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
Q01389 UniProt NPD GO	BCK1_YEAST	Serine/threonine-protein kinase BCK1/SLK1/SSP31 (EC 2.7.11.1)	0.95	-	nuc	0	Cytoplasm (Potential)	intracellular [TAS]			1478
Q92212 UniProt NPD GO	STE20_CANAL	Serine/threonine-protein kinase CST20 (EC 2.7.11.1)	0.95	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1228
Q59LR2 UniProt NPD GO	ATR_CANAL	Serine/threonine-protein kinase MEC1 (EC 2.7.11.1) (DNA-damage checkpoint kinase MEC1) (Mitosis entr ...	0.95	+	gol	0	Nucleus. Localizes to nuclear DNA repair foci in response to DNA double strand breaks (By similarity ...				2325
P38111 UniProt NPD GO	ATR_YEAST	Serine/threonine-protein kinase MEC1 (EC 2.7.11.1) (DNA-damage checkpoint kinase MEC1) (Mitosis entr ...	0.95	-	nuc	0	Nucleus. Localizes to nuclear DNA repair foci in response to DNA double strand breaks. The recruitme ...	mitochondrion [IDA] nucleus [IC]			2368
Q7TT50 UniProt NPD GO	MRCKB_MOUSE	Serine/threonine-protein kinase MRCK beta (EC 2.7.11.1) (CDC42-binding protein kinase beta) (Myotoni ...	0.95	+	nuc	0	Cytoplasm (By similarity). Displays a dispersed punctate distribution and concentrates along the cel ...	intercellular junction [ISS] leading edge [ISS]			1713
Q7Z8E9 UniProt NPD GO	STE20_MAGGR	Serine/threonine-protein kinase MST20 (EC 2.7.11.1)	0.95	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				914
P46549 UniProt NPD GO	SULU_CAEEL	Serine/threonine-protein kinase SULU (EC 2.7.11.1) (Protein kinase 18)	0.95	-	nuc	0					982
Q9H2K8 UniProt NPD GO	TAOK3_HUMAN	Serine/threonine-protein kinase TAO3 (EC 2.7.11.1) (Thousand and one amino acid protein 3) (Jun kina ...	0.95	-	nuc	0	Cytoplasm. Cell membrane; peripheral membrane protein. Also localized to the peripheral cell membran ...				898
Q9I9E0 UniProt NPD GO	TAOK3_CHICK	Serine/threonine-protein kinase TAO3 (EC 2.7.11.1) (Thousand and one amino acid protein 3) (Kinase f ...	0.95	-	nuc	0	Cytoplasm (By similarity)				898
Q07538 UniProt NPD GO	PRP4_SCHPO	Serine/threonine-protein kinase prp4 (EC 2.7.11.1)	0.95	+	nuc	0					477
Q4WHP3 UniProt NPD GO	STE20_ASPFU	Serine/threonine-protein kinase ste20 (EC 2.7.11.1)	0.95	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				986
Q863C2 UniProt NPD GO	SRY_AXIPR	Sex-determining region Y protein (Testis-determining factor)	0.95	+	nuc	0	Nucleus				229
Q9BH08 UniProt NPD GO	SRY_CERNI	Sex-determining region Y protein (Testis-determining factor)	0.95	+	nuc	0	Nucleus				229
Q863B7 UniProt NPD GO	SRY_ELADA	Sex-determining region Y protein (Testis-determining factor)	0.95	+	nuc	0	Nucleus				229
P08032 UniProt NPD GO	SPTA1_MOUSE	Spectrin alpha chain, erythrocyte (Erythroid alpha-spectrin)	0.95	-	nuc	0		spectrin [TAS]			2415
Q8S9L0 UniProt NPD GO	SPL10_ARATH	Squamosa promoter-binding-like protein 10	0.95	+	nuc	0	Nucleus (Probable)				396
Q9FZK0 UniProt NPD GO	SPL11_ARATH	Squamosa promoter-binding-like protein 11	0.95	+	nuc	0	Nucleus (Probable)				393
Q90988 UniProt NPD GO	SMC2_CHICK	Structural maintenance of chromosome 2 (Chromosome scaffold protein ScII)	0.95	+	nuc	0	Nucleus. Cytoplasm. In interphase cells, the majority of the condensin complex is found in the cytop ...				1189
P97690 UniProt NPD GO	SMC3_RAT	Structural maintenance of chromosome 3 (Chondroitin sulfate proteoglycan 6) (Chromosome segregation ...	0.95	-	nuc	0	Nucleus (By similarity). Associates with chromatin. Before prophase it is scattered along chromosome ...	basement membrane [IDA] cohesin complex [ISS] cytoplasm [ISS] nuclear matrix [ISS] spindle pole [ISS]			1191
O13710 UniProt NPD GO	SMC5_SCHPO	Structural maintenance of chromosome 5 (DNA repair protein spr18) (SMC partner of rad18)	0.95	-	nuc	0	Nucleus (Potential)	nucleus [IDA] Smc5-Smc6 complex [IDA]			1065
P70279 UniProt NPD GO	SURF6_MOUSE	Surfeit locus protein 6	0.95	+	nuc	0	Nucleus; nucleoplasm. Granular component of the nucleolus	granular component [IDA]			355
Q4R764 UniProt NPD GO	SYCP3_MACFA	Synaptonemal complex protein 3 (SCP-3)	0.95	-	nuc	0	Nucleus (By similarity). In tripartite segments of synaptonemal complexes, irrespective of whether t ...				236
Q2TBI2 UniProt NPD GO	THAP4_BOVIN	THAP domain-containing protein 4	0.95	-	nuc	0					570
Q03560 UniProt NPD GO	YKD1_CAEEL	TPR repeat-containing protein B0464.2	0.95	+	nuc	0					1150
Q9NRE2 UniProt NPD GO	TSH2_HUMAN	Teashirt homolog 2 (Zinc finger protein 218) (Ovarian cancer-related protein 10-2) (OVC10-2)	0.95	+	nuc	0	Nucleus (Probable)				1034
Q68FE9 UniProt NPD GO	TSH2_MOUSE	Teashirt homolog 2 (Zinc finger protein 218) (SDCCAG33-like protein)	0.95	+	nuc	0	Nucleus (Probable)				1030
Q63HK5 UniProt NPD GO	TSH3_HUMAN	Teashirt homolog 3 (Zinc finger protein 537)	0.95	-	nuc	0	Nucleus (Probable)				1081
Q8CGV9 UniProt NPD GO	TSH3_MOUSE	Teashirt homolog 3 (Zinc finger protein 537)	0.95	-	nuc	0	Nucleus (Probable)				1081
Q6PR54 UniProt NPD GO	RIF1_MOUSE	Telomere-associated protein RIF1 (Rap1-interacting factor 1 homolog) (mRif1)	0.95	-	nuc	0	Nucleus. Exhibits ATM- and TP53BP1-dependent localization to uncapped or aberrant telomeres and to D ...	chromosome, telomeric region [IDA] female pronucleus [IDA] male pronucleus [IDA] nucleus [IDA]			2419
O55036 UniProt NPD GO	TERF1_CRIGR	Telomeric repeat-binding factor 1 (TTAGGG repeat-binding factor 1) (Fragment)	0.95	-	nuc	0	Nucleus (By similarity). Colocalizes with telomeric DNA in interphase and metaphase cells and is loc ...				438
Q8IWB6 UniProt NPD GO	TEX14_HUMAN	Testis-expressed protein 14 (Testis-expressed sequence 14)	0.95	-	nuc	0	Cytoplasm. Detected in the intercellular bridges that connect male germ cell daughter cells after ce ...		605792		1497
P53804 UniProt NPD GO	TTC3_HUMAN	Tetratricopeptide repeat protein 3 (TPR repeat protein 3) (TPR repeat protein D)	0.95	+	nuc	0			602259		2025
Q02777 UniProt NPD GO	THA_RANCA	Thyroid hormone receptor alpha	0.95	+	nuc	0	Nucleus				418
O97716 UniProt NPD GO	THA_PIG	Thyroid hormone receptor alpha (C-erbA-alpha) (c-erbA-1)	0.95	+	nuc	0	Nucleus				506
Q91241 UniProt NPD GO	THAA_PAROL	Thyroid hormone receptor alpha A (THR-alpha-A)	0.95	+	nuc	0	Nucleus				416
Q9R1X4 UniProt NPD GO	TIM_MOUSE	Timeless homolog (mTim)	0.95	+	nuc	0	Nucleus	nucleus [IDA]			1197
P70062 UniProt NPD GO	T7L1A_XENLA	Transcription factor 7-like 1-A (HMG box transcription factor 3-A) (TCF-3-A) (xTcf-3)	0.95	+	nuc	0	Cytoplasm. Nucleus			1G3J	554
Q90ZB6 UniProt NPD GO	T7L1B_XENLA	Transcription factor 7-like 1-B (HMG box transcription factor 3-B) (TCF-3-B) (xTcf-3)	0.95	+	nuc	0	Nucleus				551
P70063 UniProt NPD GO	T7L1C_XENLA	Transcription factor 7-like 1-C (HMG box transcription factor 3-C) (TCF-3-C) (xTcf-3c)	0.95	+	nuc	0	Nucleus (By similarity)				550
P05412 UniProt NPD GO	JUN_HUMAN	Transcription factor AP-1 (Activator protein 1) (AP1) (Proto-oncogene c-jun) (V-jun avian sarcoma vi ...	0.95	+	nuc	0	Nucleus	nuclear chromosome [TAS]	165160	1T2K	331
P12981 UniProt NPD GO	JUN_COTJA	Transcription factor AP-1 (Proto-oncogene c-jun)	0.95	+	nuc	0	Nucleus				313
Q12734 UniProt NPD GO	CSR2_YEAST	Transcription factor CSR2 (CHS5 SPA2 rescue protein 2)	0.95	+	nuc	0	Cytoplasm. Nucleus	nucleus [IDA]			1121
Q9BG91 UniProt NPD GO	SOX9_CALJA	Transcription factor SOX-9	0.95	+	nuc	0	Nucleus (Potential)				509
P48434 UniProt NPD GO	SOX9_CHICK	Transcription factor SOX-9	0.95	+	nuc	0	Nucleus (Potential)				494
P48436 UniProt NPD GO	SOX9_HUMAN	Transcription factor SOX-9	0.95	+	nuc	0	Nucleus (Potential)	nucleus [TAS]	114290	1SX9	509
P61753 UniProt NPD GO	SOX9_MACMU	Transcription factor SOX-9	0.95	+	nuc	0	Nucleus (Potential)				509
Q04887 UniProt NPD GO	SOX9_MOUSE	Transcription factor SOX-9	0.95	+	nuc	0	Nucleus (Potential)	nucleus [IDA]			507
O18896 UniProt NPD GO	SOX9_PIG	Transcription factor SOX-9	0.95	+	nuc	0	Nucleus (Potential)				509
P61754 UniProt NPD GO	SOX9_PONPY	Transcription factor SOX-9	0.95	+	nuc	0	Nucleus (Potential)				509
P46678 UniProt NPD GO	TFC5_YEAST	Transcription factor TFIIIB B'' component (TFIIIB90)	0.95	+	nuc	0	Nucleus	transcription factor TFIIIB complex [TAS]			594

You are viewing entries 2101 to 2150 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.