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
P38216 UniProt NPD GO	YBM6_YEAST	Uncharacterized protein YBR016W	0.36	-	nuc	0		plasma membrane [IDA]			128
P39000 UniProt NPD GO	YES6_YEAST	Uncharacterized protein YER096W	0.36	-	nuc	0		prospore membrane [IDA]			512
P53120 UniProt NPD GO	YGO0_YEAST	Uncharacterized protein YGL140C	0.36	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				1219
P38756 UniProt NPD GO	YHG3_YEAST	Uncharacterized protein YHR003C	0.36	-	mit	0		mitochondrial outer membrane [IDA] mitochondrion [IDA]			429
Q03212 UniProt NPD GO	YM40_YEAST	Uncharacterized protein YMR171C	0.36	-	exc	1 *		endosome [IDA]			550
P82331 UniProt NPD GO	UT114_PEA	Unknown protein from 2D-PAGE of thylakoid (Spot 114) (Fragment)	0.36	-		0	Plastid; chloroplast; chloroplast thylakoid				15
P55089 UniProt NPD GO	UCN1_HUMAN	Urocortin precursor	0.36	-	exc	0	Secreted protein		600945		124
P06869 UniProt NPD GO	UROK_MOUSE	Urokinase-type plasminogen activator precursor (EC 3.4.21.73) (uPA) (U-plasminogen activator) [Conta ...	0.36	-	exc	0					433
P57747 UniProt NPD GO	VATD_SUBDO	Vacuolar ATP synthase subunit D (EC 3.6.3.14) (V-ATPase D subunit) (Vacuolar proton pump D subunit)	0.36	-	mit	0					250
Q9U5N0 UniProt NPD GO	VATH_MANSE	Vacuolar ATP synthase subunit H (EC 3.6.3.14) (V-ATPase H subunit) (Vacuolar proton pump subunit H)	0.36	-	nuc	0					475
Q9UI12 UniProt NPD GO	VATH_HUMAN	Vacuolar ATP synthase subunit H (EC 3.6.3.14) (V-ATPase H subunit) (Vacuolar proton pump subunit H) ...	0.36	-	cyt	0		hydrogen-transporting ATPase V1 domain [NAS]	608861		483
Q03308 UniProt NPD GO	VPS16_YEAST	Vacuolar protein sorting-associated protein VPS16	0.36	-	nuc	0	Cytoplasm	HOPS complex [IPI] vacuolar membrane (sensu Fungi) [IDA]			798
P40335 UniProt NPD GO	VPS26_YEAST	Vacuolar protein sorting/targeting protein VPS26	0.36	-	nuc	0		endosome [IPI] retromer complex [TAS]			379
Q8C1W1 UniProt NPD GO	VASH_MOUSE	Vasohibin	0.36	-	nuc	0	Secreted protein (By similarity)				375
P17668 UniProt NPD GO	NEU3_CATCO	Vasotocin-neurophysin VT 1 precursor [Contains: Vasotocin (VT); Neurophysin VT 1]	0.36	-	nuc	0	Secreted protein				152
Q07662 UniProt NPD GO	NEU3_ONCMA	Vasotocin-neurophysin VT 1 precursor [Contains: Vasotocin (VT); Neurophysin VT 1]	0.36	-	nuc	1 *	Secreted protein				155
Q10497 UniProt NPD GO	YDGB_SCHPO	Very hypothetical protein C26F1.11 in chromosome I	0.36	-	nuc	0					105
Q9MZA9 UniProt NPD GO	VIME_SHEEP	Vimentin (Fragment)	0.36	-	mit	0					153
P48671 UniProt NPD GO	VIM1_CARAU	Vimentin A1 (Fragment)	0.36	-	nuc	0					170
P07225 UniProt NPD GO	PROS_HUMAN	Vitamin K-dependent protein S precursor	0.36	-	exc	0	Secreted protein	extracellular region [NAS]	176880	1Z6C	676
O88602 UniProt NPD GO	CCG2_MOUSE	Voltage-dependent calcium channel gamma-2 subunit (Neuronal voltage-gated calcium channel gamma-2 su ...	0.36	-	end	4 *	Membrane; multi-pass membrane protein				323
Q8VHW2 UniProt NPD GO	CCG8_MOUSE	Voltage-dependent calcium channel gamma-8 subunit (Neuronal voltage-gated calcium channel gamma-8 su ...	0.36	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				423
Q8VHW5 UniProt NPD GO	CCG8_RAT	Voltage-dependent calcium channel gamma-8 subunit (Neuronal voltage-gated calcium channel gamma-8 su ...	0.36	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				421
Q8R2E6 UniProt NPD GO	V1A11_MOUSE	Vomeronasal type-1 receptor A11	0.36	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				318
Q5J3F6 UniProt NPD GO	V1A16_RAT	Vomeronasal type-1 receptor A16 (Vomeronasal receptor 6) (Pheromone receptor VN6)	0.36	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				310
Q5J3G9 UniProt NPD GO	VN1A7_RAT	Vomeronasal type-1 receptor A7	0.36	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				314
Q9EP79 UniProt NPD GO	VN1A7_MOUSE	Vomeronasal type-1 receptor A7 (Vomeronasal receptor 3) (Pheromone receptor VN3)	0.36	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				309
Q5J3E5 UniProt NPD GO	VN1A8_RAT	Vomeronasal type-1 receptor A8	0.36	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				314
Q9ESH5 UniProt NPD GO	WFDC1_MOUSE	WAP four-disulfide core domain protein 1 precursor (Prostate stromal protein ps20) (ps20 growth inhi ...	0.36	-	exc	0	Secreted protein (Potential)				211
P59823 UniProt NPD GO	IRPL1_MOUSE	X-linked interleukin-1 receptor accessory protein-like 1 precursor (IL1RAPL-1)	0.36	-	nuc	1	Membrane; single-pass type I membrane protein				695
Q6J2U6 UniProt NPD GO	ZN313_RAT	Zinc finger protein 313	0.36	-	nuc	0					229
Q02526 UniProt NPD GO	ZFP41_MOUSE	Zinc finger protein 41 (Zfp-41) (CtFIN92) (Fragment)	0.36	-	nuc	0	Nucleus				105
Q9H609 UniProt NPD GO	ZN576_HUMAN	Zinc finger protein 576	0.36	-	nuc	0	Nucleus (Potential)				170
Q969S3 UniProt NPD GO	ZN622_HUMAN	Zinc finger protein 622 (Zinc finger-like protein 9)	0.36	-	nuc	0	Cytoplasm. Nucleus		608694		477
Q90Y35 UniProt NPD GO	ZN622_CHICK	Zinc finger protein 622 (Zn-finger protein C47)	0.36	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				405
P51506 UniProt NPD GO	ZNF80_PANTR	Zinc finger protein 80	0.36	-	nuc	0	Nucleus (Probable)				273
Q21059 UniProt NPD GO	NAS34_CAEEL	Zinc metalloproteinase nas-34 precursor (EC 3.4.24.21) (Nematode astacin 34) (Defective hatching pro ...	0.36	-	exc	0	Secreted protein (Potential)				605
Q63065 UniProt NPD GO	PDK1_RAT	[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (EC 2.7.11.2) (Pyruva ...	0.36	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]			434
O42794 UniProt NPD GO	KAPR_COLTR	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit)	0.36	-	nuc	0					404
P31324 UniProt NPD GO	KAP3_MOUSE	cAMP-dependent protein kinase type II-beta regulatory subunit	0.36	-	cyt	0					415
P48565 UniProt NPD GO	PALH_YEAST	pH-response regulator protein palH/RIM21 (Regulator of IME2 protein 21)	0.36	-	end	6	Cell membrane; multi-pass membrane protein (Potential)				533
P15456 UniProt NPD GO	12S2_ARATH	12S seed storage protein CRB precursor [Contains: 12S seed storage protein CRB alpha chain (12S seed ...	0.35	-	mit	0					455
P16330 UniProt NPD GO	CN37_MOUSE	2',3'-cyclic-nucleotide 3'-phosphodiesterase (EC 3.1.4.37) (CNP) (CNPase)	0.35	-	mit	0	Membrane. Firmly bound to membrane structures of brain white matter	membrane fraction [IDA]			420
P46465 UniProt NPD GO	PRS6A_ORYSA	26S protease regulatory subunit 6A homolog (TAT-binding protein homolog 1) (TBP-1)	0.35	-	nuc	0	Cytoplasm (Potential). Nucleus (Potential)				429
Q9WTV5 UniProt NPD GO	PSD9_RAT	26S proteasome non-ATPase regulatory subunit 9 (26S proteasome regulatory subunit p27) (Transactivat ...	0.35	-	nuc	0					222
P82917 UniProt NPD GO	RT18C_BOVIN	28S ribosomal protein S18c, mitochondrial precursor (MRP-S18-c) (Mrps18c) (MRP-S18-1)	0.35	-	nuc	0	Mitochondrion				143
P12684 UniProt NPD GO	HMDH2_YEAST	3-hydroxy-3-methylglutaryl-coenzyme A reductase 2 (EC 1.1.1.34) (HMG-CoA reductase 2)	0.35	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [TAS] nuclear envelope [TAS]			1045
P42732 UniProt NPD GO	RR13_ARATH	30S ribosomal protein S13, chloroplast precursor (CS13)	0.35	-	mit	0	Plastid; chloroplast				169
Q9BYD1 UniProt NPD GO	RM13_HUMAN	39S ribosomal protein L13, mitochondrial (L13mt) (MRP-L13)	0.35	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [NAS]	610200		178
Q9D8P4 UniProt NPD GO	RM17_MOUSE	39S ribosomal protein L17, mitochondrial precursor (L17mt) (MRP-L17)	0.35	-	nuc	0	Mitochondrion (Potential)	mitochondrial inner membrane [IDA]			176

You are viewing entries 35501 to 35550 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.