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
P98159 UniProt NPD GO	NUDEL_DROME	Serine protease nudel precursor (EC 3.4.21.-)	0.90	-	nuc	1 *	Secreted protein; extracellular space; extracellular matrix				2616
O14338 UniProt NPD GO	YB33_SCHPO	Serine-rich protein C2F12.03c in chromosome II	0.90	-	nuc	0	Nucleus				891
Q802A6 UniProt NPD GO	STK4_SQUAC	Serine/threonine-protein kinase 3/4 (EC 2.7.11.1) (STE20-like kinase MST1/2) (sMST1/2)	0.90	-	nuc	0	Cytoplasm; the caspase-cleaved form cycles between nucleus and cytoplasm (By similarity)				491
Q9Y2A5 UniProt NPD GO	DUET_HUMAN	Serine/threonine-protein kinase Duet (EC 2.7.11.1) (Serine/threonine kinase with Dbl- and pleckstrin ...	0.90	-	nuc	0	Cytoplasm. Cytoskeleton. Associated with the cytoskeleton	actin cytoskeleton [TAS]	608128		1289
Q62726 UniProt NPD GO	ICK_RAT	Serine/threonine-protein kinase ICK (EC 2.7.11.22) (Intestinal cell kinase) (MAK-related kinase) (MR ...	0.90	-	nuc	0	Cytoplasm	cytoplasm [IEP]			629
P20793 UniProt NPD GO	MAK_RAT	Serine/threonine-protein kinase MAK (EC 2.7.11.22) (Male germ cell-associated kinase)	0.90	-	nuc	0					622
Q96J92 UniProt NPD GO	WNK4_HUMAN	Serine/threonine-protein kinase WNK4 (EC 2.7.11.1) (Protein kinase with no lysine 4) (Protein kinase ...	0.90	+	nuc	0	Cell membrane; cell-cell junction; tight junction (By similarity). Present exclusively in intercellu ...	tight junction [ISS]	601844		1243
Q8T0S6 UniProt NPD GO	HIPPO_DROME	Serine/threonine-protein kinase hippo (EC 2.7.11.1) (STE20-like kinase MST) (dMST) (Drosophila homol ...	0.90	-	nuc	0					669
Q07657 UniProt NPD GO	SHS1_YEAST	Seventh homolog of septin 1 (Septation protein 7)	0.90	-	nuc	0	Membrane; peripheral membrane protein (By similarity). Bud neck (By similarity). Present at the bud ...	septin ring [IDA]			551
Q8IN81 UniProt NPD GO	FRU_DROME	Sex determination protein fruitless	0.90	+	nuc	0	Nucleus (Potential)	nucleus [NAS]			955
P51501 UniProt NPD GO	SRY_CALJA	Sex-determining region Y protein (Testis-determining factor)	0.90	+	nuc	0	Nucleus				227
Q9BG90 UniProt NPD GO	SRY_MACMU	Sex-determining region Y protein (Testis-determining factor)	0.90	+	nuc	0	Nucleus				204
Q12136 UniProt NPD GO	SAS10_YEAST	Something about silencing protein 10 (U3 small nucleolar RNA-associated protein 3) (U3 snoRNA-associ ...	0.90	+	nuc	0	Nucleus; nucleolus	nucleus [IDA] small nucleolar ribonucleoprotein complex [IPI]			610
Q4WZF1 UniProt NPD GO	MVP1_ASPFU	Sorting nexin mvp1	0.90	-	nuc	0	Cytoplasm (By similarity)				729
Q6BHN9 UniProt NPD GO	SNX41_DEBHA	Sorting nexin-41	0.90	-	nuc	0	Endosome; endosomal membrane; peripheral membrane protein (By similarity). Intracellular membrane; p ...				670
Q6CWX3 UniProt NPD GO	SNX41_KLULA	Sorting nexin-41	0.90	-	nuc	0	Endosome; endosomal membrane; peripheral membrane protein (By similarity). Intracellular membrane; p ...				575
P35308 UniProt NPD GO	HSP1_PANPA	Sperm protamine P1 (Cysteine-rich protamine)	0.90	-	nuc	0	Nucleus	nucleoplasm [ISS]			49
P35309 UniProt NPD GO	HSP1_PANTR	Sperm protamine P1 (Cysteine-rich protamine)	0.90	+	mit	0	Nucleus	nucleoplasm [ISS]			50
O75391 UniProt NPD GO	SPAG7_HUMAN	Sperm-associated antigen 7	0.90	-	nuc	0	Nucleus (Potential)		610056	2CPM	227
Q7TNE3 UniProt NPD GO	SPAG7_MOUSE	Sperm-associated antigen 7	0.90	-	nuc	0	Nucleus (Potential)				227
Q80VP2 UniProt NPD GO	SPAT7_MOUSE	Spermatogenesis-associated protein 7 homolog	0.90	+	mit	0					582
Q15637 UniProt NPD GO	SF01_HUMAN	Splicing factor 1 (Zinc finger protein 162) (Transcription factor ZFM1) (Zinc finger gene in MEN1 lo ...	0.90	+	nuc	0	Nucleus	nucleus [NAS] ribosome [NAS] spliceosome complex [IDA]	601516	1K1G	638
Q68FU8 UniProt NPD GO	SF04_RAT	Splicing factor 4	0.90	-	nuc	0	Nucleus (Probable)				644
P36629 UniProt NPD GO	U2AF2_SCHPO	Splicing factor U2AF 59 kDa subunit (U2 auxiliary factor 59 kDa subunit) (U2 snRNP auxiliary factor ...	0.90	+	nuc	0	Nucleus	commitment complex [IDA] snRNP U2 [TAS]			517
P90978 UniProt NPD GO	U2AF2_CAEEL	Splicing factor U2AF 65 kDa subunit (U2 auxiliary factor 65 kDa subunit) (U2 snRNP auxiliary factor ...	0.90	+	nuc	0	Nucleus				496
Q8VCC9 UniProt NPD GO	SPON1_MOUSE	Spondin-1 precursor (F-spondin)	0.90	+	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				807
P35446 UniProt NPD GO	SPON1_RAT	Spondin-1 precursor (F-spondin)	0.90	+	nuc	0	Secreted protein; extracellular space; extracellular matrix			1VEX	807
Q03868 UniProt NPD GO	SPO71_YEAST	Sporulation-specific protein 71	0.90	-	nuc	0		spore wall (sensu Fungi) [IMP]			1245
Q6C8M8 UniProt NPD GO	ATG26_YARLI	Sterol 3-beta-glucosyltransferase (EC 2.4.1.173) (Autophagy-related protein 26)	0.90	-	mit	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				1424
Q60429 UniProt NPD GO	SRBP2_CRIGR	Sterol regulatory element-binding protein 2 (SREBP-2) (Sterol regulatory element-binding transcripti ...	0.90	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Golgi apparatus; ...				1139
O42649 UniProt NPD GO	SMC3_SCHPO	Structural maintenance of chromosome 3 (Cohesin complex Psm3 subunit)	0.90	-	nuc	0	Nucleus. Associates with chromatin. Before prophase it is scattered along chromosome arms. At anapha ...	chromosome [IDA] mitotic cohesin complex [TAS]			1194
P78524 UniProt NPD GO	ST5_HUMAN	Suppression of tumorigenicity 5 (HeLa tumor suppression 1) (DENN domain-containing protein 2B)	0.90	+	mit	0			140750		1137
Q80TY4 UniProt NPD GO	ST18_MOUSE	Suppression of tumorigenicity protein 18	0.90	-	nuc	0	Nucleus (By similarity)				1045
O60284 UniProt NPD GO	ST18_HUMAN	Suppression of tumorigenicity protein 18 (Zinc finger protein 387)	0.90	-	nuc	0	Nucleus			2CS8	1047
Q9NQ55 UniProt NPD GO	SSF1_HUMAN	Suppressor of SWI4 1 homolog (Ssf-1) (Peter Pan homolog)	0.90	-	nuc	0	Nucleus; nucleolus	nucleus [IDA]	607793		473
Q91ZA6 UniProt NPD GO	SOCS4_MOUSE	Suppressor of cytokine signaling 4 (SOCS-4) (Suppressor of cytokine signaling 7) (SOCS-7)	0.90	-	nuc	0					436
Q6A028 UniProt NPD GO	SWP70_MOUSE	Switch-associated protein 70 (SWAP-70)	0.90	-	nuc	0	Cytoplasm (By similarity). Cell membrane (By similarity). Nucleus (By similarity). In resting B-cell ...	nucleus [IDA]			585
Q8VHQ7 UniProt NPD GO	SYTL4_RAT	Synaptotagmin-like protein 4 (Exophilin-2) (Granuphilin)	0.90	-	nuc	0	Membrane; peripheral membrane protein. Detected close to the plasma membrane and on secretory granul ...	extrinsic to plasma membrane [ISS]			672
O95935 UniProt NPD GO	TBX18_HUMAN	T-box transcription factor TBX18 (T-box protein 18)	0.90	+	nuc	0	Nucleus (Potential)	nucleus [NAS]	604613		607
Q6PDZ2 UniProt NPD GO	TAF1C_MOUSE	TATA box-binding protein-associated factor, RNA polymerase I, subunit C (TATA box-binding protein-as ...	0.90	-	nuc	0	Nucleus (By similarity)	RNA polymerase I transcription factor complex [TAS]			836
Q8C0G2 UniProt NPD GO	T3JAM_MOUSE	TRAF3-interacting JNK-activating modulator (TRAF3-interacting protein 3)	0.90	-	nuc	1	Membrane; single-pass type IV membrane protein (Potential)				513
Q5DTH5 UniProt NPD GO	TSH1_MOUSE	Teashirt homolog 1 (Serologically defined colon cancer antigen 3 homolog)	0.90	-	nuc	0	Nucleus (Probable)				1084
O76332 UniProt NPD GO	TERT_OXYTR	Telomerase reverse transcriptase (EC 2.7.7.49) (Telomerase catalytic subunit) (Telomerase subunit P1 ...	0.90	+	nuc	0	Nucleus				1132
Q8NEE8 UniProt NPD GO	TTC16_HUMAN	Tetratricopeptide repeat protein 16 (TPR repeat protein 16)	0.90	-	nuc	0					873
P36598 UniProt NPD GO	THI1_SCHPO	Thiamine repressible genes regulatory protein thi1 (Transcription factor ntf1)	0.90	+	nuc	0	Nucleus (Probable)				775
Q9W785 UniProt NPD GO	THA_SALSA	Thyroid hormone receptor alpha	0.90	+	nuc	0	Nucleus				416
O42295 UniProt NPD GO	THA_APTPA	Thyroid hormone receptor alpha (Fragment)	0.90	+	nuc	0	Nucleus				402
Q62383 UniProt NPD GO	SPT6H_MOUSE	Transcription elongation factor SPT6	0.90	+	nuc	0	Nucleus (Probable)				1726
Q4PI89 UniProt NPD GO	SPT6_USTMA	Transcription elongation factor SPT6 (Chromatin elongation factor SPT6)	0.90	+	nuc	0	Nucleus (By similarity)				1723
O14776 UniProt NPD GO	TCRG1_HUMAN	Transcription elongation regulator 1 (TATA box-binding protein-associated factor 2S) (Transcription ...	0.90	-	nuc	0	Nucleus	nucleus [TAS]	605409		1098

You are viewing entries 4401 to 4450 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.