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
Q2HJ67 UniProt NPD GO	HXA5_BOVIN	Homeobox protein Hox-A5	0.62	+	nuc	0	Nucleus (By similarity)				270
Q9YGT4 UniProt NPD GO	HXB6B_BRARE	Homeobox protein Hox-B6b (Hox-A7)	0.62	+	nuc	0	Nucleus (By similarity)				224
P18864 UniProt NPD GO	HXB7_RAT	Homeobox protein Hox-B7	0.62	+	nuc	0	Nucleus				219
P31262 UniProt NPD GO	HXC5_NOTVI	Homeobox protein Hox-C5 (NvHbox-3.4) (Fragment)	0.62	+	nuc	0	Nucleus				71
Q9PWM5 UniProt NPD GO	HXC6B_BRARE	Homeobox protein Hox-C6b	0.62	+	nuc	0	Nucleus (By similarity)				227
P18866 UniProt NPD GO	HXC8_RAT	Homeobox protein Hox-C8 (R4) (Fragment)	0.62	+	nuc	0	Nucleus				108
P14159 UniProt NPD GO	HXD4_SHEEP	Homeobox protein Hox-D4 (Homeobox protein Hox-8.1) (OHox-8.1) (Fragment)	0.62	-	nuc	0	Nucleus (Potential)				46
P10628 UniProt NPD GO	HXD4_MOUSE	Homeobox protein Hox-D4 (Hox-4.2) (Hox-5.1)	0.62	+	nuc	0	Nucleus				250
P15856 UniProt NPD GO	ABDA_APIME	Homeobox protein abdominal-A homolog (H15) (Fragment)	0.62	+	nuc	0	Nucleus (Probable)				74
P56666 UniProt NPD GO	KNOX8_MAIZE	Homeobox protein knotted-1-like 8 (Fragment)	0.62	-	nuc	0	Nucleus (Probable)				85
Q8WP28 UniProt NPD GO	HIPK4_MACFA	Homeodomain-interacting protein kinase 4 (EC 2.7.11.1)	0.62	-	nuc	0	Cytoplasm (Probable)				616
P53187 UniProt NPD GO	HOP2_YEAST	Homologous pairing protein 2	0.62	-	nuc	0	Nucleus	condensed nuclear chromosome [IDA]			203
P53947 UniProt NPD GO	YNF8_YEAST	Hypothetical 35.0 kDa protein in ARP5-OMP2 intergenic region	0.62	+	nuc	1	Membrane; multi-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			316
P36083 UniProt NPD GO	YKH5_YEAST	Hypothetical 52.1 kDa protein in SMY1-MUD2 intergenic region	0.62	-	nuc	0		cytoplasm [IDA]			450
Q04847 UniProt NPD GO	YM8A_YEAST	Hypothetical 64.4 kDa protein in PET111-TIF11 intergenic region	0.62	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			553
P38769 UniProt NPD GO	YHJ5_YEAST	Hypothetical 72.3 kDa protein in SLT2-PUT2 intergenic region	0.62	-	nuc	0					630
P47139 UniProt NPD GO	YJ68_YEAST	Hypothetical 74.1 kDa protein in ACR1-YUH1 intergenic region	0.62	-	nuc	0		cytoplasm [IDA] mitochondrion [IDA]			655
O13674 UniProt NPD GO	YCQ9_SCHPO	Hypothetical RNA-binding protein C74.09 in chromosome III	0.62	-	nuc	0					654
O13920 UniProt NPD GO	YDWH_SCHPO	Hypothetical protein C23C11.17 in chromosome I	0.62	-	mit	1					485
Q9Y7T1 UniProt NPD GO	YCJ5_SCHPO	Hypothetical protein C63.05 in chromosome III	0.62	-	nuc	0					323
Q8ST90 UniProt NPD GO	Y201_ENCCU	Hypothetical protein ECU02_0010/ECU04_1710	0.62	-	mit	0					220
Q8SWH7 UniProt NPD GO	Y205_ENCCU	Hypothetical protein ECU02_0050	0.62	-	nuc	0					523
Q8SW86 UniProt NPD GO	Y2F4_ENCCU	Hypothetical protein ECU02_1540	0.62	+	exc	0					616
Q8SV64 UniProt NPD GO	Y6G1_ENCCU	Hypothetical protein ECU06_1610	0.62	-	exc	0					607
Q9C104 UniProt NPD GO	YKT5_SCHPO	Hypothetical protein PB1E7.05 in chromosome I	0.62	-	nuc	0					1076
Q09416 UniProt NPD GO	YRM7_CAEEL	Hypothetical protein R06F6.7 precursor	0.62	-	exc	1 *					120
Q10043 UniProt NPD GO	YRP1_CAEEL	Hypothetical protein R10H1.1	0.62	-	nuc	0					161
P91478 UniProt NPD GO	YOK3_CAEEL	Hypothetical protein T20F5.3 in chromosome I	0.62	-	nuc	1					369
P34595 UniProt NPD GO	YOD3_CAEEL	Hypothetical protein ZC262.3 in chromosome III	0.62	-	nuc	1					773
Q6ZMZ0 UniProt NPD GO	IBRD3_HUMAN	IBR domain-containing protein 3	0.62	-	mit	2	Membrane; multi-pass membrane protein (Potential)				486
Q8VYE2 UniProt NPD GO	TIM50_ARATH	Import inner membrane translocase subunit TIM50, mitochondrial precursor	0.62	-	mit	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein	mitochondrion [IDA]			376
Q9W0S3 UniProt NPD GO	TI50B_DROME	Import inner membrane translocase subunit TIM50-B, mitochondrial precursor	0.62	-	mit	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)	mitochondrial inner membrane presequence tr... [ISS] nuclear speck [ISS]			409
O15131 UniProt NPD GO	IMA5_HUMAN	Importin alpha-6 subunit (Karyopherin alpha-5 subunit)	0.62	-	nuc	0	Cytoplasm		604545		536
Q9EPL8 UniProt NPD GO	IPO7_MOUSE	Importin-7 (Imp7) (Ran-binding protein 7) (RanBP7)	0.62	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				1038
P08476 UniProt NPD GO	INHBA_HUMAN	Inhibin beta A chain precursor (Activin beta-A chain) (Erythroid differentiation protein) (EDF)	0.62	+	nuc	0	Secreted protein	extracellular region [TAS]	147290	2B0U	426
P23677 UniProt NPD GO	IP3KA_HUMAN	Inositol-trisphosphate 3-kinase A (EC 2.7.1.127) (Inositol 1,4,5-trisphosphate 3-kinase A) (IP3K A) ...	0.62	-	nuc	0			147521	1W2F	461
Q7TS72 UniProt NPD GO	IP3KC_MOUSE	Inositol-trisphosphate 3-kinase C (EC 2.7.1.127) (Inositol 1,4,5-trisphosphate 3-kinase C) (IP3K-C)	0.62	-	nuc	0	Nucleus. Cytoplasm. Shuttles actively between nucleus and cytoplasm with both nuclear import and nuc ...				678
P53410 UniProt NPD GO	ISL2_CHICK	Insulin gene enhancer protein ISL-2 (Islet-2) (Fragment)	0.62	+	nuc	0	Nucleus				319
Q4R7B1 UniProt NPD GO	INT10_MACFA	Integrator complex subunit 10	0.62	-	cyt	0	Nucleus (By similarity)				699
Q9NVR2 UniProt NPD GO	INT10_HUMAN	Integrator complex subunit 10 (Int10)	0.62	-	cyt	0	Nucleus				710
Q865Y4 UniProt NPD GO	IFNG_PAPAN	Interferon gamma precursor (IFN-gamma)	0.62	-	mit	0	Secreted protein (By similarity)				165
Q13325 UniProt NPD GO	IFIT5_HUMAN	Interferon-induced protein with tetratricopeptide repeats 5 (IFIT-5) (Retinoic acid- and interferon- ...	0.62	-	cyt	0					482
P78413 UniProt NPD GO	IRX4_HUMAN	Iroquois-class homeodomain protein IRX-4 (Iroquois homeobox protein 4) (Homeodomain protein IRXA3)	0.62	-	nuc	0	Nucleus (Probable)		606199		519
Q9ZPC0 UniProt NPD GO	ICS_CATRO	Isochorismate synthase, chloroplast precursor (EC 5.4.4.2)	0.62	-	mit	0	Plastid; chloroplast (Potential)				580
P48526 UniProt NPD GO	SYIM_YEAST	Isoleucyl-tRNA synthetase, mitochondrial (EC 6.1.1.5) (Isoleucine--tRNA ligase) (IleRS)	0.62	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			1002
Q6B0I6 UniProt NPD GO	JHD3D_HUMAN	JmjC domain-containing histone demethylation protein 3D (EC 1.14.11.-) (Jumonji domain-containing pr ...	0.62	-	nuc	0	Nucleus (By similarity)		609766		520
Q9ET78 UniProt NPD GO	JPH2_MOUSE	Junctophilin-2 (Junctophilin type 2) (JP-2)	0.62	+	nuc	1	Cell membrane; peripheral membrane protein. Endoplasmic reticulum; endoplasmic reticulum membrane; s ...	membrane fraction [IDA] microsome [IDA] sarcoplasmic reticulum [IDA] Z disc [IDA]			696
Q6FL35 UniProt NPD GO	SMI1_CANGA	KNR4/SMI1 homolog	0.62	+	nuc	0					584
P04104 UniProt NPD GO	K2C1_MOUSE	Keratin, type II cytoskeletal 1 (Cytokeratin-1) (CK-1) (Keratin-1) (K1) (67 kDa cytokeratin)	0.62	+	nuc	0					627
P08776 UniProt NPD GO	K2C8_XENLA	Keratin, type II cytoskeletal 8 (Cytokeratin-8) (CK-8) (Keratin-8) (K8)	0.62	-	mit	0					502

You are viewing entries 17951 to 18000 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.