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
Q689G8 UniProt NPD GO	PRR37_ORYSA	Two-component response regulator-like PRR37 (Pseudo-response regulator 37) (OsPRR37)	0.86	-	nuc	0	Nucleus (Probable)				742
P28191 UniProt NPD GO	PTP1_CAEEL	Tyrosine-protein phosphatase 1 (EC 3.1.3.48) (Protein-tyrosine phosphatase 1)	0.86	-	nuc	0					1026
P35832 UniProt NPD GO	PTP99_DROME	Tyrosine-protein phosphatase 99A precursor (EC 3.1.3.48) (Receptor-linked protein-tyrosine phosphata ...	0.86	-	exc	1	Membrane; single-pass type I membrane protein				1301
Q9W0G1 UniProt NPD GO	PTP61_DROME	Tyrosine-protein phosphatase non-receptor type 61F (EC 3.1.3.48) (dPTP61F)	0.86	+	nuc	1	Isoform A: Cytoplasm. Isoform B: Nucleus. Isoform A associates with the membranes of the reticular n ...	cytoplasm [IDA] mitochondrial envelope [IDA] nucleus [IDA]			548
Q5R761 UniProt NPD GO	SNUT2_PONPY	U4/U6.U5 tri-snRNP-associated protein 2 (Inactive ubiquitin-specific peptidase 39)	0.86	-	nuc	0	Nucleus (By similarity)				565
Q53GS9 UniProt NPD GO	SNUT2_HUMAN	U4/U6.U5 tri-snRNP-associated protein 2 (U4/U6.U5 tri-snRNP-associated 65 kDa protein) (65K) (Inacti ...	0.86	-	nuc	0	Nucleus				565
Q01408 UniProt NPD GO	UVE1_NEUCR	UV-damage endonuclease (EC 3.-.-.-) (UV-endonuclease UVE-1)	0.86	-	nuc	0					656
Q04748 UniProt NPD GO	YMV6_YEAST	Uncharacterized protein YMR066W	0.86	-	mit	0		mitochondrion [IDA]			898
P53901 UniProt NPD GO	YNP2_YEAST	Uncharacterized protein YNL152W	0.86	-	nuc	0		cytoplasm [IDA]			409
Q9V7N5 UniProt NPD GO	VATC_DROME	Vacuolar ATP synthase subunit C (EC 3.6.3.14) (V-ATPase C subunit) (Vacuolar proton pump C subunit)	0.86	-	nuc	0					714
P67964 UniProt NPD GO	VEGFA_CHICK	Vascular endothelial growth factor A precursor (VEGF-A) (Vascular permeability factor) (VPF)	0.86	+	nuc	0					216
P67965 UniProt NPD GO	VEGFA_COTJA	Vascular endothelial growth factor A precursor (VEGF-A) (Vascular permeability factor) (VPF)	0.86	+	nuc	0		extracellular region [NAS]			216
P35969 UniProt NPD GO	VGFR1_MOUSE	Vascular endothelial growth factor receptor 1 precursor (EC 2.7.10.1) (VEGFR-1) (Tyrosine-protein ki ...	0.86	-	nuc	0	Membrane; single-pass type I membrane protein				1333
P50551 UniProt NPD GO	VASP_CANFA	Vasodilator-stimulated phosphoprotein (VASP)	0.86	-	nuc	0	Cytoplasm. Targeted to stress fibers and focal adhesions through interaction with a number of protei ...				383
P29788 UniProt NPD GO	VTNC_MOUSE	Vitronectin precursor (Serum-spreading factor) (S-protein)	0.86	-	exc	0	Secreted protein; extracellular space	extracellular matrix (sensu Metazoa) [IDA]			478
O75717 UniProt NPD GO	WDHD1_HUMAN	WD repeat and HMG-box DNA-binding protein 1 (Acidic nucleoplasmic DNA-binding protein 1) (And-1)	0.86	+	nuc	0	Nucleus; nucleoplasm (By similarity)	cytoplasm [TAS] nucleoplasm [TAS]	608126		1129
P47025 UniProt NPD GO	YJL2_YEAST	WD repeat protein YJL112W	0.86	-	nuc	0		mitochondrial outer membrane [IDA]			714
P32330 UniProt NPD GO	YKM1_YEAST	WD repeat protein YKL121W	0.86	-	nuc	0					852
Q8R5H6 UniProt NPD GO	WASF1_MOUSE	Wiskott-Aldrich syndrome protein family member 1 (WASP-family protein member 1) (Protein WAVE-1)	0.86	+	nuc	0	Cytoplasm (By similarity). Dot-like pattern in the cytoplasm. Concentrated in Rac-regulated membrane ...	lamellipodium [IDA] mitochondrial outer membrane [IDA] mitochondrion [IDA]			559
Q9R1S4 UniProt NPD GO	XBP1_RAT	X box-binding protein 1 (Hepatocarcinogenesis-related transcription factor) (HTF)	0.86	+	exc	1	Nucleus				267
Q61806 UniProt NPD GO	XL3B_MOUSE	X-linked lymphocyte-regulated protein 3A (XLR-related protein A12)	0.86	-	nuc	0					226
Q9UGR2 UniProt NPD GO	Z3H7B_HUMAN	Zinc finger CCCH-type domain-containing protein 7B (Rotavirus 'X'-associated non-structural protein) ...	0.86	-	nuc	0	Nucleus (Probable)				993
Q9C086 UniProt NPD GO	ZNHI4_HUMAN	Zinc finger HIT domain-containing protein 4 (PAP-1-associated protein 1) (PAPA-1) (High mobility gro ...	0.86	+	nuc	0	Nucleus; nucleolus				343
O88553 UniProt NPD GO	ZFP37_RAT	Zinc finger protein 37 (Zfp-37)	0.86	-	nuc	0	Nucleus (Probable)				601
Q96N95 UniProt NPD GO	ZN396_HUMAN	Zinc finger protein 396 (Zinc finger and SCAN domain-containing protein 14)	0.86	-	nuc	0	Isoform 1, isoform 2: Nucleus. Isoform 2: Cytoplasm	cytoplasm [IMP] nucleus [IMP]	609600		335
Q63HK3 UniProt NPD GO	ZN694_HUMAN	Zinc finger protein 694	0.86	-	nuc	0	Nucleus (Probable)				967
Q4V8A8 UniProt NPD GO	ZFP90_RAT	Zinc finger protein 90 (Zfp-90)	0.86	-	nuc	0	Nucleus (By similarity)				633
Q8NEA6 UniProt NPD GO	GLIS3_HUMAN	Zinc finger protein GLIS3 (GLI-similar 3) (Zinc finger protein 515)	0.86	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			774
Q8IX07 UniProt NPD GO	FOG1_HUMAN	Zinc finger protein ZFPM1 (Zinc finger protein multitype 1) (Friend of GATA protein 1) (Friend of GA ...	0.86	-	nuc	0	Nucleus (By similarity)		601950		1004
Q6ZN30 UniProt NPD GO	BNC2_HUMAN	Zinc finger protein basonuclin-2	0.86	+	nuc	0	Nucleus		608669		1099
Q8BMQ3 UniProt NPD GO	BNC2_MOUSE	Zinc finger protein basonuclin-2	0.86	+	nuc	0	Nucleus	nucleus [IDA]			1127
P41073 UniProt NPD GO	PEP_DROME	Zinc finger protein on ecdysone puffs	0.86	-	nuc	0	Nucleus. It is associated with the active ecdysone-regulated loci on polytene chromosomes, and on so ...	heterogeneous nuclear ribonucleoprotein com... [IDA] polytene chromosome puff [IDA]			716
Q5R7F2 UniProt NPD GO	ZHX2_PONPY	Zinc fingers and homeoboxes protein 2 (Zinc finger and homeodomain protein 2)	0.86	-	mit	0	Nucleus (By similarity)				837
Q9Y6X8 UniProt NPD GO	ZHX2_HUMAN	Zinc fingers and homeoboxes protein 2 (Zinc finger and homeodomain protein 2) (Alpha-fetoprotein reg ...	0.86	-	mit	0	Nucleus	nucleus [IDA]	609185		837
P79145 UniProt NPD GO	CREM_CANFA	cAMP-responsive element modulator	0.86	+	nuc	0	Nucleus				344
Q03060 UniProt NPD GO	CREM_HUMAN	cAMP-responsive element modulator	0.86	+	nuc	0	Nucleus	nucleus [NAS]	123812		332
Q6FU45 UniProt NPD GO	RNA14_CANGA	mRNA 3'-end processing protein RNA14	0.86	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nucleus and/or cytoplasm (By similarity)				646
Q16533 UniProt NPD GO	SNPC1_HUMAN	snRNA-activating protein complex subunit 1 (SNAPc subunit 1) (snRNA-activating protein complex 43 kD ...	0.86	+	nuc	0	Nucleus		600591		368
Q5KJW1 UniProt NPD GO	TRM10_CRYNE	tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.31) (tRNA methyltransferase 10)	0.86	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				429
Q9NQ50 UniProt NPD GO	RM40_HUMAN	39S ribosomal protein L40, mitochondrial precursor (L40mt) (MRP-40) (Nuclear localization signal-con ...	0.85	+	nuc	0	Mitochondrion (By similarity)	mitochondrial ribosome [ISS] nucleus [TAS]	605089		206
P47838 UniProt NPD GO	RS6_CHICK	40S ribosomal protein S6	0.85	+	nuc	0					249
Q6C169 UniProt NPD GO	RS6_YARLI	40S ribosomal protein S6	0.85	-	nuc	0					242
O48549 UniProt NPD GO	RS6A_ARATH	40S ribosomal protein S6-1	0.85	-	nuc	0					250
P51430 UniProt NPD GO	RS6B_ARATH	40S ribosomal protein S6-2	0.85	-	nuc	0					249
Q03782 UniProt NPD GO	SNU56_YEAST	56 kDa U1 small nuclear ribonucleoprotein component	0.85	-	nuc	0	Nucleus	commitment complex [IPI] snRNP U1 [IDA]			492
Q42347 UniProt NPD GO	RL241_ARATH	60S ribosomal protein L24-1	0.85	-	nuc	0					164
P79244 UniProt NPD GO	RL37_BOVIN	60S ribosomal protein L37	0.85	-	nuc	0					96
Q9D823 UniProt NPD GO	RL37_MOUSE	60S ribosomal protein L37	0.85	-	nuc	0					96
P61928 UniProt NPD GO	RL37_RAT	60S ribosomal protein L37	0.85	-	nuc	0					96
P61927 UniProt NPD GO	RL37_HUMAN	60S ribosomal protein L37 (G1.16)	0.85	-	nuc	0			604181		96

You are viewing entries 6351 to 6400 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.