6P6N5 UniProt NPD GO	SPRE3_MOUSE	Sprouty-related, EVH1 domain-containing protein 3 (Spred-3)	0.49	-	nuc	0	Membrane; peripheral membrane protein	plasma membrane [IDA]			408
Q9UJZ1 UniProt NPD GO	STML2_HUMAN	Stomatin-like protein 2 (SLP-2) (EPB72-like 2)	0.49	-	mit	0	Membrane; peripheral membrane protein. Cytoplasm. Associated with the cytoskeleton	cytoskeleton [TAS]	608292		356
Q7TN29 UniProt NPD GO	SMP1L_MOUSE	Stromal membrane-associated protein 1-like (Stromal membrane-associated protein 2)	0.49	-	nuc	0	Cytoplasm. Detected in multiple foci throughout the cytoplasm and in juxtanuclear structures				428
Q6FWS8 UniProt NPD GO	DHSB_CANGA	Succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (EC 1.3.5.1) (IP)	0.49	-	mit	0	Mitochondrion; mitochondrial inner membrane				253
P80353 UniProt NPD GO	2SS4_CAPMA	Sweet protein mabinlin-4 (Mabinlin IV) (MAB IV) [Contains: Sweet protein mabinlin-4 chain A; Sweet p ...	0.49	-	mit	0					100
O62732 UniProt NPD GO	SYN1_CANFA	Synapsin-1 (Synapsin I) (Fragment)	0.49	-	nuc	0	Synapse				415

You are viewing entries 25901 to 25950 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.