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
Q9GL65 UniProt NPD GO	TLR4_BOVIN	Toll-like receptor 4 precursor (CD284 antigen)	0.50	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	lipopolysaccharide receptor complex [ISS]			841
Q2KIJ9 UniProt NPD GO	TCAL1_BOVIN	Transcription elongation factor A protein-like 1 (TCEA-like protein 1) (Transcription elongation fac ...	0.50	-	nuc	0	Nucleus (By similarity)				159
Q64152 UniProt NPD GO	BTF3_MOUSE	Transcription factor BTF3 (RNA polymerase B transcription factor 3)	0.50	-	nuc	0	Nucleus				204
Q03062 UniProt NPD GO	HES5_RAT	Transcription factor HES-5 (Hairy and enhancer of split 5)	0.50	-	nuc	0	Nucleus				166
O15525 UniProt NPD GO	MAFG_HUMAN	Transcription factor MafG (V-maf musculoaponeurotic fibrosarcoma oncogene homolog G) (hMAF)	0.50	-	nuc	0	Nucleus		602020		162
Q9JHX2 UniProt NPD GO	SP5_MOUSE	Transcription factor Sp5	0.50	-	nuc	0	Nucleus				398
Q62880 UniProt NPD GO	TAF9B_RAT	Transcription initiation factor TFIID subunit 9B (Transcription initiation factor TFIID subunit 9-li ...	0.50	-	nuc	0	Nucleus (By similarity)				258
P13434 UniProt NPD GO	HAP3_YEAST	Transcriptional activator HAP3 (UAS2 regulatory protein A)	0.50	-	nuc	0	Nucleus	CCAAT-binding factor complex [TAS] nucleus [IC]			144
Q00978 UniProt NPD GO	IRTF_HUMAN	Transcriptional regulator ISGF3 subunit gamma (Interferon regulatory factor 9) (IRF-9) (IFN-alpha-re ...	0.50	-	nuc	0	Cytoplasm. Nucleus. Translocated into the nucleus upon activation by IFN-alpha/beta	cytoplasm [TAS] nucleus [TAS]	147574		393
Q9NQ03 UniProt NPD GO	SCRT2_HUMAN	Transcriptional repressor scratch 2 (Scratch homolog 2 zinc finger protein)	0.50	-	nuc	0	Nucleus (Potential)				307
Q80U63 UniProt NPD GO	MFN2_MOUSE	Transmembrane GTPase MFN2 (EC 3.6.5.-) (Mitofusin-2) (Hypertension-related protein 1) (Mitochondrial ...	0.50	-	nuc	1	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein. Colocalizes with BAX durin ...	cytosol [ISS] intrinsic to mitochondrial outer membrane [ISS] microtubule cytoskeleton [IDA]			757
Q9UDY6 UniProt NPD GO	TRI10_HUMAN	Tripartite motif-containing protein 10 (RING finger protein 9) (B30-RING finger protein)	0.50	-	cyt	0	Cytoplasm	intracellular [NAS]	605701		481
Q9BYV6 UniProt NPD GO	TRI55_HUMAN	Tripartite motif-containing protein 55 (Muscle-specific RING finger protein 2) (MuRF2) (MURF-2) (RIN ...	0.50	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Nuclear under atrophic conditions and upon mecha ...	microtubule [NAS]	606469		548
P34785 UniProt NPD GO	TBG_ANEPH	Tubulin gamma chain (Gamma tubulin)	0.50	-	cyt	0					472
Q9WU72 UniProt NPD GO	TN13B_MOUSE	Tumor necrosis factor ligand superfamily member 13B (B cell-activating factor) (BAFF) (CD257 antigen ...	0.50	-	nuc	0	Cell membrane; single-pass type II membrane protein. Processed form: Secreted protein. Also exists a ...				309
Q9Y275 UniProt NPD GO	TN13B_HUMAN	Tumor necrosis factor ligand superfamily member 13B (TNF- and APOL-related leukocyte expressed ligan ...	0.50	-	cyt	1 *	Cell membrane; single-pass type II membrane protein. Processed form: Secreted protein. Also exists a ...	soluble fraction [TAS]	603969	1OTZ	285
P25445 UniProt NPD GO	TNR6_HUMAN	Tumor necrosis factor receptor superfamily member 6 precursor (FASLG receptor) (Apoptosis-mediating ...	0.50	-	exc	0	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2, isoform 3, isoform 4, isof ...	cytosol [NAS] soluble fraction [TAS]	134637	1DDF	335
Q9BDP2 UniProt NPD GO	TNR6_MACMU	Tumor necrosis factor receptor superfamily member 6 precursor (FASLG receptor) (Apoptosis-mediating ...	0.50	+	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				333
P08630 UniProt NPD GO	BTKL_DROME	Tyrosine-protein kinase Btk29A (EC 2.7.10.2) (Dsrc28C)	0.50	-	nuc	0	Ring canals	cytoplasm [IDA] plasma membrane [IDA] ring canal (sensu Insecta) [IDA]			786
P43378 UniProt NPD GO	PTN9_HUMAN	Tyrosine-protein phosphatase non-receptor type 9 (EC 3.1.3.48) (Protein-tyrosine phosphatase MEG2) ( ...	0.50	-	cyt	0	Cytoplasm (Probable)		600768		593
Q9QZM0 UniProt NPD GO	UBQL2_MOUSE	Ubiquilin-2 (Protein linking IAP with cytoskeleton 2) (PLIC-2) (Ubiquitin-like product Chap1/Dsk2) ( ...	0.50	-	nuc	0	Cytoplasm. Nucleus. Associated with fibers and membrane-associated				638
Q92995 UniProt NPD GO	UBP13_HUMAN	Ubiquitin carboxyl-terminal hydrolase 13 (EC 3.1.2.15) (Ubiquitin thioesterase 13) (Ubiquitin-specif ...	0.50	-	cyt	0			603591		863
Q80SY4 UniProt NPD GO	MIB1_MOUSE	Ubiquitin ligase protein MIB1 (EC 6.3.2.-) (Mind bomb homolog 1) (DAPK-interacting protein 1) (DIP-1 ...	0.50	-	cyt	0	Cytoplasm. Cell membrane. Localizes to the plasma membrane	cytoplasmic vesicle [IDA]			1006
P28496 UniProt NPD GO	YKA8_YEAST	Uncharacterized TLC domain-containing protein YKL008C	0.50	+	end	7	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [TAS]			418
Q8TBR5 UniProt NPD GO	CS023_HUMAN	Uncharacterized protein C19orf23	0.50	-	nuc	0					109
Q9BQ89 UniProt NPD GO	CT055_HUMAN	Uncharacterized protein C20orf55	0.50	-	nuc	0					295
P40023 UniProt NPD GO	YEM5_YEAST	Uncharacterized protein YER035W	0.50	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			145
P53972 UniProt NPD GO	YNC2_YEAST	Uncharacterized protein YNL022C	0.50	-	cyt	0		nucleus [IDA]			490
P53956 UniProt NPD GO	YNE6_YEAST	Uncharacterized protein YNL046W	0.50	-	mit	2	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			172
P53719 UniProt NPD GO	YN87_YEAST	Uncharacterized protein YNR014W	0.50	-	nuc	0		cytoplasm [IDA]			212
P21814 UniProt NPD GO	UTMP_SHEEP	Uterine milk protein precursor (UTMP)	0.50	-	mit	0					429
P36062 UniProt NPD GO	AVT3_YEAST	Vacuolar amino acid transporter 3	0.50	-	end	10	Vacuole; vacuolar membrane; multi-pass membrane protein	vacuole [IMP]			692
Q19954 UniProt NPD GO	VPS41_CAEEL	Vacuolar assembly protein VPS41 homolog	0.50	-	cyt	0					759
P23643 UniProt NPD GO	VPS3_YEAST	Vacuolar protein sorting-associated protein VPS3	0.50	-	nuc	0	Cytoplasm	cytoplasm [TAS]			1011
P97946 UniProt NPD GO	VEGFD_MOUSE	Vascular endothelial growth factor D precursor (VEGF-D) (c-fos-induced growth factor) (FIGF)	0.50	-	nuc	0	Secreted protein	extracellular region [IDA]			358
Q10262 UniProt NPD GO	YD2E_SCHPO	Very hypothetical protein C56F8.14c in chromosome I	0.50	-	nuc	0					131
O43089 UniProt NPD GO	YHSE_SCHPO	Very hypothetical protein C947.14c in chromosome II	0.50	-	nuc	0					103
Q04674 UniProt NPD GO	YMU7_YEAST	Very hypothetical protein YMR057C	0.50	-	nuc	0					123
Q96AJ9 UniProt NPD GO	VTI1A_HUMAN	Vesicle transport through interaction with t-SNAREs homolog 1A (Vesicle transport v-SNARE protein Vt ...	0.50	-	nuc	0					203
Q9UEU0 UniProt NPD GO	VTI1B_HUMAN	Vesicle transport through interaction with t-SNAREs homolog 1B (Vesicle transport v-SNARE protein Vt ...	0.50	-	cyt	1	Intracytoplasmic membrane; single-pass type IV membrane protein. Cytoplasmic granules		603207		232
Q17162 UniProt NPD GO	VINC_BRUMA	Vinculin	0.50	-	nuc	0	Cytoskeleton (By similarity). Cell membrane; cell-cell junction; adherens junction; cytoplasmic side ...				993
P02774 UniProt NPD GO	VTDB_HUMAN	Vitamin D-binding protein precursor (DBP) (Group-specific component) (Gc-globulin) (VDB)	0.50	-	exc	0	Secreted protein	extracellular region [NAS]	139200	1MA9	474
P04070 UniProt NPD GO	PROC_HUMAN	Vitamin K-dependent protein C precursor (EC 3.4.21.69) (Autoprothrombin IIA) (Anticoagulant protein ...	0.50	+	end	0		extracellular region [NAS]	176860	2PCT	461
P31394 UniProt NPD GO	PROC_RAT	Vitamin K-dependent protein C precursor (EC 3.4.21.69) (Autoprothrombin IIA) (Anticoagulant protein ...	0.50	+	mit	0					461
P07293 UniProt NPD GO	CAC1S_RABIT	Voltage-dependent L-type calcium channel subunit alpha-1S (Voltage-gated calcium channel subunit alp ...	0.50	+	end	19	Membrane; multi-pass membrane protein			1T3L	1873
Q8VHX0 UniProt NPD GO	CCG3_RAT	Voltage-dependent calcium channel gamma-3 subunit (Neuronal voltage-gated calcium channel gamma-3 su ...	0.50	-	end	4 *	Membrane; multi-pass membrane protein				315
Q5J3K5 UniProt NPD GO	V1A15_RAT	Vomeronasal type-1 receptor A15 (Vomeronasal receptor 2) (Pheromone receptor VN2)	0.50	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				336
Q9H1Z4 UniProt NPD GO	WDR13_HUMAN	WD repeat protein 13	0.50	-	mit	0	Nucleus		300512		485
Q6DKP5 UniProt NPD GO	WDR13_PANTR	WD repeat protein 13	0.50	-	mit	0	Nucleus (By similarity)				485
Q7ZVR1 UniProt NPD GO	WDR75_BRARE	WD repeat protein 75	0.50	-	cyt	0	Nucleus; nucleolus (By similarity)				832

You are viewing entries 25301 to 25350 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.