Citrus Sinensis ID: 021437

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-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310--

MSVALSLMTFNLHEDQQEDSPNSWVKRRDLCISVITSYSPMILCTQQGVKSQLDYLQQCLPAYDQFGVSRKGPEDTSDEHCTIFYDKEKVELLEGGTFWLSESPSVPGSKAWGAEVPCIATWATFQLKGVEPPGFSFQIVNTNMDEFTARARRRSALLTWQHIASLPPSLPVIYCGGFNTQKESTTGRFLLGRSREHGVVGDMRDAWPNARMRKNVSLIRTYHGFKGNKQGALEFLKLIFRALCLCWDRQTQDLHIDWILFRGRSLIPGSCEVVNDNIDGYYPSSHYPIFAEFMLPRTVRVIEQPNSTQEEN

cccEEEEEEEcccccccccccccHHHHHHHHHHHHHHccccEEEEcccccccHHHHHHccccccEEEEEcccccccccccEEEEEEcccEEEEEEcEEEEccccccccccccccccccEEEEEEEEEccccccccEEEEEEcccccccHHHHHHHHHHHHHHHHHccccccEEEEccccccccccHHHHHcccccccccccccccHHHHHHHccccccccccccccccccccHHHHHHHHHHcccccccccccccEEEEEEEcccccccEEEEcccccccccccccccEEEEEEEEcccccccccccccccc

ccccEEEEEEEEEEcccccccccHHHHHHHHHHHHHHccccEEEHHHHHHHHHHHHHHHcccccEEEEEccccccccccEEEEEEEcccEEEEccccEEEccccccccccccccccccEEEEEEEEEccccccccEEEEEEcccccccHHHHHHHHHHHHHHHHHHcccccEEEEcccccccccHHHHHHHcccHHHHcccccccccHHHHcccccccccccccccccccccccccEEEccccccccccccccccEEEEEEEcccEEEEEEEEEccccccccccccccEEEEEEEcccccEccccccccccc

MSVALSLMTFNlhedqqedspnswvkrRDLCISVITsyspmilctQQGVKSQLDYLQQClpaydqfgvsrkgpedtsdehctiFYDKEKVELLEGgtfwlsespsvpgskawgaevpciATWATfqlkgveppgfsfQIVNTNMDEFTARARRRSALLTWQHiaslppslpviycggfntqkesttgrfllgrsrehgvvgdmrdawpnarmRKNVSLIRTYHGFKGNKQGALEFLKLIFRALCLCWDRQTQDLHIDWIlfrgrslipgscevvndnidgyypsshypifaefmlprtvrvieqpnstqeen

MSVALSLMTfnlhedqqedspnswvkRRDLCISVITSYSPMILCTQQGVKSQLDYLQQCLPAYDQFGVSRKGPEDTSDEHCTIFYDKEKVELLEGGTFWLSESPSVPGSKAWGAEVPCIATWATFQLKGVEPPGFSFQIVNTNMDEFTARARRRSALLTWQHIASLPPSLPVIYCGGFNTqkesttgrfllgrsrehgvvgdmrdawpnarMRKNVSLIRTYHGFKGNKQGALEFLKLIFRALCLCWDRQTQDLHIDWILFRGRSLIPGSCEVVNDNIDGYYPSSHYPIFAEFMLPRTVRVIeqpnstqeen

MSVALSLMTFNLHEDQQEDSPNSWVKRRDLCISVITSYSPMILCTQQGVKSQLDYLQQCLPAYDQFGVSRKGPEDTSDEHCTIFYDKEKVELLEGGTFWLSESPSVPGSKAWGAEVPCIATWATFQLKGVEPPGFSFQIVNTNMDEFTararrrsaLLTWQHIASLPPSLPVIYCGGFNTQKESTTGRFLLGRSREHGVVGDMRDAWPNARMRKNVSLIRTYHGFKGNKQGALEFLKLIFRALCLCWDRQTQDLHIDWILFRGRSLIPGSCEVVNDNIDGYYPSSHYPIFAEFMLPRTVRVIEQPNSTQEEN

***********************WVKRRDLCISVITSYSPMILCTQQGVKSQLDYLQQCLPAYDQFGVS*********EHCTIFYDKEKVELLEGGTFWLSESPSVPGSKAWGAEVPCIATWATFQLKGVEPPGFSFQIVNTNMDEFTARARRRSALLTWQHIASLPPSLPVIYCGGFNTQKESTTGRFLLGRSREHGVVGDMRDAWPNARMRKNVSLIRTYHGFKGNKQGALEFLKLIFRALCLCWDRQTQDLHIDWILFRGRSLIPGSCEVVNDNIDGYYPSSHYPIFAEFMLPRTVRVI**********

MSVALSLMTFNLH**********WVKRRDLCISVITSYSPMILCTQQGVKSQLDYLQQCLPAYDQFGV********SDEHCTIFYDKEKVELLEGGTFWLSESPSVPGSKAWGAEVPCIATWATFQLKGVEPPGFSFQIVNTNMDEFTARARRRSALLTWQHIASLPPSLPVIYCGGFNTQKESTTGRFLLGRSREHGVVGDMRDAWPNARMRKNVSLIRTYHGFKGNKQGALEFLKLIFRALCLCWDRQTQDLHIDWILFRGRSLIPGSCEVVNDNIDGYYPSSHYPIFAEFMLPRTVRVIEQ********

**VALSLMTFNLHEDQQEDSPNSWVKRRDLCISVITSYSPMILCTQQGVKSQLDYLQQCLPAYDQFGVSRKGPEDTSDEHCTIFYDKEKVELLEGGTFWLSESPSVPGSKAWGAEVPCIATWATFQLKGVEPPGFSFQIVNTNMDEFTARARRRSALLTWQHIASLPPSLPVIYCGGFNTQKESTTGRFLLGRSREHGVVGDMRDAWPNARMRKNVSLIRTYHGFKGNKQGALEFLKLIFRALCLCWDRQTQDLHIDWILFRGRSLIPGSCEVVNDNIDGYYPSSHYPIFAEFMLPRTVR************

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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		312	2.2.26 [Sep-21-2011]
Q24239		354	Protein angel OS=Drosophi	yes	no	0.532	0.468	0.232	0.0004

>sp\|Q24239\|ANGEL_DROME Protein angel OS=Drosophila melanogaster GN=angel PE=1 SV=2	Back alignment and function desciption

 Score = 45.8 bits (107), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 41/176 (23%), Positives = 72/176 (40%), Gaps = 10/176 (5%)

Query: 23  SWVKRRDLCISVITSYSPMILCTQQGVKSQLDYLQQCLPAYD--QFGVSRKGPEDTSDEH 80
           SW +R+   +  +    P ILC Q+     L  L Q L   +  +     K       + 
Sbjct: 97  SWQRRQQNLLRELLKLDPDILCLQEMQFDHLPVLVQRLRMGNGKKLAYVYKKKTGCRTDG 156

Query: 81  CTIFYDKEKVELLEGGTFWLSESPSVPGSKAWGAEVPCIATWATFQLKGVEPPGFSFQIV 140
           C I YD  K ELL+     L +      ++        +A +A F+ K  +     F + 
Sbjct: 157 CAIVYDSSKFELLDHQAVELYDQAVALLNR------DNVALFARFRFKKQQEQQKEFVVA 210

Query: 141 NTNMDEFTARARRRSALL--TWQHIASLPPSLPVIYCGGFNTQKESTTGRFLLGRS 194
            T++   T R+  R A +    + + S     P++  G FN+  +S+   FL+G++
Sbjct: 211 TTHLLFNTKRSDVRCAQVERILEELQSFSTDTPIVLTGDFNSLPDSSPIEFLVGKN 266

Drosophila melanogaster (taxid: 7227)

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		312
356500657		310	PREDICTED: uncharacterized protein LOC10	0.977	0.983	0.888	1e-165
356562569		310	PREDICTED: uncharacterized protein LOC10	0.993	1.0	0.878	1e-164
225445865		310	PREDICTED: uncharacterized protein LOC10	0.993	1.0	0.878	1e-163
118484521		315	unknown [Populus trichocarpa]	0.996	0.987	0.871	1e-163
224088280		307	predicted protein [Populus trichocarpa]	0.977	0.993	0.878	1e-162
145350190		316	endonuclease/exonuclease/phosphatase dom	0.971	0.958	0.828	1e-155
297802942		320	hypothetical protein ARALYDRAFT_913382 [	0.971	0.946	0.817	1e-155
449457883		308	PREDICTED: uncharacterized protein LOC10	0.971	0.983	0.844	1e-152
242072524		308	hypothetical protein SORBIDRAFT_06g00336	0.967	0.980	0.821	1e-151
218196473		311	hypothetical protein OsI_19281 [Oryza sa	0.974	0.977	0.812	1e-150

>gi\|356500657\|ref\|XP_003519148.1\| PREDICTED: uncharacterized protein LOC100783799 [Glycine max]	Back alignment and taxonomy information

 Score =  587 bits (1513), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 271/305 (88%), Positives = 295/305 (96%)

Query: 1   MSVALSLMTFNLHEDQQEDSPNSWVKRRDLCISVITSYSPMILCTQQGVKSQLDYLQQCL 60
           MSV+L++MTFNLH+D+ +DSPNSW KRRD+CISVITSYSP+ILCTQQGVK+QLD+LQQ L
Sbjct: 1   MSVSLTVMTFNLHDDEPQDSPNSWEKRRDMCISVITSYSPIILCTQQGVKAQLDFLQQGL 60

Query: 61  PAYDQFGVSRKGPEDTSDEHCTIFYDKEKVELLEGGTFWLSESPSVPGSKAWGAEVPCIA 120
           P YDQFG+SRKGP+DT+D+HCTIFYDKEKVELLEGGTFWLSESPSVPGS +WG+EVPCIA
Sbjct: 61  PGYDQFGISRKGPQDTTDQHCTIFYDKEKVELLEGGTFWLSESPSVPGSMSWGSEVPCIA 120

Query: 121 TWATFQLKGVEPPGFSFQIVNTNMDEFTARARRRSALLTWQHIASLPPSLPVIYCGGFNT 180
           TWATFQLKGVEPPGFSFQIVNTNMDEF+ RARRRSALLTWQHIASLPPSLPV+YCGGFNT
Sbjct: 121 TWATFQLKGVEPPGFSFQIVNTNMDEFSPRARRRSALLTWQHIASLPPSLPVVYCGGFNT 180

Query: 181 QKESTTGRFLLGRSREHGVVGDMRDAWPNARMRKNVSLIRTYHGFKGNKQGALEFLKLIF 240
           QKESTTGRFLLGRSREHGVVGDMRDAWP+AR+RKNVSLI TYHGFKG+KQG LEFLKLIF
Sbjct: 181 QKESTTGRFLLGRSREHGVVGDMRDAWPSARVRKNVSLIHTYHGFKGDKQGTLEFLKLIF 240

Query: 241 RALCLCWDRQTQDLHIDWILFRGRSLIPGSCEVVNDNIDGYYPSSHYPIFAEFMLPRTVR 300
           RALCLCWDRQTQDLHIDWILFRGRSLIP SCEVVNDNIDGYYPSSH+PIFAEFMLPRTVR
Sbjct: 241 RALCLCWDRQTQDLHIDWILFRGRSLIPVSCEVVNDNIDGYYPSSHFPIFAEFMLPRTVR 300

Query: 301 VIEQP 305
           ++E P
Sbjct: 301 MLESP 305

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|356562569\|ref\|XP_003549542.1\| PREDICTED: uncharacterized protein LOC100784843 [Glycine max]	Back alignment and taxonomy information

>gi\|225445865\|ref\|XP_002278804.1\| PREDICTED: uncharacterized protein LOC100263811 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|118484521\|gb\|ABK94135.1\| unknown [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|224088280\|ref\|XP_002308403.1\| predicted protein [Populus trichocarpa] gi\|222854379\|gb\|EEE91926.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi|145350190|ref|NP_194819.3| endonuclease/exonuclease/phosphatase domain-containing protein [Arabidopsis thaliana] gi|186515019|ref|NP_001119082.1| endonuclease/exonuclease/phosphatase domain-containing protein [Arabidopsis thaliana] gi|332660427|gb|AEE85827.1| endonuclease/exonuclease/phosphatase domain-containing protein [Arabidopsis thaliana] gi|332660428|gb|AEE85828.1| endonuclease/exonuclease/phosphatase domain-containing protein [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|297802942\|ref\|XP_002869355.1\| hypothetical protein ARALYDRAFT_913382 [Arabidopsis lyrata subsp. lyrata] gi\|297315191\|gb\|EFH45614.1\| hypothetical protein ARALYDRAFT_913382 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|449457883\|ref\|XP_004146677.1\| PREDICTED: uncharacterized protein LOC101208977 [Cucumis sativus] gi\|449503165\|ref\|XP_004161866.1\| PREDICTED: uncharacterized LOC101208977 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|242072524\|ref\|XP_002446198.1\| hypothetical protein SORBIDRAFT_06g003360 [Sorghum bicolor] gi\|241937381\|gb\|EES10526.1\| hypothetical protein SORBIDRAFT_06g003360 [Sorghum bicolor]	Back alignment and taxonomy information

>gi\|218196473\|gb\|EEC78900.1\| hypothetical protein OsI_19281 [Oryza sativa Indica Group]	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		312
TAIR\|locus:2126654		316	AT4G30900 "AT4G30900" [Arabido	1.0	0.987	0.787	5.5e-141
CGD\|CAL0003679		363	orf19.5295 [Candida albicans (	0.516	0.443	0.3	1e-09
UNIPROTKB\|Q5A5V5		363	EEP1 "Potential Endonuclease/E	0.516	0.443	0.3	1e-09
UNIPROTKB\|G4NI36		296	MGG_09360 "Endonuclease/exonuc	0.605	0.638	0.272	1.3e-07
UNIPROTKB\|G4N2Z1		309	MGG_07632 "Endonuclease/exonuc	0.711	0.718	0.246	1.3e-06
CGD\|CAL0004444		303	orf19.2059 [Candida albicans (	0.496	0.511	0.290	3.8e-05
UNIPROTKB\|Q5AD08		303	EEP2 "Potential Endonuclease/E	0.496	0.511	0.290	3.8e-05

TAIR\|locus:2126654 AT4G30900 "AT4G30900" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1379 (490.5 bits), Expect = 5.5e-141, P = 5.5e-141
 Identities = 249/316 (78%), Positives = 283/316 (89%)

Query:     1 MSVALSLMTFNLHEDQQEDSPNSWVKRRDLCISVITSYSPMILCTQQGVKSQLDYLQQCL 60
             MSV+LS+M+FNLH+D  E+SPNSW+KR+DLC++VITSYSP++LCTQQGVKSQLDYLQQ L
Sbjct:     1 MSVSLSVMSFNLHDDLPEESPNSWLKRKDLCLTVITSYSPIVLCTQQGVKSQLDYLQQGL 60

Query:    61 PAYDQFGVSRKGPEDTSDEHCTIFYDKEKVELLEGGTFWLSESPSVPGSKAWGAEVPCIA 120
             PAYDQFG+SR GP D +DEHCTIF++KEKVELLEGGTFWLSESPSVPGS AWG+ VPCIA
Sbjct:    61 PAYDQFGISRTGPGDANDEHCTIFFNKEKVELLEGGTFWLSESPSVPGSTAWGSAVPCIA 120

Query:   121 TWATFQLKGVEPPGFSFQIVNTNMDEFTXXXXXXXXLLTWQHIASLPPSLPVIYCGGFNT 180
             TWATFQLKG EPPGFSFQIVNTN+DE +        LLTWQHIASLPP+LPV+YCGGFNT
Sbjct:   121 TWATFQLKGAEPPGFSFQIVNTNLDEISPRARRRSALLTWQHIASLPPTLPVVYCGGFNT 180

Query:   181 QKESTTGRFLLGRSREHGVVGDMRDAWPNARMRKNVSLIRTYHGFKGNKQGALEFLKLIF 240
             QKESTTGRFLLGRSREHGVVGDMRDAWP+AR+RKNV+LIRTYH FKG+KQG +EFLKLIF
Sbjct:   181 QKESTTGRFLLGRSREHGVVGDMRDAWPSARVRKNVALIRTYHDFKGDKQGTVEFLKLIF 240

Query:   241 RALCLCWDRQTQDLHIDWILFRGRSLIPGSCEVVNDNIDGYYPSSHYPIFAEFMLPRTVR 300
             RALCLCWDRQTQDLH DWIL+RGRS++P  CE+VND ID  YPSSHYP+FAEFMLPR+VR
Sbjct:   241 RALCLCWDRQTQDLHTDWILYRGRSIVPVMCEIVNDKIDDLYPSSHYPVFAEFMLPRSVR 300

Query:   301 VIEQ--PNST--QEEN 312
             ++E   P S   QEE+
Sbjct:   301 MLEPTPPVSAPAQEES 316

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0005886 "plasma membrane" evidence=IDA

CGD\|CAL0003679 orf19.5295 [Candida albicans (taxid:5476)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5A5V5 EEP1 "Potential Endonuclease/Exonuclease/Phosphatase" [Candida albicans SC5314 (taxid:237561)]	Back alignment and assigned GO terms

UNIPROTKB\|G4NI36 MGG_09360 "Endonuclease/exonuclease/phosphatase" [Magnaporthe oryzae 70-15 (taxid:242507)]	Back alignment and assigned GO terms

UNIPROTKB\|G4N2Z1 MGG_07632 "Endonuclease/exonuclease/phosphatase" [Magnaporthe oryzae 70-15 (taxid:242507)]	Back alignment and assigned GO terms

CGD\|CAL0004444 orf19.2059 [Candida albicans (taxid:5476)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5AD08 EEP2 "Potential Endonuclease/Exonuclease/Phosphatase" [Candida albicans SC5314 (taxid:237561)]	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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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:
	estExt_fgenesh4_pg.C_LG_VI1224	SubName- Full=Putative uncharacterized protein; (307 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

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		312
cd09083		252	cd09083, EEP-1, Exonuclease-Endonuclease-Phosphata	5e-94
cd08372		241	cd08372, EEP, Exonuclease-Endonuclease-Phosphatase	1e-06
COG3568		259	COG3568, ElsH, Metal-dependent hydrolase [General	7e-05
cd09096		280	cd09096, Deadenylase_nocturnin, C-terminal deadeny	3e-04

>gnl\|CDD\|197317 cd09083, EEP-1, Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1	Back alignment and domain information

 Score =  278 bits (714), Expect = 5e-94
 Identities = 102/288 (35%), Positives = 137/288 (47%), Gaps = 36/288 (12%)

Query: 6   SLMTFNLHEDQQEDSPNSWVKRRDLCISVITSYSPMILCTQQGVKSQLDYLQQCLPAYDQ 65
            +MTFN+  D   D  NSW  R+DL   +I  Y P I+ TQ+ +  QL  L++ LP YD 
Sbjct: 1   RVMTFNIRYDNPSDGENSWENRKDLVAELIKFYDPDIIGTQEALPHQLADLEELLPEYDW 60

Query: 66  FGVSRKGPEDTSDEHCTIFYDKEKVELLEGGTFWLSESPSVPGSKAWGAEVPCIATWATF 125
            GV R   ++   E   IFY K++ ELL+ GTFWLSE+P V GSK W A +P I TWA F
Sbjct: 61  IGVGRDDGKE-KGEFSAIFYRKDRFELLDSGTFWLSETPDVVGSKGWDAALPRICTWARF 119

Query: 126 QLKGVEPPGFSFQIVNTNMDEFTARARRRSALLTWQHIASLPPSLPVIYCGGFNTQKEST 185
           + K     G  F + NT++D     AR  SA L  + I  +   LPVI  G FN + +S 
Sbjct: 120 KDKKT---GKEFYVFNTHLDHVGEEAREESAKLILERIKEIAGDLPVILTGDFNAEPDSE 176

Query: 186 TGRFLLGRSREHGVVGDMRDAWPNARMRKNVSLIRTYHGFKGNKQGALEFLKLIFRALCL 245
             + L          G ++DA   A          T+HGFKG   G              
Sbjct: 177 PYKTLTS--------GGLKDARDTAATTDG-GPEGTFHGFKGPPGG-------------- 213

Query: 246 CWDRQTQDLHIDWILFRGRSLIPGSCEVVNDNIDGYYPSSHYPIFAEF 293
                     ID+I      +   S E++ D  DG YPS H+P+ A+ 
Sbjct: 214 --------SRIDYIFVSP-GVKVLSYEILTDRYDGRYPSDHFPVVADL 252

This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins. Length = 252

>gnl\|CDD\|197306 cd08372, EEP, Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily	Back alignment and domain information

>gnl\|CDD\|226098 COG3568, ElsH, Metal-dependent hydrolase [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|197330 cd09096, Deadenylase_nocturnin, C-terminal deadenylase domain of nocturnin and related domains	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		312
PLN03144		606	Carbon catabolite repressor protein 4 homolog; Pro	100.0
PRK11756		268	exonuclease III; Provisional	99.97
TIGR03395		283	sphingomy sphingomyelin phosphodiesterase. Members	99.96
smart00476		276	DNaseIc deoxyribonuclease I. Deoxyribonuclease I c	99.96
COG3568		259	ElsH Metal-dependent hydrolase [General function p	99.96
PRK05421		263	hypothetical protein; Provisional	99.94
COG0708		261	XthA Exonuclease III [DNA replication, recombinati	99.93
TIGR00195		254	exoDNase_III exodeoxyribonuclease III. The model b	99.93
PTZ00297		1452	pantothenate kinase; Provisional	99.92
KOG2338		495	consensus Transcriptional effector CCR4-related pr	99.91
PRK13911		250	exodeoxyribonuclease III; Provisional	99.9
TIGR00633		255	xth exodeoxyribonuclease III (xth). This family is	99.9
KOG3873		422	consensus Sphingomyelinase family protein [Signal	99.86
KOG2756		349	consensus Predicted Mg2+-dependent phosphodiestera	99.85
PF03372		249	Exo_endo_phos: Endonuclease/Exonuclease/phosphatas	99.78
COG2374		798	Predicted extracellular nuclease [General function	99.76
PRK15251		271	cytolethal distending toxin subunit CdtB; Provisio	99.75
COG5239		378	CCR4 mRNA deadenylase, exonuclease subunit and rel	99.72
COG3021		309	Uncharacterized protein conserved in bacteria [Fun	99.71
KOG0620		361	consensus Glucose-repressible alcohol dehydrogenas	99.62
smart00128		310	IPPc Inositol polyphosphate phosphatase, catalytic	99.44
KOG0566		1080	consensus Inositol-1,4,5-triphosphate 5-phosphatas	99.08
PF14529		119	Exo_endo_phos_2: Endonuclease-reverse transcriptas	98.65
COG5411		460	Phosphatidylinositol 5-phosphate phosphatase [Sign	98.39
PLN03191		621	Type I inositol-1,4,5-trisphosphate 5-phosphatase	98.37
KOG1294		335	consensus Apurinic/apyrimidinic endonuclease and r	98.07
PTZ00312		356	inositol-1,4,5-triphosphate 5-phosphatase; Provisi	94.59
KOG1976		391	consensus Inositol polyphosphate 5-phosphatase, ty	93.34

>PLN03144 Carbon catabolite repressor protein 4 homolog; Provisional	Back alignment and domain information

Probab=100.00  E-value=1.8e-33  Score=265.07  Aligned_cols=192  Identities=16%  Similarity=0.220  Sum_probs=144.2

Q ss_pred             CccEEEEEeecCCCC---------CCCCCCcHHHHHHHHHHHHhhcCCcEEEEcCCCcccHHH-HHhcCCCCceEeeecC
Q 021437            2 SVALSLMTFNLHEDQ---------QEDSPNSWVKRRDLCISVITSYSPMILCTQQGVKSQLDY-LQQCLPAYDQFGVSRK   71 (312)
Q Consensus         2 ~~~l~v~T~Nv~~~~---------~~~~~~~w~~r~~~i~~~i~~~~pDIi~LQEv~~~~~~~-l~~~l~~y~~~~~~~~   71 (312)
                      +.++|||||||....         -++....|+.|+..|++.|..++|||||||||...++++ +...|..|.|.+....
T Consensus       252 ~~~frVmSYNILAd~ya~~dly~ycp~~aL~W~yRk~lIl~EI~~~~aDIICLQEV~~~~~~d~~~p~L~~~GY~Gv~~~  331 (606)
T PLN03144        252 AGTFTVLSYNILSDLYATSDMYSYCPPWALSWTYRRQNLLREIVGYRADILCLQEVQSDHFEEFFAPELDKHGYQALYKK  331 (606)
T ss_pred             CCCEEEEEeeeccccccCcccccCCCccccCHHHHHHHHHHHHHhcCCCEEEEeecCHHHHHHHHHhhhhhcCceEEEeC
Confidence            457999999998653         123467899999999999999999999999999888865 4556755555444332


Q ss_pred             CCC------CCCCceEEEEEeCCCcEEEeeeeEe-----ccCCCCCCCCcccCccCCc-----eEEEEEeeeccC-----
Q 021437           72 GPE------DTSDEHCTIFYDKEKVELLEGGTFW-----LSESPSVPGSKAWGAEVPC-----IATWATFQLKGV-----  130 (312)
Q Consensus        72 ~~~------~~~~~~~ai~~~~~~~~~~~~~~~~-----l~~~p~~~~~~~~~~~~~r-----~~~~~~~~~~~~-----  130 (312)
                      ..+      ....+++||||++++|++++...+.     ++..+...++.+++..++|     +++++.|+.+.+     
T Consensus       332 Kt~~~~~~~~~~~DGcAIFyr~drFeLv~~~~ief~~~~lslt~~~~~s~~~~~~l~Rl~kdNVAliv~Le~k~~~~~~~  411 (606)
T PLN03144        332 KTTEVYTGNTYVIDGCATFFRRDRFSLVKKYEVEFNKAAQSLTEALIPSAQKKAALNRLLKDNVALIVVLEAKFGNQGAD  411 (606)
T ss_pred             CCCccccccccCCceeEEEEECcceEEEEeeeeeccchhhccCccccccccchhhhhhhccCcEEEEEEEEEeccccccc
Confidence            111      1246789999999999999886653     3333444344455666777     788999988621     


Q ss_pred             -CCCCcEEEEEeccCCC--ccHHHHHHHHHHHHHHHHhcC--CCCCEEEEecCCCCCCchhHHhhhcc
Q 021437          131 -EPPGFSFQIVNTNMDE--FTARARRRSALLTWQHIASLP--PSLPVIYCGGFNTQKESTTGRFLLGR  193 (312)
Q Consensus       131 -~~~g~~~~v~~~Hl~~--~~~~~r~~~~~~l~~~l~~~~--~~~pvIv~GDfN~~~~~~~~~~l~~~  193 (312)
                       ...++.|.|+||||.+  ...+.|..|+..|++.|+++.  .+.|+|||||||+.|++..|+.|..+
T Consensus       412 ~~~~~~~l~VaNTHL~~~p~~~dvRl~Q~~~Ll~~l~~~~~~~~~PvIlcGDFNS~P~S~vy~lLt~G  479 (606)
T PLN03144        412 NGGKRQLLCVANTHIHANQELKDVKLWQVHTLLKGLEKIAASADIPMLVCGDFNSVPGSAPHCLLATG  479 (606)
T ss_pred             CCCCccEEEEEEeeeccCCccchhHHHHHHHHHHHHHHHhhcCCCceEEeccCCCCCCChhhhhhhcC
Confidence             0114579999999954  456789999999999998764  36799999999999999999998764

>PRK11756 exonuclease III; Provisional	Back alignment and domain information

>TIGR03395 sphingomy sphingomyelin phosphodiesterase	Back alignment and domain information

>smart00476 DNaseIc deoxyribonuclease I	Back alignment and domain information

>COG3568 ElsH Metal-dependent hydrolase [General function prediction only]	Back alignment and domain information

>PRK05421 hypothetical protein; Provisional	Back alignment and domain information

>COG0708 XthA Exonuclease III [DNA replication, recombination, and repair]	Back alignment and domain information

>TIGR00195 exoDNase_III exodeoxyribonuclease III	Back alignment and domain information

>PTZ00297 pantothenate kinase; Provisional	Back alignment and domain information

>KOG2338 consensus Transcriptional effector CCR4-related protein [Transcription]	Back alignment and domain information

>PRK13911 exodeoxyribonuclease III; Provisional	Back alignment and domain information

>TIGR00633 xth exodeoxyribonuclease III (xth)	Back alignment and domain information

>KOG3873 consensus Sphingomyelinase family protein [Signal transduction mechanisms]	Back alignment and domain information

>KOG2756 consensus Predicted Mg2+-dependent phosphodiesterase TTRAP [Signal transduction mechanisms]	Back alignment and domain information

>PF03372 Exo_endo_phos: Endonuclease/Exonuclease/phosphatase family Subset of Pfam family Subset of Pfam family; InterPro: IPR005135 This domain is found in a large number of proteins including magnesium dependent endonucleases and phosphatases involved in intracellular signalling []	Back alignment and domain information

>COG2374 Predicted extracellular nuclease [General function prediction only]	Back alignment and domain information

>PRK15251 cytolethal distending toxin subunit CdtB; Provisional	Back alignment and domain information

>COG5239 CCR4 mRNA deadenylase, exonuclease subunit and related nucleases [RNA processing and modification]	Back alignment and domain information

>COG3021 Uncharacterized protein conserved in bacteria [Function unknown]	Back alignment and domain information

>KOG0620 consensus Glucose-repressible alcohol dehydrogenase transcriptional effector CCR4 and related proteins [Transcription]	Back alignment and domain information

>smart00128 IPPc Inositol polyphosphate phosphatase, catalytic domain homologues	Back alignment and domain information

>KOG0566 consensus Inositol-1,4,5-triphosphate 5-phosphatase (synaptojanin), INP51/INP52/INP53 family [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>PF14529 Exo_endo_phos_2: Endonuclease-reverse transcriptase ; PDB: 2EI9_A 1WDU_B	Back alignment and domain information

>COG5411 Phosphatidylinositol 5-phosphate phosphatase [Signal transduction mechanisms]	Back alignment and domain information

>PLN03191 Type I inositol-1,4,5-trisphosphate 5-phosphatase 2; Provisional	Back alignment and domain information

>KOG1294 consensus Apurinic/apyrimidinic endonuclease and related enzymes [Replication, recombination and repair]	Back alignment and domain information

>PTZ00312 inositol-1,4,5-triphosphate 5-phosphatase; Provisional	Back alignment and domain information

>KOG1976 consensus Inositol polyphosphate 5-phosphatase, type I [Lipid transport and metabolism]	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		312
3g6s_A		267	Crystal Structure Of The EndonucleaseEXONUCLEASEPHO		2e-22
3mpr_A		298	Crystal Structure Of EndonucleaseEXONUCLEASEPHOSPHA		2e-19
3l1w_A		257	The Crystal Structure Of A Functionally Unknown Con		6e-12

>pdb|3G6S|A Chain A, Crystal Structure Of The EndonucleaseEXONUCLEASEPHOSPHATASE (BVU_0621) FROM Bacteroides Vulgatus. Northeast Structural Genomics Consortium Target Bvr56d Length = 267

Back alignment and structure

Iteration: 1

Score = 102 bits (255), Expect = 2e-22, Method: Compositional matrix adjust. Identities = 73/238 (30%), Positives = 102/238 (42%), Gaps = 24/238 (10%) Query: 9 TFNLHEDQQEDSPNSWVKRRDLCISVITSYSPMILCTQQGVKSQLDYLQQCLPAYDQFGV 68 TFN+ D +DS N+W R+D I + I+ Q+ + +Q L+ LP YD GV Sbjct: 8 TFNIRYDNPQDSLNNWQYRKDRVCQFIKDHELDIVGXQEVLHNQFQDLRAGLPEYDGIGV 67 Query: 69 SRKGPEDTSDEHCTIFYDKEKVELLEGGTFWLSESPSVPGSKAWGAEVPCIATWATFQLK 128 R + T+ E+ +FY K+K E+L+ TFWL+E+P G W A IATWA F+ K Sbjct: 68 GRDDGK-TAGEYAPLFYRKDKYEVLDSNTFWLAENPDSVGXXGWDAVCVRIATWAKFKDK 126 Query: 129 GVEPPGFSFQIVNTNMDEFTXXXXXXXXLLTWQHIASLPPSLPVIYCGGFNTQKES---- 184 G F VNT+ D LL + I + P + G FN S Sbjct: 127 AT---GKIFXAVNTHFDHVGEEARRQSALLIIRKIKEIVGERPAVVTGDFNVTDASDAYE 183 Query: 185 --TTGRFLLGRSREHGVVGDMRDAWPNARMRKNVSLIRTYHGFKGNKQGALEFLKLIF 240 TT F+ +DA+ A V T+H F E + IF Sbjct: 184 TITTNEFV------------XKDAYKTAARVTGVDY--TFHDFARIPAEDCEKIDFIF 227

PyMOL of 3g6s

>pdb|3MPR|A Chain A, Crystal Structure Of EndonucleaseEXONUCLEASEPHOSPHATASE FAMILY Protein From Bacteroides Thetaiotaomicron, Northeast Structural Genomics Consortium Target Btr318a Length = 298

Back alignment and structure

>pdb|3L1W|A Chain A, The Crystal Structure Of A Functionally Unknown Conserved Protein From Enterococcus Faecalis V583 Length = 257

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		312
3g6s_A		267	Putative endonuclease/exonuclease/phosphatase fami	9e-67
3l1w_A		257	Uncharacterized protein; APC29019.2, conserved pro	1e-62
3mpr_A		298	Putative endonuclease/exonuclease/phosphatase FAM	2e-59
3teb_A		266	Endonuclease/exonuclease/phosphatase; PSI-biology,	1e-20
3ngq_A		398	CCR4-NOT transcription complex subunit 6-like; alp	5e-18
1zwx_A		301	SMCL, sphingomyelinase-C; dnase1-like fold, beta-h	1e-13
2ddr_A		306	Sphingomyelin phosphodiesterase; DNAse I like fold	1e-13
3i41_A		317	Beta-hemolysin; beta toxin, sphingomyelinase, toxi	5e-10
2a40_B		260	Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse	2e-09

>3g6s_A Putative endonuclease/exonuclease/phosphatase family protein; alpha-beta protein, structural genomics, PSI-2; 2.50A {Bacteroides vulgatus atcc 8482} Length = 267	Back alignment and structure

 Score =  209 bits (532), Expect = 9e-67
 Identities = 82/293 (27%), Positives = 117/293 (39%), Gaps = 34/293 (11%)

Query: 5   LSLMTFNLHEDQQEDSPNSWVKRRDLCISVITSYSPMILCTQQGVKSQLDYLQQCLPAYD 64
           +   TFN+  D  +DS N+W  R+D     I  +   I+  Q+ + +Q   L+  LP YD
Sbjct: 4   VRWATFNIRYDNPQDSLNNWQYRKDRVCQFIKDHELDIVGMQEVLHNQFQDLRAGLPEYD 63

Query: 65  QFGVSRKGPEDTSDEHCTIFYDKEKVELLEGGTFWLSESPSVPGSKAWGAEVPCIATWAT 124
             GV R     T+ E+  +FY K+K E+L+  TFWL+E+P   G   W A    IATWA 
Sbjct: 64  GIGVGRD-DGKTAGEYAPLFYRKDKYEVLDSNTFWLAENPDSVGMMGWDAVCVRIATWAK 122

Query: 125 FQLKGVEPPGFSFQIVNTNMDEFTARARRRSALLTWQHIASLPPSLPVIYCGGFNTQKES 184
           F+ K     G  F  VNT+ D     ARR+SALL  + I  +    P +  G FN    S
Sbjct: 123 FKDK---ATGKIFMAVNTHFDHVGEEARRQSALLIIRKIKEIVGERPAVVTGDFNVTDAS 179

Query: 185 TTGRFLLGRSREHGVVGDMRDAWPNARMRKNVSLIRTYHGFKGNKQGALEFLKLIFRALC 244
                +            M+DA+  A     V    T+H F                   
Sbjct: 180 DAYETITTNE------FVMKDAYKTAARVTGVD--YTFHDFARIP--------------- 216

Query: 245 LCWDRQTQDLHIDWILFRGRSLIPGSCEVVNDNIDGYYPSSHYPIFAEFMLPR 297
                      ID+I    + L+      +   +     S H P  A+  L  
Sbjct: 217 -----AEDCEKIDFIFVTPQVLV--KSCEIPAEVPEALLSDHNPQLADLELEH 262

PyMOL of 3g6s

>3l1w_A Uncharacterized protein; APC29019.2, conserved protein, enterococcus faecalis V583, PSI-2, MCSG, structural genomics; 1.60A {Enterococcus faecalis} Length = 257	Back alignment and structure

>3mpr_A Putative endonuclease/exonuclease/phosphatase FAM protein; structural genomics, PSI-2, protein structure initiative; HET: MSE PEG; 1.90A {Bacteroides thetaiotaomicron} Length = 298	Back alignment and structure

>3teb_A Endonuclease/exonuclease/phosphatase; PSI-biology, MCSG, midwest center for structural genomics; 2.99A {Leptotrichia buccalis c-1013-b} Length = 266	Back alignment and structure

>3ngq_A CCR4-NOT transcription complex subunit 6-like; alpha/beta sandwich fold, hydrolase; HET: 1PS; 1.80A {Homo sapiens} PDB: 3ngo_A 3ngn_A Length = 398	Back alignment and structure

>1zwx_A SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpin, hydrolase; 1.90A {Listeria ivanovii} SCOP: d.151.1.3 Length = 301	Back alignment and structure

>2ddr_A Sphingomyelin phosphodiesterase; DNAse I like folding, riken structural genomics/proteomics initiative, RSGI, structural genomics, hydrolase; 1.40A {Bacillus cereus} SCOP: d.151.1.3 PDB: 2dds_A 2ddt_A* 2uyr_X Length = 306	Back alignment and structure

>3i41_A Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1.75A {Staphylococcus aureus} PDB: 3i46_A 3i48_A 3i5v_A* 3k55_A Length = 317	Back alignment and structure

>2a40_B Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse I, ARP2/3, structural protein; HET: HIC NAG ATP; 1.80A {Bos taurus} SCOP: d.151.1.1 PDB: 1dnk_A* 2a3z_B* 2a41_B* 2a42_B* 2d1k_B* 2dnj_A* 3cjc_D* 3dni_A* 1atn_D* Length = 260	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		312
3g6s_A		267	Putative endonuclease/exonuclease/phosphatase fami	100.0
3mpr_A		298	Putative endonuclease/exonuclease/phosphatase FAM	100.0
3l1w_A		257	Uncharacterized protein; APC29019.2, conserved pro	100.0
4gz1_A		256	Tyrosyl-DNA phosphodiesterase 2; protein-DNA compl	100.0
4f1h_A		250	Tyrosyl-DNA phosphodiesterase 2; hydrolase-DNA com	100.0
3ngq_A		398	CCR4-NOT transcription complex subunit 6-like; alp	100.0
4fva_A		256	5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosy	100.0
3teb_A		266	Endonuclease/exonuclease/phosphatase; PSI-biology,	100.0
4gew_A		362	5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosy	100.0
1zwx_A		301	SMCL, sphingomyelinase-C; dnase1-like fold, beta-h	99.97
3i41_A		317	Beta-hemolysin; beta toxin, sphingomyelinase, toxi	99.97
2ddr_A		306	Sphingomyelin phosphodiesterase; DNAse I like fold	99.96
1ako_A		268	Exonuclease III; AP-endonuclease, DNA repair; 1.70	99.96
2jc4_A		256	Exodeoxyribonuclease III; hydrolase, repair phosph	99.96
4b8c_D		727	Glucose-repressible alcohol dehydrogenase transcr	99.96
1vyb_A		238	ORF2 contains A reverse transcriptase domain; endo	99.95
2a40_B		260	Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse	99.95
2j63_A		467	AP-endonuclease; base excision repair, lyase; 2.48	99.94
1wdu_A		245	TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA	99.94
2voa_A		257	AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP	99.94
2o3h_A		285	DNA-(apurinic or apyrimidinic site) lyase; APE, en	99.94
1hd7_A		318	DNA-(apurinic or apyrimidinic site) lyase; DNA rep	99.94
3g91_A		265	MTH0212, exodeoxyribonuclease; double-strand speci	99.93
2jc5_A		259	Exodeoxyribonuclease; hydrolase, repair phosphodie	99.93
2imq_X		282	Salivary nitrophorin; ferrous heme, beta-sandwich,	99.91
2ei9_A		240	Non-LTR retrotransposon R1BMKS ORF2 protein; four	99.89
2f1n_A		262	CDT B, cytolethal distending toxin subunit B; E.co	99.8
1sr4_B		261	CDT B, cytolethal distending toxin protein B; bact	99.79
1i9z_A		347	Synaptojanin, phosphatidylinositol phosphate phosp	99.78
2xsw_A		357	72 kDa inositol polyphosphate 5-phosphatase; inosi	99.67
3mtc_A		313	Type II inositol-1,4,5-trisphosphate 5-phosphatas;	99.57
4a9c_A		316	Phosphatidylinositol-3,4,5-trisphosphate 5-phosph;	99.39

>3g6s_A Putative endonuclease/exonuclease/phosphatase family protein; alpha-beta protein, structural genomics, PSI-2; 2.50A {Bacteroides vulgatus atcc 8482}	Back alignment and structure

Probab=100.00  E-value=9.1e-43  Score=304.34  Aligned_cols=260  Identities=32%  Similarity=0.494  Sum_probs=216.2

Q ss_pred             ccEEEEEeecCCCCCCCCCCcHHHHHHHHHHHHhhcCCcEEEEcCCCcccHHHHHhcCCCCceEeeecCCCCCCCCceEE
Q 021437            3 VALSLMTFNLHEDQQEDSPNSWVKRRDLCISVITSYSPMILCTQQGVKSQLDYLQQCLPAYDQFGVSRKGPEDTSDEHCT   82 (312)
Q Consensus         3 ~~l~v~T~Nv~~~~~~~~~~~w~~r~~~i~~~i~~~~pDIi~LQEv~~~~~~~l~~~l~~y~~~~~~~~~~~~~~~~~~a   82 (312)
                      .+||||||||++....++...|..|++.|.++|++.+||||||||+...+++.|.+.|.+|.+++.++.. +...+.+++
T Consensus         2 ~~l~v~t~Ni~~~~~~~~~~~~~~r~~~i~~~i~~~~~DIv~LQEv~~~~~~~l~~~l~~y~~~~~~~~~-~~~~g~~~a   80 (267)
T 3g6s_A            2 TDVRWATFNIRYDNPQDSLNNWQYRKDRVCQFIKDHELDIVGMQEVLHNQFQDLRAGLPEYDGIGVGRDD-GKTAGEYAP   80 (267)
T ss_dssp             EEEEEEEEECCCCCGGGGGGSGGGTHHHHHHHHHHTTCSEEEEESBCHHHHHHHHHHCTTEEEECCCTTT-SSSSSCBCC
T ss_pred             CcEEEEEEEeccCCCCccccCHHHHHHHHHHHHHHcCCCEEEEecCCHHHHHHHHHhccCCcEEEecCCC-CCcCCceeE
Confidence            5799999999988766667789999999999999999999999999998888999888889998766642 334566799


Q ss_pred             EEEeCCCcEEEeeeeEeccCCCCCCCCcccCccCCceEEEEEeeeccCCCCCcEEEEEeccCCCccHHHHHHHHHHHHHH
Q 021437           83 IFYDKEKVELLEGGTFWLSESPSVPGSKAWGAEVPCIATWATFQLKGVEPPGFSFQIVNTNMDEFTARARRRSALLTWQH  162 (312)
Q Consensus        83 i~~~~~~~~~~~~~~~~l~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~g~~~~v~~~Hl~~~~~~~r~~~~~~l~~~  162 (312)
                      |+|++++++++....++++..|..+++.+|+...+|.++++.|+....   |+.+.|+|+|+++.+...|.+|++.+++.
T Consensus        81 il~~~s~~~~~~~~~~~l~~~~~~~~~~~~~~~~~R~~~~~~~~~~~~---~~~~~v~~~Hl~~~~~~~R~~q~~~l~~~  157 (267)
T 3g6s_A           81 LFYRKDKYEVLDSNTFWLAENPDSVGMMGWDAVCVRIATWAKFKDKAT---GKIFMAVNTHFDHVGEEARRQSALLIIRK  157 (267)
T ss_dssp             EEEETTTEEEEEEEEEESSSCTTSTTCCCTTCSSCCEEEEEEEEETTT---CCEEEEEEEECCSSCHHHHHHHHHHHHHH
T ss_pred             EEEEccceEEEecccEecCCCCCccccccccccCcceEEEEEEEEcCC---CCEEEEEEeCCCCCCHHHHHHHHHHHHHH
Confidence            999999999999999999988887766778888899999999987654   78999999999998889999999999999


Q ss_pred             HHhcCCCCCEEEEecCCCCCCchhHHhhhcccccCCccccccchhhhhhhcCCCCCcccccCCCCCCcchhHHHHHHHhh
Q 021437          163 IASLPPSLPVIYCGGFNTQKESTTGRFLLGRSREHGVVGDMRDAWPNARMRKNVSLIRTYHGFKGNKQGALEFLKLIFRA  242 (312)
Q Consensus       163 l~~~~~~~pvIv~GDfN~~~~~~~~~~l~~~~~~~g~~~~l~d~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~  242 (312)
                      ++++..+.|+|||||||+.+.+..++.+.+.+.      .|.|++..+...  .+...||+.+.+...            
T Consensus       158 l~~~~~~~pvIl~GDfN~~~~~~~~~~l~~~~~------~l~d~~~~~~~~--~~~~~T~~~~~~~~~------------  217 (267)
T 3g6s_A          158 IKEIVGERPAVVTGDFNVTDASDAYETITTNEF------VMKDAYKTAARV--TGVDYTFHDFARIPA------------  217 (267)
T ss_dssp             HHHHTTTSCEEEEEECSSCTTSHHHHHHHSSSS------CCEEHHHHCSEE--EECSCSBCTTTTSCG------------
T ss_pred             HHHhcCCCCEEEEeECCCCCCCHHHHHhhcCCc------chhhhHhhhccc--cCCCCCEeCCCCCCC------------
Confidence            998766789999999999999999999987310      288998765421  134568776654210            


Q ss_pred             hhccccCCCCCCceeEEEecCCceeeeeEEeecCCCCCcCCCCCcceEEEEEec
Q 021437          243 LCLCWDRQTQDLHIDWILFRGRSLIPGSCEVVNDNIDGYYPSSHYPIFAEFMLP  296 (312)
Q Consensus       243 ~~~~~~~~~~~~riD~I~~s~~~~~~~~~~v~~~~~~~~~~SDH~pV~a~~~~~  296 (312)
                              ....||||||+++ .+++.+++++....++ ++|||+||+|++...
T Consensus       218 --------~~~~riD~I~~s~-~~~~~~~~v~~~~~~~-~~SDH~PV~a~~~~~  261 (267)
T 3g6s_A          218 --------EDCEKIDFIFVTP-QVLVKSCEIPAEVPEA-LLSDHNPQLADLELE  261 (267)
T ss_dssp             --------GGCCCCEEEEECT-TSEEEEEEECCCCSSS-CCCSBCCEEEEEEEC
T ss_pred             --------CCCCcEeEEEeCC-CceEEEEEEecCCCCC-CCCCcccEEEEEEec
Confidence                    0358999999998 5899999998875545 789999999999864

PyMOL of 3g6s

>3mpr_A Putative endonuclease/exonuclease/phosphatase FAM protein; structural genomics, PSI-2, protein structure initiative; HET: MSE PEG; 1.90A {Bacteroides thetaiotaomicron}	Back alignment and structure

>3l1w_A Uncharacterized protein; APC29019.2, conserved protein, enterococcus faecalis V583, PSI-2, MCSG, structural genomics; 1.60A {Enterococcus faecalis}	Back alignment and structure

>4gz1_A Tyrosyl-DNA phosphodiesterase 2; protein-DNA complex, DNA repair, 5'-DNA END processing, endonuclease/exonuclease/phosphatase domain; HET: DNA EPE; 1.50A {Mus musculus} PDB: 4gyz_A* 4gz0_A* 4gz2_A*	Back alignment and structure

>4f1h_A Tyrosyl-DNA phosphodiesterase 2; hydrolase-DNA complex; HET: DNA; 1.66A {Danio rerio} PDB: 4fpv_A* 4f1h_B*	Back alignment and structure

>3ngq_A CCR4-NOT transcription complex subunit 6-like; alpha/beta sandwich fold, hydrolase; HET: 1PS; 1.80A {Homo sapiens} PDB: 3ngo_A 3ngn_A	Back alignment and structure

>4fva_A 5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosyl-DNA diesterase, hydrolase; HET: EDO; 2.07A {Caenorhabditis elegans}	Back alignment and structure

>3teb_A Endonuclease/exonuclease/phosphatase; PSI-biology, MCSG, midwest center for structural genomics; 2.99A {Leptotrichia buccalis c-1013-b}	Back alignment and structure

>4gew_A 5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosyl-DNA diesterase, hydrolase; 2.35A {Caenorhabditis elegans} PDB: 4f1i_A	Back alignment and structure

>1zwx_A SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpin, hydrolase; 1.90A {Listeria ivanovii} SCOP: d.151.1.3	Back alignment and structure

>3i41_A Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1.75A {Staphylococcus aureus} PDB: 3i46_A 3i48_A 3i5v_A* 3k55_A	Back alignment and structure

>2ddr_A Sphingomyelin phosphodiesterase; DNAse I like folding, riken structural genomics/proteomics initiative, RSGI, structural genomics, hydrolase; 1.40A {Bacillus cereus} SCOP: d.151.1.3 PDB: 2dds_A 2ddt_A* 2uyr_X	Back alignment and structure

>1ako_A Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Escherichia coli} SCOP: d.151.1.1	Back alignment and structure

>2jc4_A Exodeoxyribonuclease III; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: 1PE; 1.90A {Neisseria meningitidis}	Back alignment and structure

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}	Back alignment and structure

>1vyb_A ORF2 contains A reverse transcriptase domain; endonuclease, APE-1 type, retrotransposition, retrotransposon, transferase; 1.8A {Homo sapiens} SCOP: d.151.1.1 PDB: 2v0s_A 2v0r_A	Back alignment and structure

>2a40_B Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse I, ARP2/3, structural protein; HET: HIC NAG ATP; 1.80A {Bos taurus} SCOP: d.151.1.1 PDB: 1dnk_A* 2a3z_B* 2a41_B* 2a42_B* 2d1k_B* 2dnj_A* 3cjc_D* 3dni_A* 1atn_D*	Back alignment and structure

>2j63_A AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania major}	Back alignment and structure

>1wdu_A TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA binding protein; 2.40A {Bombyx mori} SCOP: d.151.1.1	Back alignment and structure

>2voa_A AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease, lyase; 1.7A {Archaeoglobus fulgidus}	Back alignment and structure

>2o3h_A DNA-(apurinic or apyrimidinic site) lyase; APE, endonuclease; 1.90A {Homo sapiens} PDB: 1bix_A 1dew_A* 1de8_B* 1de9_A* 2o3c_A	Back alignment and structure

>1hd7_A DNA-(apurinic or apyrimidinic site) lyase; DNA repair, endonuclease, APE1, HAP1, REF-1; 1.95A {Homo sapiens} SCOP: d.151.1.1 PDB: 1e9n_A 3u8u_A 2isi_A	Back alignment and structure

>3g91_A MTH0212, exodeoxyribonuclease; double-strand specific 3'-5' exonuclease, AP endonuclease; HET: PG4; 1.23A {Methanothermobacter thermautotrophicusorganism_taxid} PDB: 3fzi_A 3g0a_A 3g1k_A 3g2c_A 3g3c_A* 3g3y_A* 3g4t_A* 3g00_A 3g0r_A* 3g2d_A* 3g38_A 3g8v_A* 3ga6_A	Back alignment and structure

>2jc5_A Exodeoxyribonuclease; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: BCN DIO GOL; 1.50A {Neisseria meningitidis}	Back alignment and structure

>2imq_X Salivary nitrophorin; ferrous heme, beta-sandwich, transport protein; HET: HEM; 1.30A {Cimex lectularius} SCOP: d.151.1.2 PDB: 1ntf_A* 1y21_A* 1yjh_A* 1si6_X*	Back alignment and structure

>2ei9_A Non-LTR retrotransposon R1BMKS ORF2 protein; four layered alpha beta sandwich, gene regulation; 2.00A {Bombyx mori}	Back alignment and structure

>2f1n_A CDT B, cytolethal distending toxin subunit B; E.coli, DNAse I, microbatch; 1.73A {Escherichia coli} SCOP: d.151.1.1	Back alignment and structure

>1sr4_B CDT B, cytolethal distending toxin protein B; bacterial, virulence, DNA damage, genotoxin, cytotoxins, cell cycle, apoptosis, lectin; 2.00A {Haemophilus ducreyi} SCOP: d.151.1.1 PDB: 2f2f_B	Back alignment and structure

>1i9z_A Synaptojanin, phosphatidylinositol phosphate phosphatase; spsynaptojanin, IPP5C, IP3, IP2,, hydrolase; HET: 2IP; 1.80A {Schizosaccharomyces pombe} SCOP: d.151.1.2 PDB: 1i9y_A*	Back alignment and structure

>2xsw_A 72 kDa inositol polyphosphate 5-phosphatase; inositol signalling, SGC stockholm, structural genomics CONS hydrolase; 1.90A {Homo sapiens}	Back alignment and structure

>3mtc_A Type II inositol-1,4,5-trisphosphate 5-phosphatas; INPP5BA,phosphoinositide 5-phosphatase, inositol signalling, phosphatase, magnesium; HET: PIF; 2.40A {Homo sapiens} PDB: 3n9v_A	Back alignment and structure

>4a9c_A Phosphatidylinositol-3,4,5-trisphosphate 5-phosph; SGC, signalling, structural genomics consortium stockholm, magnesium binding, hydrolase; HET: B5F; 2.10A {Homo sapiens} PDB: 3nr8_B*	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		312
d2ddra1		299	d.151.1.3 (A:7-305) Sphingomyelin phosphodiesteras	8e-15
d1zwxa1		293	d.151.1.3 (A:41-333) Sphingomyelin phosphodiestera	7e-12
d1sr4b_		261	d.151.1.1 (B:) Cytolethal distending toxin subunit	2e-10
d2f1na1		250	d.151.1.1 (A:1-250) Cytolethal distending toxin su	3e-06
d2a40b1		260	d.151.1.1 (B:1-260) Deoxyribonuclease I {Cow (Bos	5e-06

>d2ddra1 d.151.1.3 (A:7-305) Sphingomyelin phosphodiesterase C {Bacillus cereus [TaxId: 1396]} Length = 299	Back information, alignment and structure


class: Alpha and beta proteins (a+b)
fold: DNase I-like
superfamily: DNase I-like
family: Sphingomyelin phosphodiesterase-like
domain: Sphingomyelin phosphodiesterase C
species: Bacillus cereus [TaxId: 1396]

 Score = 71.2 bits (172), Expect = 8e-15
 Identities = 32/304 (10%), Positives = 82/304 (26%), Gaps = 21/304 (6%)

Query: 5   LSLMTFNLHEDQQEDSPN-SWVKRRDLCISVITSYSPMILCTQQGVKSQLDYLQQCLPAY 63
           L +MT N++       PN    +R DL  +     +  ++   +   +            
Sbjct: 4   LKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDNSASDRLLGNLKK 63

Query: 64  DQFGVSRKGPEDTSDEHCTIFYDKEKVELLEGGTFWLSESPSVPGSKAWGAEVPCIATWA 123
           +    +      +  E      +       +GG   +S+ P     +   A+       +
Sbjct: 64  EYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVSKWPIAEKIQYVFAKGCGPDNLS 123

Query: 124 TFQLKGV--EPPGFSFQIVNTNMD----------EFTARARRRSALLTWQHIASLPPSLP 171
                    +       ++ T++             + R  +   +  +    ++P +  
Sbjct: 124 NKGFVYTKIKKNDRFVHVIGTHLQAEDSMCGKTSPASVRTNQLKEIQDFIKNKNIPNNEY 183

Query: 172 VIYCGGFNTQKESTTGRFLLGRSREHGVVGDMRDAWPNARMRKNVSLIRTYHGFKGNKQG 231
           V+  G  N  K +         +     +     ++       + +          +   
Sbjct: 184 VLIGGDMNVNKINAENNNDSEYASMFKTLNASVPSYTGHTATWDATTNSIAKYNFPDSPA 243

Query: 232 ALEFLKLIFRALCLCWDRQTQDLHIDWILFRGRSLIPGSCEVVNDNIDGYYPSSHYPIFA 291
             E+L  I               +I+  + + +S    +             S HYP+ A
Sbjct: 244 --EYLDYII-----ASKDHANPSYIENKVLQPKS-PQWTVTSWFQKYTYNDYSDHYPVEA 295

Query: 292 EFML 295
              +
Sbjct: 296 TISM 299

PyMOL of d2ddra1

>d1zwxa1 d.151.1.3 (A:41-333) Sphingomyelin phosphodiesterase C {Listeria ivanovii [TaxId: 1638]} Length = 293	Back information, alignment and structure

>d1sr4b_ d.151.1.1 (B:) Cytolethal distending toxin subunit B {Haemophilus ducreyi [TaxId: 730]} Length = 261	Back information, alignment and structure

>d2f1na1 d.151.1.1 (A:1-250) Cytolethal distending toxin subunit B {Escherichia coli [TaxId: 562]} Length = 250	Back information, alignment and structure

>d2a40b1 d.151.1.1 (B:1-260) Deoxyribonuclease I {Cow (Bos taurus) [TaxId: 9913]} Length = 260	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		312
d2ddra1		299	Sphingomyelin phosphodiesterase C {Bacillus cereus	99.95
d1zwxa1		293	Sphingomyelin phosphodiesterase C {Listeria ivanov	99.95
d2a40b1		260	Deoxyribonuclease I {Cow (Bos taurus) [TaxId: 9913	99.92
d1vyba_		236	Endonuclease domain of LINE-1 reverse transcriptas	99.92
d2f1na1		250	Cytolethal distending toxin subunit B {Escherichia	99.9
d1sr4b_		261	Cytolethal distending toxin subunit B {Haemophilus	99.9
d1wdua_		228	Endonuclease domain of TRAS1 retrotransposon (ORF2	99.89
d1hd7a_		275	DNA repair endonuclease Hap1 {Human (Homo sapiens)	99.86
d2imqx1		280	Salivary nitrophorin {Bedbug (Cimex lectularius) [	99.81
d1akoa_		268	DNA-repair enzyme exonuclease III {Escherichia col	99.8
d1i9za_		345	Synaptojanin, IPP5C domain {Fission yeast (Schizos	99.69

>d2ddra1 d.151.1.3 (A:7-305) Sphingomyelin phosphodiesterase C {Bacillus cereus [TaxId: 1396]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: DNase I-like
superfamily: DNase I-like
family: Sphingomyelin phosphodiesterase-like
domain: Sphingomyelin phosphodiesterase C
species: Bacillus cereus [TaxId: 1396]

Probab=99.95  E-value=2.7e-27  Score=205.82  Aligned_cols=172  Identities=13%  Similarity=0.051  Sum_probs=103.7

Q ss_pred             CccEEEEEeecCCCCCCC-CCCcHHHHHHHHHHHHhhcCCcEEEEcCCCcccH-HHHHhcC-CCCceEeeecC-------
Q 021437            2 SVALSLMTFNLHEDQQED-SPNSWVKRRDLCISVITSYSPMILCTQQGVKSQL-DYLQQCL-PAYDQFGVSRK-------   71 (312)
Q Consensus         2 ~~~l~v~T~Nv~~~~~~~-~~~~w~~r~~~i~~~i~~~~pDIi~LQEv~~~~~-~~l~~~l-~~y~~~~~~~~-------   71 (312)
                      +.+||||||||++..... ....+..|.+.|.+.|...+|||||||||...+. +.+.+.+ ..|.+......       
T Consensus         1 ~~tl~v~s~Nv~~~~~~~~~~~~~~~r~~~i~~~i~~~~~DIi~LQEv~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~   80 (299)
T d2ddra1           1 NDTLKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDNSASDRLLGNLKKEYPNQTAVLGRSSGSEW   80 (299)
T ss_dssp             CCEEEEEEEEEEECCTTTCTTSCHHHHHHHHHHCSTTCSCSEEEEEEECCHHHHHHHHHHHTTTCCEECCCTTSCCSTTS
T ss_pred             CCceEEEEEECCccccccCCCcCHHHHHHHHHHHHHhcCCCEEEEEccCCcchHHHHHHHHHHhcCceeeeccccccccc
Confidence            468999999999765322 2334678889999999999999999999986543 3344433 33433211110       


Q ss_pred             -------CCCCCCCceEEEEEeCCCcEEEeeeeEeccCCCCCCCCcccCccCCceEEEEEeeeccCCCCCcEEEEEeccC
Q 021437           72 -------GPEDTSDEHCTIFYDKEKVELLEGGTFWLSESPSVPGSKAWGAEVPCIATWATFQLKGVEPPGFSFQIVNTNM  144 (312)
Q Consensus        72 -------~~~~~~~~~~ai~~~~~~~~~~~~~~~~l~~~p~~~~~~~~~~~~~r~~~~~~~~~~~~~~~g~~~~v~~~Hl  144 (312)
                             ........+++++.+   +++.....+.......      .+....+.+....+...     +..|.|+++||
T Consensus        81 ~~~~~~~~~~~~~~~g~~~~s~---~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~-----~~~~~v~~~Hl  146 (299)
T d2ddra1          81 DKTLGNYSSSTPEDGGVAIVSK---WPIAEKIQYVFAKGCG------PDNLSNKGFVYTKIKKN-----DRFVHVIGTHL  146 (299)
T ss_dssp             SEEEESCCTTCSSCCCCEEEES---SCEEEEEEEECSCCC----------CCCCEEEEEEEEET-----TEEEEEEEEEC
T ss_pred             ceeeecccccccccceeEEEEE---eecccceeeeeecccC------cccccceeEEEEEEecC-----CeEEEEEEccc
Confidence                   001112234556543   3444333333222111      11223355555554443     78999999999


Q ss_pred             CCccH--------HHHHHHHHHHHHHHHhc--CCCCCEEEEecCCCCCCchhH
Q 021437          145 DEFTA--------RARRRSALLTWQHIASL--PPSLPVIYCGGFNTQKESTTG  187 (312)
Q Consensus       145 ~~~~~--------~~r~~~~~~l~~~l~~~--~~~~pvIv~GDfN~~~~~~~~  187 (312)
                      ++...        ..|..+++.+.+.+...  ..+.|+|+|||||..+.+..+
T Consensus       147 ~~~~~~~~~~~~~~~r~~q~~~~~~~~~~~~~~~~~~vi~~GDfN~~~~~~~~  199 (299)
T d2ddra1         147 QAEDSMCGKTSPASVRTNQLKEIQDFIKNKNIPNNEYVLIGGDMNVNKINAEN  199 (299)
T ss_dssp             CCC-------CHHHHHHHHHHHHHHHHHHHTCCTTSCEEEEEECCCCCTTTSS
T ss_pred             cCCCCccchhhhHHHHHHHHHHHhhhhhhhcccccceEEEEecCCCCccchhh
Confidence            87422        34677777777777643  346799999999998866443

PyMOL of d2ddra1

>d1zwxa1 d.151.1.3 (A:41-333) Sphingomyelin phosphodiesterase C {Listeria ivanovii [TaxId: 1638]}	Back information, alignment and structure

>d2a40b1 d.151.1.1 (B:1-260) Deoxyribonuclease I {Cow (Bos taurus) [TaxId: 9913]}	Back information, alignment and structure

>d1vyba_ d.151.1.1 (A:) Endonuclease domain of LINE-1 reverse transcriptase homolog {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2f1na1 d.151.1.1 (A:1-250) Cytolethal distending toxin subunit B {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1sr4b_ d.151.1.1 (B:) Cytolethal distending toxin subunit B {Haemophilus ducreyi [TaxId: 730]}	Back information, alignment and structure

>d1wdua_ d.151.1.1 (A:) Endonuclease domain of TRAS1 retrotransposon (ORF2) {Silkworm (Bombyx mori) [TaxId: 7091]}	Back information, alignment and structure

>d1hd7a_ d.151.1.1 (A:) DNA repair endonuclease Hap1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2imqx1 d.151.1.2 (X:3-282) Salivary nitrophorin {Bedbug (Cimex lectularius) [TaxId: 79782]}	Back information, alignment and structure

>d1akoa_ d.151.1.1 (A:) DNA-repair enzyme exonuclease III {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1i9za_ d.151.1.2 (A:) Synaptojanin, IPP5C domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}	Back information, alignment and structure