Citrus Sinensis ID: 030072

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180---
Protein Sequence
MAYQQSLNLRIHSFWRSLNCFRKKFSKPQRTGNTLFNIKRFDLARLSSSQSTKGSCCLSINLSTNVRGVGRANFHSIVTSISDQTLSVEALDPVKFEESAVNPKPSNGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCPSCMSMFHVPI
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccEEEEEccHHHHHHHHHHHHHHcccccccccccccEEHHHHHHHHHHHHHHcccccEEEEEEccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHccccccccccccEccccccccccccccccccccccccEEEEEEcccccHccccccccccccccccccccccccccccccccccccccccccEEEEEcHHHHHHHHHHHHHHHHHccccHccccccHHHHHHHHHHHHHHHHHHHccccEEEEEccccEEEEEEccc
Coil and Loop (DISEMBL)
mayqqslnLRIHSFWRSLNCfrkkfskpqrtgntlfnikrfdlarlsssqstkgscclsinlstnvrgvgrANFHSIVTSIsdqtlsvealdpvkfeesavnpkpsngrvmliDGTSIIYRAYYKILAKLHhghlshadgngdWVLTIFSALSLIIDVLEfipshvavcfscpscmsmfhvpi
Flexible Loop (DISEMBL)
mayqqslnlriHSFWRSLNCFrkkfskpqrtgntlfniKRFDLARlsssqstkgscCLSINLSTNVRGVGRANFHSIVTSISDQTLSVEALDPVKFeesavnpkpsngrvmLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCPSCMSMFHVPI
Low Complexity Region (SEG)
MAYQQSLNLRIHSFWRSLNCFRKKFSKPQRTGNTLFNIKRFDLARLSSSQSTKGSCCLSINLSTNVRGVGRANFHSIVTSISDQTLSVEALDPVKFEESAVNPKPSNGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCPSCMSMFHVPI
Disordered region (IsUnstruct)
******LNLRIHSFWRSLNCFRKKFSKPQRTGNTLFNIKRFDLARL******KGSCCLSINLSTNVRGVGRANFHSIVTSISDQTLSVEALD***************GRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCPSCMSMFH***
Disordered Region (DISOPRED)
*******NLRIHSFWRSLNCFRKKFSKPQRTGNTLF************************************************************************RVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCPSCMSMFHVPI
Disordered Region (DISEMBL)
MAYQQSLNLRIHSFWRSLNCFRKKFSKPQRTGNTLFNIKRFDLAR*********SCCLSINLSTNVRGVGRANFHSIVTSISDQTLSVEALDPVKFEESAVNPKPSNGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCPSCMSMFHVPI
Disordered Region (DISPRO)
MAYQQSLNLRIHSFWRSLNCFRKKFSKPQRTGNTLFNIKRFDLARLSSSQSTKGSCCLSINLS*****************************************PSNGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCPSCMSMFHVPI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAYQQSLNLRIHSFWRSLNCFRKKFSKPQRTGNTLFNIKRFDLARLSSSQSTKGSCCLSINLSTNVRGVGRANFHSIVTSISDQTLSVEALDPVKFEESAVNPKPSNGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCPSCMSMFHVPI
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	183
359478321	441	PREDICTED: DNA polymerase I-like [Vitis	0.928	0.385	0.526	1e-38
255579460	180	hypothetical protein RCOM_0547690 [Ricin	0.918	0.933	0.527	1e-36
357475547	491	DNA polymerase I [Medicago truncatula] g	0.683	0.254	0.581	5e-30
449453197	461	PREDICTED: DNA polymerase I-like [Cucumi	0.770	0.305	0.487	8e-29
297816476	454	hypothetical protein ARALYDRAFT_485561 [	0.852	0.343	0.497	1e-28
449480947	112	PREDICTED: DNA polymerase I, thermostabl	0.437	0.714	0.737	2e-28
42565846	425	5'-3' exonuclease-like protein [Arabidop	0.825	0.355	0.508	2e-28
145332811	413	5'-3' exonuclease-like protein [Arabidop	0.825	0.365	0.508	3e-28
145332809	448	5'-3' exonuclease-like protein [Arabidop	0.825	0.337	0.508	3e-28
238480047	365	5'-3' exonuclease-like protein [Arabidop	0.825	0.413	0.508	3e-28

>gi|359478321|ref|XP_002275974.2| PREDICTED: DNA polymerase I-like [Vitis vinifera] gi|296084279|emb|CBI24667.3| unnamed protein product [Vitis vinifera]

 Score =  164 bits (416), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 91/173 (52%), Positives = 120/173 (69%), Gaps = 3/173 (1%)

Query: 1   MAYQQSLNLRIHSFWRSLNCFRKKFSKPQRTGNTLFNIKRFDLARLSSSQSTKGSCCLSI 60
           MA  +S +  I   W +LNC+R  FS+ Q+ GN    ++R +L    S  S KG C LS 
Sbjct: 1   MACYRSSHHHIRFLWGNLNCWRSSFSRTQKIGNNSCCLQRRNLIHSPSILSRKGCCTLSN 60

Query: 61  NLSTNVRGVGR--ANFHSIVTSISDQTLSVEA-LDPVKFEESAVNPKPSNGRVMLIDGTS 117
           +L +++  V    +  ++ ++S S++ L   A +D V  +E  ++   SNGRVMLIDGTS
Sbjct: 61  SLDSSIHEVAHTISYGNTTISSKSERKLCQGAFVDSVDHKERKMDISSSNGRVMLIDGTS 120

Query: 118 IIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCF 170
           IIYRAYYK+LAKLHHG+LSHADGNGDWVLTIF+ALSLI+DVL+FIPSHVAV F
Sbjct: 121 IIYRAYYKLLAKLHHGYLSHADGNGDWVLTIFAALSLIVDVLDFIPSHVAVVF 173

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255579460|ref|XP_002530573.1| hypothetical protein RCOM_0547690 [Ricinus communis] gi|223529872|gb|EEF31803.1| hypothetical protein RCOM_0547690 [Ricinus communis]

 Score =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 95/180 (52%), Positives = 113/180 (62%), Gaps = 12/180 (6%)

Query: 1   MAYQQSLNLRIHS-FWRSLNCFRKKFSKPQRTGNTLFNIKRFDLARLSSSQSTKGSCCLS 59
           MAY QSLNLR+ S  WR+ N   +K  + +R G+ L N+K       SS+ S KG   +S
Sbjct: 1   MAYCQSLNLRVQSSLWRNFNYLGEKLKRARRVGSFLSNLKTLVQIHPSSTLSKKGFYGIS 60

Query: 60  INLSTNVRGVGRANFHSIVTSISDQTLSVEA--LDPVKFEESAVNP---------KPSNG 108
              S   +     +  S  TS  +  +  +    D +K+EE  VN           PSNG
Sbjct: 61  STSSALPQDACVTSRSSTFTSSEELHMPHQGAIFDSIKYEERLVNTTSQSDVANSSPSNG 120

Query: 109 RVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAV 168
           R+MLIDGTSIIYRAYYK+LAKLHHGHLS ADGNGDWVLTIFSALSLIIDVLEFIPSHV V
Sbjct: 121 RLMLIDGTSIIYRAYYKLLAKLHHGHLSQADGNGDWVLTIFSALSLIIDVLEFIPSHVVV 180

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357475547|ref|XP_003608059.1| DNA polymerase I [Medicago truncatula] gi|355509114|gb|AES90256.1| DNA polymerase I [Medicago truncatula]

 Score =  136 bits (342), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 75/129 (58%), Positives = 87/129 (67%), Gaps = 4/129 (3%)

Query: 42  DLARLSSSQSTKGSCCLSINLSTNVRGVGRANFHSIVTSISDQTLSVEALDPVKFEESAV 101
           +L R S +  +KG CC+S  L ++  GV  A   S  T      +S  A  PV       
Sbjct: 47  NLLRSSRAPLSKGFCCVS--LDSHKDGVVSAT--SPSTGTVPPEISYGAAQPVHIGSVTN 102

Query: 102 NPKPSNGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEF 161
               +NGRVMLIDGTS+I+RAYYK+LAKLHHGHL+HADGNGDWVLTIFSALS IIDVLEF
Sbjct: 103 ADAAANGRVMLIDGTSVIHRAYYKLLAKLHHGHLAHADGNGDWVLTIFSALSFIIDVLEF 162

Query: 162 IPSHVAVCF 170
           IPSHV V F
Sbjct: 163 IPSHVVVVF 171

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449453197|ref|XP_004144345.1| PREDICTED: DNA polymerase I-like [Cucumis sativus]

 Score =  132 bits (331), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 78/160 (48%), Positives = 95/160 (59%), Gaps = 19/160 (11%)

Query: 21  FRKKFSKPQRTGNTLFNIKRFDLARLSSSQSTKGSCCLSINLSTNVRGVGRANFHSIVTS 80
           F  KF  P R   +   I  F     S   S KG C  S ++++       AN    V +
Sbjct: 43  FTSKFPHPFRFSTSSSRIHSF--PSFSLLLSPKGYCSSSGSINS-------ANTMDTVPT 93

Query: 81  ISDQTLSVEALDPVKFEESAVNP----------KPSNGRVMLIDGTSIIYRAYYKILAKL 130
               + S      V+F++S  NP           P++ RVMLIDGTSII+RAYYK+LAKL
Sbjct: 94  YHGSSASTRCQPMVQFQDSLSNPLTFKEDTGIDNPADARVMLIDGTSIIFRAYYKLLAKL 153

Query: 131 HHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCF 170
           HHGHLSHADGNGDWVLTIF+ALSLI+DVLE +PSHVAV F
Sbjct: 154 HHGHLSHADGNGDWVLTIFTALSLIVDVLEIMPSHVAVVF 193

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297816476|ref|XP_002876121.1| hypothetical protein ARALYDRAFT_485561 [Arabidopsis lyrata subsp. lyrata] gi|297321959|gb|EFH52380.1| hypothetical protein ARALYDRAFT_485561 [Arabidopsis lyrata subsp. lyrata]

 Score =  131 bits (329), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 85/171 (49%), Positives = 110/171 (64%), Gaps = 15/171 (8%)

Query: 6   SLNLRIHS--FWRSLNCFRKKFSKPQRTGNTLFNIKRFDLARLSSSQSTKGSCCLSINLS 63
           +L+L  HS   WR+L CF +      R GN L N +   L   S ++S K  C  + NL 
Sbjct: 24  TLHLYHHSRFLWRNL-CFTR------RIGN-LCN-RNSSLISPSLARSAKYYCSSTCNLD 74

Query: 64  TNVRGVGR--ANFHSIVTSISDQTLSVEALD-PVKFEES-AVNPKPSNGRVMLIDGTSII 119
             V  +    A+ + + +  S+  ++ E +  P K EE  A     SNGRVMLIDGTSII
Sbjct: 75  AAVSEISNDAASGNMLTSYKSEDVVAPETIKYPFKSEERVASTAASSNGRVMLIDGTSII 134

Query: 120 YRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCF 170
           YRAYYK+LA+L+HGHL+HADGN DWVLTIFS+LSL+IDVL+F+PSHVAV F
Sbjct: 135 YRAYYKLLARLNHGHLAHADGNADWVLTIFSSLSLLIDVLKFLPSHVAVVF 185

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449480947|ref|XP_004156037.1| PREDICTED: DNA polymerase I, thermostable-like [Cucumis sativus]

 Score =  130 bits (328), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 59/80 (73%), Positives = 69/80 (86%)

Query: 92  DPVKFEESAVNPKPSNGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSA 151
           +P+ F+E      P++ RVMLIDGTSII+RAYYK+LAKLHHGHLSHADGNGDWVLTIF+A
Sbjct: 28  NPLTFKEDTGIDNPADARVMLIDGTSIIFRAYYKLLAKLHHGHLSHADGNGDWVLTIFTA 87

Query: 152 LSLIIDVLEFIPSHVAVCFS 171
           LSLI+DVLE +PSHVAV F 
Sbjct: 88  LSLIVDVLEIMPSHVAVVFD 107

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42565846|ref|NP_190773.2| 5'-3' exonuclease-like protein [Arabidopsis thaliana] gi|145362483|ref|NP_974414.2| 5'-3' exonuclease-like protein [Arabidopsis thaliana] gi|109946597|gb|ABG48477.1| At3g52050 [Arabidopsis thaliana] gi|332645358|gb|AEE78879.1| 5'-3' exonuclease-like protein [Arabidopsis thaliana] gi|332645359|gb|AEE78880.1| 5'-3' exonuclease-like protein [Arabidopsis thaliana]

 Score =  130 bits (327), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 86/169 (50%), Positives = 108/169 (63%), Gaps = 18/169 (10%)

Query: 6   SLNLRIHS--FWRSLNCFRKKFSKPQRTGNTLFNIKRFDLARLSSSQSTKGSCC-LSINL 62
           +L+L  HS   WR+L CF      P+  GN L N +   L   S ++S K  C  ++++ 
Sbjct: 2   TLHLYHHSRFLWRNL-CF------PRSVGN-LCN-RNCSLISPSLARSAKYYCSSVAVSE 52

Query: 63  STNVRGVGRANFHSIVTSISDQTLSVEALDPVKFEES-AVNPKPSNGRVMLIDGTSIIYR 121
            +N    G     S +TSIS+         P K EE  A     SNGRVMLIDGTSIIYR
Sbjct: 53  FSNEAASG-----STLTSISEDVTPQSIKYPFKSEERVASTAASSNGRVMLIDGTSIIYR 107

Query: 122 AYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCF 170
           AYYK+LA+L+HGHL+HADGN DWVLTIFS+LSL+IDVL+F+PSHVAV F
Sbjct: 108 AYYKLLARLNHGHLAHADGNADWVLTIFSSLSLLIDVLKFLPSHVAVVF 156

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145332811|ref|NP_001078271.1| 5'-3' exonuclease-like protein [Arabidopsis thaliana] gi|332645361|gb|AEE78882.1| 5'-3' exonuclease-like protein [Arabidopsis thaliana]

 Score =  130 bits (326), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 86/169 (50%), Positives = 108/169 (63%), Gaps = 18/169 (10%)

Query: 6   SLNLRIHS--FWRSLNCFRKKFSKPQRTGNTLFNIKRFDLARLSSSQSTKGSCC-LSINL 62
           +L+L  HS   WR+L CF      P+  GN L N +   L   S ++S K  C  ++++ 
Sbjct: 2   TLHLYHHSRFLWRNL-CF------PRSVGN-LCN-RNCSLISPSLARSAKYYCSSVAVSE 52

Query: 63  STNVRGVGRANFHSIVTSISDQTLSVEALDPVKFEES-AVNPKPSNGRVMLIDGTSIIYR 121
            +N    G     S +TSIS+         P K EE  A     SNGRVMLIDGTSIIYR
Sbjct: 53  FSNEAASG-----STLTSISEDVTPQSIKYPFKSEERVASTAASSNGRVMLIDGTSIIYR 107

Query: 122 AYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCF 170
           AYYK+LA+L+HGHL+HADGN DWVLTIFS+LSL+IDVL+F+PSHVAV F
Sbjct: 108 AYYKLLARLNHGHLAHADGNADWVLTIFSSLSLLIDVLKFLPSHVAVVF 156

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145332809|ref|NP_001078270.1| 5'-3' exonuclease-like protein [Arabidopsis thaliana] gi|332645360|gb|AEE78881.1| 5'-3' exonuclease-like protein [Arabidopsis thaliana]

 Score =  130 bits (326), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 86/169 (50%), Positives = 108/169 (63%), Gaps = 18/169 (10%)

Query: 6   SLNLRIHS--FWRSLNCFRKKFSKPQRTGNTLFNIKRFDLARLSSSQSTKGSCC-LSINL 62
           +L+L  HS   WR+L CF      P+  GN L N +   L   S ++S K  C  ++++ 
Sbjct: 25  TLHLYHHSRFLWRNL-CF------PRSVGN-LCN-RNCSLISPSLARSAKYYCSSVAVSE 75

Query: 63  STNVRGVGRANFHSIVTSISDQTLSVEALDPVKFEES-AVNPKPSNGRVMLIDGTSIIYR 121
            +N    G     S +TSIS+         P K EE  A     SNGRVMLIDGTSIIYR
Sbjct: 76  FSNEAASG-----STLTSISEDVTPQSIKYPFKSEERVASTAASSNGRVMLIDGTSIIYR 130

Query: 122 AYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCF 170
           AYYK+LA+L+HGHL+HADGN DWVLTIFS+LSL+IDVL+F+PSHVAV F
Sbjct: 131 AYYKLLARLNHGHLAHADGNADWVLTIFSSLSLLIDVLKFLPSHVAVVF 179

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|238480047|ref|NP_001154673.1| 5'-3' exonuclease-like protein [Arabidopsis thaliana] gi|332645362|gb|AEE78883.1| 5'-3' exonuclease-like protein [Arabidopsis thaliana]

 Score =  130 bits (326), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 86/169 (50%), Positives = 108/169 (63%), Gaps = 18/169 (10%)

Query: 6   SLNLRIHS--FWRSLNCFRKKFSKPQRTGNTLFNIKRFDLARLSSSQSTKGSCC-LSINL 62
           +L+L  HS   WR+L CF      P+  GN L N +   L   S ++S K  C  ++++ 
Sbjct: 25  TLHLYHHSRFLWRNL-CF------PRSVGN-LCN-RNCSLISPSLARSAKYYCSSVAVSE 75

Query: 63  STNVRGVGRANFHSIVTSISDQTLSVEALDPVKFEES-AVNPKPSNGRVMLIDGTSIIYR 121
            +N    G     S +TSIS+         P K EE  A     SNGRVMLIDGTSIIYR
Sbjct: 76  FSNEAASG-----STLTSISEDVTPQSIKYPFKSEERVASTAASSNGRVMLIDGTSIIYR 130

Query: 122 AYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCF 170
           AYYK+LA+L+HGHL+HADGN DWVLTIFS+LSL+IDVL+F+PSHVAV F
Sbjct: 131 AYYKLLARLNHGHLAHADGNADWVLTIFSSLSLLIDVLKFLPSHVAVVF 179

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	183
TAIR|locus:2083775	448	AT3G52050 [Arabidopsis thalian	0.825	0.337	0.508	6.9e-31

TAIR|locus:2083775 AT3G52050 [Arabidopsis thaliana (taxid:3702)]

 Score = 340 (124.7 bits), Expect = 6.9e-31, P = 6.9e-31
 Identities = 86/169 (50%), Positives = 108/169 (63%)

Query:     6 SLNLRIHS--FWRSLNCFRKKFSKPQRTGNTLFNIKRFDLARLSSSQSTKGSCC-LSINL 62
             +L+L  HS   WR+L CF      P+  GN L N +   L   S ++S K  C  ++++ 
Sbjct:    25 TLHLYHHSRFLWRNL-CF------PRSVGN-LCN-RNCSLISPSLARSAKYYCSSVAVSE 75

Query:    63 STNVRGVGRANFHSIVTSISDQTLSVEALDPVKFEES-AVNPKPSNGRVMLIDGTSIIYR 121
              +N    G     S +TSIS+         P K EE  A     SNGRVMLIDGTSIIYR
Sbjct:    76 FSNEAASG-----STLTSISEDVTPQSIKYPFKSEERVASTAASSNGRVMLIDGTSIIYR 130

Query:   122 AYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCF 170
             AYYK+LA+L+HGHL+HADGN DWVLTIFS+LSL+IDVL+F+PSHVAV F
Sbjct:   131 AYYKLLARLNHGHLAHADGNADWVLTIFSSLSLLIDVLKFLPSHVAVVF 179


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.324   0.135   0.412    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      183       183   0.00076  110 3  11 22  0.37    32
                                                     31  0.40    35


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  592 (63 KB)
  Total size of DFA:  161 KB (2096 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  16.04u 0.15s 16.19t   Elapsed:  00:00:01
  Total cpu time:  16.04u 0.15s 16.19t   Elapsed:  00:00:01
  Start:  Fri May 10 07:04:11 2013   End:  Fri May 10 07:04:12 2013

GO:0003677 "DNA binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008409 "5'-3' exonuclease activity" evidence=IEA

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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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	183
smart00475	259	smart00475, 53EXOc, 5'-3' exonuclease	4e-09
cd09859	174	cd09859, PIN_53EXO, PIN domain of the 5'-3' exonuc	7e-09
PRK05755	880	PRK05755, PRK05755, DNA polymerase I; Provisional	0.002

>gnl|CDD|214682 smart00475, 53EXOc, 5'-3' exonuclease

 Score = 54.1 bits (131), Expect = 4e-09
 Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 13/66 (19%)

Query: 108 GRVMLIDGTSIIYRAYYKILAKLHHGHLSH---ADGNGDWVLTIFSALSLIIDVLEFIPS 164
            +++L+DG+S+ +RAY+  L  L +          G    +L +           E  P+
Sbjct: 1   KKLLLVDGSSLAFRAYFA-LPPLKNSKGEPTNAVYGFLRMLLKLIK---------EEKPT 50

Query: 165 HVAVCF 170
           +VAV F
Sbjct: 51  YVAVVF 56

Length = 259

>gnl|CDD|189029 cd09859, PIN_53EXO, PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs

 Score = 52.4 bits (127), Expect = 7e-09
 Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 8/62 (12%)

Query: 110 VMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVL-EFIPSHVAV 168
           ++LIDG+S+++RAYY +              +G+    ++  L++++ +L E  P+HVAV
Sbjct: 1   LLLIDGSSLLFRAYYALPP-------LTNSDDGEPTNAVYGFLNMLLKLLKEEKPTHVAV 53

Query: 169 CF 170
            F
Sbjct: 54  AF 55

The 5'-3' exonuclease (53EXO) PIN (PilT N terminus) domain of multi-domain DNA polymerase I and single domain protein homologs are included in this family. Taq contains a polymerase domain for synthesizing a new DNA strand and a 53EXO PIN domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO PIN domain recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The 53EXO PIN domain cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN domain with a helical arch/clamp region (I domain) of variable length (approximately 16 residues in 53EXO PIN domains) and a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA/RNA binding. The active site includes a set of conserved acidic residues that are essential for binding divalent metal ions required for nuclease activity. Length = 174

>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional

 Score = 38.1 bits (90), Expect = 0.002
 Identities = 21/66 (31%), Positives = 38/66 (57%), Gaps = 14/66 (21%)

Query: 109 RVMLIDGTSIIYRAYYKILAKLHHGHLSHADG---NGDWVLTIFSALSLIIDVL-EFIPS 164
            ++LIDG+S+++RA+Y +        L ++DG        +  F  L++++ +L E  P+
Sbjct: 3   TLLLIDGSSLLFRAFYAL-----LPTLRNSDGLPTG---AVYGF--LNMLLKLLKEEKPT 52

Query: 165 HVAVCF 170
           HVAV F
Sbjct: 53  HVAVAF 58

Length = 880

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	183
PF02739	169	5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolv	99.7
smart00475	259	53EXOc 5'-3' exonuclease.	99.61
PHA00439	286	exonuclease	99.58
PRK09482	256	flap endonuclease-like protein; Provisional	99.57
PRK14976	281	5'-3' exonuclease; Provisional	99.56
TIGR00593	887	pola DNA polymerase I. This family is based on the	99.52
cd00008	240	53EXOc 5'-3' exonuclease; T5 type 5'-3' exonucleas	99.48
PRK05755	880	DNA polymerase I; Provisional	99.43
COG0258	310	Exo 5'-3' exonuclease (including N-terminal domain	99.33
PHA02567	304	rnh RnaseH; Provisional	98.95
TIGR03674	338	fen_arch flap structure-specific endonuclease. End	98.69
PTZ00217	393	flap endonuclease-1; Provisional	98.65
cd00128	316	XPG Xeroderma pigmentosum G N- and I-regions (XPGN	98.3
PF00752	101	XPG_N: XPG N-terminal domain; InterPro: IPR006085	96.06
smart00485	99	XPGN Xeroderma pigmentosum G N-region. domain in n	95.46
PF05991	166	NYN_YacP: YacP-like NYN domain; InterPro: IPR01029	92.03

>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities

Probab=99.70  E-value=1.2e-17  Score=135.44  Aligned_cols=62  Identities=31%  Similarity=0.646  Sum_probs=55.4

Q ss_pred             CcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCCCc
Q 030072          108 GRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCPSC  175 (183)
Q Consensus       108 ~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~gk  175 (183)
                      ++|+||||++|+||+|||.+..    ++  .+++|+|||||+||++||+++++ ++|+|++||||.+++
T Consensus         1 k~llLIDg~~l~~Ra~~a~~~~----~l--~~~~G~~t~ai~g~~~~l~~l~~~~~p~~~vv~fD~~~~   63 (169)
T PF02739_consen    1 KKLLLIDGNSLLFRAYYALPKD----PL--RNSDGEPTNAIYGFLRMLLKLLKDFKPDYVVVAFDSKGP   63 (169)
T ss_dssp             -EEEEEEHHHHHHHCCCCCTTS----T---BETTSEB-HHHHHHHHHHHHHHHHTTEEEEEEEEEBSSC
T ss_pred             CeEEEEechHHHHHHHHhhccC----CC--cCCCCCChHHHHHHHHHHHHHHHHcCCceEEEEecCCCc
Confidence            4799999999999999999843    56  89999999999999999999999 999999999998876

The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....

>smart00475 53EXOc 5'-3' exonuclease

Probab=99.61  E-value=1e-15  Score=131.79  Aligned_cols=59  Identities=25%  Similarity=0.590  Sum_probs=54.7

Q ss_pred             cEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCCCc
Q 030072          109 RVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCPSC  175 (183)
Q Consensus       109 kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~gk  175 (183)
                      +++||||++++||+|||.+      .+  .+++|.||||++||+++++++++ ++|+|++||||.+++
T Consensus         2 ~lllIDg~~~i~R~~~a~~------~l--~~~~G~~t~a~~g~~~~l~~l~~~~~p~~~~~~fD~~~~   61 (259)
T smart00475        2 KLLLVDGSSLAFRAYFALP------PL--KNSKGEPTNAVYGFLRMLLKLIKEEKPTYVAVVFDAKGK   61 (259)
T ss_pred             cEEEEeCcHHHHHHHHCCC------cc--cCCCCCcccHHHHHHHHHHHHHHHcCCCeEEEEEeCCCC
Confidence            5999999999999999986      45  88999999999999999999999 999999999997654

>PHA00439 exonuclease

Probab=99.58  E-value=3.4e-15  Score=131.66  Aligned_cols=65  Identities=12%  Similarity=0.137  Sum_probs=54.6

Q ss_pred             CCcEEEEecchHHHhhccccccccc-cCCCcccCCCCceeehhHHHHHHHHHHHh----hCCCEEEEEEeCCC
Q 030072          107 NGRVMLIDGTSIIYRAYYKILAKLH-HGHLSHADGNGDWVLTIFSALSLIIDVLE----FIPSHVAVCFSCPS  174 (183)
Q Consensus       107 ~~kLLLIDGssLlFRAYYA~p~~~~-~~~L~~~ns~G~PTnAVyGFl~mLlkLLk----~~PthIaVaFDs~g  174 (183)
                      .++|+||||++|+||||||.....+ ..++  .+++|.||||+|||++||+++++    ++|+|++|||| ++
T Consensus         5 ~~~llLIDG~~l~fRA~~A~~~~~~~~~~l--~~~~G~~t~A~~gf~~~L~kl~~~~k~~~p~~i~vaFD-~~   74 (286)
T PHA00439          5 DKGVLVMDGDYLVFQAMAAAEVETDWGEDI--WTLECDHAKARQILEDSIKSYKTRKKAWKDAPIVLAFT-DS   74 (286)
T ss_pred             CCcEEEEeCcHHHHHHHHccCcccccCCCC--CCCCCeeccHHHHHHHHHHHHHHhhccCCCCeEEEEEC-CC
Confidence            6689999999999999999842110 0035  79999999999999999999996    48999999999 44

>PRK09482 flap endonuclease-like protein; Provisional

Probab=99.57  E-value=4.3e-15  Score=128.78  Aligned_cols=58  Identities=16%  Similarity=0.167  Sum_probs=51.9

Q ss_pred             CcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCCCccc
Q 030072          108 GRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCPSCMS  177 (183)
Q Consensus       108 ~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~gk~s  177 (183)
                      ++|+||||++|+||+|||.+           +++|. |||||||+++|+++++ ++|+|++||||.+++++
T Consensus         3 ~~llLiDg~~l~~R~~~a~~-----------~~~g~-t~av~gf~~~l~~ll~~~~p~~i~v~fD~~~~~~   61 (256)
T PRK09482          3 NHLLIIDALNLIRRIHAVQP-----------SPNDI-NACVETCQHALDKLIRHSQPTHAVAVFDGDARSS   61 (256)
T ss_pred             CeEEEEeCcHHHHHHHhCCC-----------CCCCc-chHHHHHHHHHHHHHHHcCCCEEEEEEeCCCCCc
Confidence            46999999999999999974           24577 9999999999999999 99999999999987653

>PRK14976 5'-3' exonuclease; Provisional

Probab=99.56  E-value=6.3e-15  Score=128.19  Aligned_cols=65  Identities=29%  Similarity=0.519  Sum_probs=56.2

Q ss_pred             CcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCCCcc
Q 030072          108 GRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCPSCM  176 (183)
Q Consensus       108 ~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~gk~  176 (183)
                      ++++||||++++||+|||.....  ..+  .+++|.||||++||+++|+++++ ++|+|++||||.++++
T Consensus         3 ~~~lliDg~~~~~ra~~a~~~~~--~~l--~~~~G~~t~a~~gf~~~l~~ll~~~~p~~~~v~fD~~~~~   68 (281)
T PRK14976          3 KKALLIDGNSLIFRSYYATLKQG--PKL--KNNKGLPTNAIHTFLTMIFKILKKLNPSYILIAFDAGRKT   68 (281)
T ss_pred             CcEEEEeCcHHHHHHHHccCccC--CCc--cCCCCCCchHHHHHHHHHHHHHHhcCCCEEEEEEECCCCc
Confidence            46999999999999999974221  135  89999999999999999999999 9999999999986543

>TIGR00593 pola DNA polymerase I

Probab=99.52  E-value=1.2e-14  Score=143.19  Aligned_cols=61  Identities=28%  Similarity=0.549  Sum_probs=55.2

Q ss_pred             EEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCCCcc
Q 030072          110 VMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCPSCM  176 (183)
Q Consensus       110 LLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~gk~  176 (183)
                      |+||||++++||+|||.+..    ++  .+++|.||||||||++||+++++ ++|+|++||||.++++
T Consensus         1 l~lIDg~~l~~Ra~~a~~~~----~l--~~~~G~~t~av~Gf~~~l~~ll~~~~p~~i~v~FD~~~~t   62 (887)
T TIGR00593         1 LLLIDGHSLAFRAYFALKNK----PL--TNSKGEPTNAVYGFTKMLLKLLKEEKPTYVAVAFDSGTPT   62 (887)
T ss_pred             CEEEeCcHHHHHHHHCCCcc----cC--cCCCCCEecHHHHHHHHHHHHHHhcCCCEEEEEEcCCCCc
Confidence            58999999999999999632    35  89999999999999999999999 9999999999987643

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes

Probab=99.48  E-value=6.1e-14  Score=118.69  Aligned_cols=59  Identities=31%  Similarity=0.635  Sum_probs=53.4

Q ss_pred             cEEEEecchHHHhhccccccccccCCCcccCC-CCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCCCc
Q 030072          109 RVMLIDGTSIIYRAYYKILAKLHHGHLSHADG-NGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCPSC  175 (183)
Q Consensus       109 kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns-~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~gk  175 (183)
                      +++||||++++||+|||.+      .+  .+. +|.||||++||+++++++++ ++|+|++||||.+++
T Consensus         2 ~~llIDg~~l~yr~~~a~~------~~--~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~~~~fD~~~~   62 (240)
T cd00008           2 RLLLIDGSSLAYRAYFALP------PL--KNSPKGLPTNAVYGFLNMLLKLIKEYKPTYVAVVFDAGGK   62 (240)
T ss_pred             cEEEEEChHHHHHHHHCCC------Cc--CCCCCCcCchHHHHHHHHHHHHHHhcCCCeEEEEEeCCCC
Confidence            6999999999999999986      23  566 89999999999999999999 999999999998743

They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.

>PRK05755 DNA polymerase I; Provisional

Probab=99.43  E-value=1.8e-13  Score=133.51  Aligned_cols=61  Identities=31%  Similarity=0.636  Sum_probs=55.2

Q ss_pred             CcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCCCc
Q 030072          108 GRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCPSC  175 (183)
Q Consensus       108 ~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~gk  175 (183)
                      ++++||||++++||+|||.+.     .+  .+++|.|||||+||+++++++++ ++|+|++||||.+++
T Consensus         2 ~~~~liDg~~~~~r~~~a~~~-----~~--~~~~g~~~~a~~g~~~~l~~~~~~~~p~~~~v~fD~~~~   63 (880)
T PRK05755          2 KTLLLIDGSSLLFRAFYALLP-----TL--RNSDGLPTGAVYGFLNMLLKLLKEEKPTHVAVAFDAKGK   63 (880)
T ss_pred             CeEEEEeCcHHHHHHHHCCCC-----cc--cCCCCCcccHHHHHHHHHHHHHHhcCCCEEEEEEECCCC
Confidence            469999999999999999831     45  89999999999999999999999 999999999998654

>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]

Probab=99.33  E-value=2.2e-12  Score=112.17  Aligned_cols=64  Identities=27%  Similarity=0.471  Sum_probs=57.1

Q ss_pred             CCCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCCCcc
Q 030072          106 SNGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCPSCM  176 (183)
Q Consensus       106 ~~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~gk~  176 (183)
                      ..+++++|||++++||+|||++..     +  .+.+|.||||++||.+||.++++ .+|+|.+||||.+.++
T Consensus         9 ~~~~l~~IDg~~~lyr~~~a~~~~-----~--~~~~g~~~~~~~~~~~~l~~~~~~~~~~~~~~vFD~~~~t   73 (310)
T COG0258           9 KSGKLLLIDGSSLLYRALHALPQP-----L--GNPLGDPTGAVSGFLGMLYRLIRLLEPTHPVVVFDGKPPT   73 (310)
T ss_pred             ccCcEEEEechHHHHHHHHhcchh-----c--CCCCCCCccHHHHHHHHHHHHHHhcCCCcEEEEEcCCCCc
Confidence            355799999999999999999732     4  78999999999999999999999 9999999999995543

>PHA02567 rnh RnaseH; Provisional

Probab=98.95  E-value=1.2e-09  Score=97.63  Aligned_cols=58  Identities=17%  Similarity=0.132  Sum_probs=50.4

Q ss_pred             CCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehh-HHHHHHHHHHHh-hCC--CEEEEEEeCCC
Q 030072          107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTI-FSALSLIIDVLE-FIP--SHVAVCFSCPS  174 (183)
Q Consensus       107 ~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAV-yGFl~mLlkLLk-~~P--thIaVaFDs~g  174 (183)
                      +..++||||++|+||+|||.        +  .+++|.++||| ++|+++|.++++ ++|  +|++||||.++
T Consensus        13 ~~~~~LiDgs~i~~~~~~a~--------l--~~~~~~~~~~ir~~v~nsL~~~v~~~k~~~~~i~vaFD~~~   74 (304)
T PHA02567         13 KEGVNLIDFSQIIIATIMAN--------F--KPKDKINEAMVRHLVLNSIRYNVKKFKEEYPEIVLAFDNSK   74 (304)
T ss_pred             CCCEEEEehHHHHHHHHHhh--------C--CCCCCCcHHHHHHHHHHHHHHHHHHhcCCCCeEEEEEeCCC
Confidence            45699999999999999994        3  78889999999 559999999999 655  55999999875

>TIGR03674 fen_arch flap structure-specific endonuclease

Probab=98.69  E-value=1.4e-08  Score=90.51  Aligned_cols=64  Identities=20%  Similarity=0.286  Sum_probs=53.1

Q ss_pred             CCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh--hCCCEEEEEEeCCCcc
Q 030072          107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE--FIPSHVAVCFSCPSCM  176 (183)
Q Consensus       107 ~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk--~~PthIaVaFDs~gk~  176 (183)
                      .+++++|||++++||+||+.... .+.++  .+++|.||++++||+.+++++++  .+|   ++|||.+.+.
T Consensus        20 ~gk~vaIDas~~L~r~~~a~~~~-~g~~l--~~~~G~~t~~l~g~~~~~~~ll~~~i~P---v~VFDG~~p~   85 (338)
T TIGR03674        20 SGKVVAVDAFNALYQFLSSIRQP-DGTPL--MDSRGRITSHLSGLFYRTINLLENGIKP---VYVFDGKPPE   85 (338)
T ss_pred             CCCEEEEeHHHHHHHHHHHHhcc-ccchh--hhccCCCcHHHHHHHHHHHHHHHCCCeE---EEEECCCChh
Confidence            45699999999999999997521 12245  89999999999999999999998  556   9999987653

Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA

>PTZ00217 flap endonuclease-1; Provisional

Probab=98.65  E-value=3.1e-08  Score=90.34  Aligned_cols=64  Identities=25%  Similarity=0.360  Sum_probs=52.7

Q ss_pred             CCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh--hCCCEEEEEEeCCCc
Q 030072          107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE--FIPSHVAVCFSCPSC  175 (183)
Q Consensus       107 ~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk--~~PthIaVaFDs~gk  175 (183)
                      .++.++|||++++||+|||.+...++.++  .+++|.+|++|+||+..+++|++  .+|   ++|||.+.+
T Consensus        27 ~gk~vaIDa~~~lyr~~~a~~~~~~~~~l--~~~~G~~t~~l~g~~~r~~~Ll~~gikP---v~VFDG~~p   92 (393)
T PTZ00217         27 FGRVIAIDASMALYQFLIAIRDDSQGGNL--TNEAGEVTSHISGLFNRTIRLLEAGIKP---VYVFDGKPP   92 (393)
T ss_pred             CCcEEEEeHHHHHHHHHHHcccccccccc--hhccCCccHHHHHHHHHHHHHHHCCCCE---EEEEcCCCc
Confidence            44799999999999999998631122245  89999999999999999999998  577   689997653

>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases

Probab=98.30  E-value=1e-06  Score=76.66  Aligned_cols=60  Identities=13%  Similarity=0.135  Sum_probs=49.8

Q ss_pred             CCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHhhCCCEEEEEEeCCCc
Q 030072          107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCPSC  175 (183)
Q Consensus       107 ~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk~~PthIaVaFDs~gk  175 (183)
                      .++.++|||++++||+||+....        ...+|.|+++++||++.+.++++++ -+.++|||...+
T Consensus        23 ~gk~laID~~~~l~r~~~a~~~~--------~~~~g~~~~~l~~~~~rl~~L~~~~-i~pvfVFDG~~~   82 (316)
T cd00128          23 RGKKVAIDASIWLYQFLKACRQE--------LGSGGETTSHLQGFFYRTCRLLELG-IKPVFVFDGKPP   82 (316)
T ss_pred             CCcEEEecHHHHHHHHHHHhhhh--------ccCCCCCcHHHHHHHHHHHHHHHCC-CEEEEEEcCCCc
Confidence            44689999999999999997522        3478999999999999999999855 478889997644

XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.

>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer

Probab=96.06  E-value=0.011  Score=43.40  Aligned_cols=57  Identities=16%  Similarity=0.139  Sum_probs=38.4

Q ss_pred             cEEEEecchHHHhhccccccccccCCCcccCCCCce-eehhHHHHHHHHHHHhhCCCEEEEEEeCCCc
Q 030072          109 RVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDW-VLTIFSALSLIIDVLEFIPSHVAVCFSCPSC  175 (183)
Q Consensus       109 kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~P-TnAVyGFl~mLlkLLk~~PthIaVaFDs~gk  175 (183)
                      +.+-|||+.++||.+++....     +    ..+.+ +..+.+++..+..|++++= ..++|||...+
T Consensus        27 ~~vaID~s~wl~~~~~~~~~~-----~----~~~~~~~~~~~~~~~r~~~L~~~gI-~PifVFDG~~~   84 (101)
T PF00752_consen   27 KRVAIDASCWLHQFLFSCREE-----L----GQGVGTDSHLRGLFSRLCRLLEHGI-KPIFVFDGKPP   84 (101)
T ss_dssp             CEEEEEHHHHHHHHHHHSBCT-----T----SCB-BS-HHHHHHHHHHHHHHHTTE-EEEEEE--STT
T ss_pred             CEEEEEcHHHHHHHHHHhHHH-----h----ccccchHHHHHHHHHHHHHHHHCCC-EEEEEECCCCc
Confidence            679999999999999987522     1    12222 4778888888888887332 34799998654

People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair [, ]. XP-G can be corrected by a 133 Kd nuclear protein, XPGC []. XPGC is an acidic protein that confers normal UV resistance in expressing cells []. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms [, ]. XPGC cleaves one strand of the duplex at the border with the single-stranded region []. XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases [, ]; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents the N-terminal of XPG.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1A77_A 1A76_A 1MC8_B 3QEB_Z 3QEA_Z 3QE9_Y 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A ....

>smart00485 XPGN Xeroderma pigmentosum G N-region

Probab=95.46  E-value=0.022  Score=41.72  Aligned_cols=58  Identities=19%  Similarity=0.174  Sum_probs=41.4

Q ss_pred             CcEEEEecchHHHhhccccccccccCCCcccCCCCceee-hhHHHHHHHHHHHhhCCCEEEEEEeCCCc
Q 030072          108 GRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVL-TIFSALSLIIDVLEFIPSHVAVCFSCPSC  175 (183)
Q Consensus       108 ~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTn-AVyGFl~mLlkLLk~~PthIaVaFDs~gk  175 (183)
                      ++.+-||++..+||.+++....     .    ..+.+.. .+.+++..+..|++++-+ .+++||...+
T Consensus        24 g~~vaIDa~~wl~~~~~~~~~~-----~----~~~~~~~~~l~~~~~rl~~L~~~~I~-PifVFDG~~~   82 (99)
T smart00485       24 GKTLAIDASIWLYQFLTACREK-----L----GTPLPNSKHLMGLFYRTCRLLEFGIK-PIFVFDGKPP   82 (99)
T ss_pred             CceEeccHHHHHHHHHHHHhhh-----h----cCCCCchHHHHHHHHHHHHHHHCCCe-EEEEECCCCc
Confidence            4688999999999999986422     1    1123334 888999999988884333 4789997654

domain in nucleases

>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana

Probab=92.03  E-value=0.17  Score=41.10  Aligned_cols=53  Identities=23%  Similarity=0.284  Sum_probs=31.2

Q ss_pred             EEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHhhCCCEEEEEEeCC
Q 030072          111 MLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCP  173 (183)
Q Consensus       111 LLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk~~PthIaVaFDs~  173 (183)
                      |||||++++|.    ++.      +.....++.--.|=--++.+|..+..+....++||||..
T Consensus         1 LlIDGYNli~~----~~~------l~~~~~~~~l~~aR~~Li~~L~~y~~~~~~~v~VVFDa~   53 (166)
T PF05991_consen    1 LLIDGYNLIHA----WPE------LRSLAERGDLEAARERLIEMLSEYAQFSGYEVIVVFDAY   53 (166)
T ss_pred             CeEcchhhhCC----CHH------HHhhcCcCCHHHHHHHHHHHHHHHhcccCCEEEEEEeCC
Confidence            69999999975    331      100111222234444555555554445668999999974

The function of this family is unknown.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	183
1exn_A	290	5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent	4e-07
1bgx_T	832	TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi	2e-06

>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A Length = 290

 Score = 47.7 bits (114), Expect = 4e-07
 Identities = 13/77 (16%), Positives = 24/77 (31%), Gaps = 17/77 (22%)

Query: 95  KFEESAVNPKPSNGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSL 154
           KF E       S   +M++DGT++ +R  +                         S +S 
Sbjct: 6   KFIEEEEAEMASRRNLMIVDGTNLGFRFKH---NNSKKP-------------FASSYVST 49

Query: 155 IIDVLE-FIPSHVAVCF 170
           I  + + +      V  
Sbjct: 50  IQSLAKSYSARTTIVLG 66

>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A* Length = 832

 Score = 46.4 bits (111), Expect = 2e-06
 Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 14/68 (20%)

Query: 106 SNGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADG---NGDWVLTIFSALSLIIDVLEFI 162
             GRV+L+DG  + YR ++ +        L+ + G          ++     ++  L+  
Sbjct: 10  PKGRVLLVDGHHLAYRTFHAL------KGLTTSRGEPVQA-----VYGFAKSLLKALKED 58

Query: 163 PSHVAVCF 170
              V V F
Sbjct: 59  GDAVIVVF 66

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	183
3h7i_A	305	Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonu	99.36
1exn_A	290	5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent	99.22
1bgx_T	832	TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi	99.16
3q8k_A	341	Flap endonuclease 1; helix-3 turn-helix, hydrophob	99.14
1rxw_A	336	Flap structure-specific endonuclease; helical clam	99.1
1b43_A	340	Protein (FEN-1); nuclease, DNA repair, DNA replica	99.09
2izo_A	346	FEN1, flap structure-specific endonuclease; hydrol	99.03
1a76_A	326	Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea	99.02
3ory_A	363	Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco	98.93
1ul1_X	379	Flap endonuclease-1; protein complex, DNA-binding	98.89
3qe9_Y	352	Exonuclease 1; exonuclease, hydrolase-DNA complex;	97.29

>3h7i_A Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonuclease, hydrolase, endonuclease; 1.50A {Enterobacteria phage T4} PDB: 2ihn_A 3h8w_A 3h8j_A 1tfr_A 3h8s_A

Probab=99.36  E-value=4e-13  Score=118.33  Aligned_cols=57  Identities=14%  Similarity=0.074  Sum_probs=50.7

Q ss_pred             CCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHH-HHHHHHHHHhh----CCCEEEEEEeCC
Q 030072          107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFS-ALSLIIDVLEF----IPSHVAVCFSCP  173 (183)
Q Consensus       107 ~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyG-Fl~mLlkLLk~----~PthIaVaFDs~  173 (183)
                      +++++||||++|+||||++.        +  .+.+|.|||||+| |++||+++++.    +|+|++||||.+
T Consensus        12 ~~~llLIDgssl~~ra~~~~--------f--~~~~g~~tnav~ggf~~~L~~ll~~~k~~~P~~iavaFD~~   73 (305)
T 3h7i_A           12 KEGICLIDFSQIALSTALVN--------F--PDKEKINLSMVRHLILNSIKFNVKKAKTLGYTKIVLCIDNA   73 (305)
T ss_dssp             SCCEEEEEHHHHHHHHHHHH--------S--CSSSCCCHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCC
T ss_pred             CCCEEEEeccHHHHHHHHHh--------c--CCCCCcchHHHHHHHHHHHHHHHHhhhccCCCEEEEEecCC
Confidence            45799999999999998642        4  7889999999987 99999999984    999999999976

>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A

Probab=99.22  E-value=4.4e-12  Score=110.16  Aligned_cols=53  Identities=17%  Similarity=0.133  Sum_probs=46.6

Q ss_pred             CCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCCCc
Q 030072          107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCPSC  175 (183)
Q Consensus       107 ~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~gk  175 (183)
                      +++++||||++++||+||.              ++|.|  |++||++|++++++ ++|+|++||||.+++
T Consensus        18 ~~~lllIDg~~llyRa~~~--------------~~G~p--av~Gf~~~l~~ll~~~~p~~~vvvFD~~~~   71 (290)
T 1exn_A           18 RRNLMIVDGTNLGFRFKHN--------------NSKKP--FASSYVSTIQSLAKSYSARTTIVLGDKGKS   71 (290)
T ss_dssp             -CEEEEEEHHHHHHHHHHH--------------CSSSC--CHHHHHHHHHHHHHHTTEEEEEEECCBSCC
T ss_pred             CCCEEEEECcHHHHHHHhC--------------CCCch--HHHHHHHHHHHHHHHcCCCeEEEEEcCCCc
Confidence            4579999999999999982              24778  99999999999999 999999999997654

>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A*

Probab=99.16  E-value=3.4e-12  Score=123.37  Aligned_cols=60  Identities=25%  Similarity=0.455  Sum_probs=54.8

Q ss_pred             CCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCCCc
Q 030072          107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCPSC  175 (183)
Q Consensus       107 ~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~gk  175 (183)
                      +++++||||++++||+|||.+      ++  .+++|.|||||+||++++.++++ ++ +|++||||.+++
T Consensus        11 ~~~~llIDg~~~l~ra~~a~~------~l--~~~~G~~t~av~gf~~~l~~ll~~~~-~~~v~vFDg~~~   71 (832)
T 1bgx_T           11 KGRVLLVDGHHLAYRTFHALK------GL--TTSRGEPVQAVYGFAKSLLKALKEDG-DAVIVVFDAKAP   71 (832)
T ss_dssp             CTTSCCCCCSTHHHHTTSSCT------TC--BCSSSCBCSSSTTHHHHHHHGGGTCC-SCCCCCCCCSSS
T ss_pred             CCCEEEEEChHHHHHHHhcCC------cc--ccCCCcEehHHHHHHHHHHHHHHHcC-CeEEEEEcCCCc
Confidence            446999999999999999997      56  89999999999999999999999 77 999999997654

>3q8k_A Flap endonuclease 1; helix-3 turn-helix, hydrophobic wedge, 3' flap binding site, hydrolase-DNA complex, DNA repair, replication; HET: DNA; 2.20A {Homo sapiens} PDB: 3q8l_A* 3q8m_A*

Probab=99.14  E-value=2e-11  Score=107.07  Aligned_cols=63  Identities=19%  Similarity=0.254  Sum_probs=53.1

Q ss_pred             CCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh--hCCCEEEEEEeCCCcc
Q 030072          107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE--FIPSHVAVCFSCPSCM  176 (183)
Q Consensus       107 ~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk--~~PthIaVaFDs~gk~  176 (183)
                      .+++++|||++++||+|||.+..  +.++  .+++|.||+||+||+++++++++  .+|.|   |||.++++
T Consensus        26 ~gk~l~IDgs~~lyr~~~a~~~~--~~~l--~~~~G~~T~al~g~~~~~~~ll~~~i~P~~---VFDg~~~~   90 (341)
T 3q8k_A           26 FGRKVAIDASMSIYQFLIAVRQG--GDVL--QNEEGETTSHLMGMFYRTIRMMENGIKPVY---VFDGKPPQ   90 (341)
T ss_dssp             TTCEEEEEHHHHHHHHHHHCEET--TEEC--BCTTSCBCHHHHHHHHHHHHHHTTTCEEEE---EECCCCCG
T ss_pred             CCCEEEEecHHHHHHHHHccccc--cCCC--CCCCCCCchHHHHHHHHHHHHHHCCCCceE---EEeCCCcc
Confidence            34699999999999999998731  1146  89999999999999999999998  77877   69988654

>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3 turn-helix, hydrophobic wedge, 3' FLA site, hydrolase-DNA complex; 2.00A {Archaeoglobus fulgidus} SCOP: a.60.7.1 c.120.1.2 PDB: 1rxv_A

Probab=99.10  E-value=5.3e-11  Score=103.00  Aligned_cols=62  Identities=18%  Similarity=0.229  Sum_probs=51.9

Q ss_pred             CcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-h-CCCEEEEEEeCCCc
Q 030072          108 GRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-F-IPSHVAVCFSCPSC  175 (183)
Q Consensus       108 ~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~-~PthIaVaFDs~gk  175 (183)
                      +++++|||++++||+||+.+.. .+.++  .+++|.||+|++||+++++++++ . +|   +||||.+++
T Consensus        21 ~~~l~IDg~~~l~r~~~a~~~~-~~~~l--~~~~G~~t~a~~g~~~~l~~ll~~~i~P---v~vFDg~~~   84 (336)
T 1rxw_A           21 GKKIAVDAFNTLYQFISIIRQP-DGTPL--KDSQGRITSHLSGILYRVSNMVEVGIRP---VFVFDGEPP   84 (336)
T ss_dssp             TCEEEEEHHHHHHHHHHHSBCT-TSCBC--BCTTSCBCHHHHHHHHHHHHHHHHTCEE---EEEECCSCC
T ss_pred             CCEEEEEhHHHHHHHHHhhccc-cCCcc--cccCCCccHHHHHHHHHHHHHHHCCCEE---EEEEcCCCC
Confidence            3699999999999999998521 11135  89999999999999999999999 4 77   999997765

>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication, transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1 c.120.1.2 PDB: 1mc8_A

Probab=99.09  E-value=1.1e-10  Score=101.08  Aligned_cols=64  Identities=20%  Similarity=0.240  Sum_probs=54.2

Q ss_pred             CcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHhhCCCEEEEEEeCCCc
Q 030072          108 GRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCPSC  175 (183)
Q Consensus       108 ~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk~~PthIaVaFDs~gk  175 (183)
                      +++++|||++++||+|||.+.. .+.++  .+++|.||++++||+++++++++ .|.+.+||||.+.+
T Consensus        21 g~~l~ID~~~~l~r~~~a~~~~-~~~~l--~~~~G~~t~~l~g~~~~l~~ll~-~~i~pv~VFDG~~~   84 (340)
T 1b43_A           21 GKKIAIDALNAIYQFLSTIRQK-DGTPL--MDSKGRITSHLSGLFYRTINLME-AGIKPVYVFDGEPP   84 (340)
T ss_dssp             TCEEEEEHHHHHHHHHHHSBCT-TSCBC--BCTTSCBCHHHHHHHHHHHHHHH-TTCEEEEEECCSCC
T ss_pred             CCEEEEEhHHHHHHHHHHhccc-cCCcc--ccccCCchHHHHHHHHHHHHHHh-CCCEEEEEecCCCc
Confidence            4699999999999999998521 11245  89999999999999999999987 78999999997654

>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-BIND excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus}

Probab=99.03  E-value=1.5e-10  Score=100.89  Aligned_cols=62  Identities=24%  Similarity=0.330  Sum_probs=49.6

Q ss_pred             CcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh--hCCCEEEEEEeCCCc
Q 030072          108 GRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE--FIPSHVAVCFSCPSC  175 (183)
Q Consensus       108 ~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk--~~PthIaVaFDs~gk  175 (183)
                      +++++|||++++||+|||.+.. .+.++  .+++|.||++++||+++++++++  .+|   +||||.+.+
T Consensus        18 ~~~l~IDg~~~l~r~~~a~~~~-~g~~l--~~~~G~~t~al~g~~~~~~~ll~~~i~P---v~vFDG~~~   81 (346)
T 2izo_A           18 GKRVSIDGYNALYQFLAAIRQP-DGTPL--MDSQGRVTSHLSGLFYRTINILEEGVIP---IYVFDGKPP   81 (346)
T ss_dssp             TEEEEEEHHHHHHHHHHSCCCC----CC--BCSSSCBCHHHHHHHHHHHHHHHHTEEE---EEEECC---
T ss_pred             CCEEEEEhHHHHHHHHHhcccc-ccccc--cccCCCccHHHHHHHHHHHHHHHCCCcE---EEEECCCCc
Confidence            4699999999999999998621 11145  89999999999999999999998  667   899997654

>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA replication, RTH, RAD27, DNA repair; 2.00A {Methanocaldococcus jannaschii} SCOP: a.60.7.1 c.120.1.2 PDB: 1a77_A

Probab=99.02  E-value=2.1e-10  Score=98.95  Aligned_cols=62  Identities=21%  Similarity=0.316  Sum_probs=51.0

Q ss_pred             CcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh--hCCCEEEEEEeCCCc
Q 030072          108 GRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE--FIPSHVAVCFSCPSC  175 (183)
Q Consensus       108 ~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk--~~PthIaVaFDs~gk  175 (183)
                      +++++|||++++||+|||.+.. .+.++  .+++|.||++++||+.++++++.  .+|   +||||.+.+
T Consensus        21 ~~~l~IDg~~~l~r~~~a~~~~-~~~~l--~~~~G~~t~~l~g~~~~l~~ll~~~i~P---v~vFDG~~~   84 (326)
T 1a76_A           21 GKKVAIDGMNALYQFLTSIRLR-DGSPL--RNRKGEITSAYNGVFYKTIHLLENDITP---IWVFDGEPP   84 (326)
T ss_dssp             TCEEEEEHHHHHHHHHHHSBCT-TSCBC--BCTTSCBCHHHHHHHHHHHHHHHTTCEE---EEEECCCSS
T ss_pred             CCEEEEEhHHHHHHHHHhhccc-ccccc--ccccCCccHHHHHHHHHHHHHHHCCCeE---EEEEeCcCc
Confidence            4699999999999999998621 01135  89999999999999999999955  667   899997654

>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus}

Probab=98.93  E-value=6.6e-10  Score=98.48  Aligned_cols=64  Identities=22%  Similarity=0.353  Sum_probs=50.6

Q ss_pred             CCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh--hCCCEEEEEEeCCCcc
Q 030072          107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE--FIPSHVAVCFSCPSCM  176 (183)
Q Consensus       107 ~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk--~~PthIaVaFDs~gk~  176 (183)
                      .+++++|||++++||+|++.+.. .+.+|  .+++|.||+||+||+.+++++++  .+|   ++|||.+.++
T Consensus        34 ~gk~l~IDg~~~l~r~~~~~~~~-~g~~l--~~~~G~~T~al~gf~~r~~~ll~~~i~P---v~VFDg~~p~   99 (363)
T 3ory_A           34 HGKIIVIDGYNALYQFLAAIRQP-DGTPL--MDNNGRITSHLSGLFYRTINIVEAGIKP---VYVFDGKPPE   99 (363)
T ss_dssp             TTCEEEEEHHHHHHHHHHHCBCT-TSCBC--BCTTSCBCHHHHHHHHHHHHHHHTTCEE---EEEECSSCGG
T ss_pred             CCCEEEEehHHHHHHHHHhhhcc-CCCcc--CCCCCCCccHHHHHHHHHHHHHHcCCCc---EEEEcCCCcc
Confidence            34799999999999977765421 11246  89999999999999999999887  677   5779987643

>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A {Homo sapiens} SCOP: a.60.7.1 c.120.1.2

Probab=98.89  E-value=6.8e-10  Score=98.11  Aligned_cols=61  Identities=20%  Similarity=0.285  Sum_probs=43.1

Q ss_pred             CcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh--hCCCEEEEEEeCCCc
Q 030072          108 GRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE--FIPSHVAVCFSCPSC  175 (183)
Q Consensus       108 ~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk--~~PthIaVaFDs~gk  175 (183)
                      +++++|||++++||+|||.+..  +..+  .+++|.||++|+||+.+++++++  .+|.|   |||.+.+
T Consensus        27 g~~l~IDg~~~lyr~~~a~~~~--~~~l--~~~~G~~t~~l~g~~~~~~~ll~~~i~P~~---VFDG~~~   89 (379)
T 1ul1_X           27 GRKVAIDASMSIYQFLIAVRQG--GDVL--QNEEGETTSHLMGMFYRTIRMMENGIKPVY---VFDGKPP   89 (379)
T ss_dssp             TCCEEEEHHHHHHHHHSCC-----------------CCHHHHHHHHHHHHHHHTTCCEEE---EECCSCC
T ss_pred             CCEEEEEchHHHHHHHHhCCCc--cccc--CcCCCCCchHHHHHHHHHHHHHHCCCCeEE---EEeCCCc
Confidence            3699999999999999998631  1135  89999999999999999999999  67766   7997654

>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A {Homo sapiens} PDB: 3qeb_Z* 3qea_Z*

Probab=97.29  E-value=0.00023  Score=62.65  Aligned_cols=59  Identities=10%  Similarity=0.034  Sum_probs=48.0

Q ss_pred             CcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHhhCCCEEEEEEeCCCc
Q 030072          108 GRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCPSC  175 (183)
Q Consensus       108 ~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk~~PthIaVaFDs~gk  175 (183)
                      ++.+.|||++++||++|+...         ....|.||+++.||+...++++....-..++|||.+..
T Consensus        24 Gk~vaIDas~wL~~~~~~~~~---------~l~~G~~t~~l~~~~~r~l~~L~~~gI~PvfVFDG~~~   82 (352)
T 3qe9_Y           24 GQVVAVDTYCWLHKGAIACAE---------KLAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTL   82 (352)
T ss_dssp             TSEEEEETHHHHHHHHHHTHH---------HHHTTCCCCHHHHHHHHHHHHHHHTTCEEEEEECCSCC
T ss_pred             CcEEEEecHHHHHHhhhccch---------hhcCCCCcHHHHHHHHHHHHHHHHcCCEEEEEECCCCc
Confidence            468999999999999988642         23589999999999999999887233677899998764

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	183
d1cmwa2	164	c.120.1.2 (A:10-173) 5' to 3' exonuclease domain o	8e-06
d1xo1a2	167	c.120.1.2 (A:19-185) T5 5'-exonuclease {Bacterioph	0.001

>d1cmwa2 c.120.1.2 (A:10-173) 5' to 3' exonuclease domain of DNA polymerase Taq {Thermus aquaticus [TaxId: 271]} Length = 164

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: 5' to 3' exonuclease domain of DNA polymerase Taq
species: Thermus aquaticus [TaxId: 271]

 Score = 41.8 bits (97), Expect = 8e-06
 Identities = 15/69 (21%), Positives = 26/69 (37%), Gaps = 8/69 (11%)

Query: 107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHV 166
            GRV+L+DG  + YR +        H         G+ V  ++     ++  L+     V
Sbjct: 2   KGRVLLVDGHHLAYRTF--------HALKGLTTSRGEPVQAVYGFAKSLLKALKEDGDAV 53

Query: 167 AVCFSCPSC 175
            V F   + 
Sbjct: 54  IVVFDAKAP 62

>d1xo1a2 c.120.1.2 (A:19-185) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]} Length = 167

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: T5 5'-exonuclease
species: Bacteriophage T5 [TaxId: 10726]

 Score = 35.4 bits (81), Expect = 0.001
 Identities = 8/66 (12%), Positives = 20/66 (30%), Gaps = 15/66 (22%)

Query: 109 RVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAV 168
            +M++DGT++ +R               H +    +  +  S +  +     +      V
Sbjct: 3   NLMIVDGTNLGFRFK-------------HNNSKKPFASSYVSTIQSLAK--SYSARTTIV 47

Query: 169 CFSCPS 174
                 
Sbjct: 48  LGDKGK 53

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	183
d1cmwa2	164	5' to 3' exonuclease domain of DNA polymerase Taq	99.6
d1xo1a2	167	T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]	99.21
d1tfra2	169	T4 RNase H {Bacteriophage T4 [TaxId: 10665]}	99.03
d1a77a2	207	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met	95.66
d1b43a2	219	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr	95.41
d1rxwa2	217	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc	95.35
d1ul1x2	216	Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo	95.2

>d1cmwa2 c.120.1.2 (A:10-173) 5' to 3' exonuclease domain of DNA polymerase Taq {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: 5' to 3' exonuclease domain of DNA polymerase Taq
species: Thermus aquaticus [TaxId: 271]

Probab=99.60  E-value=5.7e-16  Score=120.36  Aligned_cols=63  Identities=24%  Similarity=0.426  Sum_probs=57.0

Q ss_pred             CCCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHhhCCCEEEEEEeCCCcc
Q 030072          106 SNGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCPSCM  176 (183)
Q Consensus       106 ~~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk~~PthIaVaFDs~gk~  176 (183)
                      ++++++||||++++||+|||.+      .+  .+++|.|++||+||+++|.+++++.|++++|+||.+++.
T Consensus         1 p~~~~lLIDg~~l~~R~~~a~~------~~--~~~~g~~~~~i~gf~~~l~~~~~~~~~~~~v~~d~~~~~   63 (164)
T d1cmwa2           1 PKGRVLLVDGHHLAYRTFHALK------GL--TTSRGEPVQAVYGFAKSLLKALKEDGDAVIVVFDAKAPS   63 (164)
T ss_dssp             CCEEEEEEETTHHHHHHHTSST------TC--BCTTSCBCHHHHHHHHHHHHHHHHCCSEEEEECCCSSSC
T ss_pred             CCCeEEEEeChHHHHHHHHcCC------cc--cCCCCCeeHHHHHHHHHHHHHHhcCCceEEEEEeccccc
Confidence            3678999999999999999997      45  789999999999999999999997799999999987654

>d1xo1a2 c.120.1.2 (A:19-185) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]}

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: T5 5'-exonuclease
species: Bacteriophage T5 [TaxId: 10726]

Probab=99.21  E-value=2.5e-12  Score=100.27  Aligned_cols=53  Identities=17%  Similarity=0.083  Sum_probs=42.5

Q ss_pred             CCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCCCc
Q 030072          107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCPSC  175 (183)
Q Consensus       107 ~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~gk  175 (183)
                      +++++||||++|+||+||+..                ++++++||+++|.++++ ++|++++||||.+++
T Consensus         1 k~~~lliDg~~l~~R~~~~~~----------------~~~~~~~f~~~l~~l~~~~~~~~iiv~~d~~~~   54 (167)
T d1xo1a2           1 RRNLMIVDGTNLGFRFKHNNS----------------KKPFASSYVSTIQSLAKSYSARTTIVLGDKGKS   54 (167)
T ss_dssp             CCEEEEEEHHHHHTTC-----------------------CCHHHHHHHHHHHHHHTTEEEEEEECCBSCC
T ss_pred             CCeEEEEcChHHHHHHHHcCC----------------CcCHHHHHHHHHHHHHHHcCCCEEEEEEeCCCC
Confidence            357999999999999998743                57889999999999999 999999999997654

>d1tfra2 c.120.1.2 (A:12-180) T4 RNase H {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: T4 RNase H
species: Bacteriophage T4 [TaxId: 10665]

Probab=99.03  E-value=6.8e-11  Score=93.04  Aligned_cols=59  Identities=10%  Similarity=0.130  Sum_probs=47.2

Q ss_pred             CCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHH----HHHHHHHHHh-hCCCEEEEEEeCCCc
Q 030072          107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFS----ALSLIIDVLE-FIPSHVAVCFSCPSC  175 (183)
Q Consensus       107 ~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyG----Fl~mLlkLLk-~~PthIaVaFDs~gk  175 (183)
                      +++++||||++++||+||+..          .++++.+++++++    .++++.+.++ ++|++++||||.+++
T Consensus         1 k~~~~liD~s~~~~~~~~~~~----------~~~~~~~~~~~~h~~lnsi~~~~k~~~~~~p~~viv~~D~~~~   64 (169)
T d1tfra2           1 KEGICLIDFSQIALSTALVNF----------PDKEKINLSMVRHLILNSIKFNVKKAKTLGYTKIVLCIDNAKS   64 (169)
T ss_dssp             CCEEEEEEHHHHHHHHHHHHS----------CTTSCCCHHHHHHHHHHHHHHHHHHHHHTTEEEEEEECCCCTT
T ss_pred             CCCEEEEechHHHHHHHHHhc----------cCCCCCChhHHHHHHHHHHHHHHHHhhhcCCCeEEEEEeCCCC
Confidence            358999999999999999875          4556788888866    3455556667 889999999997654

>d1a77a2 c.120.1.2 (A:2-208) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=95.66  E-value=0.011  Score=45.69  Aligned_cols=64  Identities=19%  Similarity=0.209  Sum_probs=48.6

Q ss_pred             CcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHhhCCCEEEEEEeCCCc
Q 030072          108 GRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCPSC  175 (183)
Q Consensus       108 ~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk~~PthIaVaFDs~gk  175 (183)
                      ++.+-||++.++||.-++.... .+.++  .+..|.++..+.+++..+..+++++ =..++|||...+
T Consensus        20 gk~vaIDas~~L~~~l~~~~~~-~~~~l--~~~~g~~~~~l~~~~~~~~~ll~~~-I~pifVFDG~~~   83 (207)
T d1a77a2          20 GKKVAIDGMNALYQFLTSIRLR-DGSPL--RNRKGEITSAYNGVFYKTIHLLEND-ITPIWVFDGEPP   83 (207)
T ss_dssp             TCEEEEEHHHHHHHHHHHSBCT-TSCBC--BCTTSCBCHHHHHHHHHHHHHHHTT-CEEEEEECCCTT
T ss_pred             CCEEEEEChHHHHHHHHHhhcc-cCchh--hhccCCcCHHHHHHHHHHHHHHHcC-CeEEEEECCCCc
Confidence            3579999999999977765432 11234  7889999999999999999888754 446778998644

>d1b43a2 c.120.1.2 (A:1-219) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.41  E-value=0.02  Score=44.60  Aligned_cols=65  Identities=20%  Similarity=0.207  Sum_probs=48.7

Q ss_pred             CCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHhhCCCEEEEEEeCCCc
Q 030072          107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCPSC  175 (183)
Q Consensus       107 ~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk~~PthIaVaFDs~gk  175 (183)
                      +++.+-||++.++||.-++.... .+.++  .+.+|.++..+.+|+..+..+++++ =..+++||...+
T Consensus        19 ~gk~iaIDas~~L~k~l~~~~~~-~~~~l--~~~~~~~~~~l~~~~~r~~~Ll~~~-I~pVFVFDG~~~   83 (219)
T d1b43a2          19 YGKKIAIDALNAIYQFLSTIRQK-DGTPL--MDSKGRITSHLSGLFYRTINLMEAG-IKPVYVFDGEPP   83 (219)
T ss_dssp             TTCEEEEEHHHHHHHHHHHSBCT-TSCBC--BCTTSCBCHHHHHHHHHHHHHHHTT-CEEEEEECCSCC
T ss_pred             CCCEEEEEChHHHHHHHHHhccc-ccchh--hhccCCCchHHHHHHHHHHHHHHcC-CeEEEEeCCCCC
Confidence            34578899999999976665422 12234  7889999999999999999888743 456789997643

>d1rxwa2 c.120.1.2 (A:3-219) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.35  E-value=0.021  Score=44.32  Aligned_cols=65  Identities=15%  Similarity=0.185  Sum_probs=49.6

Q ss_pred             CCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHhhCCCEEEEEEeCCCc
Q 030072          107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCPSC  175 (183)
Q Consensus       107 ~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk~~PthIaVaFDs~gk  175 (183)
                      +++.+-||++.++||.-++.... .+.++  .+..|.++..+.+|+..+..+++++ =..++|||...+
T Consensus        18 ~Gk~vAIDas~wL~k~l~~~~~~-~~~~l--~~~~~~~~~~l~~~~~ri~~l~~~~-I~pifVFDG~~p   82 (217)
T d1rxwa2          18 SGKKIAVDAFNTLYQFISIIRQP-DGTPL--KDSQGRITSHLSGILYRVSNMVEVG-IRPVFVFDGEPP   82 (217)
T ss_dssp             TTCEEEEEHHHHHHHHHHHSBCT-TSCBC--BCTTSCBCHHHHHHHHHHHHHHHHT-CEEEEEECCSCC
T ss_pred             CCCEEEEECHHHHHHHHHHhccc-cCCch--hhccCCccHHHHHHHHHHHHHHHcC-CeEEEEECCCCC
Confidence            34689999999999976665322 11134  7889999999999999999888844 557888998654

>d1ul1x2 c.120.1.2 (X:2-217) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.20  E-value=0.013  Score=45.00  Aligned_cols=60  Identities=17%  Similarity=0.185  Sum_probs=39.7

Q ss_pred             cEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHhhCCCEEEEEEeCC
Q 030072          109 RVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCP  173 (183)
Q Consensus       109 kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk~~PthIaVaFDs~  173 (183)
                      +.+.||++.++||..++....  ...+  .+..|.++..+.+++..+..+++++ =..++|||..
T Consensus        28 k~vaIDas~~l~~~l~~~~~~--~~~l--~~~~~~~~~~l~~~~~~~~~l~~~~-I~pifVFDG~   87 (216)
T d1ul1x2          28 RKVAIDASMSIYQFLIAVRQG--GDVL--QNEEGETTSHLMGMFYRTIRMMENG-IKPVYVFDGK   87 (216)
T ss_dssp             CCEEEEHHHHHHHHHSCC-----------------CCHHHHHHHHHHHHHHHTT-CCEEEEECCS
T ss_pred             CEEEEEeHHHHHHHHHHhccc--cchh--hccCCCCcHHHHHHHHHHHHHHHcC-CeEEEEEcCC
Confidence            579999999999998886432  1134  6788999999999999988888743 3468889984