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
P59544 UniProt NPD GO	T2R50_HUMAN	Taste receptor type 2 member 50 (T2R50) (T2R51)	0.23	-	end	7 *	Membrane; multi-pass membrane protein		609627		299
Q646G4 UniProt NPD GO	TA2R8_PAPHA	Taste receptor type 2 member 8 (T2R8)	0.23	-	end	7 *	Membrane; multi-pass membrane protein				309
Q9ESC2 UniProt NPD GO	TNMD_RAT	Tenomodulin (TeM) (rTeM) (Chondromodulin-I-like protein) (ChM1L) (rChM1L) (Myodulin)	0.23	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)	cell surface [NAS]			317
Q2QLB2 UniProt NPD GO	TES_HORSE	Testin	0.23	-	nuc	0					421
Q9SEU6 UniProt NPD GO	TRXM4_ARATH	Thioredoxin M-type 4, chloroplast precursor (TRX-M4)	0.23	-	mit	0	Plastid; chloroplast (By similarity)				193
Q00063 UniProt NPD GO	THRC_ASHGO	Threonine synthase (EC 4.2.3.1) (TS)	0.23	-	cyt	0					512
P24557 UniProt NPD GO	THAS_HUMAN	Thromboxane-A synthase (EC 5.3.99.5) (TXA synthase) (TXS) (Cytochrome P450 5A1)	0.23	-	end	0	Membrane; multi-pass membrane protein		274180		533
O76511 UniProt NPD GO	TYSY_DROME	Thymidylate synthase (EC 2.1.1.45) (TS) (TSase)	0.23	-	cyt	0					321
Q8HYB7 UniProt NPD GO	PERT_CANFA	Thyroid peroxidase precursor (EC 1.11.1.8) (TPO)	0.23	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				933
Q3UA06 UniProt NPD GO	TRP13_MOUSE	Thyroid receptor-interacting protein 13 (Thyroid hormone receptor interactor 13) (Trip-13)	0.23	-	cyt	0					432
Q15645 UniProt NPD GO	TRP13_HUMAN	Thyroid receptor-interacting protein 13 (Thyroid hormone receptor interactor 13) (Trip-13) (Human pa ...	0.23	-	cyt	0		nucleus [TAS]	604507		432
P04066 UniProt NPD GO	FUCO_HUMAN	Tissue alpha-L-fucosidase precursor (EC 3.2.1.51) (Alpha-L-fucosidase I) (Alpha-L-fucoside fucohydro ...	0.23	-	end	0	Lysosome	cytoplasm [IC]	230000		461
P62389 UniProt NPD GO	NXS5_ENHSC	Toxin 5	0.23	-	nuc	0	Secreted protein				60
P01414 UniProt NPD GO	TXFS2_DENPO	Toxin FS-2 (FS2)	0.23	-	mit	0	Secreted protein			1TFS	60
Q07338 UniProt NPD GO	TXPH_PYETR	Toxin tox21A precursor (Insect-selective neurotoxin TxP-I homolog)	0.23	-	exc	0	Secreted protein (By similarity)				289
P37114 UniProt NPD GO	TCMO_MEDSA	Trans-cinnamate 4-monooxygenase (EC 1.14.13.11) (Cinnamic acid 4-hydroxylase) (CA4H) (C4H) (P450C4H) ...	0.23	-	end	0					506
Q4I5W5 UniProt NPD GO	SPT4_GIBZE	Transcription elongation factor SPT4 (Chromatin elongation factor SPT4)	0.23	-	nuc	0	Nucleus. Centromere and heterochromatin (By similarity)				99
P52654 UniProt NPD GO	TF2AA_DROME	Transcription initiation factor IIA subunit 1 (dTFIIA-L) [Contains: Transcription initiation factor ...	0.23	-	nuc	0	Nucleus				366
Q15544 UniProt NPD GO	TAF11_HUMAN	Transcription initiation factor TFIID subunit 11 (Transcription initiation factor TFIID 28 kDa subun ...	0.23	-	nuc	0	Nucleus	transcription factor TFIID complex [IDA]	600772	1BH9	211
Q9H808 UniProt NPD GO	TLE6_HUMAN	Transducin-like enhancer protein 6	0.23	-	nuc	0	Nucleus (By similarity)				449
P29401 UniProt NPD GO	TKT_HUMAN	Transketolase (EC 2.2.1.1) (TK)	0.23	-	cyt	0			606781		623
Q5R1W6 UniProt NPD GO	TKT_PANTR	Transketolase (EC 2.2.1.1) (TK)	0.23	-	cyt	0					623
Q6P7C7 UniProt NPD GO	GPNMB_RAT	Transmembrane glycoprotein NMB precursor	0.23	-	end	1	Membrane; single-pass type I membrane protein (Potential)				572
Q9NUM4 UniProt NPD GO	T106B_HUMAN	Transmembrane protein 106B	0.23	-	mit	1	Membrane; single-pass membrane protein (Potential)				274
Q9DCF1 UniProt NPD GO	TMM25_MOUSE	Transmembrane protein 25 precursor	0.23	-	end	1	Isoform 1: Cell membrane; single-pass type I membrane protein (Potential). Isoform 2: Secreted prote ...				365
Q9UIK5 UniProt NPD GO	TEFF2_HUMAN	Transmembrane protein with EGF-like and two follistatin-like domains 2 precursor (Transmembrane prot ...	0.23	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]	605734		374
Q29554 UniProt NPD GO	ECHA_PIG	Trifunctional enzyme subunit alpha, mitochondrial precursor (TP-alpha) (78 kDa gastrin-binding prote ...	0.23	-	mit	0	Mitochondrion; mitochondrial matrix				763
Q9XSB8 UniProt NPD GO	TPP1_CANFA	Tripeptidyl-peptidase 1 precursor (EC 3.4.14.9) (Tripeptidyl-peptidase I) (TPP-I) (Tripeptidyl amino ...	0.23	-	end	0	Lysosome				563
P81428 UniProt NPD GO	FA10V_TROCA	Trocarin precursor (EC 3.4.21.6) (Venom coagulation factor Xa-like protease) [Contains: Trocarin lig ...	0.23	-	exc	0	Secreted protein				455
O13831 UniProt NPD GO	TRP_SCHPO	Tryptophan synthase (EC 4.2.1.20)	0.23	-	nuc	0					697
P20802 UniProt NPD GO	TBB_ACHKL	Tubulin beta chain (Beta tubulin)	0.23	-	cyt	0	Cytoplasm				444
O17449 UniProt NPD GO	TBB1_MANSE	Tubulin beta-1 chain (Beta-1 tubulin)	0.23	-	cyt	0					447
P25862 UniProt NPD GO	TBB1_AVESA	Tubulin beta-1 chain (Beta-1 tubulin) (Fragment)	0.23	-	cyt	0					386
P29501 UniProt NPD GO	TBB2_PEA	Tubulin beta-2 chain (Beta-2 tubulin) (Fragment)	0.23	-	cyt	0					447
Q9UJT1 UniProt NPD GO	TBD_HUMAN	Tubulin delta chain (Delta tubulin)	0.23	-	cyt	0	Centrosome. Associated with centrioles. Cytoplasm. Nucleus. Both cytoplasmic and nuclear	centriole [TAS]	607344		453
Q8NG68 UniProt NPD GO	TTL_HUMAN	Tubulin--tyrosine ligase (EC 6.3.2.25) (TTL)	0.23	-	cyt	0			608291		377
O00220 UniProt NPD GO	TR10A_HUMAN	Tumor necrosis factor receptor superfamily member 10A precursor (Death receptor 4) (TNF-related apop ...	0.23	-	nuc	1	Membrane; single-pass type I membrane protein	integral to membrane [IC]	603611		468
Q84W55 UniProt NPD GO	IP5PC_ARATH	Type II inositol-1,4,5-trisphosphate 5-phosphatase 12 (EC 3.1.3.36) (At5PTase12) (FRAGILE FIBER3 pro ...	0.23	-	mit	0					1101
P25044 UniProt NPD GO	PTP1_YEAST	Tyrosine-protein phosphatase 1 (EC 3.1.3.48) (Protein-tyrosine phosphatase 1) (PTPase 1)	0.23	-	nuc	0	Cytoplasm	cytoplasm [IDA] mitochondrion [IDA]			335
Q8WZJ9 UniProt NPD GO	HUT1_SCHPO	UDP-galactose transporter homolog 1	0.23	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				322
Q8VCW4 UniProt NPD GO	UN93B_MOUSE	UNC93 homolog B1 (UNC-93B protein)	0.23	-	end	12	Membrane; multi-pass membrane protein (Potential)				598
Q23202 UniProt NPD GO	YOM4_CAEEL	UPF0023 protein W06E11.4	0.23	-	nuc	0					253
P36039 UniProt NPD GO	YKU7_YEAST	UPF0347 protein YKL207W	0.23	-	cyt	3 *	Membrane; multi-pass membrane protein (Potential)				282
Q5RC24 UniProt NPD GO	UCR6_PONPY	Ubiquinol-cytochrome c reductase complex 14 kDa protein (EC 1.10.2.2) (Complex III subunit VI)	0.23	-	cyt	0	Mitochondrion; mitochondrial inner membrane				110
P84589 UniProt NPD GO	UBIQ_LUMTE	Ubiquitin (Fragment)	0.23	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				63
Q8WUN7 UniProt NPD GO	UBTD2_HUMAN	Ubiquitin domain-containing protein 2 (Dendritic cell-derived ubiquitin-like protein) (DC-UbP) (Ubiq ...	0.23	-	nuc	0	Cytoplasm			1TTN	234
Q8R4T2 UniProt NPD GO	SIAH2_RAT	Ubiquitin ligase SIAH2 (EC 6.3.2.-) (Seven in absentia homolog 2) (Siah-2)	0.23	-	nuc	0	Cytoplasm. Predominantly. Nucleus (Probable). Partially (Probable)				325
O43255 UniProt NPD GO	SIAH2_HUMAN	Ubiquitin ligase SIAH2 (EC 6.3.2.-) (Seven in absentia homolog 2) (Siah-2) (hSiah2)	0.23	-	nuc	0	Cytoplasm. Predominantly. Nucleus (Probable). Partially (Probable)	cytoplasm [TAS]	602213		324
Q06986 UniProt NPD GO	SIAH2_MOUSE	Ubiquitin ligase SIAH2 (EC 6.3.2.-) (Seven in absentia homolog 2) (Siah-2) (mSiah2)	0.23	-	nuc	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). Partially (By similarity)				325
Q9VL00 UniProt NPD GO	OTUBL_DROME	Ubiquitin thioesterase otubain-like protein (EC 3.4.-.-) (Ubiquitin-specific-processing protease otu ...	0.23	-	cyt	0					262

You are viewing entries 47951 to 48000 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.