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
P53789 UniProt NPD GO	VTDB_RABIT	Vitamin D-binding protein precursor (DBP) (Group-specific component) (Gc-globulin) (VDB)	0.47	-	exc	0	Secreted protein				476
Q91V09 UniProt NPD GO	WDR13_MOUSE	WD repeat protein 13	0.47	-	mit	0	Nucleus (By similarity)				485
Q8NA75 UniProt NPD GO	WD21C_HUMAN	WD repeat protein 21C	0.47	-	mit	0					395
Q5RF51 UniProt NPD GO	WDR57_PONPY	WD repeat protein 57	0.47	-	mit	0	Nucleus (By similarity)				357
O80946 UniProt NPD GO	WBC1_ARATH	White-brown complex homolog protein 1	0.47	-	end	6	Membrane; multi-pass membrane protein (By similarity)				740
Q9MYW6 UniProt NPD GO	XDH_FELCA	Xanthine dehydrogenase/oxidase [Includes: Xanthine dehydrogenase (EC 1.17.1.4) (XD); Xanthine oxidas ...	0.47	-	nuc	0	Peroxisome (By similarity)				1330
Q9CWV7 UniProt NPD GO	ZSWM1_MOUSE	Zinc finger SWIM domain-containing protein 1	0.47	-	nuc	0		nucleus [IDA]			455
Q9HCK0 UniProt NPD GO	ZBT26_HUMAN	Zinc finger and BTB domain-containing protein 26 (Zinc finger protein 481) (Zinc finger protein Bior ...	0.47	-	nuc	0	Nucleus (Probable)				441
Q5TC79 UniProt NPD GO	ZBT37_HUMAN	Zinc finger and BTB domain-containing protein 37	0.47	-	nuc	0	Nucleus (Probable)				503
Q14584 UniProt NPD GO	ZN266_HUMAN	Zinc finger protein 266 (Zinc finger protein HZF1)	0.47	-	nuc	0	Nucleus (Probable)		604751		549
Q02525 UniProt NPD GO	ZFP39_MOUSE	Zinc finger protein 39 (Zfp-39) (CtFIN33) (Fragment)	0.47	-	nuc	0	Nucleus				201
Q5R5Y7 UniProt NPD GO	ZN436_PONPY	Zinc finger protein 436	0.47	-	nuc	0	Nucleus (Potential)				470
P15621 UniProt NPD GO	ZNF44_HUMAN	Zinc finger protein 44 (Zinc finger protein KOX7) (Gonadotropin-inducible transcription repressor 2) ...	0.47	-	nuc	0	Nucleus (Probable)		194542		589
Q6ZNH5 UniProt NPD GO	ZN497_HUMAN	Zinc finger protein 497	0.47	-	nuc	0	Nucleus (Potential)				498
Q5EBM4 UniProt NPD GO	ZN542_HUMAN	Zinc finger protein 542	0.47	-	nuc	0	Nucleus (Probable)				241
Q8TC21 UniProt NPD GO	ZN596_HUMAN	Zinc finger protein 596	0.47	-	nuc	0	Nucleus (Probable)				498
Q8WXB4 UniProt NPD GO	ZN606_HUMAN	Zinc finger protein 606 (Zinc finger protein 328)	0.47	-	nuc	0	Nucleus (Potential)				792
Q05481 UniProt NPD GO	ZNF91_HUMAN	Zinc finger protein 91 (Zinc finger protein HTF10) (HPF7)	0.47	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	603971		1191
P17349 UniProt NPD GO	DIS1_TRIEL	Zinc metalloproteinase elegantin-1 precursor (EC 3.4.24.-) [Contains: Disintegrin elegantin-1a; Disi ...	0.47	-	nuc	0	Secreted protein				481
Q9NP56 UniProt NPD GO	PDE7B_HUMAN	cAMP-specific 3',5'-cyclic phosphodiesterase 7B (EC 3.1.4.17)	0.47	-	nuc	0			604645	1LXW	450
P29974 UniProt NPD GO	CNGA1_MOUSE	cGMP-gated cation channel alpha 1 (CNG channel alpha 1) (CNG-1) (CNG1) (Cyclic nucleotide-gated chan ...	0.47	+	nuc	2	Membrane; multi-pass membrane protein	membrane fraction [IDA] photoreceptor outer segment [IDA]			684
Q01159 UniProt NPD GO	MCE1_YEAST	mRNA capping enzyme subunit alpha (mRNA guanylyltransferase) (EC 2.7.7.50) (GTP--RNA guanylyltransfe ...	0.47	-	cyt	0	Nucleus	nucleus [IPI]			459
P53720 UniProt NPD GO	DUS2_YEAST	tRNA-dihydrouridine synthase 2 (EC 1.-.-.-) (SMM1 protein)	0.47	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			384
Q91XI1 UniProt NPD GO	DUS3L_MOUSE	tRNA-dihydrouridine synthase 3-like (EC 1.-.-.-)	0.47	-	cyt	0					637
Q28BT8 UniProt NPD GO	DUS3L_XENTR	tRNA-dihydrouridine synthase 3-like (EC 1.-.-.-)	0.47	+	cyt	0					639
Q8BMZ5 UniProt NPD GO	SEN34_MOUSE	tRNA-splicing endonuclease subunit Sen34 (EC 3.1.27.9) (tRNA-intron endonuclease Sen34) (Leukocyte r ...	0.47	-	nuc	0	Nucleus (By similarity). Nucleus; nucleolus (By similarity). May be transiently localized in the nuc ...				316
Q25538 UniProt NPD GO	1433_NEOCA	14-3-3 protein homolog	0.46	-	nuc	0					266
P09543 UniProt NPD GO	CN37_HUMAN	2',3'-cyclic-nucleotide 3'-phosphodiesterase (EC 3.1.4.37) (CNP) (CNPase)	0.46	-	mit	0	Membrane. Firmly bound to membrane structures of brain white matter		123830	1WOJ	421
Q12250 UniProt NPD GO	RPN5_YEAST	26S proteasome regulatory subunit RPN5 (Proteasome non-ATPase subunit 5)	0.46	-	nuc	0		proteasome regulatory particle, lid subcomp... [IDA]			444
P62302 UniProt NPD GO	RS13_SOYBN	40S ribosomal protein S13	0.46	-	mit	0					151
Q9XVP0 UniProt NPD GO	RS15_CAEEL	40S ribosomal protein S15	0.46	-	cyt	0					150
Q9UTQ6 UniProt NPD GO	RS15B_SCHPO	40S ribosomal protein S15-B	0.46	-	cyt	0					154
Q8SRP2 UniProt NPD GO	RS18_ENCCU	40S ribosomal protein S18	0.46	-	nuc	0	Cytoplasm				153
Q71UM5 UniProt NPD GO	RS27L_HUMAN	40S ribosomal protein S27-like protein	0.46	+	nuc	0					83
Q6ZWY3 UniProt NPD GO	RS27L_MOUSE	40S ribosomal protein S27-like protein	0.46	+	nuc	0					83
P24051 UniProt NPD GO	RS27L_RAT	40S ribosomal protein S27-like protein	0.46	+	nuc	0					83
Q5EG47 UniProt NPD GO	AAPK1_MOUSE	5'-AMP-activated protein kinase catalytic subunit alpha-1 (EC 2.7.11.1) (AMPK alpha-1 chain)	0.46	-	nuc	0					548
Q02284 UniProt NPD GO	5HT1F_MOUSE	5-hydroxytryptamine 1F receptor (5-HT-1F) (Serotonin receptor 1F) (5-HT-1E-beta)	0.46	-	end	7 *	Membrane; multi-pass membrane protein				366
P07953 UniProt NPD GO	F261_RAT	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 (6PF-2-K/Fru-2,6-P2ASE liver isozyme) [Include ...	0.46	-	cyt	0		6-phosphofructo-2-kinase/fructose-2,6-bipho... [ISS]		1TIP	470
O60825 UniProt NPD GO	F262_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 (6PF-2-K/Fru-2,6-P2ASE heart-type isozyme) (PF ...	0.46	-	nuc	0			171835		505
P90521 UniProt NPD GO	K6PF_DICDI	6-phosphofructokinase (EC 2.7.1.11) (Phosphofructokinase) (Phosphohexokinase)	0.46	-	nuc	0					834
P48157 UniProt NPD GO	RL11_LEIMA	60S ribosomal protein L11	0.46	+	cyt	0					188
O59931 UniProt NPD GO	RL13_CANAL	60S ribosomal protein L13	0.46	-	nuc	0					202
P14329 UniProt NPD GO	RL19_DICDI	60S ribosomal protein L19 (Vegetative-specific protein V14) (22 kDa calmodulin-binding protein)	0.46	-	nuc	0					186
P34113 UniProt NPD GO	RL3_DICDI	60S ribosomal protein L3	0.46	-	mit	0	Cytoplasm				397
Q8NKF4 UniProt NPD GO	RL3_ASPFU	60S ribosomal protein L3 (Allergen Asp f 23)	0.46	+	mit	0	Cytoplasm				392
Q9V597 UniProt NPD GO	RL31_DROME	60S ribosomal protein L31	0.46	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [NAS]			124
Q758D8 UniProt NPD GO	RL39_ASHGO	60S ribosomal protein L39	0.46	-	mit	0					50
Q96499 UniProt NPD GO	RL44_GOSHI	60S ribosomal protein L44	0.46	-	nuc	0					104
P27075 UniProt NPD GO	RL44_CANTR	60S ribosomal protein L44 (60S ribosomal protein L41)	0.46	-	nuc	0					105

You are viewing entries 27351 to 27400 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.