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
P80002 UniProt NPD GO	PRT2_SEPOF	Spermatid-specific protein T2 [Contains: Spermatid-specific protein T2B; Sperm protamine SP2]	0.80	+	nuc	0	Nucleus				77
Q16629 UniProt NPD GO	SFRS7_HUMAN	Splicing factor, arginine/serine-rich 7 (Splicing factor 9G8)	0.80	+	nuc	0	Nucleus	nucleus [TAS]	600572		238
P40511 UniProt NPD GO	SPO22_YEAST	Sporulation-specific protein 22	0.80	-	nuc	0					975
Q9UPU9 UniProt NPD GO	SAMD4_HUMAN	Sterile alpha motif domain-containing protein 4	0.80	-	nuc	0					529
Q9Y751 UniProt NPD GO	ATG26_PICPA	Sterol 3-beta-glucosyltransferase (EC 2.4.1.173) (Autophagy-related protein 26) (UDP-glycosyltransfe ...	0.80	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Found in perivacuolar punctate structures and micr ...				1211
O59793 UniProt NPD GO	BIS1_SCHPO	Stress response protein bis1	0.80	+	nuc	0	Nucleus. During mitosis associates with the spindle microtubules				384
Q9W6S3 UniProt NPD GO	SIN1_CHICK	Stress-activated map kinase-interacting protein 1 (SAPK-interacting protein 1)	0.80	+	nuc	0					522
P50533 UniProt NPD GO	SMC2_XENLA	Structural maintenance of chromosome 2 (Chromosome-associated protein E) (Chromosome assembly protei ...	0.80	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). In interphase cells, the majority of the condens ...				1203
Q9ERA5 UniProt NPD GO	SMC4_MICAR	Structural maintenance of chromosomes 4-like 1 protein (Chromosome-associated polypeptide C) (XCAP-C ...	0.80	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). In interphase cells, the majority of the condens ...	condensin complex [ISS] nucleus [ISS]			1243
Q5F4B2 UniProt NPD GO	SWP70_CHICK	Switch-associated protein 70 (SWAP-70)	0.80	-	nuc	0	Cytoplasm (By similarity). Cell membrane (By similarity). Nucleus (By similarity). In resting B-cell ...				586
Q8K402 UniProt NPD GO	TBX22_MOUSE	T-box transcription factor TBX22 (T-box protein 22)	0.80	-	nuc	0	Nucleus (Potential)				517
Q9N428 UniProt NPD GO	TCL2_CAEEL	T-cell defective protein 2	0.80	+	nuc	0	Nucleus. Cytoplasm. Cytoplasmic in neurons and nuclear in T-cells				435
Q9NU19 UniProt NPD GO	TB22B_HUMAN	TBC1 domain family member 22B	0.80	-	nuc	0					505
O74995 UniProt NPD GO	TFH47_SCHPO	TFIIH basal transcription factor complex p47 subunit (Suppressor of stem-loop protein 1 homolog) (SS ...	0.80	-	nuc	0	Nucleus (Potential)	transcription factor TFIIH complex [TAS]			421
O70422 UniProt NPD GO	TF2H4_MOUSE	TFIIH basal transcription factor complex p52 subunit (Basic transcription factor 52 kDa subunit) (BT ...	0.80	+	cyt	0	Nucleus				463
Q8CHW1 UniProt NPD GO	THAP1_MOUSE	THAP domain-containing protein 1	0.80	+	nuc	0	Nucleus; nucleoplasm (By similarity). And PML nuclear bodies (By similarity)				210
Q9BUZ4 UniProt NPD GO	TRAF4_HUMAN	TNF receptor-associated factor 4 (Cysteine-rich domain associated with RING and Traf domains protein ...	0.80	-	nuc	0	Cytoplasm. Nucleus	nucleus [TAS]	602464		470
Q61382 UniProt NPD GO	TRAF4_MOUSE	TNF receptor-associated factor 4 (Cysteine-rich motif associated to RING and Traf domains protein 1) ...	0.80	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				470
O00939 UniProt NPD GO	TERT_EUPAE	Telomerase reverse transcriptase (EC 2.7.7.49) (Telomerase catalytic subunit) (Telomerase subunit P1 ...	0.80	+	nuc	0	Nucleus				1031
O43086 UniProt NPD GO	ELG1_SCHPO	Telomere length regulation protein elg1 (Telomere elongation suppressor elg1)	0.80	-	nuc	0		Elg1 RFC-like complex [IDA]			920
O75448 UniProt NPD GO	TR100_HUMAN	Thyroid hormone receptor-associated protein complex 100 kDa component (Trap100) (Thyroid hormone rec ...	0.80	-	mit	0	Nucleus	mediator complex [NAS] nucleus [IDA]	607000		989
Q9H3H9 UniProt NPD GO	TCAL2_HUMAN	Transcription elongation factor A protein-like 2 (TCEA-like protein 2) (Transcription elongation fac ...	0.80	-	nuc	0	Nucleus (Probable)				227
Q4WWH6 UniProt NPD GO	SPT6_ASPFU	Transcription elongation factor spt6 (Chromatin elongation factor spt6)	0.80	+	cyt	0	Nucleus (By similarity)				1420
P36402 UniProt NPD GO	TCF7_HUMAN	Transcription factor 7 (T-cell-specific transcription factor 1) (TCF-1) (T-cell factor 1)	0.80	+	nuc	0	Nucleus		189908		383
P43692 UniProt NPD GO	GATA5_CHICK	Transcription factor GATA-5 (GATA-binding factor 5)	0.80	-	nuc	0	Nucleus				391
Q92994 UniProt NPD GO	TF3B_HUMAN	Transcription factor IIIB 90 kDa subunit (TFIIIB90) (hTFIIIB90) (B-related factor 1) (BRF-1) (hBRF) ...	0.80	-	nuc	0	Nucleus (By similarity)	transcription factor TFIIIB complex [NAS]	604902		677
Q91731 UniProt NPD GO	SOX11_XENLA	Transcription factor SOX-11 (xSOX-11)	0.80	-	nuc	0	Nucleus (Potential)				382
P40646 UniProt NPD GO	SOX7_MOUSE	Transcription factor SOX-7 (mSOX7)	0.80	+	nuc	0	Nucleus (Probable)				380
Q22703 UniProt NPD GO	TDP1_CAEEL	Transcription factor dpl-1	0.80	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			598
P98152 UniProt NPD GO	TF65_CHICK	Transcription factor p65 (Nuclear factor NF-kappa-B p65 subunit)	0.80	-	nuc	0	Nucleus. Cytoplasm. Nuclear, but also found in the cytoplasm in an inactive form complexed to an inh ...				558
Q8VI33 UniProt NPD GO	TAF9_MOUSE	Transcription initiation factor TFIID subunit 9 (Transcription initiation factor TFIID 31 kDa subuni ...	0.80	-	nuc	0	Nucleus (By similarity)				264
Q9EPI8 UniProt NPD GO	MTERF_RAT	Transcription termination factor, mitochondrial precursor (mTERF) (Mitochondrial transcription termi ...	0.80	-	mit	0	Mitochondrion				374
P19018 UniProt NPD GO	TRA2_DROME	Transformer-2 sex-determining protein	0.80	-	nuc	0					264
Q8K1S5 UniProt NPD GO	TIEG3_MOUSE	Transforming growth factor-beta-inducible early growth response protein 3 (TGFB-inducible early grow ...	0.80	-	nuc	0	Nucleus (Probable)	nucleus [IC]			502
Q2T9Z0 UniProt NPD GO	TRI17_BOVIN	Tripartite motif-containing protein 17	0.80	+	nuc	0					475
Q61037 UniProt NPD GO	TSC2_MOUSE	Tuberin (Tuberous sclerosis 2 homolog protein)	0.80	-	end	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). At steady state fo ...				1814
Q9XSK8 UniProt NPD GO	P73_CERAE	Tumor protein p73 (p53-like transcription factor) (p53-related protein)	0.80	+	nuc	0	Nucleus				637
O15350 UniProt NPD GO	P73_HUMAN	Tumor protein p73 (p53-like transcription factor) (p53-related protein)	0.80	+	nuc	0	Nucleus		601990	1DXS	636
Q8MI03 UniProt NPD GO	TWST1_PANTR	Twist-related protein 1	0.80	-	nuc	0	Nucleus (By similarity)				201
Q93WK5 UniProt NPD GO	APRR7_ARATH	Two-component response regulator-like APRR7 (Pseudo-response regulator 7)	0.80	+	nuc	0	Nucleus	mitochondrion [IDA]			727
Q689G6 UniProt NPD GO	PRR95_ORYSA	Two-component response regulator-like PRR95 (Pseudo-response regulator 95) (OsPRR95)	0.80	+	nuc	0	Nucleus (Probable)				623
Q9FUR2 UniProt NPD GO	IP5P2_ARATH	Type I inositol-1,4,5-trisphosphate 5-phosphatase 2 (EC 3.1.3.56) (At5PTase2)	0.80	-	nuc	0					646
Q9Z139 UniProt NPD GO	ROR1_MOUSE	Tyrosine-protein kinase transmembrane receptor ROR1 precursor (EC 2.7.10.1) (Neurotrophic tyrosine k ...	0.80	-	exc	1	Membrane; single-pass type I membrane protein				937
O13453 UniProt NPD GO	PMP1_SCHPO	Tyrosine-protein phosphatase pmp1 (EC 3.1.3.48)	0.80	-	nuc	0		cytoplasm [IDA]			278
P42945 UniProt NPD GO	UTP10_YEAST	U3 small nucleolar RNA-associated protein 10 (U3 snoRNA-associated protein 10)	0.80	+	end	0	Nucleus; nucleolus	mitochondrion [IDA] small nucleolar ribonucleoprotein complex [IPI]			1769
Q28BP9 UniProt NPD GO	UBXD8_XENTR	UBX domain-containing protein 8	0.80	+	cyt	0	Cytoplasm (By similarity)				445
O76064 UniProt NPD GO	RNF8_HUMAN	Ubiquitin ligase protein RNF8 (EC 6.3.2.-) (RING finger protein 8)	0.80	-	nuc	0	Nucleus			2CSW	485
Q17551 UniProt NPD GO	RPM1_CAEEL	Ubiquitin ligase protein rpm-1 (EC 6.3.2.-) (Pam/highwire/rpm-1 protein) (Regulator of presynaptic m ...	0.80	+	nuc	0	Nucleus (By similarity)				3766
P52488 UniProt NPD GO	UBA2_YEAST	Ubiquitin-activating enzyme E1-like (Polymerase-interacting protein 2)	0.80	-	nuc	0	Nucleus	nucleus [IDA]			636
Q7S304 UniProt NPD GO	BRE1_NEUCR	Ubiquitin-protein ligase bre-1 (EC 6.3.2.-)	0.80	-	nuc	0	Nucleus (By similarity)				707

You are viewing entries 9151 to 9200 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.