Citrus Sinensis ID: 030242

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180

MFKKFSAEEVSAQNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYLNDGLWKVSWI

cccccccccccccccccHHHHHHHHHHHHHHccccccHHcccccccccEEEEEEEccEEEEEEccEEEEEEEcccccccEEEEcccccccccEEEEcccHHHHHccccccccccEEccccccccccccccEEEEEEcccccEEEEEEEEccHHHHHHcccccEEEEEEEEcccccccccc

ccccccHHcccccHHccHHHHHHHHHHHHHHccccHHHHHHHccccccEEEEEEccEEEEEEEccEEEEEEEcccccccHHHHHHccccccccEEEcccHHHHHHccccEccccccccccccccccccccEEEEEEEccccEEEEEEEEEcHHHHHHHcccccEEEEEEcccccEEEEEc

MFKKFSAEEVSAQNQVKASVQRKIRQSIadeypglepvlddllpkksplIVAKCQNHlnlvlvnnvplffnirdgpymptlrllhqYPNIMKKLQVDRGAIKFVLSGanimcpgltspggsldeevgaetpvAIMAEGKQHALAIGFTKMSAKDIKAINkgigvdnmhylndglwkvswi

mfkkfsaeevsaqnqvkasvqRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINkgigvdnmhylndglwkvswi

MFKKFSAEEVSAQNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHlnlvlvnnvPLFFNIRDGPYMPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYLNDGLWKVSWI

*******************************YPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTS**********AETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYLNDGLWKVSW*

MFKK*********************QSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYLNDGLWKVSWI

**********************KIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYLNDGLWKVSWI

*FKKFSAEEVSAQNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYLNDGLWKVSWI

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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MFKKFSAEEVSAQNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYLNDGLWKVSWI

no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		180	2.2.26 [Sep-21-2011]
Q9ULC4		181	Malignant T-cell-amplifie	yes	no	0.966	0.961	0.573	1e-54
Q2KIE4		181	Malignant T-cell-amplifie	yes	no	0.966	0.961	0.573	1e-54
Q5PPY1		181	Malignant T-cell-amplifie	N/A	no	0.966	0.961	0.585	1e-54
Q9DB27		181	Malignant T-cell-amplifie	yes	no	0.966	0.961	0.573	1e-54
Q9CQ21		181	Malignant T-cell-amplifie	no	no	0.966	0.961	0.562	7e-54
Q6DER1		181	Malignant T-cell-amplifie	yes	no	0.966	0.961	0.573	2e-53
Q6NRJ7		181	Malignant T-cell-amplifie	N/A	no	0.966	0.961	0.573	7e-53
Q5ZI42		181	Malignant T-cell-amplifie	yes	no	0.966	0.961	0.568	8e-53
Q4G009		182	Malignant T-cell-amplifie	no	no	0.927	0.917	0.571	2e-52
Q7ZV34		181	Malignant T-cell-amplifie	yes	no	0.966	0.961	0.556	8e-52

>sp\|Q9ULC4\|MCTS1_HUMAN Malignant T-cell-amplified sequence 1 OS=Homo sapiens GN=MCTS1 PE=1 SV=1	Back alignment and function desciption

 Score =  212 bits (539), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 101/176 (57%), Positives = 132/176 (75%), Gaps = 2/176 (1%)

Query: 1   MFKKFSAEE-VSAQNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLN 59
           MFKKF  +E VS   Q+K SV + I+  + +++PG+EP L+ ++PKK P+ + +C  H+ 
Sbjct: 1   MFKKFDEKENVSNCIQLKTSVIKGIKNQLIEQFPGIEPWLNQIMPKKDPVKIVRCHEHIE 60

Query: 60  LVLVNNVPLFFNIRDGPYMPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPG 119
           ++ VN   LFF  R+GP+ PTLRLLH+YP I+   QVD+GAIKFVLSGANIMCPGLTSPG
Sbjct: 61  ILTVNGELLFFRQREGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPG 120

Query: 120 GSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYLNDGLW 175
             L      +T VAIMAEGKQHAL +G  KMSA+DI+ +NKGIG++N+HYLNDGLW
Sbjct: 121 AKL-YPAAVDTIVAIMAEGKQHALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLW 175

Anti-oncogene that play a role in cell cycle regulation; decreases cell doubling time and anchorage-dependent growth; shortens the duration of G1 transit time and G1/S transition. When constituvely expressed, increases CDK4 and CDK6 kinases activity and CCND1/cyclin D1 protein level, as well as G1 cyclin/CDK complex formation. Plays a role as translation enhancer; Recruits the density-regulated protein/DENR and binds to the cap complex of the 5'-terminus of mRNAs, subsequently altering the mRNA translation profile; Up-regulates protein levels of BCL2L2, TFDP1, MRE11A, CCND1 and E2F1, while mRNA levels remains constant. Hyperactivates DNA damage signaling pathway; increased gamma-irradiation-induced phosphorylation of histone H2AX, and induces damage foci formation. Increases the overall number of chromosomal abnormalities such as larger chromosomes formation and multiples chromosomal fusions when overexpressed in gamma-irradiated cells. May play a role in promoting lymphoid tumor development: lymphoid cell lines overexpressing MCTS1 exhibit increased growth rates and display increased protection against apoptosis. May contribute to the pathogenesis and progression of breast cancer via promotion of angiogenesis through the decline of inhibitory THBS1/thrombospondin-1, and inhibition of apoptosis. Involved in the process of proteasome degradation to down-regulate Tumor suppressor p53/TP53 in breast cancer cell; Positively regulates phosphorylation of MAPK1 and MAPK3.
Homo sapiens (taxid: 9606)

>sp\|Q2KIE4\|MCTS1_BOVIN Malignant T-cell-amplified sequence 1 OS=Bos taurus GN=MCTS1 PE=2 SV=1	Back alignment and function description

>sp\|Q5PPY1\|MCS1A_XENLA Malignant T-cell-amplified sequence 1-A OS=Xenopus laevis GN=mcts1-a PE=2 SV=1	Back alignment and function description

>sp\|Q9DB27\|MCTS1_MOUSE Malignant T-cell-amplified sequence 1 OS=Mus musculus GN=Mcts1 PE=2 SV=1	Back alignment and function description

>sp\|Q9CQ21\|MCTS2_MOUSE Malignant T-cell-amplified sequence 2 OS=Mus musculus GN=Mcts2 PE=2 SV=1	Back alignment and function description

>sp\|Q6DER1\|MCTS1_XENTR Malignant T-cell-amplified sequence 1 OS=Xenopus tropicalis GN=mcts1 PE=2 SV=1	Back alignment and function description

>sp\|Q6NRJ7\|MCS1B_XENLA Malignant T-cell-amplified sequence 1-B OS=Xenopus laevis GN=mcts1-b PE=2 SV=1	Back alignment and function description

>sp\|Q5ZI42\|MCTS1_CHICK Malignant T-cell-amplified sequence 1 OS=Gallus gallus GN=MCTS1 PE=2 SV=1	Back alignment and function description

>sp\|Q4G009\|MCTS1_RAT Malignant T-cell-amplified sequence 1 OS=Rattus norvegicus GN=Mcts1 PE=2 SV=1	Back alignment and function description

>sp\|Q7ZV34\|MCTS1_DANRE Malignant T-cell-amplified sequence 1 OS=Danio rerio GN=mcts1 PE=2 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		180
118483544		252	unknown [Populus trichocarpa]	0.994	0.710	0.932	2e-95
224125114		181	predicted protein [Populus trichocarpa]	1.0	0.994	0.927	1e-94
359487647		429	PREDICTED: uncharacterized protein LOC10	0.983	0.412	0.932	2e-94
224123656		181	predicted protein [Populus trichocarpa]	1.0	0.994	0.916	6e-94
255542784		403	60S ribosomal protein L18, putative [Ric	0.961	0.429	0.947	6e-94
357464025		181	Malignant T cell-amplified sequence 1-A	0.988	0.983	0.921	9e-94
296089721		181	unnamed protein product [Vitis vinifera]	1.0	0.994	0.911	1e-93
449435988		389	PREDICTED: uncharacterized protein LOC10	0.977	0.452	0.926	2e-93
351725351		181	uncharacterized protein LOC100305623 [Gl	0.988	0.983	0.921	3e-93
356509216		181	PREDICTED: malignant T cell-amplified se	0.988	0.983	0.921	6e-93

>gi\|118483544\|gb\|ABK93670.1\| unknown [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  353 bits (905), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 167/179 (93%), Positives = 175/179 (97%)

Query: 1   MFKKFSAEEVSAQNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNL 60
           MFKKFS++EVS+QNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIV KCQNHLNL
Sbjct: 1   MFKKFSSDEVSSQNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVVKCQNHLNL 60

Query: 61  VLVNNVPLFFNIRDGPYMPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGG 120
           V+VNNVPLFFNIRDGPYMPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGG
Sbjct: 61  VVVNNVPLFFNIRDGPYMPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGG 120

Query: 121 SLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYLNDGLWKVSW 179
           +LD+EV AETPVAIMAEGKQHALAIGFTKMSAKDIK INKGIGVDNMHYLNDGLWK+ +
Sbjct: 121 ALDDEVDAETPVAIMAEGKQHALAIGFTKMSAKDIKTINKGIGVDNMHYLNDGLWKLHY 179

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224125114\|ref\|XP_002319503.1\| predicted protein [Populus trichocarpa] gi\|118483047\|gb\|ABK93433.1\| unknown [Populus trichocarpa] gi\|222857879\|gb\|EEE95426.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|359487647\|ref\|XP_002283392.2\| PREDICTED: uncharacterized protein LOC100259659 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224123656\|ref\|XP_002330175.1\| predicted protein [Populus trichocarpa] gi\|118484569\|gb\|ABK94158.1\| unknown [Populus trichocarpa] gi\|222871631\|gb\|EEF08762.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|255542784\|ref\|XP_002512455.1\| 60S ribosomal protein L18, putative [Ricinus communis] gi\|223548416\|gb\|EEF49907.1\| 60S ribosomal protein L18, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|357464025\|ref\|XP_003602294.1\| Malignant T cell-amplified sequence 1-A [Medicago truncatula] gi\|355491342\|gb\|AES72545.1\| Malignant T cell-amplified sequence 1-A [Medicago truncatula]	Back alignment and taxonomy information

>gi\|296089721\|emb\|CBI39540.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449435988\|ref\|XP_004135776.1\| PREDICTED: uncharacterized protein LOC101207642 [Cucumis sativus] gi\|449524956\|ref\|XP_004169487.1\| PREDICTED: uncharacterized protein LOC101228164 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|351725351\|ref\|NP_001238113.1\| uncharacterized protein LOC100305623 [Glycine max] gi\|255626117\|gb\|ACU13403.1\| unknown [Glycine max]	Back alignment and taxonomy information

>gi\|356509216\|ref\|XP_003523347.1\| PREDICTED: malignant T cell-amplified sequence 1-like [Glycine max]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		180
TAIR\|locus:2195336		181	AT1G09150 [Arabidopsis thalian	0.983	0.977	0.824	2.7e-75
UNIPROTKB\|F1RX51		181	Ssc.3881 "Uncharacterized prot	0.966	0.961	0.562	5.8e-50
UNIPROTKB\|Q2KIE4		181	MCTS1 "Malignant T-cell-amplif	0.966	0.961	0.562	1.5e-49
UNIPROTKB\|F6UN31		181	MCTS1 "Uncharacterized protein	0.966	0.961	0.562	1.5e-49
UNIPROTKB\|J9P226		181	LOC487150 "Uncharacterized pro	0.966	0.961	0.562	1.5e-49
UNIPROTKB\|Q9ULC4		181	MCTS1 "Malignant T-cell-amplif	0.966	0.961	0.562	1.5e-49
MGI\|MGI:1916245		181	Mcts1 "malignant T cell amplif	0.966	0.961	0.562	1.5e-49
UNIPROTKB\|A6QLG1		181	LOC515358 "Uncharacterized pro	0.966	0.961	0.556	4.1e-49
MGI\|MGI:1913655		181	Mcts2 "malignant T cell amplif	0.966	0.961	0.551	1.8e-48
DICTYBASE\|DDB_G0271910		182	DDB_G0271910 "MCTS1 family pro	0.972	0.961	0.539	6e-48

TAIR\|locus:2195336 AT1G09150 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 759 (272.2 bits), Expect = 2.7e-75, P = 2.7e-75
 Identities = 146/177 (82%), Positives = 155/177 (87%)

Query:     1 MFKKFSAEEVSAQNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHXXX 60
             MFKKF  EE+S+QNQVKASVQR+IRQSI DEYPGLE V++DLLPKK PLIV KC NH   
Sbjct:     1 MFKKFCLEEISSQNQVKASVQRRIRQSIQDEYPGLESVMEDLLPKKIPLIVVKCPNHLTL 60

Query:    61 XXXXXXPLFFNIRDGPYMPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGG 120
                   PLFF IRDGPYMPTLRLLHQYPNIMK+ QVDRGAIKFVLSGANIMCPGLTSPGG
Sbjct:    61 VVVNNVPLFFCIRDGPYMPTLRLLHQYPNIMKRFQVDRGAIKFVLSGANIMCPGLTSPGG 120

Query:   121 SLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYLNDGLWKV 177
              LD+EV AE PVAI AEGKQHALAIGFTKMSAKDIK+INKGIGVDNMHYLNDGLWK+
Sbjct:   121 VLDQEVEAERPVAIYAEGKQHALAIGFTKMSAKDIKSINKGIGVDNMHYLNDGLWKM 177

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0005829 "cytosol" evidence=IDA

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

GO:0009086 "methionine biosynthetic process" evidence=RCA

UNIPROTKB\|F1RX51 Ssc.3881 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|Q2KIE4 MCTS1 "Malignant T-cell-amplified sequence 1" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|F6UN31 MCTS1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|J9P226 LOC487150 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|Q9ULC4 MCTS1 "Malignant T-cell-amplified sequence 1" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

MGI\|MGI:1916245 Mcts1 "malignant T cell amplified sequence 1" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|A6QLG1 LOC515358 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

MGI\|MGI:1913655 Mcts2 "malignant T cell amplified sequence 2" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0271910 DDB_G0271910 "MCTS1 family protein" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q86KL4	MCTS1_DICDI	No assigned EC number	0.5738	0.9722	0.9615	yes	no
Q5ZI42	MCTS1_CHICK	No assigned EC number	0.5681	0.9666	0.9613	yes	no
Q75AA8	TMA20_ASHGO	No assigned EC number	0.4945	0.9944	0.9889	yes	no
Q5PPY1	MCS1A_XENLA	No assigned EC number	0.5852	0.9666	0.9613	N/A	no
P89886	TMA20_YEAST	No assigned EC number	0.4722	0.9833	0.9779	yes	no
Q6DER1	MCTS1_XENTR	No assigned EC number	0.5738	0.9666	0.9613	yes	no
Q2KIE4	MCTS1_BOVIN	No assigned EC number	0.5738	0.9666	0.9613	yes	no
Q9DB27	MCTS1_MOUSE	No assigned EC number	0.5738	0.9666	0.9613	yes	no
P87313	TMA20_SCHPO	No assigned EC number	0.4887	0.9833	0.9779	yes	no
Q6NRJ7	MCS1B_XENLA	No assigned EC number	0.5738	0.9666	0.9613	N/A	no
Q9ULC4	MCTS1_HUMAN	No assigned EC number	0.5738	0.9666	0.9613	yes	no
Q7ZV34	MCTS1_DANRE	No assigned EC number	0.5568	0.9666	0.9613	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	grail3.0016013002	SubName- Full=Putative uncharacterized protein; (182 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	fgenesh4_pg.C_scaffold_1866000002	annotation not avaliable (150 aa)	•	•	0.448
	eugene3.00190939	hypothetical protein (258 aa)	•	•	0.443
	estExt_fgenesh4_pm.C_LG_XIII0470	SubName- Full=Putative uncharacterized protein; (271 aa)	•	•	0.435
	fgenesh4_pg.C_LG_X000844	hypothetical protein (338 aa)	•		0.409

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		180
cd11609		77	cd11609, MCT1_N, N-terminal domain of multiple cop	1e-42
COG2016		161	COG2016, COG2016, Predicted RNA-binding protein (c	3e-40
PRK14560		160	PRK14560, PRK14560, putative RNA-binding protein;	4e-27
TIGR00451		107	TIGR00451, unchar_dom_2, uncharacterized domain 2	1e-26
TIGR03684		150	TIGR03684, arCOG00985, arCOG04150 universal archae	1e-26
cd11580		72	cd11580, eIF2D_N_like, N-terminal domain of eIF2D,	5e-19
pfam01472		74	pfam01472, PUA, PUA domain	5e-17
smart00359		76	smart00359, PUA, Putative RNA-binding Domain in Ps	7e-11
cd11610		76	cd11610, eIF2D_N, N-terminal domain of eIF2D and r	1e-10
PRK13795		636	PRK13795, PRK13795, hypothetical protein; Provisio	2e-08
PRK13794		479	PRK13794, PRK13794, hypothetical protein; Provisio	5e-05
TIGR00425		322	TIGR00425, CBF5, rRNA pseudouridine synthase, puta	7e-05
COG5270		202	COG5270, COG5270, PUA domain (predicted RNA-bindin	0.001
PRK04270		300	PRK04270, PRK04270, H/ACA RNA-protein complex comp	0.002

>gnl\|CDD\|211422 cd11609, MCT1_N, N-terminal domain of multiple copies T cell malignancies 1 and related proteins	Back alignment and domain information

 Score =  136 bits (346), Expect = 1e-42
 Identities = 42/77 (54%), Positives = 58/77 (75%)

Query: 3  KKFSAEEVSAQNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVL 62
          K F  E+VS Q Q+K+SVQR IR  + ++YP LEP +D++LPKK PL++ KC +H+ L++
Sbjct: 1  KFFEKEDVSGQTQLKSSVQRGIRAKLLEQYPLLEPYIDEILPKKEPLVLVKCHDHIELLV 60

Query: 63 VNNVPLFFNIRDGPYMP 79
          VN  PLFF  RDGPY+P
Sbjct: 61 VNGEPLFFQHRDGPYIP 77

This N-terminal domain of MCT-1 (multiple copies T cell malignancies 1), also known as MCTS-1 (malignant T cell-amplified sequence 1), co-occurs with a PUA domain. MCT-1, together with DENR (density regulated protein), has been shown to have similar function as eIF2D translation initiation factor (also known as ligatin), which is involved in the recruitment and delivery of aminoacyl-tRNAs to the P-site of the eukaryotic ribosome in a GTP-independent manner. Length = 77

>gnl\|CDD\|224927 COG2016, COG2016, Predicted RNA-binding protein (contains PUA domain) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|237757 PRK14560, PRK14560, putative RNA-binding protein; Provisional	Back alignment and domain information

>gnl\|CDD\|129543 TIGR00451, unchar_dom_2, uncharacterized domain 2	Back alignment and domain information

>gnl\|CDD\|234310 TIGR03684, arCOG00985, arCOG04150 universal archaeal PUA-domain protein	Back alignment and domain information

>gnl\|CDD\|211421 cd11580, eIF2D_N_like, N-terminal domain of eIF2D, malignant T cell-amplified sequence 1 and related proteins	Back alignment and domain information

>gnl\|CDD\|201816 pfam01472, PUA, PUA domain	Back alignment and domain information

>gnl\|CDD\|214635 smart00359, PUA, Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase	Back alignment and domain information

>gnl\|CDD\|211423 cd11610, eIF2D_N, N-terminal domain of eIF2D and related proteins	Back alignment and domain information

>gnl\|CDD\|237510 PRK13795, PRK13795, hypothetical protein; Provisional	Back alignment and domain information

>gnl\|CDD\|237509 PRK13794, PRK13794, hypothetical protein; Provisional	Back alignment and domain information

>gnl\|CDD\|232971 TIGR00425, CBF5, rRNA pseudouridine synthase, putative	Back alignment and domain information

>gnl\|CDD\|227595 COG5270, COG5270, PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|179806 PRK04270, PRK04270, H/ACA RNA-protein complex component Cbf5p; Reviewed	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		180
KOG2523		181	consensus Predicted RNA-binding protein with PUA d	100.0
PRK14560		160	putative RNA-binding protein; Provisional	100.0
COG2016		161	Predicted RNA-binding protein (contains PUA domain	100.0
TIGR03684		150	arCOG00985 arCOG04150 universal archaeal PUA-domai	100.0
KOG2522		560	consensus Filamentous baseplate protein Ligatin, c	100.0
TIGR00451		107	unchar_dom_2 uncharacterized domain 2. This unchar	99.96
PRK13534		639	7-cyano-7-deazaguanine tRNA-ribosyltransferase; Pr	99.91
PRK13795		636	hypothetical protein; Provisional	99.88
PRK13794		479	hypothetical protein; Provisional	99.85
COG1370		155	Prefoldin, molecular chaperone implicated in de no	99.85
TIGR00432		540	arcsn_tRNA_tgt tRNA-guanine transglycosylase, arch	99.8
PF01472		74	PUA: PUA domain; InterPro: IPR002478 The PUA (Pseu	99.79
COG5270		202	PUA domain (predicted RNA-binding domain) [Transla	99.61
smart00359		77	PUA Putative RNA-binding Domain in PseudoUridine s	99.29
TIGR00425		322	CBF5 rRNA pseudouridine synthase, putative. This f	99.23
PRK04270		300	H/ACA RNA-protein complex component Cbf5p; Reviewe	99.15
PRK05429		372	gamma-glutamyl kinase; Provisional	98.96
COG1549		519	Queuine tRNA-ribosyltransferases, contain PUA doma	98.94
TIGR01027		363	proB glutamate 5-kinase. Bacterial ProB proteins h	98.69
PF09183		65	DUF1947: Domain of unknown function (DUF1947); Int	98.41
PRK08557		417	hypothetical protein; Provisional	98.29
PRK13402		368	gamma-glutamyl kinase; Provisional	97.98
PF14810		74	TGT_C2: Patch-forming domain C2 of tRNA-guanine tr	97.85
COG0263		369	ProB Glutamate 5-kinase [Amino acid transport and	97.42
KOG2529		395	consensus Pseudouridine synthase [Translation, rib	96.16
PRK14124		308	tRNA pseudouridine synthase B; Provisional	96.11
PF03657		162	UPF0113: Uncharacterised protein family (UPF0113);	90.64
KOG3492		180	consensus Ribosome biogenesis protein NIP7 [Transl	90.09
PRK00130		290	truB tRNA pseudouridine synthase B; Provisional	86.95
PF09157		58	TruB-C_2: Pseudouridine synthase II TruB, C-termin	84.33
COG0130		271	TruB Pseudouridine synthase [Translation, ribosoma	81.41
PRK05033		312	truB tRNA pseudouridine synthase B; Provisional	80.91

>KOG2523 consensus Predicted RNA-binding protein with PUA domain [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

Probab=100.00  E-value=3e-47  Score=290.00  Aligned_cols=178  Identities=66%  Similarity=1.091  Sum_probs=172.1

Q ss_pred             CCCCCCC-CCcccccccCHHHHHHHHHHHHhHCCCCchhhcccCCCCCceEEEEeeCceEEEEECCEEEEEEecCCCcch
Q 030242            1 MFKKFSA-EEVSAQNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMP   79 (180)
Q Consensus         1 MFkK~~~-~~~k~~~~l~~sd~kkLr~~i~~~f~~~~~~~~~l~p~~~~v~~~k~~~~~~~y~~dg~pl~f~~~~~~~~P   79 (180)
                      ||||+.. +.+++++++|+|-+|-+|+.+.++||.+..-+++++|+|+++.+.||.+++.+|+++|.++||+.+||.|+|
T Consensus         1 mfkkf~~ke~i~~~~~~Kssvq~~i~~kl~~~yp~le~~~~ellpKk~~~~vikC~d~i~L~s~~G~~~fF~~~dg~~~P   80 (181)
T KOG2523|consen    1 MFKKFDLKEDISSSTQLKSSVQRGIKAKLVDQYPGLEQVIDELLPKKEQYKVIKCKDHIELLSVNGEVLFFCHRDGPYIP   80 (181)
T ss_pred             CcccccchhhhhcchhhHHHHHHHHHHHHHHhCcchHHHHHHhccCCCceEEEEccCeeEEEEeCCEEEEEEecCCCccc
Confidence            8999965 789999999999999999999999998777789999999999999999999999999999999999999999


Q ss_pred             hhHhhhcCCCCCcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCC
Q 030242           80 TLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAIN  159 (180)
Q Consensus        80 Tl~~l~~~p~~~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~  159 (180)
                      |+++|+++|..+|.+.||.||++|+++|||+|+||++.+.+.+++.+++|+.|+|+++++..++|||.+.||++||.+..
T Consensus        81 TLRllhk~p~~~~~~qvD~GAIkfvlsGAnIMcPGlts~g~~l~~~~ekd~~V~i~aeGK~~alAiG~~~ms~kei~s~n  160 (181)
T KOG2523|consen   81 TLRLLHKYPFIFPHVQVDRGAIKFVLSGANIMCPGLTSPGAKLPPGVEKDTIVAIMAEGKEHALAIGLTKMSAKEIKSVN  160 (181)
T ss_pred             hhHHHhhCCCccceEEecCcceeeeecCCceEcccCCCCcccCCCCccCCCEEEEEecCchhhhhhhhhhhcHHHHHhhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cceEEEEEEEEcccccCcc
Q 030242          160 KGIGVDNMHYLNDGLWKVS  178 (180)
Q Consensus       160 kG~av~v~H~~~D~Lw~~~  178 (180)
                      ||.++++.|++||.||.+.
T Consensus       161 KGiGIE~~H~l~DgLw~~~  179 (181)
T KOG2523|consen  161 KGIGIENYHYLNDGLWKMK  179 (181)
T ss_pred             cCCceEEEEecCCchhhee
Confidence            9999999999999999875

>PRK14560 putative RNA-binding protein; Provisional	Back alignment and domain information

>COG2016 Predicted RNA-binding protein (contains PUA domain) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>TIGR03684 arCOG00985 arCOG04150 universal archaeal PUA-domain protein	Back alignment and domain information

>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>TIGR00451 unchar_dom_2 uncharacterized domain 2	Back alignment and domain information

>PRK13534 7-cyano-7-deazaguanine tRNA-ribosyltransferase; Provisional	Back alignment and domain information

>PRK13795 hypothetical protein; Provisional	Back alignment and domain information

>PRK13794 hypothetical protein; Provisional	Back alignment and domain information

>COG1370 Prefoldin, molecular chaperone implicated in de novo protein folding, alpha subunit [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>TIGR00432 arcsn_tRNA_tgt tRNA-guanine transglycosylase, archaeosine-15-forming	Back alignment and domain information

>PF01472 PUA: PUA domain; InterPro: IPR002478 The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was named after the proteins in which it was first found []	Back alignment and domain information

>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase	Back alignment and domain information

>TIGR00425 CBF5 rRNA pseudouridine synthase, putative	Back alignment and domain information

>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed	Back alignment and domain information

>PRK05429 gamma-glutamyl kinase; Provisional	Back alignment and domain information

>COG1549 Queuine tRNA-ribosyltransferases, contain PUA domain [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>TIGR01027 proB glutamate 5-kinase	Back alignment and domain information

>PF09183 DUF1947: Domain of unknown function (DUF1947); InterPro: IPR015266 Members of this entry are a set of hypothetical archaeal proteins	Back alignment and domain information

>PRK08557 hypothetical protein; Provisional	Back alignment and domain information

>PRK13402 gamma-glutamyl kinase; Provisional	Back alignment and domain information

>PF14810 TGT_C2: Patch-forming domain C2 of tRNA-guanine transglycosylase; PDB: 1J2B_A 1IT8_A 1IT7_B 1IQ8_A	Back alignment and domain information

>COG0263 ProB Glutamate 5-kinase [Amino acid transport and metabolism]	Back alignment and domain information

>KOG2529 consensus Pseudouridine synthase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PRK14124 tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PF03657 UPF0113: Uncharacterised protein family (UPF0113); InterPro: IPR005155 This entry represents PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain containing proteins such as the ribosomal biogenesis factor NIP7 [, ]	Back alignment and domain information

>KOG3492 consensus Ribosome biogenesis protein NIP7 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PRK00130 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

>PF09157 TruB-C_2: Pseudouridine synthase II TruB, C-terminal; InterPro: IPR015240 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones	Back alignment and domain information

>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PRK05033 truB tRNA pseudouridine synthase B; Provisional	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		180
3r90_A		188	Crystal Structure Of Malignant T Cell-Amplified Seq		2e-46
3d79_A		179	Crystal Structure Of Hypothetical Protein Ph0734.1		3e-09

>pdb|3R90|A Chain A, Crystal Structure Of Malignant T Cell-Amplified Sequence 1 Protein Length = 188

Back alignment and structure

Iteration: 1

Score = 181 bits (459), Expect = 2e-46, Method: Compositional matrix adjust. Identities = 96/176 (54%), Positives = 124/176 (70%), Gaps = 2/176 (1%) Query: 1 MFKKFSAEE-VSAQNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHXX 59 MFKKF +E VS Q+K SV + I+ + +++PG+EP L+ ++PKK P+ + +C H Sbjct: 1 MFKKFDEKENVSNCIQLKTSVIKGIKNQLIEQFPGIEPWLNQIMPKKDPVKIVRCHEHIE 60 Query: 60 XXXXXXXPLFFNIRDGPYMPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPG 119 LFF R+GP+ PTLRLLH+YP I+ QVD+GAIKFVLSGANIMCPGLTSPG Sbjct: 61 ILTVNGELLFFRQREGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPG 120 Query: 120 GSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYLNDGLW 175 L +T VAIMA G HAL +G KMSA+DI+ +NKGIG++N+HYLNDGLW Sbjct: 121 AKL-YPAAVDTIVAIMAAGAAHALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLW 175

PyMOL of 3r90

>pdb|3D79|A Chain A, Crystal Structure Of Hypothetical Protein Ph0734.1 From Hyperthermophilic Archaea Pyrococcus Horikoshii Ot3 Length = 179

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		180
3r90_A		188	Malignant T cell-amplified sequence 1; structural	8e-73
3d79_A		179	PUA domain, putative uncharacterized protein PH073	8e-58
2cx0_A		187	Hypothetical protein APE0525; PUA domain, structur	2e-57
1q7h_A		153	Conserved hypothetical protein; structural genomic	4e-45
3zv0_C		195	H/ACA ribonucleoprotein complex subunit 4; cell cy	7e-15
2aus_C		334	Pseudouridine synthase; isomerase, structural prot	7e-05
2apo_A		357	Probable tRNA pseudouridine synthase B; protein-pr	9e-05

>3r90_A Malignant T cell-amplified sequence 1; structural genomics consortium, surface entropy reduction, S binding protein; 1.70A {Homo sapiens} Length = 188	Back alignment and structure

 Score =  216 bits (552), Expect = 8e-73
 Identities = 98/177 (55%), Positives = 129/177 (72%), Gaps = 2/177 (1%)

Query: 1   MFKKFSAEE-VSAQNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLN 59
           MFKKF  +E VS   Q+K SV + I+  + +++PG+EP L+ ++PKK P+ + +C  H+ 
Sbjct: 1   MFKKFDEKENVSNCIQLKTSVIKGIKNQLIEQFPGIEPWLNQIMPKKDPVKIVRCHEHIE 60

Query: 60  LVLVNNVPLFFNIRDGPYMPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPG 119
           ++ VN   LFF  R+GP+ PTLRLLH+YP I+   QVD+GAIKFVLSGANIMCPGLTSPG
Sbjct: 61  ILTVNGELLFFRQREGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPG 120

Query: 120 GSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYLNDGLWK 176
             L      +T VAIMA G  HAL +G  KMSA+DI+ +NKGIG++N+HYLNDGLW 
Sbjct: 121 AKL-YPAAVDTIVAIMAAGAAHALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWH 176

PyMOL of 3r90

>3d79_A PUA domain, putative uncharacterized protein PH0734; unknown function; 1.73A {Pyrococcus horikoshii} Length = 179	Back alignment and structure

>2cx0_A Hypothetical protein APE0525; PUA domain, structural genomics, NPPSFA, national project on structural and functional analyses; 1.80A {Aeropyrum pernix} SCOP: b.122.1.1 d.17.6.4 PDB: 2cx1_A* 1zs7_A Length = 187	Back alignment and structure

>1q7h_A Conserved hypothetical protein; structural genomics, MCSG, PSI, PR structure initiative; 2.10A {Thermoplasma acidophilum dsm 1728} SCOP: b.122.1.1 d.17.6.2 Length = 153	Back alignment and structure

>3zv0_C H/ACA ribonucleoprotein complex subunit 4; cell cycle, RNP assembly, X-linked dyskeratosis congenita; 2.80A {Saccharomyces cerevisiae} Length = 195	Back alignment and structure

>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A Length = 334	Back alignment and structure

>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: b.122.1.1 d.265.1.2 Length = 357	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		180
3r90_A		188	Malignant T cell-amplified sequence 1; structural	100.0
3d79_A		179	PUA domain, putative uncharacterized protein PH073	100.0
2cx0_A		187	Hypothetical protein APE0525; PUA domain, structur	100.0
1q7h_A		153	Conserved hypothetical protein; structural genomic	100.0
1iq8_A		582	Archaeosine tRNA-guanine transglycosylase; (alpha/	99.91
3zv0_C		195	H/ACA ribonucleoprotein complex subunit 4; cell cy	99.9
2q07_A		306	Uncharacterized protein AF0587; monomer, structura	99.9
2p38_A		166	Protein involved in ribosomal biogenesis; two alph	99.62
3u28_A		400	H/ACA ribonucleoprotein complex subunit 4; pseudou	99.12
1sqw_A		188	Saccharomyces cerevisiae NIP7P homolog; PUA, unkno	98.95
2j5v_A		367	Glutamate 5-kinase; proline biosynthesis, gamma gl	98.65
2aus_C		334	Pseudouridine synthase; isomerase, structural prot	98.65
2apo_A		357	Probable tRNA pseudouridine synthase B; protein-pr	98.53
1r3e_A		309	TRNA pseudouridine synthase B; RNA modification, p	86.68
3c0k_A		396	UPF0064 protein YCCW; PUA domain, adoMet dependent	83.77
1k8w_A		327	TRNA pseudouridine synthase B; protein-RNA complex	81.24

>3r90_A Malignant T cell-amplified sequence 1; structural genomics consortium, surface entropy reduction, S binding protein; 1.70A {Homo sapiens}	Back alignment and structure

Probab=100.00  E-value=1.5e-55  Score=349.40  Aligned_cols=177  Identities=55%  Similarity=1.004  Sum_probs=165.7

Q ss_pred             CCCCC-CCCCcccccccCHHHHHHHHHHHHhHCCCCchhhcccCCCCCceEEEEeeCceEEEEECCEEEEEEecCCCcch
Q 030242            1 MFKKF-SAEEVSAQNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMP   79 (180)
Q Consensus         1 MFkK~-~~~~~k~~~~l~~sd~kkLr~~i~~~f~~~~~~~~~l~p~~~~v~~~k~~~~~~~y~~dg~pl~f~~~~~~~~P   79 (180)
                      ||||+ +.+++|++++||+||+|+||+.+.+|||..++.+++|||+++.+++.|++++.++|++||+|+||+.++|.++|
T Consensus         1 MFkk~~~~~~vk~~~~lk~Sd~kkLr~~l~~qf~~~~~~~d~l~pkk~~v~~~k~~~~~~iy~~~~~pl~f~~~dg~l~P   80 (188)
T 3r90_A            1 MFKKFDEKENVSNCIQLKTSVIKGIKNQLIEQFPGIEPWLNQIMPKKDPVKIVRCHEHIEILTVNGELLFFRQREGPFYP   80 (188)
T ss_dssp             CCTTCCHHHHEEEEEECCHHHHHHHHHHHHHHCGGGGGGHHHHSCTTSCEEEEEEGGGEEEEEETTEEEEEEETTCCCEE
T ss_pred             CCCCCcCccCccccEeccHHHHHHHHHHHHHHcCCchhhHHhhCCCCCCEEEEEeCCeEEEEEECCEEEEEEeCCCeEec
Confidence            99996 23689999999999999999999999997656788999999999999999999999999999999998889999


Q ss_pred             hhHhhhcCCCCCcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCC
Q 030242           80 TLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAIN  159 (180)
Q Consensus        80 Tl~~l~~~p~~~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~  159 (180)
                      |||+||++|.++|+|+||++|+++|++|||||+|||+...+.+ ++|++||+|+|++++++.++|||+++||++||.+..
T Consensus        81 Tl~~l~~~p~~lp~v~Vd~~av~~v~~GA~Lm~PGv~~~~~~~-~~i~~Gd~V~V~~~~~~~~vAVG~a~mss~e~~~~~  159 (188)
T 3r90_A           81 TLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKL-YPAAVDTIVAIMAAGAAHALCVGVMKMSAEDIEKVN  159 (188)
T ss_dssp             CHHHHHHSGGGSCEEEECGGGHHHHTTTCCEETHHHHSTTCBC-CCCCTTCEEEEEETTCSSCSEEEEESSCHHHHHHHC
T ss_pred             hHHHHhhCcccCCEEEEChhHHHHhhcCCccccCeEEccCCCc-ccccCCCEEEEEECCCCcEEEEEEEEeCHHHHhhcC
Confidence            9999999999999999999999999999999999999965544 479999999999977899999999999999999899


Q ss_pred             cceEEEEEEEEcccccCcc
Q 030242          160 KGIGVDNMHYLNDGLWKVS  178 (180)
Q Consensus       160 kG~av~v~H~~~D~Lw~~~  178 (180)
                      +|+||+++|++||+||+++
T Consensus       160 kG~aV~v~H~~~D~LW~~~  178 (188)
T 3r90_A          160 KGIGIENIHYLNDGLWHMK  178 (188)
T ss_dssp             CSEEEEEEEETTSHHHHHC
T ss_pred             CcEEEEEEEEECchhhhcC
Confidence            9999999999999999876

PyMOL of 3r90

>3d79_A PUA domain, putative uncharacterized protein PH0734; unknown function; 1.73A {Pyrococcus horikoshii}	Back alignment and structure

>2cx0_A Hypothetical protein APE0525; PUA domain, structural genomics, NPPSFA, national project on structural and functional analyses; 1.80A {Aeropyrum pernix} SCOP: b.122.1.1 d.17.6.4 PDB: 2cx1_A* 1zs7_A	Back alignment and structure

>1q7h_A Conserved hypothetical protein; structural genomics, MCSG, PSI, PR structure initiative; 2.10A {Thermoplasma acidophilum dsm 1728} SCOP: b.122.1.1 d.17.6.2	Back alignment and structure

>1iq8_A Archaeosine tRNA-guanine transglycosylase; (alpha/beta)8 barrel, riken structural genomics/proteomics initiative, RSGI; 2.20A {Pyrococcus horikoshii} SCOP: b.122.1.1 c.1.20.1 d.17.6.1 PDB: 1it7_A* 1it8_A* 1j2b_A	Back alignment and structure

>3zv0_C H/ACA ribonucleoprotein complex subunit 4; cell cycle, RNP assembly, X-linked dyskeratosis congenita; 2.80A {Saccharomyces cerevisiae}	Back alignment and structure

>2q07_A Uncharacterized protein AF0587; monomer, structural genomics, PSI-2, protein structure initiative; 2.04A {Archaeoglobus fulgidus dsm 4304} SCOP: b.122.1.1 c.18.1.4 d.17.6.5	Back alignment and structure

>2p38_A Protein involved in ribosomal biogenesis; two alpha/beta domains, PUA domain, biosynthetic protein; 1.80A {Pyrococcus abyssi}	Back alignment and structure

>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A	Back alignment and structure

>1sqw_A Saccharomyces cerevisiae NIP7P homolog; PUA, unknown function; 1.90A {Homo sapiens} SCOP: b.122.1.1 d.17.6.3 PDB: 1t5y_A	Back alignment and structure

>2j5v_A Glutamate 5-kinase; proline biosynthesis, gamma glutamyl kinase, amino-acid biosynthesis, transferase, feedback regulation, PUA domain; HET: RGP; 2.5A {Escherichia coli} PDB: 2j5t_A* 2w21_A	Back alignment and structure

>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A	Back alignment and structure

>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: b.122.1.1 d.265.1.2	Back alignment and structure

>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima} SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A	Back alignment and structure

>3c0k_A UPF0064 protein YCCW; PUA domain, adoMet dependent methyltransferase fold; 2.00A {Escherichia coli K12}	Back alignment and structure

>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		180
d1q7ha1		85	b.122.1.1 (A:69-153) Hypothetical protein Ta1423,	1e-21
d2cx1a1		93	b.122.1.1 (A:91-183) Hypothetical protein APE0525,	2e-20
d2apoa1		85	b.122.1.1 (A:247-331) Pseudouridine synthase II Tr	6e-16
d1r3ea1		81	b.122.1.1 (A:238-318) Pseudouridine synthase II Tr	7e-15
d1iq8a3		77	b.122.1.1 (A:506-582) Archaeosine tRNA-guanine tra	3e-14
d2ey4a1		84	b.122.1.1 (A:253-336) Pseudouridine synthase II Tr	5e-14
d2q07a1		68	b.122.1.1 (A:460-527) Uncharacterized protein AF05	4e-05

>d1q7ha1 b.122.1.1 (A:69-153) Hypothetical protein Ta1423, C-terminal domain {Archaeon Thermoplasma acidophilum [TaxId: 2303]} Length = 85	Back information, alignment and structure


class: All beta proteins
fold: PUA domain-like
superfamily: PUA domain-like
family: PUA domain
domain: Hypothetical protein Ta1423, C-terminal domain
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

 Score = 82.1 bits (203), Expect = 1e-21
 Identities = 20/86 (23%), Positives = 42/86 (48%), Gaps = 5/86 (5%)

Query: 92  KKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMS 151
             + VD GA   +L+G+++  PG+ S   S+ +       + + +  K + +A+G  +M 
Sbjct: 3   NIVTVDEGAEPHILNGSDLFAPGIVSMDDSIRKG----DMIFVKSS-KGYFIAVGMAEMD 57

Query: 152 AKDIKAINKGIGVDNMHYLNDGLWKV 177
           A ++ A  +G     +H+  D L + 
Sbjct: 58  AGEVMATKRGKAARIIHFPGDELIRA 83

PyMOL of d1q7ha1

>d2cx1a1 b.122.1.1 (A:91-183) Hypothetical protein APE0525, C-terminal domain {Archaeon Aeropyrum pernix [TaxId: 56636]} Length = 93	Back information, alignment and structure

>d2apoa1 b.122.1.1 (A:247-331) Pseudouridine synthase II TruB, C-terminal domain {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 85	Back information, alignment and structure

>d1r3ea1 b.122.1.1 (A:238-318) Pseudouridine synthase II TruB, C-terminal domain {Thermotoga maritima [TaxId: 2336]} Length = 81	Back information, alignment and structure

>d1iq8a3 b.122.1.1 (A:506-582) Archaeosine tRNA-guanine transglycosylase, C3 domain {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Length = 77	Back information, alignment and structure

>d2ey4a1 b.122.1.1 (A:253-336) Pseudouridine synthase II TruB, C-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 84	Back information, alignment and structure

>d2q07a1 b.122.1.1 (A:460-527) Uncharacterized protein AF0587 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 68	Back information, alignment and structure

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		180
d2cx1a1		93	Hypothetical protein APE0525, C-terminal domain {A	99.92
d1q7ha1		85	Hypothetical protein Ta1423, C-terminal domain {Ar	99.92
d2apoa1		85	Pseudouridine synthase II TruB, C-terminal domain	99.85
d2ey4a1		84	Pseudouridine synthase II TruB, C-terminal domain	99.84
d1iq8a3		77	Archaeosine tRNA-guanine transglycosylase, C3 doma	99.81
d1r3ea1		81	Pseudouridine synthase II TruB, C-terminal domain	99.77
d2q07a1		68	Uncharacterized protein AF0587 {Archaeoglobus fulg	99.68
d2cx1a2		90	Hypothetical protein APE0525, N-terminal domain {A	98.11
d2as0a1		72	Hypothetical protein PH1915, N-terminal domain {Ar	98.03
d1q7ha2		66	Hypothetical protein Ta1423, N-terminal domain {Ar	97.55
d1sqwa1		76	Nip7p homolog, C-terminal domain {Human (Homo sapi	96.34
d1iq8a4		145	Archaeosine tRNA-guanine transglycosylase, C2 doma	96.07
d1k8wa3		62	Pseudouridine synthase II TruB, C-terminal domain	90.55
d2b78a1		68	Hypothetical protein SMu776, N-terminal domain {St	82.66

>d2cx1a1 b.122.1.1 (A:91-183) Hypothetical protein APE0525, C-terminal domain {Archaeon Aeropyrum pernix [TaxId: 56636]}	Back information, alignment and structure

class: All beta proteins
fold: PUA domain-like
superfamily: PUA domain-like
family: PUA domain
domain: Hypothetical protein APE0525, C-terminal domain
species: Archaeon Aeropyrum pernix [TaxId: 56636]

Probab=99.92  E-value=7.6e-26  Score=158.44  Aligned_cols=83  Identities=23%  Similarity=0.472  Sum_probs=77.4

Q ss_pred             cEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhc----CCcceEEEEE
Q 030242           92 KKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKA----INKGIGVDNM  167 (180)
Q Consensus        92 p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~----~~kG~av~v~  167 (180)
                      ..|+||++|+++|++|||||+|||+.    ++++|++||+|+|++++++.++|+|++.+|++||..    ..+|++++++
T Consensus         2 g~i~vd~gA~~al~~GA~Lm~pGIv~----~~g~f~~Gd~V~I~~~~~~~~iAvG~~~~~s~ei~~~~g~~~kG~~v~~l   77 (93)
T d2cx1a1           2 GVVLVDKGAAIALAKGAHLMIPGVVG----VEGSFTRGDVVAALYHETRTPVMVGVAEVDSSALEKLYREKARGRAVRRV   77 (93)
T ss_dssp             EEEEECHHHHHHHHTTCCEEGGGEEE----EEECCCTTCEEEEEETTTTEEEEEEEESSCHHHHHHHHHHTCCSEEEEEE
T ss_pred             CEEEECcCHHHHHHCCCCcCccccEE----CCCCCCCCCEEEEEECCCCeEEEEEEEecCHHHHHHHhccCCCceEEEEE
Confidence            46899999999999999999999998    778999999999999778899999999999999865    5799999999


Q ss_pred             EEEcccccCcc
Q 030242          168 HYLNDGLWKVS  178 (180)
Q Consensus       168 H~~~D~Lw~~~  178 (180)
                      |++||+||+++
T Consensus        78 h~~gD~lw~~~   88 (93)
T d2cx1a1          78 HRLGDALWELA   88 (93)
T ss_dssp             EETTSHHHHHH
T ss_pred             EEechhhhhhh
Confidence            99999999875

PyMOL of d2cx1a1

>d1q7ha1 b.122.1.1 (A:69-153) Hypothetical protein Ta1423, C-terminal domain {Archaeon Thermoplasma acidophilum [TaxId: 2303]}	Back information, alignment and structure

>d2apoa1 b.122.1.1 (A:247-331) Pseudouridine synthase II TruB, C-terminal domain {Archaeon Methanococcus jannaschii [TaxId: 2190]}	Back information, alignment and structure

>d2ey4a1 b.122.1.1 (A:253-336) Pseudouridine synthase II TruB, C-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d1iq8a3 b.122.1.1 (A:506-582) Archaeosine tRNA-guanine transglycosylase, C3 domain {Archaeon Pyrococcus horikoshii [TaxId: 53953]}	Back information, alignment and structure

>d1r3ea1 b.122.1.1 (A:238-318) Pseudouridine synthase II TruB, C-terminal domain {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d2q07a1 b.122.1.1 (A:460-527) Uncharacterized protein AF0587 {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d2cx1a2 d.17.6.4 (A:1-90) Hypothetical protein APE0525, N-terminal domain {Archaeon Aeropyrum pernix [TaxId: 56636]}	Back information, alignment and structure

>d2as0a1 b.122.1.9 (A:1-72) Hypothetical protein PH1915, N-terminal domain {Archaeon Pyrococcus horikoshii [TaxId: 53953]}	Back information, alignment and structure

>d1q7ha2 d.17.6.2 (A:3-68) Hypothetical protein Ta1423, N-terminal domain {Archaeon Thermoplasma acidophilum [TaxId: 2303]}	Back information, alignment and structure

>d1sqwa1 b.122.1.1 (A:95-170) Nip7p homolog, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1iq8a4 d.17.6.1 (A:361-505) Archaeosine tRNA-guanine transglycosylase, C2 domain {Archaeon Pyrococcus horikoshii [TaxId: 53953]}	Back information, alignment and structure

>d1k8wa3 b.122.1.1 (A:251-312) Pseudouridine synthase II TruB, C-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d2b78a1 b.122.1.9 (A:1-68) Hypothetical protein SMu776, N-terminal domain {Streptococcus mutans [TaxId: 1309]}	Back information, alignment and structure