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
O04856 UniProt NPD GO	PP11_TOBAC	Serine/threonine-protein phosphatase PP1 isozyme 1 (EC 3.1.3.16)	0.35	-	cyt	0					317
P23734 UniProt NPD GO	PP12_TRYBB	Serine/threonine-protein phosphatase PP1(5.9) (EC 3.1.3.16)	0.35	-	mit	0					346
P48461 UniProt NPD GO	PP11_DROME	Serine/threonine-protein phosphatase alpha-1 isoform (EC 3.1.3.16)	0.35	-	mit	0					327
P90837 UniProt NPD GO	SRE32_CAEEL	Serpentine receptor class epsilon-32 (Protein sre-32)	0.35	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				361
Q91X20 UniProt NPD GO	ASH2L_MOUSE	Set1/Ash2 histone methyltransferase complex subunit ASH2 (ASH2-like protein)	0.35	-	nuc	0	Nucleus (Probable)				623
O01671 UniProt NPD GO	SXL_MEGSC	Sex-lethal homolog	0.35	-	nuc	0	Nucleus (By similarity)				321
O60902 UniProt NPD GO	SHOX2_HUMAN	Short stature homeobox protein 2 (Paired-related homeobox protein SHOT) (Homeobox protein Og12X)	0.35	+	nuc	0	Nucleus		602504		331
Q9JMI9 UniProt NPD GO	TRPC3_RAT	Short transient receptor potential channel 3 (TrpC3)	0.35	-	end	6	Membrane; multi-pass membrane protein (Probable)				736
Q95LH0 UniProt NPD GO	SIG12_PANTR	Sialic acid-binding Ig-like lectin 12 precursor (Siglec-12) (Sialic acid-binding Ig-like lectin-like ...	0.35	-	exc	1	Membrane; single-pass type I membrane protein				597
Q00179 UniProt NPD GO	SRP54_ASPNG	Signal recognition particle 54 kDa protein homolog	0.35	-	cyt	0	Cytoplasm				534
Q9Y3P8 UniProt NPD GO	SIT1_HUMAN	Signaling threshold-regulating transmembrane adapter 1 precursor (Suppression-inducing transmembrane ...	0.35	-	exc	1 *	Cell membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [IDA]	604964		196
Q9HCE7 UniProt NPD GO	SMUF1_HUMAN	Smad ubiquitination regulatory factor 1 (EC 6.3.2.-) (Ubiquitin--protein ligase SMURF1) (Smad-specif ...	0.35	-	mit	0		intracellular [TAS]	605568		757
Q08782 UniProt NPD GO	CCL2_CAVPO	Small inducible cytokine A2 precursor (CCL2) (Monocyte chemotactic protein 1) (MCP-1) (Monocyte chem ...	0.35	-	exc	0	Secreted protein				120
O97919 UniProt NPD GO	CCL5_BOVIN	Small inducible cytokine A5 precursor (CCL5) (T-cell-specific RANTES protein) (SIS-delta)	0.35	-	exc	1 *	Secreted protein				91
O95715 UniProt NPD GO	SCYBE_HUMAN	Small inducible cytokine B14 precursor (CXCL14) (Chemokine BRAK)	0.35	-	nuc	0	Secreted protein		604186		99
Q2TBS9 UniProt NPD GO	SMU1_BOVIN	Smu-1 suppressor of mec-8 and unc-52 protein homolog	0.35	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				513
Q76B40 UniProt NPD GO	SMU1_CRIGR	Smu-1 suppressor of mec-8 and unc-52 protein homolog	0.35	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				513
Q2TAY7 UniProt NPD GO	SMU1_HUMAN	Smu-1 suppressor of mec-8 and unc-52 protein homolog	0.35	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				513
Q3UKJ7 UniProt NPD GO	SMU1_MOUSE	Smu-1 suppressor of mec-8 and unc-52 protein homolog	0.35	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				513
P26432 UniProt NPD GO	SL9A3_RABIT	Sodium/hydrogen exchanger 3 (Na(+)/H(+) exchanger 3) (NHE-3) (Solute carrier family 9 member 3)	0.35	-	end	13 *	Membrane; multi-pass membrane protein				832
Q92030 UniProt NPD GO	AT1A1_ANGAN	Sodium/potassium-transporting ATPase alpha-1 chain precursor (EC 3.6.3.9) (Sodium pump 1) (Na+/K+ AT ...	0.35	+	end	8	Membrane; multi-pass membrane protein	sodium:potassium-exchanging ATPase complex [ISS]			1022
Q43846 UniProt NPD GO	SSY3_SOLTU	Soluble starch synthase 3, chloroplast precursor (EC 2.4.1.21) (SS III) (Soluble starch synthase III ...	0.35	-	mit	0	Or: Plastid; chloroplast. Or: Plastid; amyloplast. Soluble and granule-bound (By similarity)				1230
P79894 UniProt NPD GO	SOML2_SPAAU	Somatolactin-2 precursor (SL)	0.35	-	mit	0	Secreted protein				231
P87384 UniProt NPD GO	SMS1_RANRI	Somatostatin 1 precursor (PSS1) [Contains: Somatostatin-14 (S-I) (SSS1)]	0.35	-	exc	0	Secreted protein				115
Q9W7F0 UniProt NPD GO	SMS1_PROAN	Somatostatin-1 precursor (Somatostatin I) (PSS1) [Contains: Somatostatin-27; Somatostatin-14]	0.35	-	exc	0	Secreted protein				115
Q5R613 UniProt NPD GO	SNX6_PONPY	Sorting nexin-6	0.35	-	cyt	0					406
Q9PU13 UniProt NPD GO	SPD1A_XENLA	Speedy protein 1-A (Spy1-A) (XSpy1-A) (Rapid inducer of G2/M progression in oocytes A) (RINGO-A) (p3 ...	0.35	-	mit	0	Nucleus (By similarity)	nucleus [ISS]			299
Q8TAD1 UniProt NPD GO	SPNXE_HUMAN	Sperm protein associated with the nucleus on the X chromosome E (Nuclear-associated protein SPAN-Xe) ...	0.35	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Associated with nuclear craters (By similarity)				97
P21623 UniProt NPD GO	DIT1_YEAST	Spore wall maturation protein DIT1	0.35	-	cyt	0					536
Q8R4L0 UniProt NPD GO	SLAP2_MOUSE	Src-like-adapter 2 (Src-like adapter protein 2) (SLAP-2)	0.35	-	nuc	0	Cytoplasm. Cell membrane. Cytoplasmic vesicle. Endosome; late endosome. Localized to the plasma memb ...	cytoplasm [ISS] cytoplasmic membrane-bound vesicle [IDA] endosome membrane [ISS] late endosome [IDA] plasma membrane [ISS]			258
P26793 UniProt NPD GO	RAD27_YEAST	Structure-specific endonuclease RAD27	0.35	-	nuc	0	Nucleus (Probable)	nucleus [IMP]			382
Q9CQA3 UniProt NPD GO	DHSB_MOUSE	Succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (EC 1.3.5.1) (Ip) ...	0.35	-	nuc	0	Mitochondrion; mitochondrial inner membrane (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			282
Q02045 UniProt NPD GO	MLR5_HUMAN	Superfast myosin regulatory light chain 2 (MyLC-2) (MYLC2) (Myosin regulatory light chain 5)	0.35	-	mit	0		muscle myosin [TAS]	160782		173
Q960T2 UniProt NPD GO	SAP47_DROME	Synapse-associated protein of 47 kDa	0.35	-	cyt	0		synapse [IDA]			551
P24506 UniProt NPD GO	SY62_DISOM	Synaptotagmin B (Synaptic vesicle protein O-p65-B)	0.35	-	nuc	1	Synaptic vesicles in neurons				439
P34693 UniProt NPD GO	SYT1_CAEEL	Synaptotagmin-1 (Synaptotagmin I)	0.35	-	nuc	1	Synaptic vesicles and vesicle-like structures	integral to synaptic vesicle membrane [TAS]			441
P93654 UniProt NPD GO	SYP22_ARATH	Syntaxin-22 (AtSYP22) (AtVAM3)	0.35	-	nuc	1	Prevacuolar compartment; prevacuolar compartment membrane; single-pass type IV membrane protein. Vac ...				268
P91809 UniProt NPD GO	TBP_STRPU	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (TB ...	0.35	+	nuc	0	Nucleus				265
P24155 UniProt NPD GO	MEPD_RAT	Thimet oligopeptidase (EC 3.4.24.15) (Endo-oligopeptidase A) (Endopeptidase 24.15) (PZ-peptidase) (S ...	0.35	-	cyt	0	Cytoplasm				686
Q715T0 UniProt NPD GO	TXND3_MOUSE	Thioredoxin domain-containing protein 3 (Spermatid-specific thioredoxin-2) (Sptrx-2)	0.35	-	cyt	0	Cytoplasm				586
Q9NSU2 UniProt NPD GO	TREX1_HUMAN	Three prime repair exonuclease 1 (EC 3.1.11.2) (3'-5' exonuclease TREX1) (DNase III)	0.35	-	nuc	1	Nucleus (By similarity)	nuclear envelope [NAS]	606605		369
O00142 UniProt NPD GO	KITM_HUMAN	Thymidine kinase 2, mitochondrial precursor (EC 2.7.1.21) (Mt-TK)	0.35	-	mit	0	Mitochondrion		609560		266
Q62381 UniProt NPD GO	TLL1_MOUSE	Tolloid-like protein 1 precursor (EC 3.4.24.-) (mTll)	0.35	-	exc	0	Secreted protein (Probable)				1013
O57382 UniProt NPD GO	TLL2_XENLA	Tolloid-like protein 2 precursor (EC 3.4.24.-) (Xenopus tolloid) (Metalloprotease xolloid)	0.35	-	vac	2 *	Secreted protein				1019
Q9BZA0 UniProt NPD GO	TTY10_HUMAN	Transcript Y 10 protein	0.35	-	nuc	0					68
Q9CZY2 UniProt NPD GO	TCAL8_MOUSE	Transcription elongation factor A protein-like 8 (TCEA-like protein 8) (Transcription elongation fac ...	0.35	-	nuc	0	Nucleus (Probable)				117
Q6I7R5 UniProt NPD GO	TCAL8_RAT	Transcription elongation factor A protein-like 8 (TCEA-like protein 8) (Transcription elongation fac ...	0.35	-	nuc	0	Nucleus (Probable)				117
Q60539 UniProt NPD GO	TCF15_MESAU	Transcription factor 15 (bHLH-EC2 protein) (Paraxis) (Meso1)	0.35	-	nuc	0	Nucleus (By similarity)				195
Q9BIB4 UniProt NPD GO	YMYD_CAEEL	Transcription initiation factor IIA small chain homolog	0.35	-	nuc	0	Nucleus (Potential)				139
P49906 UniProt NPD GO	TAF11_DROME	Transcription initiation factor TFIID subunit 11 (Transcription initiation factor TFIID 28 kDa subun ...	0.35	-	nuc	0	Nucleus				196

You are viewing entries 36251 to 36300 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.