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
Q673L6 UniProt NPD GO	TERT_RAT	Telomerase reverse transcriptase (EC 2.7.7.49) (Telomerase catalytic subunit)	0.68	-	nuc	0	Nucleus				1125
O14746 UniProt NPD GO	TERT_HUMAN	Telomerase reverse transcriptase (EC 2.7.7.49) (Telomerase catalytic subunit) (HEST2) (Telomerase-as ...	0.68	-	nuc	0	Nucleus	chromosome, telomeric region [IC] telomerase holoenzyme complex [IDA]	187270	2BCK	1132
Q6ZPJ0 UniProt NPD GO	TEX2_MOUSE	Testis-expressed sequence 2 protein	0.68	-	nuc	2	Membrane; multi-pass membrane protein (Potential)				1128
Q9BXA7 UniProt NPD GO	TSSK1_HUMAN	Testis-specific serine/threonine-protein kinase 1 (EC 2.7.11.1) (TSSK-1) (Testis-specific kinase 1) ...	0.68	-	nuc	0					367
Q8K2W3 UniProt NPD GO	TXD11_MOUSE	Thioredoxin domain-containing protein 11	0.68	+	mit	0	Endoplasmic reticulum (By similarity)				948
O57568 UniProt NPD GO	THA_SPAAU	Thyroid hormone receptor alpha (Fragment)	0.68	+	nuc	0	Nucleus				129
P37242 UniProt NPD GO	THB1_MOUSE	Thyroid hormone receptor beta-1	0.68	+	cyt	0	Nucleus	nucleus [TAS]			461
Q95168 UniProt NPD GO	ZO2_CANFA	Tight junction protein ZO-2 (Zonula occludens 2 protein) (Zona occludens 2 protein) (Tight junction ...	0.68	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side (By similarity). Nucleus (By similarity ...				1174
Q5I2M5 UniProt NPD GO	TLR9_BOVIN	Toll-like receptor 9 precursor (CD289 antigen)	0.68	-	end	0	Membrane; single-pass type I membrane protein (By similarity)				1029
P23771 UniProt NPD GO	GATA3_HUMAN	Trans-acting T-cell-specific transcription factor GATA-3 (GATA-binding factor 3)	0.68	-	nuc	0	Nucleus		146255		443
Q4KLL0 UniProt NPD GO	TCEA1_RAT	Transcription elongation factor A protein 1 (Transcription elongation factor S-II protein 1)	0.68	+	nuc	0	Nucleus (By similarity)				301
P23193 UniProt NPD GO	TCEA1_HUMAN	Transcription elongation factor A protein 1 (Transcription elongation factor S-II protein 1) (Transc ...	0.68	+	nuc	0	Nucleus		601425	1TFI	301
P10711 UniProt NPD GO	TCEA1_MOUSE	Transcription elongation factor A protein 1 (Transcription elongation factor S-II protein 1) (Transc ...	0.68	+	nuc	0	Nucleus	nucleoplasm [IDA]			301
Q63799 UniProt NPD GO	TCEA2_RAT	Transcription elongation factor A protein 2 (Transcription elongation factor S-II protein 2) (Testis ...	0.68	-	nuc	0	Nucleus	nucleus [TAS]			299
O00267 UniProt NPD GO	SPT5H_HUMAN	Transcription elongation factor SPT5 (hSPT5) (DRB sensitivity-inducing factor large subunit) (DSIF l ...	0.68	-	nuc	0	Nucleus		602102		1087
Q6NZH6 UniProt NPD GO	TFCP2_XENTR	Transcription factor CP2	0.68	-	nuc	0	Nucleus (By similarity)				507
P15806 UniProt NPD GO	TFE2_MOUSE	Transcription factor E2-alpha (Immunoglobulin enhancer-binding factor E12/E47) (Transcription factor ...	0.68	-	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IDA]			651
Q61501 UniProt NPD GO	E2F1_MOUSE	Transcription factor E2F1 (E2F-1)	0.68	+	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA] transcription factor complex [IDA]			430
Q9BWX5 UniProt NPD GO	GATA5_HUMAN	Transcription factor GATA-5 (GATA-binding factor 5)	0.68	-	nuc	0	Nucleus (By similarity)				397
Q9H6I2 UniProt NPD GO	SOX17_HUMAN	Transcription factor SOX-17	0.68	+	nuc	0	Nucleus (Potential)				414
P53784 UniProt NPD GO	SOX3_MOUSE	Transcription factor SOX-3	0.68	+	nuc	0	Nucleus				375
O75410 UniProt NPD GO	TACC1_HUMAN	Transforming acidic coiled-coil-containing protein 1 (Taxin 1) (Gastric cancer antigen Ga55)	0.68	-	nuc	0	Cytoplasm. Nucleus. Nucleus during interphase. Weakly concentrated at centrosomes during mitosis		605301		805
P47023 UniProt NPD GO	YJL4_YEAST	Transposon Ty4 48.0 kDa hypothetical protein	0.68	-	nuc	0					414
Q9Y577 UniProt NPD GO	TRI17_HUMAN	Tripartite motif-containing protein 17 (Testis RING finger protein) (RING finger protein 16)	0.68	-	nuc	0			606123		477
Q9BZR9 UniProt NPD GO	TRIM8_HUMAN	Tripartite motif-containing protein 8 (RING finger protein 27) (Glioblastoma-expressed RING finger p ...	0.68	-	nuc	0			606125		551
O44572 UniProt NPD GO	TNNI4_CAEEL	Troponin I 4 (TnI 4)	0.68	+	nuc	0					194
P27768 UniProt NPD GO	TNNI2_RAT	Troponin I, fast skeletal muscle (Troponin I, fast-twitch isoform)	0.68	-	nuc	0					181
Q9GKK5 UniProt NPD GO	TBG1_CANFA	Tubulin gamma-1 chain (Gamma-1 tubulin) (Gamma-tubulin complex component 1) (GCP-1)	0.68	+	cyt	0	Centrosome (By similarity)	centrosome [ISS] cytoplasm [ISS] gamma-tubulin complex [ISS] polar microtubule [ISS] spindle pole body [ISS]			451
P83887 UniProt NPD GO	TBG1_MOUSE	Tubulin gamma-1 chain (Gamma-1 tubulin) (Gamma-tubulin complex component 1) (GCP-1)	0.68	+	cyt	0	Centrosome (By similarity)	condensed nuclear chromosome [IDA] cytoplasm [IDA] cytoplasmic microtubule [IDA] gamma-tubulin complex [ISS] pericentriolar material [IDA] polar microtubule [ISS] spindle pole body [ISS]			451
P83888 UniProt NPD GO	TBG1_RAT	Tubulin gamma-1 chain (Gamma-1 tubulin) (Gamma-tubulin complex component 1) (GCP-1)	0.68	+	cyt	0	Centrosome (By similarity)	centrosome [ISS] cytoplasm [ISS] gamma-tubulin complex [ISS] polar microtubule [ISS] spindle pole body [ISS]			451
P23330 UniProt NPD GO	TBG1_XENLA	Tubulin gamma-1 chain (Gamma-1 tubulin) (xGAM)	0.68	+	cyt	0		centrosome [ISS] cytoplasm [ISS] gamma-tubulin complex [ISS] polar microtubule [ISS] spindle pole body [ISS]			451
P61407 UniProt NPD GO	TDRD6_MOUSE	Tudor domain-containing protein 6	0.68	-	mit	0		polar granule [IDA]			2134
P19438 UniProt NPD GO	TNR1A_HUMAN	Tumor necrosis factor receptor superfamily member 1A precursor (p60) (TNF-R1) (TNF-RI) (TNFR-I) (p55 ...	0.68	-	nuc	2 *	Cell membrane; single-pass type I membrane protein. Secreted protein	extracellular region [NAS] integral to plasma membrane [TAS]	142680	1TNR	455
Q63199 UniProt NPD GO	TNR6_RAT	Tumor necrosis factor receptor superfamily member 6 precursor (FASLG receptor) (Apoptosis-mediating ...	0.68	-	exc	1	Membrane; single-pass type I membrane protein	caveola [IEP]			324
Q04604 UniProt NPD GO	TYRO_RANNI	Tyrosinase precursor (EC 1.14.18.1) (Monophenol monooxygenase)	0.68	-	nuc	1	Melanosome; melanosomal membrane; single-pass type I membrane protein				532
O42091 UniProt NPD GO	TY3H_ANGAN	Tyrosine 3-monooxygenase (EC 1.14.16.2) (Tyrosine 3-hydroxylase) (TH)	0.68	-	cyt	0					488
P35992 UniProt NPD GO	PTP10_DROME	Tyrosine-protein phosphatase 10D precursor (EC 3.1.3.48) (Receptor-linked protein-tyrosine phosphata ...	0.68	-	nuc	1	Membrane; single-pass type I membrane protein				1631
P35821 UniProt NPD GO	PTN1_MOUSE	Tyrosine-protein phosphatase non-receptor type 1 (EC 3.1.3.48) (Protein-tyrosine phosphatase 1B) (PT ...	0.68	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...				432
Q04305 UniProt NPD GO	UTP15_YEAST	U3 small nucleolar RNA-associated protein 15 (U3 snoRNA-associated protein 15)	0.68	-	mit	0	Nucleus; nucleolus	small nucleolar ribonucleoprotein complex [IPI]			513
P32571 UniProt NPD GO	UBP4_YEAST	Ubiquitin carboxyl-terminal hydrolase 4 (EC 3.1.2.15) (Ubiquitin thioesterase 4) (Ubiquitin-specific ...	0.68	-	nuc	0		membrane fraction [IDA] mitochondrion [IDA] proteasome complex (sensu Eukaryota) [IPI]			926
Q8BWR4 UniProt NPD GO	UBP40_MOUSE	Ubiquitin carboxyl-terminal hydrolase 40 (EC 3.1.2.15) (Ubiquitin thioesterase 40) (Ubiquitin-specif ...	0.68	-	cyt	0					1140
Q9UBT2 UniProt NPD GO	ULE1B_HUMAN	Ubiquitin-like 1-activating enzyme E1B (SUMO-1-activating enzyme subunit 2) (Anthracycline-associate ...	0.68	-	mit	0				1Y8R	640
P79457 UniProt NPD GO	UTY_MOUSE	Ubiquitously transcribed Y chromosome tetratricopeptide repeat protein (Ubiquitously transcribed TPR ...	0.68	-	nuc	0	Nucleus (Potential)				1212
Q5EA86 UniProt NPD GO	CA037_BOVIN	Uncharacterized protein C1orf37 homolog	0.68	-	nuc	1					376
Q96HY6 UniProt NPD GO	CT116_HUMAN	Uncharacterized protein C20orf116 precursor	0.68	-	exc	1 *	Secreted protein (Potential)				314
Q9NUG4 UniProt NPD GO	CT160_HUMAN	Uncharacterized protein C20orf160	0.68	-	nuc	0					571
P30643 UniProt NPD GO	YNE4_CAEEL	Uncharacterized protein R08D7.4	0.68	+	nuc	0					121
P40078 UniProt NPD GO	YEV6_YEAST	Uncharacterized protein YER126C	0.68	-	nuc	0		nucleus [IDA]			261
P53272 UniProt NPD GO	YG34_YEAST	Uncharacterized protein YGR122W	0.68	-	nuc	0		cytoplasm [IDA]			402
P38815 UniProt NPD GO	YHQ5_YEAST	Uncharacterized protein YHR105W	0.68	-	nuc	0		endosome [IDA]			214

You are viewing entries 15001 to 15050 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.