Citrus Sinensis ID: 039224

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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-------18
Protein Sequence
MPRPSTSYRRKKVEKEELPEDTELYRFFSYIYNTNQGIDNAVPVLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEVSLIIYYTCC
Secondary Structure (PSIPRED)
ccccccHHHccHHHHHccccHHHHHccccccccccccccccccEEEEcccccccccHHHHHHHccccHHHHHHHHHHHHHHHHcccccEEEEEEccccccccccEEEEccEEEEEcccccHHHHHHHHHHHHHccccccEEEEcccHHHHHHHHHcccEEEcHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccccccEEEccccccccHHHHcccEEEEcccccccccEEEEEcccHHHccHHHHHHHHHcccHHHHHHHHHHHHHHHHHccccEEEEEEEcEEccccccEEEEEEEEEEEccHHHHHHHHHHHHHHHHHccccEEEEEEccHHHHHHHHHccHHHccHHHHHHHHHHEEEHccc
Coil and Loop (DISEMBL)
mprpstsyrrkkvekeelpedteLYRFFSYIYNtnqgidnavpvllvdgynvcgywpklenhfIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALmsglpthkeefigvdivfpgetcadAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEVSLIIYYTCC
Flexible Loop (DISEMBL)
mprpstsyrrkkvekeelpedtelYRFFSYIYNTNQGIDNAVPVLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEVSLIIYYTCC
Low Complexity Region (SEG)
MPRPSTSYRRKKVEKEELPEDTELYRFFSYIYNTNQGIDNAVPVLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEVSLIIYYTCC
Disordered region (IsUnstruct)
**********************ELYRFFSYIYNTNQGIDNAVPVLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEVSLIIYYTC*
Disordered Region (DISOPRED)
*******************************************VLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGL****EEFIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEVSLIIYYTCC
Disordered Region (DISEMBL)
****************ELPEDTELYRFFSYIYNTNQGIDNAVPVLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEVSLIIYYTCC
Disordered Region (DISPRO)
******SYRRKKVEKEELPEDTELYRFFSYIYNTNQGIDNAVPVLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEVSLIIYYTCC
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MPRPSTSYRRKKVEKEELPEDTELYRFFSYIYNTNQGIDNAVPVLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEVSLIIYYTCC
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

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	179	2.2.26 [Sep-21-2011]
P37574	170	Uncharacterized protein Y	yes	no	0.703	0.741	0.374	1e-12

>sp|P37574|YACP_BACSU Uncharacterized protein YacP OS=Bacillus subtilis (strain 168) GN=yacP PE=4 SV=1

 Score = 72.4 bits (176), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 49/131 (37%), Positives = 76/131 (58%), Gaps = 5/131 (3%)

Query: 42  VPVLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDA-LMSG 100
           + +LLVDGYN+ G WP+L++       + AR  LI+++ E+      +V+VVFDA L+ G
Sbjct: 1   MDILLVDGYNMIGAWPQLKD-LKANSFEEARDVLIQKMAEYQSYTGNRVIVVFDAHLVKG 59

Query: 101 LPTHKEEFIGVDIVFPGET-CADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAF 159
           L   K+    V+++F  E   AD  IEK   AL  +   ++ V TSD+ +Q A +G GA 
Sbjct: 60  LE-KKQTNHRVEVIFTKENETADERIEKLAQALN-NIATQIHVATSDYTEQWAIFGQGAL 117

Query: 160 VWSSKALVSEV 170
             S++ L+ EV
Sbjct: 118 RKSARELLREV 128

Bacillus subtilis (strain 168) (taxid: 224308)

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	179
255556685	303	conserved hypothetical protein [Ricinus	0.944	0.557	0.794	7e-78
118488713	297	unknown [Populus trichocarpa]	0.944	0.569	0.770	5e-75
225465306	282	PREDICTED: uncharacterized protein LOC10	0.944	0.599	0.770	8e-75
224070772	253	predicted protein [Populus trichocarpa]	0.944	0.667	0.770	1e-74
449431908	304	PREDICTED: uncharacterized protein LOC10	0.955	0.562	0.75	7e-74
449525788	259	PREDICTED: uncharacterized protein LOC10	0.944	0.652	0.758	6e-73
356522105	286	PREDICTED: uncharacterized protein LOC10	0.944	0.590	0.744	1e-71
334184110	243	uncharacterized protein [Arabidopsis tha	0.949	0.699	0.773	6e-70
30677998	308	uncharacterized protein [Arabidopsis tha	0.949	0.551	0.773	1e-69
334184108	260	uncharacterized protein [Arabidopsis tha	0.949	0.653	0.773	1e-69

>gi|255556685|ref|XP_002519376.1| conserved hypothetical protein [Ricinus communis] gi|223541443|gb|EEF42993.1| conserved hypothetical protein [Ricinus communis]

 Score =  295 bits (754), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 135/170 (79%), Positives = 157/170 (92%), Gaps = 1/170 (0%)

Query: 2   PRPSTSYRRKKVEKEELPEDTELYRFFSY-IYNTNQGIDNAVPVLLVDGYNVCGYWPKLE 60
           P+P+TSYR+KKV+KE+LPEDTELYR  +  +Y TNQ ID+AVPVLLVDGYNVCGYWPKL+
Sbjct: 83  PKPATSYRKKKVQKEDLPEDTELYRDPTLSLYYTNQVIDDAVPVLLVDGYNVCGYWPKLK 142

Query: 61  NHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGETC 120
            HF+ GRLD+ARQKLI+EL+ FSM+REVKVV VFDA+MSGLPTHKE FIG+D+VF GE+C
Sbjct: 143 KHFMNGRLDIARQKLIDELITFSMLREVKVVAVFDAMMSGLPTHKETFIGIDVVFSGESC 202

Query: 121 ADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEV 170
           ADAWIEKE+VALREDGCPKVWVVTSD +QQHAA+GAGAFVWSSKALVSE+
Sbjct: 203 ADAWIEKEVVALREDGCPKVWVVTSDRMQQHAAHGAGAFVWSSKALVSEI 252

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118488713|gb|ABK96167.1| unknown [Populus trichocarpa]

 Score =  285 bits (729), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 131/170 (77%), Positives = 152/170 (89%), Gaps = 1/170 (0%)

Query: 2   PRPSTSYRRKKVEKEELPEDTELYRFFSY-IYNTNQGIDNAVPVLLVDGYNVCGYWPKLE 60
           P+PSTSYRRKKVEKE+LPEDTELYR  +  +Y TNQ ++  VPVLLVDGYNVCGYW KL+
Sbjct: 77  PKPSTSYRRKKVEKEDLPEDTELYRDPTLSLYYTNQIVETGVPVLLVDGYNVCGYWAKLK 136

Query: 61  NHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGETC 120
            HF+ GRLD+ARQKLI+ELV FS+ R+VKVVVVFDA+MSGLPTHKE F GVD++F GE+C
Sbjct: 137 KHFVNGRLDIARQKLIDELVAFSLARDVKVVVVFDAMMSGLPTHKENFAGVDVIFTGESC 196

Query: 121 ADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEV 170
           ADAWIEKE+VAL+EDGCPKVWVVTSDH+ QHAA+GAGAF+WS KALVSEV
Sbjct: 197 ADAWIEKEVVALKEDGCPKVWVVTSDHIHQHAAHGAGAFIWSCKALVSEV 246

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225465306|ref|XP_002269195.1| PREDICTED: uncharacterized protein LOC100265963 [Vitis vinifera] gi|297739435|emb|CBI29617.3| unnamed protein product [Vitis vinifera]

 Score =  285 bits (728), Expect = 8e-75,   Method: Compositional matrix adjust.
 Identities = 131/170 (77%), Positives = 153/170 (90%), Gaps = 1/170 (0%)

Query: 2   PRPSTSYRRKKVEKEELPEDTELYRFFS-YIYNTNQGIDNAVPVLLVDGYNVCGYWPKLE 60
           P+P+TSYRRKKV+K++LPEDTELY   +  +Y TNQGID AVPVLLVDGYNVCGYW KL+
Sbjct: 64  PKPATSYRRKKVQKDDLPEDTELYHDPTVTLYYTNQGIDTAVPVLLVDGYNVCGYWMKLK 123

Query: 61  NHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGETC 120
            HF+ GRLD+ARQKLI+ELV FS++REVKVVVVFDA+MSGLPTHKE F G+D+V+ GE+C
Sbjct: 124 KHFVNGRLDIARQKLIDELVTFSLLREVKVVVVFDAMMSGLPTHKENFAGIDVVYSGESC 183

Query: 121 ADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEV 170
           ADAWIEKE+VALREDGCPKVWVVTSD+ QQ AA+GAGAFVWS KALVSE+
Sbjct: 184 ADAWIEKEVVALREDGCPKVWVVTSDNCQQQAAHGAGAFVWSCKALVSEI 233

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224070772|ref|XP_002303229.1| predicted protein [Populus trichocarpa] gi|222840661|gb|EEE78208.1| predicted protein [Populus trichocarpa]

 Score =  284 bits (726), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 131/170 (77%), Positives = 152/170 (89%), Gaps = 1/170 (0%)

Query: 2   PRPSTSYRRKKVEKEELPEDTELYRFFSY-IYNTNQGIDNAVPVLLVDGYNVCGYWPKLE 60
           P+PSTSYRRKKVEKE+LPEDTELYR  +  +Y TNQ ++  VPVLLVDGYNVCGYW KL+
Sbjct: 33  PKPSTSYRRKKVEKEDLPEDTELYRDPTLSLYYTNQIVETGVPVLLVDGYNVCGYWAKLK 92

Query: 61  NHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGETC 120
            HF+ GRLD+ARQKLI+ELV FS+ R+VKVVVVFDA+MSGLPTHKE F GVD++F GE+C
Sbjct: 93  KHFVNGRLDIARQKLIDELVAFSLARDVKVVVVFDAIMSGLPTHKENFAGVDVIFTGESC 152

Query: 121 ADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEV 170
           ADAWIEKE+VAL+EDGCPKVWVVTSDH+ QHAA+GAGAF+WS KALVSEV
Sbjct: 153 ADAWIEKEVVALKEDGCPKVWVVTSDHIHQHAAHGAGAFIWSCKALVSEV 202

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449431908|ref|XP_004133742.1| PREDICTED: uncharacterized protein LOC101212837 [Cucumis sativus]

 Score =  281 bits (719), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 129/172 (75%), Positives = 153/172 (88%), Gaps = 1/172 (0%)

Query: 1   MPRPSTSYRRKKVEKEELPEDTELYRFFSY-IYNTNQGIDNAVPVLLVDGYNVCGYWPKL 59
           +P+P+TSYRRKKVEKE+LPEDTELYR  +  +Y+TNQGIDN  PVLLVDGYNVCGYW KL
Sbjct: 85  VPKPATSYRRKKVEKEDLPEDTELYRDPTLALYHTNQGIDNVFPVLLVDGYNVCGYWVKL 144

Query: 60  ENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGET 119
           + HF+ GRLDVARQKLI+EL+ FSM+REVKVVVVFDA++SGLPTHKE F G+D+V+ GE+
Sbjct: 145 KKHFMNGRLDVARQKLIDELITFSMLREVKVVVVFDAMLSGLPTHKENFAGIDVVYSGES 204

Query: 120 CADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEVS 171
           CAD WIE E+VAL+EDGCPKVWVVTSD   QHAA+GAGAF+WS KALVSE++
Sbjct: 205 CADTWIETEVVALKEDGCPKVWVVTSDVCHQHAAHGAGAFIWSCKALVSEIN 256

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449525788|ref|XP_004169898.1| PREDICTED: uncharacterized protein LOC101230835, partial [Cucumis sativus]

 Score =  278 bits (711), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 129/170 (75%), Positives = 151/170 (88%), Gaps = 1/170 (0%)

Query: 1   MPRPSTSYRRKKVEKEELPEDTELYRFFSY-IYNTNQGIDNAVPVLLVDGYNVCGYWPKL 59
           +P+P+TSYRRKKVEKE+LPEDTELYR  +  +Y+TNQGIDN  PVLLVDGYNVCGYW KL
Sbjct: 90  VPKPATSYRRKKVEKEDLPEDTELYRDPTLALYHTNQGIDNVFPVLLVDGYNVCGYWVKL 149

Query: 60  ENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGET 119
           + HF+ GRLDVARQKLI+EL+ FSM+REVKVVVVFDA++SGLPTHKE F G+D+V+ GE+
Sbjct: 150 KKHFMNGRLDVARQKLIDELITFSMLREVKVVVVFDAMLSGLPTHKENFAGIDVVYSGES 209

Query: 120 CADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSE 169
           CAD WIE E+VAL+EDGCPKVWVVTSD   QHAA+GAGAF+WS KALVSE
Sbjct: 210 CADTWIETEVVALKEDGCPKVWVVTSDVCHQHAAHGAGAFIWSCKALVSE 259

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356522105|ref|XP_003529690.1| PREDICTED: uncharacterized protein LOC100804585 [Glycine max]

 Score =  273 bits (699), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 128/172 (74%), Positives = 148/172 (86%), Gaps = 3/172 (1%)

Query: 2   PRPSTSYRRKKVEKEELPEDTELYR--FFSYIYNTNQGI-DNAVPVLLVDGYNVCGYWPK 58
           PRPSTSYR+KKVEKE+   DT+LYR    S  Y   QGI DNAVPVLLVDGYNVCGYW K
Sbjct: 66  PRPSTSYRKKKVEKEDDVVDTDLYRDPTTSLYYTNQQGILDNAVPVLLVDGYNVCGYWMK 125

Query: 59  LENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGE 118
           L+ HF+KGRLD+ARQKLI+EL+ FSM+REVK+VVVFDA+MSGLPTHKE+F G+DI+F GE
Sbjct: 126 LKKHFVKGRLDIARQKLIDELLTFSMLREVKIVVVFDAMMSGLPTHKEDFAGLDIIFSGE 185

Query: 119 TCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEV 170
           TCAD WIEKE+ AL+EDGCPKVWVVTSDH  Q AA+GAGAF+WS KALV+E+
Sbjct: 186 TCADTWIEKEVAALKEDGCPKVWVVTSDHCHQQAAHGAGAFIWSCKALVTEI 237

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334184110|ref|NP_001189501.1| uncharacterized protein [Arabidopsis thaliana] gi|330250485|gb|AEC05579.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  268 bits (686), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 133/172 (77%), Positives = 157/172 (91%), Gaps = 2/172 (1%)

Query: 1   MPRPSTSYRRKKVEKEELPEDTELYRF-FSYIYNTNQGI-DNAVPVLLVDGYNVCGYWPK 58
           M +P+TSYR+KKVEK+ELP+D+ELYR   + +Y TNQG+ D+AVPVLLVDGYNVCGYW K
Sbjct: 22  MAKPATSYRKKKVEKDELPDDSELYRDPTNTLYYTNQGLLDDAVPVLLVDGYNVCGYWMK 81

Query: 59  LENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGE 118
           L+ HF+KGRLDVARQKL++ELV FSM++EVKVVVVFDALMSGLPTHKE+F GVD++F GE
Sbjct: 82  LKKHFMKGRLDVARQKLVDELVSFSMVKEVKVVVVFDALMSGLPTHKEDFAGVDVIFSGE 141

Query: 119 TCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEV 170
           TCADAWIEKE+VALREDGCPKVWVVTSD  QQ AA+GAGA++WSSKALVSE+
Sbjct: 142 TCADAWIEKEVVALREDGCPKVWVVTSDVCQQQAAHGAGAYIWSSKALVSEI 193

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30677998|ref|NP_178346.2| uncharacterized protein [Arabidopsis thaliana] gi|26449562|dbj|BAC41907.1| unknown protein [Arabidopsis thaliana] gi|28950879|gb|AAO63363.1| At2g02410 [Arabidopsis thaliana] gi|330250483|gb|AEC05577.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  267 bits (683), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 133/172 (77%), Positives = 157/172 (91%), Gaps = 2/172 (1%)

Query: 1   MPRPSTSYRRKKVEKEELPEDTELYRF-FSYIYNTNQGI-DNAVPVLLVDGYNVCGYWPK 58
           M +P+TSYR+KKVEK+ELP+D+ELYR   + +Y TNQG+ D+AVPVLLVDGYNVCGYW K
Sbjct: 87  MAKPATSYRKKKVEKDELPDDSELYRDPTNTLYYTNQGLLDDAVPVLLVDGYNVCGYWMK 146

Query: 59  LENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGE 118
           L+ HF+KGRLDVARQKL++ELV FSM++EVKVVVVFDALMSGLPTHKE+F GVD++F GE
Sbjct: 147 LKKHFMKGRLDVARQKLVDELVSFSMVKEVKVVVVFDALMSGLPTHKEDFAGVDVIFSGE 206

Query: 119 TCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEV 170
           TCADAWIEKE+VALREDGCPKVWVVTSD  QQ AA+GAGA++WSSKALVSE+
Sbjct: 207 TCADAWIEKEVVALREDGCPKVWVVTSDVCQQQAAHGAGAYIWSSKALVSEI 258

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334184108|ref|NP_001189500.1| uncharacterized protein [Arabidopsis thaliana] gi|330250484|gb|AEC05578.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  267 bits (682), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 133/172 (77%), Positives = 157/172 (91%), Gaps = 2/172 (1%)

Query: 1   MPRPSTSYRRKKVEKEELPEDTELYRF-FSYIYNTNQGI-DNAVPVLLVDGYNVCGYWPK 58
           M +P+TSYR+KKVEK+ELP+D+ELYR   + +Y TNQG+ D+AVPVLLVDGYNVCGYW K
Sbjct: 39  MAKPATSYRKKKVEKDELPDDSELYRDPTNTLYYTNQGLLDDAVPVLLVDGYNVCGYWMK 98

Query: 59  LENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGE 118
           L+ HF+KGRLDVARQKL++ELV FSM++EVKVVVVFDALMSGLPTHKE+F GVD++F GE
Sbjct: 99  LKKHFMKGRLDVARQKLVDELVSFSMVKEVKVVVVFDALMSGLPTHKEDFAGVDVIFSGE 158

Query: 119 TCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEV 170
           TCADAWIEKE+VALREDGCPKVWVVTSD  QQ AA+GAGA++WSSKALVSE+
Sbjct: 159 TCADAWIEKEVVALREDGCPKVWVVTSDVCQQQAAHGAGAYIWSSKALVSEI 210

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	179
TAIR|locus:2056206	308	AT2G02410 "AT2G02410" [Arabido	0.949	0.551	0.773	6.1e-71
UNIPROTKB|Q724H0	170	LMOf2365_0254 "Putative unchar	0.687	0.723	0.392	1.8e-16
UNIPROTKB|Q3A9P5	168	CHY_2334 "Putative uncharacter	0.692	0.738	0.343	1.2e-12
TIGR_CMR|CHY_2334	168	CHY_2334 "conserved hypothetic	0.692	0.738	0.343	1.2e-12
UNIPROTKB|Q81VU8	170	BAS0092 "Uncharacterized prote	0.692	0.729	0.302	8.4e-10
TIGR_CMR|BA_0092	170	BA_0092 "conserved hypothetica	0.692	0.729	0.302	8.4e-10

TAIR|locus:2056206 AT2G02410 "AT2G02410" [Arabidopsis thaliana (taxid:3702)]

 Score = 718 (257.8 bits), Expect = 6.1e-71, P = 6.1e-71
 Identities = 133/172 (77%), Positives = 157/172 (91%)

Query:     1 MPRPSTSYRRKKVEKEELPEDTELYRF-FSYIYNTNQGI-DNAVPVLLVDGYNVCGYWPK 58
             M +P+TSYR+KKVEK+ELP+D+ELYR   + +Y TNQG+ D+AVPVLLVDGYNVCGYW K
Sbjct:    87 MAKPATSYRKKKVEKDELPDDSELYRDPTNTLYYTNQGLLDDAVPVLLVDGYNVCGYWMK 146

Query:    59 LENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGE 118
             L+ HF+KGRLDVARQKL++ELV FSM++EVKVVVVFDALMSGLPTHKE+F GVD++F GE
Sbjct:   147 LKKHFMKGRLDVARQKLVDELVSFSMVKEVKVVVVFDALMSGLPTHKEDFAGVDVIFSGE 206

Query:   119 TCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEV 170
             TCADAWIEKE+VALREDGCPKVWVVTSD  QQ AA+GAGA++WSSKALVSE+
Sbjct:   207 TCADAWIEKEVVALREDGCPKVWVVTSDVCQQQAAHGAGAYIWSSKALVSEI 258

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

UNIPROTKB|Q724H0 LMOf2365_0254 "Putative uncharacterized protein" [Listeria monocytogenes serotype 4b str. F2365 (taxid:265669)]

 Score = 204 (76.9 bits), Expect = 1.8e-16, P = 1.8e-16
 Identities = 51/130 (39%), Positives = 79/130 (60%)

Query:    44 VLLVDGYNVCGYWPKLENHFIKGR-LDVARQKLIEELVEFSMIREVKVVVVFDA-LMSGL 101
             +LLVDGYNV G WP+L   F+K R L+ AR KL+E + E+      +VVVVFDA  + G+
Sbjct:     4 ILLVDGYNVIGAWPELS--FLKDRDLEAARDKLVEWMAEYQSYTGYRVVVVFDAQFVRGV 61

Query:   102 PTHKEEFIGVDIVFPGET-CADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFV 160
                 +++  V++VF  E   AD +IE++ +  +     ++ V TSD+ +Q A +G GA  
Sbjct:    62 KRKSKKY-QVEVVFTHEDETADEYIEQKAIEWKNVRT-QIMVATSDYTEQWAIFGQGALR 119

Query:   161 WSSKALVSEV 170
              SS+ L+ E+
Sbjct:   120 ISSRELLFEI 129

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q3A9P5 CHY_2334 "Putative uncharacterized protein" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 45/131 (34%), Positives = 75/131 (57%)

Query:    45 LLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTH 104
             +L+DGYN+   WP+L     +  L+ AR+ L E L+ +  +   +V++V+DA      + 
Sbjct:     5 VLIDGYNLLFNWPELNKLKDETSLEHAREVLKERLINYRALTGREVIIVYDAHQQK-ESR 63

Query:   105 KEEF-IGVDIVFP--GETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVW 161
             +E F  G+ +VF   GET AD +IEK++  L      +V+VVT D LQQ   +G GA   
Sbjct:    64 REFFEAGITVVFTESGET-ADHFIEKKVQELLPGN--RVYVVTQDELQQKLIFGYGALRI 120

Query:   162 SSKALVSEVSL 172
             S + L++++ +
Sbjct:   121 SLRELLNDLKI 131

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|CHY_2334 CHY_2334 "conserved hypothetical protein" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 45/131 (34%), Positives = 75/131 (57%)

Query:    45 LLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTH 104
             +L+DGYN+   WP+L     +  L+ AR+ L E L+ +  +   +V++V+DA      + 
Sbjct:     5 VLIDGYNLLFNWPELNKLKDETSLEHAREVLKERLINYRALTGREVIIVYDAHQQK-ESR 63

Query:   105 KEEF-IGVDIVFP--GETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVW 161
             +E F  G+ +VF   GET AD +IEK++  L      +V+VVT D LQQ   +G GA   
Sbjct:    64 REFFEAGITVVFTESGET-ADHFIEKKVQELLPGN--RVYVVTQDELQQKLIFGYGALRI 120

Query:   162 SSKALVSEVSL 172
             S + L++++ +
Sbjct:   121 SLRELLNDLKI 131

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q81VU8 BAS0092 "Uncharacterized protein" [Bacillus anthracis (taxid:1392)]

 Score = 141 (54.7 bits), Expect = 8.4e-10, P = 8.4e-10
 Identities = 39/129 (30%), Positives = 69/129 (53%)

Query:    44 VLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDAL-MSGLP 102
             +L+VDGYN+ G W  L+       L  +R  LI+++ ++      KV++VFDA  + G+ 
Sbjct:     4 ILIVDGYNIIGAWGDLKK-LRDVDLQSSRDALIDKMADYQGYTGTKVMIVFDAYTVHGIE 62

Query:   103 THKEEFIGVDIVFPGET-CADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVW 161
                ++   V+++F  +   AD  IE+  + LR     +++V TSD+ +Q   +  GA   
Sbjct:    63 KKMKQS-RVEVIFTRKNQTADEKIEQLAIELRNINT-QIYVATSDYTEQWVIFAQGALRK 120

Query:   162 SSKALVSEV 170
             S++ L  EV
Sbjct:   121 SARELELEV 129

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|BA_0092 BA_0092 "conserved hypothetical protein" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 141 (54.7 bits), Expect = 8.4e-10, P = 8.4e-10
 Identities = 39/129 (30%), Positives = 69/129 (53%)

Query:    44 VLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDAL-MSGLP 102
             +L+VDGYN+ G W  L+       L  +R  LI+++ ++      KV++VFDA  + G+ 
Sbjct:     4 ILIVDGYNIIGAWGDLKK-LRDVDLQSSRDALIDKMADYQGYTGTKVMIVFDAYTVHGIE 62

Query:   103 THKEEFIGVDIVFPGET-CADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVW 161
                ++   V+++F  +   AD  IE+  + LR     +++V TSD+ +Q   +  GA   
Sbjct:    63 KKMKQS-RVEVIFTRKNQTADEKIEQLAIELRNINT-QIYVATSDYTEQWVIFAQGALRK 120

Query:   162 SSKALVSEV 170
             S++ L  EV
Sbjct:   121 SARELELEV 129


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        0.322   0.138   0.429    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      179       179   0.00089  109 3  11 22  0.40    32
                                                     31  0.39    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:  6
  No. of states in DFA:  599 (64 KB)
  Total size of DFA:  176 KB (2102 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:  17.17u 0.08s 17.25t   Elapsed:  00:00:02
  Total cpu time:  17.18u 0.08s 17.26t   Elapsed:  00:00:02
  Start:  Tue May 21 01:52:24 2013   End:  Tue May 21 01:52:26 2013

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

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

Fail to connect to STRING server

---

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	179
pfam05991	165	pfam05991, NYN_YacP, YacP-like NYN domain	5e-49
COG3688	173	COG3688, COG3688, Predicted RNA-binding protein co	3e-27

>gnl|CDD|218845 pfam05991, NYN_YacP, YacP-like NYN domain

 Score =  155 bits (395), Expect = 5e-49
 Identities = 53/128 (41%), Positives = 75/128 (58%), Gaps = 3/128 (2%)

Query: 45  LLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDA-LMSGLPT 103
           LLVDGYNV G WP+L+    +G L+ AR KL+E L  +   +  +V+VVFDA  + G   
Sbjct: 1   LLVDGYNVIGAWPELKKLKDRGSLEAARDKLLEILANYQAFKGYRVIVVFDAHYVPGSEE 60

Query: 104 HKEEFIGVDIVFPGE-TCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWS 162
             E++ G+++VF  E   AD++IEK +  L      +V VVTSD  +Q   +G GA   S
Sbjct: 61  EYEKYGGIEVVFTKEGETADSYIEKLVAELNRRKK-QVTVVTSDRAEQWTIFGRGALRIS 119

Query: 163 SKALVSEV 170
           S+ L  EV
Sbjct: 120 SRELAEEV 127

This family consists of bacterial proteins related to YacP. This family is uncharacterized functionally, but it has been suggested that these proteins are nucleases due to them containing a NYN domain. NYN (for N4BP1, YacP-like Nuclease) domains were discovered by Anantharaman and Aravind. Based on gene neighborhoods it was suggested that the bacterial YacP proteins interact with the Ribonuclease III and TrmH methylase in a processome complex that catalyzes the maturation of rRNA and tRNA. Length = 165

>gnl|CDD|226213 COG3688, COG3688, Predicted RNA-binding protein containing a PIN domain [General function prediction only]

 Score =  100 bits (251), Expect = 3e-27
 Identities = 52/131 (39%), Positives = 74/131 (56%), Gaps = 7/131 (5%)

Query: 44  VLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPT 103
           +LLVDGYN+ G WP+L+    +  L+ AR KLIE L E+      K++VVFDA    +P 
Sbjct: 5   ILLVDGYNMIGAWPELKQLKDRNGLEAARDKLIEALAEYQSFTGYKIIVVFDAHY--VPG 62

Query: 104 HKEEFI--GVDIVFP--GETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAF 159
              E+    V +V+   GET AD++IE+ +  LR     +V V TSD  +Q   +G GA 
Sbjct: 63  VGREYKNHRVSVVYTKEGET-ADSFIERYVAELRNAATHQVIVATSDRAEQWTIFGQGAL 121

Query: 160 VWSSKALVSEV 170
             S++ L  EV
Sbjct: 122 RMSARELYQEV 132

Length = 173

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	179
COG3688	173	Predicted RNA-binding protein containing a PIN dom	100.0
PF05991	166	NYN_YacP: YacP-like NYN domain; InterPro: IPR01029	100.0
smart00475	259	53EXOc 5'-3' exonuclease.	98.27
PF02739	169	5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolv	98.18
PRK14976	281	5'-3' exonuclease; Provisional	98.14
cd00008	240	53EXOc 5'-3' exonuclease; T5 type 5'-3' exonucleas	98.01
PRK09482	256	flap endonuclease-like protein; Provisional	97.81
PHA02567	304	rnh RnaseH; Provisional	97.72
PHA00439	286	exonuclease	97.72
PRK05755	880	DNA polymerase I; Provisional	97.56
TIGR00593	887	pola DNA polymerase I. This family is based on the	97.04
PF02639	130	DUF188: Uncharacterized BCR, YaiI/YqxD family COG1	96.71
COG0258	310	Exo 5'-3' exonuclease (including N-terminal domain	96.67
PRK00124	151	hypothetical protein; Validated	96.16
PF11977	155	RNase_Zc3h12a: Zc3h12a-like Ribonuclease NYN domai	96.0
COG1671	150	Uncharacterized protein conserved in bacteria [Fun	95.34
COG2454	211	Uncharacterized conserved protein [Function unknow	95.12
COG1412	136	Uncharacterized proteins of PilT N-term./Vapc supe	95.02
PTZ00217	393	flap endonuclease-1; Provisional	93.91
TIGR03674	338	fen_arch flap structure-specific endonuclease. End	92.12
cd06167	149	LabA_like LabA_like proteins. A well conserved gro	92.02
PRK13764	602	ATPase; Provisional	91.92
PF13638	133	PIN_4: PIN domain; PDB: 2HWW_C 2HWX_A 2DOK_B 2HWY_	91.12
PF00752	101	XPG_N: XPG N-terminal domain; InterPro: IPR006085	90.38
PF04900	101	Fcf1: Fcf1; InterPro: IPR006984 This family is com	88.78
PRK04358	217	hypothetical protein; Provisional	87.4
TIGR03875	206	RNA_lig_partner RNA ligase partner, MJ_0950 family	86.63
TIGR00288	160	conserved hypothetical protein TIGR00288. This fam	85.53
smart00485	99	XPGN Xeroderma pigmentosum G N-region. domain in n	85.51
COG1212	247	KdsB CMP-2-keto-3-deoxyoctulosonic acid synthetase	85.06
cd00128	316	XPG Xeroderma pigmentosum G N- and I-regions (XPGN	84.92
PF01927	147	Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 T	81.02
PF08745	205	UPF0278: UPF0278 family; InterPro: IPR022785 This	80.02

>COG3688 Predicted RNA-binding protein containing a PIN domain [General function prediction only]

Probab=100.00  E-value=2.3e-44  Score=289.58  Aligned_cols=134  Identities=37%  Similarity=0.549  Sum_probs=124.1

Q ss_pred             CCccEEEEecccccCccccchhhhcCCCHHHHHHHHHHHHHhccccCCceEEEEEcCCCCCCCCCceeecCeEEEeCCC-
Q 039224           40 NAVPVLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGE-  118 (179)
Q Consensus        40 ~~~~~lIVDGYNvI~a~p~L~~~~~~~~Le~AR~~Li~~L~~y~~~~g~~V~VVFDa~~~~~~~~~~~~~gi~VvfT~~-  118 (179)
                      |.+.+|||||||+||+||.|+.+..+.+||.||++||+.|++|+.+.|++|+|||||+..++.+......+|+|+||++ 
T Consensus         1 ~~~~iLLVDGYNmIgaWp~Lk~lkd~~~LE~AR~~LIe~l~~Y~s~~g~~iivVFDA~~v~g~~~~~~~~~vsvvyT~~~   80 (173)
T COG3688           1 MKMRILLVDGYNMIGAWPELKQLKDRNGLEAARDKLIEALAEYQSFTGYKIIVVFDAHYVPGVGREYKNHRVSVVYTKEG   80 (173)
T ss_pred             CCceEEEeccchhccccHHHHHHHhhccHHHHHHHHHHHHHHhhcccCceEEEEEEccccccccccccccceEEEEecCC
Confidence            5778999999999999999999877779999999999999999999999999999999988776666778899999999 


Q ss_pred             CChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHHhCCceEecHHHHHHHHHHH
Q 039224          119 TCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEVSLI  173 (179)
Q Consensus       119 ~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~~~GA~~iSs~ef~~~l~~~  173 (179)
                      +|||++|||++.+++.....+|.|||||.++|++++|+||.|+||+||+.+++.+
T Consensus        81 ETADs~IEr~~~el~~~~t~~V~VaTSD~~EQ~~Ifg~GA~r~Sarel~~ev~~~  135 (173)
T COG3688          81 ETADSFIERYVAELRNAATHQVIVATSDRAEQWTIFGQGALRMSARELYQEVETI  135 (173)
T ss_pred             ccHHHHHHHHHHHHhccccceEEEEeCchhhhhhhhccchHHHhHHHHHHHHHHH
Confidence            6999999999999995444589999999999999999999999999999999875

>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=100.00  E-value=3.7e-43  Score=283.34  Aligned_cols=130  Identities=38%  Similarity=0.561  Sum_probs=118.5

Q ss_pred             EEEecccccCccccchhhhcCCCHHHHHHHHHHHHHhccccCCceEEEEEcCCCCCC-CCCceeecCeEEEeCCC-CChH
Q 039224           45 LLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGL-PTHKEEFIGVDIVFPGE-TCAD  122 (179)
Q Consensus        45 lIVDGYNvI~a~p~L~~~~~~~~Le~AR~~Li~~L~~y~~~~g~~V~VVFDa~~~~~-~~~~~~~~gi~VvfT~~-~TAD  122 (179)
                      ||||||||||+||+|+.+...++|+.||++|++.|.+|++.+|++|+|||||+..++ .+..+..+||+|+||++ +|||
T Consensus         1 LlIDGYNli~~~~~l~~~~~~~~l~~aR~~Li~~L~~y~~~~~~~v~VVFDa~~~~~~~~~~~~~~gi~Vvft~~~~tAD   80 (166)
T PF05991_consen    1 LLIDGYNLIHAWPELRSLAERGDLEAARERLIEMLSEYAQFSGYEVIVVFDAYKVPGGSEEREEYGGIEVVFTKEGETAD   80 (166)
T ss_pred             CeEcchhhhCCCHHHHhhcCcCCHHHHHHHHHHHHHHHhcccCCEEEEEEeCCcCCCCCceeeeeCceEEEECCCCCCHH
Confidence            699999999999999996557899999999999999999999999999999998655 44455778999999998 6999


Q ss_pred             HHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHHhCCceEecHHHHHHHHHHHHh
Q 039224          123 AWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEVSLIIY  175 (179)
Q Consensus       123 ~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~~~GA~~iSs~ef~~~l~~~~~  175 (179)
                      +|||+++.++.+. +.+|+|||||+++|++|+++||.+|||++|+.+++....
T Consensus        81 ~~Ie~~v~~~~~~-~~~v~VVTSD~~iq~~~~~~GA~~iss~ef~~~l~~~~~  132 (166)
T PF05991_consen   81 DYIERLVRELKNR-PRQVTVVTSDREIQRAARGRGAKRISSEEFLRELKAAKR  132 (166)
T ss_pred             HHHHHHHHHhccC-CCeEEEEeCCHHHHHHHhhCCCEEEcHHHHHHHHHHHHH
Confidence            9999999999963 379999999999999999999999999999999987654

The function of this family is unknown.

>smart00475 53EXOc 5'-3' exonuclease

Probab=98.27  E-value=2.2e-06  Score=73.95  Aligned_cols=125  Identities=22%  Similarity=0.253  Sum_probs=80.3

Q ss_pred             cEEEEecccccC----ccccchhhhcCCCHHHHHHHHHHHHHhccc-cCCceEEEEEcCCCCC------------CCCCc
Q 039224           43 PVLLVDGYNVCG----YWPKLENHFIKGRLDVARQKLIEELVEFSM-IREVKVVVVFDALMSG------------LPTHK  105 (179)
Q Consensus        43 ~~lIVDGYNvI~----a~p~L~~~~~~~~Le~AR~~Li~~L~~y~~-~~g~~V~VVFDa~~~~------------~~~~~  105 (179)
                      +++||||+|+|+    +.|.|..  ..+..-.|-..++..|..... .+-..++||||+....            ....+
T Consensus         2 ~lllIDg~~~i~R~~~a~~~l~~--~~G~~t~a~~g~~~~l~~l~~~~~p~~~~~~fD~~~~~~R~~l~p~YKa~R~~~p   79 (259)
T smart00475        2 KLLLVDGSSLAFRAYFALPPLKN--SKGEPTNAVYGFLRMLLKLIKEEKPTYVAVVFDAKGKTFRHELYPEYKANRPKTP   79 (259)
T ss_pred             cEEEEeCcHHHHHHHHCCCcccC--CCCCcccHHHHHHHHHHHHHHHcCCCeEEEEEeCCCCccccchhHHHHhCCCCCC
Confidence            589999999997    5555433  133445666677777777654 4446799999984210            01111


Q ss_pred             ee-------------ecCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHHh--------C---CceEe
Q 039224          106 EE-------------FIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYG--------A---GAFVW  161 (179)
Q Consensus       106 ~~-------------~~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~~--------~---GA~~i  161 (179)
                      +.             .-|+.++-.+.-.||+.|--++......| ..++|+|+|+...+.+-.        .   +...+
T Consensus        80 e~L~~q~~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~g-~~~~IvS~DkDl~ql~~~~v~~~~~~~~~~~~~~~  158 (259)
T smart00475       80 DELLEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEG-YEVRIVSGDKDLLQLVSDKVSVLDPTKGIKEFELY  158 (259)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHhCC-CeEEEEeCCCcHhhcCCCCEEEEeccCCCCccEEE
Confidence            11             14675544434499999999999877543 689999999998877521        1   12456


Q ss_pred             cHHHHHHHH
Q 039224          162 SSKALVSEV  170 (179)
Q Consensus       162 Ss~ef~~~l  170 (179)
                      +.+++.+..
T Consensus       159 ~~~~v~~~~  167 (259)
T smart00475      159 TPENVIEKY  167 (259)
T ss_pred             cHHHHHHHh
Confidence            666665543

>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=98.18  E-value=2.1e-06  Score=69.64  Aligned_cols=111  Identities=23%  Similarity=0.215  Sum_probs=71.6

Q ss_pred             ccEEEEeccccc----Cccc--cchhhhcCCCHHHHHHHHHHHHHhccc-cCCceEEEEEcCCCCC-----CCC------
Q 039224           42 VPVLLVDGYNVC----GYWP--KLENHFIKGRLDVARQKLIEELVEFSM-IREVKVVVVFDALMSG-----LPT------  103 (179)
Q Consensus        42 ~~~lIVDGYNvI----~a~p--~L~~~~~~~~Le~AR~~Li~~L~~y~~-~~g~~V~VVFDa~~~~-----~~~------  103 (179)
                      +++|||||.|++    |+.|  .+... ..... .|-.-+++.|..... .+...++|+||+....     .+.      
T Consensus         1 k~llLIDg~~l~~Ra~~a~~~~~l~~~-~G~~t-~ai~g~~~~l~~l~~~~~p~~~vv~fD~~~~~fR~~l~p~YKanR~   78 (169)
T PF02739_consen    1 KKLLLIDGNSLLFRAYYALPKDPLRNS-DGEPT-NAIYGFLRMLLKLLKDFKPDYVVVAFDSKGPTFRKELYPEYKANRK   78 (169)
T ss_dssp             -EEEEEEHHHHHHHCCCCCTTST-BET-TSEB--HHHHHHHHHHHHHHHHTTEEEEEEEEEBSSCHHHHHCCTTTTHHHH
T ss_pred             CeEEEEechHHHHHHHHhhccCCCcCC-CCCCh-HHHHHHHHHHHHHHHHcCCceEEEEecCCCcchHHHHHHHHHhCCC
Confidence            478999999999    4445  33331 12122 355667777777654 3446799999987530     011      


Q ss_pred             -Cce-------------eecCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHHh
Q 039224          104 -HKE-------------EFIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYG  155 (179)
Q Consensus       104 -~~~-------------~~~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~~  155 (179)
                       .++             ..-|+.++-.++-.||++|--++......+ ..|+|||+|+.+.+.+..
T Consensus        79 ~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~-~~v~IvS~DkD~~QLv~~  143 (169)
T PF02739_consen   79 PMPEELIPQLPYIKELLEALGIPVLEVPGYEADDVIATLAKKASEEG-FEVIIVSGDKDLLQLVDE  143 (169)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTSEEEEETTB-HHHHHHHHHHHHHHTT-CEEEEE-SSGGGGGGTCS
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCCEecCCCCcHHHHHHHHHhhhccCC-CEEEEEcCCCCHHHhcCC
Confidence             011             013888776544499999999999998754 689999999998887755

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 ....

>PRK14976 5'-3' exonuclease; Provisional

Probab=98.14  E-value=1.3e-05  Score=69.84  Aligned_cols=128  Identities=20%  Similarity=0.188  Sum_probs=83.3

Q ss_pred             CCccEEEEecccccCc----c----ccchhhhcCCCHHHHHHHHHHHHHhccc-cCCceEEEEEcCCCCC----------
Q 039224           40 NAVPVLLVDGYNVCGY----W----PKLENHFIKGRLDVARQKLIEELVEFSM-IREVKVVVVFDALMSG----------  100 (179)
Q Consensus        40 ~~~~~lIVDGYNvI~a----~----p~L~~~~~~~~Le~AR~~Li~~L~~y~~-~~g~~V~VVFDa~~~~----------  100 (179)
                      |.++++||||+|+|+.    .    |.+..  ..+.-..|-.-+++.|..... .+-..++||||+....          
T Consensus         1 m~~~~lliDg~~~~~ra~~a~~~~~~~l~~--~~G~~t~a~~gf~~~l~~ll~~~~p~~~~v~fD~~~~~~R~~l~p~YK   78 (281)
T PRK14976          1 MMKKALLIDGNSLIFRSYYATLKQGPKLKN--NKGLPTNAIHTFLTMIFKILKKLNPSYILIAFDAGRKTFRHQLYDEYK   78 (281)
T ss_pred             CCCcEEEEeCcHHHHHHHHccCccCCCccC--CCCCCchHHHHHHHHHHHHHHhcCCCEEEEEEECCCCcccccccHHHh
Confidence            4557999999999974    1    22222  233444566667777777664 3446799999985311          


Q ss_pred             --CCCCcee-------------ecCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHH--------hCC
Q 039224          101 --LPTHKEE-------------FIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAY--------GAG  157 (179)
Q Consensus       101 --~~~~~~~-------------~~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~--------~~G  157 (179)
                        ....++.             .-|+.++=.++-.||+.|--++......+ ..|+|||+|+...+.+-        ..|
T Consensus        79 anR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~~g-~~v~IvS~DkDl~ql~~~~v~~~~~~~~  157 (281)
T PRK14976         79 QGRKKTPESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQN-ITVLIYSSDKDLLQLVNENTDVLLKKKG  157 (281)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHCC-CeEEEEeCCCCcCccCCCCeEEEEecCC
Confidence              0111110             12777776655599999999999887653 58999999999977762        233


Q ss_pred             --ceEecHHHHHHHH
Q 039224          158 --AFVWSSKALVSEV  170 (179)
Q Consensus       158 --A~~iSs~ef~~~l  170 (179)
                        -..++.+.+.++.
T Consensus       158 ~~~~~~~~~~v~~~~  172 (281)
T PRK14976        158 TSHFILNTNNFFELY  172 (281)
T ss_pred             CCcEEEcHHHHHHHh
Confidence              2467777766554

>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=98.01  E-value=2.1e-05  Score=66.86  Aligned_cols=109  Identities=26%  Similarity=0.233  Sum_probs=70.7

Q ss_pred             cEEEEecccccCc----cccchhhhcCCCHHHHHHHHHHHHHhccc-cCCceEEEEEcCCCCC------------CCCCc
Q 039224           43 PVLLVDGYNVCGY----WPKLENHFIKGRLDVARQKLIEELVEFSM-IREVKVVVVFDALMSG------------LPTHK  105 (179)
Q Consensus        43 ~~lIVDGYNvI~a----~p~L~~~~~~~~Le~AR~~Li~~L~~y~~-~~g~~V~VVFDa~~~~------------~~~~~  105 (179)
                      ++++|||+|+++.    .+.+.. ...+....|-..++..|..+.. .+-..+++|||+....            ....+
T Consensus         2 ~~llIDg~~l~yr~~~a~~~~~~-~~~g~~t~ai~g~~~~l~~~~~~~~p~~~~~~fD~~~~~~R~~l~p~YK~~R~~~p   80 (240)
T cd00008           2 RLLLIDGSSLAYRAYFALPPLKN-SPKGLPTNAVYGFLNMLLKLIKEYKPTYVAVVFDAGGKTFRHELYPEYKANRKKMP   80 (240)
T ss_pred             cEEEEEChHHHHHHHHCCCCcCC-CCCCcCchHHHHHHHHHHHHHHhcCCCeEEEEEeCCCCcccccccHHHHcCCCCCC
Confidence            5899999999964    222211 0022334566666666666654 3345799999997311            00111


Q ss_pred             ee-------------ecCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHH
Q 039224          106 EE-------------FIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAA  153 (179)
Q Consensus       106 ~~-------------~~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a  153 (179)
                      +.             .-|+.++=.++-.||+.|--++......| ..++|+|+|..+.+.+
T Consensus        81 ~~l~~q~~~~~~~l~~~gi~~i~~~~~EADD~ia~la~~~~~~g-~~~~I~S~DkD~~ql~  140 (240)
T cd00008          81 EELREQIPLIKELLEALGIPVLEIEGYEADDVIGTLAKKAEAEG-YKVVIVSGDKDLLQLV  140 (240)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHcC-CeEEEEeCCCChhhhC
Confidence            10             02777765554599999999998877653 6899999999998876

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.

>PRK09482 flap endonuclease-like protein; Provisional

Probab=97.81  E-value=5.4e-05  Score=65.60  Aligned_cols=108  Identities=17%  Similarity=0.153  Sum_probs=66.1

Q ss_pred             ccEEEEecccccCccccchhhhcCCCHHHHHHHHHHHHHhccc-cCCceEEEEEcCCCCC--------------CCCCce
Q 039224           42 VPVLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSM-IREVKVVVVFDALMSG--------------LPTHKE  106 (179)
Q Consensus        42 ~~~lIVDGYNvI~a~p~L~~~~~~~~Le~AR~~Li~~L~~y~~-~~g~~V~VVFDa~~~~--------------~~~~~~  106 (179)
                      +++|||||+|+++..  +.......+.-.|=--++..|..... ..-..++|+||+....              ....++
T Consensus         3 ~~llLiDg~~l~~R~--~~a~~~~~g~t~av~gf~~~l~~ll~~~~p~~i~v~fD~~~~~~~fR~~l~p~YKa~R~~~Pe   80 (256)
T PRK09482          3 NHLLIIDALNLIRRI--HAVQPSPNDINACVETCQHALDKLIRHSQPTHAVAVFDGDARSSGWRHQLLPDYKAGRKPMPE   80 (256)
T ss_pred             CeEEEEeCcHHHHHH--HhCCCCCCCcchHHHHHHHHHHHHHHHcCCCEEEEEEeCCCCCcccHHHHhHHHhcCCCCCcH
Confidence            369999999999742  11100011123444444555555443 3335689999985321              011111


Q ss_pred             e-------------ecCeEEEeCCCC-ChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHH
Q 039224          107 E-------------FIGVDIVFPGET-CADAWIEKEIVALREDGCPKVWVVTSDHLQQHAA  153 (179)
Q Consensus       107 ~-------------~~gi~VvfT~~~-TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a  153 (179)
                      .             .-|+.++ ...+ .||++|--++.+..+.+ ..|++||+|+.+.+.+
T Consensus        81 ~l~~Q~~~i~~~l~~~gi~~~-~~~g~EADDvIatla~~~~~~~-~~v~I~S~DKDl~Qlv  139 (256)
T PRK09482         81 ALQQGLPAIRAAFEELGIDSW-HADGNEADDLIATLAVKVAQAG-HQATIVSTDKGYCQLL  139 (256)
T ss_pred             HHHHHHHHHHHHHHhCCCCEe-ccCCcCHHHHHHHHHHHHHHCC-CeEEEEECCCCccccC
Confidence            1             1377664 4455 99999999999887653 6899999999987765

>PHA02567 rnh RnaseH; Provisional

Probab=97.72  E-value=0.0001  Score=65.50  Aligned_cols=119  Identities=18%  Similarity=0.149  Sum_probs=75.9

Q ss_pred             CccEEEEecccccCccc--cchhhhcCCCHHHHHHHHHHHHHhccc-cC--CceEEEEEcCCCCC-------------CC
Q 039224           41 AVPVLLVDGYNVCGYWP--KLENHFIKGRLDVARQKLIEELVEFSM-IR--EVKVVVVFDALMSG-------------LP  102 (179)
Q Consensus        41 ~~~~lIVDGYNvI~a~p--~L~~~~~~~~Le~AR~~Li~~L~~y~~-~~--g~~V~VVFDa~~~~-------------~~  102 (179)
                      +..++||||.|++++.=  .|... ...+-..-|..+++.|..... .+  .-.++|+||+...+             ..
T Consensus        13 ~~~~~LiDgs~i~~~~~~a~l~~~-~~~~~~~ir~~v~nsL~~~v~~~k~~~~~i~vaFD~~~~~tfR~elyp~YKAnR~   91 (304)
T PHA02567         13 KEGVNLIDFSQIIIATIMANFKPK-DKINEAMVRHLVLNSIRYNVKKFKEEYPEIVLAFDNSKSGYWRRDIAWYYKKNRK   91 (304)
T ss_pred             CCCEEEEehHHHHHHHHHhhCCCC-CCCcHHHHHHHHHHHHHHHHHHhcCCCCeEEEEEeCCCCCCchhhhhhHhhcCCC
Confidence            67899999999995431  23221 133445556667777776543 22  23599999996311             01


Q ss_pred             CCcee---------------e------cCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHHhCCceEe
Q 039224          103 THKEE---------------F------IGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVW  161 (179)
Q Consensus       103 ~~~~~---------------~------~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~~~GA~~i  161 (179)
                      ..++.               .      -|+.++-.+.-.||++|--++......| ..|+|||+|+.+.+.+..-|...+
T Consensus        92 ~~Peel~~q~~~l~~~l~~ii~el~~~~gi~~l~~~g~EADDvIgTLA~k~~~~g-~~VvIvS~DKDl~QLv~~~~v~~~  170 (304)
T PHA02567         92 KDREESPWDWEGLFEAINKIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSAEG-RPVLIVSSDGDFTQLHKYPGVKQW  170 (304)
T ss_pred             CCChHHHHHHHHhhhhHHHHHHHHHHHCCCCEEEeCCccHHHHHHHHHHHHHhCC-CcEEEEeCCCChhhccCCCCeEEe
Confidence            11111               0      1666554444599999999999888653 689999999999888753455544

>PHA00439 exonuclease

Probab=97.72  E-value=9.3e-05  Score=65.22  Aligned_cols=111  Identities=14%  Similarity=0.056  Sum_probs=71.7

Q ss_pred             CccEEEEecccccC----cc-------ccchhhhcCCCHHHHHHHHHHHHHhccc----cCCceEEEEEcCCCCC-----
Q 039224           41 AVPVLLVDGYNVCG----YW-------PKLENHFIKGRLDVARQKLIEELVEFSM----IREVKVVVVFDALMSG-----  100 (179)
Q Consensus        41 ~~~~lIVDGYNvI~----a~-------p~L~~~~~~~~Le~AR~~Li~~L~~y~~----~~g~~V~VVFDa~~~~-----  100 (179)
                      ++.+|||||+++++    +.       +.+..  ..+..-.|+.-++++|..+..    ++--.++|+||+..+-     
T Consensus         5 ~~~llLIDG~~l~fRA~~A~~~~~~~~~~l~~--~~G~~t~A~~gf~~~L~kl~~~~k~~~p~~i~vaFD~~~tfR~ely   82 (286)
T PHA00439          5 DKGVLVMDGDYLVFQAMAAAEVETDWGEDIWT--LECDHAKARQILEDSIKSYKTRKKAWKDAPIVLAFTDSVNWRKEVV   82 (286)
T ss_pred             CCcEEEEeCcHHHHHHHHccCcccccCCCCCC--CCCeeccHHHHHHHHHHHHHHhhccCCCCeEEEEECCCCChHhhhh
Confidence            67899999999996    33       12321  234455677777777777653    3556799999964310     


Q ss_pred             ------CCCCce----------e--ecCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHH
Q 039224          101 ------LPTHKE----------E--FIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAA  153 (179)
Q Consensus       101 ------~~~~~~----------~--~~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a  153 (179)
                            .+..++          .  ..|+.++-...-.||++|--++......+..+|+|||+|+.+.+.+
T Consensus        83 p~YKanR~~~p~~~~~~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~~g~~~vvIvS~DKDl~QLv  153 (286)
T PHA00439         83 PTYKANRKAKRKPVGYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLFGFKKAVLVSCDKDFKTIP  153 (286)
T ss_pred             hHhcCCCCCCCCchhhHHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHHCCCCeEEEEeCCCCHhhcC
Confidence                  000000          0  1355444333349999999999887754323899999999988875

>PRK05755 DNA polymerase I; Provisional

Probab=97.56  E-value=0.00022  Score=70.56  Aligned_cols=108  Identities=24%  Similarity=0.255  Sum_probs=72.9

Q ss_pred             cEEEEecccccCc-c----ccchhhhcCCCHHHHHHHHHHHHHhccc-cCCceEEEEEcCCCCC------------CCCC
Q 039224           43 PVLLVDGYNVCGY-W----PKLENHFIKGRLDVARQKLIEELVEFSM-IREVKVVVVFDALMSG------------LPTH  104 (179)
Q Consensus        43 ~~lIVDGYNvI~a-~----p~L~~~~~~~~Le~AR~~Li~~L~~y~~-~~g~~V~VVFDa~~~~------------~~~~  104 (179)
                      +++||||+|+++. +    |.+..  ..+..-.|-.-+++.|..+.. .+-..++||||+....            .+..
T Consensus         3 ~~~liDg~~~~~r~~~a~~~~~~~--~~g~~~~a~~g~~~~l~~~~~~~~p~~~~v~fD~~~~~~R~~~~~~YK~~R~~~   80 (880)
T PRK05755          3 TLLLIDGSSLLFRAFYALLPTLRN--SDGLPTGAVYGFLNMLLKLLKEEKPTHVAVAFDAKGKTFRHELYPEYKANRPPM   80 (880)
T ss_pred             eEEEEeCcHHHHHHHHCCCCcccC--CCCCcccHHHHHHHHHHHHHHhcCCCEEEEEEECCCCccccccCHHHhCCCCCC
Confidence            5899999999974 2    33322  133445666777777777664 4456799999984310            0111


Q ss_pred             cee-------------ecCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHH
Q 039224          105 KEE-------------FIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAA  153 (179)
Q Consensus       105 ~~~-------------~~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a  153 (179)
                      ++.             .-|+.++-.++-.||+.|--++......| ..++|+|+|+.+-+.+
T Consensus        81 p~~l~~q~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~-~~~~i~S~DkD~~ql~  141 (880)
T PRK05755         81 PEDLREQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEAAG-YEVLIVTGDKDLLQLV  141 (880)
T ss_pred             cHHHHHHHHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHHhCC-CcEEEEcCCCChhhhC
Confidence            110             14776665544599999999998877653 6899999999988776

>TIGR00593 pola DNA polymerase I

Probab=97.04  E-value=0.0013  Score=65.76  Aligned_cols=107  Identities=22%  Similarity=0.218  Sum_probs=65.0

Q ss_pred             EEEEecccccCc----cc--cchhhhcCCCHHHHHHHHHHHHHhccc-cCCceEEEEEcCCCCC------------CCCC
Q 039224           44 VLLVDGYNVCGY----WP--KLENHFIKGRLDVARQKLIEELVEFSM-IREVKVVVVFDALMSG------------LPTH  104 (179)
Q Consensus        44 ~lIVDGYNvI~a----~p--~L~~~~~~~~Le~AR~~Li~~L~~y~~-~~g~~V~VVFDa~~~~------------~~~~  104 (179)
                      ++||||+|+|+.    .|  .|..  ..+.--.|---++.+|..... .+-..++||||+..+.            .+..
T Consensus         1 l~lIDg~~l~~Ra~~a~~~~~l~~--~~G~~t~av~Gf~~~l~~ll~~~~p~~i~v~FD~~~~tfR~~~~~~YKa~R~~~   78 (887)
T TIGR00593         1 LLLIDGHSLAFRAYFALKNKPLTN--SKGEPTNAVYGFTKMLLKLLKEEKPTYVAVAFDSGTPTFRHEAYAEYKANRAPT   78 (887)
T ss_pred             CEEEeCcHHHHHHHHCCCcccCcC--CCCCEecHHHHHHHHHHHHHHhcCCCEEEEEEcCCCCcchHHHHHHHHhCCCCC
Confidence            489999999963    22  1211  112222333334444444432 3345799999986421            0111


Q ss_pred             cee-------------ecCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHH
Q 039224          105 KEE-------------FIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAA  153 (179)
Q Consensus       105 ~~~-------------~~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a  153 (179)
                      ++.             .-||.++-.++-.||++|--++......| ..|+|||+|+...+.+
T Consensus        79 Pe~l~~Q~~~i~~~l~~~gi~~i~~~g~EADDiIatla~~~~~~g-~~v~IvS~DkDllQLv  139 (887)
T TIGR00593        79 PEELIEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEKEG-YEVRIISGDKDLLQLV  139 (887)
T ss_pred             hHHHHHHHHHHHHHHHHCCCcEEeeCCccHHHHHHHHHHHHHhCC-CcEEEEECCCChhhcC
Confidence            111             13676654433499999999999887653 6899999999988776

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

>PF02639 DUF188: Uncharacterized BCR, YaiI/YqxD family COG1671; InterPro: IPR003791 This entry describes proteins of unknown function

Probab=96.71  E-value=0.0039  Score=48.99  Aligned_cols=70  Identities=17%  Similarity=0.118  Sum_probs=52.3

Q ss_pred             cccCCceEEEEEcCCCCCCCCCceeecCeEEEeCCC--CChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHHhCCceE
Q 039224           83 SMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGE--TCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFV  160 (179)
Q Consensus        83 ~~~~g~~V~VVFDa~~~~~~~~~~~~~gi~VvfT~~--~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~~~GA~~  160 (179)
                      +...+..+++|=|......     ....+++++-..  ..||.||-..+..       .=+|||.|--+...+.++||.+
T Consensus         6 a~r~~i~vi~Van~~h~~~-----~~~~~~~i~Vd~g~DaaD~~I~~~~~~-------gDiVITqDigLA~~~l~Kga~v   73 (130)
T PF02639_consen    6 AKRYGIPVIFVANYSHRLP-----RSPYVEMIVVDSGFDAADFYIVNHAKP-------GDIVITQDIGLASLLLAKGAYV   73 (130)
T ss_pred             HHHHCCEEEEEeCCCccCC-----CCCCeEEEEECCCCChHHHHHHHcCCC-------CCEEEECCHHHHHHHHHCCCEE
Confidence            3455688888888653321     125667777765  5999999885432       3579999999999999999999


Q ss_pred             ecHH
Q 039224          161 WSSK  164 (179)
Q Consensus       161 iSs~  164 (179)
                      |+++
T Consensus        74 l~~r   77 (130)
T PF02639_consen   74 LNPR   77 (130)
T ss_pred             ECCC
Confidence            9976

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

Probab=96.67  E-value=0.0024  Score=55.96  Aligned_cols=115  Identities=18%  Similarity=0.128  Sum_probs=69.5

Q ss_pred             CCccEEEEecccccCcccc-chhhhcCCCHH--HHHHHHHHHHHhccc-cCCceEEEEEcCCCCCC--------C-CCce
Q 039224           40 NAVPVLLVDGYNVCGYWPK-LENHFIKGRLD--VARQKLIEELVEFSM-IREVKVVVVFDALMSGL--------P-THKE  106 (179)
Q Consensus        40 ~~~~~lIVDGYNvI~a~p~-L~~~~~~~~Le--~AR~~Li~~L~~y~~-~~g~~V~VVFDa~~~~~--------~-~~~~  106 (179)
                      ..+++++|||+|+++.+=. ++..+......  .|=.-+..+|.+... .+-..++|||||..+..        . .+..
T Consensus         9 ~~~~l~~IDg~~~lyr~~~a~~~~~~~~~g~~~~~~~~~~~~l~~~~~~~~~~~~~~vFD~~~~tfR~~~~~~yK~~R~~   88 (310)
T COG0258           9 KSGKLLLIDGSSLLYRALHALPQPLGNPLGDPTGAVSGFLGMLYRLIRLLEPTHPVVVFDGKPPTFRHELLEEYKANREK   88 (310)
T ss_pred             ccCcEEEEechHHHHHHHHhcchhcCCCCCCCccHHHHHHHHHHHHHHhcCCCcEEEEEcCCCCcchHHHHHHHHhCCCc
Confidence            3458999999999865521 10001111111  155666777766654 33389999999953210        0 0001


Q ss_pred             -ee----------------cCeEEEeCCCC-ChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHHhC
Q 039224          107 -EF----------------IGVDIVFPGET-CADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGA  156 (179)
Q Consensus       107 -~~----------------~gi~VvfT~~~-TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~~~  156 (179)
                       ..                -|+... .-.+ .||+.|+-++....+.| ..++++|+|....+.+-..
T Consensus        89 ~~p~~l~~q~~~i~~~~~~~~~~~l-~~~G~eadd~i~t~A~~a~~~g-~~~~I~S~DkD~lql~~~~  154 (310)
T COG0258          89 EMPDELAPQIPILTELLVALGIPLL-ELMGIEADDPIETLAQKAYKKG-DVVLIISGDKDLLQLVSPN  154 (310)
T ss_pred             cCHHHHHHHHHHHHHHHHHhCcHhh-hcCCCCcchhHHHHHHHHHhcC-CeEEEEeCCcchhhhcCCC
Confidence             00                133222 2223 69999999999888543 6899999999998887554

>PRK00124 hypothetical protein; Validated

Probab=96.16  E-value=0.021  Score=46.19  Aligned_cols=71  Identities=18%  Similarity=-0.004  Sum_probs=50.0

Q ss_pred             ccCCceEEEEEcCCCCCCCCCceeecCeEEEeCCC--CChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHHhCCceEe
Q 039224           84 MIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGE--TCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVW  161 (179)
Q Consensus        84 ~~~g~~V~VVFDa~~~~~~~~~~~~~gi~VvfT~~--~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~~~GA~~i  161 (179)
                      ...+..+++|=+-...-.   ......++.++-..  ..||.||.+.+..       .=+|||.|--+...+.++||.+|
T Consensus        21 ~r~~i~v~~Vas~n~~~~---~~~~~~v~~v~V~~g~D~AD~~Iv~~~~~-------gDiVIT~Di~LAa~~l~Kga~vl   90 (151)
T PRK00124         21 ERHGIPVTLVASFNHFLR---VPYSPFIRTVYVDAGFDAADNEIVQLAEK-------GDIVITQDYGLAALALEKGAIVL   90 (151)
T ss_pred             HHHCCeEEEEEeCCcccC---CCCCCceEEEEeCCCCChHHHHHHHhCCC-------CCEEEeCCHHHHHHHHHCCCEEE
Confidence            345577788774222110   11234567777765  5999999885442       36899999999999999999999


Q ss_pred             cHH
Q 039224          162 SSK  164 (179)
Q Consensus       162 Ss~  164 (179)
                      +++
T Consensus        91 ~pr   93 (151)
T PRK00124         91 NPR   93 (151)
T ss_pred             CCC
Confidence            975

>PF11977 RNase_Zc3h12a: Zc3h12a-like Ribonuclease NYN domain; InterPro: IPR021869 This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes []

Probab=96.00  E-value=0.0085  Score=47.59  Aligned_cols=92  Identities=21%  Similarity=0.215  Sum_probs=44.7

Q ss_pred             ccEEEEecccccCccccchhhhcCCCHHHHHHHHHHHHHhccccCCceEEEEEcCCCC----CC-CCCc----eeecCeE
Q 039224           42 VPVLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMS----GL-PTHK----EEFIGVD  112 (179)
Q Consensus        42 ~~~lIVDGYNvI~a~p~L~~~~~~~~Le~AR~~Li~~L~~y~~~~g~~V~VVFDa~~~----~~-~~~~----~~~~gi~  112 (179)
                      .+.+||||-||-  |-....    ..+.   -+-|..+.+|....|+++++|||....    .. ....    +-...=.
T Consensus         2 ~r~VVIDG~NVA--~~~~~~----~~f~---~~~i~~~v~~~~~rG~~~v~v~~~~~~~~~~~~~~~~~~~L~~l~~~~~   72 (155)
T PF11977_consen    2 LRPVVIDGSNVA--YSHGNQ----KFFS---VRGIQIAVEYFKSRGHEVVVVFPPNYRYKKLAKKSDDQEELEKLIRKGI   72 (155)
T ss_dssp             B--EEEEHHHHH--HHHTTT----TSEE---HHHHHHHHHHHHHTT---EEEEEEGGGGS-TTS-EESTCHHHHHHHTTS
T ss_pred             CCEEEEeCHHHH--hhcCCC----CCcC---HHHHHHHHHHHHHcCCCeEEEEcchhhhccccCCCChHHHHHHHHHCCe
Confidence            467999999993  211111    1111   234555666666779999999997652    11 1000    0112223


Q ss_pred             EEeCCCCC---------hHHHHHHHHHHHhhCCCCcEEEEcCCHH
Q 039224          113 IVFPGETC---------ADAWIEKEIVALREDGCPKVWVVTSDHL  148 (179)
Q Consensus       113 VvfT~~~T---------AD~~IErlv~~~~~~~~~~V~VVTSD~~  148 (179)
                      |++|+.++         +|.+|..++.+.      .-.|||+|+.
T Consensus        73 i~~tp~~~~~g~~~~~ydD~~il~~A~~~------~a~IVSND~f  111 (155)
T PF11977_consen   73 IYFTPSGSNYGSRSRNYDDRYILYYAEEK------DAVIVSNDRF  111 (155)
T ss_dssp             EEEE-EEEETTEEEEB-HHHHHHHHHHHT------T-EEE-S---
T ss_pred             EEEcCCCCCCCCcccccchHHHHHHHHHc------CCEEEeCchH
Confidence            67777654         788887776653      2467788864

It has been suggested that this domain belongs to the PIN domain superfamily []. ; PDB: 3V33_A 3V34_B 3V32_B.

>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.34  E-value=0.074  Score=43.06  Aligned_cols=75  Identities=21%  Similarity=0.145  Sum_probs=55.0

Q ss_pred             HHHhccccCCceEEEEEcCCCCCCCCCceeecCeEEEeCCC--CChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHHh
Q 039224           78 ELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGE--TCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYG  155 (179)
Q Consensus        78 ~L~~y~~~~g~~V~VVFDa~~~~~~~~~~~~~gi~VvfT~~--~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~~  155 (179)
                      .+...+...|..|++|=......    + ....++.++...  ..||.||.+++..       .=+|||.|--+...+..
T Consensus        16 ~i~r~A~r~~~~v~~Van~~~~~----~-~~~~i~~v~V~~g~DaaD~~Iv~~a~~-------gDlVVT~Di~LA~~ll~   83 (150)
T COG1671          16 EIYRVAERMGLKVTFVANFPHRV----P-PSPEIRTVVVDAGFDAADDWIVNLAEK-------GDLVVTADIPLASLLLD   83 (150)
T ss_pred             HHHHHHHHhCCeEEEEeCCCccC----C-CCCceeEEEecCCcchHHHHHHHhCCC-------CCEEEECchHHHHHHHh
Confidence            34445556678999987654332    1 335567777765  5999999885432       35899999999999999


Q ss_pred             CCceEecHH
Q 039224          156 AGAFVWSSK  164 (179)
Q Consensus       156 ~GA~~iSs~  164 (179)
                      .||.+|+++
T Consensus        84 kg~~v~~pr   92 (150)
T COG1671          84 KGAAVLNPR   92 (150)
T ss_pred             cCCEEECCC
Confidence            999999875

>COG2454 Uncharacterized conserved protein [Function unknown]

Probab=95.12  E-value=0.045  Score=46.43  Aligned_cols=101  Identities=26%  Similarity=0.222  Sum_probs=50.3

Q ss_pred             CccEEEEecccccCccc----------------cchhhhcCCCHHHHHHHHHHHHHhccc-cCCceEEEEEcCCCCCCCC
Q 039224           41 AVPVLLVDGYNVCGYWP----------------KLENHFIKGRLDVARQKLIEELVEFSM-IREVKVVVVFDALMSGLPT  103 (179)
Q Consensus        41 ~~~~lIVDGYNvI~a~p----------------~L~~~~~~~~Le~AR~~Li~~L~~y~~-~~g~~V~VVFDa~~~~~~~  103 (179)
                      +...|+||||||+=...                +++-....--+.+--++-+++|.+|-. ..-..+++.||+..+.+..
T Consensus        65 rg~~l~iDGyNvLItleSl~~g~~vlcdDg~iRDl~~~~gkyk~~E~t~~Al~lil~~lk~~~~k~vi~L~d~~vs~SGe  144 (211)
T COG2454          65 RGQDLVIDGYNVLITLESLLKGEAVLCDDGVIRDLRGVQGKYKINEKTDKALDLLLEFLKDVEPKSVIFLFDAPVSKSGE  144 (211)
T ss_pred             ccceEEEechhhhhhHHHHhcCcEEEecCchhhhhhhhccchhhhhHHHHHHHHHHHHHHHcCCceEEEEeCCCCCccHH
Confidence            34679999999983221                111000001111222334444444433 4455678888887643211


Q ss_pred             ---C-ce--eecCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHH
Q 039224          104 ---H-KE--EFIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHA  152 (179)
Q Consensus       104 ---~-~~--~~~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~  152 (179)
                         . ++  ..-+|.+-=.-..+||..+.       +.   . .|+|||..|-..
T Consensus       145 l~~~i~~~mK~~~I~g~~~lvk~~D~eLk-------~~---e-~VaTsD~~IIds  188 (211)
T COG2454         145 LAGRIEEKMKSLGIPGEASLVKNADFELK-------EL---E-VVATSDSGIIDS  188 (211)
T ss_pred             HHHHHHHHHHhcCCCceeEeccCcCHHHH-------hc---C-ceeecCeeeeee
Confidence               1 11  22344432222368887665       11   2 899999766544

>COG1412 Uncharacterized proteins of PilT N-term

Probab=95.02  E-value=0.05  Score=43.29  Aligned_cols=51  Identities=14%  Similarity=0.094  Sum_probs=43.3

Q ss_pred             ecCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHHhCCceEecHH
Q 039224          108 FIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSK  164 (179)
Q Consensus       108 ~~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~~~GA~~iSs~  164 (179)
                      ..+.+++.+ .+-||+.|.+.+.++.     .++|+|+|+++.+.++..|.-+++-+
T Consensus        74 ~er~~~~~~-~~~aDe~i~~~a~~~~-----~~iVaTnD~eLk~rlr~~GIPvi~lr  124 (136)
T COG1412          74 AERLECIHK-GRYADECLLEAALKHG-----RYIVATNDKELKRRLRENGIPVITLR  124 (136)
T ss_pred             hhccCcccc-CCChHHHHHHHHHHcC-----CEEEEeCCHHHHHHHHHcCCCEEEEe
Confidence            456788888 7788999999888764     59999999999999999998887643

/Vapc superfamily [General function prediction only]

>PTZ00217 flap endonuclease-1; Provisional

Probab=93.91  E-value=0.16  Score=46.54  Aligned_cols=36  Identities=19%  Similarity=0.131  Sum_probs=25.4

Q ss_pred             cCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHH
Q 039224          109 IGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQ  150 (179)
Q Consensus       109 ~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq  150 (179)
                      -||.++-++. .||+.+-.+..    .| .-..|+|.|..+-
T Consensus       150 ~Gip~i~AP~-EAdaq~A~L~~----~g-~v~~ViS~D~D~l  185 (393)
T PTZ00217        150 MGIPVIEAPC-EAEAQCAELVK----KG-KVYAVATEDMDAL  185 (393)
T ss_pred             cCCceEECCc-CHHHHHHHHHH----CC-CeEEEeCCCcCee
Confidence            4888887765 89997777653    22 3466899998654

>TIGR03674 fen_arch flap structure-specific endonuclease

Probab=92.12  E-value=0.26  Score=44.10  Aligned_cols=65  Identities=18%  Similarity=0.235  Sum_probs=36.4

Q ss_pred             CCCCC-CCccEEEEecccccCcccc-ch-----hhh-cCCCHHHHHHHHHHHHHhccccCCceEEEEEcCCCCC
Q 039224           35 NQGID-NAVPVLLVDGYNVCGYWPK-LE-----NHF-IKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSG  100 (179)
Q Consensus        35 ~~~~~-~~~~~lIVDGYNvI~a~p~-L~-----~~~-~~~~Le~AR~~Li~~L~~y~~~~g~~V~VVFDa~~~~  100 (179)
                      ...++ .+.+.+.|||++.||..=. .+     .+. ..+..-.+=..++..+.++. ..|.+.++||||...+
T Consensus        13 ~~~l~~~~gk~vaIDas~~L~r~~~a~~~~~g~~l~~~~G~~t~~l~g~~~~~~~ll-~~~i~Pv~VFDG~~p~   85 (338)
T TIGR03674        13 EIELEDLSGKVVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITSHLSGLFYRTINLL-ENGIKPVYVFDGKPPE   85 (338)
T ss_pred             ccCHHHhCCCEEEEeHHHHHHHHHHHHhccccchhhhccCCCcHHHHHHHHHHHHHH-HCCCeEEEEECCCChh
Confidence            33444 4567999999999984310 10     000 01111123344455555553 3568889999998643

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

>cd06167 LabA_like LabA_like proteins

Probab=92.02  E-value=0.44  Score=36.37  Aligned_cols=110  Identities=12%  Similarity=0.045  Sum_probs=59.5

Q ss_pred             cEEEEecccccCccccchhhhcCCCHHHHHHHHHHHHHhccccCCceEEEEEcCCCC--CCC--CCceeecCeEEEeCC-
Q 039224           43 PVLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMS--GLP--THKEEFIGVDIVFPG-  117 (179)
Q Consensus        43 ~~lIVDGYNvI~a~p~L~~~~~~~~Le~AR~~Li~~L~~y~~~~g~~V~VVFDa~~~--~~~--~~~~~~~gi~VvfT~-  117 (179)
                      -.++|||-|+-.+......  ...++....+.+...       ......-+|-....  ...  ...-...|++++... 
T Consensus         3 ~~ifiD~~Nl~~~~~~~~~--~~~d~~~l~~~~~~~-------~~~~~~r~y~~~~~~~~~~~~~~~L~~~g~~~~~~~~   73 (149)
T cd06167           3 VAVFIDGENLYYSLRDLGG--KRFDYRKLLEFLRDG-------GEIVLARAYGNWTSPERQRGFLDALRRLGFEPIQKPL   73 (149)
T ss_pred             EEEEEeHHHHHHHHHHhcC--CCcCHHHHHHHHHhC-------CeEEEEEEEEecCCchhHHHHHHHHHHCCcEEEEEcc
Confidence            5789999999865543321  123444333333322       22333344433321  100  011234677776554 


Q ss_pred             ------CCChHHHH-HHHHHHHhhCCCCcEEEEcCCHHHH---HHHHhCCceEe
Q 039224          118 ------ETCADAWI-EKEIVALREDGCPKVWVVTSDHLQQ---HAAYGAGAFVW  161 (179)
Q Consensus       118 ------~~TAD~~I-Erlv~~~~~~~~~~V~VVTSD~~iq---~~a~~~GA~~i  161 (179)
                            ++.+|..| .+++..+...+...+++||+|...-   +.++..|..++
T Consensus        74 ~~~~~~~~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~i~~lr~~G~~V~  127 (149)
T cd06167          74 RTRGSGKKGVDVALAIDALELAYKRRIDTIVLVSGDSDFVPLVERLRELGKRVI  127 (149)
T ss_pred             eecCCcccCccHHHHHHHHHHhhhcCCCEEEEEECCccHHHHHHHHHHcCCEEE
Confidence                  25899777 4555555544446799999998754   34556666653

A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.

>PRK13764 ATPase; Provisional

Probab=91.92  E-value=0.47  Score=45.92  Aligned_cols=101  Identities=20%  Similarity=0.140  Sum_probs=61.3

Q ss_pred             cchhhhcCCCHHHHHHH--HHHHHHhccccCCceEEEEEcCCCCCCCCCceeecCeEEEeCCCCChHHHHHHHHHHHhhC
Q 039224           58 KLENHFIKGRLDVARQK--LIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGETCADAWIEKEIVALRED  135 (179)
Q Consensus        58 ~L~~~~~~~~Le~AR~~--Li~~L~~y~~~~g~~V~VVFDa~~~~~~~~~~~~~gi~VvfT~~~TAD~~IErlv~~~~~~  135 (179)
                      +|.. .++...+..|..  .+..|.+...  +-.+.|.|.+..+.   .      -.+-..+.+..|+.|.+++.+.   
T Consensus        38 ELe~-~A~~~r~~G~~gLeeL~~L~~l~~--~g~i~ie~~~~~p~---~------~~~~~~~~gevD~~I~~~A~~~---  102 (602)
T PRK13764         38 ELEA-QANQGREIGFSGLEELKKLRELAE--EGLIELEFVGERPT---L------EQIKLAKGGEIDALIREVAKEL---  102 (602)
T ss_pred             HHHH-HhhccchhhHHHHHHHHHHHHhhc--cCceEEEEeccccc---h------hhcccccCCCHHHHHHHHHHHc---
Confidence            4555 344455555544  3444554432  23455556543211   0      0123344468999999988853   


Q ss_pred             CCCcEEEEcCCHHHHHHHHhCCceEecHHHHHHHHHHHHhh
Q 039224          136 GCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEVSLIIYY  176 (179)
Q Consensus       136 ~~~~V~VVTSD~~iq~~a~~~GA~~iSs~ef~~~l~~~~~~  176 (179)
                         .+++||+|..++..|+..|..++.-+.-.+.+.-..||
T Consensus       103 ---~~~lvT~D~~l~~~A~~~GI~V~~l~~~~~~L~ie~~~  140 (602)
T PRK13764        103 ---GATLVTSDRVQAEVARAKGIDVIYLKPEREPLEIEKFF  140 (602)
T ss_pred             ---CCEEEeCCHHHHHHHHHcCCEEEEeCCCCCccchHHHh
Confidence               58999999999999999999998766543334444444

>PF13638 PIN_4: PIN domain; PDB: 2HWW_C 2HWX_A 2DOK_B 2HWY_B 2WP8_J

Probab=91.12  E-value=0.36  Score=36.27  Aligned_cols=45  Identities=27%  Similarity=0.156  Sum_probs=33.6

Q ss_pred             CChHHHHHHHHHHHhhCC-CCcEEEEcCCHHHHHHHHhCCceEecH
Q 039224          119 TCADAWIEKEIVALREDG-CPKVWVVTSDHLQQHAAYGAGAFVWSS  163 (179)
Q Consensus       119 ~TAD~~IErlv~~~~~~~-~~~V~VVTSD~~iq~~a~~~GA~~iSs  163 (179)
                      .+.|+.|-..+..+.... ...|+++|+|..++..|.+.|-.+.|-
T Consensus        87 ~~~D~~Il~~a~~~~~~~~~~~vvLvT~D~~l~~~A~~~gi~~~~~  132 (133)
T PF13638_consen   87 QRNDDRILNCALYLQEENPGRKVVLVTNDKNLRLKARAEGIPAVSY  132 (133)
T ss_dssp             -HHHHHHHHHHHHHHHHCGCEEEEEEE--HHHHHHHHHTT--EE--
T ss_pred             cccHHHHHHHHHHHHHhcCCCeEEEEeCCHHHHHHHhhcccccccC
Confidence            599999999998887642 458999999999999999999988874

>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=90.38  E-value=0.2  Score=36.48  Aligned_cols=58  Identities=14%  Similarity=0.082  Sum_probs=30.7

Q ss_pred             ccEEEEecccccCccccchhhhcCCCH--HHHHHHHHHHHHhccccCCceEEEEEcCCCCC
Q 039224           42 VPVLLVDGYNVCGYWPKLENHFIKGRL--DVARQKLIEELVEFSMIREVKVVVVFDALMSG  100 (179)
Q Consensus        42 ~~~lIVDGYNvI~a~p~L~~~~~~~~L--e~AR~~Li~~L~~y~~~~g~~V~VVFDa~~~~  100 (179)
                      ...+-|||++.|+..-.-...-...+.  ..-...++..+..+ ...|...++||||...+
T Consensus        26 g~~vaID~s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~L-~~~gI~PifVFDG~~~~   85 (101)
T PF00752_consen   26 GKRVAIDASCWLHQFLFSCREELGQGVGTDSHLRGLFSRLCRL-LEHGIKPIFVFDGKPPP   85 (101)
T ss_dssp             TCEEEEEHHHHHHHHHHHSBCTTSCB-BS-HHHHHHHHHHHHH-HHTTEEEEEEE--STTG
T ss_pred             CCEEEEEcHHHHHHHHHHhHHHhccccchHHHHHHHHHHHHHH-HHCCCEEEEEECCCCch
Confidence            378999999999753110000000111  23334555555544 35579999999998543

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 ....

>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins

Probab=88.78  E-value=0.69  Score=34.00  Aligned_cols=40  Identities=23%  Similarity=0.005  Sum_probs=32.0

Q ss_pred             CCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHH-hCCceEec
Q 039224          118 ETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAY-GAGAFVWS  162 (179)
Q Consensus       118 ~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~-~~GA~~iS  162 (179)
                      ..+||+-|.+++...+     ..+|+|.|..+++..+ ..|.-+|.
T Consensus        50 ~~~addci~~~~~~~~-----~~~VaT~D~~Lr~~lr~~~GvPvi~   90 (101)
T PF04900_consen   50 PGSADDCILDLAGKNN-----KYIVATQDKELRRRLRKIPGVPVIY   90 (101)
T ss_pred             CcCHHHHHHHHhccCC-----eEEEEecCHHHHHHHhcCCCCCEEE
Confidence            3489999999986322     2999999999999999 77776654

>PRK04358 hypothetical protein; Provisional

Probab=87.40  E-value=1.1  Score=38.37  Aligned_cols=36  Identities=14%  Similarity=0.040  Sum_probs=32.8

Q ss_pred             cEEEEcCCHHHHHHHHhCCceEecHHHHHHHHHHHH
Q 039224          139 KVWVVTSDHLQQHAAYGAGAFVWSSKALVSEVSLII  174 (179)
Q Consensus       139 ~V~VVTSD~~iq~~a~~~GA~~iSs~ef~~~l~~~~  174 (179)
                      ..+|||+|..+|+.|...|-..+++..|...+++..
T Consensus       175 da~lvTdD~giqn~A~~LGI~~~~~~~F~~~Lee~l  210 (217)
T PRK04358        175 DAAVVSADEGIRKWAERLGLRFVDARKFPRMLEEYL  210 (217)
T ss_pred             CCEEEeCCHHHHHHHHHcCCeeecHHHHHHHHHHHH
Confidence            479999999999999999999999999998887643

>TIGR03875 RNA_lig_partner RNA ligase partner, MJ_0950 family

Probab=86.63  E-value=1.2  Score=37.86  Aligned_cols=34  Identities=15%  Similarity=0.027  Sum_probs=31.8

Q ss_pred             cEEEEcCCHHHHHHHHhCCceEecHHHHHHHHHH
Q 039224          139 KVWVVTSDHLQQHAAYGAGAFVWSSKALVSEVSL  172 (179)
Q Consensus       139 ~V~VVTSD~~iq~~a~~~GA~~iSs~ef~~~l~~  172 (179)
                      ..+|||+|..+|+.|...|-..+++..|...++.
T Consensus       171 da~lvTdD~giqn~A~~Lgi~~~~~~~f~~~L~e  204 (206)
T TIGR03875       171 DAAVVSADEGIRKWAERLGLRFVDARNFPEMLEE  204 (206)
T ss_pred             CcEEEeCcHHHHHHHHHcCCeeecHHHHHHHHHH
Confidence            5899999999999999999999999999988875

This uncharacterized protein family is found almost perfectly in the same set of genomes as the Pab1020 family described by model TIGR01209. These pairs are found mostly in Archaea, but also in a few bacteria (e.g. Alkalilimnicola ehrlichei MLHE-1, Aquifex aeolicus). While the partner protein has been described as homodimeric ligase that has RNA circularization activity, the function of this protein (also called UPF0278) is unknown.

>TIGR00288 conserved hypothetical protein TIGR00288

Probab=85.53  E-value=6.8  Score=31.98  Aligned_cols=116  Identities=22%  Similarity=0.151  Sum_probs=63.3

Q ss_pred             CCccEEEEecccccCccccchhhhcCCCHHHHHHHHHHHHHhccccCCceEEEEEcCCCCCCCCCceeecCeEEEeCCCC
Q 039224           40 NAVPVLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGET  119 (179)
Q Consensus        40 ~~~~~lIVDGYNvI~a~p~L~~~~~~~~Le~AR~~Li~~L~~y~~~~g~~V~VVFDa~~~~~~~~~~~~~gi~VvfT~~~  119 (179)
                      +++--++|||=|+-.      +.+ ..+++    .+++.|+.+....-.++.+  |++........-...|++.++++. 
T Consensus        22 ~~riAvfID~~Nv~~------~~~-~~d~~----~i~~~ls~~G~i~~~R~Y~--~a~a~~~l~~~l~~~Gf~pv~~kG-   87 (160)
T TIGR00288        22 EKKIGLLVDGPNMLR------KEF-NIDLD----EIREILSEYGDIKIGKVLL--NQYASDKLIEAVVNQGFEPIIVAG-   87 (160)
T ss_pred             CCcEEEEEeCCccCh------hhh-ccCHH----HHHHHHHhcCCeEEEEEEe--chhccHHHHHHHHHCCceEEEecC-
Confidence            555789999999952      111 23443    4556666665433223332  443322111122447888887755 


Q ss_pred             ChHHHH-HHHHHHHhhCCCCcEEEEcCCHHHHHHH---HhCCceE-------ecHHHHHHH
Q 039224          120 CADAWI-EKEIVALREDGCPKVWVVTSDHLQQHAA---YGAGAFV-------WSSKALVSE  169 (179)
Q Consensus       120 TAD~~I-Erlv~~~~~~~~~~V~VVTSD~~iq~~a---~~~GA~~-------iSs~ef~~~  169 (179)
                      +.|--| .+.+.-+-.+.-..+.+||||..-...+   +..|..+       .+|..|.+.
T Consensus        88 ~~Dv~laIDame~~~~~~iD~~vLvSgD~DF~~Lv~~lre~G~~V~v~g~~~~ts~~L~~a  148 (160)
T TIGR00288        88 DVDVRMAVEAMELIYNPNIDAVALVTRDADFLPVINKAKENGKETIVIGAEPGFSTALQNS  148 (160)
T ss_pred             cccHHHHHHHHHHhccCCCCEEEEEeccHhHHHHHHHHHHCCCEEEEEeCCCCChHHHHHh
Confidence            556433 4444444222235699999999766554   4566554       355555543

This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.

>smart00485 XPGN Xeroderma pigmentosum G N-region

Probab=85.51  E-value=0.38  Score=35.01  Aligned_cols=59  Identities=12%  Similarity=-0.112  Sum_probs=33.1

Q ss_pred             CCccEEEEecccccCccccch---hhhcCCCHHHHHHHHHHHHHhccccCCceEEEEEcCCCCC
Q 039224           40 NAVPVLLVDGYNVCGYWPKLE---NHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSG  100 (179)
Q Consensus        40 ~~~~~lIVDGYNvI~a~p~L~---~~~~~~~Le~AR~~Li~~L~~y~~~~g~~V~VVFDa~~~~  100 (179)
                      ...+.+-|||++.|+..-.-.   ......+.. .-.-++..+..+. ..|...++||||...+
T Consensus        22 l~g~~vaIDa~~wl~~~~~~~~~~~~~~~~~~~-~l~~~~~rl~~L~-~~~I~PifVFDG~~~~   83 (99)
T smart00485       22 LRGKTLAIDASIWLYQFLTACREKLGTPLPNSK-HLMGLFYRTCRLL-EFGIKPIFVFDGKPPP   83 (99)
T ss_pred             hCCceEeccHHHHHHHHHHHHhhhhcCCCCchH-HHHHHHHHHHHHH-HCCCeEEEEECCCCch
Confidence            446789999999986431100   000011111 2233444444444 4779999999998643

domain in nucleases

>COG1212 KdsB CMP-2-keto-3-deoxyoctulosonic acid synthetase [Cell envelope biogenesis, outer membrane]

Probab=85.06  E-value=2  Score=37.35  Aligned_cols=39  Identities=21%  Similarity=0.126  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHHhCCceEe
Q 039224          123 AWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVW  161 (179)
Q Consensus       123 ~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~~~GA~~i  161 (179)
                      ..|++...+..+.+..+|+|+|.|..+...+.+.|+.++
T Consensus        29 pmI~rV~e~a~~s~~~rvvVATDde~I~~av~~~G~~av   67 (247)
T COG1212          29 PMIVRVAERALKSGADRVVVATDDERIAEAVQAFGGEAV   67 (247)
T ss_pred             hHHHHHHHHHHHcCCCeEEEEcCCHHHHHHHHHhCCEEE
Confidence            468888888887667899999999999999999998865

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

Probab=84.92  E-value=0.93  Score=39.64  Aligned_cols=58  Identities=16%  Similarity=0.015  Sum_probs=33.7

Q ss_pred             CccEEEEecccccCcccc-chhh-hcCCCHHHHHHHHHHHHHhccccCCceEEEEEcCCCC
Q 039224           41 AVPVLLVDGYNVCGYWPK-LENH-FIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMS   99 (179)
Q Consensus        41 ~~~~lIVDGYNvI~a~p~-L~~~-~~~~~Le~AR~~Li~~L~~y~~~~g~~V~VVFDa~~~   99 (179)
                      +.+.+.||||+.||..-. .... ...+.-..+-..++..|..+.. .+...++||||...
T Consensus        23 ~gk~laID~~~~l~r~~~a~~~~~~~~g~~~~~l~~~~~rl~~L~~-~~i~pvfVFDG~~~   82 (316)
T cd00128          23 RGKKVAIDASIWLYQFLKACRQELGSGGETTSHLQGFFYRTCRLLE-LGIKPVFVFDGKPP   82 (316)
T ss_pred             CCcEEEecHHHHHHHHHHHhhhhccCCCCCcHHHHHHHHHHHHHHH-CCCEEEEEEcCCCc
Confidence            457899999999964310 0000 0112223344555555555553 45899999999643

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.

>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function

Probab=81.02  E-value=5.4  Score=31.36  Aligned_cols=61  Identities=13%  Similarity=0.130  Sum_probs=45.2

Q ss_pred             eecCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHHhCCc-eEecHHHHHHHHHHHH
Q 039224          107 EFIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGA-FVWSSKALVSEVSLII  174 (179)
Q Consensus       107 ~~~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~~~GA-~~iSs~ef~~~l~~~~  174 (179)
                      ..-|+.++|.. +-.|..|.+++.+      ..-+++|.|+.+...+...|+ ..+.+....+++.+.+
T Consensus        17 R~lG~Dt~~~~-~~~D~~il~~A~~------e~RillTrd~~l~~~~~~~~~~~li~~~~~~~QL~ev~   78 (147)
T PF01927_consen   17 RLLGYDTLYSR-DIDDDEILELARE------EGRILLTRDRDLLKRRRVSGGVILIRSDDPEEQLREVL   78 (147)
T ss_pred             HHCCCcEEEeC-CCChHHHHHHhhh------CCeEEEECCHHHHHHhhccCCEEEEcCCCHHHHHHHHH
Confidence            34577777776 3367777665543      346899999999999998876 7888888888877663

The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.

>PF08745 UPF0278: UPF0278 family; InterPro: IPR022785 This entry contains proteins of the UPF0278 family and proteins containing PIN domains

Probab=80.02  E-value=3.2  Score=35.28  Aligned_cols=34  Identities=18%  Similarity=0.012  Sum_probs=14.9

Q ss_pred             EEEEcCCHHHHHHHHhCCceEecHHHHHHHHHHH
Q 039224          140 VWVVTSDHLQQHAAYGAGAFVWSSKALVSEVSLI  173 (179)
Q Consensus       140 V~VVTSD~~iq~~a~~~GA~~iSs~ef~~~l~~~  173 (179)
                      -.|||+|..+|..|...|-+.+.+..|...++..
T Consensus       169 a~lvt~D~gi~~~A~~lGi~~i~~~~F~~~Leey  202 (205)
T PF08745_consen  169 AVLVTDDYGIQNWAEKLGIRFIDARDFPRMLEEY  202 (205)
T ss_dssp             --EE---HHHHHHHHHTT--EE------------
T ss_pred             CEEEeCCHhHHHHHHHCCCEEEeccccccccccc
Confidence            5799999999999999999999999998888754

Members of the UPF0278 family are uncharacterised and about 200 amino acids in length.; PDB: 2LCQ_A.

---

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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	179
3h7i_A	305	Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonu	97.64
1exn_A	290	5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent	97.46
1b43_A	340	Protein (FEN-1); nuclease, DNA repair, DNA replica	96.83
1a76_A	326	Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea	96.58
1bgx_T	832	TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi	96.36
2izo_A	346	FEN1, flap structure-specific endonuclease; hydrol	95.62
3v32_B	185	Ribonuclease ZC3H12A; rossmann-like sandwich fold,	95.51
3ix7_A	134	Uncharacterized protein TTHA0540; unknown function	95.41
1ul1_X	379	Flap endonuclease-1; protein complex, DNA-binding	94.95
3qe9_Y	352	Exonuclease 1; exonuclease, hydrolase-DNA complex;	94.87
3v33_A	223	Ribonuclease ZC3H12A; rossmann-like sandwich fold,	94.85
2dok_A	186	Telomerase-binding protein EST1A; telomerase-assoc	93.88
3q8k_A	341	Flap endonuclease 1; helix-3 turn-helix, hydrophob	93.66
3ory_A	363	Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco	93.46
3i8o_A	142	KH domain-containing protein MJ1533; APC89320.5, m	92.09
1rxw_A	336	Flap structure-specific endonuclease; helical clam	86.32
2lcq_A	165	Putative toxin VAPC6; PIN domain, Zn ribbon domain	85.61
1v96_A	149	Hypothetical protein PH0500; rossmann fold, tRNA s	85.53

>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=97.64  E-value=3.7e-05  Score=67.03  Aligned_cols=120  Identities=14%  Similarity=0.110  Sum_probs=79.2

Q ss_pred             CCccEEEEecccccCcc--ccchhhhcCCCHHHHHHHHHHHHHhccc----cCCceEEEEEcCCC-C-------CC----
Q 039224           40 NAVPVLLVDGYNVCGYW--PKLENHFIKGRLDVARQKLIEELVEFSM----IREVKVVVVFDALM-S-------GL----  101 (179)
Q Consensus        40 ~~~~~lIVDGYNvI~a~--p~L~~~~~~~~Le~AR~~Li~~L~~y~~----~~g~~V~VVFDa~~-~-------~~----  101 (179)
                      +++.++||||.+++++.  +.+.. -...+....|..+++.|.....    .+--.++|+||+.. .       +.    
T Consensus        11 ~~~~llLIDgssl~~ra~~~~f~~-~~g~~tnav~ggf~~~L~~ll~~~k~~~P~~iavaFD~~~~~tfR~elyp~YKan   89 (305)
T 3h7i_A           11 YKEGICLIDFSQIALSTALVNFPD-KEKINLSMVRHLILNSIKFNVKKAKTLGYTKIVLCIDNAKSGYWRRDFAYYYKKN   89 (305)
T ss_dssp             SSCCEEEEEHHHHHHHHHHHHSCS-SSCCCHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCCTTCCHHHHHSTTTTHH
T ss_pred             cCCCEEEEeccHHHHHHHHHhcCC-CCCcchHHHHHHHHHHHHHHHHhhhccCCCEEEEEecCCCCcchHhhhCHHhccC
Confidence            36689999999999874  22322 1234666777766666666543    35567999999751 1       00    


Q ss_pred             -CCCcee---------------------ecCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHHhCCce
Q 039224          102 -PTHKEE---------------------FIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAF  159 (179)
Q Consensus       102 -~~~~~~---------------------~~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~~~GA~  159 (179)
                       +..++.                     .-|+.++=...-.||++|--++......| .+|+|||+|+...+.+..-|..
T Consensus        90 R~~~PeeL~~Q~~~l~~Qi~p~ike~l~a~gi~~l~~~G~EADDiIgTLA~~a~~~g-~~V~IvSgDKDl~QLv~~~~V~  168 (305)
T 3h7i_A           90 RGKAREESTWDWEGYFESSHKVIDELKAYMPYIVMDIDKYEANDHIAVLVKKFSLEG-HKILIISSDGDFTQLHKYPNVK  168 (305)
T ss_dssp             HHHHHHHCSSCHHHHHHHHHHHHHHHHHHSSSEEECCTTCCHHHHHHHHHHHHHHTT-CCEEEECSSCCCGGGGGSSSEE
T ss_pred             CCCCCHHHHHHHHHhhhhhHHHHHHHHHHCCCCEEccCCccHHHHHHHHHHHHHHCC-CcEEEEeCCCCccccccCCCeE
Confidence             001111                     13677665544599999999999988764 6899999999998888533444


Q ss_pred             Ee
Q 039224          160 VW  161 (179)
Q Consensus       160 ~i  161 (179)
                      .+
T Consensus       169 ~~  170 (305)
T 3h7i_A          169 QW  170 (305)
T ss_dssp             EE
T ss_pred             EE
Confidence            43

>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=97.46  E-value=4.3e-05  Score=65.89  Aligned_cols=106  Identities=14%  Similarity=0.079  Sum_probs=68.5

Q ss_pred             CccEEEEecccccCccccchhhhcCCCHHHHHHHHHHHHHhcccc-CCceEEEEEcCCCC-------C-CCC----Cc--
Q 039224           41 AVPVLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMI-REVKVVVVFDALMS-------G-LPT----HK--  105 (179)
Q Consensus        41 ~~~~lIVDGYNvI~a~p~L~~~~~~~~Le~AR~~Li~~L~~y~~~-~g~~V~VVFDa~~~-------~-~~~----~~--  105 (179)
                      .+++++|||+|+++..=. ..  ....   |...++.+|.+.... +--.++||||+..+       + -..    .+  
T Consensus        18 ~~~lllIDg~~llyRa~~-~~--~G~p---av~Gf~~~l~~ll~~~~p~~~vvvFD~~~~tfR~~~~~~YKa~R~~~p~~   91 (290)
T 1exn_A           18 RRNLMIVDGTNLGFRFKH-NN--SKKP---FASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRLEHLPEYKGNRDEKYAQ   91 (290)
T ss_dssp             -CEEEEEEHHHHHHHHHH-HC--SSSC---CHHHHHHHHHHHHHHTTEEEEEEECCBSCCHHHHHHCTTTTHHHHHHHHT
T ss_pred             CCCEEEEECcHHHHHHHh-CC--CCch---HHHHHHHHHHHHHHHcCCCeEEEEEcCCCchhhhhCcHHHHcCCCCCCcc
Confidence            347999999999976421 11  1112   556666666655432 33468999997431       1 010    11  


Q ss_pred             -----e---ee-------------cCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHH
Q 039224          106 -----E---EF-------------IGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAA  153 (179)
Q Consensus       106 -----~---~~-------------~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a  153 (179)
                           +   ..             -||.++=.+.-.||+.|--++......| ..|+|||+|+...+.+
T Consensus        92 ~~~~~e~L~~q~~~~ikell~~~~~gip~i~~~g~EADDviatLa~~~~~~G-~~v~IvS~DkDl~Qlv  159 (290)
T 1exn_A           92 RTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLY-DHVWLISTDGDWDTLL  159 (290)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHHHTTTSCEECCTTBCHHHHHHHHHHHHGGGS-SCEEEECSCGGGGGGC
T ss_pred             ccccchhHHHhhHHHHHHHHHhhCCCCcEEEECCcCHHHHHHHHHHHHHHCC-CcEEEEeCCCChhhcC
Confidence                 1   01             4777754433499999999999887654 5899999999998876

>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=96.83  E-value=0.0023  Score=55.41  Aligned_cols=37  Identities=14%  Similarity=-0.076  Sum_probs=29.4

Q ss_pred             CeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHH
Q 039224          110 GVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHA  152 (179)
Q Consensus       110 gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~  152 (179)
                      ||.++-++ ..||+.|--+++.-     ..+.|+|+|...-..
T Consensus       143 gip~i~ap-~EADa~iA~La~~g-----~~~~i~S~D~D~l~~  179 (340)
T 1b43_A          143 GIPIVQAP-SEGEAQAAYMAAKG-----SVYASASQDYDSLLF  179 (340)
T ss_dssp             TCCEEECS-SCHHHHHHHHHHHT-----SSSEEECSSSHHHHT
T ss_pred             CCcEEEcC-hhHHHHHHHHHHcC-----CEEEEEccCCCccee
Confidence            78888887 89999998877642     457899999988654

>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=96.58  E-value=0.0045  Score=53.23  Aligned_cols=37  Identities=19%  Similarity=-0.014  Sum_probs=28.9

Q ss_pred             CeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHH
Q 039224          110 GVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHA  152 (179)
Q Consensus       110 gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~  152 (179)
                      ||.++-++. .||+.|--++..    | ..+.|+|+|..+-..
T Consensus       143 gi~~i~apg-EAD~~ia~La~~----g-~~~~I~S~D~Dll~~  179 (326)
T 1a76_A          143 GIPYVEAPS-EGEAQASYMAKK----G-DVWAVVSQDYDALLY  179 (326)
T ss_dssp             TCCEEECSS-CHHHHHHHHHHT----T-SSSEEECSSSGGGGG
T ss_pred             CCCeEECCc-cHHHHHHHHHHC----C-CEEEEecCCccccee
Confidence            788887776 999988887764    2 468899999877555

>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=96.36  E-value=0.0003  Score=68.14  Aligned_cols=111  Identities=23%  Similarity=0.195  Sum_probs=67.1

Q ss_pred             CCccEEEEecccccC----ccccchhhhcCCCHHHHHHHHHHHHHhccccCCceEEEEEcCCCCC------------CCC
Q 039224           40 NAVPVLLVDGYNVCG----YWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSG------------LPT  103 (179)
Q Consensus        40 ~~~~~lIVDGYNvI~----a~p~L~~~~~~~~Le~AR~~Li~~L~~y~~~~g~~V~VVFDa~~~~------------~~~  103 (179)
                      .+.++++|||++++|    +.|.|...  .+.--.|-..++.+|.+.....+..++|||||....            ...
T Consensus        10 ~~~~~llIDg~~~l~ra~~a~~~l~~~--~G~~t~av~gf~~~l~~ll~~~~~~~v~vFDg~~~tfR~~~~~~YKa~R~~   87 (832)
T 1bgx_T           10 PKGRVLLVDGHHLAYRTFHALKGLTTS--RGEPVQAVYGFAKSLLKALKEDGDAVIVVFDAKAPSFRHEAYGGYKAGRAP   87 (832)
T ss_dssp             CCTTSCCCCCSTHHHHTTSSCTTCBCS--SSCBCSSSTTHHHHHHHGGGTCCSCCCCCCCCSSSCSSSGGGGTTTSCCCC
T ss_pred             hCCCEEEEEChHHHHHHHhcCCccccC--CCcEehHHHHHHHHHHHHHHHcCCeEEEEEcCCCccccccchHHHHhcccc
Confidence            344699999999994    34544321  111111333455555554443337899999985321            000


Q ss_pred             Cceee-------------cCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHH
Q 039224          104 HKEEF-------------IGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAA  153 (179)
Q Consensus       104 ~~~~~-------------~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a  153 (179)
                      .++..             -||.++=.+.-.||+.|--++......| ..+.|||+|+...+.+
T Consensus        88 ~pe~l~~q~~~i~~~l~~~gi~~i~~pg~EADD~iatLa~~~~~~G-~~v~IvS~DkDllql~  149 (832)
T 1bgx_T           88 TPEDFPRQLALIKELVDLLGLARLEVPGYEADDVLASLAKKAEKEG-YEVRILTADKDLYQLL  149 (832)
T ss_dssp             CCTTSTTGGGTHHHHHHHTTCCCCCCSSSCHHHHHHHHHHHHHHHT-CCBCCCCSSTTCCTTC
T ss_pred             ChHHHHHHHHHHHHHHHHCCCCEEEeCCccHHHHHHHHHHHHHHcC-CeEEEEeCCCChhhcC
Confidence            11110             2676665544499999999998876543 5799999999887664

>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=95.62  E-value=0.01  Score=51.52  Aligned_cols=39  Identities=15%  Similarity=-0.041  Sum_probs=29.5

Q ss_pred             cCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHH
Q 039224          109 IGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAA  153 (179)
Q Consensus       109 ~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a  153 (179)
                      -||.++-++. .||+.|--++..    | ..+.|+|+|..+-..+
T Consensus       139 ~gi~~i~ap~-EADa~ia~La~~----g-~~~~I~S~D~D~l~~~  177 (346)
T 2izo_A          139 MGIPIVQAPS-EGEAEAAYLNKL----G-LSWAAASQDYDAILFG  177 (346)
T ss_dssp             HTCCEEECSS-CHHHHHHHHHHT----T-SSSEEECSSSHHHHTT
T ss_pred             CCCCEEEcCC-cHHHHHHHHHhC----C-CeEEEECCCCCcceec
Confidence            3777777766 999998777652    2 5689999999887654

>3v32_B Ribonuclease ZC3H12A; rossmann-like sandwich fold, RNAse, cytoplastic, hydrolase; 2.00A {Homo sapiens} PDB: 3v34_A

Probab=95.51  E-value=0.005  Score=49.98  Aligned_cols=93  Identities=22%  Similarity=0.137  Sum_probs=55.4

Q ss_pred             CccEEEEecccccCccccchhhhcCCCHHHHHHHHHHHHHhccccCCceEEEEEcCCCC-CCC--CCc--------eeec
Q 039224           41 AVPVLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMS-GLP--THK--------EEFI  109 (179)
Q Consensus        41 ~~~~lIVDGYNvI~a~p~L~~~~~~~~Le~AR~~Li~~L~~y~~~~g~~V~VVFDa~~~-~~~--~~~--------~~~~  109 (179)
                      ..+.+||||-||.++...- .     .+ ..|  -|....+|....|++.++||+.... ..+  ...        +-..
T Consensus        23 ~lR~IVIDGsNVA~~~g~~-~-----~F-s~r--gI~~aV~yf~~rGh~~v~VfvP~~r~~~~~~~~~~~d~~~L~~L~~   93 (185)
T 3v32_B           23 DLRPVVIDGSNVAMSHGNK-E-----VF-SCR--GILLAVNWFLERGHTDITVFVPSWRKEQPRPDVPITDQHILRELEK   93 (185)
T ss_dssp             CBCCEEEEHHHHHHHHTTT-T-----SE-EHH--HHHHHHHHHHHTTCCCEEEEEEGGGGSCCCTTSCEECTHHHHHHHH
T ss_pred             CCCeEEEeCHHHHhhhCCC-C-----Cc-CHH--HHHHHHHHHHHcCCCceEEEechHhhhcccccCCCCCHHHHHHHHH
Confidence            3467899999999755321 1     11 122  3455566667889998888987642 111  000        0001


Q ss_pred             CeEEEeCCCCC---------hHHHHHHHHHHHhhCCCCcEEEEcCCHH
Q 039224          110 GVDIVFPGETC---------ADAWIEKEIVALREDGCPKVWVVTSDHL  148 (179)
Q Consensus       110 gi~VvfT~~~T---------AD~~IErlv~~~~~~~~~~V~VVTSD~~  148 (179)
                      -=-|+||+.++         +|.+|..++.+..      -.|||+|+.
T Consensus        94 ~g~l~~TPs~~~~g~~~~~ydD~~il~~A~~~~------g~IVSND~~  135 (185)
T 3v32_B           94 KKILVFTPSRRVGGKRVVCYDDRFIVKLAYESD------GIVVSNDTY  135 (185)
T ss_dssp             TTCEEEECCCC-------CCHHHHHHHHHHHTT------CEEECSCCC
T ss_pred             CCCEEECCCcccCCCcccCccHHHHHHHHHHcC------CEEEeCccH
Confidence            12366777642         7888888877643      468898853

>3ix7_A Uncharacterized protein TTHA0540; unknown function, thermus thermophilus HB8, structural genom 2, protein structure initiative; HET: MSE; 2.15A {Thermus thermophilus}

Probab=95.41  E-value=0.024  Score=43.69  Aligned_cols=47  Identities=23%  Similarity=0.107  Sum_probs=42.2

Q ss_pred             CCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHHhCCceEecHHHHHHHH
Q 039224          118 ETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEV  170 (179)
Q Consensus       118 ~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~~~GA~~iSs~ef~~~l  170 (179)
                      .+.+|+.|.+++.++.      .+|||+|..++..|...|..++.-.+|..-+
T Consensus        83 ~~~vD~~ll~lA~~~~------~~lvTnD~~L~kvA~~~GI~Vl~l~~l~~al  129 (134)
T 3ix7_A           83 GESVDEKLLFLARDLE------AALVTNDHALLQMARIYGVKALSIQALAQAL  129 (134)
T ss_dssp             CSSHHHHHHHHHHHTT------CEEEESCHHHHHHHHHTTCCEEEHHHHHHHT
T ss_pred             cccHHHHHHHHHHHhC------CEEEeCCHHHHHHHHHCCCeEEehHHHHHhh
Confidence            3689999999998864      6999999999999999999999999987755

>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=94.95  E-value=0.027  Score=49.53  Aligned_cols=38  Identities=16%  Similarity=-0.085  Sum_probs=30.0

Q ss_pred             CeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHH
Q 039224          110 GVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAA  153 (179)
Q Consensus       110 gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a  153 (179)
                      ||.++-++. .||+.|--++...     ..+.|+|+|..+-...
T Consensus       148 Gi~~i~apg-EADd~iA~La~~g-----~~~~iiS~D~Dll~~g  185 (379)
T 1ul1_X          148 GIPYLDAPS-EAEASCAALVKAG-----KVYAAATEDMDCLTFG  185 (379)
T ss_dssp             TCCEEECSS-CHHHHHHHHHHHT-----SSSEEECSCTHHHHTT
T ss_pred             CCCeecCCC-cHHHHHHHHHhcC-----CeEEEEecCcCccccc
Confidence            788887777 9999998887752     3477999999987764

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

Probab=94.87  E-value=0.024  Score=49.69  Aligned_cols=36  Identities=28%  Similarity=0.162  Sum_probs=27.1

Q ss_pred             CeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHH
Q 039224          110 GVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQH  151 (179)
Q Consensus       110 gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~  151 (179)
                      ||.++-++ ..||+.|--+...    | ..+.|+|+|..+-.
T Consensus       141 gIp~i~ap-~EADaqiA~La~~----g-~~~~I~S~D~Dll~  176 (352)
T 3qe9_Y          141 GVDCLVAP-YEADAQLAYLNKA----G-IVQAIITEDSALLA  176 (352)
T ss_dssp             TCEEEECS-SCHHHHHHHHHHT----T-SCSEEECSCGGGGG
T ss_pred             CCcEEECC-cchHHHHHHHHHC----C-CeEEEEeCCcCccc
Confidence            78888654 7999999777662    2 46789999998643

>3v33_A Ribonuclease ZC3H12A; rossmann-like sandwich fold, RNAse, cytoplastic, hydrolase; 2.00A {Homo sapiens}

Probab=94.85  E-value=0.0069  Score=50.57  Aligned_cols=93  Identities=22%  Similarity=0.143  Sum_probs=55.3

Q ss_pred             CccEEEEecccccCccccchhhhcCCCHHHHHHHHHHHHHhccccCCceEEEEEcCCCC-CCC--CCc--------eeec
Q 039224           41 AVPVLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMS-GLP--THK--------EEFI  109 (179)
Q Consensus        41 ~~~~lIVDGYNvI~a~p~L~~~~~~~~Le~AR~~Li~~L~~y~~~~g~~V~VVFDa~~~-~~~--~~~--------~~~~  109 (179)
                      ..+.+||||-||.++...- .     .+ .+|  -|....+|....|++.++||+.... ..+  ...        +-..
T Consensus        23 ~lR~IVIDGsNVA~~~g~~-~-----~F-s~r--gI~~aV~yF~~RGh~~V~VfvP~~r~~~~~~~~~~~d~~~L~~L~k   93 (223)
T 3v33_A           23 DLRPVVIDGSNVAMSHGNK-E-----VF-SCR--GILLAVNWFLERGHTDITVFVPSWRKEQPRPDVPITDQHILRELEK   93 (223)
T ss_dssp             CBCCEEEEHHHHHHHSSST-T-----SE-EHH--HHHHHHHHHHTTTCCCEEEEEEGGGGSCCCTTSCEESTHHHHHHHH
T ss_pred             cCCeEEEeCHHHHhhhCCC-C-----Cc-CHH--HHHHHHHHHHHcCCCceEEEechhhhccccccCCCCcHHHHHHHHH
Confidence            3467899999999765421 1     11 122  5666677778899998888876532 111  000        0011


Q ss_pred             CeEEEeCCCC---------ChHHHHHHHHHHHhhCCCCcEEEEcCCHH
Q 039224          110 GVDIVFPGET---------CADAWIEKEIVALREDGCPKVWVVTSDHL  148 (179)
Q Consensus       110 gi~VvfT~~~---------TAD~~IErlv~~~~~~~~~~V~VVTSD~~  148 (179)
                      -=-|+||+..         -+|.+|..++.+..      -.|||+|+.
T Consensus        94 ~g~L~~TPs~~v~G~r~~sydD~~iL~~A~~~~------g~IVSND~y  135 (223)
T 3v33_A           94 KKILVFTPSRRVGGKRVVCYDDRFIVKLAYESD------GIVVSNDTY  135 (223)
T ss_dssp             TTCEEEECEEEETTEEEECCHHHHHHHHHHHTT------CEEECSCCC
T ss_pred             CCCEEECCCCCcCCccccccchHHHHHHHHHcC------CEEEeCccH
Confidence            1236667654         27888888777632      468888864

>2dok_A Telomerase-binding protein EST1A; telomerase-associated protein, unknown function; 1.80A {Homo sapiens} PDB: 2hww_A 2hwx_A

Probab=93.88  E-value=0.11  Score=41.00  Aligned_cols=53  Identities=17%  Similarity=0.036  Sum_probs=44.7

Q ss_pred             CCChHHHHHHHHHHHhhCC---------------CCcEEEEcCCHHHHHHHHhCCceEecHHHHHHHH
Q 039224          118 ETCADAWIEKEIVALREDG---------------CPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEV  170 (179)
Q Consensus       118 ~~TAD~~IErlv~~~~~~~---------------~~~V~VVTSD~~iq~~a~~~GA~~iSs~ef~~~l  170 (179)
                      ..++|+.|-+.+..+.+..               ...|++||.|..++.-|.+.|-.+++-.+|.++.
T Consensus       116 ~~~~D~~IL~~a~~l~~~~~~~~~~~~~~~~~~~~~~vvLvTnD~nLr~KA~~~Gi~~~~~~~~~~~~  183 (186)
T 2dok_A          116 LGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVKALTRNVPVRDIPAFLTWA  183 (186)
T ss_dssp             -CCHHHHHHHHHHTTCCCCGGGGCCC---CCCEEEEEEEEECCCHHHHHHHHHTTCCEECHHHHHHHH
T ss_pred             CCCccHHHHHHHHHHHHhcccccccccccccccCCCcEEEEeCcHHHHHHHHHCCCeeCcHHHHHHHh
Confidence            3599999999998875321               1369999999999999999999999999999874

>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=93.66  E-value=0.044  Score=47.73  Aligned_cols=38  Identities=18%  Similarity=0.011  Sum_probs=29.7

Q ss_pred             CeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHH
Q 039224          110 GVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAA  153 (179)
Q Consensus       110 gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a  153 (179)
                      ||.++-++. .||+.|--++..    + ..+.|+|+|...-..+
T Consensus       148 gip~i~ap~-EADd~ia~La~~----g-~v~~i~s~D~D~l~~~  185 (341)
T 3q8k_A          148 GIPYLDAPS-EAEASCAALVKA----G-KVYAAATEDMDCLTFG  185 (341)
T ss_dssp             TCCEEECSS-CHHHHHHHHHHT----T-SSSEEECSCTHHHHTT
T ss_pred             CCCEEECCc-cHHHHHHHHHhc----C-CeEEEEcCCccccccC
Confidence            788888876 999999888774    2 3466889999887664

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

Probab=93.46  E-value=0.047  Score=48.03  Aligned_cols=38  Identities=13%  Similarity=-0.016  Sum_probs=28.5

Q ss_pred             CeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHH
Q 039224          110 GVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAA  153 (179)
Q Consensus       110 gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a  153 (179)
                      ||.++-++. .||+.|-.+++    .| ..+.|+|+|...-..+
T Consensus       157 GIp~i~apg-EADaqiA~La~----~g-~~~~I~S~D~D~l~fg  194 (363)
T 3ory_A          157 GIPWVQAPA-EGEAQAAYIVK----KG-DAYASASQDYDSLLFG  194 (363)
T ss_dssp             TCCEEECSS-CHHHHHHHHHH----TT-SCSEEECSSSHHHHTT
T ss_pred             CCCEEEeCc-cHHHHHHHHHH----CC-CeEEEECCCcCccccC
Confidence            788888876 69998766653    22 5789999999887643

>3i8o_A KH domain-containing protein MJ1533; APC89320.5, methanocaldococcus jannaschii DSM 2661, structural genomics, PSI-2; 2.64A {Methanocaldococcus jannaschii}

Probab=92.09  E-value=0.21  Score=38.76  Aligned_cols=87  Identities=22%  Similarity=0.204  Sum_probs=56.3

Q ss_pred             cchhhhcCCCHHHHHHH--HHHHHHhccccCCceEEEEEcCCCCCCCCCceeecCeEEEeCCCCChHHHHHHHHHHHhhC
Q 039224           58 KLENHFIKGRLDVARQK--LIEELVEFSMIREVKVVVVFDALMSGLPTHKEEFIGVDIVFPGETCADAWIEKEIVALRED  135 (179)
Q Consensus        58 ~L~~~~~~~~Le~AR~~--Li~~L~~y~~~~g~~V~VVFDa~~~~~~~~~~~~~gi~VvfT~~~TAD~~IErlv~~~~~~  135 (179)
                      +|.. .++...+..|.-  .++.|.+.+......+.++  +..   +...      ++-|++.+..|+.|.+++.++.  
T Consensus        41 EL~~-~a~~~r~~GrrGLe~L~~L~~~~~~~~i~vei~--~~r---~~~~------~i~~~~~~~vD~~l~~lA~~~~--  106 (142)
T 3i8o_A           41 ELEY-QANMGREIGYKGIEELRKLIEKASEHNIKVEYY--GER---PTRE------EIFLAKSGEIDAMIRKVAKETN--  106 (142)
T ss_dssp             HHHH-HHTTTCHHHHHHHHHHHHHHHHHHHTTCCEEEE--SCC---CCHH------HHHSCCSSSHHHHHHHHHHHTT--
T ss_pred             HHHH-HHHccchhhHHHHHHHHHHHHHhhccCceEEEe--ccc---Cchh------hhccccCCcHHHHHHHHHHHhC--
Confidence            4555 244455666663  4666666554445555544  211   1111      1123445689999999998864  


Q ss_pred             CCCcEEEEcCCHHHHHHHHhCCceEec
Q 039224          136 GCPKVWVVTSDHLQQHAAYGAGAFVWS  162 (179)
Q Consensus       136 ~~~~V~VVTSD~~iq~~a~~~GA~~iS  162 (179)
                          .+|+|+|..++..|...|..++.
T Consensus       107 ----a~lvTnD~~l~kvA~~~GI~V~~  129 (142)
T 3i8o_A          107 ----SILLTSDWIQYNLAKAQGIEAYF  129 (142)
T ss_dssp             ----CEEEESCHHHHHHHHHTTCCEEE
T ss_pred             ----CEEEcCCHHHHHHHHHcCCEEEE
Confidence                58999999999999999998875

>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=86.32  E-value=0.37  Score=41.33  Aligned_cols=39  Identities=13%  Similarity=0.030  Sum_probs=25.8

Q ss_pred             cCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHH
Q 039224          109 IGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAA  153 (179)
Q Consensus       109 ~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a  153 (179)
                      -||.++-++. .||.-+-.+.    ..| ..+.|+|+|...-+.+
T Consensus       141 ~gi~~i~apg-eAEA~lA~la----~~g-~~~~I~S~D~Dllql~  179 (336)
T 1rxw_A          141 MGIPFVDAPS-EGEAQAAYMA----AKG-DVEYTGSQDYDSLLFG  179 (336)
T ss_dssp             TTCCEEECSS-CHHHHHHHHH----HTT-SSSEEECSSSHHHHTT
T ss_pred             CCCCEEEcCc-hHHHHHHHHH----HcC-CeeEEEcCCCCcceec
Confidence            4788887765 4555444433    333 5789999999887654

>2lcq_A Putative toxin VAPC6; PIN domain, Zn ribbon domain, ribosome biogenesis, metal BIN protein; NMR {Pyrococcus horikoshii}

Probab=85.61  E-value=0.91  Score=34.87  Aligned_cols=46  Identities=20%  Similarity=0.019  Sum_probs=38.9

Q ss_pred             CChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHHhCCceEecHHHHHHHH
Q 039224          119 TCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEV  170 (179)
Q Consensus       119 ~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~~~GA~~iSs~ef~~~l  170 (179)
                      ..||..+..++.++.      ..|+|+|..+|+.|...|-.+++..++++++
T Consensus        83 s~~D~~lIaLA~~l~------~~lvT~D~~l~~vA~~~Gv~v~~~~~~i~~~  128 (165)
T 2lcq_A           83 SKADIEVLALAYELK------GEIFSDDYNVQNIASLLGLRFRTLKRGIKKV  128 (165)
T ss_dssp             CHHHHHHHHHHHHHT------CCEECCCHHHHHHHHHTTCCEECCSCCCSSC
T ss_pred             CHHHHHHHHhHHHhC------CeEEcCcHHHHHHHHHCCCeEEchhhhcccc
Confidence            479999999999875      3789999999999999999999877555443

>1v96_A Hypothetical protein PH0500; rossmann fold, tRNA synthetase, nucleotide binding protein, structural genomics; 1.75A {Pyrococcus horikoshii} SCOP: c.120.1.1 PDB: 1ye5_A 1y82_A

Probab=85.53  E-value=1.2  Score=32.56  Aligned_cols=48  Identities=17%  Similarity=0.126  Sum_probs=36.9

Q ss_pred             CChHHHHHHHHHHHhhCCCCcEEEEcCCH-HHHHHHHhCCceEecHHHHHHHHHHH
Q 039224          119 TCADAWIEKEIVALREDGCPKVWVVTSDH-LQQHAAYGAGAFVWSSKALVSEVSLI  173 (179)
Q Consensus       119 ~TAD~~IErlv~~~~~~~~~~V~VVTSD~-~iq~~a~~~GA~~iSs~ef~~~l~~~  173 (179)
                      ..+|.+|-..+...+      +++||.|. ..+. +.+.|-.++++.+|+++++..
T Consensus        95 ~~~D~lIaA~A~~~~------~~lvT~D~kdf~~-i~~~~i~~i~~~efl~~~~~~  143 (149)
T 1v96_A           95 DMEDIITATTAIYTN------SLLVTDDPKRYEP-IRRFGLDTMPLDKFIKEVELM  143 (149)
T ss_dssp             CHHHHHHHHHHHHHT------CEEEESCHHHHGG-GGGGTCCEEEHHHHHHHHHHH
T ss_pred             CHhHHHHHHHHHHcC------CEEEECCHHHHhh-hhhCCeeecCHHHHHHHHHHH
Confidence            358998887776543      47999995 5554 567899999999999988654

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	179
d1xo1a2	167	T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]	98.6
d1cmwa2	164	5' to 3' exonuclease domain of DNA polymerase Taq	98.51
d1tfra2	169	T4 RNase H {Bacteriophage T4 [TaxId: 10665]}	98.25
d1ul1x2	216	Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo	92.71
d1o4wa_	125	Hypothetical protein AF0591 {Archaeon Archaeoglobu	89.67
d1v96a1	148	Hypothetical protein PH0500 {Pyrococcus horikoshii	84.41
d1vh1a_	246	CMP:2-keto-3-deoxy-manno-octonic acid (CMP-KDO)syn	83.88

>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=98.60  E-value=1.5e-08  Score=78.46  Aligned_cols=107  Identities=11%  Similarity=0.045  Sum_probs=68.7

Q ss_pred             CccEEEEecccccCccccchhhhcCCCHHHHHHHHHHHHHhccc-cCCceEEEEEcCCCC-------CC-CCCc----ee
Q 039224           41 AVPVLLVDGYNVCGYWPKLENHFIKGRLDVARQKLIEELVEFSM-IREVKVVVVFDALMS-------GL-PTHK----EE  107 (179)
Q Consensus        41 ~~~~lIVDGYNvI~a~p~L~~~~~~~~Le~AR~~Li~~L~~y~~-~~g~~V~VVFDa~~~-------~~-~~~~----~~  107 (179)
                      ++++|||||.|+++.|-.-.      .-..+...+++.|..+.. +....++|+||+..+       +. ..++    +.
T Consensus         1 k~~~lliDg~~l~~R~~~~~------~~~~~~~~f~~~l~~l~~~~~~~~iiv~~d~~~~~~R~~l~p~YKanR~~~~~~   74 (167)
T d1xo1a2           1 RRNLMIVDGTNLGFRFKHNN------SKKPFASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRLEHLPEYAGNRDEKYAQ   74 (167)
T ss_dssp             CCEEEEEEHHHHHTTC-------------CCHHHHHHHHHHHHHHTTEEEEEEECCBSCCHHHHTTCTTCC---------
T ss_pred             CCeEEEEcChHHHHHHHHcC------CCcCHHHHHHHHHHHHHHHcCCCEEEEEEeCCCCCcccccchhhhhcCCCCchh
Confidence            46899999999998763211      112234456677776654 455678999995431       10 1110    00


Q ss_pred             -----------------------ecCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHH
Q 039224          108 -----------------------FIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAY  154 (179)
Q Consensus       108 -----------------------~~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~  154 (179)
                                             ..|+.++..++-.||++|--++......+ ..|+|||||+.+.+.+.
T Consensus        75 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~EADDiIa~l~~~~~~~~-~~v~IvS~DkD~~QLv~  143 (167)
T d1xo1a2          75 RTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLY-DHVWLISTDGDWDTLLT  143 (167)
T ss_dssp             -----------CHHHHHHHHHHHHTTSCEECCTTBCHHHHHHHHHHHHGGGS-SCEEEECSCGGGGGGCB
T ss_pred             cccchhHHHHHHHHHHHHHHHHhhccccEEEeccccchhHHHHHHHHhhcCC-CEEEEEeCCccHHHhee
Confidence                                   11566666555699999999998877653 68999999999988763

>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=98.51  E-value=6.5e-08  Score=74.31  Aligned_cols=111  Identities=22%  Similarity=0.173  Sum_probs=75.4

Q ss_pred             CccEEEEecccccC----ccccchhhhcCCCHHHHHHHHHHHHHhccccCCceEEEEEcCCCCC------------CCCC
Q 039224           41 AVPVLLVDGYNVCG----YWPKLENHFIKGRLDVARQKLIEELVEFSMIREVKVVVVFDALMSG------------LPTH  104 (179)
Q Consensus        41 ~~~~lIVDGYNvI~----a~p~L~~~~~~~~Le~AR~~Li~~L~~y~~~~g~~V~VVFDa~~~~------------~~~~  104 (179)
                      ++++|||||.|+++    +.|.+..  ..+.--.|-..++..|........-.++|+||+....            ....
T Consensus         2 ~~~~lLIDg~~l~~R~~~a~~~~~~--~~g~~~~~i~gf~~~l~~~~~~~~~~~~v~~d~~~~~~R~~l~p~YK~~R~~~   79 (164)
T d1cmwa2           2 KGRVLLVDGHHLAYRTFHALKGLTT--SRGEPVQAVYGFAKSLLKALKEDGDAVIVVFDAKAPSFRHEAYGGYKAGRAPT   79 (164)
T ss_dssp             CEEEEEEETTHHHHHHHTSSTTCBC--TTSCBCHHHHHHHHHHHHHHHHCCSEEEEECCCSSSCTTGGGGSTTTSCCCCC
T ss_pred             CCeEEEEeChHHHHHHHHcCCcccC--CCCCeeHHHHHHHHHHHHHHhcCCceEEEEEecccccchhhhhhhhhhccccC
Confidence            45899999999996    5555433  1122223556666666666555567789999876421            0011


Q ss_pred             cee-------------ecCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHH
Q 039224          105 KEE-------------FIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAY  154 (179)
Q Consensus       105 ~~~-------------~~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~  154 (179)
                      ++.             ..|+.++..+.-.||++|--++......+ .+|+|||||+...+.+.
T Consensus        80 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~EADDvIa~la~~~~~~~-~~v~IvS~DkD~~QLv~  141 (164)
T d1cmwa2          80 PEDFPRQLALIKELVDLLGLARLEVPGYEADDVLASLAKKAEKEG-YEVRILTADKDLYQLLS  141 (164)
T ss_dssp             CSSHHHHHHHHHHHHHHTTCEEECCTTSCHHHHHHHHHHHHHHTT-EEEEEECSSGGGGGSCC
T ss_pred             chhHHHHHHHHHHHHhhcCceEEEecCcchHHHHHHHHHHhcccc-ceEEEecCCCChHHhee
Confidence            111             13888877766699999999999988653 58999999999888763

>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=98.25  E-value=1.3e-06  Score=67.80  Aligned_cols=120  Identities=18%  Similarity=0.159  Sum_probs=81.5

Q ss_pred             CccEEEEecccccCcc--ccchhhhcCCCHHHHHHHHHHHHHhccc----cCCceEEEEEcCCCCC------CC---CCc
Q 039224           41 AVPVLLVDGYNVCGYW--PKLENHFIKGRLDVARQKLIEELVEFSM----IREVKVVVVFDALMSG------LP---THK  105 (179)
Q Consensus        41 ~~~~lIVDGYNvI~a~--p~L~~~~~~~~Le~AR~~Li~~L~~y~~----~~g~~V~VVFDa~~~~------~~---~~~  105 (179)
                      +.+++||||-|+.++.  ...+. ....+...+|..+++.|..+..    ..--+|+|+||+....      .+   +++
T Consensus         1 k~~~~liD~s~~~~~~~~~~~~~-~~~~~~~~~~h~~lnsi~~~~k~~~~~~p~~viv~~D~~~~~~~R~~l~p~YKanR   79 (169)
T d1tfra2           1 KEGICLIDFSQIALSTALVNFPD-KEKINLSMVRHLILNSIKFNVKKAKTLGYTKIVLCIDNAKSGYWRRDFAYYYKKNR   79 (169)
T ss_dssp             CCEEEEEEHHHHHHHHHHHHSCT-TSCCCHHHHHHHHHHHHHHHHHHHHHTTEEEEEEECCCCTTCCGGGGTCTTTTC--
T ss_pred             CCCEEEEechHHHHHHHHHhccC-CCCCChhHHHHHHHHHHHHHHHHhhhcCCCeEEEEEeCCCCCchhhhhHHHHhhCC
Confidence            4589999999998543  22222 2355777888877777765542    4456899999975311      01   110


Q ss_pred             ----ee---------------------ecCeEEEeCCCCChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHHhCCceE
Q 039224          106 ----EE---------------------FIGVDIVFPGETCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFV  160 (179)
Q Consensus       106 ----~~---------------------~~gi~VvfT~~~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~~~GA~~  160 (179)
                          +.                     .-|+.+++.+.-.||++|--++.++...+ ..|+++|||+..-+.+..-+...
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~EADDvIa~la~~~~~~~-~~vvIvS~DkD~~QLv~~~~V~~  158 (169)
T d1tfra2          80 GKAREESTWDWEGYFESSHKVIDELKAYMPYIVMDIDKYEADDHIAVLVKKFSLEG-HKILIISSDGDFTQLHKYPNVKQ  158 (169)
T ss_dssp             -------CCCHHHHHHHHHHHHHHHHHHSSSEEECCTTCCHHHHHHHHHHHHHHTT-CCEEEECCCGGGGGGTTSTTEEE
T ss_pred             CCCcccchhhhhHHHHHHHHHHHHHHHHhhhhccccCCcccccHHHHHHHHHHHCC-CcEEEEeCCCCHHHhCcCCCeEE
Confidence                00                     13788877766799999999999987654 68999999999988775445555


Q ss_pred             ec
Q 039224          161 WS  162 (179)
Q Consensus       161 iS  162 (179)
                      .+
T Consensus       159 ~~  160 (169)
T d1tfra2         159 WS  160 (169)
T ss_dssp             EE
T ss_pred             ee
Confidence            54

>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=92.71  E-value=0.18  Score=38.30  Aligned_cols=56  Identities=14%  Similarity=0.056  Sum_probs=28.3

Q ss_pred             ccEEEEecccccCccccchhhhcCCCHH----HHHHHHHH---HHHhccccCCceEEEEEcCCCC
Q 039224           42 VPVLLVDGYNVCGYWPKLENHFIKGRLD----VARQKLIE---ELVEFSMIREVKVVVVFDALMS   99 (179)
Q Consensus        42 ~~~lIVDGYNvI~a~p~L~~~~~~~~Le----~AR~~Li~---~L~~y~~~~g~~V~VVFDa~~~   99 (179)
                      ...+.|||++.|+.+-.-... ....+.    .....|+.   .+..+. ..+.+.+.||||...
T Consensus        27 gk~vaIDas~~l~~~l~~~~~-~~~~l~~~~~~~~~~l~~~~~~~~~l~-~~~I~pifVFDG~~~   89 (216)
T d1ul1x2          27 GRKVAIDASMSIYQFLIAVRQ-GGDVLQNEEGETTSHLMGMFYRTIRMM-ENGIKPVYVFDGKPP   89 (216)
T ss_dssp             TCCEEEEHHHHHHHHHSCC--------------CCHHHHHHHHHHHHHH-HTTCCEEEEECCSCC
T ss_pred             CCEEEEEeHHHHHHHHHHhcc-ccchhhccCCCCcHHHHHHHHHHHHHH-HcCCeEEEEEcCCCC
Confidence            358999999998754211000 000111    11122222   233333 258999999999754

>d1o4wa_ c.120.1.1 (A:) Hypothetical protein AF0591 {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: PIN domain
domain: Hypothetical protein AF0591
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=89.67  E-value=0.26  Score=34.70  Aligned_cols=38  Identities=16%  Similarity=0.047  Sum_probs=31.6

Q ss_pred             CChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHHhCCceEec
Q 039224          119 TCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWS  162 (179)
Q Consensus       119 ~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~~~GA~~iS  162 (179)
                      ..||+-|..++.+.      .++|+|.|..++..++..|..+++
T Consensus        76 ~~~Dd~il~~a~~~------~~iv~T~D~~Lr~~~~~~GVpvi~  113 (125)
T d1o4wa_          76 SEGDPSLIEAAEKY------GCILITNDKELKRKAKQRGIPVGY  113 (125)
T ss_dssp             SCSHHHHHHHHHHH------TCEEECCCHHHHHHHHHTTCCEEC
T ss_pred             CcHHHHHHHHHhhC------CeEEEecCHHHHHHHHHcCCcEEE
Confidence            46898887776653      379999999999999999988775

>d1v96a1 c.120.1.1 (A:2-149) Hypothetical protein PH0500 {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: PIN domain
domain: Hypothetical protein PH0500
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=84.41  E-value=0.64  Score=33.64  Aligned_cols=50  Identities=16%  Similarity=0.153  Sum_probs=41.7

Q ss_pred             CChHHHHHHHHHHHhhCCCCcEEEEcCCHHHHHHHHhCCceEecHHHHHHHHHHHH
Q 039224          119 TCADAWIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWSSKALVSEVSLII  174 (179)
Q Consensus       119 ~TAD~~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~~~GA~~iSs~ef~~~l~~~~  174 (179)
                      +.+|.+|-..+..+.      .++||.|..--..+...|-.+++.++|+++++-+.
T Consensus        94 ~~~D~lIAAtAi~~~------~~LVT~n~kdF~~i~~~Gl~vi~~~~~l~~~~~~~  143 (148)
T d1v96a1          94 DMEDIITATTAIYTN------SLLVTDDPKRYEPIRRFGLDTMPLDKFIKEVELMV  143 (148)
T ss_dssp             CHHHHHHHHHHHHHT------CEEEESCHHHHGGGGGGTCCEEEHHHHHHHHHHHH
T ss_pred             ChhHHHHHHHHHHcC------CEEEeCCHHHhhHHHHCCceEecHHHHHHHHHHhh
Confidence            367888877766643      68999998888888889999999999999998664

>d1vh1a_ c.68.1.13 (A:) CMP:2-keto-3-deoxy-manno-octonic acid (CMP-KDO)synthetase {Escherichia coli, KdsB [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Nucleotide-diphospho-sugar transferases
superfamily: Nucleotide-diphospho-sugar transferases
family: Cytidylytransferase
domain: CMP:2-keto-3-deoxy-manno-octonic acid (CMP-KDO)synthetase
species: Escherichia coli, KdsB [TaxId: 562]

Probab=83.88  E-value=0.91  Score=33.68  Aligned_cols=39  Identities=26%  Similarity=0.236  Sum_probs=29.3

Q ss_pred             HHHHHHHHHhhCCCCcEEEEcCCHHHHHHHHhCCceEec
Q 039224          124 WIEKEIVALREDGCPKVWVVTSDHLQQHAAYGAGAFVWS  162 (179)
Q Consensus       124 ~IErlv~~~~~~~~~~V~VVTSD~~iq~~a~~~GA~~iS  162 (179)
                      .|+..+.++...+-.+|+|+|+|..+...+...|+.++-
T Consensus        28 LI~~~i~~a~~s~i~~iiVsTd~~~i~~~~~~~g~~v~~   66 (246)
T d1vh1a_          28 MIVHVLERARESGAERIIVATDHEDVARAVEAAGGEVCM   66 (246)
T ss_dssp             HHHHHHHHHHHTTCSEEEEEESCHHHHHHHHHTTCEEEE
T ss_pred             HHHHHHHHHHHcCCCcEEEEecCccccchhhccccccee
Confidence            344444444443346899999999999999999998763