Psyllid ID: psy1206

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-
Protein Sequence
MTLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFIDLCILLGCDYCDSIRGIGPKRAIELLYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIADPETIELVADVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFTIRREEKRKSRCQYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQYQYQYQCQCQCQCQCQYQY
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHHHcccccHHHHHHHHHHHHHHcccccHHHHHHHHHHHcccEEccccHHHHHHHHHHHcccEEEEEccccccccccccEEEEccccccccccccccEEHHHHHccccccHHHHHHHHHHHccccccccccccHHHHHHHHHHcccHHHHHHHHHcccccccccccHHHHHHHHccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccccHHHHHHHHccHHHHHHHHHccccccccccHHHHHHHHHccccccccccccHHcccccccccccHHHHccHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHcccEEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHcccccccHHHHHHHHHHHHHHcccccccccccccEEccccHHHHHHHHHHHcccEEEcccccccccccccccccccccEEEEEEEEEEEEEEEEEccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHccccccccccHHccccccEccccHHHHHHHHHHHccccEEEccccHHHHccccEEEEcccccEEEEccccccEEEHHHHHccccHHHHHHHHHHHccccccccccccHHHHHHHHHHcccHHHHHHHHccccccccccccHHHHHHHHcccccccHccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHcccHHHHHHHcccccccccccccHHHHHHHHHccccccHHHcHHHHcccccHHHHccEEEEEccccEEEHEEEEcccccEcEcccccEcHHHHHHHHHHHHHHHcccEEEEEEcccccccccccHHHHHccHHHccHHHHHHHHcccHHcccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHccccccccccEEcccHHHHHHHHHHHHHHHHHHHHHHHccccccccccEcEcEEEEEEEEEEEEEEEEEEEEEcccEcEcEccc
Coil and Loop (DISEMBL)
mtlkwsdpdedgLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFFTIRReekrkapcEAEAQCAAMVKAGKVYAtatedmdaltFGSNILLRHMTfsearklpvqeFHLEKVLEGMELSHEEFIDLCILLGcdycdsirgiGPKRAIELIKEHRSIEKILEnidtkkytvpegwlyKEARElfrhpevadpetiEFIDLCILLGcdycdsirgigPKRAIELLYSFIDLCILLGcdycdsirgiGPKRAIELIKEHRSIEKILEnidtkkytvpegwlYKEARElfrhpeiadpetIELVADVAPSSIRESRKICIDASMSLYQFLIAVRSEgnqlmsvdgeptshlmgTFYRTIRLVEhglkpiyvfdgkpptlksgelNKRMEKREDAQKALAKAQEqgklkwsdpdedgLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFTIRREEKRKSRCQYQCQyqcqyqcqyqcqcqcqcqcqcqcqcqyQYQYQYQYQYQYQYQYqcqcqcqcqcqyqy
Flexible Loop (DISEMBL)
mtlkwsdpdedgLVKYLCGDKNFAEDRIRNGAKKllkarssttqgrldsfftirreekrkapcEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKilenidtkkytvpEGWLYKEARELFRHPEVADPETIEFIDLCILLGCDYCDSIRGIGPKRAIELLYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKilenidtkkytvpeGWLYKEARELFRHpeiadpetielVADVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKpiyvfdgkpptlksgelNKRMEKREDAQKALAKaqeqgklkwsdpdedGLVKYLCGDKNFAEDRIRNGAKKllkarstttqgrldsfftirreekrKSRCQYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQYQYQYQCQCQCQCQCQYQY
Low Complexity Region (SEG)
MTLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFIDLCILLGCDYCDSIRGIGPKRAIELLYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIADPETIELVADVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFTIRREEKRKSRcqyqcqyqcqyqcqyqcqcqcqcqcqcqcqcqyqyqyqyqyqyqyqyqyqcqcqcqcqcqyqy
Disordered region (IsUnstruct)
************LVKYLCGDKNFAEDRI*********************FFTI**********EAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFIDLCILLGCDYCDSIRGIGPKRAIELLYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIADPETIELVADVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFD******************************************GLVKYLCGDKNFAEDRIRNGAKKLL********GRLDSFFTIRREEKRKSRCQYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQYQYQYQCQCQCQCQCQY**
Disordered Region (DISOPRED)
MTLKWSDPDEDGLVKYLCG**************KLLKARSSTTQGRLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFIDLCILLGCDYCDSIRGIGPKRAIELLYSFIDLCILLGCDYCD*********************************VPEGWLYKEARELFRHPEIADPETIELVADVAPSSIRESRKICIDASMSLYQFLIAVRSEGN*****DGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSG********************************************************LLKARSTTTQGRLDSFFTIRREEKRKSRCQYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQYQYQYQCQCQCQCQCQYQ*
Disordered Region (DISEMBL)
********DEDGLVKYLCGDKNFAEDRIRNGAKKL*********GRLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFIDLCILLGCDYCDSIRGIGPKRAIELLYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIADPETIELVADVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNK***********************SDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFTIRREEKRKSRCQYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQYQYQYQCQCQC********
Disordered Region (DISPRO)
MTLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFIDLCILLGCDYCDSIRGIGPKRAIELLYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIADPETIELVADVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFTIRREEKRKSRCQYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQYQYQYQCQCQCQCQCQYQY
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFIDLCILLGCDYCDSIRGIGPKRAIELLYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIADPETIELVADVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGExxxxxxxxxxxxxxxxxxxxxGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFTIRREEKRKSRCQYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQYQYQYQCQCQCQCQCQYQY
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	531	2.2.26 [Sep-21-2011]
Q178M1	380	Flap endonuclease 1 OS=Ae	N/A	N/A	0.254	0.355	0.781	5e-65
Q7Q323	383	Flap endonuclease 1 OS=An	yes	N/A	0.254	0.352	0.788	2e-63
A7RRJ0	377	Flap endonuclease 1 OS=Ne	N/A	N/A	0.254	0.358	0.732	3e-61
D3TQJ5	382	Flap endonuclease 1 OS=Gl	N/A	N/A	0.254	0.353	0.753	4e-59
B4KNM1	388	Flap endonuclease 1 OS=Dr	N/A	N/A	0.254	0.347	0.753	1e-58
B4J6M4	388	Flap endonuclease 1 OS=Dr	N/A	N/A	0.254	0.347	0.746	1e-58
B5DUR8	386	Flap endonuclease 1 OS=Dr	yes	N/A	0.254	0.349	0.739	3e-58
B1H158	382	Flap endonuclease 1 OS=Xe	yes	N/A	0.254	0.353	0.704	3e-58
B4MR84	388	Flap endonuclease 1 OS=Dr	N/A	N/A	0.254	0.347	0.746	4e-58
B4GIM3	386	Flap endonuclease 1 OS=Dr	N/A	N/A	0.254	0.349	0.739	4e-58

>sp|Q178M1|FEN1_AEDAE Flap endonuclease 1 OS=Aedes aegypti GN=Fen1 PE=3 SV=1

 Score =  249 bits (635), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 111/142 (78%), Positives = 131/142 (92%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           APCEAEAQCAA+VK GKVYATATEDMDALTFGSNILLRH+TFSEARK+PVQEF+ +K+L+
Sbjct: 155 APCEAEAQCAALVKGGKVYATATEDMDALTFGSNILLRHLTFSEARKMPVQEFNYDKILQ 214

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
           G+EL+ +EFIDLCILLGCDYCDSIRGIGPK+A+ELI +HR+IEKILEN+DTKKY VPE W
Sbjct: 215 GLELTRDEFIDLCILLGCDYCDSIRGIGPKKAVELINKHRTIEKILENLDTKKYVVPENW 274

Query: 181 LYKEARELFRHPEVADPETIEF 202
            Y++AR LF+ PEVA+PE +E 
Sbjct: 275 NYQQARVLFKEPEVANPEEVEL 296

Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structurs that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in repairing mitochondrial DNA.
Aedes aegypti (taxid: 7159)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -

>sp|Q7Q323|FEN1_ANOGA Flap endonuclease 1 OS=Anopheles gambiae GN=Fen1 PE=3 SV=2

 Score =  244 bits (622), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 112/142 (78%), Positives = 130/142 (91%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           APCEAEAQCAA+V+AGKVYATATEDMDALTFGSNILLRH+TFSEARK+PVQEF  EKVL+
Sbjct: 155 APCEAEAQCAALVRAGKVYATATEDMDALTFGSNILLRHLTFSEARKMPVQEFAYEKVLK 214

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
           G EL+ +EFIDLCILLGCDYCD+IRGIGPK+AIELI +HRSIEKILE++D +KY VPEGW
Sbjct: 215 GFELTQDEFIDLCILLGCDYCDTIRGIGPKKAIELINKHRSIEKILEHLDRQKYIVPEGW 274

Query: 181 LYKEARELFRHPEVADPETIEF 202
            Y++AR+LF+ PEV D +TIE 
Sbjct: 275 NYEQARKLFKEPEVQDADTIEL 296

Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structurs that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in repairing mitochondrial DNA.

Anopheles gambiae (taxid: 7165)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|A7RRJ0|FEN1_NEMVE Flap endonuclease 1 OS=Nematostella vectensis GN=FEN1 PE=3 SV=1

 Score =  236 bits (603), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 104/142 (73%), Positives = 127/142 (89%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           APCEAEAQCAA+VK+GKVYAT TEDMDALTFG+ ++LRH+TFSEA+K+P++EFHL+ VL 
Sbjct: 155 APCEAEAQCAALVKSGKVYATGTEDMDALTFGTTVMLRHLTFSEAKKMPIKEFHLQNVLS 214

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
              LS +EFIDLCILLGCDYCDSI+GIGPKR+++LI++HRSI+KILENIDT K+  PE W
Sbjct: 215 EAGLSQDEFIDLCILLGCDYCDSIKGIGPKRSVDLIRQHRSIDKILENIDTSKHPPPENW 274

Query: 181 LYKEARELFRHPEVADPETIEF 202
           LYKEARELF++PEV +PE IE 
Sbjct: 275 LYKEARELFKNPEVRNPEEIEL 296

Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structurs that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in repairing mitochondrial DNA.

Nematostella vectensis (taxid: 45351)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|D3TQJ5|FEN1_GLOMM Flap endonuclease 1 OS=Glossina morsitans morsitans GN=Fen1 PE=2 SV=1

 Score =  229 bits (584), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 107/142 (75%), Positives = 121/142 (85%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           APCEAEAQCAA+VKAGKVYATATEDMDALTFGS ILLRH+TFSEARK+PV+EF   KVL+
Sbjct: 155 APCEAEAQCAALVKAGKVYATATEDMDALTFGSGILLRHLTFSEARKMPVKEFSYAKVLD 214

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
           G  L+ +EFIDLCILLGCDYCD IRGIGPKRA EL+  ++ IE ILE ID KKYTVPE W
Sbjct: 215 GFGLTSQEFIDLCILLGCDYCDGIRGIGPKRATELMNSYKDIETILEKIDRKKYTVPEDW 274

Query: 181 LYKEARELFRHPEVADPETIEF 202
            Y+ ARELF +PEVADP ++E 
Sbjct: 275 NYQIARELFVNPEVADPSSLEL 296

Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structurs that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in repairing mitochondrial DNA.

Glossina morsitans morsitans (taxid: 37546)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|B4KNM1|FEN1_DROMO Flap endonuclease 1 OS=Drosophila mojavensis GN=Fen1 PE=3 SV=1

 Score =  228 bits (581), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 107/142 (75%), Positives = 123/142 (86%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           APCEAEAQCAA+VKAGKVYATATEDMDALTFGS  LLR++T+SEARK+PV+EF  +KVL+
Sbjct: 155 APCEAEAQCAALVKAGKVYATATEDMDALTFGSCKLLRYLTYSEARKMPVKEFSYDKVLQ 214

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
           G+EL+ +EFIDLCIL+GCDYCDSI+GIGPKRAIELIK +R IE ILENIDT KY VPE W
Sbjct: 215 GLELTSKEFIDLCILMGCDYCDSIKGIGPKRAIELIKTYRDIETILENIDTSKYIVPENW 274

Query: 181 LYKEARELFRHPEVADPETIEF 202
            Y+ ARELF  PEV D  TI+ 
Sbjct: 275 NYQRARELFVEPEVTDASTIDL 296

Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structurs that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in repairing mitochondrial DNA.

Drosophila mojavensis (taxid: 7230)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|B4J6M4|FEN1_DROGR Flap endonuclease 1 OS=Drosophila grimshawi GN=Fen1 PE=3 SV=1

 Score =  227 bits (579), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 106/142 (74%), Positives = 123/142 (86%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           APCEAEAQCAA+VKAGKVYATATEDMDALTFGS  LLR++T+SEARK+PV+EF  +KVL+
Sbjct: 155 APCEAEAQCAALVKAGKVYATATEDMDALTFGSCKLLRYLTYSEARKMPVKEFSYDKVLQ 214

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
           G+EL+ +EFIDLCIL+GCDYC+SIRG+GPKRAIELIK +R IE ILENIDT KY VPE W
Sbjct: 215 GLELTSKEFIDLCILMGCDYCESIRGVGPKRAIELIKSYRDIETILENIDTNKYAVPENW 274

Query: 181 LYKEARELFRHPEVADPETIEF 202
            YK ARELF  P+V D  TI+ 
Sbjct: 275 NYKRARELFIEPDVTDASTIDL 296

Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structurs that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in repairing mitochondrial DNA.

Drosophila grimshawi (taxid: 7222)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|B5DUR8|FEN1_DROPS Flap endonuclease 1 OS=Drosophila pseudoobscura pseudoobscura GN=Fen1 PE=3 SV=1

 Score =  226 bits (577), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 105/142 (73%), Positives = 123/142 (86%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           APCEAEAQCAA+VKAGKVYATATEDMDALTFGS  LLR++T+SEARK+PV+EF  +K+LE
Sbjct: 155 APCEAEAQCAALVKAGKVYATATEDMDALTFGSTKLLRYLTYSEARKMPVKEFSYDKLLE 214

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
           G+E+++ EFIDLCILLGCDYC+SI+GIGPKRAIELI  +R IE IL+N+DT KYTVPE W
Sbjct: 215 GLEVNNREFIDLCILLGCDYCESIKGIGPKRAIELINNYRDIETILDNLDTSKYTVPENW 274

Query: 181 LYKEARELFRHPEVADPETIEF 202
            YK ARELF  PEVAD   I+ 
Sbjct: 275 NYKVARELFIEPEVADASAIDL 296

Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structurs that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in repairing mitochondrial DNA.

Drosophila pseudoobscura pseudoobscura (taxid: 46245)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|B1H158|FEN1_XENTR Flap endonuclease 1 OS=Xenopus tropicalis GN=fen1 PE=2 SV=1

 Score =  226 bits (577), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 100/142 (70%), Positives = 125/142 (88%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           APCEAEA CAA+VKAGKVYA ATEDMDALTFG+ +LLRH+T SEA+KLP+QEFHL +V++
Sbjct: 155 APCEAEATCAALVKAGKVYAAATEDMDALTFGTPVLLRHLTASEAKKLPIQEFHLNRVMQ 214

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
            M +SHE+F+DLCILLG DYC++IRGIGPKRAI+LI++H+SIE+I++NID KKY +PE W
Sbjct: 215 DMGVSHEQFVDLCILLGSDYCETIRGIGPKRAIDLIRQHKSIEEIVDNIDLKKYPIPENW 274

Query: 181 LYKEARELFRHPEVADPETIEF 202
           L+KEAR+LF  PEV D E+ E 
Sbjct: 275 LHKEARQLFLEPEVVDTESTEL 296

Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structurs that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in repairing mitochondrial DNA.

Xenopus tropicalis (taxid: 8364)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|B4MR84|FEN1_DROWI Flap endonuclease 1 OS=Drosophila willistoni GN=Fen1 PE=3 SV=1

 Score =  226 bits (576), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 106/142 (74%), Positives = 123/142 (86%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           APCEAEAQCAA+VKAGKVYATATEDMDALTFGS+ LLR++T+SEARK+PV+EF  EK+L+
Sbjct: 155 APCEAEAQCAALVKAGKVYATATEDMDALTFGSSKLLRYLTYSEARKMPVKEFTYEKLLQ 214

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
           G+EL+  EFIDLCILLGCDYC+SI+GIGPKRAIELI  +R IE IL+N+DT KYTVPE W
Sbjct: 215 GLELNQREFIDLCILLGCDYCESIKGIGPKRAIELINSYRDIETILDNLDTSKYTVPENW 274

Query: 181 LYKEARELFRHPEVADPETIEF 202
            YK ARELF  PEVAD   I+ 
Sbjct: 275 NYKVARELFIEPEVADASAIDL 296

Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structurs that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in repairing mitochondrial DNA.

Drosophila willistoni (taxid: 7260)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|B4GIM3|FEN1_DROPE Flap endonuclease 1 OS=Drosophila persimilis GN=Fen1 PE=3 SV=1

 Score =  226 bits (576), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 105/142 (73%), Positives = 123/142 (86%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           APCEAEAQCAA+VKAGKVYATATEDMDALTFGS  LLR++T+SEARK+PV+EF  +K+LE
Sbjct: 155 APCEAEAQCAALVKAGKVYATATEDMDALTFGSTKLLRYLTYSEARKMPVKEFSYDKLLE 214

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
           G+E+++ EFIDLCILLGCDYC+SI+GIGPKRAIELI  +R IE IL+N+DT KYTVPE W
Sbjct: 215 GLEVNNREFIDLCILLGCDYCESIKGIGPKRAIELINNYRDIETILDNLDTSKYTVPENW 274

Query: 181 LYKEARELFRHPEVADPETIEF 202
            YK ARELF  PEVAD   I+ 
Sbjct: 275 NYKVARELFIEPEVADASAIDL 296

Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structurs that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in repairing mitochondrial DNA.

Drosophila persimilis (taxid: 7234)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

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	531
157169412	380	flap endonuclease-1 [Aedes aegypti] gi|1	0.254	0.355	0.781	4e-63
110766831	379	PREDICTED: flap endonuclease 1 [Apis mel	0.254	0.356	0.781	6e-62
58390636	383	AGAP011448-PA [Anopheles gambiae str. PE	0.254	0.352	0.788	1e-61
380015033	383	PREDICTED: flap endonuclease 1-like [Api	0.254	0.352	0.774	1e-61
193659550	380	PREDICTED: flap endonuclease 1 [Acyrthos	0.256	0.357	0.762	3e-61
312385968	385	hypothetical protein AND_00127 [Anophele	0.254	0.350	0.781	4e-61
350416440	381	PREDICTED: flap endonuclease 1-like [Bom	0.254	0.354	0.753	1e-59
156398094	377	predicted protein [Nematostella vectensi	0.254	0.358	0.732	2e-59
242014497	380	Flap endonuclease 1-B, putative [Pedicul	0.254	0.355	0.746	2e-59
340717150	381	PREDICTED: LOW QUALITY PROTEIN: flap end	0.254	0.354	0.760	2e-59

>gi|157169412|ref|XP_001651504.1| flap endonuclease-1 [Aedes aegypti] gi|122094730|sp|Q178M1.1|FEN1_AEDAE RecName: Full=Flap endonuclease 1; Short=FEN-1; AltName: Full=Flap structure-specific endonuclease 1 gi|108878396|gb|EAT42621.1| AAEL005870-PA [Aedes aegypti]

 Score =  249 bits (635), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 111/142 (78%), Positives = 131/142 (92%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           APCEAEAQCAA+VK GKVYATATEDMDALTFGSNILLRH+TFSEARK+PVQEF+ +K+L+
Sbjct: 155 APCEAEAQCAALVKGGKVYATATEDMDALTFGSNILLRHLTFSEARKMPVQEFNYDKILQ 214

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
           G+EL+ +EFIDLCILLGCDYCDSIRGIGPK+A+ELI +HR+IEKILEN+DTKKY VPE W
Sbjct: 215 GLELTRDEFIDLCILLGCDYCDSIRGIGPKKAVELINKHRTIEKILENLDTKKYVVPENW 274

Query: 181 LYKEARELFRHPEVADPETIEF 202
            Y++AR LF+ PEVA+PE +E 
Sbjct: 275 NYQQARVLFKEPEVANPEEVEL 296

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|110766831|ref|XP_395769.3| PREDICTED: flap endonuclease 1 [Apis mellifera]

 Score =  244 bits (624), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 111/142 (78%), Positives = 130/142 (91%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           APCEAEAQCAAMVKAGKV+ATATEDMDALTFG NILLR +TFSEARK+PVQEFH +KVLE
Sbjct: 155 APCEAEAQCAAMVKAGKVFATATEDMDALTFGCNILLRRLTFSEARKMPVQEFHQDKVLE 214

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
           G+ELSH+EFIDLCI+LGCDY +SI+G+GPKRAIELIK HR++EKI+EN+DTKK+ +PE W
Sbjct: 215 GLELSHDEFIDLCIMLGCDYTNSIKGVGPKRAIELIKTHRTLEKIIENLDTKKFPIPEDW 274

Query: 181 LYKEARELFRHPEVADPETIEF 202
            YK+AR LF+ PEV DPETI+ 
Sbjct: 275 NYKQARLLFQEPEVTDPETIDL 296

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|58390636|ref|XP_317855.2| AGAP011448-PA [Anopheles gambiae str. PEST] gi|74802123|sp|Q7Q323.2|FEN1_ANOGA RecName: Full=Flap endonuclease 1; Short=FEN-1; AltName: Full=Flap structure-specific endonuclease 1 gi|55237026|gb|EAA13029.2| AGAP011448-PA [Anopheles gambiae str. PEST]

 Score =  244 bits (622), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 112/142 (78%), Positives = 130/142 (91%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           APCEAEAQCAA+V+AGKVYATATEDMDALTFGSNILLRH+TFSEARK+PVQEF  EKVL+
Sbjct: 155 APCEAEAQCAALVRAGKVYATATEDMDALTFGSNILLRHLTFSEARKMPVQEFAYEKVLK 214

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
           G EL+ +EFIDLCILLGCDYCD+IRGIGPK+AIELI +HRSIEKILE++D +KY VPEGW
Sbjct: 215 GFELTQDEFIDLCILLGCDYCDTIRGIGPKKAIELINKHRSIEKILEHLDRQKYIVPEGW 274

Query: 181 LYKEARELFRHPEVADPETIEF 202
            Y++AR+LF+ PEV D +TIE 
Sbjct: 275 NYEQARKLFKEPEVQDADTIEL 296

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380015033|ref|XP_003691516.1| PREDICTED: flap endonuclease 1-like [Apis florea]

 Score =  243 bits (621), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 110/142 (77%), Positives = 130/142 (91%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           APCEAEAQCAAMVKAGKV+ATATEDMDALTFG NILLR +TFSEARK+PVQEFH +KVLE
Sbjct: 155 APCEAEAQCAAMVKAGKVFATATEDMDALTFGCNILLRRLTFSEARKMPVQEFHQDKVLE 214

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
           G+ELSH+EFIDLCI+LGCDY +SI+G+GPKRAIELIK HR++EKI+EN+DTKK+ +PE W
Sbjct: 215 GLELSHDEFIDLCIMLGCDYTNSIKGVGPKRAIELIKTHRTLEKIVENLDTKKFPIPEDW 274

Query: 181 LYKEARELFRHPEVADPETIEF 202
            YK+AR LF+ PE+ DPETI+ 
Sbjct: 275 NYKQARLLFQKPEITDPETIDL 296

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193659550|ref|XP_001944971.1| PREDICTED: flap endonuclease 1 [Acyrthosiphon pisum]

 Score =  242 bits (618), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 109/143 (76%), Positives = 129/143 (90%)

Query: 60  KAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVL 119
           +APCEAEAQCAAMVKAGKVYATATEDMDALTFGS +LLRHMTFSEARK+P+QEF L+ VL
Sbjct: 154 EAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSPVLLRHMTFSEARKMPIQEFQLDSVL 213

Query: 120 EGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEG 179
           E ME+S +EFIDLCILLGCDYC+SI+G+GPKRAIEL+++++S+E I+EN+DTKKY VPE 
Sbjct: 214 ETMEMSRDEFIDLCILLGCDYCNSIKGVGPKRAIELMRQYKSLENIIENLDTKKYQVPED 273

Query: 180 WLYKEARELFRHPEVADPETIEF 202
           W YKEAR LF  PE+ DPETI+ 
Sbjct: 274 WPYKEARRLFIEPEITDPETIDL 296

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312385968|gb|EFR30352.1| hypothetical protein AND_00127 [Anopheles darlingi]

 Score =  242 bits (617), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 111/142 (78%), Positives = 127/142 (89%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           APCEAEAQCAA+VKAGKVYATATEDMDALTFGSNILLRH+TFSEARK+PVQEFH EKVL+
Sbjct: 155 APCEAEAQCAALVKAGKVYATATEDMDALTFGSNILLRHLTFSEARKMPVQEFHYEKVLK 214

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
           G EL+ +EFID+CILLGCDYCD+IRGIGPK+AIELI +HRSIE+ILE++D  KY VPE W
Sbjct: 215 GFELTADEFIDMCILLGCDYCDTIRGIGPKKAIELINKHRSIEQILEHLDKSKYVVPEDW 274

Query: 181 LYKEARELFRHPEVADPETIEF 202
            Y++AR LF+ PEVAD   IE 
Sbjct: 275 NYQQARRLFKEPEVADAAEIEL 296

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350416440|ref|XP_003490949.1| PREDICTED: flap endonuclease 1-like [Bombus impatiens]

 Score =  237 bits (605), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 107/142 (75%), Positives = 127/142 (89%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           APCEAEAQCAA+VKAGKV+ATATEDMDALTFG N+LLR +TFSEARK+PVQEFH +KVL+
Sbjct: 155 APCEAEAQCAALVKAGKVFATATEDMDALTFGCNVLLRRLTFSEARKMPVQEFHFDKVLK 214

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
            + L+H+EFIDLCI+LGCDY  SI+G+GPKRAIELIK HRS+EKI+EN+DTKK+ +PE W
Sbjct: 215 DLGLNHDEFIDLCIMLGCDYTSSIKGVGPKRAIELIKTHRSLEKIVENLDTKKFPIPEDW 274

Query: 181 LYKEARELFRHPEVADPETIEF 202
            YKEAR LF+ PEV DPETI+ 
Sbjct: 275 NYKEARLLFQEPEVTDPETIDL 296

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156398094|ref|XP_001638024.1| predicted protein [Nematostella vectensis] gi|317374916|sp|A7RRJ0.1|FEN1_NEMVE RecName: Full=Flap endonuclease 1; Short=FEN-1; AltName: Full=Flap structure-specific endonuclease 1 gi|156225141|gb|EDO45961.1| predicted protein [Nematostella vectensis]

 Score =  236 bits (603), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 104/142 (73%), Positives = 127/142 (89%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           APCEAEAQCAA+VK+GKVYAT TEDMDALTFG+ ++LRH+TFSEA+K+P++EFHL+ VL 
Sbjct: 155 APCEAEAQCAALVKSGKVYATGTEDMDALTFGTTVMLRHLTFSEAKKMPIKEFHLQNVLS 214

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
              LS +EFIDLCILLGCDYCDSI+GIGPKR+++LI++HRSI+KILENIDT K+  PE W
Sbjct: 215 EAGLSQDEFIDLCILLGCDYCDSIKGIGPKRSVDLIRQHRSIDKILENIDTSKHPPPENW 274

Query: 181 LYKEARELFRHPEVADPETIEF 202
           LYKEARELF++PEV +PE IE 
Sbjct: 275 LYKEARELFKNPEVRNPEEIEL 296

Source: Nematostella vectensis

Species: Nematostella vectensis

Genus: Nematostella

Family: Edwardsiidae

Order: Actiniaria

Class: Anthozoa

Phylum: Cnidaria

Superkingdom: Eukaryota

>gi|242014497|ref|XP_002427926.1| Flap endonuclease 1-B, putative [Pediculus humanus corporis] gi|212512410|gb|EEB15188.1| Flap endonuclease 1-B, putative [Pediculus humanus corporis]

 Score =  236 bits (602), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 106/142 (74%), Positives = 128/142 (90%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           APCEAEAQCAA+VKAGKVYATATEDMDALTFGSNI+LRH+TFSEARK+PVQE +L+KVL 
Sbjct: 155 APCEAEAQCAALVKAGKVYATATEDMDALTFGSNIILRHLTFSEARKMPVQEIYLDKVLA 214

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
            +E++  EFIDLCILLGCDYCDSI+GIGPKRAIELIK+H+S+EKILEN+D+ KY VPE W
Sbjct: 215 ELEMTQNEFIDLCILLGCDYCDSIKGIGPKRAIELIKKHKSLEKILENLDSGKYVVPEDW 274

Query: 181 LYKEARELFRHPEVADPETIEF 202
           +++EAR+LF +P+V D   +E 
Sbjct: 275 IFQEARKLFINPDVCDASNVEL 296

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340717150|ref|XP_003397050.1| PREDICTED: LOW QUALITY PROTEIN: flap endonuclease 1-like [Bombus terrestris]

 Score =  236 bits (602), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 108/142 (76%), Positives = 125/142 (88%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           APCEAEAQCAA+VKAGKV+ATATEDMDALTFG NILLR +TFSEARK+PVQEFH +KVLE
Sbjct: 155 APCEAEAQCAALVKAGKVFATATEDMDALTFGCNILLRRLTFSEARKMPVQEFHFDKVLE 214

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
            + L+H EFIDLCI+LGCDY  SI+G+GPKRAIELIK H S+EKI+EN+DTKK+++PE W
Sbjct: 215 DLGLNHNEFIDLCIMLGCDYTSSIKGVGPKRAIELIKTHGSLEKIVENLDTKKFSIPEDW 274

Query: 181 LYKEARELFRHPEVADPETIEF 202
            YKEAR LF+ PEV DPETI  
Sbjct: 275 NYKEARLLFQEPEVTDPETINM 296

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	531
ZFIN|ZDB-GENE-031112-11	380	fen1 "flap structure-specific	0.331	0.463	0.587	2.5e-73
FB|FBgn0025832	385	Fen1 "Flap endonuclease 1" [Dr	0.265	0.366	0.730	6e-72
UNIPROTKB|P70054	382	fen1-b "Flap endonuclease 1-B"	0.265	0.369	0.680	1.6e-71
UNIPROTKB|P70040	382	fen1-a "Flap endonuclease 1-A"	0.329	0.458	0.568	5.3e-71
UNIPROTKB|Q5ZLN4	381	FEN1 "Flap endonuclease 1" [Ga	0.331	0.461	0.570	6.8e-69
RGD|621821	380	Fen1 "flap structure-specific	0.333	0.465	0.556	1.1e-68
UNIPROTKB|J9PB88	380	FEN1 "Flap endonuclease 1" [Ca	0.333	0.465	0.556	1.8e-68
UNIPROTKB|P39748	380	FEN1 "Flap endonuclease 1" [Ho	0.333	0.465	0.556	2.3e-68
UNIPROTKB|Q58DH8	380	FEN1 "Flap endonuclease 1" [Bo	0.265	0.371	0.666	6e-68
UNIPROTKB|F1RKS3	380	FEN1 "Flap endonuclease 1" [Su	0.265	0.371	0.673	6e-68

ZFIN|ZDB-GENE-031112-11 fen1 "flap structure-specific endonuclease 1" [Danio rerio (taxid:7955)]

 Score = 559 (201.8 bits), Expect = 2.5e-73, Sum P(2) = 2.5e-73
 Identities = 104/177 (58%), Positives = 134/177 (75%)

Query:    25 EDRIRNGAKKLLKARSSTTQGRLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATE 84
             ++ I   +K+L+K      +       ++      +APCEAEA CAA+VKAGKVYATATE
Sbjct:   120 QENIDKFSKRLVKVTKQHNE-ECKKLLSLMGVPYIEAPCEAEASCAALVKAGKVYATATE 178

Query:    85 DMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDSI 144
             DMD LTFG+ +LLRH+T SEA+KLP+QEFH  ++L+ MEL+H++FIDLCILLGCDYC +I
Sbjct:   179 DMDGLTFGTTVLLRHLTASEAKKLPIQEFHFSRILQDMELTHQQFIDLCILLGCDYCGTI 238

Query:   145 RGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIE 201
             +GIGPKRAI+LIK+H SIE+ILENID  K+  PE WLYKEAR LF  PEV D  +++
Sbjct:   239 KGIGPKRAIDLIKQHGSIEEILENIDPNKHPAPEDWLYKEARGLFLEPEVVDGTSVD 295

GO:0016788 "hydrolase activity, acting on ester bonds" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0060041 "retina development in camera-type eye" evidence=IMP

GO:0046872 "metal ion binding" evidence=IEA

GO:0004527 "exonuclease activity" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

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

GO:0017108 "5'-flap endonuclease activity" evidence=IEA

GO:0043137 "DNA replication, removal of RNA primer" evidence=IEA

GO:0006284 "base-excision repair" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

FB|FBgn0025832 Fen1 "Flap endonuclease 1" [Drosophila melanogaster (taxid:7227)]

 Score = 556 (200.8 bits), Expect = 6.0e-72, Sum P(2) = 6.0e-72
 Identities = 103/141 (73%), Positives = 124/141 (87%)

Query:    61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
             APCEAEAQCAA+VKAGKVYATATEDMDALTFGS  LLR++T+SEARK+PV+EF  +K+LE
Sbjct:   155 APCEAEAQCAALVKAGKVYATATEDMDALTFGSTKLLRYLTYSEARKMPVKEFSYDKLLE 214

Query:   121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
             G+ +++ EFIDLCILLGCDYC+SI+GIGPKRAIELI  +R IE IL+N+D+ KYTVPE W
Sbjct:   215 GLAINNREFIDLCILLGCDYCESIKGIGPKRAIELINTYRDIETILDNLDSSKYTVPENW 274

Query:   181 LYKEARELFRHPEVADPETIE 201
              YK ARELF  PEVAD ++I+
Sbjct:   275 NYKVARELFIEPEVADADSID 295

GO:0005634 "nucleus" evidence=IC

GO:0048256 "flap endonuclease activity" evidence=ISS

GO:0006281 "DNA repair" evidence=ISS

GO:0004519 "endonuclease activity" evidence=ISS

GO:0003677 "DNA binding" evidence=IEA

GO:0022008 "neurogenesis" evidence=IMP

UNIPROTKB|P70054 fen1-b "Flap endonuclease 1-B" [Xenopus laevis (taxid:8355)]

 Score = 545 (196.9 bits), Expect = 1.6e-71, Sum P(2) = 1.6e-71
 Identities = 96/141 (68%), Positives = 123/141 (87%)

Query:    61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
             APCEAEA CAA+VKAGKVYA ATEDMDALTFG+ +LLRH+T SEA+KLP+QEFHL +V +
Sbjct:   155 APCEAEATCAALVKAGKVYAAATEDMDALTFGTPVLLRHLTASEAKKLPIQEFHLNRVFQ 214

Query:   121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
              + ++HE+F+DLCILLG DYC++IRGIGPKRAI+LI++H++IE+I++NID KKY +PE W
Sbjct:   215 DIGINHEQFVDLCILLGSDYCETIRGIGPKRAIDLIRQHKTIEEIIDNIDLKKYPIPENW 274

Query:   181 LYKEARELFRHPEVADPETIE 201
             L+KEAR+LF  PEV D +  E
Sbjct:   275 LHKEARQLFLEPEVIDADITE 295

GO:0005634 "nucleus" evidence=IDA

GO:0006260 "DNA replication" evidence=IPI

GO:0006284 "base-excision repair" evidence=ISS

GO:0017108 "5'-flap endonuclease activity" evidence=IDA

UNIPROTKB|P70040 fen1-a "Flap endonuclease 1-A" [Xenopus laevis (taxid:8355)]

 Score = 543 (196.2 bits), Expect = 5.3e-71, Sum P(2) = 5.3e-71
 Identities = 100/176 (56%), Positives = 133/176 (75%)

Query:    26 DRIRNGAKKLLKARSSTTQGRLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATED 85
             + I    K+L+K      +       T+       APCEAEA CAA+VKAGKVYA ATED
Sbjct:   121 ENIEKFTKRLVKVTKQHNE-ECKKLLTLMGIPYVDAPCEAEATCAALVKAGKVYAAATED 179

Query:    86 MDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDSIR 145
             MDALTFG+ +LLRH+T SEA+KLP+QEFHL +V++ + ++HE+F+DLCILLG DYC++IR
Sbjct:   180 MDALTFGTPVLLRHLTASEAKKLPIQEFHLNRVIQDIGITHEQFVDLCILLGSDYCETIR 239

Query:   146 GIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIE 201
             GIGPKRAI+LI++H++I++I++NID KKY VPE WL+KEA+ LF  PEV D +  E
Sbjct:   240 GIGPKRAIDLIRQHKTIDEIIDNIDLKKYPVPENWLHKEAKHLFLEPEVVDTDITE 295

GO:0005634 "nucleus" evidence=IDA

GO:0006260 "DNA replication" evidence=IPI

GO:0006284 "base-excision repair" evidence=IDA

GO:0017108 "5'-flap endonuclease activity" evidence=IDA

UNIPROTKB|Q5ZLN4 FEN1 "Flap endonuclease 1" [Gallus gallus (taxid:9031)]

 Score = 543 (196.2 bits), Expect = 6.8e-69, Sum P(2) = 6.8e-69
 Identities = 101/177 (57%), Positives = 135/177 (76%)

Query:    25 EDRIRNGAKKLLKARSSTTQGRLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATE 84
             E  I   +K+L+K     T         +      +AP EAEA CA +VKAGKVYA ATE
Sbjct:   120 EANIEKFSKRLVKVTQQHTD-ECKKLLMLMGIPYVEAPGEAEASCATLVKAGKVYAAATE 178

Query:    85 DMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDSI 144
             DMD LTFGS +L+RH+T SEA+KLP+QEFHL +VL+ + L+ E+F+DLCILLGCDYC+SI
Sbjct:   179 DMDCLTFGSPVLMRHLTASEAKKLPIQEFHLNRVLQDLGLTWEQFVDLCILLGCDYCESI 238

Query:   145 RGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIE 201
             RGIGPKRA+ELIK+H++IE+I+++IDTKKY +PE WL+KEA++LF  P+V +P+ +E
Sbjct:   239 RGIGPKRAVELIKQHKTIEEIIQHIDTKKYPLPENWLHKEAQKLFLEPDVINPDDVE 295

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006284 "base-excision repair" evidence=IEA

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

GO:0017108 "5'-flap endonuclease activity" evidence=IEA

GO:0043137 "DNA replication, removal of RNA primer" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0030145 "manganese ion binding" evidence=IEA

RGD|621821 Fen1 "flap structure-specific endonuclease 1" [Rattus norvegicus (taxid:10116)]

 Score = 535 (193.4 bits), Expect = 1.1e-68, Sum P(2) = 1.1e-68
 Identities = 99/178 (55%), Positives = 131/178 (73%)

Query:    24 AEDRIRNGAKKLLKARSSTTQGRLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATAT 83
             AE+ +    K+L+K              ++       AP EAEA CAA+ KAGKVYA AT
Sbjct:   119 AEEEVEKFTKRLVKVTKQHND-ECKHLLSLMGIPYLDAPSEAEASCAALAKAGKVYAAAT 177

Query:    84 EDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDS 143
             EDMD LTFGS +L+RH+T SEA+KLP+QEFHL +VL+ + L+ E+F+DLCILLG DYC+S
Sbjct:   178 EDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRVLQELGLNQEQFVDLCILLGSDYCES 237

Query:   144 IRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIE 201
             +RGIGPKRA++LI++H+SIE+I+  +D  KY VPE WL+KEAR+LF  PEV DPE++E
Sbjct:   238 VRGIGPKRAVDLIQKHKSIEEIVRRLDPSKYPVPENWLHKEARQLFLEPEVLDPESVE 295

GO:0000287 "magnesium ion binding" evidence=IEA;ISO

GO:0003677 "DNA binding" evidence=IEA;ISO

GO:0004523 "ribonuclease H activity" evidence=IEA;ISO

GO:0004527 "exonuclease activity" evidence=ISO;NAS

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0006260 "DNA replication" evidence=ISO

GO:0006281 "DNA repair" evidence=ISO

GO:0006284 "base-excision repair" evidence=IEA

GO:0007613 "memory" evidence=IMP

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

GO:0017108 "5'-flap endonuclease activity" evidence=IEA;ISO

GO:0030145 "manganese ion binding" evidence=IEA;ISO

GO:0043137 "DNA replication, removal of RNA primer" evidence=IEA;ISO

GO:0048256 "flap endonuclease activity" evidence=ISO

UNIPROTKB|J9PB88 FEN1 "Flap endonuclease 1" [Canis lupus familiaris (taxid:9615)]

 Score = 535 (193.4 bits), Expect = 1.8e-68, Sum P(2) = 1.8e-68
 Identities = 99/178 (55%), Positives = 132/178 (74%)

Query:    24 AEDRIRNGAKKLLKARSSTTQGRLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATAT 83
             AE+ +    K+L+K              ++       AP EAEA CAA+VKAGKVYA AT
Sbjct:   119 AEEEVEKFTKRLVKVTKQHND-ECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAAT 177

Query:    84 EDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDS 143
             EDMD LTFGS +L+RH+T SEA+KLP+QEFHL ++L+ + L+ E+F+DLCILLG DYC+S
Sbjct:   178 EDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLNRILQELGLNQEQFVDLCILLGSDYCES 237

Query:   144 IRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIE 201
             IRGIGPKRA++LI++H+SIE+I+  +D  KY VPE WL+KEA++LF  PEV DPE++E
Sbjct:   238 IRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAQQLFLEPEVLDPESVE 295

GO:0005739 "mitochondrion" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0043137 "DNA replication, removal of RNA primer" evidence=IEA

GO:0017108 "5'-flap endonuclease activity" evidence=IEA

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

GO:0006284 "base-excision repair" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

UNIPROTKB|P39748 FEN1 "Flap endonuclease 1" [Homo sapiens (taxid:9606)]

 Score = 532 (192.3 bits), Expect = 2.3e-68, Sum P(2) = 2.3e-68
 Identities = 99/178 (55%), Positives = 130/178 (73%)

Query:    24 AEDRIRNGAKKLLKARSSTTQGRLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATAT 83
             AE  +    K+L+K              ++       AP EAEA CAA+VKAGKVYA AT
Sbjct:   119 AEQEVEKFTKRLVKVTKQHND-ECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAAT 177

Query:    84 EDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDS 143
             EDMD LTFGS +L+RH+T SEA+KLP+QEFHL ++L+ + L+ E+F+DLCILLG DYC+S
Sbjct:   178 EDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCES 237

Query:   144 IRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIE 201
             IRGIGPKRA++LI++H+SIE+I+  +D  KY VPE WL+KEA +LF  PEV DPE++E
Sbjct:   238 IRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVE 295

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0007613 "memory" evidence=IEA

GO:0030145 "manganese ion binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0048015 "phosphatidylinositol-mediated signaling" evidence=NAS

GO:0006260 "DNA replication" evidence=NAS

GO:0006281 "DNA repair" evidence=NAS;TAS

GO:0017108 "5'-flap endonuclease activity" evidence=IDA;IMP

GO:0003677 "DNA binding" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

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

GO:0004523 "ribonuclease H activity" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0043137 "DNA replication, removal of RNA primer" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

GO:0004527 "exonuclease activity" evidence=TAS

GO:0008309 "double-stranded DNA specific exodeoxyribonuclease activity" evidence=TAS

GO:0003684 "damaged DNA binding" evidence=TAS

GO:0003690 "double-stranded DNA binding" evidence=TAS

GO:0004519 "endonuclease activity" evidence=TAS

GO:0006302 "double-strand break repair" evidence=TAS

GO:0009650 "UV protection" evidence=TAS

GO:0000084 "S phase of mitotic cell cycle" evidence=TAS

GO:0000278 "mitotic cell cycle" evidence=TAS

GO:0000722 "telomere maintenance via recombination" evidence=TAS

GO:0000723 "telomere maintenance" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006271 "DNA strand elongation involved in DNA replication" evidence=TAS

GO:0006284 "base-excision repair" evidence=TAS

GO:0032201 "telomere maintenance via semi-conservative replication" evidence=TAS

UNIPROTKB|Q58DH8 FEN1 "Flap endonuclease 1" [Bos taurus (taxid:9913)]

 Score = 531 (192.0 bits), Expect = 6.0e-68, Sum P(2) = 6.0e-68
 Identities = 94/141 (66%), Positives = 121/141 (85%)

Query:    61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
             AP EAEA CAA+VKAGKVYA ATEDMD LTFGS +L+RH+T SEA+KLP+QEFHL ++L+
Sbjct:   155 APSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQ 214

Query:   121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
              + L+ E+F+DLCILLG DYC+SIRGIGPKRA++LI++H+SIE+I+  +D  KY VPE W
Sbjct:   215 ELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENW 274

Query:   181 LYKEARELFRHPEVADPETIE 201
             L+KEA++LF  PEV DPE++E
Sbjct:   275 LHKEAQQLFLEPEVLDPESVE 295

GO:0005739 "mitochondrion" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0030145 "manganese ion binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0043137 "DNA replication, removal of RNA primer" evidence=IEA

GO:0017108 "5'-flap endonuclease activity" evidence=IEA

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

GO:0006284 "base-excision repair" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

UNIPROTKB|F1RKS3 FEN1 "Flap endonuclease 1" [Sus scrofa (taxid:9823)]

 Score = 531 (192.0 bits), Expect = 6.0e-68, Sum P(2) = 6.0e-68
 Identities = 95/141 (67%), Positives = 120/141 (85%)

Query:    61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
             AP EAEA CAA+VKAGKVYA ATEDMD LTFGS +L+RH+T SEA+KLP+QEFHL +VL+
Sbjct:   155 APSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRVLQ 214

Query:   121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
              + L+ E+F+DLCILLG DYC+SIRGIGPKRA++LI++H+SIE+I+  +D  KY VPE W
Sbjct:   215 ELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENW 274

Query:   181 LYKEARELFRHPEVADPETIE 201
             L+KEA++LF  PEV DPE +E
Sbjct:   275 LHKEAQQLFLEPEVLDPEAVE 295

GO:0005739 "mitochondrion" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0030145 "manganese ion binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0043137 "DNA replication, removal of RNA primer" evidence=IEA

GO:0017108 "5'-flap endonuclease activity" evidence=IEA

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

GO:0006284 "base-excision repair" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

---

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 EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	531
PTZ00217	393	PTZ00217, PTZ00217, flap endonuclease-1; Provision	8e-83
cd09867	261	cd09867, PIN_FEN1, PIN domain of Flap Endonuclease	4e-48
PTZ00217	393	PTZ00217, PTZ00217, flap endonuclease-1; Provision	1e-43
cd09907	70	cd09907, H3TH_FEN1-Euk, H3TH domain of Flap Endonu	4e-42
cd09907	70	cd09907, H3TH_FEN1-Euk, H3TH domain of Flap Endonu	2e-40
PRK03980	292	PRK03980, PRK03980, flap endonuclease-1; Provision	7e-40
TIGR03674	338	TIGR03674, fen_arch, flap structure-specific endon	5e-37
PTZ00217	393	PTZ00217, PTZ00217, flap endonuclease-1; Provision	5e-36
cd09901	73	cd09901, H3TH_FEN1-like, H3TH domains of Flap endo	7e-33
cd09867	261	cd09867, PIN_FEN1, PIN domain of Flap Endonuclease	1e-32
cd09901	73	cd09901, H3TH_FEN1-like, H3TH domains of Flap endo	4e-31
TIGR03674	338	TIGR03674, fen_arch, flap structure-specific endon	7e-31
pfam00752	100	pfam00752, XPG_N, XPG N-terminal domain	3e-26
COG0258	310	COG0258, Exo, 5'-3' exonuclease (including N-termi	4e-26
smart00485	99	smart00485, XPGN, Xeroderma pigmentosum G N-region	4e-26
cd09897	68	cd09897, H3TH_FEN1-XPG-like, H3TH domains of Flap	2e-25
cd09897	68	cd09897, H3TH_FEN1-XPG-like, H3TH domains of Flap	1e-24
PRK03980	292	PRK03980, PRK03980, flap endonuclease-1; Provision	3e-23
cd00128	209	cd00128, PIN_FEN1_EXO1-like, PIN domains of Flap E	2e-22
smart00484	73	smart00484, XPGI, Xeroderma pigmentosum G I-region	2e-22
cd09867	261	cd09867, PIN_FEN1, PIN domain of Flap Endonuclease	2e-19
cd09867	261	cd09867, PIN_FEN1, PIN domain of Flap Endonuclease	3e-19
cd00128	209	cd00128, PIN_FEN1_EXO1-like, PIN domains of Flap E	4e-19
PTZ00217	393	PTZ00217, PTZ00217, flap endonuclease-1; Provision	1e-18
PTZ00217	393	PTZ00217, PTZ00217, flap endonuclease-1; Provision	9e-18
cd09853	163	cd09853, PIN_StructSpec-5'-nucleases, PIN domains	1e-16
cd09868	249	cd09868, PIN_XPG, PIN domain of Xeroderma pigmento	4e-16
cd09903	65	cd09903, H3TH_FEN1-Arc, H3TH domain of Flap Endonu	1e-15
cd00080	71	cd00080, H3TH_StructSpec-5'-nucleases, H3TH domain	2e-15
cd00080	71	cd00080, H3TH_StructSpec-5'-nucleases, H3TH domain	6e-15
PRK03980	292	PRK03980, PRK03980, flap endonuclease-1; Provision	1e-14
COG0258	310	COG0258, Exo, 5'-3' exonuclease (including N-termi	2e-14
cd09903	65	cd09903, H3TH_FEN1-Arc, H3TH domain of Flap Endonu	3e-14
COG0258	310	COG0258, Exo, 5'-3' exonuclease (including N-termi	8e-14
cd09908	73	cd09908, H3TH_EXO1, H3TH domain of Exonuclease-1,	1e-13
TIGR00600	1034	TIGR00600, rad2, DNA excision repair protein (rad2	3e-13
pfam00867	46	pfam00867, XPG_I, XPG I-region	6e-13
TIGR03674	338	TIGR03674, fen_arch, flap structure-specific endon	7e-13
cd09908	73	cd09908, H3TH_EXO1, H3TH domain of Exonuclease-1,	8e-13
PRK03980	292	PRK03980, PRK03980, flap endonuclease-1; Provision	1e-11
PRK03980	292	PRK03980, PRK03980, flap endonuclease-1; Provision	1e-11
cd09900	52	cd09900, H3TH_XPG-like, H3TH domains of Flap endon	1e-11
cd09856	207	cd09856, PIN_FEN1-like, PIN domain of Flap Endonuc	2e-11
cd09900	52	cd09900, H3TH_XPG-like, H3TH domains of Flap endon	7e-11
TIGR03674	338	TIGR03674, fen_arch, flap structure-specific endon	1e-10
TIGR03674	338	TIGR03674, fen_arch, flap structure-specific endon	3e-10
TIGR00600	1034	TIGR00600, rad2, DNA excision repair protein (rad2	5e-09
smart00475	259	smart00475, 53EXOc, 5'-3' exonuclease	8e-09
cd09900	52	cd09900, H3TH_XPG-like, H3TH domains of Flap endon	2e-08
smart00279	36	smart00279, HhH2, Helix-hairpin-helix class 2 (Pol	2e-08
cd09898	73	cd09898, H3TH_53EXO, H3TH domain of the 5'-3' exon	2e-08
pfam01367	100	pfam01367, 5_3_exonuc, 5'-3' exonuclease, C-termin	2e-08
cd09898	73	cd09898, H3TH_53EXO, H3TH domain of the 5'-3' exon	4e-08
pfam01367	100	pfam01367, 5_3_exonuc, 5'-3' exonuclease, C-termin	4e-08
smart00279	36	smart00279, HhH2, Helix-hairpin-helix class 2 (Pol	8e-08
cd09904	97	cd09904, H3TH_XPG, H3TH domain of Xeroderma pigmen	8e-08
cd09904	97	cd09904, H3TH_XPG, H3TH domain of Xeroderma pigmen	1e-07
cd09868	249	cd09868, PIN_XPG, PIN domain of Xeroderma pigmento	3e-07
TIGR00593	887	TIGR00593, pola, DNA polymerase I	3e-07
smart00475	259	smart00475, 53EXOc, 5'-3' exonuclease	4e-07
cd09870	239	cd09870, PIN_YEN1, PIN domain of Yeast Endonucleas	1e-06
smart00279	36	smart00279, HhH2, Helix-hairpin-helix class 2 (Pol	3e-06
PRK05755	880	PRK05755, PRK05755, DNA polymerase I; Provisional	3e-06
TIGR00593	887	TIGR00593, pola, DNA polymerase I	1e-05
cd09853	163	cd09853, PIN_StructSpec-5'-nucleases, PIN domains	2e-05
PRK05755	880	PRK05755, PRK05755, DNA polymerase I; Provisional	3e-05
PRK14976	281	PRK14976, PRK14976, 5'-3' exonuclease; Provisional	3e-05
cd09856	207	cd09856, PIN_FEN1-like, PIN domain of Flap Endonuc	4e-05
cd09869	233	cd09869, PIN_GEN1, PIN domain of Gap Endonuclease	5e-05
cd09857	210	cd09857, PIN_EXO1, PIN domain of Exonuclease-1, a	7e-05
PRK14976	281	PRK14976, PRK14976, 5'-3' exonuclease; Provisional	1e-04
cd09869	233	cd09869, PIN_GEN1, PIN domain of Gap Endonuclease	1e-04
cd09852	120	cd09852, PIN_SF, PIN (PilT N terminus) domain: Sup	6e-04
PRK09482	256	PRK09482, PRK09482, flap endonuclease-like protein	0.002
PRK09482	256	PRK09482, PRK09482, flap endonuclease-like protein	0.004

>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional

 Score =  262 bits (672), Expect = 8e-83
 Identities = 93/143 (65%), Positives = 117/143 (81%)

Query: 60  KAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVL 119
           +APCEAEAQCA +VK GKVYA ATEDMDALTFG+ +LLR++ FSEA+K P+QE +L  VL
Sbjct: 156 EAPCEAEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTVL 215

Query: 120 EGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEG 179
           E + LS ++FIDLCIL GCDYCD+I+GIGPK A +LIK+++SIE+ILE++D  KY VPE 
Sbjct: 216 EELGLSMDQFIDLCILCGCDYCDTIKGIGPKTAYKLIKKYKSIEEILEHLDKTKYPVPEN 275

Query: 180 WLYKEARELFRHPEVADPETIEF 202
           + YKEARELF +PEV   E I+ 
Sbjct: 276 FDYKEARELFLNPEVTPAEEIDL 298

Length = 393

>gnl|CDD|189037 cd09867, PIN_FEN1, PIN domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs

 Score =  167 bits (425), Expect = 4e-48
 Identities = 73/147 (49%), Positives = 91/147 (61%), Gaps = 17/147 (11%)

Query: 304 ELVADVAPSSIR----ESRKICIDASMSLYQFLIAVRSE-GNQLMSVDGEPTSHLMGTFY 358
           +L+AD A   I       RKI IDAS +LYQFLIA+R   G  L +  GE TSHL G FY
Sbjct: 5   KLIADGAIKEIELKDLFGRKIAIDASNALYQFLIAIRQPDGTPLTNSAGEVTSHLSGLFY 64

Query: 359 RTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDG 418
           RTIRL+E+G+KP+YVFDGKPP LKSGEL KR E+RE+A++ L +A+E+G       D + 
Sbjct: 65  RTIRLLENGIKPVYVFDGKPPELKSGELEKRRERREEAEEKLEEAKEEG-------DAEE 117

Query: 419 LVKYLCGDK--NFAEDRIRNGAKKLLK 443
             KY    K        I    KKLL+
Sbjct: 118 ARKY---AKRTVRVTKEIVEECKKLLR 141

Flap endonuclease-1 (FEN1) is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes (long-patch base excision repair) in eukaryotes and archaea. Interaction between FEN1 and PCNA (Proliferating cell nuclear antigen) is an essential prerequisite to FEN1's DNA replication functionality and stimulates FEN1 nuclease activity by 10-50 fold. FEN1 belongs to the FEN1-EXO1-like family of structure-specific, 5' nucleases. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region (I domain) of variable length (approximately 45 residues in FEN1 PIN domains) and a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. Nucleases within this group also have a carboxylate-rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+/Mn2+). FEN1 has a C-terminal extension containing residues forming the consensus PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA. Length = 261

>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional

 Score =  159 bits (403), Expect = 1e-43
 Identities = 63/115 (54%), Positives = 82/115 (71%), Gaps = 11/115 (9%)

Query: 303 IELVADVAPSSIRES-------RKICIDASMSLYQFLIAVRSEGNQLMSV---DGEPTSH 352
            + +AD AP++I+E        R I IDASM+LYQFLIA+R   +Q  ++    GE TSH
Sbjct: 7   SKFLADKAPNAIKEQELKNYFGRVIAIDASMALYQFLIAIRD-DSQGGNLTNEAGEVTSH 65

Query: 353 LMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQG 407
           + G F RTIRL+E G+KP+YVFDGKPP LKSGEL KR E+RE+A++ L KA E+G
Sbjct: 66  ISGLFNRTIRLLEAGIKPVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEG 120

Length = 393

>gnl|CDD|188627 cd09907, H3TH_FEN1-Euk, H3TH domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease: Eukaryotic homologs

 Score =  144 bits (366), Expect = 4e-42
 Identities = 54/70 (77%), Positives = 62/70 (88%)

Query: 127 EEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAR 186
           E+FIDLCILLGCDYC+SI+GIGPK A++LIK+H+SIEKILENID  KY VPE W YKEAR
Sbjct: 1   EQFIDLCILLGCDYCESIKGIGPKTALKLIKKHKSIEKILENIDKSKYPVPEDWPYKEAR 60

Query: 187 ELFRHPEVAD 196
           ELF +PEV D
Sbjct: 61  ELFLNPEVTD 70

Members of this subgroup include the H3TH (helix-3-turn-helix) domains of eukaryotic Flap endonuclease-1 (FEN1), 5' nucleases. FEN1 is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes (long-patch base excision repair) in eukaryotes and archaea. Interaction between FEN1 and PCNA (Proliferating cell nuclear antigen) is an essential prerequisite to FEN1's DNA replication functionality and stimulates FEN1 nuclease activity by 10-50 fold. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this subfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Also, FEN1 has a C-terminal extension containing residues forming the consensus PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA. Length = 70

>gnl|CDD|188627 cd09907, H3TH_FEN1-Euk, H3TH domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease: Eukaryotic homologs

 Score =  139 bits (354), Expect = 2e-40
 Identities = 52/68 (76%), Positives = 60/68 (88%)

Query: 232 FIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAREL 291
           FIDLCILLGCDYC+SI+GIGPK A++LIK+H+SIEKILENID  KY VPE W YKEAREL
Sbjct: 3   FIDLCILLGCDYCESIKGIGPKTALKLIKKHKSIEKILENIDKSKYPVPEDWPYKEAREL 62

Query: 292 FRHPEIAD 299
           F +PE+ D
Sbjct: 63  FLNPEVTD 70

Members of this subgroup include the H3TH (helix-3-turn-helix) domains of eukaryotic Flap endonuclease-1 (FEN1), 5' nucleases. FEN1 is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes (long-patch base excision repair) in eukaryotes and archaea. Interaction between FEN1 and PCNA (Proliferating cell nuclear antigen) is an essential prerequisite to FEN1's DNA replication functionality and stimulates FEN1 nuclease activity by 10-50 fold. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this subfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Also, FEN1 has a C-terminal extension containing residues forming the consensus PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA. Length = 70

>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional

 Score =  146 bits (370), Expect = 7e-40
 Identities = 60/151 (39%), Positives = 88/151 (58%), Gaps = 15/151 (9%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFH------ 114
           AP E EAQ A M K G  +A  ++D D+L FG+  L+R++T S  RKLP +  +      
Sbjct: 102 APSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNVYVEVKPE 161

Query: 115 ---LEKVLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT 171
              LE+VL+ + ++ E+ ID+ IL+G DY   I+GIGPK A++LIK+H  +EK+LE    
Sbjct: 162 LIELEEVLKELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKKHGDLEKVLEERG- 220

Query: 172 KKYTVPEGWLYKEARELFRHPEVADPETIEF 202
                 E   Y E RE F +P V D   +++
Sbjct: 221 -----FEIENYDEIREFFLNPPVTDDYELKW 246

Length = 292

>gnl|CDD|234306 TIGR03674, fen_arch, flap structure-specific endonuclease

 Score =  139 bits (352), Expect = 5e-37
 Identities = 58/152 (38%), Positives = 88/152 (57%), Gaps = 15/152 (9%)

Query: 60  KAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFH----- 114
           +AP E EAQ A M K G V    ++D D+L FG+  L+R++T S  RKLP +  +     
Sbjct: 148 QAPSEGEAQAAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNIYVEVKP 207

Query: 115 ----LEKVLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENID 170
               LE+VL  + ++ E+ ID+ IL+G DY + ++GIGPK A++LIKEH  +EK+L    
Sbjct: 208 ELIELEEVLSELGITREQLIDIAILVGTDYNEGVKGIGPKTALKLIKEHGDLEKVL---K 264

Query: 171 TKKYTVPEGWLYKEARELFRHPEVADPETIEF 202
            +   +     Y E RE F +P V D   +++
Sbjct: 265 ARGEDIEN---YDEIREFFLNPPVTDDYELKW 293

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. Length = 338

>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional

 Score =  137 bits (348), Expect = 5e-36
 Identities = 48/74 (64%), Positives = 61/74 (82%)

Query: 232 FIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAREL 291
           FIDLCIL GCDYCD+I+GIGPK A +LIK+++SIE+ILE++D  KY VPE + YKEAREL
Sbjct: 225 FIDLCILCGCDYCDTIKGIGPKTAYKLIKKYKSIEEILEHLDKTKYPVPENFDYKEAREL 284

Query: 292 FRHPEIADPETIEL 305
           F +PE+   E I+L
Sbjct: 285 FLNPEVTPAEEIDL 298

Length = 393

>gnl|CDD|188621 cd09901, H3TH_FEN1-like, H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 (eukaryotic) and EXO1

 Score =  119 bits (301), Expect = 7e-33
 Identities = 40/73 (54%), Positives = 49/73 (67%), Gaps = 3/73 (4%)

Query: 127 EEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKY---TVPEGWLYK 183
           E+FIDLCIL GCDY  SI GIGPK A +LIK+H+SIEK+L+ + + K     VP    +K
Sbjct: 1   EQFIDLCILSGCDYLPSIPGIGPKTAYKLIKKHKSIEKVLKALRSNKKKKVPVPYEEPFK 60

Query: 184 EARELFRHPEVAD 196
           EAR  F H  V D
Sbjct: 61  EARLTFLHQRVYD 73

The 5' nucleases within this family are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. This family includes the H3TH (helix-3-turn-helix) domains of eukaryotic Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), and other eukaryotic homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Length = 73

>gnl|CDD|189037 cd09867, PIN_FEN1, PIN domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs

 Score =  125 bits (316), Expect = 1e-32
 Identities = 36/65 (55%), Positives = 48/65 (73%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           AP EAEAQCA +VK G VYA A++D D+L FG+  L+R++T S  +K+P +E  LEKVLE
Sbjct: 150 APSEAEAQCAYLVKKGDVYAVASQDYDSLLFGAPRLVRNLTISGKKKVPPEEIELEKVLE 209

Query: 121 GMELS 125
            +EL 
Sbjct: 210 ELELK 214

Flap endonuclease-1 (FEN1) is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes (long-patch base excision repair) in eukaryotes and archaea. Interaction between FEN1 and PCNA (Proliferating cell nuclear antigen) is an essential prerequisite to FEN1's DNA replication functionality and stimulates FEN1 nuclease activity by 10-50 fold. FEN1 belongs to the FEN1-EXO1-like family of structure-specific, 5' nucleases. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region (I domain) of variable length (approximately 45 residues in FEN1 PIN domains) and a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. Nucleases within this group also have a carboxylate-rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+/Mn2+). FEN1 has a C-terminal extension containing residues forming the consensus PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA. Length = 261

>gnl|CDD|188621 cd09901, H3TH_FEN1-like, H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 (eukaryotic) and EXO1

 Score =  114 bits (289), Expect = 4e-31
 Identities = 38/71 (53%), Positives = 47/71 (66%), Gaps = 3/71 (4%)

Query: 232 FIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKY---TVPEGWLYKEA 288
           FIDLCIL GCDY  SI GIGPK A +LIK+H+SIEK+L+ + + K     VP    +KEA
Sbjct: 3   FIDLCILSGCDYLPSIPGIGPKTAYKLIKKHKSIEKVLKALRSNKKKKVPVPYEEPFKEA 62

Query: 289 RELFRHPEIAD 299
           R  F H  + D
Sbjct: 63  RLTFLHQRVYD 73

The 5' nucleases within this family are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. This family includes the H3TH (helix-3-turn-helix) domains of eukaryotic Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), and other eukaryotic homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Length = 73

>gnl|CDD|234306 TIGR03674, fen_arch, flap structure-specific endonuclease

 Score =  122 bits (308), Expect = 7e-31
 Identities = 59/152 (38%), Positives = 83/152 (54%), Gaps = 20/152 (13%)

Query: 296 EIADPETIELVADVAPSSIRESRKICIDASMSLYQFLIAVRSE-GNQLMSVDGEPTSHLM 354
           ++   E IEL  D+        + + +DA  +LYQFL ++R   G  LM   G  TSHL 
Sbjct: 7   DLLAKEEIEL-EDL------SGKVVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITSHLS 59

Query: 355 GTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKWSDP 414
           G FYRTI L+E+G+KP+YVFDGKPP LK+  L +R E RE+A++   +A E+G       
Sbjct: 60  GLFYRTINLLENGIKPVYVFDGKPPELKAETLEERREIREEAEEKWEEALEKG------- 112

Query: 415 DEDGLVKYLCGDK--NFAEDRIRNGAKKLLKA 444
           D +   KY    +  +     I   +KKLL  
Sbjct: 113 DLEEARKY---AQRSSRLTSEIVESSKKLLDL 141

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. Length = 338

>gnl|CDD|216098 pfam00752, XPG_N, XPG N-terminal domain

 Score =  102 bits (256), Expect = 3e-26
 Identities = 47/97 (48%), Positives = 62/97 (63%), Gaps = 8/97 (8%)

Query: 303 IELVADVAPSSIR--ESRKICIDASMSLYQFLIAVRSE-GNQLMSVDGEPTSHLMGTFYR 359
           ++ VA + P  I   E + + IDAS+ LYQFL AVR + GN L +     TSHLMG F R
Sbjct: 9   LKPVALIRPVDIEALEGKTLAIDASIWLYQFLKAVRDQLGNALQN-----TSHLMGFFSR 63

Query: 360 TIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDA 396
             RL + G+KPI+VFDG PP LK+  L KR  +R++A
Sbjct: 64  LCRLKDFGIKPIFVFDGGPPPLKAETLQKRSARRQEA 100

Length = 100

>gnl|CDD|223336 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]

 Score =  108 bits (271), Expect = 4e-26
 Identities = 44/142 (30%), Positives = 68/142 (47%), Gaps = 9/142 (6%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
            P E  AQ A   K G V    + D D L   S      +  +  +  P +   LE+V E
Sbjct: 122 DPIETLAQKAY--KKGDVVLIISGDKDLLQLVSP---NVLVINGKKGEPEKFLDLEEVEE 176

Query: 121 -GMELSHEEFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVP 177
               L+ E+ IDL  L+G   D    ++GIGPK A++L++E+ S+E + EN+D  K    
Sbjct: 177 KFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLDIIKKKTR 236

Query: 178 EGWLYKEARELFRHPEVADPET 199
           E  L ++  + F    +A  +T
Sbjct: 237 E-KLLEDKEKAFLSKPLATIKT 257

Length = 310

>gnl|CDD|214690 smart00485, XPGN, Xeroderma pigmentosum G N-region

 Score =  101 bits (255), Expect = 4e-26
 Identities = 45/82 (54%), Positives = 55/82 (67%), Gaps = 6/82 (7%)

Query: 316 ESRKICIDASMSLYQFLIAVRSE-GNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVF 374
             + + IDAS+ LYQFL A R + G  L +       HLMG FYRT RL+E G+KPI+VF
Sbjct: 23  RGKTLAIDASIWLYQFLTACREKLGTPLPNS-----KHLMGLFYRTCRLLEFGIKPIFVF 77

Query: 375 DGKPPTLKSGELNKRMEKREDA 396
           DGKPP LKS  L KR E+RE+A
Sbjct: 78  DGKPPPLKSETLAKRRERREEA 99

domain in nucleases. Length = 99

>gnl|CDD|188617 cd09897, H3TH_FEN1-XPG-like, H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases

 Score = 99.2 bits (248), Expect = 2e-25
 Identities = 37/68 (54%), Positives = 48/68 (70%), Gaps = 3/68 (4%)

Query: 127 EEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKY---TVPEGWLYK 183
           E+FIDLCIL GCDY   + GIGPK A++LIKE+ S+EK+L+ +   K     VP  + YK
Sbjct: 1   EQFIDLCILSGCDYLPGLPGIGPKTALKLIKEYGSLEKVLKALRDDKKDKVPVPYDFPYK 60

Query: 184 EARELFRH 191
           +ARELF H
Sbjct: 61  KARELFLH 68

The 5' nucleases within this family are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. This family includes the H3TH (helix-3-turn-helix) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), Xeroderma pigmentosum complementation group G (XPG) nuclease, and other eukaryotic and archaeal homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. With the except of the Mkt1-like proteins, the nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Length = 68

>gnl|CDD|188617 cd09897, H3TH_FEN1-XPG-like, H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases

 Score = 96.5 bits (241), Expect = 1e-24
 Identities = 36/66 (54%), Positives = 46/66 (69%), Gaps = 3/66 (4%)

Query: 232 FIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKY---TVPEGWLYKEA 288
           FIDLCIL GCDY   + GIGPK A++LIKE+ S+EK+L+ +   K     VP  + YK+A
Sbjct: 3   FIDLCILSGCDYLPGLPGIGPKTALKLIKEYGSLEKVLKALRDDKKDKVPVPYDFPYKKA 62

Query: 289 RELFRH 294
           RELF H
Sbjct: 63  RELFLH 68

The 5' nucleases within this family are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. This family includes the H3TH (helix-3-turn-helix) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), Xeroderma pigmentosum complementation group G (XPG) nuclease, and other eukaryotic and archaeal homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. With the except of the Mkt1-like proteins, the nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Length = 68

>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional

 Score = 99.5 bits (249), Expect = 3e-23
 Identities = 45/104 (43%), Positives = 62/104 (59%), Gaps = 12/104 (11%)

Query: 343 MSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAK 402
           M   G  TSHL G FYRTI L+E+G+KP+YVFDGKPP LK+ E+ +R E RE+A++   +
Sbjct: 1   MDSKGRITSHLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREEAEEKYEE 60

Query: 403 AQEQGKLKWSDPDEDGLVKYLCGDK--NFAEDRIRNGAKKLLKA 444
           A+E+G       D +   KY    +  +   D I   +KKLL  
Sbjct: 61  AKEEG-------DLEEARKY---AQRSSRLTDEIVEDSKKLLDL 94

Length = 292

>gnl|CDD|189020 cd00128, PIN_FEN1_EXO1-like, PIN domains of Flap Endonuclease-1 (FEN1)-like and Exonuclease-1 (EXO1)-like nucleases, structure-specific, divalent-metal-ion dependent, 5' nucleases

 Score = 95.3 bits (237), Expect = 2e-22
 Identities = 44/99 (44%), Positives = 59/99 (59%), Gaps = 5/99 (5%)

Query: 311 PSSIRE--SRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGL 368
            S+I +   +K+ ID +  LYQFL + R    Q +   GE TS L G FYRTI+L E+G+
Sbjct: 12  GSAIEDLNGKKVAIDVNHYLYQFLTSKRE---QYLDAIGEFTSSLKGYFYRTIKLFENGI 68

Query: 369 KPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQG 407
            PI+VFDG PP LKS    KR E R +A+ +  +A   G
Sbjct: 69  TPIFVFDGGPPYLKSEASGKRTEARAEAEISSTEASYIG 107

PIN (PilT N terminus) domain of Flap Endonuclease-1 (FEN1) and Exonuclease-1 (EXO1)-like nucleases: FEN1, EXO1, Mkt1, Gap endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN domain with a helical arch/clamp region (I domain) of variable length (approximately 30 to 800 residues) and a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. Most nucleases within this family also have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+/Mn2+). Some nucleases in this family have C-terminal extensions that act as interaction sites for other proteins. Length = 209

>gnl|CDD|214689 smart00484, XPGI, Xeroderma pigmentosum G I-region

 Score = 90.7 bits (226), Expect = 2e-22
 Identities = 31/64 (48%), Positives = 40/64 (62%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           AP EAEAQCA + K+G V A  TED D L FG+  L R++ FS  +KL  +   LE VL+
Sbjct: 10  APYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLEFRIIDLESVLK 69

Query: 121 GMEL 124
            + L
Sbjct: 70  ELGL 73

domain in nucleases. Length = 73

>gnl|CDD|189037 cd09867, PIN_FEN1, PIN domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs

 Score = 87.9 bits (219), Expect = 2e-19
 Identities = 30/58 (51%), Positives = 44/58 (75%)

Query: 400 LAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFF 457
           L K  E+ +LKW +PDE+GL+K+L  + +F+EDR+R   ++L KA+  +TQGRLDSFF
Sbjct: 204 LEKVLEELELKWKEPDEEGLIKFLVEEHDFSEDRVRKAIERLKKAKKKSTQGRLDSFF 261

Flap endonuclease-1 (FEN1) is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes (long-patch base excision repair) in eukaryotes and archaea. Interaction between FEN1 and PCNA (Proliferating cell nuclear antigen) is an essential prerequisite to FEN1's DNA replication functionality and stimulates FEN1 nuclease activity by 10-50 fold. FEN1 belongs to the FEN1-EXO1-like family of structure-specific, 5' nucleases. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region (I domain) of variable length (approximately 45 residues in FEN1 PIN domains) and a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. Nucleases within this group also have a carboxylate-rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+/Mn2+). FEN1 has a C-terminal extension containing residues forming the consensus PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA. Length = 261

>gnl|CDD|189037 cd09867, PIN_FEN1, PIN domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs

 Score = 87.2 bits (217), Expect = 3e-19
 Identities = 27/51 (52%), Positives = 40/51 (78%)

Query: 1   MTLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFF 51
           + LKW +PDE+GL+K+L  + +F+EDR+R   ++L KA+  +TQGRLDSFF
Sbjct: 211 LELKWKEPDEEGLIKFLVEEHDFSEDRVRKAIERLKKAKKKSTQGRLDSFF 261

Flap endonuclease-1 (FEN1) is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes (long-patch base excision repair) in eukaryotes and archaea. Interaction between FEN1 and PCNA (Proliferating cell nuclear antigen) is an essential prerequisite to FEN1's DNA replication functionality and stimulates FEN1 nuclease activity by 10-50 fold. FEN1 belongs to the FEN1-EXO1-like family of structure-specific, 5' nucleases. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region (I domain) of variable length (approximately 45 residues in FEN1 PIN domains) and a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. Nucleases within this group also have a carboxylate-rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+/Mn2+). FEN1 has a C-terminal extension containing residues forming the consensus PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA. Length = 261

>gnl|CDD|189020 cd00128, PIN_FEN1_EXO1-like, PIN domains of Flap Endonuclease-1 (FEN1)-like and Exonuclease-1 (EXO1)-like nucleases, structure-specific, divalent-metal-ion dependent, 5' nucleases

 Score = 85.7 bits (212), Expect = 4e-19
 Identities = 29/65 (44%), Positives = 36/65 (55%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           AP EAEAQ A + K+G V A  TED D L +G    +R MTF    K  +  F L K+L 
Sbjct: 144 APYEAEAQLAYLAKSGHVIAAITEDTDCLMYGVPRFIRGMTFPNKEKRFIDRFRLSKILG 203

Query: 121 GMELS 125
            +EL 
Sbjct: 204 KLELF 208

PIN (PilT N terminus) domain of Flap Endonuclease-1 (FEN1) and Exonuclease-1 (EXO1)-like nucleases: FEN1, EXO1, Mkt1, Gap endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN domain with a helical arch/clamp region (I domain) of variable length (approximately 30 to 800 residues) and a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. Most nucleases within this family also have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+/Mn2+). Some nucleases in this family have C-terminal extensions that act as interaction sites for other proteins. Length = 209

>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional

 Score = 87.8 bits (218), Expect = 1e-18
 Identities = 30/63 (47%), Positives = 45/63 (71%)

Query: 405 EQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFTIRREEK 464
           E+  LKW++PDE+GL K+L  +KNF E+R+    ++L KA++  TQ RLDSFFT  ++  
Sbjct: 294 EEIDLKWNEPDEEGLKKFLVKEKNFNEERVEKYIERLKKAKTKKTQTRLDSFFTATKKPI 353

Query: 465 RKS 467
           +KS
Sbjct: 354 KKS 356

Length = 393

>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional

 Score = 85.1 bits (211), Expect = 9e-18
 Identities = 29/64 (45%), Positives = 46/64 (71%)

Query: 3   LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFFTIRREEKRKAP 62
           LKW++PDE+GL K+L  +KNF E+R+    ++L KA++  TQ RLDSFFT  ++  +K+ 
Sbjct: 298 LKWNEPDEEGLKKFLVKEKNFNEERVEKYIERLKKAKTKKTQTRLDSFFTATKKPIKKSN 357

Query: 63  CEAE 66
            +A+
Sbjct: 358 SKAK 361

Length = 393

>gnl|CDD|189023 cd09853, PIN_StructSpec-5'-nucleases, PIN domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination

 Score = 76.9 bits (189), Expect = 1e-16
 Identities = 34/95 (35%), Positives = 46/95 (48%), Gaps = 10/95 (10%)

Query: 319 KICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHG--LKPIYVFDG 376
           K+ ID S   YQFL   R +  +     GE TS   G FY  I L ++   + PI VFDG
Sbjct: 1   KVAIDGSNLGYQFLHNNRKDKEK-----GELTSFASGYFYTIISLAKNYSAITPIVVFDG 55

Query: 377 KPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKW 411
             P L+   L +  E R+   +A A+A E+ K   
Sbjct: 56  GKPVLRLEHLPEYKENRD---EAEAEATEEEKRLD 87

Structure-specific 5' nucleases are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner. The family includes the PIN (PilT N terminus) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the PIN domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4- and T5-5' nucleases, and other homologs. These nucleases contain a PIN domain with a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, the nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+). Length = 163

>gnl|CDD|189038 cd09868, PIN_XPG, PIN domain of Xeroderma pigmentosum complementation group G (XPG) nuclease, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs

 Score = 77.7 bits (192), Expect = 4e-16
 Identities = 40/109 (36%), Positives = 59/109 (54%), Gaps = 13/109 (11%)

Query: 309 VAPSSIR------ESRKICIDASMSLYQFLIAVR-SEGNQLMSVDGEPTSHLMGTFYRTI 361
           + PS         E +++ IDAS+ +YQFL  +R  EGN L        +HL+G F R  
Sbjct: 10  LEPSGRPVRLETLEGKRLAIDASIWIYQFLKGMRDREGNAL------KNAHLLGFFRRIC 63

Query: 362 RLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLK 410
           +L+ +G+KP++VFDG  P LK   L KR ++RE A+    K  E+    
Sbjct: 64  KLLFYGIKPVFVFDGGAPELKRRTLAKRRQQREKAEINAKKTAEKLLAS 112

The Xeroderma pigmentosum complementation group G (XPG) nuclease plays a central role in nucleotide excision repair (NER) in cleaving DNA bubble structures or loops. XPG is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region (I domain). In XPG PIN domains, this arch region can be quite variable and extensive (400 - 800 residues) in length and is required for NER activity and for efficient processing of bubble substrates. Inserted within the PIN domain of these 5' nucleases is a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. Nucleases within this group also have a carboxylate-rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+/Mn2+). Length = 249

>gnl|CDD|188623 cd09903, H3TH_FEN1-Arc, H3TH domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease: Archaeal homologs

 Score = 71.5 bits (176), Expect = 1e-15
 Identities = 27/71 (38%), Positives = 45/71 (63%), Gaps = 7/71 (9%)

Query: 127 EEFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEA 185
           E+ ID+ IL+G DY    ++GIGPK A++L+KE+  +EK+L    + +  + +    +E 
Sbjct: 1   EQLIDIAILVGTDYNPGGVKGIGPKTALKLVKEYGDLEKVLR---SVEDEIVD---PEEI 54

Query: 186 RELFRHPEVAD 196
           RE+F +P V D
Sbjct: 55  REIFLNPPVTD 65

Members of this subgroup include the H3TH (helix-3-turn-helix) domains of archaeal Flap endonuclease-1 (FEN1), 5' nucleases. FEN1 is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes (long-patch base excision repair) in eukaryotes and archaea. Interaction between FEN1 and PCNA (Proliferating cell nuclear antigen) is an essential prerequisite to FEN1's DNA replication functionality and stimulates FEN1 nuclease activity by 10-50 fold. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this subfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Also, FEN1 has a C-terminal extension containing residues forming the consensus PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA. Length = 65

>gnl|CDD|188616 cd00080, H3TH_StructSpec-5'-nucleases, H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination

 Score = 70.9 bits (174), Expect = 2e-15
 Identities = 27/71 (38%), Positives = 39/71 (54%), Gaps = 10/71 (14%)

Query: 127 EEFIDLCILLGCDYCD--SIRGIGPKRAIELIKEHRSIEKILENID--------TKKYTV 176
           E+FIDLC L+GCDY D   + GIGPK A +L  ++ S+E ILEN+D          +   
Sbjct: 1   EQFIDLCALVGCDYSDNPGVPGIGPKTAAKLALKYGSLEGILENLDELKGKKREKLEEPK 60

Query: 177 PEGWLYKEARE 187
              +L ++   
Sbjct: 61  EYAFLSRKLAT 71

The 5' nucleases of this superfamily are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. The superfamily includes the H3TH (helix-3-turn-helix) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the H3TH domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4 RNase H, T5-5'nuclease, and other homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the C-terminal region of the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. Typically, the nucleases within this superfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one or two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Length = 71

>gnl|CDD|188616 cd00080, H3TH_StructSpec-5'-nucleases, H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination

 Score = 69.3 bits (170), Expect = 6e-15
 Identities = 26/69 (37%), Positives = 37/69 (53%), Gaps = 10/69 (14%)

Query: 232 FIDLCILLGCDYCD--SIRGIGPKRAIELIKEHRSIEKILENID--------TKKYTVPE 281
           FIDLC L+GCDY D   + GIGPK A +L  ++ S+E ILEN+D          +     
Sbjct: 3   FIDLCALVGCDYSDNPGVPGIGPKTAAKLALKYGSLEGILENLDELKGKKREKLEEPKEY 62

Query: 282 GWLYKEARE 290
            +L ++   
Sbjct: 63  AFLSRKLAT 71

The 5' nucleases of this superfamily are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. The superfamily includes the H3TH (helix-3-turn-helix) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the H3TH domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4 RNase H, T5-5'nuclease, and other homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the C-terminal region of the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. Typically, the nucleases within this superfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one or two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Length = 71

>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional

 Score = 73.7 bits (182), Expect = 1e-14
 Identities = 30/73 (41%), Positives = 42/73 (57%), Gaps = 6/73 (8%)

Query: 233 IDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELF 292
           ID+ IL+G DY   I+GIGPK A++LIK+H  +EK+LE          E   Y E RE F
Sbjct: 180 IDIAILVGTDYNPGIKGIGPKTALKLIKKHGDLEKVLEERG------FEIENYDEIREFF 233

Query: 293 RHPEIADPETIEL 305
            +P + D   ++ 
Sbjct: 234 LNPPVTDDYELKW 246

Length = 292

>gnl|CDD|223336 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]

 Score = 73.9 bits (182), Expect = 2e-14
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 3/73 (4%)

Query: 232 FIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAR 289
            IDL  L+G   D    ++GIGPK A++L++E+ S+E + EN+D  K    E  L ++  
Sbjct: 186 LIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLDIIKKKTRE-KLLEDKE 244

Query: 290 ELFRHPEIADPET 302
           + F    +A  +T
Sbjct: 245 KAFLSKPLATIKT 257

Length = 310

>gnl|CDD|188623 cd09903, H3TH_FEN1-Arc, H3TH domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease: Archaeal homologs

 Score = 67.2 bits (165), Expect = 3e-14
 Identities = 25/68 (36%), Positives = 43/68 (63%), Gaps = 7/68 (10%)

Query: 233 IDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAREL 291
           ID+ IL+G DY    ++GIGPK A++L+KE+  +EK+L    + +  + +    +E RE+
Sbjct: 4   IDIAILVGTDYNPGGVKGIGPKTALKLVKEYGDLEKVLR---SVEDEIVD---PEEIREI 57

Query: 292 FRHPEIAD 299
           F +P + D
Sbjct: 58  FLNPPVTD 65

Members of this subgroup include the H3TH (helix-3-turn-helix) domains of archaeal Flap endonuclease-1 (FEN1), 5' nucleases. FEN1 is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes (long-patch base excision repair) in eukaryotes and archaea. Interaction between FEN1 and PCNA (Proliferating cell nuclear antigen) is an essential prerequisite to FEN1's DNA replication functionality and stimulates FEN1 nuclease activity by 10-50 fold. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this subfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Also, FEN1 has a C-terminal extension containing residues forming the consensus PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA. Length = 65

>gnl|CDD|223336 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]

 Score = 72.0 bits (177), Expect = 8e-14
 Identities = 31/91 (34%), Positives = 43/91 (47%), Gaps = 7/91 (7%)

Query: 311 PSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPT---SHLMGTFYRTIRLVEHG 367
               +  + + ID S  LY+ L A+      L +  G+PT   S  +G  YR IRL+E  
Sbjct: 5   QLMNKSGKLLLIDGSSLLYRALHALPQ---PLGNPLGDPTGAVSGFLGMLYRLIRLLEP- 60

Query: 368 LKPIYVFDGKPPTLKSGELNKRMEKREDAQK 398
             P+ VFDGKPPT +   L +    RE    
Sbjct: 61  THPVVVFDGKPPTFRHELLEEYKANREKEMP 91

Length = 310

>gnl|CDD|188628 cd09908, H3TH_EXO1, H3TH domain of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease

 Score = 65.7 bits (161), Expect = 1e-13
 Identities = 29/73 (39%), Positives = 45/73 (61%), Gaps = 3/73 (4%)

Query: 127 EEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT-KKYTVPEGWL--YK 183
           E+F  +CIL GCDY  S+ GIG K+A +L++ HR+IEK+++ +    K  VP  +   ++
Sbjct: 1   EKFRHMCILSGCDYLPSLPGIGLKKAYKLVRRHRTIEKVIKALRFDGKKEVPPDYEEGFQ 60

Query: 184 EARELFRHPEVAD 196
           +A   F H  V D
Sbjct: 61  KALLTFLHQRVFD 73

Exonuclease-1 (EXO1) is involved in multiple, eukaryotic DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity), DNA repair processes (DNA mismatch repair (MMR) and post-replication repair (PRR), recombination, and telomere integrity. EXO1 functions in the MMS2 error-free branch of the PRR pathway in the maintenance and repair of stalled replication forks. Studies also suggest that EXO1 plays both structural and catalytic roles during MMR-mediated mutation avoidance. Members of this subgroup include the H3TH (helix-3-turn-helix) domains of EXO1 and other similar eukaryotic 5' nucleases. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. These nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. EXO1 nucleases also have C-terminal Mlh1- and Msh2-binding domains which allow interaction with MMR and PRR proteins, respectively. Length = 73

>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2)

 Score = 72.2 bits (177), Expect = 3e-13
 Identities = 35/99 (35%), Positives = 57/99 (57%), Gaps = 8/99 (8%)

Query: 309 VAPSSIRESRKICIDASMSLYQFLIAVR-SEGNQLMSVDGEPTSHLMGTFYRTIRLVEHG 367
           V+P ++ E +++ +D S+ L Q L  VR  EGN + +      SHL+  F+R  +L+   
Sbjct: 17  VSPETL-EGKRLAVDISIWLNQALKGVRDREGNAIKN------SHLLTLFHRLCKLLFFR 69

Query: 368 LKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQ 406
           ++PI+VFDG  P LK   L KR ++R+ A +   K  E+
Sbjct: 70  IRPIFVFDGGAPLLKRQTLAKRRQRRDGASEDARKTAEK 108

All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 1034

>gnl|CDD|216163 pfam00867, XPG_I, XPG I-region

 Score = 62.8 bits (154), Expect = 6e-13
 Identities = 20/33 (60%), Positives = 23/33 (69%)

Query: 61 APCEAEAQCAAMVKAGKVYATATEDMDALTFGS 93
          AP EAEAQCA +VK G V A  +ED D L FG+
Sbjct: 10 APYEAEAQCAYLVKTGLVDAVISEDSDLLLFGA 42

Length = 46

>gnl|CDD|234306 TIGR03674, fen_arch, flap structure-specific endonuclease

 Score = 69.6 bits (171), Expect = 7e-13
 Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 6/73 (8%)

Query: 233 IDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELF 292
           ID+ IL+G DY + ++GIGPK A++LIKEH  +EK+L     +   +     Y E RE F
Sbjct: 227 IDIAILVGTDYNEGVKGIGPKTALKLIKEHGDLEKVL---KARGEDIEN---YDEIREFF 280

Query: 293 RHPEIADPETIEL 305
            +P + D   ++ 
Sbjct: 281 LNPPVTDDYELKW 293

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. Length = 338

>gnl|CDD|188628 cd09908, H3TH_EXO1, H3TH domain of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease

 Score = 63.4 bits (155), Expect = 8e-13
 Identities = 26/67 (38%), Positives = 41/67 (61%), Gaps = 3/67 (4%)

Query: 231 SFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT-KKYTVPEGWL--YKE 287
            F  +CIL GCDY  S+ GIG K+A +L++ HR+IEK+++ +    K  VP  +   +++
Sbjct: 2   KFRHMCILSGCDYLPSLPGIGLKKAYKLVRRHRTIEKVIKALRFDGKKEVPPDYEEGFQK 61

Query: 288 ARELFRH 294
           A   F H
Sbjct: 62  ALLTFLH 68

Exonuclease-1 (EXO1) is involved in multiple, eukaryotic DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity), DNA repair processes (DNA mismatch repair (MMR) and post-replication repair (PRR), recombination, and telomere integrity. EXO1 functions in the MMS2 error-free branch of the PRR pathway in the maintenance and repair of stalled replication forks. Studies also suggest that EXO1 plays both structural and catalytic roles during MMR-mediated mutation avoidance. Members of this subgroup include the H3TH (helix-3-turn-helix) domains of EXO1 and other similar eukaryotic 5' nucleases. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. These nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. EXO1 nucleases also have C-terminal Mlh1- and Msh2-binding domains which allow interaction with MMR and PRR proteins, respectively. Length = 73

>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional

 Score = 65.2 bits (160), Expect = 1e-11
 Identities = 18/50 (36%), Positives = 35/50 (70%)

Query: 408 KLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFF 457
           +LKW +PD++G++++L  + +F+E+R++   ++L KA     Q  LDS+F
Sbjct: 243 ELKWKEPDKEGIIEFLVEEHDFSEERVKKALERLEKAVKEKKQTTLDSWF 292

Length = 292

>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional

 Score = 65.2 bits (160), Expect = 1e-11
 Identities = 18/50 (36%), Positives = 34/50 (68%)

Query: 2   TLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFF 51
            LKW +PD++G++++L  + +F+E+R++   ++L KA     Q  LDS+F
Sbjct: 243 ELKWKEPDKEGIIEFLVEEHDFSEERVKKALERLEKAVKEKKQTTLDSWF 292

Length = 292

>gnl|CDD|188620 cd09900, H3TH_XPG-like, H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 (archaeal), GEN1, YEN1, and XPG

 Score = 59.0 bits (144), Expect = 1e-11
 Identities = 22/49 (44%), Positives = 30/49 (61%), Gaps = 1/49 (2%)

Query: 127 EEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSI-EKILENIDTKKY 174
           E+ I L +LLG DY   + GIGPK A+EL+KE     EK LE+ +  + 
Sbjct: 1   EQLILLALLLGTDYNPGVPGIGPKTALELLKEFGEDLEKFLESEEILEA 49

The 5' nucleases within this family are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. This family includes the H3TH (helix-3-turn-helix) domains of archaeal Flap Endonuclease-1 (FEN1), Gap Endonuclease 1 (GEN1), Yeast Endonuclease 1 (YEN1), Xeroderma pigmentosum complementation group G (XPG) nuclease, and other eukaryotic and archaeal homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. With the except of the Mkt1-like proteins, the nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Length = 52

>gnl|CDD|189026 cd09856, PIN_FEN1-like, PIN domain of Flap Endonuclease-1 (FEN1)-like, structure-specific, divalent-metal-ion dependent, 5' nucleases

 Score = 62.9 bits (153), Expect = 2e-11
 Identities = 26/83 (31%), Positives = 38/83 (45%), Gaps = 1/83 (1%)

Query: 301 ETIELVADVAPSSIRESRKICIDASMSLYQFLIAVR-SEGNQLMSVDGEPTSHLMGTFYR 359
           E +E      P      ++I IDAS  L++ L   R   G +           L+  F R
Sbjct: 4   EFLEPQKSRIPKEQLRGKRIAIDASGWLFEALTIQRIRIGPRSSRSYSTTGPALINLFSR 63

Query: 360 TIRLVEHGLKPIYVFDGKPPTLK 382
              L+   ++PI+VFDG+PP LK
Sbjct: 64  LKELLSLDVEPIFVFDGEPPKLK 86

PIN (PilT N terminus) domain of Flap Endonuclease-1 (FEN1)-like nucleases: FEN1, Gap endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN domain with a helical arch/clamp region (I domain) of variable length (approximately 30 to 800 residues) and a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. Most nucleases within this family also have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+/Mn2+). Some nucleases in this family have C-terminal extensions that act as interaction sites for other proteins. Length = 207

>gnl|CDD|188620 cd09900, H3TH_XPG-like, H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 (archaeal), GEN1, YEN1, and XPG

 Score = 57.1 bits (139), Expect = 7e-11
 Identities = 21/47 (44%), Positives = 28/47 (59%), Gaps = 1/47 (2%)

Query: 232 FIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSI-EKILENIDTKKY 277
            I L +LLG DY   + GIGPK A+EL+KE     EK LE+ +  + 
Sbjct: 3   LILLALLLGTDYNPGVPGIGPKTALELLKEFGEDLEKFLESEEILEA 49

The 5' nucleases within this family are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. This family includes the H3TH (helix-3-turn-helix) domains of archaeal Flap Endonuclease-1 (FEN1), Gap Endonuclease 1 (GEN1), Yeast Endonuclease 1 (YEN1), Xeroderma pigmentosum complementation group G (XPG) nuclease, and other eukaryotic and archaeal homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. With the except of the Mkt1-like proteins, the nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Length = 52

>gnl|CDD|234306 TIGR03674, fen_arch, flap structure-specific endonuclease

 Score = 62.7 bits (153), Expect = 1e-10
 Identities = 19/50 (38%), Positives = 32/50 (64%), Gaps = 1/50 (2%)

Query: 2   TLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFF 51
            LKW  PD++G++++LC + +F+EDR+    ++L  A  S  Q  LD +F
Sbjct: 290 ELKWRKPDKEGIIEFLCDEHDFSEDRVERALERLEAAYKS-KQKTLDRWF 338

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. Length = 338

>gnl|CDD|234306 TIGR03674, fen_arch, flap structure-specific endonuclease

 Score = 61.5 bits (150), Expect = 3e-10
 Identities = 18/50 (36%), Positives = 33/50 (66%), Gaps = 1/50 (2%)

Query: 408 KLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFF 457
           +LKW  PD++G++++LC + +F+EDR+    ++L  A   + Q  LD +F
Sbjct: 290 ELKWRKPDKEGIIEFLCDEHDFSEDRVERALERLEAAYK-SKQKTLDRWF 338

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. Length = 338

>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2)

 Score = 58.8 bits (142), Expect = 5e-09
 Identities = 31/98 (31%), Positives = 52/98 (53%), Gaps = 3/98 (3%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           AP EAEAQCA +    +   T T+D D   FG+  + ++  F++ +   V+ +    +  
Sbjct: 791 APMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNF-FNQNKF--VEYYQYVDIHN 847

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKE 158
            + L   + I+L  LLG DY + I  +GP  A+E++ E
Sbjct: 848 QLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNE 885

All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 1034

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

 Score = 56.1 bits (136), Expect = 8e-09
 Identities = 27/62 (43%), Positives = 37/62 (59%), Gaps = 4/62 (6%)

Query: 112 EFHLEKVLEGMELSHEEFIDLCILLGCDYCDSIRG---IGPKRAIELIKEHRSIEKILEN 168
            +  E V+E   L+ E+ ID   L+G D  D+I G   IG K A +L+KE  S+E ILEN
Sbjct: 157 LYTPENVIEKYGLTPEQIIDYKALMG-DSSDNIPGVPGIGEKTAAKLLKEFGSLENILEN 215

Query: 169 ID 170
           +D
Sbjct: 216 LD 217

Length = 259

>gnl|CDD|188620 cd09900, H3TH_XPG-like, H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 (archaeal), GEN1, YEN1, and XPG

 Score = 49.8 bits (120), Expect = 2e-08
 Identities = 17/39 (43%), Positives = 22/39 (56%)

Query: 201 EFIDLCILLGCDYCDSIRGIGPKRAIELLYSFIDLCILL 239
           + I L +LLG DY   + GIGPK A+ELL  F +     
Sbjct: 2   QLILLALLLGTDYNPGVPGIGPKTALELLKEFGEDLEKF 40

The 5' nucleases within this family are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. This family includes the H3TH (helix-3-turn-helix) domains of archaeal Flap Endonuclease-1 (FEN1), Gap Endonuclease 1 (GEN1), Yeast Endonuclease 1 (YEN1), Xeroderma pigmentosum complementation group G (XPG) nuclease, and other eukaryotic and archaeal homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. With the except of the Mkt1-like proteins, the nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Length = 52

>gnl|CDD|197623 smart00279, HhH2, Helix-hairpin-helix class 2 (Pol1 family) motifs

 Score = 49.8 bits (120), Expect = 2e-08
 Identities = 18/36 (50%), Positives = 26/36 (72%), Gaps = 4/36 (11%)

Query: 127 EEFIDLCILLGCDYCD---SIRGIGPKRAIELIKEH 159
           E+FID  IL+G DY D    ++GIGPK A++L++E 
Sbjct: 2   EQFIDYAILVG-DYSDNIPGVKGIGPKTALKLLREF 36

Length = 36

>gnl|CDD|188618 cd09898, H3TH_53EXO, H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs

 Score = 50.9 bits (123), Expect = 2e-08
 Identities = 22/53 (41%), Positives = 31/53 (58%), Gaps = 10/53 (18%)

Query: 127 EEFIDLCILLGCDYCDS------IRGIGPKRAIELIKEHRSIEKILENIDTKK 173
           E+ ID   L+G    DS      + GIGPK A +L++E+ S+E IL N+D  K
Sbjct: 2   EQIIDYLALVG----DSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDELK 50

H3TH (helix-3-turn-helix) domains of the 5'-3' exonuclease (53EXO) of mutli-domain DNA polymerase I and single domain protein homologs are included in this family. Taq DNA polymerase I contains a polymerase domain for synthesizing a new DNA strand and a 53EXO domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The 53EXO cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+ or Mn2+ or Zn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Length = 73

>gnl|CDD|216458 pfam01367, 5_3_exonuc, 5'-3' exonuclease, C-terminal SAM fold

 Score = 51.4 bits (124), Expect = 2e-08
 Identities = 23/50 (46%), Positives = 31/50 (62%), Gaps = 4/50 (8%)

Query: 127 EEFIDLCILLGCDYCDSI---RGIGPKRAIELIKEHRSIEKILENIDTKK 173
           E+ ID   L+G D  D+I    GIG K A +L+KE+ S+E I EN+D  K
Sbjct: 4   EQIIDYKALVG-DSSDNIPGVPGIGEKTAAKLLKEYGSLENIYENLDKLK 52

Length = 100

>gnl|CDD|188618 cd09898, H3TH_53EXO, H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs

 Score = 50.1 bits (121), Expect = 4e-08
 Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 10/51 (19%)

Query: 232 FIDLCILLGCDYCDS------IRGIGPKRAIELIKEHRSIEKILENIDTKK 276
            ID   L+G    DS      + GIGPK A +L++E+ S+E IL N+D  K
Sbjct: 4   IIDYLALVG----DSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDELK 50

H3TH (helix-3-turn-helix) domains of the 5'-3' exonuclease (53EXO) of mutli-domain DNA polymerase I and single domain protein homologs are included in this family. Taq DNA polymerase I contains a polymerase domain for synthesizing a new DNA strand and a 53EXO domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The 53EXO cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+ or Mn2+ or Zn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Length = 73

>gnl|CDD|216458 pfam01367, 5_3_exonuc, 5'-3' exonuclease, C-terminal SAM fold

 Score = 51.0 bits (123), Expect = 4e-08
 Identities = 22/48 (45%), Positives = 29/48 (60%), Gaps = 4/48 (8%)

Query: 232 FIDLCILLGCDYCDSI---RGIGPKRAIELIKEHRSIEKILENIDTKK 276
            ID   L+G D  D+I    GIG K A +L+KE+ S+E I EN+D  K
Sbjct: 6   IIDYKALVG-DSSDNIPGVPGIGEKTAAKLLKEYGSLENIYENLDKLK 52

Length = 100

>gnl|CDD|197623 smart00279, HhH2, Helix-hairpin-helix class 2 (Pol1 family) motifs

 Score = 47.8 bits (115), Expect = 8e-08
 Identities = 17/34 (50%), Positives = 24/34 (70%), Gaps = 4/34 (11%)

Query: 232 FIDLCILLGCDYCD---SIRGIGPKRAIELIKEH 262
           FID  IL+G DY D    ++GIGPK A++L++E 
Sbjct: 4   FIDYAILVG-DYSDNIPGVKGIGPKTALKLLREF 36

Length = 36

>gnl|CDD|188624 cd09904, H3TH_XPG, H3TH domain of Xeroderma pigmentosum complementation group G (XPG) nuclease, a structure-specific, divalent-metal-ion dependent, 5' nuclease

 Score = 49.9 bits (120), Expect = 8e-08
 Identities = 23/97 (23%), Positives = 44/97 (45%), Gaps = 3/97 (3%)

Query: 201 EFIDLCILLGCDYCDSIRGIGPKRAIELLYSFIDLCILLGCDYCDSIRGIGPKRAIELIK 260
           + I L +LLG DY + + GIGP  A+E+L  F     L    + D      P+++ +   
Sbjct: 2   KLIRLALLLGSDYTEGVSGIGPVNAMEILSEFPGEEDL--EKFKDWWENAQPEKSEDSDN 59

Query: 261 EHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEI 297
           + +  ++  +N   K   +P G+        + +P +
Sbjct: 60  DKQEFKRKHKNY-LKNLILPPGFPSPAVINAYLNPNV 95

The Xeroderma pigmentosum complementation group G (XPG) nuclease plays a central role in nucleotide excision repair (NER) in cleaving DNA bubble structures or loops. XPG is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Members of this subgroup include the H3TH (helix-3-turn-helix) domains of XPG and other similar eukaryotic 5' nucleases. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. These nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Length = 97

>gnl|CDD|188624 cd09904, H3TH_XPG, H3TH domain of Xeroderma pigmentosum complementation group G (XPG) nuclease, a structure-specific, divalent-metal-ion dependent, 5' nuclease

 Score = 49.6 bits (119), Expect = 1e-07
 Identities = 21/95 (22%), Positives = 36/95 (37%), Gaps = 27/95 (28%)

Query: 127 EEFIDLCILLGCDYCDSIRGIGPKRAIELIKE--------------HRSIEKILENIDT- 171
           ++ I L +LLG DY + + GIGP  A+E++ E                +  +  E+ D  
Sbjct: 1   DKLIRLALLLGSDYTEGVSGIGPVNAMEILSEFPGEEDLEKFKDWWENAQPEKSEDSDND 60

Query: 172 ------------KKYTVPEGWLYKEARELFRHPEV 194
                       K   +P G+        + +P V
Sbjct: 61  KQEFKRKHKNYLKNLILPPGFPSPAVINAYLNPNV 95

The Xeroderma pigmentosum complementation group G (XPG) nuclease plays a central role in nucleotide excision repair (NER) in cleaving DNA bubble structures or loops. XPG is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Members of this subgroup include the H3TH (helix-3-turn-helix) domains of XPG and other similar eukaryotic 5' nucleases. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. These nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Length = 97

>gnl|CDD|189038 cd09868, PIN_XPG, PIN domain of Xeroderma pigmentosum complementation group G (XPG) nuclease, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs

 Score = 51.5 bits (124), Expect = 3e-07
 Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEAR 106
           AP EAEAQCA + + G V    T+D D   FG+  + ++  F+  +
Sbjct: 155 APMEAEAQCAILNQLGLVDGVITDDSDVFLFGAKRVYKNF-FNGNK 199

The Xeroderma pigmentosum complementation group G (XPG) nuclease plays a central role in nucleotide excision repair (NER) in cleaving DNA bubble structures or loops. XPG is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region (I domain). In XPG PIN domains, this arch region can be quite variable and extensive (400 - 800 residues) in length and is required for NER activity and for efficient processing of bubble substrates. Inserted within the PIN domain of these 5' nucleases is a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. Nucleases within this group also have a carboxylate-rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+/Mn2+). Length = 249

>gnl|CDD|233038 TIGR00593, pola, DNA polymerase I

 Score = 53.1 bits (128), Expect = 3e-07
 Identities = 25/65 (38%), Positives = 39/65 (60%), Gaps = 4/65 (6%)

Query: 112 EFHLEKVLEGMELSHEEFIDLCILLGCDYCDSI---RGIGPKRAIELIKEHRSIEKILEN 168
           E   E V+E   ++ ++ +DL  L+G D  D+I   +GIG K A +L++E  S+E I EN
Sbjct: 156 EITPEYVVEKYGVTPDQLVDLKALVG-DSSDNIPGVKGIGEKTAAKLLQEFGSLENIYEN 214

Query: 169 IDTKK 173
           +D  K
Sbjct: 215 LDQIK 219

All proteins in this family for which functions are known are DNA polymerases Many also have an exonuclease motif. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 887

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

 Score = 51.1 bits (123), Expect = 4e-07
 Identities = 22/45 (48%), Positives = 28/45 (62%), Gaps = 4/45 (8%)

Query: 232 FIDLCILLGCDYCDSIRG---IGPKRAIELIKEHRSIEKILENID 273
            ID   L+G D  D+I G   IG K A +L+KE  S+E ILEN+D
Sbjct: 174 IIDYKALMG-DSSDNIPGVPGIGEKTAAKLLKEFGSLENILENLD 217

Length = 259

>gnl|CDD|189040 cd09870, PIN_YEN1, PIN domain of Yeast Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and fungal homologs

 Score = 49.2 bits (118), Expect = 1e-06
 Identities = 18/38 (47%), Positives = 25/38 (65%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLR 98
           AP EAEA+CA + + G V A  + D DAL FG+  ++R
Sbjct: 129 APGEAEAECARLQRLGIVDAVLSNDSDALMFGATRVIR 166

Yeast Endonuclease 1 (YEN1) is a Holliday junction resolvase which promotes reciprocal exchange during mitotic recombination to maintain genome integrity in budding yeast. YEN1 is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region (I domain) of variable length (approximately 15 - 50 residues in YEN1 PIN domains) and a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. Nucleases within this group also have a carboxylate-rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+/Mn2+). Length = 239

>gnl|CDD|197623 smart00279, HhH2, Helix-hairpin-helix class 2 (Pol1 family) motifs

 Score = 43.6 bits (104), Expect = 3e-06
 Identities = 17/31 (54%), Positives = 22/31 (70%), Gaps = 4/31 (12%)

Query: 202 FIDLCILLGCDYCD---SIRGIGPKRAIELL 229
           FID  IL+G DY D    ++GIGPK A++LL
Sbjct: 4   FIDYAILVG-DYSDNIPGVKGIGPKTALKLL 33

Length = 36

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

 Score = 49.7 bits (120), Expect = 3e-06
 Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 10/61 (16%)

Query: 116 EKVLEGMELSHEEFIDLCILLGCDYCDS------IRGIGPKRAIELIKEHRSIEKILENI 169
           E+V+E   ++ E+ ID   L+G    DS      + GIG K A +L++E+ S+E + EN+
Sbjct: 162 EEVVEKYGVTPEQIIDYLALMG----DSSDNIPGVPGIGEKTAAKLLQEYGSLEGLYENL 217

Query: 170 D 170
           D
Sbjct: 218 D 218

Length = 880

>gnl|CDD|233038 TIGR00593, pola, DNA polymerase I

 Score = 47.7 bits (114), Expect = 1e-05
 Identities = 21/48 (43%), Positives = 30/48 (62%), Gaps = 4/48 (8%)

Query: 232 FIDLCILLGCDYCDSI---RGIGPKRAIELIKEHRSIEKILENIDTKK 276
            +DL  L+G D  D+I   +GIG K A +L++E  S+E I EN+D  K
Sbjct: 173 LVDLKALVG-DSSDNIPGVKGIGEKTAAKLLQEFGSLENIYENLDQIK 219

All proteins in this family for which functions are known are DNA polymerases Many also have an exonuclease motif. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 887

>gnl|CDD|189023 cd09853, PIN_StructSpec-5'-nucleases, PIN domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination

 Score = 44.5 bits (105), Expect = 2e-05
 Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 10/57 (17%)

Query: 62  PCEAEAQCAAMVKAGK----VYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFH 114
           P EAE   A +VK G     V A  + D D LT G++        S    L  +E+H
Sbjct: 113 PSEAEDMAAYLVKKGGHLYDVVALISTDGDWLTLGTD------KVSRFSFLTRREYH 163

Structure-specific 5' nucleases are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner. The family includes the PIN (PilT N terminus) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the PIN domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4- and T5-5' nucleases, and other homologs. These nucleases contain a PIN domain with a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, the nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+). Length = 163

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

 Score = 46.6 bits (112), Expect = 3e-05
 Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 17/61 (27%)

Query: 219 GIGPKRAIELLYSFIDLCILLGCDYCDS------IRGIGPKRAIELIKEHRSIEKILENI 272
           G+ P++        ID   L+G    DS      + GIG K A +L++E+ S+E + EN+
Sbjct: 169 GVTPEQ-------IIDYLALMG----DSSDNIPGVPGIGEKTAAKLLQEYGSLEGLYENL 217

Query: 273 D 273
           D
Sbjct: 218 D 218

Length = 880

>gnl|CDD|237877 PRK14976, PRK14976, 5'-3' exonuclease; Provisional

 Score = 45.7 bits (109), Expect = 3e-05
 Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 4/68 (5%)

Query: 106 RKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDSIRG---IGPKRAIELIKEHRSI 162
           +       +     E   +  ++ ID   L+G D  D+I+G   IGPK AI+L+ ++ +I
Sbjct: 156 KGTSHFILNTNNFFELYGIEPKQIIDYKGLVG-DSSDNIKGVKGIGPKTAIKLLNKYGNI 214

Query: 163 EKILENID 170
           E I ENID
Sbjct: 215 ENIYENID 222

Length = 281

>gnl|CDD|189026 cd09856, PIN_FEN1-like, PIN domain of Flap Endonuclease-1 (FEN1)-like, structure-specific, divalent-metal-ion dependent, 5' nucleases

 Score = 44.4 bits (105), Expect = 4e-05
 Identities = 17/49 (34%), Positives = 23/49 (46%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLP 109
           AP E EAQCA +  +G V    + D D L FG+  + R+ T        
Sbjct: 114 APGEGEAQCAYLQVSGAVDGILSNDSDTLLFGAEKVYRNFTKFYKESFV 162

PIN (PilT N terminus) domain of Flap Endonuclease-1 (FEN1)-like nucleases: FEN1, Gap endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN domain with a helical arch/clamp region (I domain) of variable length (approximately 30 to 800 residues) and a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. Most nucleases within this family also have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+/Mn2+). Some nucleases in this family have C-terminal extensions that act as interaction sites for other proteins. Length = 207

>gnl|CDD|189039 cd09869, PIN_GEN1, PIN domain of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs

 Score = 44.7 bits (106), Expect = 5e-05
 Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 8/76 (10%)

Query: 318 RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGK 377
           +++ +D S  + +    V+            P  HL   F+RT  L+  G+ P++V DG 
Sbjct: 25  KRVAVDLSCWVVESQTVVKYFV--------VPKPHLRNLFFRTRYLIALGVLPVFVVDGA 76

Query: 378 PPTLKSGELNKRMEKR 393
            P LK   + KR + +
Sbjct: 77  APPLKLPVIIKRNQLQ 92

Gap Endonuclease 1 (GEN1) is a Holliday junction resolvase reported to symmetrically cleave Holliday junctions and allow religation without additional processing. GEN1 is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region (I domain) of variable length (approximately 30 - 50 residues in GEN1 PIN domains) and a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. Nucleases within this group also have a carboxylate-rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+/Mn2+). Length = 233

>gnl|CDD|189027 cd09857, PIN_EXO1, PIN domain of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs

 Score = 43.6 bits (104), Expect = 7e-05
 Identities = 27/101 (26%), Positives = 47/101 (46%), Gaps = 8/101 (7%)

Query: 311 PSSIRESR--KICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEH-G 367
           P  I E +  ++ +DA   L++   +   E        G+PT   +    + + ++ H G
Sbjct: 16  PVHISEYKGKRVAVDAYSWLHRGAYSCAEELAL-----GKPTDKYVQYCMKRVNMLLHYG 70

Query: 368 LKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGK 408
           +KPI VFDG P   K G   +R E+RE+  +   +   +G 
Sbjct: 71  IKPILVFDGGPLPSKKGTEEERRERREENLEKALELLREGN 111

Exonuclease-1 (EXO1) is involved in multiple, eukaryotic DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity), DNA repair processes (DNA mismatch repair (MMR) and post-replication repair (PRR)), recombination, and telomere integrity. EXO1 functions in the MMS2 error-free branch of the PRR pathway in the maintenance and repair of stalled replication forks. Studies also suggest that EXO1 plays both structural and catalytic roles during MMR-mediated mutation avoidance. EXO1 belongs to the FEN1-EXO1-like family of structure-specific, 5' nucleases. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region (I domain) of variable length (approximately 43 residues in EXO1 PIN domains) and a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. Nucleases within this group also have a carboxylate-rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+/Mn2+). EXO1 nucleases also have C-terminal Mlh1- and Msh2-binding domains which allow interaction with MMR and PRR proteins, respectively. Length = 210

>gnl|CDD|237877 PRK14976, PRK14976, 5'-3' exonuclease; Provisional

 Score = 43.8 bits (104), Expect = 1e-04
 Identities = 25/72 (34%), Positives = 34/72 (47%), Gaps = 13/72 (18%)

Query: 214 CDSIRGIGPK----RAIELLYS-----FIDLCILLGCDYCDSIRG---IGPKRAIELIKE 261
               +G             LY       ID   L+G D  D+I+G   IGPK AI+L+ +
Sbjct: 152 LLKKKGTSHFILNTNNFFELYGIEPKQIIDYKGLVG-DSSDNIKGVKGIGPKTAIKLLNK 210

Query: 262 HRSIEKILENID 273
           + +IE I ENID
Sbjct: 211 YGNIENIYENID 222

Length = 281

>gnl|CDD|189039 cd09869, PIN_GEN1, PIN domain of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs

 Score = 43.5 bits (103), Expect = 1e-04
 Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 6/78 (7%)

Query: 60  KAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVL 119
           +A  EAEA CA +   G V    T+D DA  +G+  + R+   SE     V  + +  + 
Sbjct: 136 QAAGEAEALCAELNSEGLVDGCITQDSDAFLYGARTVYRNFQMSEKGG-YVDCYDMSDIK 194

Query: 120 EGMELS-----HEEFIDL 132
             ++LS      E FID 
Sbjct: 195 SKLDLSWRQPDLELFIDF 212

Gap Endonuclease 1 (GEN1) is a Holliday junction resolvase reported to symmetrically cleave Holliday junctions and allow religation without additional processing. GEN1 is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region (I domain) of variable length (approximately 30 - 50 residues in GEN1 PIN domains) and a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. Nucleases within this group also have a carboxylate-rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+/Mn2+). Length = 233

>gnl|CDD|189022 cd09852, PIN_SF, PIN (PilT N terminus) domain: Superfamily

 Score = 39.4 bits (92), Expect = 6e-04
 Identities = 19/72 (26%), Positives = 22/72 (30%)

Query: 21  KNFAEDRIRNGAKKLLKARSSTTQGRLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYA 80
               E +     KK   A        L     I          EA+AQ AA+ K G V A
Sbjct: 41  LLKLEAQKGLRRKKGRVAELLLRDLELLDLMGIPVVHAPGDLYEADAQIAALAKKGHVVA 100

Query: 81  TATEDMDALTFG 92
             T D D     
Sbjct: 101 LITNDSDLRQKA 112

PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+). The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins. Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly. Length = 120

>gnl|CDD|181896 PRK09482, PRK09482, flap endonuclease-like protein; Provisional

 Score = 39.9 bits (94), Expect = 0.002
 Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 16/75 (21%)

Query: 124 LSHEEFIDLCILLGCDYCDS------IRGIGPKRAIELIKEHRSIEKILENIDTKKYTVP 177
           +  ++  D   L G     S      + GIGPK A EL+ + RS+E I E++D     +P
Sbjct: 165 VEPQQLPDYWGLAG----ISSSKIPGVAGIGPKSAAELLNQFRSLENIYESLD----ALP 216

Query: 178 EGWLYK--EARELFR 190
           E W  K  E +E+ R
Sbjct: 217 EKWRKKLEEHKEMAR 231

Length = 256

>gnl|CDD|181896 PRK09482, PRK09482, flap endonuclease-like protein; Provisional

 Score = 38.7 bits (91), Expect = 0.004
 Identities = 21/49 (42%), Positives = 30/49 (61%), Gaps = 6/49 (12%)

Query: 247 IRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYK--EARELFR 293
           + GIGPK A EL+ + RS+E I E++D     +PE W  K  E +E+ R
Sbjct: 187 VAGIGPKSAAELLNQFRSLENIYESLD----ALPEKWRKKLEEHKEMAR 231

Length = 256

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	531
PTZ00217	393	flap endonuclease-1; Provisional	100.0
PRK03980	292	flap endonuclease-1; Provisional	100.0
TIGR03674	338	fen_arch flap structure-specific endonuclease. End	100.0
cd00128	316	XPG Xeroderma pigmentosum G N- and I-regions (XPGN	100.0
TIGR00600	1034	rad2 DNA excision repair protein (rad2). All prote	100.0
KOG2519|consensus	449		100.0
KOG2518|consensus	556		100.0
smart00475	259	53EXOc 5'-3' exonuclease.	99.96
PTZ00217	393	flap endonuclease-1; Provisional	99.95
PRK14976	281	5'-3' exonuclease; Provisional	99.95
KOG2519|consensus	449		99.95
cd00008	240	53EXOc 5'-3' exonuclease; T5 type 5'-3' exonucleas	99.95
PRK09482	256	flap endonuclease-like protein; Provisional	99.94
TIGR03674	338	fen_arch flap structure-specific endonuclease. End	99.94
KOG2520|consensus	815		99.93
TIGR00593	887	pola DNA polymerase I. This family is based on the	99.93
PRK05755	880	DNA polymerase I; Provisional	99.91
COG0258	310	Exo 5'-3' exonuclease (including N-terminal domain	99.91
PF00867	94	XPG_I: XPG I-region; InterPro: IPR006086 This entr	99.89
PRK03980	292	flap endonuclease-1; Provisional	99.85
cd00128	316	XPG Xeroderma pigmentosum G N- and I-regions (XPGN	99.85
TIGR00600	1034	rad2 DNA excision repair protein (rad2). All prote	99.82
PF00752	101	XPG_N: XPG N-terminal domain; InterPro: IPR006085	99.81
smart00485	99	XPGN Xeroderma pigmentosum G N-region. domain in n	99.8
PHA00439	286	exonuclease	99.8
smart00484	73	XPGI Xeroderma pigmentosum G I-region. domain in n	99.76
KOG2518|consensus	556		99.7
PHA02567	304	rnh RnaseH; Provisional	99.53
cd00080	75	HhH2_motif Helix-hairpin-helix class 2 (Pol1 famil	99.46
COG0258	310	Exo 5'-3' exonuclease (including N-terminal domain	99.24
PF02739	169	5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolv	99.17
PF01367	101	5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold	99.13
cd00080	75	HhH2_motif Helix-hairpin-helix class 2 (Pol1 famil	99.1
smart00279	36	HhH2 Helix-hairpin-helix class 2 (Pol1 family) mot	98.96
smart00279	36	HhH2 Helix-hairpin-helix class 2 (Pol1 family) mot	98.6
cd00008	240	53EXOc 5'-3' exonuclease; T5 type 5'-3' exonucleas	98.31
PF12813	246	XPG_I_2: XPG domain containing	98.22
PRK14976	281	5'-3' exonuclease; Provisional	98.16
smart00475	259	53EXOc 5'-3' exonuclease.	98.15
KOG2520|consensus	815		97.87
PRK09482	256	flap endonuclease-like protein; Provisional	97.76
PRK05755	880	DNA polymerase I; Provisional	97.64
TIGR00593	887	pola DNA polymerase I. This family is based on the	97.61
PF01367	101	5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold	96.97
PF12826	64	HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS	96.61
PRK14602	203	ruvA Holliday junction DNA helicase RuvA; Provisio	96.16
PRK13901	196	ruvA Holliday junction DNA helicase RuvA; Provisio	95.86
PRK14601	183	ruvA Holliday junction DNA helicase RuvA; Provisio	95.79
PRK14600	186	ruvA Holliday junction DNA helicase RuvA; Provisio	95.78
PRK14603	197	ruvA Holliday junction DNA helicase RuvA; Provisio	95.73
PRK14606	188	ruvA Holliday junction DNA helicase RuvA; Provisio	95.69
PRK14604	195	ruvA Holliday junction DNA helicase RuvA; Provisio	95.69
COG0632	201	RuvA Holliday junction resolvasome, DNA-binding su	95.59
COG5366	531	Protein involved in propagation of M2 dsRNA satell	95.33
PRK14605	194	ruvA Holliday junction DNA helicase RuvA; Provisio	95.09
TIGR00084	191	ruvA Holliday junction DNA helicase, RuvA subunit.	95.0
PRK00116	192	ruvA Holliday junction DNA helicase RuvA; Reviewed	94.09
PF02739	169	5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolv	93.94
PRK07956	665	ligA NAD-dependent DNA ligase LigA; Validated	91.05
TIGR00575	652	dnlj DNA ligase, NAD-dependent. The member of this	89.74
PF10391	52	DNA_pol_lambd_f: Fingers domain of DNA polymerase	88.96
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	87.74
PF12826	64	HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS	87.11
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	85.63
PF00633	30	HHH: Helix-hairpin-helix motif; InterPro: IPR00044	84.38
PF04599	425	Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 P	84.06
PRK14667	567	uvrC excinuclease ABC subunit C; Provisional	83.82
PHA00439	286	exonuclease	83.55
PRK14669	624	uvrC excinuclease ABC subunit C; Provisional	83.2
PHA03065	438	Hypothetical protein; Provisional	82.38
TIGR00194	574	uvrC excinuclease ABC, C subunit. This family cons	81.57
PRK14670	574	uvrC excinuclease ABC subunit C; Provisional	81.48
PF00633	30	HHH: Helix-hairpin-helix motif; InterPro: IPR00044	81.02
PF14520	60	HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU	80.3
COG0272	667	Lig NAD-dependent DNA ligase (contains BRCT domain	80.26

>PTZ00217 flap endonuclease-1; Provisional

Probab=100.00  E-value=1.1e-44  Score=383.25  Aligned_cols=245  Identities=51%  Similarity=0.831  Sum_probs=212.7

Q ss_pred             ceeecccCCCCCcchhH------HhHH----------------HHHHhhccCCCH---HHHHHHHhhcCCccccCCCchh
Q psy1206          12 GLVKYLCGDKNFAEDRI------RNGA----------------KKLLKARSSTTQ---GRLDSFFTIRREEKRKAPCEAE   66 (531)
Q Consensus        12 ~~~a~~~~~~~f~~~~~------R~~~----------------~~~~k~~~~~t~---~~i~~lL~~~gIp~vvAPyEAD   66 (531)
                      -++.||.+.++++..++      |..+                ..++++...+|+   +.++++|+++||||++||||||
T Consensus        83 Pv~VFDG~~p~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~r~~~vt~~~~~~~~~lL~~~Gip~i~AP~EAd  162 (393)
T PTZ00217         83 PVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPCEAE  162 (393)
T ss_pred             EEEEEcCCCchhhHHHHHHHHHHHHHhHHHHHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCCceEECCcCHH
Confidence            46899998888876542      2222                123444455666   4578899999999999999999


Q ss_pred             HHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcCCCCCCCCCC
Q psy1206          67 AQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDSIRG  146 (531)
Q Consensus        67 Aq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G~DY~pGIpG  146 (531)
                      ||||+|++.|++|+|+|+|+|+|+||++.|+++++.++..+.+++.++++.+++.+|++++||+|+|+|+||||+|||||
T Consensus       163 aq~A~L~~~g~v~~ViS~D~D~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~iL~G~Dy~pgi~G  242 (393)
T PTZ00217        163 AQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTVLEELGLSMDQFIDLCILCGCDYCDTIKG  242 (393)
T ss_pred             HHHHHHHHCCCeEEEeCCCcCeeecCCcEEEEcccccccCCCCeEEEEHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCC
Confidence            99999999999999999999999999999999987654444467899999999999999999999999999999999999


Q ss_pred             ccHHHHHHHHHHcCCHHHHHHHhhhcCCCCCCCCcHHHHHHHhcCCCcCCCCCcccccccccccccccccccCCChhhhH
Q psy1206         147 IGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFIDLCILLGCDYCDSIRGIGPKRAI  226 (531)
Q Consensus       147 IG~ktA~kLI~~~~sle~il~~l~~~~~~ip~~f~~~~A~~~f~~p~V~d~~~~~~v~Ls~~~~~d~cesl~~~Gp~~~~  226 (531)
                      ||+|||++||++|+|+|+|+++++.                                                       
T Consensus       243 IG~ktA~~Li~~~gsle~il~~~~~-------------------------------------------------------  267 (393)
T PTZ00217        243 IGPKTAYKLIKKYKSIEEILEHLDK-------------------------------------------------------  267 (393)
T ss_pred             ccHHHHHHHHHHcCCHHHHHHHHHh-------------------------------------------------------
Confidence            9999999999999999999987632                                                       


Q ss_pred             hHHhhhhhhhhhccCccccCCCCCchHHHHHHHHhhccHHHHHHHHhhCCCCCCCcchHHHHHHHhcCCcccCccccccc
Q psy1206         227 ELLYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIADPETIELV  306 (531)
Q Consensus       227 el~e~F~~~CiLsGCDY~~~i~giG~k~A~kli~k~~s~~~vi~~l~~~~~~vP~~y~~~~A~~~F~~~~V~dP~~~~Lv  306 (531)
                                                                      .++.+|++|+|.+|+.+|+||.|+||.+    
T Consensus       268 ------------------------------------------------~k~~~p~~~~~~~~~~~f~~p~V~~~~~----  295 (393)
T PTZ00217        268 ------------------------------------------------TKYPVPENFDYKEARELFLNPEVTPAEE----  295 (393)
T ss_pred             ------------------------------------------------cCCCCCCCCChHHHHHHhcCCCcCCCCC----
Confidence                                                            1245799999999999999999999831    


Q ss_pred             cccCCCcccccceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHH
Q psy1206         307 ADVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGEL  386 (531)
Q Consensus       307 ~~~aP~~i~~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~  386 (531)
                                                                                                      
T Consensus       296 --------------------------------------------------------------------------------  295 (393)
T PTZ00217        296 --------------------------------------------------------------------------------  295 (393)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             HHHHHHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhccCCcCccccccccchhh
Q psy1206         387 NKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFTIRREE  463 (531)
Q Consensus       387 ~kR~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~rld~ff~~~~~~  463 (531)
                                          -+++|+.||.+++++|++.+..|..++|.+.+.+|.+++++.+|+|||+||++.++.
T Consensus       296 --------------------~~l~w~~pD~~~l~~fl~~e~~f~~~rv~~~i~rl~~~~~~~~Q~~l~~ff~~~~~~  352 (393)
T PTZ00217        296 --------------------IDLKWNEPDEEGLKKFLVKEKNFNEERVEKYIERLKKAKTKKTQTRLDSFFTATKKP  352 (393)
T ss_pred             --------------------CCCCCCCCCHHHHHHHHHhccCCCHHHHHHHHHHHHHHhccCccCCHHHhcCCCCCc
Confidence                                136799999999999999999999999999999999999999999999999998664

>PRK03980 flap endonuclease-1; Provisional

Probab=100.00  E-value=2.6e-41  Score=345.11  Aligned_cols=160  Identities=35%  Similarity=0.549  Sum_probs=134.7

Q ss_pred             CccceeecccCCCCCcchhH------HhHHH----------------HHHhhccCCCH---HHHHHHHhhcCCccccCCC
Q psy1206           9 DEDGLVKYLCGDKNFAEDRI------RNGAK----------------KLLKARSSTTQ---GRLDSFFTIRREEKRKAPC   63 (531)
Q Consensus         9 d~~~~~a~~~~~~~f~~~~~------R~~~~----------------~~~k~~~~~t~---~~i~~lL~~~gIp~vvAPy   63 (531)
                      ...-++.||.+.++++.++.      |..+.                +++++...+|+   +.++++|+++||||++|||
T Consensus        25 gi~PvfVFDG~~p~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~~a~k~~~~~~~vt~~~~~~~k~lL~~~GIp~i~AP~  104 (292)
T PRK03980         25 GIKPVYVFDGKPPELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQRSSRLTDEIVEDSKKLLDLMGIPYVQAPS  104 (292)
T ss_pred             CCEEEEEECCCCchHHHHHHHHHHHHHHHhHHHHHHHHHcCCHHHHHHHHhccccCCHHHHHHHHHHHHHCCCCEEecCc
Confidence            34458999999888875543      22221                22333445565   4578899999999999999


Q ss_pred             chhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccC---------CcEEecHHHHHHhCCCCHHHHHHHHh
Q psy1206          64 EAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKL---------PVQEFHLEKVLEGMELSHEEFIDLCI  134 (531)
Q Consensus        64 EADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~---------~v~~~~~~~i~~~lglt~eqfid~~i  134 (531)
                      |||||||+|++.|++|+|+|+|+|+|+||+++|+++++..+.+++         ..+.++.+.+++.+|++++||+|+|+
T Consensus       105 EAEAq~A~L~~~g~vd~V~S~D~D~l~fg~~~vir~l~~~~~~~~p~~~~~~~~~~e~~~~~~vl~~lgl~~~q~id~~i  184 (292)
T PRK03980        105 EGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNVYVEVKPELIELEEVLKELGITREQLIDIAI  184 (292)
T ss_pred             hHHHHHHHHHHCCCeEEEecCCcCeeeecCCEEEEeecccccccCccccccccccceeeeHHHHHHHhCCCHHHHHHHHH
Confidence            999999999999999999999999999999999999977654322         34579999999999999999999999


Q ss_pred             HcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206         135 LLGCDYCDSIRGIGPKRAIELIKEHRSIEKILEN  168 (531)
Q Consensus       135 L~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~  168 (531)
                      |+||||+|||||||+|||++||++|+|+|+|+++
T Consensus       185 L~G~Dy~~GI~GIG~ktA~kLi~~~~sle~i~~~  218 (292)
T PRK03980        185 LVGTDYNPGIKGIGPKTALKLIKKHGDLEKVLEE  218 (292)
T ss_pred             hcCCCCCCCCCCccHHHHHHHHHHCCCHHHHHHh
Confidence            9999999999999999999999999999999873

>TIGR03674 fen_arch flap structure-specific endonuclease

Probab=100.00  E-value=7.2e-37  Score=318.41  Aligned_cols=158  Identities=34%  Similarity=0.527  Sum_probs=133.3

Q ss_pred             ceeecccCCCCCcchh------HHhHHHHH----------------HhhccCCCH---HHHHHHHhhcCCccccCCCchh
Q psy1206          12 GLVKYLCGDKNFAEDR------IRNGAKKL----------------LKARSSTTQ---GRLDSFFTIRREEKRKAPCEAE   66 (531)
Q Consensus        12 ~~~a~~~~~~~f~~~~------~R~~~~~~----------------~k~~~~~t~---~~i~~lL~~~gIp~vvAPyEAD   66 (531)
                      -++.||.+.++|+..+      .|..+.+.                .++...+|+   +.++++|+++||||++||+|||
T Consensus        75 Pv~VFDG~~p~~K~~~~~~R~~~r~~a~~~~~~~~~~g~~~~a~~~~~r~~~~~~~~~~~~k~lL~~~Gip~i~AP~EAe  154 (338)
T TIGR03674        75 PVYVFDGKPPELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPSEGE  154 (338)
T ss_pred             EEEEECCCChhhhHhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCCeEEECCccHH
Confidence            4899999998886333      34443222                223344555   4578999999999999999999


Q ss_pred             HHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccC---------CcEEecHHHHHHhCCCCHHHHHHHHhHcC
Q psy1206          67 AQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKL---------PVQEFHLEKVLEGMELSHEEFIDLCILLG  137 (531)
Q Consensus        67 Aq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~---------~v~~~~~~~i~~~lglt~eqfid~~iL~G  137 (531)
                      ||||+|++.|.||+|+|+|+|+|+||+++|+++++..+.++.         ..+.++.+.+++.+|++++||+|+|+|+|
T Consensus       155 aq~a~L~~~g~vd~v~S~D~D~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~e~~~~~~v~~~lgl~~~q~id~~iL~G  234 (338)
T TIGR03674       155 AQAAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNIYVEVKPELIELEEVLSELGITREQLIDIAILVG  234 (338)
T ss_pred             HHHHHHHHCCCeeEEecCCcCeeeecCCEEEEecccccccCCCcccccccccceeeeHHHHHHHhCCCHHHHHHHHHhcC
Confidence            999999999999999999999999999999999876553221         34568999999999999999999999999


Q ss_pred             CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHh
Q psy1206         138 CDYCDSIRGIGPKRAIELIKEHRSIEKILENI  169 (531)
Q Consensus       138 ~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l  169 (531)
                      |||+|||||||+|||++||++|+|+|+|++++
T Consensus       235 ~dyn~Gv~GIG~ktA~kli~~~gsie~il~~~  266 (338)
T TIGR03674       235 TDYNEGVKGIGPKTALKLIKEHGDLEKVLKAR  266 (338)
T ss_pred             CCCCCCCCCccHHHHHHHHHHcCCHHHHHHhh
Confidence            99999999999999999999999999998764

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

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

Probab=100.00  E-value=1.5e-35  Score=305.48  Aligned_cols=213  Identities=36%  Similarity=0.492  Sum_probs=171.4

Q ss_pred             ccceeecccCCCCCcchh------HHhHHHH----------------HHhhccCCCH---HHHHHHHhhcCCccccCCCc
Q psy1206          10 EDGLVKYLCGDKNFAEDR------IRNGAKK----------------LLKARSSTTQ---GRLDSFFTIRREEKRKAPCE   64 (531)
Q Consensus        10 ~~~~~a~~~~~~~f~~~~------~R~~~~~----------------~~k~~~~~t~---~~i~~lL~~~gIp~vvAPyE   64 (531)
                      ...++.||.+.+++++.+      .|.++..                +..+...+++   +.++++|+++||||++||||
T Consensus        71 i~pvfVFDG~~~~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~gi~~i~ap~E  150 (316)
T cd00128          71 IKPVFVFDGKPPPLKAETLAKRRERREEAEEEAKEALEKGLEEEAKKLERRAVRVTPQMIEEAKELLRLMGIPYIVAPYE  150 (316)
T ss_pred             CEEEEEEcCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhccCcCCHHHHHHHHHHHHHcCCCEEECCcC
Confidence            347889999888887433      2322211                1112223444   56788999999999999999


Q ss_pred             hhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcCCCCCCCC
Q psy1206          65 AEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDSI  144 (531)
Q Consensus        65 ADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G~DY~pGI  144 (531)
                      ||||||+|+++|.+|+|+|+|||+|+||+++|+++++..+.  ..++.++.+.+.+.+|++++||+|+|+|+||||+|||
T Consensus       151 Adaq~a~l~~~g~v~~i~S~DsD~l~fg~~~vi~~~~~~~~--~~~~~~~~~~~~~~lgl~~~q~id~~~L~G~Dy~~gv  228 (316)
T cd00128         151 AEAQCAYLAKKGLVDAIITEDSDLLLFGAPRVYRNLFDSGA--KPVEEIDLEKILKELGLTREKLIDLAILLGCDYTEGI  228 (316)
T ss_pred             HHHHHHHHHhCCCeeEEEecCCCeeeecCceEEEecccCCC--CceEEEEHHHHHHHcCCCHHHHHHHHHhcCCCCCCCC
Confidence            99999999999999999999999999999999999876441  2467899999999999999999999999999999999


Q ss_pred             CCccHHHHHHHHHHcCCHHHHHHHhhhcCCCCCCCCcHHHHHHHhcCCCcCCC-CCcccccccccccccccccccCCChh
Q psy1206         145 RGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADP-ETIEFIDLCILLGCDYCDSIRGIGPK  223 (531)
Q Consensus       145 pGIG~ktA~kLI~~~~sle~il~~l~~~~~~ip~~f~~~~A~~~f~~p~V~d~-~~~~~v~Ls~~~~~d~cesl~~~Gp~  223 (531)
                      ||||+|||++||++|+|++.+++++......+|.+|++..++..|.+|.|.+. ....|..........++....+|.+.
T Consensus       229 ~giG~k~A~~li~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~f~~p~~~~~~~~~~~~~p~~~~l~~~~~~~~~~~~~  308 (316)
T cd00128         229 PGIGPVTALKLIKKYGDIEKDIERLKKKLYRSPEDFPLKEAREFFLNPEVTDDFIDLRWRDPDEEGIIEFLCKEHGFNED  308 (316)
T ss_pred             CCccHHHHHHHHHHcCChHHHHHHHHHhCccCCCcCChHHHHHHHcCCCCCCCCCceeecCCCHHHHHHHccCCCCCCHH
Confidence            99999999999999999999999999887788899999999999999998875 44555444333333444445556543


Q ss_pred             h
Q psy1206         224 R  224 (531)
Q Consensus       224 ~  224 (531)
                      +
T Consensus       309 r  309 (316)
T cd00128         309 R  309 (316)
T ss_pred             H
Confidence            3

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.

>TIGR00600 rad2 DNA excision repair protein (rad2)

Probab=100.00  E-value=8.3e-35  Score=333.23  Aligned_cols=228  Identities=22%  Similarity=0.380  Sum_probs=184.6

Q ss_pred             CCCHHH---HHHHHhhcCCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHH
Q psy1206          41 STTQGR---LDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEK  117 (531)
Q Consensus        41 ~~t~~~---i~~lL~~~gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~  117 (531)
                      .+|+.+   ++++|++||||||+||+|||||||+|++.|+||+|+|+|+|+|+||+++|++++...+   ..+..|+.++
T Consensus       768 ~vt~~m~~~~~~LL~~~GIP~i~AP~EAEAqcA~L~~~G~vd~V~TeDsD~llFGa~~v~rn~~~~~---~~ve~~~~~~  844 (1034)
T TIGR00600       768 EVTGQMILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFNQN---KFVEYYQYVD  844 (1034)
T ss_pred             cCCHHHHHHHHHHHHHCCCCeeeCCccHHHHHHHHHhCCCeEEEEccccceeccCCceeeecccCCC---CceEEeeHHH
Confidence            566654   5788999999999999999999999999999999999999999999999999985322   2578899999


Q ss_pred             HHHhCCCCHHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcC--CHHHHHHH---hhhcCCCCCCCCcHHHHHHHhcCC
Q psy1206         118 VLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHR--SIEKILEN---IDTKKYTVPEGWLYKEARELFRHP  192 (531)
Q Consensus       118 i~~~lglt~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~--sle~il~~---l~~~~~~ip~~f~~~~A~~~f~~p  192 (531)
                      +++.+|+++++|+++|+|+||||++||||||++||++||++|+  +++.+++.   +...             .   ...
T Consensus       845 i~~~lglt~~qli~laiL~G~DY~~GI~GIGpktAl~li~~~~~~~le~L~~f~~w~~~~-------------~---~~~  908 (1034)
T TIGR00600       845 IHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEFPGDGLEPLLKFKEWWHEA-------------Q---KDK  908 (1034)
T ss_pred             HHHHhCCCHHHHHHHHHeeCCCCCCCCCcccHHHHHHHHHHcCCCCHHHHHHHHHHHHHh-------------h---hcc
Confidence            9999999999999999999999999999999999999999999  47776642   2110             0   000


Q ss_pred             CcCCCCCcccccccccccccccccccCCChhhhHhHHhhhhhhhhhccCccccCCCCCchHHHHHHHHhhccHHHHHHHH
Q psy1206         193 EVADPETIEFIDLCILLGCDYCDSIRGIGPKRAIELLYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENI  272 (531)
Q Consensus       193 ~V~d~~~~~~v~Ls~~~~~d~cesl~~~Gp~~~~el~e~F~~~CiLsGCDY~~~i~giG~k~A~kli~k~~s~~~vi~~l  272 (531)
                      .. .+.                       +                         .        ++.          ...
T Consensus       909 ~~-~~~-----------------------~-------------------------~--------~~~----------~~~  921 (1034)
T TIGR00600       909 KK-REN-----------------------P-------------------------N--------DTK----------VKK  921 (1034)
T ss_pred             cc-ccc-----------------------c-------------------------c--------hhh----------hhh
Confidence            00 000                       0                         0        000          000


Q ss_pred             hhCCCCCCCcchHHHHHHHhcCCcccCccccccccccCCCcccccceeeecccchHHHHHHHHhhcCccccCCCCCCcch
Q psy1206         273 DTKKYTVPEGWLYKEARELFRHPEIADPETIELVADVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSH  352 (531)
Q Consensus       273 ~~~~~~vP~~y~~~~A~~~F~~~~V~dP~~~~Lv~~~aP~~i~~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tsh  352 (531)
                      +..++.+|++|++..++.+|++|.|-+.                                                    
T Consensus       922 ~~~~~~lp~~FP~~~V~~~yl~P~V~~~----------------------------------------------------  949 (1034)
T TIGR00600       922 KLRLLQLTPGFPNPAVADAYLRPVVDDS----------------------------------------------------  949 (1034)
T ss_pred             cccccccCCCCCcHHHHHHhcCCCCCCC----------------------------------------------------
Confidence            1123569999999999999999998643                                                    


Q ss_pred             hhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHHHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchH
Q psy1206         353 LMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAED  432 (531)
Q Consensus       353 l~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~  432 (531)
                                                                           .+.+.|+.||.++++.|++.+..+..+
T Consensus       950 -----------------------------------------------------~~~f~W~~PD~e~L~~Fl~~~~gws~e  976 (1034)
T TIGR00600       950 -----------------------------------------------------KGSFLWGKPDLDKIREFCQRYFGWNRE  976 (1034)
T ss_pred             -----------------------------------------------------cCCCCCCCCCHHHHHHHHHHccCCCHH
Confidence                                                                 134689999999999999999999999


Q ss_pred             HHHHHHHHHHH-HhccCCcCcccccccc
Q psy1206         433 RIRNGAKKLLK-ARSTTTQGRLDSFFTI  459 (531)
Q Consensus       433 ~~~~~~~~ll~-~~~~~~~~rld~ff~~  459 (531)
                      ++.+.+.++++ +..+.+|+|||+||++
T Consensus       977 Rv~~~l~plikk~~~~~~Q~~ld~FF~~ 1004 (1034)
T TIGR00600       977 KTDEVLLPVLKKLNAQQTQLRIDSFFRL 1004 (1034)
T ss_pred             HHHHHHHHHHHHHHccCCccCHHHhhCc
Confidence            99999999987 5567889999999995

All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG2519|consensus

Probab=100.00  E-value=7.8e-34  Score=298.04  Aligned_cols=250  Identities=46%  Similarity=0.798  Sum_probs=211.7

Q ss_pred             CccceeecccCCCCCcchhHHhHHHHH----------------------HhhccCCCH---HHHHHHHhhcCCccccCCC
Q psy1206           9 DEDGLVKYLCGDKNFAEDRIRNGAKKL----------------------LKARSSTTQ---GRLDSFFTIRREEKRKAPC   63 (531)
Q Consensus         9 d~~~~~a~~~~~~~f~~~~~R~~~~~~----------------------~k~~~~~t~---~~i~~lL~~~gIp~vvAPy   63 (531)
                      +.+.++-||.+-+.++.++........                      .++-..+|-   .-.+.+|..|||||+.||+
T Consensus        74 gi~Pv~VfDG~pP~lKs~e~~kR~~rr~~a~~~~~~~~e~~~~~~~~k~~~r~vkvtk~~~dEak~LL~lmGIp~i~ap~  153 (449)
T KOG2519|consen   74 GIKPVYVFDGKPPDLKSQELAKRSERRSEADKELKPAKEAGAKENMEKFFSRLVKVTKQHNDEAKRLLSLMGIPVLDAPG  153 (449)
T ss_pred             CCcEEEEECCCCCCcchHHHHHHHHHhhhhhhhhhhHHHhhhHHHHHHHHHHHhhhcchhhHHHHHHHHHcCCeeecCCc
Confidence            455788899888888755432222111                      111111111   2467899999999999999


Q ss_pred             chhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcCCCCCCC
Q psy1206          64 EAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDS  143 (531)
Q Consensus        64 EADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G~DY~pG  143 (531)
                      ||+||||+|++.|.|++++|+|||.|.||++.+++++..+.+++.++.+|+++.+++.++++.++|+|+|+|+||||+++
T Consensus       154 EAEAqCA~Lnk~g~V~~~at~DsD~l~fg~~~~lr~l~~s~~~~~pv~e~~~~~il~~l~l~~~~fidL~lLlGCDYc~~  233 (449)
T KOG2519|consen  154 EAEAQCAALNKAGKVYAVATEDSDALTFGAPVKLRHLIHSLASGLPVSEYDMSRILEGLGLSRESFIDLCLLLGCDYCPT  233 (449)
T ss_pred             hHHHHHHHHhhcCceeeeeccccchhhccCHHHHHHhccchhcCCCeEEeeHHHHHHHhcccHHHHHHHHHHhcCccccc
Confidence            99999999999999999999999999999999999987765666799999999999999999999999999999999999


Q ss_pred             CCCccHHHHHHHHHHcCCHHHHHHHhhhcCCCCCCCCcHHHHHHHhcCCCcCCCCCcccccccccccccccccccCCChh
Q psy1206         144 IRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFIDLCILLGCDYCDSIRGIGPK  223 (531)
Q Consensus       144 IpGIG~ktA~kLI~~~~sle~il~~l~~~~~~ip~~f~~~~A~~~f~~p~V~d~~~~~~v~Ls~~~~~d~cesl~~~Gp~  223 (531)
                      |.|||+++|++||++|++++++++-                                                       
T Consensus       234 I~Gig~~~al~lir~~~~i~~ile~-------------------------------------------------------  258 (449)
T KOG2519|consen  234 IRGIGPKKALKLIRQHGDIENILEI-------------------------------------------------------  258 (449)
T ss_pred             ccccChHHHHHHHHHhcCHHHHhhh-------------------------------------------------------
Confidence            9999999999999999998888752                                                       


Q ss_pred             hhHhHHhhhhhhhhhccCccccCCCCCchHHHHHHHHhhccHHHHHHHHhhCCCCCCCcchHHHHHHHhcCCcccCcccc
Q psy1206         224 RAIELLYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIADPETI  303 (531)
Q Consensus       224 ~~~el~e~F~~~CiLsGCDY~~~i~giG~k~A~kli~k~~s~~~vi~~l~~~~~~vP~~y~~~~A~~~F~~~~V~dP~~~  303 (531)
                                                                     ....+.++||++|++..|+..|..+.|-+|+..
T Consensus       259 -----------------------------------------------~~~~~~~~ip~~w~~~~~r~~f~~p~~~~~~~~  291 (449)
T KOG2519|consen  259 -----------------------------------------------NSDLKEYPIPEDWSYKLARKLFLEPEFPNPESI  291 (449)
T ss_pred             -----------------------------------------------ccchhhcCCCCCccHHHHHHHhcCcccCCccce
Confidence                                                           001235789999999999999999999888421


Q ss_pred             ccccccCCCcccccceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcch
Q psy1206         304 ELVADVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKS  383 (531)
Q Consensus       304 ~Lv~~~aP~~i~~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~  383 (531)
                                                                                                      
T Consensus       292 --------------------------------------------------------------------------------  291 (449)
T KOG2519|consen  292 --------------------------------------------------------------------------------  291 (449)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhccCCcCccccccccchhh
Q psy1206         384 GELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFTIRREE  463 (531)
Q Consensus       384 ~~~~kR~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~rld~ff~~~~~~  463 (531)
                                             =++.|..||++++.+|++.+..|..+++.....+++..++..+|||+|+||+..++-
T Consensus       292 -----------------------~~i~w~~pd~~~li~fl~~~~~f~~~rv~~~~~kl~~~~~~~~qgrl~~f~~~~~~~  348 (449)
T KOG2519|consen  292 -----------------------LDLKWKTPDTEGLIQFLVGEKQFNEERVRKGIRKLKSSLKLGTQGRLDSFFKRIPKG  348 (449)
T ss_pred             -----------------------eecccCCCChHHHHHHHHhhhccCHHHHhhhhHHHhhhhccccccchhhhhcccCCC
Confidence                                   246899999999999999889999999999999999999999999999999997763

>KOG2518|consensus

Probab=100.00  E-value=4.1e-34  Score=303.03  Aligned_cols=188  Identities=28%  Similarity=0.399  Sum_probs=159.5

Q ss_pred             HHHhhccCCCHHHH---HHHHhhcCCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCc
Q psy1206          34 KLLKARSSTTQGRL---DSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPV  110 (531)
Q Consensus        34 ~~~k~~~~~t~~~i---~~lL~~~gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v  110 (531)
                      ..|..+.++|++++   .++|+..||+|||||||||||||||++.|+|++|||||||+++|||++||++|+..|.    .
T Consensus       117 ~~fqr~VdIT~~ma~~lI~~~r~~nVe~IVAPyEADAQlayL~~~~~i~~IITEDSDLl~fGc~~vifK~d~~G~----~  192 (556)
T KOG2518|consen  117 ECFQRCVDITPEMAHKLIQYLRSQNVEYIVAPYEADAQLAYLEREGIVDAIITEDSDLLVFGCKKVIFKMDSFGN----G  192 (556)
T ss_pred             HHHHHhccCcHHHHHHHHHHHHHcCCceEecCccccchhHHHHhcCcceEEEeccccccccCchhheeeccCCCC----c
Confidence            35888889999764   5567788999999999999999999999999999999999999999999999986553    2


Q ss_pred             EEecHHHHHHhC----CCCHHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHH-HhhhcCCCCCCCCc--HH
Q psy1206         111 QEFHLEKVLEGM----ELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILE-NIDTKKYTVPEGWL--YK  183 (531)
Q Consensus       111 ~~~~~~~i~~~l----glt~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~-~l~~~~~~ip~~f~--~~  183 (531)
                      ..++...+.+..    +++.++|+.||+|+||||++||||||.+||+++|++|.+.+.++. .+...+..+|++|.  |.
T Consensus       193 le~~~~~l~~~~~l~~~~~~ekfr~mciLSGCDYl~slpGvGl~tA~k~l~k~~~~d~vi~~~~~~~~l~Vpd~y~~~F~  272 (556)
T KOG2518|consen  193 LEINRSKLPECKPLGDKFTEEKFRRMCILSGCDYLSSLPGVGLATAHKLLSKYNTPDRVIISHLLKKKLTVPDDYIENFE  272 (556)
T ss_pred             ccccHhhhhhccccccccCHHHHHHHHHhcCCcccccCccccHHHHHHHHHhcCcHHHHHHHHHhccCCcCCHHHHHHHH
Confidence            344555554433    478999999999999999999999999999999999999999865 45566788999996  99


Q ss_pred             HHHHHhcCCCcCCCCCcccccccccccccccccccCCChhhh
Q psy1206         184 EARELFRHPEVADPETIEFIDLCILLGCDYCDSIRGIGPKRA  225 (531)
Q Consensus       184 ~A~~~f~~p~V~d~~~~~~v~Ls~~~~~d~cesl~~~Gp~~~  225 (531)
                      +|..+|+|+.||||..+++++|++.+....-+.+.+.|+...
T Consensus       273 ~A~~tF~hQrVydP~~k~~~~L~~~~~~l~~~~~~~~g~~~~  314 (556)
T KOG2518|consen  273 RANLTFLHQRVYDPIEKKLIHLNPIEDELDNEDLEFLGPLKD  314 (556)
T ss_pred             HHHHhhhhhheeCchHhhhhcCCchhhhcchhhHhhcccccC
Confidence            999999999999999999999999765443355566665443

>smart00475 53EXOc 5'-3' exonuclease

Probab=99.96  E-value=1.5e-29  Score=254.80  Aligned_cols=158  Identities=27%  Similarity=0.307  Sum_probs=136.4

Q ss_pred             CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCH-------HHHHHHHhhcCCccccCC-CchhHHHHHHHHc---
Q psy1206           7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ-------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVKA---   75 (531)
Q Consensus         7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~-------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r~---   75 (531)
                      +|++ ++++||.+.++|     |++.++.||++|..+|       +.++++|+++|||++.+| |||||+||+|+++   
T Consensus        48 ~p~~-~~~~fD~~~~~~-----R~~l~p~YKa~R~~~pe~L~~q~~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~  121 (259)
T smart00475       48 KPTY-VAVVFDAKGKTF-----RHELYPEYKANRPKTPDELLEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEA  121 (259)
T ss_pred             CCCe-EEEEEeCCCCcc-----ccchhHHHHhCCCCCCHHHHHHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHh
Confidence            7999 999999776666     5556788899998888       467899999999999887 6999999999974   


Q ss_pred             -CCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcC--CCCCCCCCCccHHHH
Q psy1206          76 -GKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLG--CDYCDSIRGIGPKRA  152 (531)
Q Consensus        76 -G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G--~DY~pGIpGIG~ktA  152 (531)
                       |..++|+|+|+|++++++++|......++..  ....++.+.+.+.+|++|+||+|+++|+|  |||+|||||||+|||
T Consensus       122 ~g~~~~IvS~DkDl~ql~~~~v~~~~~~~~~~--~~~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGV~GIG~KtA  199 (259)
T smart00475      122 EGYEVRIVSGDKDLLQLVSDKVSVLDPTKGIK--EFELYTPENVIEKYGLTPEQIIDYKALMGDSSDNIPGVPGIGEKTA  199 (259)
T ss_pred             CCCeEEEEeCCCcHhhcCCCCEEEEeccCCCC--ccEEEcHHHHHHHhCcCHHHHHHHHHHhCCcccCCCCCCCCCHHHH
Confidence             7889999999999999998774322223221  24579999999999999999999999999  999999999999999


Q ss_pred             HHHHHHcCCHHHHHHHhhhc
Q psy1206         153 IELIKEHRSIEKILENIDTK  172 (531)
Q Consensus       153 ~kLI~~~~sle~il~~l~~~  172 (531)
                      .+||++|+|+|+|+++++..
T Consensus       200 ~~Ll~~ygsle~i~~~~~~~  219 (259)
T smart00475      200 AKLLKEFGSLENILENLDKL  219 (259)
T ss_pred             HHHHHHhCCHHHHHHHHHHH
Confidence            99999999999999998763

>PTZ00217 flap endonuclease-1; Provisional

Probab=99.95  E-value=2.2e-28  Score=259.19  Aligned_cols=136  Identities=51%  Similarity=0.774  Sum_probs=127.1

Q ss_pred             ccccccCCCcccc-------cceeeecccchHHHHHHHHhh--cCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEee
Q psy1206         304 ELVADVAPSSIRE-------SRKICIDASMSLYQFLIAVRS--EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVF  374 (531)
Q Consensus       304 ~Lv~~~aP~~i~~-------gk~iAIDa~~~lyqfl~~ir~--~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVF  374 (531)
                      .++.+++|.++.+       |++||||||+|||||++++|+  +|.+|+|+.|++|+||+|+|+|+++|+++||+|||||
T Consensus         8 ~~l~~~~p~~~~~~~l~~l~gk~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~G~~t~~l~g~~~r~~~Ll~~gikPv~VF   87 (393)
T PTZ00217          8 KFLADKAPNAIKEQELKNYFGRVIAIDASMALYQFLIAIRDDSQGGNLTNEAGEVTSHISGLFNRTIRLLEAGIKPVYVF   87 (393)
T ss_pred             HHHhhhccccccccCHHHhCCcEEEEeHHHHHHHHHHHcccccccccchhccCCccHHHHHHHHHHHHHHHCCCCEEEEE
Confidence            3556666666654       899999999999999999996  6889999999999999999999999999999999999


Q ss_pred             cCCCCCcchHHHHHHHHHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhcc
Q psy1206         375 DGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARST  447 (531)
Q Consensus       375 DG~pp~lK~~~~~kR~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~  447 (531)
                      ||+||++|++++++|+++|+++.+++++|.++|+.+       +|++|++| +..++++|++.+++||++||=
T Consensus        88 DG~~p~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~-------~a~k~~~r-~~~vt~~~~~~~~~lL~~~Gi  152 (393)
T PTZ00217         88 DGKPPELKSGELEKRRERREEAEEELEKAIEEGDDE-------EIKKQSKR-TVRVTKEQNEDAKKLLRLMGI  152 (393)
T ss_pred             cCCCchhhHHHHHHHHHHHHHhHHHHHHHHhcCCHH-------HHHHHHhh-cccCCHHHHHHHHHHHHHcCC
Confidence            999999999999999999999999999999999977       99999998 999999999999999999983

>PRK14976 5'-3' exonuclease; Provisional

Probab=99.95  E-value=1.4e-27  Score=243.09  Aligned_cols=157  Identities=24%  Similarity=0.302  Sum_probs=134.7

Q ss_pred             CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCH-------HHHHHHHhhcCCccccCC-CchhHHHHHHHHc---
Q psy1206           7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ-------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVKA---   75 (531)
Q Consensus         7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~-------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r~---   75 (531)
                      .|++ .+|+||.+.++|     |++.++.||++|..+|       +.++++|+++|||++.+| |||||+||+|+++   
T Consensus        54 ~p~~-~~v~fD~~~~~~-----R~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~  127 (281)
T PRK14976         54 NPSY-ILIAFDAGRKTF-----RHQLYDEYKQGRKKTPESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSK  127 (281)
T ss_pred             CCCE-EEEEEECCCCcc-----cccccHHHhcCCCCCCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHH
Confidence            7898 999999876665     4556788899998888       357889999999999999 6999999999864   


Q ss_pred             -CCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcC--CCCCCCCCCccHHHH
Q psy1206          76 -GKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLG--CDYCDSIRGIGPKRA  152 (531)
Q Consensus        76 -G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G--~DY~pGIpGIG~ktA  152 (531)
                       |.-..|+|+|+|++++++++|.......+.   ....++.+.+.+.+|++|+||+|+++|+|  |||+|||||||+|||
T Consensus       128 ~g~~v~IvS~DkDl~ql~~~~v~~~~~~~~~---~~~~~~~~~v~~~~gv~p~q~~d~~aL~GD~sDnipGVpGIG~KtA  204 (281)
T PRK14976        128 QNITVLIYSSDKDLLQLVNENTDVLLKKKGT---SHFILNTNNFFELYGIEPKQIIDYKGLVGDSSDNIKGVKGIGPKTA  204 (281)
T ss_pred             CCCeEEEEeCCCCcCccCCCCeEEEEecCCC---CcEEEcHHHHHHHhCcCHHHHHHHHHHhCCccCCCCCCCcccHHHH
Confidence             666789999999999999876332222221   24679999999999999999999999999  999999999999999


Q ss_pred             HHHHHHcCCHHHHHHHhhhc
Q psy1206         153 IELIKEHRSIEKILENIDTK  172 (531)
Q Consensus       153 ~kLI~~~~sle~il~~l~~~  172 (531)
                      .+||++|||+|+|++++++.
T Consensus       205 ~~LL~~~gsle~i~~~~~~~  224 (281)
T PRK14976        205 IKLLNKYGNIENIYENIDKI  224 (281)
T ss_pred             HHHHHHcCCHHHHHHhHHHH
Confidence            99999999999999998764

>KOG2519|consensus

Probab=99.95  E-value=2.7e-28  Score=256.40  Aligned_cols=133  Identities=53%  Similarity=0.822  Sum_probs=126.1

Q ss_pred             ccccccCCCcccc-------cceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecC
Q psy1206         304 ELVADVAPSSIRE-------SRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDG  376 (531)
Q Consensus       304 ~Lv~~~aP~~i~~-------gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG  376 (531)
                      +++++++|+++++       ||+||||||||||||++++|+.    ++..|++|+||.|+||||++|+++||+|||||||
T Consensus         8 ~v~~d~a~~~ir~~~~~~f~~kkVAID~s~~lyqfl~~v~~~----~~~~~~~~~HL~g~f~Rt~~l~~~gi~Pv~VfDG   83 (449)
T KOG2519|consen    8 KVIADVAPPCIRKNPIKFFFGKKVAIDASMWLYQFLIVVRSC----RNEAGEPTSHLMGMFYRTIRLIENGIKPVYVFDG   83 (449)
T ss_pred             HHHHHhchHHhhhccHHHhcCceEEEecceeHhhHhhhhccc----cccCCCchHHHHHHHHHHHHHHHcCCcEEEEECC
Confidence            4678999999988       7999999999999999999975    6778999999999999999999999999999999


Q ss_pred             CCCCcchHHHHHHHHHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhccC
Q psy1206         377 KPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTT  448 (531)
Q Consensus       377 ~pp~lK~~~~~kR~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~  448 (531)
                      +||+||+.+++||.++|.+|.+.++.+.+.|..+       ...+|+.| ..+++..-.+++++||..||--
T Consensus        84 ~pP~lKs~e~~kR~~rr~~a~~~~~~~~e~~~~~-------~~~k~~~r-~vkvtk~~~dEak~LL~lmGIp  147 (449)
T KOG2519|consen   84 KPPDLKSQELAKRSERRSEADKELKPAKEAGAKE-------NMEKFFSR-LVKVTKQHNDEAKRLLSLMGIP  147 (449)
T ss_pred             CCCCcchHHHHHHHHHhhhhhhhhhhHHHhhhHH-------HHHHHHHH-HhhhcchhhHHHHHHHHHcCCe
Confidence            9999999999999999999999999999999977       99999998 9999999999999999999975

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

Probab=99.95  E-value=3.3e-27  Score=235.30  Aligned_cols=154  Identities=25%  Similarity=0.273  Sum_probs=132.6

Q ss_pred             CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCH-------HHHHHHHhhcCCccccCC-CchhHHHHHHHH----
Q psy1206           7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ-------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVK----   74 (531)
Q Consensus         7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~-------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r----   74 (531)
                      +|++ .+++||.+.++|+     ++..+.||++|..+|       +.++++|+++|||++.+| +||||+||+|++    
T Consensus        49 ~p~~-~~~~fD~~~~~~R-----~~l~p~YK~~R~~~p~~l~~q~~~~~~~l~~~gi~~i~~~~~EADD~ia~la~~~~~  122 (240)
T cd00008          49 KPTY-VAVVFDAGGKTFR-----HELYPEYKANRKKMPEELREQIPLIKELLEALGIPVLEIEGYEADDVIGTLAKKAEA  122 (240)
T ss_pred             CCCe-EEEEEeCCCCccc-----ccccHHHHcCCCCCCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHH
Confidence            6888 9999998756664     445677899998777       457889999999999988 699999999985    


Q ss_pred             cCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcC--CCCCCCCCCccHHHH
Q psy1206          75 AGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLG--CDYCDSIRGIGPKRA  152 (531)
Q Consensus        75 ~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G--~DY~pGIpGIG~ktA  152 (531)
                      .|...+|+|+|+|++++++++|..... .     ....++.+.+.+.+|++|+||+|+++|+|  |||+|||||||+|||
T Consensus       123 ~g~~~~I~S~DkD~~ql~~~~v~~~~~-~-----~~~~i~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA  196 (240)
T cd00008         123 EGYKVVIVSGDKDLLQLVSDNVKVVSP-M-----KKKLVTEENVIEKYGVTPAQIIDYKALMGDSSDNIPGVPGIGEKTA  196 (240)
T ss_pred             cCCeEEEEeCCCChhhhCCCCEEEEeC-C-----CceEEeHHHHHHHhCcCHHHHHHHHHHcCCcccCCCCCCccCHHHH
Confidence            578889999999999998887643211 1     13568999999999999999999999999  999999999999999


Q ss_pred             HHHHHHcCCHHHHHHHhhhc
Q psy1206         153 IELIKEHRSIEKILENIDTK  172 (531)
Q Consensus       153 ~kLI~~~~sle~il~~l~~~  172 (531)
                      .+||++|+|+|+|+++++..
T Consensus       197 ~~Ll~~~gsle~i~~~~~~~  216 (240)
T cd00008         197 AKLLKEYGSLEGILENLDKI  216 (240)
T ss_pred             HHHHHHhCCHHHHHHhHHHH
Confidence            99999999999999998764

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=99.94  E-value=1.2e-26  Score=232.76  Aligned_cols=155  Identities=19%  Similarity=0.227  Sum_probs=132.4

Q ss_pred             CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCH-------HHHHHHHhhcCCccccCC-CchhHHHHHHHHc---
Q psy1206           7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ-------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVKA---   75 (531)
Q Consensus         7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~-------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r~---   75 (531)
                      +|+| ++|+||.+.++   ..+|++.++.||++|..+|       +.|++++.++|||++..| |||||+||+|+++   
T Consensus        46 ~p~~-i~v~fD~~~~~---~~fR~~l~p~YKa~R~~~Pe~l~~Q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~  121 (256)
T PRK09482         46 QPTH-AVAVFDGDARS---SGWRHQLLPDYKAGRKPMPEALQQGLPAIRAAFEELGIDSWHADGNEADDLIATLAVKVAQ  121 (256)
T ss_pred             CCCE-EEEEEeCCCCC---cccHHHHhHHHhcCCCCCcHHHHHHHHHHHHHHHhCCCCEeccCCcCHHHHHHHHHHHHHH
Confidence            7999 99999986554   1146667888999998888       467899999999999988 5999999999863   


Q ss_pred             -CCEEEEEcCCCccccccCCeEE-EeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcC--CCCCCCCCCccHHH
Q psy1206          76 -GKVYATATEDMDALTFGSNILL-RHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLG--CDYCDSIRGIGPKR  151 (531)
Q Consensus        76 -G~vd~ViSeDsDlL~fg~~~Vi-~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G--~DY~pGIpGIG~kt  151 (531)
                       |.-..|+|.|+|++++..++|. .+.  ..     .+.++.+.+.+.+|++|+|++|+.+|+|  +||+|||||||+||
T Consensus       122 ~~~~v~I~S~DKDl~Qlv~~~v~~~~~--~~-----~~~~~~~~v~~~~Gv~P~q~~D~~aL~GD~sDnIpGVpGIG~Kt  194 (256)
T PRK09482        122 AGHQATIVSTDKGYCQLLSPTIQIRDY--FQ-----KRWLDAPFIEQEFGVEPQQLPDYWGLAGISSSKIPGVAGIGPKS  194 (256)
T ss_pred             CCCeEEEEECCCCccccCCCCeEEEec--cc-----cccCCHHHHHHHhCCCHHHHHHHHHHhCCCccCCCCCCCcChHH
Confidence             6666789999999999988763 322  11     2358999999999999999999999999  99999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHhhhc
Q psy1206         152 AIELIKEHRSIEKILENIDTK  172 (531)
Q Consensus       152 A~kLI~~~~sle~il~~l~~~  172 (531)
                      |.+||++|||+|+|++++++.
T Consensus       195 A~~LL~~~gsle~i~~~~~~~  215 (256)
T PRK09482        195 AAELLNQFRSLENIYESLDAL  215 (256)
T ss_pred             HHHHHHHhCCHHHHHHhHHHh
Confidence            999999999999999998653

>TIGR03674 fen_arch flap structure-specific endonuclease

Probab=99.94  E-value=5e-27  Score=244.72  Aligned_cols=128  Identities=42%  Similarity=0.659  Sum_probs=122.3

Q ss_pred             CcccccceeeecccchHHHHHHHHhh-cCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHH
Q psy1206         312 SSIRESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRM  390 (531)
Q Consensus       312 ~~i~~gk~iAIDa~~~lyqfl~~ir~-~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~  390 (531)
                      -....|++||||||+|||||++++|+ +|.+++|++|++|+||+|+|+|+++|+++||+|||||||+||++|.+++++|+
T Consensus        16 l~~~~gk~vaIDas~~L~r~~~a~~~~~g~~l~~~~G~~t~~l~g~~~~~~~ll~~~i~Pv~VFDG~~p~~K~~~~~~R~   95 (338)
T TIGR03674        16 LEDLSGKVVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITSHLSGLFYRTINLLENGIKPVYVFDGKPPELKAETLEERR   95 (338)
T ss_pred             HHHhCCCEEEEeHHHHHHHHHHHHhccccchhhhccCCCcHHHHHHHHHHHHHHHCCCeEEEEECCCChhhhHhhHHHHH
Confidence            34456999999999999999999998 79999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhcc
Q psy1206         391 EKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARST  447 (531)
Q Consensus       391 ~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~  447 (531)
                      ++|++|.+++++++++|+.+       +|++|++| +..++++|++.+++||++||=
T Consensus        96 ~~r~~a~~~~~~~~~~g~~~-------~a~~~~~r-~~~~~~~~~~~~k~lL~~~Gi  144 (338)
T TIGR03674        96 EIREEAEEKWEEALEKGDLE-------EARKYAQR-SSRLTSEIVESSKKLLDLMGI  144 (338)
T ss_pred             HHHHHHHHHHHHHHHcCCHH-------HHHHHHhh-cCCCCHHHHHHHHHHHHHcCC
Confidence            99999999999999999987       99999998 899999999999999999983

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

>KOG2520|consensus

Probab=99.93  E-value=2.3e-26  Score=256.94  Aligned_cols=184  Identities=24%  Similarity=0.408  Sum_probs=150.1

Q ss_pred             CCCHHH---HHHHHhhcCCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHH
Q psy1206          41 STTQGR---LDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEK  117 (531)
Q Consensus        41 ~~t~~~---i~~lL~~~gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~  117 (531)
                      .+|+.+   ++++|+.+|||||+||+|||||||.|...++||+|||+|||+|+||+.+|++++. ..++  .+..|.+.+
T Consensus       462 evt~~m~~e~QElL~~fGIPyI~APmEAEAQCa~Le~~~LvdGiITDDSDV~LFGg~~VYrn~F-~knk--~ve~y~~~d  538 (815)
T KOG2520|consen  462 EVTSDMFKELQELLRLFGIPYIIAPMEAEAQCAFLEQLNLVDGIITDDSDVFLFGGTRVYRNFF-NKNK--YVEKYQLDD  538 (815)
T ss_pred             hhHHHHHHHHHHHHHHcCCceecccccHHHHHHHHHHcCCcceeecccccceeeccchhhHHHh-hcCc--cceeeehHH
Confidence            466654   5789999999999999999999999999999999999999999999999999984 3333  478899999


Q ss_pred             HHHhCCCCHHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcC---CHHHHHHHhh----------------------hc
Q psy1206         118 VLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHR---SIEKILENID----------------------TK  172 (531)
Q Consensus       118 i~~~lglt~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~---sle~il~~l~----------------------~~  172 (531)
                      +...||+++..+|-++.|+|+||+.||+|||+++|+.+|.+|+   ++..+-+++.                      ..
T Consensus       539 i~kel~l~R~~lI~lA~LlGsDYt~Gl~giGpV~AlEil~Efp~~~~l~~f~~w~~~~~~~~~~~~s~~~~~lrkkl~n~  618 (815)
T KOG2520|consen  539 IEKELGLDRPNLISLAQLLGSDYTEGLKGIGPVSALEILAEFPGDENLLKFKKWVQQTGPADKEVGSTQQKMLRKKLKNP  618 (815)
T ss_pred             HHHHHccCchhhHHHHHhcccccccCCCcccchHHHHHHHHcCCcchhHHHHHHHHHhCccccccccHHHHHHHHHhcCc
Confidence            9999999999999999999999999999999999999999999   4333322222                      12


Q ss_pred             CCCCCCCCcHHHHHHHhcCCCcCCCCC-cccccccccccccccccccCCChhhhHh
Q psy1206         173 KYTVPEGWLYKEARELFRHPEVADPET-IEFIDLCILLGCDYCDSIRGIGPKRAIE  227 (531)
Q Consensus       173 ~~~ip~~f~~~~A~~~f~~p~V~d~~~-~~~v~Ls~~~~~d~cesl~~~Gp~~~~e  227 (531)
                      +..+|.+||...+..+|+||.|.+... ..|.-..-.....++...++|.-+++++
T Consensus       619 ~~~l~~~fP~~~v~~AYLrP~VD~sk~~f~WG~pdl~~lRef~~~~fgW~~~kT~~  674 (815)
T KOG2520|consen  619 KIILPSDFPNPNVIEAYLRPEVDDSKEKFRWGKPDLDILREFMKRLFGWPDEKTDE  674 (815)
T ss_pred             ccccCcCCCchhHHHHhhCCccCCCcccccCCCCCHHHHHHHHHHHcCCCccccch
Confidence            367899999999999999999987544 3444332222345566677777666655

>TIGR00593 pola DNA polymerase I

Probab=99.93  E-value=1.3e-25  Score=258.32  Aligned_cols=156  Identities=26%  Similarity=0.333  Sum_probs=134.8

Q ss_pred             CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCH-------HHHHHHHhhcCCccccCC-CchhHHHHHHHHc---
Q psy1206           7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ-------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVKA---   75 (531)
Q Consensus         7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~-------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r~---   75 (531)
                      +|+| ++|+||.+.++|     |++.++.||++|..+|       +.++++|+++|||++.+| |||||+||+|+++   
T Consensus        48 ~p~~-i~v~FD~~~~tf-----R~~~~~~YKa~R~~~Pe~l~~Q~~~i~~~l~~~gi~~i~~~g~EADDiIatla~~~~~  121 (887)
T TIGR00593        48 KPTY-VAVAFDSGTPTF-----RHEAYAEYKANRAPTPEELIEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEK  121 (887)
T ss_pred             CCCE-EEEEEcCCCCcc-----hHHHHHHHHhCCCCChHHHHHHHHHHHHHHHHCCCcEEeeCCccHHHHHHHHHHHHHh
Confidence            7999 999999876666     5566888899998888       467899999999999888 6999999999974   


Q ss_pred             -CCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcC--CCCCCCCCCccHHHH
Q psy1206          76 -GKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLG--CDYCDSIRGIGPKRA  152 (531)
Q Consensus        76 -G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G--~DY~pGIpGIG~ktA  152 (531)
                       |+.+.|+|+|+|++++++++|.......+.   ....++.+.+.+.+|++|+||+|+++|+|  |||+|||||||+|||
T Consensus       122 ~g~~v~IvS~DkDllQLv~~~v~~~~~~~~~---~~~~~~~~~v~~~~Gv~p~q~~D~~aL~GD~sDnIpGVpGIG~KtA  198 (887)
T TIGR00593       122 EGYEVRIISGDKDLLQLVSDNVKVLIPKGKT---SFTEITPEYVVEKYGVTPDQLVDLKALVGDSSDNIPGVKGIGEKTA  198 (887)
T ss_pred             CCCcEEEEECCCChhhcCCCCEEEEeccCCC---CceEEcHHHHHHHhCCCHHHHHHHHHHcCCcccCCCCCCCcCHHHH
Confidence             888899999999999999876332112211   24569999999999999999999999999  899999999999999


Q ss_pred             HHHHHHcCCHHHHHHHhhh
Q psy1206         153 IELIKEHRSIEKILENIDT  171 (531)
Q Consensus       153 ~kLI~~~~sle~il~~l~~  171 (531)
                      .+||++|||+|+|+++++.
T Consensus       199 ~kLL~~ygsle~i~~~~~~  217 (887)
T TIGR00593       199 AKLLQEFGSLENIYENLDQ  217 (887)
T ss_pred             HHHHHHcCCHHHHHHHHHH
Confidence            9999999999999998765

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

>PRK05755 DNA polymerase I; Provisional

Probab=99.91  E-value=1.9e-24  Score=249.82  Aligned_cols=156  Identities=25%  Similarity=0.298  Sum_probs=134.1

Q ss_pred             CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCH-------HHHHHHHhhcCCccccCC-CchhHHHHHHHH----
Q psy1206           7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ-------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVK----   74 (531)
Q Consensus         7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~-------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r----   74 (531)
                      .|+| ++|+||.+.++|     |++.++.||++|..+|       +.++++|+++|||++.+| |||||+||+|++    
T Consensus        50 ~p~~-~~v~fD~~~~~~-----R~~~~~~YK~~R~~~p~~l~~q~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~  123 (880)
T PRK05755         50 KPTH-VAVAFDAKGKTF-----RHELYPEYKANRPPMPEDLREQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEA  123 (880)
T ss_pred             CCCE-EEEEEECCCCcc-----ccccCHHHhCCCCCCcHHHHHHHHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHHh
Confidence            7999 999999876666     4456788899998877       468899999999999999 699999999985    


Q ss_pred             cCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcC--CCCCCCCCCccHHHH
Q psy1206          75 AGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLG--CDYCDSIRGIGPKRA  152 (531)
Q Consensus        75 ~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G--~DY~pGIpGIG~ktA  152 (531)
                      .|..++|+|+|+|++++++++|-......+.   ....++.+.+.+.+|++|+||+|+++|+|  |||+|||||||+|||
T Consensus       124 ~~~~~~i~S~DkD~~ql~~~~v~~~~~~~~~---~~~~~~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA  200 (880)
T PRK05755        124 AGYEVLIVTGDKDLLQLVDDNVTLLDTMGVS---KNEELDPEEVVEKYGVTPEQIIDYLALMGDSSDNIPGVPGIGEKTA  200 (880)
T ss_pred             CCCcEEEEcCCCChhhhCCCCEEEeeccCCC---CCeEEcHHHHHHHHCcCHHHHHHHHHHhCCccCCCCCCCCccHHHH
Confidence            5888999999999999999876221111111   24579999999999999999999999999  899999999999999


Q ss_pred             HHHHHHcCCHHHHHHHhhh
Q psy1206         153 IELIKEHRSIEKILENIDT  171 (531)
Q Consensus       153 ~kLI~~~~sle~il~~l~~  171 (531)
                      .+||++|||+|+|+++++.
T Consensus       201 ~~Ll~~~gsle~i~~~~~~  219 (880)
T PRK05755        201 AKLLQEYGSLEGLYENLDE  219 (880)
T ss_pred             HHHHHHcCCHHHHHHhHHH
Confidence            9999999999999998875

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

Probab=99.91  E-value=6.7e-24  Score=218.73  Aligned_cols=180  Identities=26%  Similarity=0.316  Sum_probs=144.2

Q ss_pred             CCCccceeecccCCCCCcchhHHhHHHHHHhhccCC-CH-------HHHHHHHhhcCCccccCC-CchhHHHHHHHH---
Q psy1206           7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSST-TQ-------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVK---   74 (531)
Q Consensus         7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~-t~-------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r---   74 (531)
                      .|.+ .+++||.+.++|     |++..+.+|++|.. ++       +.|.+++.++|++++..+ +||||.++++++   
T Consensus        59 ~~~~-~~~vFD~~~~tf-----R~~~~~~yK~~R~~~~p~~l~~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~a~  132 (310)
T COG0258          59 EPTH-PVVVFDGKPPTF-----RHELLEEYKANREKEMPDELAPQIPILTELLVALGIPLLELMGIEADDPIETLAQKAY  132 (310)
T ss_pred             CCCc-EEEEEcCCCCcc-----hHHHHHHHHhCCCccCHHHHHHHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHHHH
Confidence            5667 999999866666     44457778888888 77       467888999999999766 699999999885   


Q ss_pred             -cCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhC-CCCHHHHHHHHhHcC--CCCCCCCCCccHH
Q psy1206          75 -AGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGM-ELSHEEFIDLCILLG--CDYCDSIRGIGPK  150 (531)
Q Consensus        75 -~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~l-glt~eqfid~~iL~G--~DY~pGIpGIG~k  150 (531)
                       .|.++.|+|+|+|+|+|+++++.......+.   +...++...+.+.+ |++|+||+|+++|+|  |||+|||||||+|
T Consensus       133 ~~g~~~~I~S~DkD~lql~~~~~~~~~~~~~~---~~~~~~~~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV~GIG~k  209 (310)
T COG0258         133 KKGDVVLIISGDKDLLQLVSPNVLVINGKKGE---PEKFLDLEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPK  209 (310)
T ss_pred             hcCCeEEEEeCCcchhhhcCCCcEEEeccCCC---CcccCCHHHHHHHHcCCCHHHHHHHHHHhCCcccCCCCCCCcCHH
Confidence             6899999999999999999996543333321   11157889999999 999999999999999  9999999999999


Q ss_pred             HHHHHHHHcCCHHHHHHHhhhcCCCCCCCCcHHHHHHHhcC-CCcCC
Q psy1206         151 RAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRH-PEVAD  196 (531)
Q Consensus       151 tA~kLI~~~~sle~il~~l~~~~~~ip~~f~~~~A~~~f~~-p~V~d  196 (531)
                      ||++||++|||+|.++++++..+ .............+|.+ +.|.+
T Consensus       210 tA~~Ll~~~gs~e~i~~~~~~~~-~~~~~~l~~~~~~afl~~~l~t~  255 (310)
T COG0258         210 TALKLLQEYGSLEGLYENLDIIK-KKTREKLLEDKEKAFLSKPLATI  255 (310)
T ss_pred             HHHHHHHHhCCHHHHHHhhhhhc-chhhHHHHHHHHHHhcCcccccc
Confidence            99999999999999999987322 11222335677888888 66655

>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment

Probab=99.89  E-value=4.7e-24  Score=183.72  Aligned_cols=88  Identities=41%  Similarity=0.629  Sum_probs=75.2

Q ss_pred             hhcCCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEecc-cc-Ccc----cCCcEEecHHHHHHhCCCC
Q psy1206          52 TIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMT-FS-EAR----KLPVQEFHLEKVLEGMELS  125 (531)
Q Consensus        52 ~~~gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~-~~-~~~----~~~v~~~~~~~i~~~lglt  125 (531)
                      +++||||++||||||||||+|+++|+||+|+|+|||+|+||+++||++++ .. +..    ...++.++.+.+++.++++
T Consensus         1 ~~~gv~~i~AP~EAeAq~A~L~~~g~vd~V~t~DsD~l~fG~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~l~   80 (94)
T PF00867_consen    1 RLMGVPYIVAPYEAEAQCAYLERNGLVDAVITEDSDLLLFGAPKVIRKLSDKSSGKCSSKSEKEVEVIDLDDILKELGLT   80 (94)
T ss_dssp             HHHT-EEEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESST-CSCCSTS-CCESEEEEEEHHHHHHHHTTS
T ss_pred             CCCCCeEEEcCchHHHHHHHHHHhcceeEEEecCCCEEeeCCCEEEEeccccccCCcccccccceEEEEHHHHHHHcCCC
Confidence            47899999999999999999999999999999999999999999999996 33 221    2458899999999999999


Q ss_pred             HHHHHHHHhHcCCC
Q psy1206         126 HEEFIDLCILLGCD  139 (531)
Q Consensus       126 ~eqfid~~iL~G~D  139 (531)
                      +++|+++|+|+|||
T Consensus        81 ~~~fi~~~iL~G~D   94 (94)
T PF00867_consen   81 REQFIDLCILCGCD   94 (94)
T ss_dssp             HHHHHHHHHHHHET
T ss_pred             HHHHHHHheecCCC
Confidence            99999999999998

Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....

>PRK03980 flap endonuclease-1; Provisional

Probab=99.85  E-value=2.1e-21  Score=198.87  Aligned_cols=96  Identities=47%  Similarity=0.750  Sum_probs=93.7

Q ss_pred             cCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHHHHHHHHHHHHHHHHcccccCCCCChhHHHHH
Q psy1206         343 MSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKY  422 (531)
Q Consensus       343 ~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~  422 (531)
                      ||++|++||||+|+|+|+++|+++||+|||||||+||++|.+++++|+++|++|.+++++|+++|+.+       +|++|
T Consensus         1 ~~~~G~~Ts~l~g~~~r~~~ll~~gi~PvfVFDG~~p~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~-------~a~k~   73 (292)
T PRK03980          1 MDSKGRITSHLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREEAEEKYEEAKEEGDLE-------EARKY   73 (292)
T ss_pred             CCCCCcCcHHHHHHHHHHHHHHHCCCEEEEEECCCCchHHHHHHHHHHHHHHHhHHHHHHHHHcCCHH-------HHHHH
Confidence            58999999999999999999999999999999999999999999999999999999999999999977       99999


Q ss_pred             HhhccccchHHHHHHHHHHHHHhc
Q psy1206         423 LCGDKNFAEDRIRNGAKKLLKARS  446 (531)
Q Consensus       423 ~~~~~~~~~~~~~~~~~~ll~~~~  446 (531)
                      +++ +.+++++|++.+++||++||
T Consensus        74 ~~~-~~~vt~~~~~~~k~lL~~~G   96 (292)
T PRK03980         74 AQR-SSRLTDEIVEDSKKLLDLMG   96 (292)
T ss_pred             Hhc-cccCCHHHHHHHHHHHHHCC
Confidence            998 99999999999999999998

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

Probab=99.85  E-value=5e-21  Score=197.64  Aligned_cols=119  Identities=45%  Similarity=0.657  Sum_probs=111.7

Q ss_pred             ccceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHHHHHH
Q psy1206         316 ESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKRED  395 (531)
Q Consensus       316 ~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~~r~~  395 (531)
                      .|++|||||++||||++++++...    .+.|.+|+|+.|+++|+.+|+++||+|||||||.+|++|.+|+.+|+++|++
T Consensus        23 ~gk~laID~~~~l~r~~~a~~~~~----~~~g~~~~~l~~~~~rl~~L~~~~i~pvfVFDG~~~~~K~~~~~~R~~~r~~   98 (316)
T cd00128          23 RGKKVAIDASIWLYQFLKACRQEL----GSGGETTSHLQGFFYRTCRLLELGIKPVFVFDGKPPPLKAETLAKRRERREE   98 (316)
T ss_pred             CCcEEEecHHHHHHHHHHHhhhhc----cCCCCCcHHHHHHHHHHHHHHHCCCEEEEEEcCCCchhhHHHHHHHHHHHHH
Confidence            689999999999999999998632    2679999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhc
Q psy1206         396 AQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARS  446 (531)
Q Consensus       396 a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~  446 (531)
                      +.+++..+.++|+.+       ++.++.++ ...+++.+++.+++||++||
T Consensus        99 ~~~~~~~~~~~~~~~-------~~~~~~~~-~~~~~~~~~~~~~~lL~~~g  141 (316)
T cd00128          99 AEEEAKEALEKGLEE-------EAKKLERR-AVRVTPQMIEEAKELLRLMG  141 (316)
T ss_pred             HHHHHHHHHHhCCHH-------HHHHHHhc-cCcCCHHHHHHHHHHHHHcC
Confidence            999999999999876       99999887 88899999999999999996

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.

>TIGR00600 rad2 DNA excision repair protein (rad2)

Probab=99.82  E-value=2e-20  Score=215.44  Aligned_cols=84  Identities=39%  Similarity=0.637  Sum_probs=77.7

Q ss_pred             ccceeeecccchHHHHHHHHhh-cCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHHHHH
Q psy1206         316 ESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKRE  394 (531)
Q Consensus       316 ~gk~iAIDa~~~lyqfl~~ir~-~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~~r~  394 (531)
                      .||+||||||+|||||+.++|. .|++++|      +||.|+|+|+++||++||+|||||||.||++|.+|+++|+++|+
T Consensus        23 ~Gk~vAIDasiWL~q~l~~vr~~~g~~l~n------~hl~g~f~Ri~~Ll~~gI~PVfVFDG~~p~lK~~t~~~R~~rR~   96 (1034)
T TIGR00600        23 EGKRLAVDISIWLNQALKGVRDREGNAIKN------SHLLTLFHRLCKLLFFRIRPIFVFDGGAPLLKRQTLAKRRQRRD   96 (1034)
T ss_pred             CCeEEEechHHHHHHHHHHHHhccCCccCC------HHHHHHHHHHHHHHHCCCeEEEEECCCCchHhHHHHHHHHHHHH
Confidence            4999999999999999999998 7888765      89999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q psy1206         395 DAQKALAKAQE  405 (531)
Q Consensus       395 ~a~~~~~~a~~  405 (531)
                      +|.+..++..+
T Consensus        97 ~a~~~a~~~~~  107 (1034)
T TIGR00600        97 GASEDARKTAE  107 (1034)
T ss_pred             HHHHHHHHHHH
Confidence            98877765554

All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>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=99.81  E-value=5.3e-20  Score=159.67  Aligned_cols=80  Identities=50%  Similarity=0.764  Sum_probs=66.0

Q ss_pred             cccccceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHHH
Q psy1206         313 SIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEK  392 (531)
Q Consensus       313 ~i~~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~~  392 (531)
                      .-..|++|||||++||||++.+.+..   +. ..+..++|+.++++|+..|+.+||+|||||||.+|++|.+|.++|+++
T Consensus        22 ~~l~g~~vaID~s~wl~~~~~~~~~~---~~-~~~~~~~~~~~~~~r~~~L~~~gI~PifVFDG~~~~~K~~~~~~R~~~   97 (101)
T PF00752_consen   22 SELRGKRVAIDASCWLHQFLFSCREE---LG-QGVGTDSHLRGLFSRLCRLLEHGIKPIFVFDGKPPPLKRETIQKRRKR   97 (101)
T ss_dssp             GGGTTCEEEEEHHHHHHHHHHHSBCT---TS-CB-BS-HHHHHHHHHHHHHHHTTEEEEEEE--STTGGCHHHHHHHHHH
T ss_pred             HHhCCCEEEEEcHHHHHHHHHHhHHH---hc-cccchHHHHHHHHHHHHHHHHCCCEEEEEECCCCchhhHHHHHHHHHH
Confidence            34568999999999999999988641   11 112227999999999999999999999999999999999999999999


Q ss_pred             HHHH
Q psy1206         393 REDA  396 (531)
Q Consensus       393 r~~a  396 (531)
                      |++|
T Consensus        98 r~~~  101 (101)
T PF00752_consen   98 REEA  101 (101)
T ss_dssp             HHHH
T ss_pred             HhcC
Confidence            9987

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

>smart00485 XPGN Xeroderma pigmentosum G N-region

Probab=99.80  E-value=3.7e-20  Score=160.32  Aligned_cols=77  Identities=61%  Similarity=0.991  Sum_probs=68.2

Q ss_pred             ccccceeeecccchHHHHHHHHhh-cCccccCCCCCCcc-hhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHH
Q psy1206         314 IRESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTS-HLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRME  391 (531)
Q Consensus       314 i~~gk~iAIDa~~~lyqfl~~ir~-~g~~l~~~~g~~ts-hl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~  391 (531)
                      ...|++|||||++||||++.+++. .+..+      .++ |+.++|+|+.+|+++||+|||||||.+|++|.+|+++|++
T Consensus        21 ~l~g~~vaIDa~~wl~~~~~~~~~~~~~~~------~~~~~l~~~~~rl~~L~~~~I~PifVFDG~~~~~K~~t~~~R~~   94 (99)
T smart00485       21 ALRGKTLAIDASIWLYQFLTACREKLGTPL------PNSKHLMGLFYRTCRLLEFGIKPIFVFDGKPPPLKSETLAKRRE   94 (99)
T ss_pred             HhCCceEeccHHHHHHHHHHHHhhhhcCCC------CchHHHHHHHHHHHHHHHCCCeEEEEECCCCchhhHHHHHHHHH
Confidence            345999999999999999999976 34433      234 9999999999999999999999999999999999999999


Q ss_pred             HHHHH
Q psy1206         392 KREDA  396 (531)
Q Consensus       392 ~r~~a  396 (531)
                      +|++|
T Consensus        95 ~r~~~   99 (99)
T smart00485       95 RREEA   99 (99)
T ss_pred             HHhcC
Confidence            99875

domain in nucleases

>PHA00439 exonuclease

Probab=99.80  E-value=2.2e-19  Score=182.37  Aligned_cols=143  Identities=15%  Similarity=0.146  Sum_probs=111.9

Q ss_pred             CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCH------HHHHHHHhhcCCccccCC-CchhHHHHHHHH----c
Q psy1206           7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVK----A   75 (531)
Q Consensus         7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r----~   75 (531)
                      +||+ ++|+|| +.+     .+|++.++.||++|..++      +.+++++.++||+++..| +||||.+|+|++    .
T Consensus        63 ~p~~-i~vaFD-~~~-----tfR~elyp~YKanR~~~p~~~~~~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~~  135 (286)
T PHA00439         63 KDAP-IVLAFT-DSV-----NWRKEVVPTYKANRKAKRKPVGYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLF  135 (286)
T ss_pred             CCCe-EEEEEC-CCC-----ChHhhhhhHhcCCCCCCCCchhhHHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHHC
Confidence            8999 999999 544     456777888999997765      578899999999999777 799999999986    3


Q ss_pred             CC-EEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcC--CCCCCCCCCccHHHH
Q psy1206          76 GK-VYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLG--CDYCDSIRGIGPKRA  152 (531)
Q Consensus        76 G~-vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G--~DY~pGIpGIG~ktA  152 (531)
                      |+ -..|+|.|+|++++....++.. . .+ .   +..++.+        .+++++|+.+|+|  +||+||||||| |||
T Consensus       136 g~~~vvIvS~DKDl~QLv~~~~~~~-~-~~-~---~~~~~~~--------~p~~~~d~~AL~GDsSDNIPGVpGIG-KTA  200 (286)
T PHA00439        136 GFKKAVLVSCDKDFKTIPNCDFLWC-T-TG-N---ILTQTPE--------TADRWHLFQTIKGDSTDGYSGIPGWG-DTA  200 (286)
T ss_pred             CCCeEEEEeCCCCHhhcCcceEEEc-c-CC-c---eEEcCcc--------cHHHHHhhhhcccccccCCCCCCCcC-HHH
Confidence            66 6678999999999976544422 1 11 1   1112322        2999999999999  99999999999 999


Q ss_pred             HHHHHH---cCCHHHHHHHhhh
Q psy1206         153 IELIKE---HRSIEKILENIDT  171 (531)
Q Consensus       153 ~kLI~~---~~sle~il~~l~~  171 (531)
                      .+||.+   |..++.++++-..
T Consensus       201 ~kLL~~~~~~~~~~~~~~sg~~  222 (286)
T PHA00439        201 EAFLENPYIFEQVEKVLKSGKR  222 (286)
T ss_pred             HHHHhCccccchhhHHhhcccc
Confidence            999998   5667777766533

>smart00484 XPGI Xeroderma pigmentosum G I-region

Probab=99.76  E-value=9.1e-19  Score=144.58  Aligned_cols=73  Identities=42%  Similarity=0.532  Sum_probs=67.5

Q ss_pred             hhcCCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCC
Q psy1206          52 TIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMEL  124 (531)
Q Consensus        52 ~~~gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lgl  124 (531)
                      +.+||||++||||||||||+|+++|++|+|+|+|+|+|+||+++||++++++++++.+++.+++..+++.+|+
T Consensus         1 ~~~gi~~i~AP~eAeAq~A~L~~~g~vdav~s~D~D~llfG~~~vi~~~~~~~~~~~~~~~i~~~~vl~~L~l   73 (73)
T smart00484        1 RLMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLEFRIIDLESVLKELGL   73 (73)
T ss_pred             CcCCCeEEEcCCcHHHHHHHHHhCCCeeEEEcCccceEecCCcEEEEecccCCCcccCeEEEEHHHHHHHcCC
Confidence            3689999999999999999999999999999999999999999999999887765567899999999998875

domain in nucleases

>KOG2518|consensus

Probab=99.70  E-value=3.6e-17  Score=174.73  Aligned_cols=117  Identities=22%  Similarity=0.333  Sum_probs=105.5

Q ss_pred             cceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHH-HHHcCCeeEEeecCCCCCcchHHHHHHHHHHHH
Q psy1206         317 SRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIR-LVEHGLKPIYVFDGKPPTLKSGELNKRMEKRED  395 (531)
Q Consensus       317 gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~-ll~~gIkPVfVFDG~pp~lK~~~~~kR~~~r~~  395 (531)
                      |++||||+|+|||+.+.++..     ....|++|+.+..+|....+ |+.+||+||.||||.|.+.|+.|..+||++|++
T Consensus        24 g~tvavD~y~WLhrg~~~Ca~-----el~~~~pT~ryi~y~ik~v~lL~~~gikPilVFDG~~LP~K~~te~~Rr~~R~~   98 (556)
T KOG2518|consen   24 GKTVAVDGYCWLHRGALACAE-----KLAKGKPTDRYIQFFIKRVKLLLSYGIKPILVFDGDPLPSKKETERKRRERRKK   98 (556)
T ss_pred             CceEEEehhhHHhhhHHhHHH-----HHhcCCChHHHHHHHHHHHHHHHhcCCeEEEEecCCCcccccccchHHHHHHHH
Confidence            899999999999999998865     33457888766666666666 589999999999999999999999999999999


Q ss_pred             HHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhc
Q psy1206         396 AQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARS  446 (531)
Q Consensus       396 a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~  446 (531)
                      ..+..++.+.+|+..       +|++|+++ +..|+++|++..++.++.+|
T Consensus        99 n~~~a~~ll~~G~~~-------~A~~~fqr-~VdIT~~ma~~lI~~~r~~n  141 (556)
T KOG2518|consen   99 NLDAAEQLLAEGKES-------NARECFQR-CVDITPEMAHKLIQYLRSQN  141 (556)
T ss_pred             hHHHHHHHHHcCCHH-------HHHHHHHH-hccCcHHHHHHHHHHHHHcC
Confidence            999999999999987       99999999 99999999999999999885

>PHA02567 rnh RnaseH; Provisional

Probab=99.53  E-value=4.2e-14  Score=144.71  Aligned_cols=123  Identities=16%  Similarity=0.058  Sum_probs=97.2

Q ss_pred             CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCHH---------------HHHHHHhhcCCccccCC-CchhHHHH
Q psy1206           7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQG---------------RLDSFFTIRREEKRKAP-CEAEAQCA   70 (531)
Q Consensus         7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~~---------------~i~~lL~~~gIp~vvAP-yEADAq~A   70 (531)
                      .|++ ++++||.+.    ...+|++.++.||++|..+|+               .+++++.++||+++..| +||||.+|
T Consensus        62 ~~~~-i~vaFD~~~----~~tfR~elyp~YKAnR~~~Peel~~q~~~l~~~l~~ii~el~~~~gi~~l~~~g~EADDvIg  136 (304)
T PHA02567         62 EYPE-IVLAFDNSK----SGYWRRDIAWYYKKNRKKDREESPWDWEGLFEAINKIVDEIKENMPYKVMKIDKAEADDIIA  136 (304)
T ss_pred             CCCe-EEEEEeCCC----CCCchhhhhhHhhcCCCCCChHHHHHHHHhhhhHHHHHHHHHHHCCCCEEEeCCccHHHHHH
Confidence            4667 899999764    233567778999999987773               35667788999999877 69999999


Q ss_pred             HHHH----cCCEEEEEcCCCccccccC-CeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcC--CCCCCC
Q psy1206          71 AMVK----AGKVYATATEDMDALTFGS-NILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLG--CDYCDS  143 (531)
Q Consensus        71 ~L~r----~G~vd~ViSeDsDlL~fg~-~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G--~DY~pG  143 (531)
                      +|++    .|.-..|+|+|+|++|+.. ++|-. ++.          ++.+.+.+++| .|+|++|+.+|+|  +|++||
T Consensus       137 TLA~k~~~~g~~VvIvS~DKDl~QLv~~~~v~~-~~~----------~~~~~V~~k~G-~P~q~iD~kaL~GDsSDNIPG  204 (304)
T PHA02567        137 VLTKKFSAEGRPVLIVSSDGDFTQLHKYPGVKQ-WSP----------MQKKWVKPKYG-SPEKDLMTKIIKGDKKDGVAS  204 (304)
T ss_pred             HHHHHHHhCCCcEEEEeCCCChhhccCCCCeEE-eec----------CCHHHHHHHhC-CHHHHHHHHHhCCcccCCcCC
Confidence            9986    4667789999999999974 55422 211          23466788999 5999999999999  999999


Q ss_pred             CCC
Q psy1206         144 IRG  146 (531)
Q Consensus       144 IpG  146 (531)
                      ||-
T Consensus       205 Vp~  207 (304)
T PHA02567        205 IKV  207 (304)
T ss_pred             CCC
Confidence            984

>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif

Probab=99.46  E-value=8e-14  Score=115.71  Aligned_cols=51  Identities=49%  Similarity=0.831  Sum_probs=49.0

Q ss_pred             hCCCCHHHHHHHHhHcC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206         121 GMELSHEEFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT  171 (531)
Q Consensus       121 ~lglt~eqfid~~iL~G--~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~  171 (531)
                      .+|++|++|+|+++|+|  |||+|||||||+|||.+||++|+++++++++++.
T Consensus         2 ~~g~~~~q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~~~~~~~~~~~~   54 (75)
T cd00080           2 KLGLTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENLDK   54 (75)
T ss_pred             CCCcCHHHHHHHHHHcCCccccCCCCCcccHHHHHHHHHHhCCHHHHHHHHHH
Confidence            58999999999999999  9999999999999999999999999999998865

HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.

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

Probab=99.24  E-value=7.2e-12  Score=129.54  Aligned_cols=110  Identities=30%  Similarity=0.404  Sum_probs=91.4

Q ss_pred             cccccceeeecccchHHHHHHHHhh-cCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHH
Q psy1206         313 SIRESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRME  391 (531)
Q Consensus       313 ~i~~gk~iAIDa~~~lyqfl~~ir~-~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~  391 (531)
                      ....|+.++||+++|+|+++++++. .++++.++.| .++|+.++++|++++.+. ++||+||||+||.+|.++.++|+.
T Consensus         7 ~~~~~~l~~IDg~~~lyr~~~a~~~~~~~~~g~~~~-~~~~~~~~l~~~~~~~~~-~~~~~vFD~~~~tfR~~~~~~yK~   84 (310)
T COG0258           7 MNKSGKLLLIDGSSLLYRALHALPQPLGNPLGDPTG-AVSGFLGMLYRLIRLLEP-THPVVVFDGKPPTFRHELLEEYKA   84 (310)
T ss_pred             hhccCcEEEEechHHHHHHHHhcchhcCCCCCCCcc-HHHHHHHHHHHHHHhcCC-CcEEEEEcCCCCcchHHHHHHHHh
Confidence            3456899999999999999999988 6777777777 899999999999999999 999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhc
Q psy1206         392 KREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARS  446 (531)
Q Consensus       392 ~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~  446 (531)
                      .|++                     +...+|..+ ...+++.|.+..+.+|+.+|
T Consensus        85 ~R~~---------------------~~p~~l~~q-~~~i~~~~~~~~~~~l~~~G  117 (310)
T COG0258          85 NREK---------------------EMPDELAPQ-IPILTELLVALGIPLLELMG  117 (310)
T ss_pred             CCCc---------------------cCHHHHHHH-HHHHHHHHHHhCcHhhhcCC
Confidence            9988                     134444444 55566666666666666665

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

Probab=99.17  E-value=2.3e-11  Score=115.83  Aligned_cols=106  Identities=17%  Similarity=0.156  Sum_probs=81.0

Q ss_pred             CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCH-------HHHHHHHhhcCCccccCC-CchhHHHHHHHH----
Q psy1206           7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ-------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVK----   74 (531)
Q Consensus         7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~-------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r----   74 (531)
                      +|++ ++++||.+.+     .+|++..+.||++|..++       +.++++++++||+++..| +||||.+|+|++    
T Consensus        50 ~p~~-~vv~fD~~~~-----~fR~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~  123 (169)
T PF02739_consen   50 KPDY-VVVAFDSKGP-----TFRKELYPEYKANRKPMPEELIPQLPYIKELLEALGIPVLEVPGYEADDVIATLAKKASE  123 (169)
T ss_dssp             TEEE-EEEEEEBSSC-----HHHHHCCTTTTHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEETTB-HHHHHHHHHHHHHH
T ss_pred             CCce-EEEEecCCCc-----chHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHCCCCEecCCCCcHHHHHHHHHhhhcc
Confidence            7888 9999997766     456667888899987777       467889999999999887 799999999986    


Q ss_pred             cCCEEEEEcCCCccccccCC--eEEEeccccCcccCCcEEecHHHHHHhC
Q psy1206          75 AGKVYATATEDMDALTFGSN--ILLRHMTFSEARKLPVQEFHLEKVLEGM  122 (531)
Q Consensus        75 ~G~vd~ViSeDsDlL~fg~~--~Vi~~l~~~~~~~~~v~~~~~~~i~~~l  122 (531)
                      .|.-..|+|+|+|++|+..+  +|.. ++..+.   ....++.+.+.++|
T Consensus       124 ~~~~v~IvS~DkD~~QLv~~~~~V~~-~~~~~~---~~~~~~~~~v~eky  169 (169)
T PF02739_consen  124 EGFEVIIVSGDKDLLQLVDENVNVYL-LDPGKK---KFKVYDPEEVEEKY  169 (169)
T ss_dssp             TTCEEEEE-SSGGGGGGTCS-TSEEE-EETTTT---CS-EB-HHHHHHHT
T ss_pred             CCCEEEEEcCCCCHHHhcCCCceEEE-eecCCC---CCEEEcHHHHhhcC
Confidence            47778899999999999999  4433 332211   35789999988764

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 ....

>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases

Probab=99.13  E-value=1.4e-12  Score=114.33  Aligned_cols=49  Identities=39%  Similarity=0.613  Sum_probs=40.3

Q ss_pred             CCHHHHHHHHhHcC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhhc
Q psy1206         124 LSHEEFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTK  172 (531)
Q Consensus       124 lt~eqfid~~iL~G--~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~~  172 (531)
                      ++|+|++|+.+|+|  +||+|||||||+|||.+||++|||+|+|+++++..
T Consensus         1 V~P~q~~D~~aL~GD~sDNIPGV~GIG~KtA~~LL~~ygsle~i~~~~~~~   51 (101)
T PF01367_consen    1 VPPEQIADYKALVGDSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDEI   51 (101)
T ss_dssp             --GHHHHHHCCCC-CCCCTB---TTSTCHCCCCCHHHHTSCHCCCCC-SSS
T ss_pred             CCHHHHHHHHHHcCCcccCCCCCCCCCHHHHHHHHHHcCCHHHHHHhHHhc
Confidence            57999999999999  99999999999999999999999999999988764

The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.

>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif

Probab=99.10  E-value=9.7e-11  Score=97.27  Aligned_cols=46  Identities=50%  Similarity=0.810  Sum_probs=43.8

Q ss_pred             Hhhhhhhhhhcc--CccccCCCCCchHHHHHHHHhhccHHHHHHHHhh
Q psy1206         229 LYSFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT  274 (531)
Q Consensus       229 ~e~F~~~CiLsG--CDY~~~i~giG~k~A~kli~k~~s~~~vi~~l~~  274 (531)
                      .++|+++|+|+|  |||+|+|||||+|+|.++|++|++++.++.+++.
T Consensus         7 ~~q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~~~~~~~~~~~~   54 (75)
T cd00080           7 PEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENLDK   54 (75)
T ss_pred             HHHHHHHHHHcCCccccCCCCCcccHHHHHHHHHHhCCHHHHHHHHHH
Confidence            579999999999  9999999999999999999999999999998864

HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.

>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs

Probab=98.96  E-value=5.7e-10  Score=80.15  Aligned_cols=34  Identities=44%  Similarity=0.851  Sum_probs=30.7

Q ss_pred             HHHHHHHHhHcC--CCCCCCCCCccHHHHHHHHHHc
Q psy1206         126 HEEFIDLCILLG--CDYCDSIRGIGPKRAIELIKEH  159 (531)
Q Consensus       126 ~eqfid~~iL~G--~DY~pGIpGIG~ktA~kLI~~~  159 (531)
                      |+||+++++|+|  +|++|||||||+|||.+||++|
T Consensus         1 p~q~~~~~~L~GD~~dni~Gv~giG~ktA~~ll~~~   36 (36)
T smart00279        1 PEQLIDYAILVGDYSDNIPGVKGIGPKTALKLLREF   36 (36)
T ss_pred             CHHHHHHHHHhCcCCCCCCCCCcccHHHHHHHHHhC
Confidence            589999999999  5666699999999999999986

>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs

Probab=98.60  E-value=3.2e-08  Score=71.17  Aligned_cols=32  Identities=50%  Similarity=0.997  Sum_probs=30.2

Q ss_pred             hhhhhhhhhccCcccc---CCCCCchHHHHHHHHhh
Q psy1206         230 YSFIDLCILLGCDYCD---SIRGIGPKRAIELIKEH  262 (531)
Q Consensus       230 e~F~~~CiLsGCDY~~---~i~giG~k~A~kli~k~  262 (531)
                      ++|+++|+|+| ||.+   +|||||+|+|.++|++|
T Consensus         2 ~q~~~~~~L~G-D~~dni~Gv~giG~ktA~~ll~~~   36 (36)
T smart00279        2 EQLIDYAILVG-DYSDNIPGVKGIGPKTALKLLREF   36 (36)
T ss_pred             HHHHHHHHHhC-cCCCCCCCCCcccHHHHHHHHHhC
Confidence            68999999999 9999   88899999999999986

>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=98.31  E-value=5.9e-07  Score=90.12  Aligned_cols=79  Identities=23%  Similarity=0.298  Sum_probs=67.4

Q ss_pred             ceeeecccchHHHHHHHHhhcCccccCC-CCCCcchhhhHHHHHHHHHHcC--CeeEEeecCCCCCcchHHHHHHHHHHH
Q psy1206         318 RKICIDASMSLYQFLIAVRSEGNQLMSV-DGEPTSHLMGTFYRTIRLVEHG--LKPIYVFDGKPPTLKSGELNKRMEKRE  394 (531)
Q Consensus       318 k~iAIDa~~~lyqfl~~ir~~g~~l~~~-~g~~tshl~g~~~R~~~ll~~g--IkPVfVFDG~pp~lK~~~~~kR~~~r~  394 (531)
                      +.++||+++.+|++..+++.    +.++ +|++|+++.|++.++.++++..  ..||+||||.+|..+.+...+.+..|.
T Consensus         2 ~~llIDg~~l~yr~~~a~~~----~~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~~~~fD~~~~~~R~~l~p~YK~~R~   77 (240)
T cd00008           2 RLLLIDGSSLAYRAYFALPP----LKNSPKGLPTNAVYGFLNMLLKLIKEYKPTYVAVVFDAGGKTFRHELYPEYKANRK   77 (240)
T ss_pred             cEEEEEChHHHHHHHHCCCC----cCCCCCCcCchHHHHHHHHHHHHHHhcCCCeEEEEEeCCCCcccccccHHHHcCCC
Confidence            47899999999999998753    3344 8999999999999999999888  899999999999999999988888886


Q ss_pred             HHHHHH
Q psy1206         395 DAQKAL  400 (531)
Q Consensus       395 ~a~~~~  400 (531)
                      +.-+.+
T Consensus        78 ~~p~~l   83 (240)
T cd00008          78 KMPEEL   83 (240)
T ss_pred             CCCHHH
Confidence            544333

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.

>PF12813 XPG_I_2: XPG domain containing

Probab=98.22  E-value=3.3e-06  Score=85.17  Aligned_cols=87  Identities=16%  Similarity=0.217  Sum_probs=66.7

Q ss_pred             HHHHHHHhhc---CCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccC----CeE-EEeccccC------cccCCc
Q psy1206          45 GRLDSFFTIR---REEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGS----NIL-LRHMTFSE------ARKLPV  110 (531)
Q Consensus        45 ~~i~~lL~~~---gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~----~~V-i~~l~~~~------~~~~~v  110 (531)
                      +.+.++|+.+   |+++++.|+|||+.||.++++.-. .|+|+|||+++|..    ..+ +..+.+..      ...+..
T Consensus         7 ~~~~e~L~~~~~~~~~~~~~~~EAD~~~A~~A~~~~~-~VLt~DSDf~I~dlg~~~~yipl~~l~~~~~~~~~~~~~i~~   85 (246)
T PF12813_consen    7 PAFIEALRESWRYGVPVVQCPGEADRECAALARKWGC-PVLTNDSDFLIHDLGQKGGYIPLDSLEWDSVPKTGSGSYISA   85 (246)
T ss_pred             HHHHHHHHHHhhcCCcEEEcCccchHHHHHHHHHcCC-eEEccCCCEEEeccCCCceEEEeeeeEeecccccCCCCeeEE
Confidence            5667888888   999999999999999999986444 78999999999998    233 33333322      123456


Q ss_pred             EEecHHHHHHhCCCCHHHHHHHHh
Q psy1206         111 QEFHLEKVLEGMELSHEEFIDLCI  134 (531)
Q Consensus       111 ~~~~~~~i~~~lglt~eqfid~~i  134 (531)
                      ..|+++.+.+.+|+.  .+..++.
T Consensus        86 ~~y~~~~i~~~l~l~--~Lp~lA~  107 (246)
T PF12813_consen   86 KVYSPDKICKRLGLP--LLPLLAY  107 (246)
T ss_pred             EEEcHHHHHHHcCCc--hhHHHHH
Confidence            779999999999999  5555555

>PRK14976 5'-3' exonuclease; Provisional

Probab=98.16  E-value=2e-06  Score=88.42  Aligned_cols=84  Identities=15%  Similarity=0.256  Sum_probs=70.2

Q ss_pred             ceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcC--CeeEEeecCCCCCcchHHHHHHHHHHHH
Q psy1206         318 RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHG--LKPIYVFDGKPPTLKSGELNKRMEKRED  395 (531)
Q Consensus       318 k~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~g--IkPVfVFDG~pp~lK~~~~~kR~~~r~~  395 (531)
                      +.++||+++.||+...+...++..+++++|.+|+++.|++..+.++++..  -.+++||||+.|..+.+....++..|.+
T Consensus         4 ~~lliDg~~~~~ra~~a~~~~~~~l~~~~G~~t~a~~gf~~~l~~ll~~~~p~~~~v~fD~~~~~~R~~l~p~YKanR~~   83 (281)
T PRK14976          4 KALLIDGNSLIFRSYYATLKQGPKLKNNKGLPTNAIHTFLTMIFKILKKLNPSYILIAFDAGRKTFRHQLYDEYKQGRKK   83 (281)
T ss_pred             cEEEEeCcHHHHHHHHccCccCCCccCCCCCCchHHHHHHHHHHHHHHhcCCCEEEEEEECCCCcccccccHHHhcCCCC
Confidence            57899999999998777543344688999999999999999999998765  6789999999999999999998888865


Q ss_pred             HHHHHH
Q psy1206         396 AQKALA  401 (531)
Q Consensus       396 a~~~~~  401 (531)
                      .-+.+.
T Consensus        84 ~p~~l~   89 (281)
T PRK14976         84 TPESLI   89 (281)
T ss_pred             CCHHHH
Confidence            444433

>smart00475 53EXOc 5'-3' exonuclease

Probab=98.15  E-value=2.1e-06  Score=87.23  Aligned_cols=79  Identities=24%  Similarity=0.386  Sum_probs=66.8

Q ss_pred             ceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCee---EEeecCCCCCcchHHHHHHHHHHH
Q psy1206         318 RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKP---IYVFDGKPPTLKSGELNKRMEKRE  394 (531)
Q Consensus       318 k~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkP---VfVFDG~pp~lK~~~~~kR~~~r~  394 (531)
                      +.++||+++.||++..+++    .+++++|++|+++.|++..+.+|++.- +|   |+||||++|....+...+.+..|+
T Consensus         2 ~lllIDg~~~i~R~~~a~~----~l~~~~G~~t~a~~g~~~~l~~l~~~~-~p~~~~~~fD~~~~~~R~~l~p~YKa~R~   76 (259)
T smart00475        2 KLLLVDGSSLAFRAYFALP----PLKNSKGEPTNAVYGFLRMLLKLIKEE-KPTYVAVVFDAKGKTFRHELYPEYKANRP   76 (259)
T ss_pred             cEEEEeCcHHHHHHHHCCC----cccCCCCCcccHHHHHHHHHHHHHHHc-CCCeEEEEEeCCCCccccchhHHHHhCCC
Confidence            3589999999999998874    378899999999999999999998864 67   999999999998888888888877


Q ss_pred             HHHHHHH
Q psy1206         395 DAQKALA  401 (531)
Q Consensus       395 ~a~~~~~  401 (531)
                      +..+.+.
T Consensus        77 ~~pe~L~   83 (259)
T smart00475       77 KTPDELL   83 (259)
T ss_pred             CCCHHHH
Confidence            5554443

>KOG2520|consensus

Probab=97.87  E-value=2.5e-05  Score=89.45  Aligned_cols=56  Identities=20%  Similarity=0.268  Sum_probs=48.7

Q ss_pred             HHHHHHHhhcCCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEec
Q psy1206          45 GRLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHM  100 (531)
Q Consensus        45 ~~i~~lL~~~gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l  100 (531)
                      .+.+.++..++...+.++.+...++-.....++++.++..|+|.+.|+....|.+.
T Consensus       229 k~~r~l~~~~~d~~~~~~~~~~~~~d~~~~~~~~~~~~e~~~~~~~~~~e~~i~~~  284 (815)
T KOG2520|consen  229 KITRKLVDLENDAPIEAKDKSETLCDGNSVSGLVDFIIESDSDILKFGGENLIKED  284 (815)
T ss_pred             HHHHHHHHhhccchhhhcccccccCCcccccchhhcccccchHHhhcccccccccc
Confidence            35677888999999999999889998888889999999999999999998776654

>PRK09482 flap endonuclease-like protein; Provisional

Probab=97.76  E-value=2.7e-05  Score=79.03  Aligned_cols=46  Identities=37%  Similarity=0.556  Sum_probs=43.0

Q ss_pred             Hhhhhhhhhhcc--CccccCCCCCchHHHHHHHHhhccHHHHHHHHhh
Q psy1206         229 LYSFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT  274 (531)
Q Consensus       229 ~e~F~~~CiLsG--CDY~~~i~giG~k~A~kli~k~~s~~~vi~~l~~  274 (531)
                      .++|.|+..|.|  .|..|++||||+|||.+|+++|+|+++|++++..
T Consensus       167 P~q~~D~~aL~GD~sDnIpGVpGIG~KtA~~LL~~~gsle~i~~~~~~  214 (256)
T PRK09482        167 PQQLPDYWGLAGISSSKIPGVAGIGPKSAAELLNQFRSLENIYESLDA  214 (256)
T ss_pred             HHHHHHHHHHhCCCccCCCCCCCcChHHHHHHHHHhCCHHHHHHhHHH
Confidence            578999999999  8899999999999999999999999999999853

>PRK05755 DNA polymerase I; Provisional

Probab=97.64  E-value=3.5e-05  Score=90.46  Aligned_cols=81  Identities=25%  Similarity=0.328  Sum_probs=69.8

Q ss_pred             ceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCee---EEeecCCCCCcchHHHHHHHHHHH
Q psy1206         318 RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKP---IYVFDGKPPTLKSGELNKRMEKRE  394 (531)
Q Consensus       318 k~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkP---VfVFDG~pp~lK~~~~~kR~~~r~  394 (531)
                      +.++||+++.+|++..++   +..+++++|.+|+++.|++..+.+|+ ++.+|   |+|||++.|.++.+...+++..|.
T Consensus         3 ~~~liDg~~~~~r~~~a~---~~~~~~~~g~~~~a~~g~~~~l~~~~-~~~~p~~~~v~fD~~~~~~R~~~~~~YK~~R~   78 (880)
T PRK05755          3 TLLLIDGSSLLFRAFYAL---LPTLRNSDGLPTGAVYGFLNMLLKLL-KEEKPTHVAVAFDAKGKTFRHELYPEYKANRP   78 (880)
T ss_pred             eEEEEeCcHHHHHHHHCC---CCcccCCCCCcccHHHHHHHHHHHHH-HhcCCCEEEEEEECCCCccccccCHHHhCCCC
Confidence            468999999999999876   34678999999999999999999999 67888   999999999999999999999886


Q ss_pred             HHHHHHHH
Q psy1206         395 DAQKALAK  402 (531)
Q Consensus       395 ~a~~~~~~  402 (531)
                      +.-+.+..
T Consensus        79 ~~p~~l~~   86 (880)
T PRK05755         79 PMPEDLRE   86 (880)
T ss_pred             CCcHHHHH
Confidence            65554443

>TIGR00593 pola DNA polymerase I

Probab=97.61  E-value=7.1e-05  Score=87.77  Aligned_cols=79  Identities=23%  Similarity=0.402  Sum_probs=68.4

Q ss_pred             eeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCee---EEeecCCCCCcchHHHHHHHHHHHHH
Q psy1206         320 ICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKP---IYVFDGKPPTLKSGELNKRMEKREDA  396 (531)
Q Consensus       320 iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkP---VfVFDG~pp~lK~~~~~kR~~~r~~a  396 (531)
                      +.||+++.||++..+++  +.++++++|++|+++.|++..+.+|++.. +|   ++||||+.|.++.+...+.+..|.+.
T Consensus         2 ~lIDg~~l~~Ra~~a~~--~~~l~~~~G~~t~av~Gf~~~l~~ll~~~-~p~~i~v~FD~~~~tfR~~~~~~YKa~R~~~   78 (887)
T TIGR00593         2 LLIDGHSLAFRAYFALK--NKPLTNSKGEPTNAVYGFTKMLLKLLKEE-KPTYVAVAFDSGTPTFRHEAYAEYKANRAPT   78 (887)
T ss_pred             EEEeCcHHHHHHHHCCC--cccCcCCCCCEecHHHHHHHHHHHHHHhc-CCCEEEEEEcCCCCcchHHHHHHHHhCCCCC
Confidence            68999999999998874  23588999999999999999999999864 78   99999999999999888888888766


Q ss_pred             HHHHH
Q psy1206         397 QKALA  401 (531)
Q Consensus       397 ~~~~~  401 (531)
                      -+.+.
T Consensus        79 Pe~l~   83 (887)
T TIGR00593        79 PEELI   83 (887)
T ss_pred             hHHHH
Confidence            65554

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

>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases

Probab=96.97  E-value=4.2e-05  Score=67.36  Aligned_cols=45  Identities=40%  Similarity=0.617  Sum_probs=34.5

Q ss_pred             hhhhhhhhhcc--CccccCCCCCchHHHHHHHHhhccHHHHHHHHhh
Q psy1206         230 YSFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT  274 (531)
Q Consensus       230 e~F~~~CiLsG--CDY~~~i~giG~k~A~kli~k~~s~~~vi~~l~~  274 (531)
                      ++|.|+-.|.|  .|-.|++||||+|||.+|+++|+|++.|+.++..
T Consensus         4 ~q~~D~~aL~GD~sDNIPGV~GIG~KtA~~LL~~ygsle~i~~~~~~   50 (101)
T PF01367_consen    4 EQIADYKALVGDSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDE   50 (101)
T ss_dssp             HHHHHHCCCC-CCCCTB---TTSTCHCCCCCHHHHTSCHCCCCC-SS
T ss_pred             HHHHHHHHHcCCcccCCCCCCCCCHHHHHHHHHHcCCHHHHHHhHHh
Confidence            57788877777  5777888999999999999999999999988753

The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.

>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B

Probab=96.61  E-value=0.002  Score=51.88  Aligned_cols=24  Identities=38%  Similarity=0.546  Sum_probs=20.4

Q ss_pred             CCCCccHHHHHHHHHHcCCHHHHH
Q psy1206         143 SIRGIGPKRAIELIKEHRSIEKIL  166 (531)
Q Consensus       143 GIpGIG~ktA~kLI~~~~sle~il  166 (531)
                      ||||||+++|..|+++|+|++++.
T Consensus         7 GI~~VG~~~ak~L~~~f~sl~~l~   30 (64)
T PF12826_consen    7 GIPGVGEKTAKLLAKHFGSLEALM   30 (64)
T ss_dssp             TSTT--HHHHHHHHHCCSCHHHHC
T ss_pred             CCCCccHHHHHHHHHHcCCHHHHH
Confidence            899999999999999999998765

>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=96.16  E-value=0.007  Score=59.63  Aligned_cols=50  Identities=20%  Similarity=0.303  Sum_probs=35.9

Q ss_pred             HHHHHHhCCCC-HHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206         115 LEKVLEGMELS-HEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT  171 (531)
Q Consensus       115 ~~~i~~~lglt-~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~  171 (531)
                      .++-...|||. .+.--.|-.|      -+|+|||||+|+.++..+ +++++...+..
T Consensus        55 rEd~~~LyGF~~~~Er~lF~~L------i~V~GIGpK~Al~iLs~~-~~~~l~~aI~~  105 (203)
T PRK14602         55 REDALELFGFATWDERQTFIVL------ISISKVGAKTALAILSQF-RPDDLRRLVAE  105 (203)
T ss_pred             ecCcceeeCCCCHHHHHHHHHH------hCCCCcCHHHHHHHHhhC-CHHHHHHHHHh
Confidence            34445678875 4555555555      468999999999999986 56888877744

>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=95.86  E-value=0.0078  Score=59.05  Aligned_cols=50  Identities=22%  Similarity=0.278  Sum_probs=35.3

Q ss_pred             HHHHHHhCCCC-HHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206         115 LEKVLEGMELS-HEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT  171 (531)
Q Consensus       115 ~~~i~~~lglt-~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~  171 (531)
                      .++-...|||. .+.--.|-.|      -+|+|||||+|+.+++.+ +++++...+..
T Consensus        53 rED~~~LYGF~t~~Er~lF~~L------isVsGIGPK~ALaILs~~-~~~el~~aI~~  103 (196)
T PRK13901         53 REDELKLFGFLNSSEREVFEEL------IGVDGIGPRAALRVLSGI-KYNEFRDAIDR  103 (196)
T ss_pred             ecCCceeeCCCCHHHHHHHHHH------hCcCCcCHHHHHHHHcCC-CHHHHHHHHHh
Confidence            44445678874 4444445555      378999999999999986 66788777644

>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=95.79  E-value=0.0087  Score=58.14  Aligned_cols=50  Identities=14%  Similarity=0.192  Sum_probs=35.3

Q ss_pred             HHHHHHhCCCC-HHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206         115 LEKVLEGMELS-HEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT  171 (531)
Q Consensus       115 ~~~i~~~lglt-~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~  171 (531)
                      .++-...|||. .+.--.|-.|      -+|+|||||+|+.+++.+ +++++...+..
T Consensus        54 rEd~~~LyGF~~~~Er~lF~~L------i~VsGIGpK~Al~ILs~~-~~~el~~aI~~  104 (183)
T PRK14601         54 KEDSNKLYGFLDKDEQKMFEML------LKVNGIGANTAMAVCSSL-DVNSFYKALSL  104 (183)
T ss_pred             ecCCceeeCCCCHHHHHHHHHH------hccCCccHHHHHHHHcCC-CHHHHHHHHHh
Confidence            44445678874 4444445555      368999999999999886 56788777644

>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=95.78  E-value=0.01  Score=57.70  Aligned_cols=50  Identities=20%  Similarity=0.246  Sum_probs=35.8

Q ss_pred             HHHHHHhCCCC-HHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206         115 LEKVLEGMELS-HEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT  171 (531)
Q Consensus       115 ~~~i~~~lglt-~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~  171 (531)
                      .++....|||. .+.--.|-.|      -+|+|||||+|+.+++.+ +++++...+..
T Consensus        54 rEd~~~LyGF~~~~Er~lF~~L------isV~GIGpK~Al~iLs~~-~~~~l~~aI~~  104 (186)
T PRK14600         54 RDNVTQLYGFLNREEQDCLRML------VKVSGVNYKTAMSILSKL-TPEQLFSAIVN  104 (186)
T ss_pred             ecCCceeeCCCCHHHHHHHHHH------hCcCCcCHHHHHHHHccC-CHHHHHHHHHc
Confidence            45555678975 4444444444      378999999999999986 66888877754

>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=95.73  E-value=0.0091  Score=58.59  Aligned_cols=50  Identities=20%  Similarity=0.262  Sum_probs=34.6

Q ss_pred             HHHHHHhCCCCHH-HHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206         115 LEKVLEGMELSHE-EFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT  171 (531)
Q Consensus       115 ~~~i~~~lglt~e-qfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~  171 (531)
                      .++-...|||... .-..|-.|      -+|+|||||+|+.+++.+ +++++.+.+..
T Consensus        53 rEd~~~LyGF~~~~Er~lF~~L------~~V~GIGpK~AL~iLs~~-~~~~l~~aI~~  103 (197)
T PRK14603         53 REDALSLYGFPDEDSLELFELL------LGVSGVGPKLALALLSAL-PPALLARALLE  103 (197)
T ss_pred             ccCCceeeCcCCHHHHHHHHHH------hCcCCcCHHHHHHHHcCC-CHHHHHHHHHh
Confidence            3444567887533 33333444      378999999999999985 66888877754

>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=95.69  E-value=0.0098  Score=57.96  Aligned_cols=50  Identities=18%  Similarity=0.272  Sum_probs=35.2

Q ss_pred             HHHHHHhCCCC-HHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206         115 LEKVLEGMELS-HEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT  171 (531)
Q Consensus       115 ~~~i~~~lglt-~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~  171 (531)
                      .++....|||. .+.--.|-.|      -+|+|||||+|+.++..+ +++++.+.+..
T Consensus        54 rEd~~~LyGF~~~~Er~lF~~L------i~V~GIGpK~AL~iLs~~-~~~el~~aI~~  104 (188)
T PRK14606         54 SQDGITLYGFSNERKKELFLSL------TKVSRLGPKTALKIISNE-DAETLVTMIAS  104 (188)
T ss_pred             ecCCceeeCCCCHHHHHHHHHH------hccCCccHHHHHHHHcCC-CHHHHHHHHHh
Confidence            44455678975 4444444455      368999999999999875 66788777644

>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=95.69  E-value=0.0097  Score=58.32  Aligned_cols=50  Identities=22%  Similarity=0.290  Sum_probs=34.9

Q ss_pred             HHHHHHhCCCC-HHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206         115 LEKVLEGMELS-HEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT  171 (531)
Q Consensus       115 ~~~i~~~lglt-~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~  171 (531)
                      .++....|||. .+.--.|-.|      -+|+|||||+|+.++..+ +++++...+..
T Consensus        54 rEd~~~LyGF~~~~Er~lF~~L------i~V~GIGpK~Al~iLs~~-~~~el~~aI~~  104 (195)
T PRK14604         54 REDALTLYGFSTPAQRQLFELL------IGVSGVGPKAALNLLSSG-TPDELQLAIAG  104 (195)
T ss_pred             ecCCceeeCCCCHHHHHHHHHH------hCcCCcCHHHHHHHHcCC-CHHHHHHHHHh
Confidence            34445678875 4444444444      368999999999999974 67888877754

>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]

Probab=95.59  E-value=0.032  Score=55.01  Aligned_cols=53  Identities=25%  Similarity=0.281  Sum_probs=36.8

Q ss_pred             EecHHHHHHhCCCCHHHHHH-HHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206         112 EFHLEKVLEGMELSHEEFID-LCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT  171 (531)
Q Consensus       112 ~~~~~~i~~~lglt~eqfid-~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~  171 (531)
                      .+-.++....|||....=.+ |..|      -+|.|||||+|+.+++.. +++++...+..
T Consensus        51 ~~vREd~~~LyGF~~~~ER~lF~~L------isVnGIGpK~ALaiLs~~-~~~~l~~aI~~  104 (201)
T COG0632          51 LVVREDAHLLYGFLTEEERELFRLL------ISVNGIGPKLALAILSNL-DPEELAQAIAN  104 (201)
T ss_pred             EeehhhHHHHcCCCCHHHHHHHHHH------HccCCccHHHHHHHHcCC-CHHHHHHHHHh
Confidence            45567778889986333333 3333      368899999999999863 56777777643

>COG5366 Protein involved in propagation of M2 dsRNA satellite of L-A virus [General function prediction only]

Probab=95.33  E-value=0.008  Score=65.00  Aligned_cols=122  Identities=25%  Similarity=0.382  Sum_probs=91.9

Q ss_pred             HHHHHHhhcCCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccC-CeEEEeccccCcccCCcEEecHHHHHHhCCC
Q psy1206          46 RLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGS-NILLRHMTFSEARKLPVQEFHLEKVLEGMEL  124 (531)
Q Consensus        46 ~i~~lL~~~gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~-~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lgl  124 (531)
                      .+..++...+|.|+++||-|..|||||....+++++ -+.+|.+++.+ +++|..+.+..+ +.++..++.....+-.-.
T Consensus       133 ~~sk~~~~~~~a~~i~~ys~~fq~AYl~~~~~~~~~-~gp~d~l~ld~vdr~il~m~fg~d-~Ppl~~~~vp~~lem~l~  210 (531)
T COG5366         133 VASKILEEKGVAVIIAPYSATFQCAYLMSAETCSYA-FGPSDILLLDGVDRIILDMSFGSD-KPPLDVFHVPRFLEMFLL  210 (531)
T ss_pred             cccccccccceEEEehhhHHHHHHHHHHHHHHHHhc-CCchHhHHHhhhhhheeecccCCC-CCCCcccccchHHHhccc
Confidence            345578889999999999999999999999999975 77999998876 788888876533 356777777776666667


Q ss_pred             CHHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHc---CCHHHHHHHh
Q psy1206         125 SHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEH---RSIEKILENI  169 (531)
Q Consensus       125 t~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~---~sle~il~~l  169 (531)
                      +-.-|...-.|.|||+++.+|.+-..-+..+....   ++-|.+...+
T Consensus       211 s~~lFya~~ll~~c~~~s~~~~C~~da~f~l~qvigd~~~qElfs~ai  258 (531)
T COG5366         211 SSRLFYALGLLLGCDFCSTIPRCATDADFSLNQVIGDMKGQELFSKAI  258 (531)
T ss_pred             ccchhhhhcccccccccccccccccchhHHHHHHHhccccHHHHHHHh
Confidence            78889999999999999999985443344444433   3344444443

>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional

Probab=95.09  E-value=0.023  Score=55.66  Aligned_cols=49  Identities=24%  Similarity=0.333  Sum_probs=34.8

Q ss_pred             HHHHHHhCCCC-HHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhh
Q psy1206         115 LEKVLEGMELS-HEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENID  170 (531)
Q Consensus       115 ~~~i~~~lglt-~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~  170 (531)
                      .++....|||. .+.--.|-.|      -+|+|||||+|+.++..++ .+.++..+.
T Consensus        54 rEd~~~LyGF~~~~Er~lF~~L------i~V~GIGpK~Al~ILs~~~-~~~l~~aI~  103 (194)
T PRK14605         54 REDALSLFGFATTEELSLFETL------IDVSGIGPKLGLAMLSAMN-AEALASAII  103 (194)
T ss_pred             ecCCceeeCCCCHHHHHHHHHH------hCCCCCCHHHHHHHHHhCC-HHHHHHHHH
Confidence            44445678875 4444444555      4799999999999999875 577777663

>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit

Probab=95.00  E-value=0.029  Score=54.78  Aligned_cols=50  Identities=26%  Similarity=0.269  Sum_probs=34.7

Q ss_pred             HHHHHHhCCCC-HHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206         115 LEKVLEGMELS-HEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT  171 (531)
Q Consensus       115 ~~~i~~~lglt-~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~  171 (531)
                      .++-...|||. .+.--.|..|      -+|||||||+|+.++..+ +++++.+.+..
T Consensus        53 red~~~LyGF~~~~Er~lF~~L------~~V~GIGpK~Al~iL~~~-~~~el~~aI~~  103 (191)
T TIGR00084        53 REDAELLFGFNTLEERELFKEL------IKVNGVGPKLALAILSNM-SPEEFVYAIET  103 (191)
T ss_pred             ecCCceeeCCCCHHHHHHHHHH------hCCCCCCHHHHHHHHhcC-CHHHHHHHHHh
Confidence            34445578874 4444444555      379999999999998764 57888777743

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed

Probab=94.09  E-value=0.054  Score=52.83  Aligned_cols=47  Identities=23%  Similarity=0.442  Sum_probs=30.2

Q ss_pred             HHHHHhCCCCHHHHHH-HHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHh
Q psy1206         116 EKVLEGMELSHEEFID-LCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENI  169 (531)
Q Consensus       116 ~~i~~~lglt~eqfid-~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l  169 (531)
                      ++....+|+....=.+ +..|.      .|||||||+|.+++..|++ +.+.+.+
T Consensus        55 d~~~~l~gF~~~~ek~~f~~L~------~i~GIGpk~A~~il~~fg~-~~l~~~i  102 (192)
T PRK00116         55 EDAILLYGFLTKEERELFRLLI------SVSGVGPKLALAILSGLSP-EELVQAI  102 (192)
T ss_pred             chhHHHcCcCCHHHHHHHHHHh------cCCCCCHHHHHHHHHhCCH-HHHHHHH
Confidence            3444557765222222 33443      4999999999999999987 5555444

>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=93.94  E-value=0.055  Score=51.79  Aligned_cols=82  Identities=24%  Similarity=0.357  Sum_probs=56.2

Q ss_pred             ceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCC--eeEEeecCCCCCcchHH----HHHHHH
Q psy1206         318 RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGL--KPIYVFDGKPPTLKSGE----LNKRME  391 (531)
Q Consensus       318 k~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gI--kPVfVFDG~pp~lK~~~----~~kR~~  391 (531)
                      +.+-||+++.+|+...+...  .++.+++|.+|+-+.|++.-+.+++..--  ..|+|||++.+....+-    -+.|..
T Consensus         2 ~llLIDg~~l~~Ra~~a~~~--~~l~~~~G~~t~ai~g~~~~l~~l~~~~~p~~~vv~fD~~~~~fR~~l~p~YKanR~~   79 (169)
T PF02739_consen    2 KLLLIDGNSLLFRAYYALPK--DPLRNSDGEPTNAIYGFLRMLLKLLKDFKPDYVVVAFDSKGPTFRKELYPEYKANRKP   79 (169)
T ss_dssp             EEEEEEHHHHHHHCCCCCTT--ST-BETTSEB-HHHHHHHHHHHHHHHHTTEEEEEEEEEBSSCHHHHHCCTTTTHHHHH
T ss_pred             eEEEEechHHHHHHHHhhcc--CCCcCCCCCChHHHHHHHHHHHHHHHHcCCceEEEEecCCCcchHHHHHHHHHhCCCC
Confidence            45789999999988776643  56889999999999999988888865543  67899999876222211    344555


Q ss_pred             HHHHHHHHHH
Q psy1206         392 KREDAQKALA  401 (531)
Q Consensus       392 ~r~~a~~~~~  401 (531)
                      ..++-...+.
T Consensus        80 ~p~~l~~q~~   89 (169)
T PF02739_consen   80 MPEELIPQLP   89 (169)
T ss_dssp             HHHHHHHHHH
T ss_pred             CCHHHHHHHH
Confidence            5555444333

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 ....

>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated

Probab=91.05  E-value=0.8  Score=52.85  Aligned_cols=124  Identities=19%  Similarity=0.274  Sum_probs=60.7

Q ss_pred             CCCCccHHHHHHHHHHc--CCHHHHHHHhhhcCC-CCCCCCcHHHHHHHhcCCCcCCCCCcccccccccccccccccccC
Q psy1206         143 SIRGIGPKRAIELIKEH--RSIEKILENIDTKKY-TVPEGWLYKEARELFRHPEVADPETIEFIDLCILLGCDYCDSIRG  219 (531)
Q Consensus       143 GIpGIG~ktA~kLI~~~--~sle~il~~l~~~~~-~ip~~f~~~~A~~~f~~p~V~d~~~~~~v~Ls~~~~~d~cesl~~  219 (531)
                      .|+|+|++++.+|+.+.  .++++++ .+..... .+| +|--+.|.+++..-.-.-  +   .+|...   .+.....+
T Consensus       449 ~I~GLG~k~i~~L~~~g~I~~i~DL~-~L~~~~L~~l~-gfG~Ksa~~ll~~Ie~sk--~---~~l~R~---l~algi~~  518 (665)
T PRK07956        449 DIDGLGEKIIEQLFEKGLIHDPADLF-KLTAEDLLGLE-GFGEKSAQNLLDAIEKSK--E---TSLARF---LYALGIRH  518 (665)
T ss_pred             CCCCcCHHHHHHHHHcCCCCCHHHHH-hcCHHHHhcCc-CcchHHHHHHHHHHHHhh--c---CCHHHh---hHhhhccC
Confidence            58999999999999874  5888888 5543222 122 343333332222111000  0   011110   11222345


Q ss_pred             CChhhhHhHHhhhhhhhhhc--cCccccCCCCCchHHHHHHHHhhccH--HHHHHHHhhCC
Q psy1206         220 IGPKRAIELLYSFIDLCILL--GCDYCDSIRGIGPKRAIELIKEHRSI--EKILENIDTKK  276 (531)
Q Consensus       220 ~Gp~~~~el~e~F~~~CiLs--GCDY~~~i~giG~k~A~kli~k~~s~--~~vi~~l~~~~  276 (531)
                      .|+..+..|...|..+--|.  .-+-+..++|||+++|..++.-+.+.  ..++..|...|
T Consensus       519 IG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG~~~A~sI~~ff~~~~~~~~i~~L~~~g  579 (665)
T PRK07956        519 VGEKAAKALARHFGSLEALRAASEEELAAVEGVGEVVAQSIVEFFAVEENRELIDELLEAG  579 (665)
T ss_pred             cCHHHHHHHHHHcCCHHHHHhCCHHHHhccCCcCHHHHHHHHHHHhhhhHHHHHHHHHHcC
Confidence            56655555555554432221  22334567777777776666655543  24455554333

>TIGR00575 dnlj DNA ligase, NAD-dependent

Probab=89.74  E-value=0.79  Score=52.79  Aligned_cols=27  Identities=26%  Similarity=0.543  Sum_probs=20.0

Q ss_pred             CCCCccHHHHHHHHHHc--CCHHHHHHHhh
Q psy1206         143 SIRGIGPKRAIELIKEH--RSIEKILENID  170 (531)
Q Consensus       143 GIpGIG~ktA~kLI~~~--~sle~il~~l~  170 (531)
                      .|+|+|++++.+|+.+.  .++++++ .|.
T Consensus       436 ~I~GLG~k~i~~L~~~g~I~~~~Dl~-~L~  464 (652)
T TIGR00575       436 DIEGLGDKVIEQLFEKKLVRSVADLY-ALK  464 (652)
T ss_pred             CCCCcCHHHHHHHHHcCCcCCHHHHH-hcC
Confidence            47889999988888764  4777777 443

The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.

>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains

Probab=88.96  E-value=0.36  Score=37.63  Aligned_cols=26  Identities=31%  Similarity=0.552  Sum_probs=18.8

Q ss_pred             CCCCCccHHHHHHHHHH-cCCHHHHHH
Q psy1206         142 DSIRGIGPKRAIELIKE-HRSIEKILE  167 (531)
Q Consensus       142 pGIpGIG~ktA~kLI~~-~~sle~il~  167 (531)
                      -+|.|||++||.+++.. ++|++++..
T Consensus         5 ~~I~GVG~~tA~~w~~~G~rtl~Dl~~   31 (52)
T PF10391_consen    5 TGIWGVGPKTARKWYAKGIRTLEDLRK   31 (52)
T ss_dssp             HTSTT--HHHHHHHHHTT--SHHHHHH
T ss_pred             hhcccccHHHHHHHHHhCCCCHHHHhh
Confidence            37899999999999985 789999944

There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=87.74  E-value=1.2  Score=51.75  Aligned_cols=39  Identities=28%  Similarity=0.440  Sum_probs=27.6

Q ss_pred             CCHHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhh
Q psy1206         124 LSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENID  170 (531)
Q Consensus       124 lt~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~  170 (531)
                      -+.+.++.+..   +   +.+||||+++|-+|+..||  ++.++.+.
T Consensus        75 ~~~~~i~~yL~---s---~~~~GIG~~~A~~iv~~fg--~~~~~~i~  113 (720)
T TIGR01448        75 TSKEGIVAYLS---S---RSIKGVGKKLAQRIVKTFG--EAAFDVLD  113 (720)
T ss_pred             CCHHHHHHHHh---c---CCCCCcCHHHHHHHHHHhC--HhHHHHHH
Confidence            35667776543   2   2488999999999999998  35555553

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B

Probab=87.11  E-value=0.3  Score=39.27  Aligned_cols=26  Identities=35%  Similarity=0.512  Sum_probs=21.0

Q ss_pred             CCCCCchHHHHHHHHhhccHHHHHHH
Q psy1206         246 SIRGIGPKRAIELIKEHRSIEKILEN  271 (531)
Q Consensus       246 ~i~giG~k~A~kli~k~~s~~~vi~~  271 (531)
                      +|||||.++|..|.++|+|++++..+
T Consensus         7 GI~~VG~~~ak~L~~~f~sl~~l~~a   32 (64)
T PF12826_consen    7 GIPGVGEKTAKLLAKHFGSLEALMNA   32 (64)
T ss_dssp             TSTT--HHHHHHHHHCCSCHHHHCC-
T ss_pred             CCCCccHHHHHHHHHHcCCHHHHHHc
Confidence            79999999999999999999887643

>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A

Probab=85.63  E-value=0.66  Score=36.55  Aligned_cols=25  Identities=44%  Similarity=0.731  Sum_probs=22.4

Q ss_pred             CCCCccHHHHHHHHHH-cCCHHHHHH
Q psy1206         143 SIRGIGPKRAIELIKE-HRSIEKILE  167 (531)
Q Consensus       143 GIpGIG~ktA~kLI~~-~~sle~il~  167 (531)
                      .|||||+++|.+|... |+|++++..
T Consensus         9 ~I~Gig~~~a~~L~~~G~~t~~~l~~   34 (60)
T PF14520_consen    9 SIPGIGPKRAEKLYEAGIKTLEDLAN   34 (60)
T ss_dssp             TSTTCHHHHHHHHHHTTCSSHHHHHT
T ss_pred             cCCCCCHHHHHHHHhcCCCcHHHHHc
Confidence            6999999999999998 899888764

...

>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]

Probab=84.38  E-value=0.8  Score=31.70  Aligned_cols=15  Identities=40%  Similarity=0.780  Sum_probs=12.2

Q ss_pred             CCCCccHHHHHHHHH
Q psy1206         143 SIRGIGPKRAIELIK  157 (531)
Q Consensus       143 GIpGIG~ktA~kLI~  157 (531)
                      .|||||++||-.++.
T Consensus        15 ~lpGIG~~tA~~I~~   29 (30)
T PF00633_consen   15 KLPGIGPKTANAILS   29 (30)
T ss_dssp             TSTT-SHHHHHHHHH
T ss_pred             hCCCcCHHHHHHHHh
Confidence            689999999998864

The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....

>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses

Probab=84.06  E-value=2.6  Score=45.98  Aligned_cols=116  Identities=23%  Similarity=0.255  Sum_probs=69.3

Q ss_pred             HHHHHHhhc--CCcccc-CCCchhHHHHHHH-----HcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHH
Q psy1206          46 RLDSFFTIR--REEKRK-APCEAEAQCAAMV-----KAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEK  117 (531)
Q Consensus        46 ~i~~lL~~~--gIp~vv-APyEADAq~A~L~-----r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~  117 (531)
                      .+.++|..+  +|.++- ....||=.+-+=+     +.|.=-.++|.|-|.|+|.+..-..++-           .+.. 
T Consensus       147 ~l~~~L~~~~~~V~IvyCDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss~D~~~KiI-----------~t~~-  214 (425)
T PF04599_consen  147 ILESSLSRLKEDVEIVYCDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSSCDTPPKII-----------KTMN-  214 (425)
T ss_pred             HHHHHHHhccCCceEEEECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeeecCchHHHH-----------HhHH-
Confidence            456667666  677774 5568887666544     3577778999999999999843222210           0111 


Q ss_pred             HHHhCCC-----CHHHHHHHHhHcCCCCCCCCCCcc--HHHHHHHHHHcC--CHHHHHHHhhhcCCCC
Q psy1206         118 VLEGMEL-----SHEEFIDLCILLGCDYCDSIRGIG--PKRAIELIKEHR--SIEKILENIDTKKYTV  176 (531)
Q Consensus       118 i~~~lgl-----t~eqfid~~iL~G~DY~pGIpGIG--~ktA~kLI~~~~--sle~il~~l~~~~~~i  176 (531)
                        +.+.+     +.---...++.-||||-||+-|+.  .++--+ +.-|.  +++++++.|.-+++..
T Consensus       215 --~~Y~~~P~~~s~YL~kL~~L~NGCDfFpGLyG~~it~~~l~~-i~LF~dFti~Ni~~SL~~kny~~  279 (425)
T PF04599_consen  215 --QLYKFIPCSKSRYLSKLTALVNGCDFFPGLYGISITKKSLNR-IKLFEDFTIDNILQSLAIKNYSL  279 (425)
T ss_pred             --hHeeecCCchHHHHHHHHHHHhcccccCCcceeEechhhccc-eeccccccHHHHHHHHhhhhhhh
Confidence              11211     222223345667899999999964  333222 33343  6789998886654433

>PRK14667 uvrC excinuclease ABC subunit C; Provisional

Probab=83.82  E-value=0.93  Score=51.36  Aligned_cols=29  Identities=21%  Similarity=0.432  Sum_probs=25.5

Q ss_pred             CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206         140 YCDSIRGIGPKRAIELIKEHRSIEKILEN  168 (531)
Q Consensus       140 Y~pGIpGIG~ktA~kLI~~~~sle~il~~  168 (531)
                      =+.+|||||+|+..+|+++|||+++|.++
T Consensus       515 ~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~A  543 (567)
T PRK14667        515 ILDKIKGIGEVKKEIIYRNFKTLYDFLKA  543 (567)
T ss_pred             ccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence            34589999999999999999999998754

>PHA00439 exonuclease

Probab=83.55  E-value=2.2  Score=44.45  Aligned_cols=60  Identities=10%  Similarity=0.158  Sum_probs=47.3

Q ss_pred             ceeeecccchHHHHHHHHhh--c-CccccCCCCCCcchhhhHHHHHHHHHHc----CCee-EEeecCC
Q psy1206         318 RKICIDASMSLYQFLIAVRS--E-GNQLMSVDGEPTSHLMGTFYRTIRLVEH----GLKP-IYVFDGK  377 (531)
Q Consensus       318 k~iAIDa~~~lyqfl~~ir~--~-g~~l~~~~g~~tshl~g~~~R~~~ll~~----gIkP-VfVFDG~  377 (531)
                      ..+-||++..+|+...++-.  + +..+++++|..|+-+.|++.-+.++++.    .-.+ |++||+.
T Consensus         7 ~llLIDG~~l~fRA~~A~~~~~~~~~~l~~~~G~~t~A~~gf~~~L~kl~~~~k~~~p~~i~vaFD~~   74 (286)
T PHA00439          7 GVLVMDGDYLVFQAMAAAEVETDWGEDIWTLECDHAKARQILEDSIKSYKTRKKAWKDAPIVLAFTDS   74 (286)
T ss_pred             cEEEEeCcHHHHHHHHccCcccccCCCCCCCCCeeccHHHHHHHHHHHHHHhhccCCCCeEEEEECCC
Confidence            57889999999998888732  1 3457899999999999999999999865    3333 5669954

>PRK14669 uvrC excinuclease ABC subunit C; Provisional

Probab=83.20  E-value=0.87  Score=52.15  Aligned_cols=28  Identities=29%  Similarity=0.444  Sum_probs=25.1

Q ss_pred             CCCCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206         141 CDSIRGIGPKRAIELIKEHRSIEKILEN  168 (531)
Q Consensus       141 ~pGIpGIG~ktA~kLI~~~~sle~il~~  168 (531)
                      +.+|||||++++.+|+++|||+++|.+.
T Consensus       554 L~~IpGIG~kr~~~LL~~FgSi~~I~~A  581 (624)
T PRK14669        554 LLEIPGVGAKTVQRLLKHFGSLERVRAA  581 (624)
T ss_pred             HhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence            3589999999999999999999998763

>PHA03065 Hypothetical protein; Provisional

Probab=82.38  E-value=2.9  Score=45.45  Aligned_cols=118  Identities=21%  Similarity=0.266  Sum_probs=69.5

Q ss_pred             HHHHHHHhhc--CCcccc-CCCchhHHHHHHH-----HcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHH
Q psy1206          45 GRLDSFFTIR--REEKRK-APCEAEAQCAAMV-----KAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLE  116 (531)
Q Consensus        45 ~~i~~lL~~~--gIp~vv-APyEADAq~A~L~-----r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~  116 (531)
                      ..+.+.|..+  +|.++- ..-.||=.+-.=+     +.|.=-.++|.|-|.|+|.+..-+-++           ..+. 
T Consensus       148 ~~l~~~L~~~~~~v~I~yCdgvDAEfvMC~~ak~~a~~~g~WPl~iStDQDtllf~s~D~~~Ki-----------I~t~-  215 (438)
T PHA03065        148 RLLESALARLGENVEIVYCDGVDAEFVMCARAKELAATTGEWPLLISTDQDTLLFSSCDRLPKI-----------IKTA-  215 (438)
T ss_pred             HHHHHHHHhccCCceEEEECCcchhHHHHHHHHHHHhhcCCCceEEeccCCeeEEEecCcHHHH-----------HHhH-
Confidence            4566677777  677774 4457776655433     357777899999999999874211111           0111 


Q ss_pred             HHHHhCCCC-----HHHHHHHHhHcCCCCCCCCCCcc--HHH--HHHHHHHcCCHHHHHHHhhhcCCCCC
Q psy1206         117 KVLEGMELS-----HEEFIDLCILLGCDYCDSIRGIG--PKR--AIELIKEHRSIEKILENIDTKKYTVP  177 (531)
Q Consensus       117 ~i~~~lglt-----~eqfid~~iL~G~DY~pGIpGIG--~kt--A~kLI~~~~sle~il~~l~~~~~~ip  177 (531)
                        -+.+.+.     .---...++.-||||.||+-|+.  +++  -.+|...| +.+++++.|..+++.+.
T Consensus       216 --~~~Y~~~P~~~t~YL~kL~~L~NGCDfFpGLyG~~it~~~l~r~~LF~dF-t~~Nv~~SL~~kny~l~  282 (438)
T PHA03065        216 --NQLYKFIPCAKTRYLSKLVALVNGCDFFPGLYGISITPKSLNRIQLFDDF-TIDNVVRSLAIKNYSLK  282 (438)
T ss_pred             --HHHheeCCChhHHHHHHHHHHHhcccccCccceEEechhhccceechhhh-hHHHHHHHHHhhhhhcc
Confidence              1122222     22222345557899999999975  333  12333333 66899988876655443

>TIGR00194 uvrC excinuclease ABC, C subunit

Probab=81.57  E-value=1.1  Score=50.92  Aligned_cols=28  Identities=32%  Similarity=0.417  Sum_probs=25.1

Q ss_pred             CCCCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206         141 CDSIRGIGPKRAIELIKEHRSIEKILEN  168 (531)
Q Consensus       141 ~pGIpGIG~ktA~kLI~~~~sle~il~~  168 (531)
                      +.+|||||+|+..+|+++|||+++|.+.
T Consensus       543 Ld~I~GIG~kr~~~LL~~Fgs~~~i~~A  570 (574)
T TIGR00194       543 LLKIPGVGEKRVQKLLKYFGSLKGIKKA  570 (574)
T ss_pred             HhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence            3589999999999999999999998754

This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.

>PRK14670 uvrC excinuclease ABC subunit C; Provisional

Probab=81.48  E-value=1.2  Score=50.53  Aligned_cols=29  Identities=31%  Similarity=0.458  Sum_probs=25.9

Q ss_pred             CCCCCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206         140 YCDSIRGIGPKRAIELIKEHRSIEKILEN  168 (531)
Q Consensus       140 Y~pGIpGIG~ktA~kLI~~~~sle~il~~  168 (531)
                      -+..|||||+++..+|+++|||+++|.++
T Consensus       515 ~L~~I~GiG~kr~~~LL~~Fgs~~~I~~A  543 (574)
T PRK14670        515 NYTKIKGIGEKKAKKILKSLGTYKDILLL  543 (574)
T ss_pred             ccccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence            45699999999999999999999998764

>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]

Probab=81.02  E-value=0.94  Score=31.37  Aligned_cols=17  Identities=35%  Similarity=0.600  Sum_probs=12.8

Q ss_pred             ccCCCCCchHHHHHHHH
Q psy1206         244 CDSIRGIGPKRAIELIK  260 (531)
Q Consensus       244 ~~~i~giG~k~A~kli~  260 (531)
                      +.++||||+++|-.++.
T Consensus        13 L~~lpGIG~~tA~~I~~   29 (30)
T PF00633_consen   13 LMKLPGIGPKTANAILS   29 (30)
T ss_dssp             HHTSTT-SHHHHHHHHH
T ss_pred             HHhCCCcCHHHHHHHHh
Confidence            45799999999987653

The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....

>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A

Probab=80.30  E-value=1.1  Score=35.23  Aligned_cols=27  Identities=41%  Similarity=0.609  Sum_probs=23.3

Q ss_pred             ccCCCCCchHHHHHHHHh-hccHHHHHH
Q psy1206         244 CDSIRGIGPKRAIELIKE-HRSIEKILE  270 (531)
Q Consensus       244 ~~~i~giG~k~A~kli~k-~~s~~~vi~  270 (531)
                      +.+|||||+++|.+|+.. ++|++.+..
T Consensus         7 L~~I~Gig~~~a~~L~~~G~~t~~~l~~   34 (60)
T PF14520_consen    7 LLSIPGIGPKRAEKLYEAGIKTLEDLAN   34 (60)
T ss_dssp             HHTSTTCHHHHHHHHHHTTCSSHHHHHT
T ss_pred             hccCCCCCHHHHHHHHhcCCCcHHHHHc
Confidence            457999999999999999 889887764

...

>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]

Probab=80.26  E-value=2.9  Score=47.98  Aligned_cols=33  Identities=21%  Similarity=0.274  Sum_probs=25.5

Q ss_pred             ccCCCCCchHHHHHHHHhhccH--HHHHHHHhhCC
Q psy1206         244 CDSIRGIGPKRAIELIKEHRSI--EKILENIDTKK  276 (531)
Q Consensus       244 ~~~i~giG~k~A~kli~k~~s~--~~vi~~l~~~~  276 (531)
                      +.+++|||.+.|..++.=+...  ..+++.|...|
T Consensus       545 l~~i~giG~~vA~si~~ff~~~~~~~li~~L~~~g  579 (667)
T COG0272         545 LASIPGIGEVVARSIIEFFANEENRELIDELLAAG  579 (667)
T ss_pred             HhhccchhHHHHHHHHHHHcCHHHHHHHHHHHHcC
Confidence            3459999999999999888765  45777776655

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	531
1ul1_X	379	Crystal Structure Of The Human Fen1-Pcna Complex Le		2e-55
1ul1_X	379	Crystal Structure Of The Human Fen1-Pcna Complex Le		2e-31
1ul1_X	379	Crystal Structure Of The Human Fen1-Pcna Complex Le		1e-13
3q8k_A	341	Crystal Structure Of Human Flap Endonuclease Fen1 (		4e-55
3q8k_A	341	Crystal Structure Of Human Flap Endonuclease Fen1 (		3e-31
3q8k_A	341	Crystal Structure Of Human Flap Endonuclease Fen1 (		9e-09
3q8m_A	341	Crystal Structure Of Human Flap Endonuclease Fen1 (		2e-54
3q8m_A	341	Crystal Structure Of Human Flap Endonuclease Fen1 (		3e-31
3q8m_A	341	Crystal Structure Of Human Flap Endonuclease Fen1 (		8e-09
2izo_A	346	Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex L		9e-22
2izo_A	346	Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex L		2e-20
3ory_A	363	Crystal Structure Of Flap Endonuclease 1 From Hyper		1e-20
3ory_A	363	Crystal Structure Of Flap Endonuclease 1 From Hyper		2e-20
1mc8_A	343	Crystal Structure Of Flap Endonuclease-1 R42e Mutan		6e-20
1mc8_A	343	Crystal Structure Of Flap Endonuclease-1 R42e Mutan		3e-08
1b43_A	340	Fen-1 From P. Furiosus Length = 340		1e-18
1b43_A	340	Fen-1 From P. Furiosus Length = 340		6e-16
1b43_A	340	Fen-1 From P. Furiosus Length = 340		3e-08
1rxv_A	336	Crystal Structure Of A. Fulgidus Fen-1 Bound To Dna		1e-17
1rxv_A	336	Crystal Structure Of A. Fulgidus Fen-1 Bound To Dna		2e-14
1a76_A	326	Flap Endonuclease-1 From Methanococcus Jannaschii L		3e-15
1a76_A	326	Flap Endonuclease-1 From Methanococcus Jannaschii L		5e-13
3qea_Z	352	Crystal Structure Of Human Exonuclease 1 Exo1 (Wt)		4e-12
3qe9_Y	352	Crystal Structure Of Human Exonuclease 1 Exo1 (D173		3e-11

>pdb|1UL1|X Chain X, Crystal Structure Of The Human Fen1-Pcna Complex Length = 379

Iteration: 1
 Score =  213 bits (542), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 94/142 (66%), Positives = 120/142 (84%)
Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           AP EAEA CAA+VKAGKVYA ATEDMD LTFGS +L+RH+T SEA+KLP+QEFHL ++L+
Sbjct: 154 APSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQ 213
Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
            + L+ E+F+DLCILLG DYC+SIRGIGPKRA++LI++H+SIE+I+  +D  KY VPE W
Sbjct: 214 ELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENW 273
Query: 181 LYKEARELFRHPEVADPETIEF 202
           L+KEA +LF  PEV DPE++E 
Sbjct: 274 LHKEAHQLFLEPEVLDPESVEL 295

>pdb|1UL1|X Chain X, Crystal Structure Of The Human Fen1-Pcna Complex Length = 379

Iteration: 1
 Score =  133 bits (335), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 64/99 (64%), Positives = 80/99 (80%), Gaps = 7/99 (7%)
Query: 304 ELVADVAPSSIRES-------RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGT 356
           +L+ADVAPS+IRE+       RK+ IDASMS+YQFLIAVR  G+ L + +GE TSHLMG 
Sbjct: 7   KLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGM 66
Query: 357 FYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKRED 395
           FYRTIR++E+G+KP+YVFDGKPP LKSGEL KR E+R +
Sbjct: 67  FYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAE 105

>pdb|1UL1|X Chain X, Crystal Structure Of The Human Fen1-Pcna Complex Length = 379

Iteration: 1
 Score = 74.3 bits (181), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 30/55 (54%), Positives = 45/55 (81%)
Query: 405 EQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFTI 459
           E  +LKWS+P+E+ L+K++CG+K F+E+RIR+G K+L K+R  +TQGRLD FF +
Sbjct: 291 ESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTQGRLDDFFKV 345

>pdb|3Q8K|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (Wt) In Complex With Product 5'-Flap Dna, Sm3+, And K+ Length = 341

Iteration: 1
 Score =  212 bits (540), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 94/142 (66%), Positives = 120/142 (84%)
Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           AP EAEA CAA+VKAGKVYA ATEDMD LTFGS +L+RH+T SEA+KLP+QEFHL ++L+
Sbjct: 154 APSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQ 213
Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
            + L+ E+F+DLCILLG DYC+SIRGIGPKRA++LI++H+SIE+I+  +D  KY VPE W
Sbjct: 214 ELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENW 273
Query: 181 LYKEARELFRHPEVADPETIEF 202
           L+KEA +LF  PEV DPE++E 
Sbjct: 274 LHKEAHQLFLEPEVLDPESVEL 295

>pdb|3Q8K|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (Wt) In Complex With Product 5'-Flap Dna, Sm3+, And K+ Length = 341

Iteration: 1
 Score =  133 bits (334), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 64/98 (65%), Positives = 79/98 (80%), Gaps = 7/98 (7%)
Query: 305 LVADVAPSSIRES-------RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTF 357
           L+ADVAPS+IRE+       RK+ IDASMS+YQFLIAVR  G+ L + +GE TSHLMG F
Sbjct: 8   LIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMF 67
Query: 358 YRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKRED 395
           YRTIR++E+G+KP+YVFDGKPP LKSGEL KR E+R +
Sbjct: 68  YRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAE 105

>pdb|3Q8K|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (Wt) In Complex With Product 5'-Flap Dna, Sm3+, And K+ Length = 341

Iteration: 1
 Score = 58.5 bits (140), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 23/45 (51%), Positives = 37/45 (82%)
Query: 405 EQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTT 449
           E  +LKWS+P+E+ L+K++CG+K F+E+RIR+G K+L K+R  +T
Sbjct: 291 ESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGST 335

>pdb|3Q8M|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (D181a) In Complex With Substrate 5'-Flap Dna And K+ Length = 341

Iteration: 1
 Score =  209 bits (533), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 93/142 (65%), Positives = 119/142 (83%)
Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           AP EAEA CAA+VKAGKVYA ATEDM  LTFGS +L+RH+T SEA+KLP+QEFHL ++L+
Sbjct: 154 APSEAEASCAALVKAGKVYAAATEDMACLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQ 213
Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
            + L+ E+F+DLCILLG DYC+SIRGIGPKRA++LI++H+SIE+I+  +D  KY VPE W
Sbjct: 214 ELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENW 273
Query: 181 LYKEARELFRHPEVADPETIEF 202
           L+KEA +LF  PEV DPE++E 
Sbjct: 274 LHKEAHQLFLEPEVLDPESVEL 295

>pdb|3Q8M|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (D181a) In Complex With Substrate 5'-Flap Dna And K+ Length = 341

Iteration: 1
 Score =  133 bits (334), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 64/98 (65%), Positives = 79/98 (80%), Gaps = 7/98 (7%)
Query: 305 LVADVAPSSIRES-------RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTF 357
           L+ADVAPS+IRE+       RK+ IDASMS+YQFLIAVR  G+ L + +GE TSHLMG F
Sbjct: 8   LIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMF 67
Query: 358 YRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKRED 395
           YRTIR++E+G+KP+YVFDGKPP LKSGEL KR E+R +
Sbjct: 68  YRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAE 105

>pdb|3Q8M|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (D181a) In Complex With Substrate 5'-Flap Dna And K+ Length = 341

Iteration: 1
 Score = 58.5 bits (140), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 23/45 (51%), Positives = 37/45 (82%)
Query: 405 EQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTT 449
           E  +LKWS+P+E+ L+K++CG+K F+E+RIR+G K+L K+R  +T
Sbjct: 291 ESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGST 335

>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex Length = 346

Iteration: 1
 Score =  101 bits (252), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 61/166 (36%), Positives = 99/166 (59%), Gaps = 14/166 (8%)
Query: 60  KAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHL---- 115
           +AP E EA+ A + K G  +A A++D DA+ FG+  L+R++T +  RKLP ++ ++    
Sbjct: 145 QAPSEGEAEAAYLNKLGLSWAAASQDYDAILFGAKRLVRNLTITGKRKLPNKDVYVEIKP 204
Query: 116 -----EKVLEGMELSHEEFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENI 169
                E +L+ + ++ E+ ID+ IL+G DY  D IRGIGP+RA+++IK++  IEK +E  
Sbjct: 205 ELIETEILLKKLGITREQLIDIGILIGTDYNPDGIRGIGPERALKIIKKYGKIEKAMEYG 264
Query: 170 DTKKYTVPEGWLYKEARELFRHPEVADPETIEFIDLCILLGCDYCD 215
           +  K  +   +   E R LF +P+V  PE  E +DL    G D  +
Sbjct: 265 EISKKDI--NFNIDEIRGLFLNPQVVKPE--EALDLNEPNGEDIIN 306

>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex Length = 346

Iteration: 1
 Score = 97.4 bits (241), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 46/94 (48%), Positives = 65/94 (69%), Gaps = 1/94 (1%)
Query: 317 SRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFD 375
            +++ ID   +LYQFL A+R  +G  LM   G  TSHL G FYRTI ++E G+ PIYVFD
Sbjct: 18  GKRVSIDGYNALYQFLAAIRQPDGTPLMDSQGRVTSHLSGLFYRTINILEEGVIPIYVFD 77
Query: 376 GKPPTLKSGELNKRMEKREDAQKALAKAQEQGKL 409
           GKPP  KS EL +R + +E+A++ L +A+ +GK+
Sbjct: 78  GKPPEQKSEELERRRKAKEEAERKLERAKSEGKI 111

>pdb|3ORY|A Chain A, Crystal Structure Of Flap Endonuclease 1 From Hyperthermophilic Archaeon Desulfurococcus Amylolyticus Length = 363

Iteration: 1
 Score = 97.8 bits (242), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 60/153 (39%), Positives = 86/153 (56%), Gaps = 14/153 (9%)
Query: 60  KAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQE------- 112
           +AP E EAQ A +VK G  YA+A++D D+L FGS  L+R++T S  RKLP +        
Sbjct: 162 QAPAEGEAQAAYIVKKGDAYASASQDYDSLLFGSPKLVRNLTISGRRKLPRKNEYVEVKP 221
Query: 113 --FHLEKVLEGMELSHEEFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENI 169
               L+K+L  + ++ E  ID+ ILLG DY  D   GIGPK+A++L+K +  IEKI + I
Sbjct: 222 ELIELDKLLVQLGITLENLIDIGILLGTDYNPDGFEGIGPKKALQLVKAYGGIEKIPKPI 281
Query: 170 DTKKYTVPEGWLYKEARELFRHPEVADPETIEF 202
                 V         ++ F  P+V D   IE+
Sbjct: 282 LKSPIEVD----VIAIKKYFLQPQVTDNYRIEW 310

>pdb|3ORY|A Chain A, Crystal Structure Of Flap Endonuclease 1 From Hyperthermophilic Archaeon Desulfurococcus Amylolyticus Length = 363

Iteration: 1
 Score = 97.1 bits (240), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 56/132 (42%), Positives = 77/132 (58%), Gaps = 9/132 (6%)
Query: 314 IRESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIY 372
           I   + I ID   +LYQFL A+R  +G  LM  +G  TSHL G FYRTI +VE G+KP+Y
Sbjct: 32  ILHGKIIVIDGYNALYQFLAAIRQPDGTPLMDNNGRITSHLSGLFYRTINIVEAGIKPVY 91
Query: 373 VFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAED 432
           VFDGKPP LK+ E+ +R   +E+A K   +A + G L+ +        +Y        E+
Sbjct: 92  VFDGKPPELKAREIERRKAVKEEAAKKYEEAVQSGDLELAR-------RYAMMSAKLTEE 144
Query: 433 RIRNGAKKLLKA 444
            +R+ AK LL A
Sbjct: 145 MVRD-AKSLLDA 155

>pdb|1MC8|A Chain A, Crystal Structure Of Flap Endonuclease-1 R42e Mutant From Pyrococcus Horikoshii Length = 343

Iteration: 1
 Score = 95.5 bits (236), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 50/94 (53%), Positives = 60/94 (63%), Gaps = 1/94 (1%)
Query: 317 SRKICIDASMSLYQFLIAVRSE-GNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFD 375
            +KI IDA  ++YQFL  +R E G  LM   G  TSHL G FYRTI L+E G+KP YVFD
Sbjct: 21  GKKIAIDALNAIYQFLSTIRQEDGTPLMDSKGRITSHLSGLFYRTINLMEAGIKPAYVFD 80
Query: 376 GKPPTLKSGELNKRMEKREDAQKALAKAQEQGKL 409
           GKPP  K  EL KR E RE+A+    +A  +G L
Sbjct: 81  GKPPEFKRKELEKRREAREEAELKWKEALAKGNL 114

>pdb|1MC8|A Chain A, Crystal Structure Of Flap Endonuclease-1 R42e Mutant From Pyrococcus Horikoshii Length = 343

Iteration: 1
 Score = 57.0 bits (136), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 22/53 (41%), Positives = 38/53 (71%)
Query: 409 LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFTIRR 461
           L W +PDE+G++K+LC + NF+E+R++NG ++L KA     Q  L+S+F  ++
Sbjct: 290 LSWKEPDEEGILKFLCDEHNFSEERVKNGIERLKKAIKAGRQSTLESWFVKKK 342

>pdb|1B43|A Chain A, Fen-1 From P. Furiosus Length = 340

Iteration: 1
 Score = 91.3 bits (225), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 53/148 (35%), Positives = 85/148 (57%), Gaps = 20/148 (13%)
Query: 60  KAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFH----- 114
           +AP E EAQ A M   G VYA+A++D D+L FG+  L+R++T +  RKLP +  +     
Sbjct: 148 QAPSEGEAQAAYMAAKGSVYASASQDYDSLLFGAPRLVRNLTITGKRKLPGKNVYVEIKP 207
Query: 115 ----LEKVLEGMELSHEEFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRS-IEKILEN 168
               LE+VL+ ++L+ E+ I+L IL+G DY    I+GIG K+A+E+++  +  + K  + 
Sbjct: 208 ELIILEEVLKELKLTREKLIELAILVGTDYNPGGIKGIGLKKALEIVRHSKDPLAKFQKQ 267
Query: 169 IDTKKYTVPEGWLYKEARELFRHPEVAD 196
            D   Y +         +E F +P V D
Sbjct: 268 SDVDLYAI---------KEFFLNPPVTD 286

>pdb|1B43|A Chain A, Fen-1 From P. Furiosus Length = 340

Iteration: 1
 Score = 82.4 bits (202), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 48/94 (51%), Positives = 64/94 (68%), Gaps = 1/94 (1%)
Query: 317 SRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFD 375
            +KI IDA  ++YQFL  +R  +G  LM   G  TSHL G FYRTI L+E G+KP+YVFD
Sbjct: 21  GKKIAIDALNAIYQFLSTIRQKDGTPLMDSKGRITSHLSGLFYRTINLMEAGIKPVYVFD 80
Query: 376 GKPPTLKSGELNKRMEKREDAQKALAKAQEQGKL 409
           G+PP  K  EL KR E RE+A++   +A E+G++
Sbjct: 81  GEPPEFKKKELEKRREAREEAEEKWREALEKGEI 114

>pdb|1B43|A Chain A, Fen-1 From P. Furiosus Length = 340

Iteration: 1
 Score = 57.0 bits (136), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 33/103 (32%), Positives = 53/103 (51%), Gaps = 20/103 (19%)
Query: 375 DGKPPTLKSGELNKRMEKREDAQKALAKAQEQG--------------------KLKWSDP 414
           D  P  +K   L K +E    ++  LAK Q+Q                      L W DP
Sbjct: 236 DYNPGGIKGIGLKKALEIVRHSKDPLAKFQKQSDVDLYAIKEFFLNPPVTDNYNLVWRDP 295
Query: 415 DEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFF 457
           DE+G++K+LC + +F+E+R++NG ++L KA  +  Q  L+S+F
Sbjct: 296 DEEGILKFLCDEHDFSEERVKNGLERLKKAIKSGKQSTLESWF 338

>pdb|1RXV|A Chain A, Crystal Structure Of A. Fulgidus Fen-1 Bound To Dna Length = 336

Iteration: 1
 Score = 88.2 bits (217), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 54/155 (34%), Positives = 81/155 (52%), Gaps = 23/155 (14%)
Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFH------ 114
           AP E EAQ A M   G V  T ++D D+L FGS  L R++  +  RKLP +  +      
Sbjct: 148 APSEGEAQAAYMAAKGDVEYTGSQDYDSLLFGSPRLARNLAITGKRKLPGKNVYVDVKPE 207
Query: 115 ---LEKVLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEH----RSIEKILE 167
              LE  L+ + L+ E+ ID+ IL+G DY + ++G+G K+A+  IK +    R+++ +  
Sbjct: 208 IIILESNLKRLGLTREQLIDIAILVGTDYNEGVKGVGVKKALNYIKTYGDIFRALKALKV 267
Query: 168 NIDTKKYTVPEGWLYKEARELFRHPEVADPETIEF 202
           NID            +E R  F +P V D   IEF
Sbjct: 268 NIDH----------VEEIRNFFLNPPVTDDYRIEF 292

>pdb|1RXV|A Chain A, Crystal Structure Of A. Fulgidus Fen-1 Bound To Dna Length = 336

Iteration: 1
 Score = 77.4 bits (189), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 36/92 (39%), Positives = 56/92 (60%), Gaps = 1/92 (1%)
Query: 317 SRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFD 375
            +KI +DA  +LYQF+  +R  +G  L    G  TSHL G  YR   +VE G++P++VFD
Sbjct: 21  GKKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSHLSGILYRVSNMVEVGIRPVFVFD 80
Query: 376 GKPPTLKSGELNKRMEKREDAQKALAKAQEQG 407
           G+PP  K  E+ +R ++R +A++    A + G
Sbjct: 81  GEPPEFKKAEIEERKKRRAEAEEMWIAALQAG 112

>pdb|1A76|A Chain A, Flap Endonuclease-1 From Methanococcus Jannaschii Length = 326

Iteration: 1
 Score = 79.7 bits (195), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 44/137 (32%), Positives = 80/137 (58%), Gaps = 14/137 (10%)
Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           AP E EAQ + M K G V+A  ++D DAL +G+  ++R++T +  +++P +   L +VLE
Sbjct: 149 APSEGEAQASYMAKKGDVWAVVSQDYDALLYGAPRVVRNLTTT--KEMP-ELIELNEVLE 205
Query: 121 GMELSHEEFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEG 179
            + +S ++ ID+ I +G DY    ++GIG KRA EL++   + + + + ++         
Sbjct: 206 DLRISLDDLIDIAIFMGTDYNPGGVKGIGFKRAYELVRSGVAKDVLKKEVE--------- 256
Query: 180 WLYKEARELFRHPEVAD 196
             Y E + +F+ P+V D
Sbjct: 257 -YYDEIKRIFKEPKVTD 272

>pdb|1A76|A Chain A, Flap Endonuclease-1 From Methanococcus Jannaschii Length = 326

Iteration: 1
 Score = 72.4 bits (176), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 37/89 (41%), Positives = 56/89 (62%), Gaps = 1/89 (1%)
Query: 316 ESRKICIDASMSLYQFLIAVR-SEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVF 374
           + +K+ ID   +LYQFL ++R  +G+ L +  GE TS   G FY+TI L+E+ + PI+VF
Sbjct: 20  KGKKVAIDGMNALYQFLTSIRLRDGSPLRNRKGEITSAYNGVFYKTIHLLENDITPIWVF 79
Query: 375 DGKPPTLKSGELNKRMEKREDAQKALAKA 403
           DG+PP LK      R E +E A+  + +A
Sbjct: 80  DGEPPKLKEKTRKVRREMKEKAELKMKEA 108

>pdb|3QEA|Z Chain Z, Crystal Structure Of Human Exonuclease 1 Exo1 (Wt) In Complex With Dna (Complex Ii) Length = 352

Iteration: 1
 Score = 69.7 bits (169), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 50/145 (34%), Positives = 76/145 (52%), Gaps = 9/145 (6%)
Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFG-SNILLRHMTFSEARKLPVQEFHLEKVL 119
           AP EA+AQ A + KAG V A  TED D L FG   ++L+   F    ++      + + L
Sbjct: 147 APYEADAQLAYLNKAGIVQAIITEDSDLLAFGCKKVILKMDQFGNGLEIDQARLGMCRQL 206
Query: 120 EGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIK--EHRSIEKILENID---TKKY 174
            G   + E+F  +CIL GCDY  S+RGIG  +A ++++   +  I K+++ I        
Sbjct: 207 -GDVFTEEKFRYMCILSGCDYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNI 265
Query: 175 TVPEGWL--YKEARELFRHPEVADP 197
           TVPE ++  +  A   F +  V DP
Sbjct: 266 TVPEDYINGFIRANNTFLYQLVFDP 290

>pdb|3QE9|Y Chain Y, Crystal Structure Of Human Exonuclease 1 Exo1 (D173a) In Complex With Dna (Complex I) Length = 352

Iteration: 1
 Score = 66.6 bits (161), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 49/145 (33%), Positives = 75/145 (51%), Gaps = 9/145 (6%)
Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFG-SNILLRHMTFSEARKLPVQEFHLEKVL 119
           AP EA+AQ A + KAG V A  TED   L FG   ++L+   F    ++      + + L
Sbjct: 147 APYEADAQLAYLNKAGIVQAIITEDSALLAFGCKKVILKMDQFGNGLEIDQARLGMCRQL 206
Query: 120 EGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIK--EHRSIEKILENID---TKKY 174
            G   + E+F  +CIL GCDY  S+RGIG  +A ++++   +  I K+++ I        
Sbjct: 207 -GDVFTEEKFRYMCILSGCDYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNI 265
Query: 175 TVPEGWL--YKEARELFRHPEVADP 197
           TVPE ++  +  A   F +  V DP
Sbjct: 266 TVPEDYINGFIRANNTFLYQLVFDP 290

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	531
3q8k_A	341	Flap endonuclease 1; helix-3 turn-helix, hydrophob	8e-63
3q8k_A	341	Flap endonuclease 1; helix-3 turn-helix, hydrophob	3e-29
3q8k_A	341	Flap endonuclease 1; helix-3 turn-helix, hydrophob	6e-29
3q8k_A	341	Flap endonuclease 1; helix-3 turn-helix, hydrophob	2e-13
3q8k_A	341	Flap endonuclease 1; helix-3 turn-helix, hydrophob	5e-13
1ul1_X	379	Flap endonuclease-1; protein complex, DNA-binding	2e-62
1ul1_X	379	Flap endonuclease-1; protein complex, DNA-binding	5e-29
1ul1_X	379	Flap endonuclease-1; protein complex, DNA-binding	2e-28
1ul1_X	379	Flap endonuclease-1; protein complex, DNA-binding	4e-16
1ul1_X	379	Flap endonuclease-1; protein complex, DNA-binding	9e-16
1rxw_A	336	Flap structure-specific endonuclease; helical clam	7e-54
1rxw_A	336	Flap structure-specific endonuclease; helical clam	6e-26
1rxw_A	336	Flap structure-specific endonuclease; helical clam	9e-23
1rxw_A	336	Flap structure-specific endonuclease; helical clam	6e-13
1rxw_A	336	Flap structure-specific endonuclease; helical clam	1e-12
3ory_A	363	Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco	6e-52
3ory_A	363	Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco	2e-27
3ory_A	363	Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco	5e-22
3ory_A	363	Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco	2e-12
3ory_A	363	Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco	5e-12
1a76_A	326	Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea	9e-50
1a76_A	326	Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea	2e-27
1a76_A	326	Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea	6e-19
1a76_A	326	Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea	1e-12
1a76_A	326	Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea	3e-12
2izo_A	346	FEN1, flap structure-specific endonuclease; hydrol	7e-49
2izo_A	346	FEN1, flap structure-specific endonuclease; hydrol	3e-27
2izo_A	346	FEN1, flap structure-specific endonuclease; hydrol	3e-20
2izo_A	346	FEN1, flap structure-specific endonuclease; hydrol	3e-13
2izo_A	346	FEN1, flap structure-specific endonuclease; hydrol	6e-13
1b43_A	340	Protein (FEN-1); nuclease, DNA repair, DNA replica	2e-46
1b43_A	340	Protein (FEN-1); nuclease, DNA repair, DNA replica	5e-27
1b43_A	340	Protein (FEN-1); nuclease, DNA repair, DNA replica	4e-18
1b43_A	340	Protein (FEN-1); nuclease, DNA repair, DNA replica	2e-14
1b43_A	340	Protein (FEN-1); nuclease, DNA repair, DNA replica	4e-14
3qe9_Y	352	Exonuclease 1; exonuclease, hydrolase-DNA complex;	2e-41
3qe9_Y	352	Exonuclease 1; exonuclease, hydrolase-DNA complex;	1e-21
3qe9_Y	352	Exonuclease 1; exonuclease, hydrolase-DNA complex;	5e-19
3qe9_Y	352	Exonuclease 1; exonuclease, hydrolase-DNA complex;	3e-04
3qe9_Y	352	Exonuclease 1; exonuclease, hydrolase-DNA complex;	3e-04
1exn_A	290	5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent	5e-07
1exn_A	290	5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent	5e-06
1bgx_T	832	TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi	1e-06
1bgx_T	832	TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi	1e-05
1igr_A	478	Insulin-like growth factor receptor 1; hormone rec	1e-04
2ahx_A	617	P180ERBB4, receptor tyrosine-protein kinase ERBB-4	2e-04
1mox_A	501	Epidermal growth factor receptor; EGFR, receptor,	3e-04
2hr7_A	486	Insulin receptor; hormone receptor, leucine rich r	4e-04

>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* Length = 341

 Score =  208 bits (530), Expect = 8e-63
 Identities = 94/142 (66%), Positives = 120/142 (84%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           AP EAEA CAA+VKAGKVYA ATEDMD LTFGS +L+RH+T SEA+KLP+QEFHL ++L+
Sbjct: 154 APSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQ 213

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
            + L+ E+F+DLCILLG DYC+SIRGIGPKRA++LI++H+SIE+I+  +D  KY VPE W
Sbjct: 214 ELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENW 273

Query: 181 LYKEARELFRHPEVADPETIEF 202
           L+KEA +LF  PEV DPE++E 
Sbjct: 274 LHKEAHQLFLEPEVLDPESVEL 295

>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* Length = 341

 Score =  117 bits (294), Expect = 3e-29
 Identities = 70/114 (61%), Positives = 89/114 (78%), Gaps = 7/114 (6%)

Query: 304 ELVADVAPSSIRES-------RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGT 356
           +L+ADVAPS+IRE+       RK+ IDASMS+YQFLIAVR  G+ L + +GE TSHLMG 
Sbjct: 7   KLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGM 66

Query: 357 FYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLK 410
           FYRTIR++E+G+KP+YVFDGKPP LKSGEL KR E+R +A+K L +AQ  G  +
Sbjct: 67  FYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQ 120

>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* Length = 341

 Score =  116 bits (292), Expect = 6e-29
 Identities = 48/75 (64%), Positives = 63/75 (84%)

Query: 232 FIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAREL 291
           F+DLCILLG DYC+SIRGIGPKRA++LI++H+SIE+I+  +D  KY VPE WL+KEA +L
Sbjct: 222 FVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQL 281

Query: 292 FRHPEIADPETIELV 306
           F  PE+ DPE++EL 
Sbjct: 282 FLEPEVLDPESVELK 296

>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* Length = 341

 Score = 70.6 bits (173), Expect = 2e-13
 Identities = 24/53 (45%), Positives = 38/53 (71%), Gaps = 3/53 (5%)

Query: 405 EQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFF 457
           E  +LKWS+P+E+ L+K++CG+K F+E+RIR+G K+L K+R       L+  F
Sbjct: 291 ESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSR---QGSTLEVLF 340

>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* Length = 341

 Score = 69.5 bits (170), Expect = 5e-13
 Identities = 23/49 (46%), Positives = 36/49 (73%), Gaps = 3/49 (6%)

Query: 3   LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFF 51
           LKWS+P+E+ L+K++CG+K F+E+RIR+G K+L K+R       L+  F
Sbjct: 295 LKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSR---QGSTLEVLF 340

>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 Length = 379

 Score =  208 bits (531), Expect = 2e-62
 Identities = 94/142 (66%), Positives = 120/142 (84%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           AP EAEA CAA+VKAGKVYA ATEDMD LTFGS +L+RH+T SEA+KLP+QEFHL ++L+
Sbjct: 154 APSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQ 213

Query: 121 GMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGW 180
            + L+ E+F+DLCILLG DYC+SIRGIGPKRA++LI++H+SIE+I+  +D  KY VPE W
Sbjct: 214 ELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENW 273

Query: 181 LYKEARELFRHPEVADPETIEF 202
           L+KEA +LF  PEV DPE++E 
Sbjct: 274 LHKEAHQLFLEPEVLDPESVEL 295

>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 Length = 379

 Score =  117 bits (294), Expect = 5e-29
 Identities = 48/75 (64%), Positives = 63/75 (84%)

Query: 232 FIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAREL 291
           F+DLCILLG DYC+SIRGIGPKRA++LI++H+SIE+I+  +D  KY VPE WL+KEA +L
Sbjct: 222 FVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQL 281

Query: 292 FRHPEIADPETIELV 306
           F  PE+ DPE++EL 
Sbjct: 282 FLEPEVLDPESVELK 296

>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 Length = 379

 Score =  115 bits (290), Expect = 2e-28
 Identities = 70/113 (61%), Positives = 88/113 (77%), Gaps = 7/113 (6%)

Query: 305 LVADVAPSSIRES-------RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTF 357
           L+ADVAPS+IRE+       RK+ IDASMS+YQFLIAVR  G+ L + +GE TSHLMG F
Sbjct: 8   LIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMF 67

Query: 358 YRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLK 410
           YRTIR++E+G+KP+YVFDGKPP LKSGEL KR E+R +A+K L +AQ  G  +
Sbjct: 68  YRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQ 120

>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 Length = 379

 Score = 79.2 bits (195), Expect = 4e-16
 Identities = 31/64 (48%), Positives = 46/64 (71%)

Query: 405 EQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFTIRREEK 464
           E  +LKWS+P+E+ L+K++CG+K F+E+RIR+G K+L K+R  +TQGRLD FF +     
Sbjct: 291 ESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTQGRLDDFFKVTGSLS 350

Query: 465 RKSR 468
              R
Sbjct: 351 SAKR 354

>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 Length = 379

 Score = 78.0 bits (192), Expect = 9e-16
 Identities = 33/73 (45%), Positives = 49/73 (67%)

Query: 3   LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFFTIRREEKRKAP 62
           LKWS+P+E+ L+K++CG+K F+E+RIR+G K+L K+R  +TQGRLD FF +         
Sbjct: 295 LKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTQGRLDDFFKVTGSLSSAKR 354

Query: 63  CEAEAQCAAMVKA 75
            E E + +   KA
Sbjct: 355 KEPEPKGSTKKKA 367

>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 Length = 336

 Score =  184 bits (468), Expect = 7e-54
 Identities = 52/151 (34%), Positives = 77/151 (50%), Gaps = 15/151 (9%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQE-------- 112
           AP E EAQ A M   G V  T ++D D+L FGS  L R++  +  RKLP +         
Sbjct: 148 APSEGEAQAAYMAAKGDVEYTGSQDYDSLLFGSPRLARNLAITGKRKLPGKNVYVDVKPE 207

Query: 113 -FHLEKVLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT 171
              LE  L+ + L+ E+ ID+ IL+G DY + ++G+G K+A+  IK +  I + L+ +  
Sbjct: 208 IIILESNLKRLGLTREQLIDIAILVGTDYNEGVKGVGVKKALNYIKTYGDIFRALKALKV 267

Query: 172 KKYTVPEGWLYKEARELFRHPEVADPETIEF 202
                      +E R  F +P V D   IEF
Sbjct: 268 NIDH------VEEIRNFFLNPPVTDDYRIEF 292

>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 Length = 336

 Score =  107 bits (269), Expect = 6e-26
 Identities = 36/92 (39%), Positives = 55/92 (59%), Gaps = 1/92 (1%)

Query: 318 RKICIDASMSLYQFLIAVRSE-GNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDG 376
           +KI +DA  +LYQF+  +R   G  L    G  TSHL G  YR   +VE G++P++VFDG
Sbjct: 22  KKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSHLSGILYRVSNMVEVGIRPVFVFDG 81

Query: 377 KPPTLKSGELNKRMEKREDAQKALAKAQEQGK 408
           +PP  K  E+ +R ++R +A++    A + G 
Sbjct: 82  EPPEFKKAEIEERKKRRAEAEEMWIAALQAGD 113

>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 Length = 336

 Score = 98.4 bits (245), Expect = 9e-23
 Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 232 FIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAREL 291
            ID+ IL+G DY + ++G+G K+A+  IK +  I + L+ +             +E R  
Sbjct: 225 LIDIAILVGTDYNEGVKGVGVKKALNYIKTYGDIFRALKALKVNIDH------VEEIRNF 278

Query: 292 FRHPEIADPETIEL 305
           F +P + D   IE 
Sbjct: 279 FLNPPVTDDYRIEF 292

>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 Length = 336

 Score = 69.1 bits (169), Expect = 6e-13
 Identities = 13/50 (26%), Positives = 31/50 (62%), Gaps = 2/50 (4%)

Query: 408 KLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFF 457
           ++++ +PD +  +++LC + +F+ +R+    +KL   +S  TQ  L+ +F
Sbjct: 289 RIEFREPDFEKAIEFLCEEHDFSRERVEKALEKLKALKS--TQATLERWF 336

>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 Length = 336

 Score = 68.3 bits (167), Expect = 1e-12
 Identities = 13/49 (26%), Positives = 30/49 (61%), Gaps = 2/49 (4%)

Query: 3   LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFF 51
           +++ +PD +  +++LC + +F+ +R+    +KL   +S  TQ  L+ +F
Sbjct: 290 IEFREPDFEKAIEFLCEEHDFSRERVEKALEKLKALKS--TQATLERWF 336

>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus} Length = 363

 Score =  180 bits (457), Expect = 6e-52
 Identities = 60/152 (39%), Positives = 85/152 (55%), Gaps = 14/152 (9%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQE-------- 112
           AP E EAQ A +VK G  YA+A++D D+L FGS  L+R++T S  RKLP +         
Sbjct: 163 APAEGEAQAAYIVKKGDAYASASQDYDSLLFGSPKLVRNLTISGRRKLPRKNEYVEVKPE 222

Query: 113 -FHLEKVLEGMELSHEEFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENID 170
              L+K+L  + ++ E  ID+ ILLG DY  D   GIGPK+A++L+K +  IEKI + I 
Sbjct: 223 LIELDKLLVQLGITLENLIDIGILLGTDYNPDGFEGIGPKKALQLVKAYGGIEKIPKPIL 282

Query: 171 TKKYTVPEGWLYKEARELFRHPEVADPETIEF 202
                V         ++ F  P+V D   IE+
Sbjct: 283 KSPIEVD----VIAIKKYFLQPQVTDNYRIEW 310

>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus} Length = 363

 Score =  112 bits (281), Expect = 2e-27
 Identities = 49/113 (43%), Positives = 69/113 (61%), Gaps = 6/113 (5%)

Query: 304 ELVADVAPSSIRE-----SRKICIDASMSLYQFLIAVRSE-GNQLMSVDGEPTSHLMGTF 357
           +++   A + I +      + I ID   +LYQFL A+R   G  LM  +G  TSHL G F
Sbjct: 17  DIIPGEAKTVIEDLRILHGKIIVIDGYNALYQFLAAIRQPDGTPLMDNNGRITSHLSGLF 76

Query: 358 YRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLK 410
           YRTI +VE G+KP+YVFDGKPP LK+ E+ +R   +E+A K   +A + G L+
Sbjct: 77  YRTINIVEAGIKPVYVFDGKPPELKAREIERRKAVKEEAAKKYEEAVQSGDLE 129

>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus} Length = 363

 Score = 96.5 bits (240), Expect = 5e-22
 Identities = 28/74 (37%), Positives = 39/74 (52%), Gaps = 5/74 (6%)

Query: 232 FIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARE 290
            ID+ ILLG DY  D   GIGPK+A++L+K +  IEKI + I      V         ++
Sbjct: 240 LIDIGILLGTDYNPDGFEGIGPKKALQLVKAYGGIEKIPKPILKSPIEVD----VIAIKK 295

Query: 291 LFRHPEIADPETIE 304
            F  P++ D   IE
Sbjct: 296 YFLQPQVTDNYRIE 309

>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus} Length = 363

 Score = 67.2 bits (164), Expect = 2e-12
 Identities = 13/54 (24%), Positives = 28/54 (51%), Gaps = 3/54 (5%)

Query: 408 KLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGR---LDSFFT 458
           +++W  PD D + + L  + +F+ DR+    ++ +KA     +G    L  +F+
Sbjct: 307 RIEWHTPDPDAVKRILVDEHDFSIDRVSTALERYVKAFKENIRGEQKGLSKWFS 360

>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus} Length = 363

 Score = 66.4 bits (162), Expect = 5e-12
 Identities = 13/53 (24%), Positives = 27/53 (50%), Gaps = 3/53 (5%)

Query: 3   LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGR---LDSFFT 52
           ++W  PD D + + L  + +F+ DR+    ++ +KA     +G    L  +F+
Sbjct: 308 IEWHTPDPDAVKRILVDEHDFSIDRVSTALERYVKAFKENIRGEQKGLSKWFS 360

>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 Length = 326

 Score =  173 bits (439), Expect = 9e-50
 Identities = 43/143 (30%), Positives = 78/143 (54%), Gaps = 14/143 (9%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           AP E EAQ + M K G V+A  ++D DAL +G+  ++R++T ++      +   L +VLE
Sbjct: 149 APSEGEAQASYMAKKGDVWAVVSQDYDALLYGAPRVVRNLTTTKE---MPELIELNEVLE 205

Query: 121 GMELSHEEFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEG 179
            + +S ++ ID+ I +G DY    ++GIG KRA EL++   + + + + +          
Sbjct: 206 DLRISLDDLIDIAIFMGTDYNPGGVKGIGFKRAYELVRSGVAKDVLKKEV---------- 255

Query: 180 WLYKEARELFRHPEVADPETIEF 202
             Y E + +F+ P+V D  ++  
Sbjct: 256 EYYDEIKRIFKEPKVTDNYSLSL 278

>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 Length = 326

 Score =  111 bits (280), Expect = 2e-27
 Identities = 37/94 (39%), Positives = 58/94 (61%), Gaps = 1/94 (1%)

Query: 318 RKICIDASMSLYQFLIAVR-SEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDG 376
           +K+ ID   +LYQFL ++R  +G+ L +  GE TS   G FY+TI L+E+ + PI+VFDG
Sbjct: 22  KKVAIDGMNALYQFLTSIRLRDGSPLRNRKGEITSAYNGVFYKTIHLLENDITPIWVFDG 81

Query: 377 KPPTLKSGELNKRMEKREDAQKALAKAQEQGKLK 410
           +PP LK      R E +E A+  + +A ++   +
Sbjct: 82  EPPKLKEKTRKVRREMKEKAELKMKEAIKKEDFE 115

>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 Length = 326

 Score = 86.8 bits (215), Expect = 6e-19
 Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 11/75 (14%)

Query: 232 FIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARE 290
            ID+ I +G DY    ++GIG KRA EL++   + + + + +            Y E + 
Sbjct: 214 LIDIAIFMGTDYNPGGVKGIGFKRAYELVRSGVAKDVLKKEV----------EYYDEIKR 263

Query: 291 LFRHPEIADPETIEL 305
           +F+ P++ D  ++ L
Sbjct: 264 IFKEPKVTDNYSLSL 278

>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 Length = 326

 Score = 68.3 bits (167), Expect = 1e-12
 Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 3/75 (4%)

Query: 386 LNKRMEKREDAQKALAKAQ--EQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLK 443
           L K +E  ++ ++   + +  +   L    PD++G++K+L  + +F  DR++    KL  
Sbjct: 251 LKKEVEYYDEIKRIFKEPKVTDNYSLSLKLPDKEGIIKFLVDENDFNYDRVKKHVDKLYN 310

Query: 444 ARST-TTQGRLDSFF 457
             +  T Q  LD++F
Sbjct: 311 LIANKTKQKTLDAWF 325

>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 Length = 326

 Score = 67.2 bits (164), Expect = 3e-12
 Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 2   TLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKA-RSSTTQGRLDSFF 51
           +L    PD++G++K+L  + +F  DR++    KL     + T Q  LD++F
Sbjct: 275 SLSLKLPDKEGIIKFLVDENDFNYDRVKKHVDKLYNLIANKTKQKTLDAWF 325

>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} Length = 346

 Score =  171 bits (434), Expect = 7e-49
 Identities = 56/150 (37%), Positives = 89/150 (59%), Gaps = 12/150 (8%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQE-------- 112
           AP E EA+ A + K G  +A A++D DA+ FG+  L+R++T +  RKLP ++        
Sbjct: 146 APSEGEAEAAYLNKLGLSWAAASQDYDAILFGAKRLVRNLTITGKRKLPNKDVYVEIKPE 205

Query: 113 -FHLEKVLEGMELSHEEFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENID 170
               E +L+ + ++ E+ ID+ IL+G DY  D IRGIGP+RA+++IK++  IEK +E  +
Sbjct: 206 LIETEILLKKLGITREQLIDIGILIGTDYNPDGIRGIGPERALKIIKKYGKIEKAMEYGE 265

Query: 171 TKKYTVPEGWLYKEARELFRHPEVADPETI 200
             K  +   +   E R LF +P+V  PE  
Sbjct: 266 ISKKDIN--FNIDEIRGLFLNPQVVKPEEA 293

>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} Length = 346

 Score =  111 bits (280), Expect = 3e-27
 Identities = 49/112 (43%), Positives = 70/112 (62%), Gaps = 8/112 (7%)

Query: 308 DVAPSSIRES-------RKICIDASMSLYQFLIAVR-SEGNQLMSVDGEPTSHLMGTFYR 359
           D+     RE        +++ ID   +LYQFL A+R  +G  LM   G  TSHL G FYR
Sbjct: 2   DLVKDVKRELSFSELKGKRVSIDGYNALYQFLAAIRQPDGTPLMDSQGRVTSHLSGLFYR 61

Query: 360 TIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKW 411
           TI ++E G+ PIYVFDGKPP  KS EL +R + +E+A++ L +A+ +GK++ 
Sbjct: 62  TINILEEGVIPIYVFDGKPPEQKSEELERRRKAKEEAERKLERAKSEGKIEE 113

>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} Length = 346

 Score = 91.2 bits (226), Expect = 3e-20
 Identities = 30/73 (41%), Positives = 45/73 (61%), Gaps = 3/73 (4%)

Query: 232 FIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARE 290
            ID+ IL+G DY  D IRGIGP+RA+++IK++  IEK +E  +  K  +   +   E R 
Sbjct: 223 LIDIGILIGTDYNPDGIRGIGPERALKIIKKYGKIEKAMEYGEISKKDIN--FNIDEIRG 280

Query: 291 LFRHPEIADPETI 303
           LF +P++  PE  
Sbjct: 281 LFLNPQVVKPEEA 293

>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} Length = 346

 Score = 70.0 bits (171), Expect = 3e-13
 Identities = 16/54 (29%), Positives = 32/54 (59%), Gaps = 4/54 (7%)

Query: 408 KLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKA----RSTTTQGRLDSFF 457
            L  ++P+ + ++  L  + NF+E+R++NG ++L KA    +  + Q  LD +F
Sbjct: 293 ALDLNEPNGEDIINILVYEHNFSEERVKNGIERLTKAIKEAKGASRQTGLDRWF 346

>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} Length = 346

 Score = 69.2 bits (169), Expect = 6e-13
 Identities = 16/53 (30%), Positives = 33/53 (62%), Gaps = 4/53 (7%)

Query: 3   LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKA----RSSTTQGRLDSFF 51
           L  ++P+ + ++  L  + NF+E+R++NG ++L KA    + ++ Q  LD +F
Sbjct: 294 LDLNEPNGEDIINILVYEHNFSEERVKNGIERLTKAIKEAKGASRQTGLDRWF 346

>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 Length = 340

 Score =  164 bits (416), Expect = 2e-46
 Identities = 51/152 (33%), Positives = 81/152 (53%), Gaps = 18/152 (11%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQE-------- 112
           AP E EAQ A M   G VYA+A++D D+L FG+  L+R++T +  RKLP +         
Sbjct: 149 APSEGEAQAAYMAAKGSVYASASQDYDSLLFGAPRLVRNLTITGKRKLPGKNVYVEIKPE 208

Query: 113 -FHLEKVLEGMELSHEEFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENID 170
              LE+VL+ ++L+ E+ I+L IL+G DY    I+GIG K+A+E+++  +          
Sbjct: 209 LIILEEVLKELKLTREKLIELAILVGTDYNPGGIKGIGLKKALEIVRHSKDPL------- 261

Query: 171 TKKYTVPEGWLYKEARELFRHPEVADPETIEF 202
             K+           +E F +P V D   + +
Sbjct: 262 -AKFQKQSDVDLYAIKEFFLNPPVTDNYNLVW 292

>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 Length = 340

 Score =  110 bits (277), Expect = 5e-27
 Identities = 48/94 (51%), Positives = 65/94 (69%), Gaps = 1/94 (1%)

Query: 318 RKICIDASMSLYQFLIAVRSE-GNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDG 376
           +KI IDA  ++YQFL  +R + G  LM   G  TSHL G FYRTI L+E G+KP+YVFDG
Sbjct: 22  KKIAIDALNAIYQFLSTIRQKDGTPLMDSKGRITSHLSGLFYRTINLMEAGIKPVYVFDG 81

Query: 377 KPPTLKSGELNKRMEKREDAQKALAKAQEQGKLK 410
           +PP  K  EL KR E RE+A++   +A E+G+++
Sbjct: 82  EPPEFKKKELEKRREAREEAEEKWREALEKGEIE 115

>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 Length = 340

 Score = 84.6 bits (209), Expect = 4e-18
 Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 9/74 (12%)

Query: 232 FIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARE 290
            I+L IL+G DY    I+GIG K+A+E+++  +            K+           +E
Sbjct: 226 LIELAILVGTDYNPGGIKGIGLKKALEIVRHSKDPL--------AKFQKQSDVDLYAIKE 277

Query: 291 LFRHPEIADPETIE 304
            F +P + D   + 
Sbjct: 278 FFLNPPVTDNYNLV 291

>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 Length = 340

 Score = 73.4 bits (180), Expect = 2e-14
 Identities = 22/50 (44%), Positives = 37/50 (74%)

Query: 408 KLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFF 457
            L W DPDE+G++K+LC + +F+E+R++NG ++L KA  +  Q  L+S+F
Sbjct: 289 NLVWRDPDEEGILKFLCDEHDFSEERVKNGLERLKKAIKSGKQSTLESWF 338

>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 Length = 340

 Score = 72.6 bits (178), Expect = 4e-14
 Identities = 23/50 (46%), Positives = 37/50 (74%)

Query: 2   TLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFF 51
            L W DPDE+G++K+LC + +F+E+R++NG ++L KA  S  Q  L+S+F
Sbjct: 289 NLVWRDPDEEGILKFLCDEHDFSEERVKNGLERLKKAIKSGKQSTLESWF 338

>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A {Homo sapiens} PDB: 3qeb_Z* 3qea_Z* Length = 352

 Score =  151 bits (383), Expect = 2e-41
 Identities = 51/153 (33%), Positives = 78/153 (50%), Gaps = 9/153 (5%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFG-SNILLRHMTFSEARKLPVQEFHLEKVL 119
           AP EA+AQ A + KAG V A  TED   L FG   ++L+   F    ++      + + L
Sbjct: 147 APYEADAQLAYLNKAGIVQAIITEDSALLAFGCKKVILKMDQFGNGLEIDQARLGMCRQL 206

Query: 120 EGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRS--IEKILENIDT---KKY 174
            G   + E+F  +CIL GCDY  S+RGIG  +A ++++   +  I K+++ I        
Sbjct: 207 -GDVFTEEKFRYMCILSGCDYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNI 265

Query: 175 TVPEGWL--YKEARELFRHPEVADPETIEFIDL 205
           TVPE ++  +  A   F +  V DP   + I L
Sbjct: 266 TVPEDYINGFIRANNTFLYQLVFDPIKRKLIPL 298

>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A {Homo sapiens} PDB: 3qeb_Z* 3qea_Z* Length = 352

 Score = 95.5 bits (237), Expect = 1e-21
 Identities = 25/95 (26%), Positives = 42/95 (44%), Gaps = 6/95 (6%)

Query: 318 RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIR-LVEHGLKPIYVFDG 376
           + + +D    L++  IA   +  +     GEPT   +G   + +  L+ HG+KPI VFDG
Sbjct: 25  QVVAVDTYCWLHKGAIACAEKLAK-----GEPTDRYVGFCMKFVNMLLSHGIKPILVFDG 79

Query: 377 KPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKW 411
                K      R E+R+       +   +GK+  
Sbjct: 80  CTLPSKKEVERSRRERRQANLLKGKQLLREGKVSE 114

>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A {Homo sapiens} PDB: 3qeb_Z* 3qea_Z* Length = 352

 Score = 87.8 bits (217), Expect = 5e-19
 Identities = 26/83 (31%), Positives = 44/83 (53%), Gaps = 7/83 (8%)

Query: 232 FIDLCILLGCDYCDSIRGIGPKRAIELIKEHRS--IEKILENIDT---KKYTVPEGWL-- 284
           F  +CIL GCDY  S+RGIG  +A ++++   +  I K+++ I        TVPE ++  
Sbjct: 215 FRYMCILSGCDYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNITVPEDYING 274

Query: 285 YKEARELFRHPEIADPETIELVA 307
           +  A   F +  + DP   +L+ 
Sbjct: 275 FIRANNTFLYQLVFDPIKRKLIP 297

>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A {Homo sapiens} PDB: 3qeb_Z* 3qea_Z* Length = 352

 Score = 42.3 bits (99), Expect = 3e-04
 Identities = 5/43 (11%), Positives = 14/43 (32%), Gaps = 1/43 (2%)

Query: 7   DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKA-RSSTTQGRLD 48
           DP +  L+     + +   + +    + +  +       G  D
Sbjct: 289 DPIKRKLIPLNAYEDDVDPETLSYAGQYVDDSIALQIALGNKD 331

>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A {Homo sapiens} PDB: 3qeb_Z* 3qea_Z* Length = 352

 Score = 42.3 bits (99), Expect = 3e-04
 Identities = 5/43 (11%), Positives = 15/43 (34%), Gaps = 1/43 (2%)

Query: 413 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARST-TTQGRLD 454
           DP +  L+     + +   + +    + +  + +     G  D
Sbjct: 289 DPIKRKLIPLNAYEDDVDPETLSYAGQYVDDSIALQIALGNKD 331

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

 Score = 50.4 bits (121), Expect = 5e-07
 Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 5/66 (7%)

Query: 112 EFHLEKVLEGMELS-HEEFIDLCILLGCDYCDSIRG---IGPKRAIELIKEHRSIEKILE 167
           E+HL  + E   +   E+FI L  ++G D  D+IRG   IG KR   +I+E  ++  I++
Sbjct: 173 EYHLRDMYEHHNVDDVEQFISLKAIMG-DLGDNIRGVEGIGAKRGYNIIREFGNVLDIID 231

Query: 168 NIDTKK 173
            +    
Sbjct: 232 QLPLPG 237

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

 Score = 47.3 bits (113), Expect = 5e-06
 Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 4/48 (8%)

Query: 232 FIDLCILLGCDYCDSIRG---IGPKRAIELIKEHRSIEKILENIDTKK 276
           FI L  ++G D  D+IRG   IG KR   +I+E  ++  I++ +    
Sbjct: 191 FISLKAIMG-DLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPG 237

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

 Score = 50.6 bits (122), Expect = 1e-06
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 10/69 (14%)

Query: 116 EKVLEGMELSHEEFIDLCILLGCDYCDS------IRGIGPKRAIELIKEHRSIEKILENI 169
             + E   L  +++ D   L G    D       ++GIG K A +L++E  S+E +L+N+
Sbjct: 166 AWLWEKYGLRPDQWADYRALTG----DESDNLPGVKGIGEKTARKLLEEWGSLEALLKNL 221

Query: 170 DTKKYTVPE 178
           D  K  + E
Sbjct: 222 DRLKPAIRE 230

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

 Score = 46.8 bits (112), Expect = 1e-05
 Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 17/69 (24%)

Query: 219 GIGPKRAIELLYSFIDLCILLGCDYCDS------IRGIGPKRAIELIKEHRSIEKILENI 272
           G+ P +       + D   L G    D       ++GIG K A +L++E  S+E +L+N+
Sbjct: 173 GLRPDQ-------WADYRALTG----DESDNLPGVKGIGEKTARKLLEEWGSLEALLKNL 221

Query: 273 DTKKYTVPE 281
           D  K  + E
Sbjct: 222 DRLKPAIRE 230

>1igr_A Insulin-like growth factor receptor 1; hormone receptor, insulin receptor family; HET: NAG FUC BMA MAN; 2.60A {Homo sapiens} SCOP: c.10.2.5 c.10.2.5 g.3.9.1 Length = 478

 Score = 43.3 bits (101), Expect = 1e-04
 Identities = 7/74 (9%), Positives = 17/74 (22%)

Query: 456 FFTIRREEKRKSRCQYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQYQY 515
           +    +  K           +     +     +   +C    +CQ         +   + 
Sbjct: 138 YIVGNKPPKECGDLCPGTMEEKPMCEKTTINNEYNYRCWTTNRCQKMCPSTCGKRACTEN 197

Query: 516 QYQCQCQCQCQCQY 529
              C  +C   C  
Sbjct: 198 NECCHPECLGSCSA 211

>2ahx_A P180ERBB4, receptor tyrosine-protein kinase ERBB-4; X-RAY crystallography, neuregulins, heparin-binding, cell CY signaling protein; HET: NAG NDG; 2.40A {Homo sapiens} PDB: 3u2p_A* Length = 617

 Score = 43.1 bits (100), Expect = 2e-04
 Identities = 5/66 (7%), Positives = 10/66 (15%)

Query: 466 KSRCQYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQYQYQYQCQCQCQC 525
            +  Q       +       +            C      Q     ++     C   C  
Sbjct: 455 STINQRIVIRDNRKAENCTAEGMVCNHLCSSDGCWGPGPDQCLSCRRFSRGRICIESCNL 514

Query: 526 QCQYQY 531
                 
Sbjct: 515 YDGEFR 520

>1mox_A Epidermal growth factor receptor; EGFR, receptor, complex, transferase-growth F complex; HET: NAG FUC BMA MAN; 2.50A {Homo sapiens} SCOP: c.10.2.5 c.10.2.5 g.3.9.1 g.3.9.1 Length = 501

 Score = 42.6 bits (99), Expect = 3e-04
 Identities = 9/67 (13%), Positives = 15/67 (22%), Gaps = 1/67 (1%)

Query: 465 RKSRCQYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQYQYQYQCQCQCQ 524
           RK R +  C+  C     Y            + +  +      +    Y       C   
Sbjct: 228 RKFRDEATCKDTCPPLMLYNPTTYQ-MDVNPEGKYSFGATCVKKCPRNYVVTDHGSCVRA 286

Query: 525 CQCQYQY 531
           C      
Sbjct: 287 CGADSYE 293

>2hr7_A Insulin receptor; hormone receptor, leucine rich repeat, transferase; HET: NAG BMA MAN FUC P33; 2.32A {Homo sapiens} Length = 486

 Score = 42.1 bits (98), Expect = 4e-04
 Identities = 5/63 (7%), Positives = 15/63 (23%)

Query: 466 KSRCQYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQYQYQYQCQCQCQC 525
                 +C   C    + +  C          +  + + +  +        + C  +  C
Sbjct: 148 NKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLC 207

Query: 526 QCQ 528
              
Sbjct: 208 CHS 210

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	531
1b43_A	340	Protein (FEN-1); nuclease, DNA repair, DNA replica	100.0
3ory_A	363	Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco	100.0
3q8k_A	341	Flap endonuclease 1; helix-3 turn-helix, hydrophob	100.0
1ul1_X	379	Flap endonuclease-1; protein complex, DNA-binding	100.0
2izo_A	346	FEN1, flap structure-specific endonuclease; hydrol	100.0
3qe9_Y	352	Exonuclease 1; exonuclease, hydrolase-DNA complex;	100.0
1a76_A	326	Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea	100.0
1rxw_A	336	Flap structure-specific endonuclease; helical clam	100.0
1exn_A	290	5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent	99.95
3ory_A	363	Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco	99.92
1bgx_T	832	TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi	99.92
3q8k_A	341	Flap endonuclease 1; helix-3 turn-helix, hydrophob	99.92
3qe9_Y	352	Exonuclease 1; exonuclease, hydrolase-DNA complex;	99.89
2izo_A	346	FEN1, flap structure-specific endonuclease; hydrol	99.87
1b43_A	340	Protein (FEN-1); nuclease, DNA repair, DNA replica	99.85
1rxw_A	336	Flap structure-specific endonuclease; helical clam	99.85
1ul1_X	379	Flap endonuclease-1; protein complex, DNA-binding	99.84
1a76_A	326	Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea	99.8
3h7i_A	305	Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonu	99.78
1exn_A	290	5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent	98.87
1bgx_T	832	TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi	98.68
2ztd_A	212	Holliday junction ATP-dependent DNA helicase RUVA;	95.57
1ixr_A	191	Holliday junction DNA helicase RUVA; heterooligome	95.5
2a1j_A	63	DNA repair endonuclease XPF; XPF, xeroderma pigmen	95.08
1cuk_A	203	RUVA protein; DNA repair, SOS response, DNA-bindin	94.79
1z00_B	84	DNA repair endonuclease XPF; helix-hairpin-helix,	94.25
2a1j_A	63	DNA repair endonuclease XPF; XPF, xeroderma pigmen	94.12
2y35_A	1140	LD22664P; hydrolase-DNA complex, RNA degradation,	93.37
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	93.15
1z00_B	84	DNA repair endonuclease XPF; helix-hairpin-helix,	93.14
4glx_A	586	DNA ligase; inhibitor, ligase-ligase inhibitor-DNA	92.8
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	92.8
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	92.65
3fqd_A	899	Protein DHP1, 5'-3' exoribonuclease 2; protein-pro	92.47
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	91.67
3b0x_A	575	DNA polymerase beta family (X family); structural	91.17
2w9m_A	578	Polymerase X; SAXS, DNA repair, DNA polymerase, DN	91.08
2owo_A	671	DNA ligase; protein-DNA complex, ligase-DNA comple	89.89
3sgi_A	615	DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tub	89.86
1kft_A	78	UVRC, excinuclease ABC subunit C; helix-hairpin-he	89.73
3pie_A	1155	5'->3' exoribonuclease (XRN1); beta berrel, tudor	89.56
2nrt_A	220	Uvrabc system protein C; UVRC, endonuclease, RNAse	89.39
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	88.24
1z00_A	89	DNA excision repair protein ERCC-1; helix-hairpin-	87.7
1x2i_A	75	HEF helicase/nuclease; alpha helix, helix-hairpin-	87.56
2a1j_B	91	DNA excision repair protein ERCC-1; XPF, xeroderma	85.02
3c65_A	226	Uvrabc system protein C; UVRC, endonuclease, nucle	84.29
2bgw_A	219	XPF endonuclease; hydrolase, structure specific en	83.87
1dgs_A	667	DNA ligase; AMP complex, NAD+-dependent; HET: DNA	80.89

>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=100.00  E-value=1.7e-40  Score=343.97  Aligned_cols=161  Identities=29%  Similarity=0.470  Sum_probs=134.3

Q ss_pred             CCCccceeecccCCCCCcchhHH------hH----HHHHHhh------------ccCCCH---HHHHHHHhhcCCccccC
Q psy1206           7 DPDEDGLVKYLCGDKNFAEDRIR------NG----AKKLLKA------------RSSTTQ---GRLDSFFTIRREEKRKA   61 (531)
Q Consensus         7 ~~d~~~~~a~~~~~~~f~~~~~R------~~----~~~~~k~------------~~~~t~---~~i~~lL~~~gIp~vvA   61 (531)
                      .|.+ .++.||.+.++|+++...      .+    +...+++            ...+|+   +.++++|+++|||+++|
T Consensus        71 ~~i~-pv~VFDG~~~~~K~~~~~~R~~~r~~~~~~~~~~yk~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~gip~i~a  149 (340)
T 1b43_A           71 AGIK-PVYVFDGEPPEFKKKELEKRREAREEAEEKWREALEKGEIEEARKYAQRATRVNEMLIEDAKKLLELMGIPIVQA  149 (340)
T ss_dssp             TTCE-EEEEECCSCCCCSSCSSTTCCCCTTHHHHHHHHHHHHSCHHHHHHHHHTSGGGTHHHHHHHHHHHHHHTCCEEEC
T ss_pred             CCCE-EEEEecCCCchhhhhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcEEEc
Confidence            5666 899999998999865432      11    1112333            233444   45789999999999999


Q ss_pred             CCchhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccC---------CcEEecHHHHHHhCCCCHHHHHHH
Q psy1206          62 PCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKL---------PVQEFHLEKVLEGMELSHEEFIDL  132 (531)
Q Consensus        62 PyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~---------~v~~~~~~~i~~~lglt~eqfid~  132 (531)
                      |||||||||+|+++|++++|+|+|+|+|+||+++|+++++.+|..+.         .++.++.+.+.+.+|++++||+|+
T Consensus       150 p~EADa~iA~La~~g~~~~i~S~D~D~l~~g~~~v~~~~~~~~~~~~p~~~~~v~~~~~~~~~~~v~~~~gl~~~q~id~  229 (340)
T 1b43_A          150 PSEGEAQAAYMAAKGSVYASASQDYDSLLFGAPRLVRNLTITGKRKLPGKNVYVEIKPELIILEEVLKELKLTREKLIEL  229 (340)
T ss_dssp             SSCHHHHHHHHHHHTSSSEEECSSSHHHHTTCSEEEESTTTCEEEECTTSSCEEEECCEEEEHHHHHHHHTCCHHHHHHH
T ss_pred             ChhHHHHHHHHHHcCCEEEEEccCCCcceecCcEEEEEeccCCCccCcccccccccceeEEEHHHHHHHhCCCHHHHHHH
Confidence            99999999999999999999999999999999999999876653322         346799999999999999999999


Q ss_pred             HhHcCCCCCC-CCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206         133 CILLGCDYCD-SIRGIGPKRAIELIKEHRSIEKILEN  168 (531)
Q Consensus       133 ~iL~G~DY~p-GIpGIG~ktA~kLI~~~~sle~il~~  168 (531)
                      |+|+||||+| ||||||+|||++||++|+|+++++++
T Consensus       230 ~~L~G~Dy~p~gv~GiG~ktA~kli~~~gsle~il~~  266 (340)
T 1b43_A          230 AILVGTDYNPGGIKGIGLKKALEIVRHSKDPLAKFQK  266 (340)
T ss_dssp             HHHHCCTTSTTCSTTCCHHHHHHHHHTCSSGGGGTGG
T ss_pred             HHhcCCCCCCCCCCCccHHHHHHHHHHcCCHHHHHcC
Confidence            9999999999 99999999999999999998876543

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

Probab=100.00  E-value=1.3e-40  Score=347.97  Aligned_cols=157  Identities=35%  Similarity=0.518  Sum_probs=132.1

Q ss_pred             eeecccCCCCCcchhH------HhHH----------------HHHHhhccCCCH---HHHHHHHhhcCCccccCCCchhH
Q psy1206          13 LVKYLCGDKNFAEDRI------RNGA----------------KKLLKARSSTTQ---GRLDSFFTIRREEKRKAPCEAEA   67 (531)
Q Consensus        13 ~~a~~~~~~~f~~~~~------R~~~----------------~~~~k~~~~~t~---~~i~~lL~~~gIp~vvAPyEADA   67 (531)
                      ++.||.+.++|+++.+      |..+                .+++.+...+|+   +.++++|+++|||+++||+||||
T Consensus        90 v~VFDg~~p~~K~~~~~~yK~~R~~~~e~l~~~~~~g~~~~a~~~~~~~~~vt~~~~~~i~~lL~~~GIp~i~apgEADa  169 (363)
T 3ory_A           90 VYVFDGKPPELKAREIERRKAVKEEAAKKYEEAVQSGDLELARRYAMMSAKLTEEMVRDAKSLLDAMGIPWVQAPAEGEA  169 (363)
T ss_dssp             EEEECSSCGGGCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHTCCCCCCCHHHHHHHHHHHHHHTCCEEECSSCHHH
T ss_pred             EEEEcCCCccchHHHHHHHHHhhhhchHHHHHHHHcCCHHHHHHHHhccccCCHHHHHHHHHHHHHCCCCEEEeCccHHH
Confidence            5679999999975542      1111                112233445565   56789999999999999999999


Q ss_pred             HHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccC---------CcEEecHHHHHHhCCCCHHHHHHHHhHcCC
Q psy1206          68 QCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKL---------PVQEFHLEKVLEGMELSHEEFIDLCILLGC  138 (531)
Q Consensus        68 q~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~---------~v~~~~~~~i~~~lglt~eqfid~~iL~G~  138 (531)
                      |||+|++.|++++|+|+|+|+|+||+++|+++++..+.++.         ..+.++.+.+.+.+|++++||+|+|+|+||
T Consensus       170 qiA~La~~g~~~~I~S~D~D~l~fg~~~v~~~l~~~~~~~~p~~~~~v~~~~~~~~~~~v~~~~gl~~~q~id~~~L~Gs  249 (363)
T 3ory_A          170 QAAYIVKKGDAYASASQDYDSLLFGSPKLVRNLTISGRRKLPRKNEYVEVKPELIELDKLLVQLGITLENLIDIGILLGT  249 (363)
T ss_dssp             HHHHHHHTTSCSEEECSSSHHHHTTCSEEEESTTTCEEEECSSTTCEEEECCEEEEHHHHHHHHTCCHHHHHHHHHHHCB
T ss_pred             HHHHHHHCCCeEEEECCCcCccccCCCeEEEEeeccccccCCccccccccceEEEcHHHHHHHhCcCHHHHHHHHHHhCC
Confidence            99999999999999999999999999999999876543211         246899999999999999999999999999


Q ss_pred             CCCC-CCCCccHHHHHHHHHHcCCHHHHHHHh
Q psy1206         139 DYCD-SIRGIGPKRAIELIKEHRSIEKILENI  169 (531)
Q Consensus       139 DY~p-GIpGIG~ktA~kLI~~~~sle~il~~l  169 (531)
                      ||+| ||||||+|||++||++|||+|+|++++
T Consensus       250 Dy~p~GVpGIG~KtA~kLl~~~gsle~il~~~  281 (363)
T 3ory_A          250 DYNPDGFEGIGPKKALQLVKAYGGIEKIPKPI  281 (363)
T ss_dssp             TTBTTCSTTCCHHHHHHHHHHHTSSTTSCGGG
T ss_pred             CCCCCCCCCcCHHHHHHHHHHcCCHHHHHHhc
Confidence            9999 999999999999999999999887765

>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=100.00  E-value=6.9e-40  Score=339.95  Aligned_cols=236  Identities=50%  Similarity=0.905  Sum_probs=200.1

Q ss_pred             eeecccCCCCCcchhHHh------H----------------HHHHHhhccCCCH---HHHHHHHhhcCCccccCCCchhH
Q psy1206          13 LVKYLCGDKNFAEDRIRN------G----------------AKKLLKARSSTTQ---GRLDSFFTIRREEKRKAPCEAEA   67 (531)
Q Consensus        13 ~~a~~~~~~~f~~~~~R~------~----------------~~~~~k~~~~~t~---~~i~~lL~~~gIp~vvAPyEADA   67 (531)
                      ...||.+.++|+++..-.      .                +.++.++...+|+   +.++++|+++|||+++|||||||
T Consensus        81 ~~VFDg~~~~~r~~~~~~yk~~R~~~~~~~~~a~r~~~pe~l~~~~~~~~~vt~~q~~~~~~lL~~~gip~i~ap~EADd  160 (341)
T 3q8k_A           81 VYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEA  160 (341)
T ss_dssp             EEEECCCCCGGGHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHTCCCCHHHHHHHHHHHHHHTCCEEECSSCHHH
T ss_pred             eEEEeCCCcccchhhhHHHHHHHhHhHHHHHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCCCEEECCccHHH
Confidence            336999999997554211      1                1112233334444   45789999999999999999999


Q ss_pred             HHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcCCCCCCCCCCc
Q psy1206          68 QCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCDSIRGI  147 (531)
Q Consensus        68 q~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G~DY~pGIpGI  147 (531)
                      |||+|++.|.+++|+|+|+|+|+||+++|++++++++.++.++..++.+.+.+.+|++|+||+|+++|+||||+||||||
T Consensus       161 ~ia~La~~g~v~~i~s~D~D~l~~~~~~v~~~~~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~~L~G~D~~~gipGi  240 (341)
T 3q8k_A          161 SCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGI  240 (341)
T ss_dssp             HHHHHHHTTSSSEEECSCTHHHHTTCSEEEESCCCCSSCCCEEEEEEHHHHHHHHTCCHHHHHHHHHHHCCSSSCCCTTC
T ss_pred             HHHHHHhcCCeEEEEcCCccccccCCcEEEEcccccccCCCceEEEcHHHHHHHhCCCHHHHHHHHHhcCCCCCCCCCCc
Confidence            99999999999999999999999999999999876544444578899999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHHcCCHHHHHHHhhhcCCCCCCCCcHHHHHHHhcCCCcCCCCCcccccccccccccccccccCCChhhhHh
Q psy1206         148 GPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFIDLCILLGCDYCDSIRGIGPKRAIE  227 (531)
Q Consensus       148 G~ktA~kLI~~~~sle~il~~l~~~~~~ip~~f~~~~A~~~f~~p~V~d~~~~~~v~Ls~~~~~d~cesl~~~Gp~~~~e  227 (531)
                      |+|||++||++|||+|+|+++++.                                                        
T Consensus       241 G~KtA~kll~~~gsle~i~~~~~~--------------------------------------------------------  264 (341)
T 3q8k_A          241 GPKRAVDLIQKHKSIEEIVRRLDP--------------------------------------------------------  264 (341)
T ss_dssp             CHHHHHHHHHHHCSHHHHHHHSCT--------------------------------------------------------
T ss_pred             cHHHHHHHHHHcCCHHHHHHHHHh--------------------------------------------------------
Confidence            999999999999999999988631                                                        


Q ss_pred             HHhhhhhhhhhccCccccCCCCCchHHHHHHHHhhccHHHHHHHHhhCCCCCCCcchHHHHHHHhcCCcccCcccccccc
Q psy1206         228 LLYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIADPETIELVA  307 (531)
Q Consensus       228 l~e~F~~~CiLsGCDY~~~i~giG~k~A~kli~k~~s~~~vi~~l~~~~~~vP~~y~~~~A~~~F~~~~V~dP~~~~Lv~  307 (531)
                                                                     .+.++|++|++.+|+.+|+||.|++|.+     
T Consensus       265 -----------------------------------------------~k~~~~~~~~~~~~r~l~l~~~V~~~~~-----  292 (341)
T 3q8k_A          265 -----------------------------------------------NKYPVPENWLHKEAHQLFLEPEVLDPES-----  292 (341)
T ss_dssp             -----------------------------------------------TTSCCCTTCCHHHHHHHHHSCCCCCTTT-----
T ss_pred             -----------------------------------------------cCCCCCcccchHHHHHHhCCCCCCCCcc-----
Confidence                                                           1236788888999999999999998832     


Q ss_pred             ccCCCcccccceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHH
Q psy1206         308 DVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELN  387 (531)
Q Consensus       308 ~~aP~~i~~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~  387 (531)
                                                                                                      
T Consensus       293 --------------------------------------------------------------------------------  292 (341)
T 3q8k_A          293 --------------------------------------------------------------------------------  292 (341)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             HHHHHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhccCCcCccccccc
Q psy1206         388 KRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFT  458 (531)
Q Consensus       388 kR~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~rld~ff~  458 (531)
                                         .++.|..||.+++++|++.+..|..++|.+.+++|.++++   |+.||+||.
T Consensus       293 -------------------~~l~~~~pd~~~l~~fl~~~~~f~~~rv~~~~~~l~~~~~---~~~l~~~~~  341 (341)
T 3q8k_A          293 -------------------VELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQ---GSTLEVLFQ  341 (341)
T ss_dssp             -------------------SCCCCCCCCHHHHHHHHTTTTCCCHHHHHHHHHHHHHHHH---HHCCCCCCC
T ss_pred             -------------------cccCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhc---cCcHhhhcC
Confidence                               2468999999999999977799999999999999999987   788999994

>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=100.00  E-value=7.8e-40  Score=343.89  Aligned_cols=210  Identities=58%  Similarity=1.048  Sum_probs=189.0

Q ss_pred             HHHHHHHhhcCCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCC
Q psy1206          45 GRLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMEL  124 (531)
Q Consensus        45 ~~i~~lL~~~gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lgl  124 (531)
                      +.++++|+++||||++||||||||||+|++.|.+++|+|+|+|+|+||+++|++++++++..+.++..++.+.+.+.+|+
T Consensus       138 ~~~~~lL~~~Gi~~i~apgEADd~iA~La~~g~~~~iiS~D~Dll~~g~~~v~~~~~~~~~~k~~~~~~~~~~v~~~~gl  217 (379)
T 1ul1_X          138 DECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGL  217 (379)
T ss_dssp             HHHHHHHHHHTCCEEECSSCHHHHHHHHHHHTSSSEEECSCTHHHHTTCSEEEECSSCCC-CCCCEEEEEHHHHHHHHTC
T ss_pred             HHHHHHHHHcCCCeecCCCcHHHHHHHHHhcCCeEEEEecCcCccccccceEEEEecccccCcCCeEEEeHHHHHHHhCC
Confidence            67899999999999999999999999999999999999999999999999999998765433356889999999999999


Q ss_pred             CHHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhhcCCCCCCCCcHHHHHHHhcCCCcCCCCCccccc
Q psy1206         125 SHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFID  204 (531)
Q Consensus       125 t~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~~~~~ip~~f~~~~A~~~f~~p~V~d~~~~~~v~  204 (531)
                      +++||+|+|+|+||||++||||||+|||++||++|+|+|+|+++++..                                
T Consensus       218 ~~~q~id~~~L~G~D~~d~IpGIG~KtA~kLl~~~gsle~i~~~~~~~--------------------------------  265 (379)
T 1ul1_X          218 NQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPN--------------------------------  265 (379)
T ss_dssp             CHHHHHHHHHHHHCSSSCCCTTCCHHHHHHHHHHSSSHHHHHTTCCCT--------------------------------
T ss_pred             CHHHHHHHHHHhCCCcCCCCCCcCHHHHHHHHHHcCCHHHHHHHHHhh--------------------------------
Confidence            999999999999999999999999999999999999999998776320                                


Q ss_pred             ccccccccccccccCCChhhhHhHHhhhhhhhhhccCccccCCCCCchHHHHHHHHhhccHHHHHHHHhhCCCCCCCcch
Q psy1206         205 LCILLGCDYCDSIRGIGPKRAIELLYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWL  284 (531)
Q Consensus       205 Ls~~~~~d~cesl~~~Gp~~~~el~e~F~~~CiLsGCDY~~~i~giG~k~A~kli~k~~s~~~vi~~l~~~~~~vP~~y~  284 (531)
                                                                                             +..+|++|.
T Consensus       266 -----------------------------------------------------------------------k~~~~~~~~  274 (379)
T 1ul1_X          266 -----------------------------------------------------------------------KYPVPENWL  274 (379)
T ss_dssp             -----------------------------------------------------------------------TSCCCSSCC
T ss_pred             -----------------------------------------------------------------------cccCCCcCC
Confidence                                                                                   124688888


Q ss_pred             HHHHHHHhcCCcccCccccccccccCCCcccccceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHH
Q psy1206         285 YKEARELFRHPEIADPETIELVADVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLV  364 (531)
Q Consensus       285 ~~~A~~~F~~~~V~dP~~~~Lv~~~aP~~i~~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll  364 (531)
                      +.+|+.+|+|+.|++|.+                                                              
T Consensus       275 ~~~ar~l~l~~~v~~~~~--------------------------------------------------------------  292 (379)
T 1ul1_X          275 HKEAHQLFLEPEVLDPES--------------------------------------------------------------  292 (379)
T ss_dssp             HHHHHHHHHSCCCCCGGG--------------------------------------------------------------
T ss_pred             HHHHHHHhcCCeeCCCCC--------------------------------------------------------------
Confidence            888999999999998731                                                              


Q ss_pred             HcCCeeEEeecCCCCCcchHHHHHHHHHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHH
Q psy1206         365 EHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKA  444 (531)
Q Consensus       365 ~~gIkPVfVFDG~pp~lK~~~~~kR~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~  444 (531)
                                                               . ++.|..||.+++++|+.++..|..+++.+.+.+|.++
T Consensus       293 -----------------------------------------~-~l~~~~pd~~~l~~fl~~~~~f~~~rv~~~~~rl~~~  330 (379)
T 1ul1_X          293 -----------------------------------------V-ELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKS  330 (379)
T ss_dssp             -----------------------------------------C-CCCCCCCCHHHHHHHTTTTSCCCHHHHHHHHHHHHHH
T ss_pred             -----------------------------------------c-cCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence                                                     1 4679999999999998887999999999999999999


Q ss_pred             hccCCcCccccccccch
Q psy1206         445 RSTTTQGRLDSFFTIRR  461 (531)
Q Consensus       445 ~~~~~~~rld~ff~~~~  461 (531)
                      +++.+|+|||+||++.+
T Consensus       331 ~~~~~q~~l~~ff~~~~  347 (379)
T 1ul1_X          331 RQGSTQGRLDDFFKVTG  347 (379)
T ss_dssp             HSCCSBCCHHHHSEEEE
T ss_pred             hccCCCCcHHhhcCCCC
Confidence            99999999999999875

>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=100.00  E-value=2.6e-39  Score=336.04  Aligned_cols=125  Identities=36%  Similarity=0.560  Sum_probs=107.3

Q ss_pred             HHHHHHHhhcCCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccC---------CcEEecH
Q psy1206          45 GRLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKL---------PVQEFHL  115 (531)
Q Consensus        45 ~~i~~lL~~~gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~---------~v~~~~~  115 (531)
                      +.++++|+++|||+++||||||||||+|++.|++++|+|+|+|+|+||+++|+++++.+|.++.         .++.++.
T Consensus       130 ~~~~~lL~~~gi~~i~ap~EADa~ia~La~~g~~~~I~S~D~D~l~~~~~~v~~~~~~~~~~~~p~~~~~~~~~~~~~~~  209 (346)
T 2izo_A          130 EESKKLLRAMGIPIVQAPSEGEAEAAYLNKLGLSWAAASQDYDAILFGAKRLVRNLTITGKRKLPNKDVYVEIKPELIET  209 (346)
T ss_dssp             HHHHHHHHHHTCCEEECSSCHHHHHHHHHHTTSSSEEECSSSHHHHTTCSEEEESSCC-----------CCCCCCEEEEH
T ss_pred             HHHHHHHHHCCCCEEEcCCcHHHHHHHHHhCCCeEEEECCCCCcceecCCeEEEEecccccccCcccccccccceEEEEH
Confidence            4678999999999999999999999999999999999999999999999999999876543211         3567999


Q ss_pred             HHHHHhCCCCHHHHHHHHhHcCCCCCC-CCCCccHHHHHHHHHHcCCHHHHHHHh
Q psy1206         116 EKVLEGMELSHEEFIDLCILLGCDYCD-SIRGIGPKRAIELIKEHRSIEKILENI  169 (531)
Q Consensus       116 ~~i~~~lglt~eqfid~~iL~G~DY~p-GIpGIG~ktA~kLI~~~~sle~il~~l  169 (531)
                      +.+.+.+|+++++|+|+|+|+||||+| ||||||+|||++||++|+|+|+|++++
T Consensus       210 ~~v~~~~gl~~~q~id~~~L~G~D~~p~Gv~GIG~KtA~kLi~~~gsle~i~~~~  264 (346)
T 2izo_A          210 EILLKKLGITREQLIDIGILIGTDYNPDGIRGIGPERALKIIKKYGKIEKAMEYG  264 (346)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHCCSSSTTCSTTCCHHHHHHHHHHSSCC-------
T ss_pred             HHHHHHcCCCHHHHHHHHHHcCCCCCCCCCCCcCHHHHHHHHHHcCCHHHHHHHH
Confidence            999999999999999999999999999 999999999999999999999998876

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

Probab=100.00  E-value=6e-39  Score=334.16  Aligned_cols=214  Identities=25%  Similarity=0.306  Sum_probs=178.6

Q ss_pred             ccceeecccCCCCCcchhH--Hh--------------------HHHHHHhhccCCCH---HHHHHHHhhcCCccccCCCc
Q psy1206          10 EDGLVKYLCGDKNFAEDRI--RN--------------------GAKKLLKARSSTTQ---GRLDSFFTIRREEKRKAPCE   64 (531)
Q Consensus        10 ~~~~~a~~~~~~~f~~~~~--R~--------------------~~~~~~k~~~~~t~---~~i~~lL~~~gIp~vvAPyE   64 (531)
                      ..-++-||.+....++.+.  |.                    ++.+.+++...+|+   +.++++|+++|||+++||||
T Consensus        71 I~PvfVFDG~~~p~Kk~~~~~Rr~~r~~~~~~~~~~~~~g~~~~a~~~f~~~~~vt~~~~~~i~~~L~~~gIp~i~ap~E  150 (352)
T 3qe9_Y           71 IKPILVFDGCTLPSKKEVERSRRERRQANLLKGKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGVDCLVAPYE  150 (352)
T ss_dssp             CEEEEEECCSCCTTTHHHHHHHHHHHHHHHHHHHHHTTSSCCHHHHHHHGGGCCCCHHHHHHHHHHHHHTTCEEEECSSC
T ss_pred             CEEEEEECCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCCcEEECCcc
Confidence            3457779988766665532  11                    12234555556777   45788999999999999999


Q ss_pred             hhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHH--HHhCC--CCHHHHHHHHhHcCCCC
Q psy1206          65 AEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKV--LEGME--LSHEEFIDLCILLGCDY  140 (531)
Q Consensus        65 ADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i--~~~lg--lt~eqfid~~iL~G~DY  140 (531)
                      ||||||+|+++|++++|+|+|+|+|+||+++|+++++..+..    ..++.+.+  .+.+|  ++++||+|+|+|+||||
T Consensus       151 ADaqiA~La~~g~~~~I~S~D~Dll~~~~~~v~~~~~~~~~~----~~~~~~~~~~~~~~g~~l~~~q~id~~~L~G~D~  226 (352)
T 3qe9_Y          151 ADAQLAYLNKAGIVQAIITEDSALLAFGCKKVILKMDQFGNG----LEIDQARLGMCRQLGDVFTEEKFRYMCILSGCDY  226 (352)
T ss_dssp             HHHHHHHHHHTTSCSEEECSCGGGGGGTCSEEEESCCTTSEE----EEEEGGGGTTCCTTCSSCCHHHHHHHHHHHCCSS
T ss_pred             hHHHHHHHHHCCCeEEEEeCCcCcccccCCeEEEeccCCCCc----EEEeHHHHHHHHHhCCCCCHHHHHHHHHhcCCCC
Confidence            999999999999999999999999999999999988765432    34666664  57888  99999999999999999


Q ss_pred             CCCCCCccHHHHHHHHHHc--CCHHHHHHHhhh---cCCCCCCCCc--HHHHHHHhcCCCcCCCCCcccccccccccccc
Q psy1206         141 CDSIRGIGPKRAIELIKEH--RSIEKILENIDT---KKYTVPEGWL--YKEARELFRHPEVADPETIEFIDLCILLGCDY  213 (531)
Q Consensus       141 ~pGIpGIG~ktA~kLI~~~--~sle~il~~l~~---~~~~ip~~f~--~~~A~~~f~~p~V~d~~~~~~v~Ls~~~~~d~  213 (531)
                      +|||||||+|||++||++|  +|++++++++.+   .+..+|++|.  |.+|+.+|+||.||||.++++++|++.+....
T Consensus       227 ~pgv~GiG~ktA~kli~~~~~~~l~~il~~~~~~l~~~~~vp~~~~~~~~~A~~~F~~q~V~dp~~~~~~~l~~~~~~~~  306 (352)
T 3qe9_Y          227 LSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNITVPEDYINGFIRANNTFLYQLVFDPIKRKLIPLNAYEDDVD  306 (352)
T ss_dssp             SCCCTTCCHHHHHHHHHHCCCSCHHHHHTTHHHHHTCCCCCCHHHHHHHHHHHHHHHHCEEEETTTTEEEESSCCCSSCC
T ss_pred             CCCCCCeeHHHHHHHHHHhCCCCHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHhCCCEEECCCCCeEeeCCCCCCCCC
Confidence            9999999999999999999  699999999875   3578999997  99999999999999999999999999887666


Q ss_pred             cccccCCChhhhHh
Q psy1206         214 CDSIRGIGPKRAIE  227 (531)
Q Consensus       214 cesl~~~Gp~~~~e  227 (531)
                      .+.+.++|+...++
T Consensus       307 ~~~~~~~G~~~~~~  320 (352)
T 3qe9_Y          307 PETLSYAGQYVDDS  320 (352)
T ss_dssp             GGGCCTTCCCCCHH
T ss_pred             hhhhhhcCCCCCHH
Confidence            66677888766554

>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=100.00  E-value=1.9e-37  Score=319.42  Aligned_cols=155  Identities=28%  Similarity=0.445  Sum_probs=132.1

Q ss_pred             cceeecccCCCCCcchhHHh----------------------HHHHHHhhccCCCH---HHHHHHHhhcCCccccCCCch
Q psy1206          11 DGLVKYLCGDKNFAEDRIRN----------------------GAKKLLKARSSTTQ---GRLDSFFTIRREEKRKAPCEA   65 (531)
Q Consensus        11 ~~~~a~~~~~~~f~~~~~R~----------------------~~~~~~k~~~~~t~---~~i~~lL~~~gIp~vvAPyEA   65 (531)
                      .-+++||.+.++|+++....                      ++.++.++...+|+   +.++++|+++|||+++|||||
T Consensus        74 ~Pv~vFDG~~~~~k~~~~~~yk~~R~~~~~~l~~~~~~g~~~~a~~~~~~~~~vt~~~~~~~~~lL~~~gi~~i~apgEA  153 (326)
T 1a76_A           74 TPIWVFDGEPPKLKEKTRKVRREMKEKAELKMKEAIKKEDFEEAAKYAKRVSYLTPKMVENCKYLLSLMGIPYVEAPSEG  153 (326)
T ss_dssp             EEEEEECCCSSCCCCSSCCSSCSSSCSSCSCCCCCCSHHHHHTTSTTGGGGCSSCHHHHHHHHHHHHHHTCCEEECSSCH
T ss_pred             eEEEEEeCcCcccchhhHHHHHHHHHhhHHHHHHHHHcCCHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCCeEECCccH
Confidence            34899998888887553210                      01112233334454   568899999999999999999


Q ss_pred             hHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcCCCCCC-CC
Q psy1206          66 EAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGCDYCD-SI  144 (531)
Q Consensus        66 DAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G~DY~p-GI  144 (531)
                      |||||+|+++|++++|+|+|+|+|+||+++|+++++.++.   .++.++.+.+.+.+|++++||+|+|+|+||||+| ||
T Consensus       154 D~~ia~La~~g~~~~I~S~D~Dll~~~~~~v~~~~~~~~~---~~~~~~~~~v~~~~gl~~~q~id~~~L~GsD~~p~Gv  230 (326)
T 1a76_A          154 EAQASYMAKKGDVWAVVSQDYDALLYGAPRVVRNLTTTKE---MPELIELNEVLEDLRISLDDLIDIAIFMGTDYNPGGV  230 (326)
T ss_dssp             HHHHHHHHHTTSSSEEECSSSGGGGGTCSEEEESSSSCSS---CCEEEEHHHHHHHHTCCHHHHHHHHHHHCCTTSTTTT
T ss_pred             HHHHHHHHHCCCEEEEecCCcccceecCCEEEEeecCCCC---ceEEEEHHHHHHHcCCCHHHHHHHHHHcCCCCCCCCC
Confidence            9999999999999999999999999999999999876653   5789999999999999999999999999999999 99


Q ss_pred             CCccHHHHHHHHHHcCCHHHHH-HHh
Q psy1206         145 RGIGPKRAIELIKEHRSIEKIL-ENI  169 (531)
Q Consensus       145 pGIG~ktA~kLI~~~~sle~il-~~l  169 (531)
                      ||||+|||++||++ +|+++++ +++
T Consensus       231 pGiG~ktA~kli~~-gsle~i~~~~~  255 (326)
T 1a76_A          231 KGIGFKRAYELVRS-GVAKDVLKKEV  255 (326)
T ss_dssp             TTCCHHHHHHHHHH-TCHHHHHHHHS
T ss_pred             CCcCHHHHHHHHHc-CCHHHHHHHHH
Confidence            99999999999999 9999998 764

>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=100.00  E-value=1.3e-33  Score=291.94  Aligned_cols=188  Identities=30%  Similarity=0.458  Sum_probs=150.2

Q ss_pred             eeecccCCCCCcchhH------HhH---------------HHHHHhhccCCCH---HHHHHHHhhcCCccccCCCchhHH
Q psy1206          13 LVKYLCGDKNFAEDRI------RNG---------------AKKLLKARSSTTQ---GRLDSFFTIRREEKRKAPCEAEAQ   68 (531)
Q Consensus        13 ~~a~~~~~~~f~~~~~------R~~---------------~~~~~k~~~~~t~---~~i~~lL~~~gIp~vvAPyEADAq   68 (531)
                      +++||.+.++|+++..      |..               +..+.++...+|+   +.++++|+++|||+++||+|||||
T Consensus        76 v~vFDg~~~~~R~~~~~~yk~~R~~~~~~~~~~~~~g~~~l~~~~~~~~~vt~~~~~~~~~lL~~~gi~~i~apgeAEA~  155 (336)
T 1rxw_A           76 VFVFDGEPPEFKKAEIEERKKRRAEAEEMWIAALQAGDKDAKKYAQAAGRVDEYIVDSAKTLLSYMGIPFVDAPSEGEAQ  155 (336)
T ss_dssp             EEEECCSCCGGGHHHHHHHHHHHHHHHHHHHHHHHHTCTTHHHHHHHHCCCCHHHHHHHHHHHHHTTCCEEECSSCHHHH
T ss_pred             EEEEcCCCCcccccchHHHHHHHHHHHHHHHHHHHhchHHHHHHHHhhccCCHHHHHHHHHHHHhCCCCEEEcCchHHHH
Confidence            8999988888875442      111               1122233344555   467899999999999999999999


Q ss_pred             HHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCccc---------CCcEEecHHHHHHhCCCCHHHHHHHHhHcCCC
Q psy1206          69 CAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARK---------LPVQEFHLEKVLEGMELSHEEFIDLCILLGCD  139 (531)
Q Consensus        69 ~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~---------~~v~~~~~~~i~~~lglt~eqfid~~iL~G~D  139 (531)
                      ||+|+++|++++|+|+|+|+++||+++|+++++..+..+         +.++.++.+.+.+.+|++|+||+|+|+|+|||
T Consensus       156 lA~la~~g~~~~I~S~D~Dllql~~~~v~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~~L~GsD  235 (336)
T 1rxw_A          156 AAYMAAKGDVEYTGSQDYDSLLFGSPRLARNLAITGKRKLPGKNVYVDVKPEIIILESNLKRLGLTREQLIDIAILVGTD  235 (336)
T ss_dssp             HHHHHHTTSSSEEECSSSHHHHTTCSEEEESCCC-------------CCCCEEEEHHHHHHHHTCCHHHHHHHHHHHCBT
T ss_pred             HHHHHHcCCeeEEEcCCCCcceecCCeEEEeccccccccCCccccccccceEEeEHHHHHHHcCCCHHHHHHHHhhcCCC
Confidence            999999999999999999999999999999887654211         14568999999999999999999999999999


Q ss_pred             CCCCCCCccHHHHHHHHHHcCCHHHHHHHhhhcCCCCCCCCcHHHHHHHhcCCCcCCCCCccccccc
Q psy1206         140 YCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFIDLC  206 (531)
Q Consensus       140 Y~pGIpGIG~ktA~kLI~~~~sle~il~~l~~~~~~ip~~f~~~~A~~~f~~p~V~d~~~~~~v~Ls  206 (531)
                      |+|||||||+|||++||++|||+|+|+++++.   .++ +  ..+++.+|.+|.|.+.+...|....
T Consensus       236 ~ipGv~GiG~KtA~kLl~~~gsle~i~~~~~~---~l~-~--~~~l~~i~~~~~v~~~~~~~~~~~d  296 (336)
T 1rxw_A          236 YNEGVKGVGVKKALNYIKTYGDIFRALKALKV---NID-H--VEEIRNFFLNPPVTDDYRIEFREPD  296 (336)
T ss_dssp             TBCCCTTCCHHHHHHHHHHHSSHHHHHHHHTC----------CHHHHHHHHSCCCCCCCCCCCCCCC
T ss_pred             CCCCCCCcCHHHHHHHHHHcCCHHHHHHhCCC---CCc-c--HHHHHHHHhCCCCCCcccccCCCCC
Confidence            99999999999999999999999999999863   122 1  3488889999999865555655443

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

Probab=99.95  E-value=5e-29  Score=253.00  Aligned_cols=153  Identities=21%  Similarity=0.239  Sum_probs=134.3

Q ss_pred             CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCH-------H--------HHHHHHhh--cCCccccCC-CchhHH
Q psy1206           7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ-------G--------RLDSFFTI--RREEKRKAP-CEAEAQ   68 (531)
Q Consensus         7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~-------~--------~i~~lL~~--~gIp~vvAP-yEADAq   68 (531)
                      .|++ .+++||.+.+     .+|++.++.||++|..+|       +        .++++|++  +|||++.+| |||||+
T Consensus        58 ~p~~-~vvvFD~~~~-----tfR~~~~~~YKa~R~~~p~~~~~~~e~L~~q~~~~ikell~~~~~gip~i~~~g~EADDv  131 (290)
T 1exn_A           58 SART-TIVLGDKGKS-----VFRLEHLPEYKGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDM  131 (290)
T ss_dssp             TEEE-EEEECCBSCC-----HHHHHHCTTTTHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHTTTSCEECCTTBCHHHH
T ss_pred             CCCe-EEEEEcCCCc-----hhhhhCcHHHHcCCCCCCccccccchhHHHhhHHHHHHHHHhhCCCCcEEEECCcCHHHH
Confidence            6888 9999997643     567777777888887666       3        36888999  999999999 599999


Q ss_pred             HHHHHHc----CCEEEEEcCCCccccccCCeE-EEeccccCcccCCcEEecHHHHHHhCCCCH-HHHHHHHhHcC--CCC
Q psy1206          69 CAAMVKA----GKVYATATEDMDALTFGSNIL-LRHMTFSEARKLPVQEFHLEKVLEGMELSH-EEFIDLCILLG--CDY  140 (531)
Q Consensus        69 ~A~L~r~----G~vd~ViSeDsDlL~fg~~~V-i~~l~~~~~~~~~v~~~~~~~i~~~lglt~-eqfid~~iL~G--~DY  140 (531)
                      ||+|+++    |..+.|+|+|+|+++|++++| +++.  .     .+..++.+.+.+.+|++| +||+|+++|+|  |||
T Consensus       132 iatLa~~~~~~G~~v~IvS~DkDl~Qlv~~~v~v~~~--~-----~~~~~~~~~v~ek~Gv~p~~q~iD~~~L~GD~sDn  204 (290)
T 1exn_A          132 AAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSF--T-----TRREYHLRDMYEHHNVDDVEQFISLKAIMGDLGDN  204 (290)
T ss_dssp             HHHHHHHHGGGSSCEEEECSCGGGGGGCCSSEEEEET--T-----TTEEECGGGHHHHHSSSSHHHHHHHHHHHCBGGGT
T ss_pred             HHHHHHHHHHCCCcEEEEeCCCChhhcCCCCEEEEEC--C-----CCEEEcHHHHHHHcCCCHHHHHHHHHHhcCCCcCC
Confidence            9999986    888889999999999999987 4432  1     357899999999999999 99999999999  999


Q ss_pred             CCCCCCccHHHHHHHHHHcCCHHHHHHHhhhc
Q psy1206         141 CDSIRGIGPKRAIELIKEHRSIEKILENIDTK  172 (531)
Q Consensus       141 ~pGIpGIG~ktA~kLI~~~~sle~il~~l~~~  172 (531)
                      +|||||||+|||.+||++|||+|+|+++++..
T Consensus       205 iPGVpGIG~KTA~kLL~~~gsle~i~~~~~~~  236 (290)
T 1exn_A          205 IRGVEGIGAKRGYNIIREFGNVLDIIDQLPLP  236 (290)
T ss_dssp             BCCCTTCCHHHHHHHHHHHCSHHHHHHHCSCS
T ss_pred             CCCCCcCCHhHHHHHHHHcCCHHHHHHHHHHh
Confidence            99999999999999999999999999999764

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

Probab=99.92  E-value=2.9e-25  Score=232.03  Aligned_cols=124  Identities=43%  Similarity=0.681  Sum_probs=120.5

Q ss_pred             cccceeeecccchHHHHHHHHhh-cCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHHHH
Q psy1206         315 RESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKR  393 (531)
Q Consensus       315 ~~gk~iAIDa~~~lyqfl~~ir~-~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~~r  393 (531)
                      ..|++||||||+|||||+.++++ +|.+|++++|++|+|+.|+|+|+++|+++||+|||||||++|++|.++.++|+.+|
T Consensus        33 l~gk~l~IDg~~~l~r~~~~~~~~~g~~l~~~~G~~T~al~gf~~r~~~ll~~~i~Pv~VFDg~~p~~K~~~~~~yK~~R  112 (363)
T 3ory_A           33 LHGKIIVIDGYNALYQFLAAIRQPDGTPLMDNNGRITSHLSGLFYRTINIVEAGIKPVYVFDGKPPELKAREIERRKAVK  112 (363)
T ss_dssp             GTTCEEEEEHHHHHHHHHHHCBCTTSCBCBCTTSCBCHHHHHHHHHHHHHHHTTCEEEEEECSSCGGGCHHHHHHHHHHH
T ss_pred             hCCCEEEEehHHHHHHHHHhhhccCCCccCCCCCCCccHHHHHHHHHHHHHHcCCCcEEEEcCCCccchHHHHHHHHHhh
Confidence            66999999999999999999997 78999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhc
Q psy1206         394 EDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARS  446 (531)
Q Consensus       394 ~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~  446 (531)
                      +++.+++.+++++|+.+       ++++|+++ +..++++|+..+++||++||
T Consensus       113 ~~~~e~l~~~~~~g~~~-------~a~~~~~~-~~~vt~~~~~~i~~lL~~~G  157 (363)
T 3ory_A          113 EEAAKKYEEAVQSGDLE-------LARRYAMM-SAKLTEEMVRDAKSLLDAMG  157 (363)
T ss_dssp             HHHHHHHHHHHHHTCHH-------HHHHHTCC-CCCCCHHHHHHHHHHHHHHT
T ss_pred             hhchHHHHHHHHcCCHH-------HHHHHHhc-cccCCHHHHHHHHHHHHHCC
Confidence            99999999999999987       99999998 99999999999999999998

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

Probab=99.92  E-value=4.9e-27  Score=267.75  Aligned_cols=152  Identities=24%  Similarity=0.280  Sum_probs=134.2

Q ss_pred             CccceeecccCCCCCcchhHHhHHHHHHhhccCCCH-------HHHHHHHhhcCCccccCC-CchhHHHHHHHH----cC
Q psy1206           9 DEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ-------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVK----AG   76 (531)
Q Consensus         9 d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~-------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r----~G   76 (531)
                      ++ .+++||.+.++|+++     ..+.||++|..++       +.++++|+++|||++++| |||||+||+|++    .|
T Consensus        60 ~~-~v~vFDg~~~tfR~~-----~~~~YKa~R~~~pe~l~~q~~~i~~~l~~~gi~~i~~pg~EADD~iatLa~~~~~~G  133 (832)
T 1bgx_T           60 DA-VIVVFDAKAPSFRHE-----AYGGYKAGRAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDVLASLAKKAEKEG  133 (832)
T ss_dssp             SC-CCCCCCCSSSCSSSG-----GGGTTTSCCCCCCTTSTTGGGTHHHHHHHTTCCCCCCSSSCHHHHHHHHHHHHHHHT
T ss_pred             Ce-EEEEEcCCCcccccc-----chHHHHhccccChHHHHHHHHHHHHHHHHCCCCEEEeCCccHHHHHHHHHHHHHHcC
Confidence            66 899999877777544     4567888887776       468999999999999999 599999999997    68


Q ss_pred             CEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcC--CCCCCCCCCccHHHHHH
Q psy1206          77 KVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLG--CDYCDSIRGIGPKRAIE  154 (531)
Q Consensus        77 ~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G--~DY~pGIpGIG~ktA~k  154 (531)
                      +.++|+|+|+|+++|++++|.+... .|      ..++.+.+.+.+|++|+||+|+++|+|  |||+|||||||+|||++
T Consensus       134 ~~v~IvS~DkDllql~~~~v~~~~~-~g------~~~~~~~v~~~~gv~p~q~id~~~L~GD~sDnipGVpGIG~KtA~k  206 (832)
T 1bgx_T          134 YEVRILTADKDLYQLLSDRIHVLHP-EG------YLITPAWLWEKYGLRPDQWADYRALTGDESDNLPGVKGIGEKTARK  206 (832)
T ss_dssp             CCBCCCCSSTTCCTTCCTTBCBCCS-SS------CCBCSTTHHHHTCCCGGGTTTTTTSSCCSSSCCCCCCCSSSCTTTT
T ss_pred             CeEEEEeCCCChhhcCcCCEEEEeC-CC------cEEcHHHHHHHHCcCHHHHHHHHHhcCCccccCCCCCCcCchHHHH
Confidence            8999999999999999999876554 32      458889999999999999999999999  99999999999999999


Q ss_pred             HHHHcCCHHHHHHHhhhcC
Q psy1206         155 LIKEHRSIEKILENIDTKK  173 (531)
Q Consensus       155 LI~~~~sle~il~~l~~~~  173 (531)
                      ||++|||+|+|++++++.+
T Consensus       207 Ll~~~gsle~i~~~~~~~~  225 (832)
T 1bgx_T          207 LLEEWGSLEALLKNLDRLK  225 (832)
T ss_dssp             TGGGTTSSCSSSSSCCCCC
T ss_pred             HHHHCCCHHHHHHHHHHhC
Confidence            9999999999999987643

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

Probab=99.92  E-value=3.2e-25  Score=230.00  Aligned_cols=135  Identities=55%  Similarity=0.850  Sum_probs=126.9

Q ss_pred             ccccccCCCcccc-------cceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecC
Q psy1206         304 ELVADVAPSSIRE-------SRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDG  376 (531)
Q Consensus       304 ~Lv~~~aP~~i~~-------gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG  376 (531)
                      +++.+++|.++++       |++||||||+||||++++++.+|.+|+|++|++|+|+.|+|+|+++|+++||+|+|||||
T Consensus         7 ~~l~~~~p~~~~~~~l~~l~gk~l~IDgs~~lyr~~~a~~~~~~~l~~~~G~~T~al~g~~~~~~~ll~~~i~P~~VFDg   86 (341)
T 3q8k_A            7 KLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDG   86 (341)
T ss_dssp             HHHHHHCGGGEEEEEGGGGTTCEEEEEHHHHHHHHHHHCEETTEECBCTTSCBCHHHHHHHHHHHHHHTTTCEEEEEECC
T ss_pred             HHHHHhhhhccccccHHHhCCCEEEEecHHHHHHHHHccccccCCCCCCCCCCchHHHHHHHHHHHHHHCCCCceEEEeC
Confidence            4677778876664       899999999999999999997788999999999999999999999999999999999999


Q ss_pred             CCCCcchHHHHHHHHHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhc
Q psy1206         377 KPPTLKSGELNKRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARS  446 (531)
Q Consensus       377 ~pp~lK~~~~~kR~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~  446 (531)
                      ++|++|.++..+|+++|+++.+++++|.++|+-+       ++.+|.++ +..++..++..++++|++||
T Consensus        87 ~~~~~r~~~~~~yk~~R~~~~~~~~~a~r~~~pe-------~l~~~~~~-~~~vt~~q~~~~~~lL~~~g  148 (341)
T 3q8k_A           87 KPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQ-------EVEKFTKR-LVKVTKQHNDECKHLLSLMG  148 (341)
T ss_dssp             CCCGGGHHHHHHHHHHHHHHHHHHHHHHTTCCHH-------HHHHHHHH-TCCCCHHHHHHHHHHHHHHT
T ss_pred             CCcccchhhhHHHHHHHhHhHHHHHHHHhcCCHH-------HHHHHHhh-cccCCHHHHHHHHHHHHHcC
Confidence            9999999999999999999999999999988765       99999998 99999999999999999998

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

Probab=99.89  E-value=1.9e-23  Score=217.49  Aligned_cols=120  Identities=21%  Similarity=0.279  Sum_probs=110.4

Q ss_pred             ccccceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHH-HHcCCeeEEeecCCCCCcchHHHHHHHHH
Q psy1206         314 IRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRL-VEHGLKPIYVFDGKPPTLKSGELNKRMEK  392 (531)
Q Consensus       314 i~~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~l-l~~gIkPVfVFDG~pp~lK~~~~~kR~~~  392 (531)
                      -..|++||||||+||||++.+++..     ++.|++|+||.|+|+|+++| +++||+|||||||+||++|+.|+.+|+++
T Consensus        21 ~l~Gk~vaIDas~wL~~~~~~~~~~-----l~~G~~t~~l~~~~~r~l~~L~~~gI~PvfVFDG~~~p~Kk~~~~~Rr~~   95 (352)
T 3qe9_Y           21 KYKGQVVAVDTYCWLHKGAIACAEK-----LAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRER   95 (352)
T ss_dssp             GGTTSEEEEETHHHHHHHHHHTHHH-----HHTTCCCCHHHHHHHHHHHHHHHTTCEEEEEECCSCCTTTHHHHHHHHHH
T ss_pred             HhCCcEEEEecHHHHHHhhhccchh-----hcCCCCcHHHHHHHHHHHHHHHHcCCEEEEEECCCCcHHHHHHHHHHHHH
Confidence            3569999999999999988766431     25799999999999999997 69999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhc
Q psy1206         393 REDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARS  446 (531)
Q Consensus       393 r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~  446 (531)
                      |+++.+++.++.++|+.+       ++++++++ +..+++.|++.++++|++||
T Consensus        96 r~~~~~~~~~~~~~g~~~-------~a~~~f~~-~~~vt~~~~~~i~~~L~~~g  141 (352)
T 3qe9_Y           96 RQANLLKGKQLLREGKVS-------EARECFTR-SINITHAMAHKVIKAARSQG  141 (352)
T ss_dssp             HHHHHHHHHHHTTSSCCH-------HHHHHHGG-GCCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhCCHH-------HHHHHHhh-cCCCCHHHHHHHHHHHHHcC
Confidence            999999999999999976       99999998 89999999999999999998

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

Probab=99.87  E-value=6.9e-23  Score=212.69  Aligned_cols=123  Identities=44%  Similarity=0.739  Sum_probs=71.8

Q ss_pred             ccceeeecccchHHHHHHHHhh-cCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHHHHH
Q psy1206         316 ESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKRE  394 (531)
Q Consensus       316 ~gk~iAIDa~~~lyqfl~~ir~-~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~~r~  394 (531)
                      .|++|||||++|||++++++++ +|.+++++.|.+|+|+.|+++|+++|+++||+|||||||++|.+|.++..+|+..|+
T Consensus        17 ~~~~l~IDg~~~l~r~~~a~~~~~g~~l~~~~G~~t~al~g~~~~~~~ll~~~i~Pv~vFDG~~~~~r~~~~~~yk~~R~   96 (346)
T 2izo_A           17 KGKRVSIDGYNALYQFLAAIRQPDGTPLMDSQGRVTSHLSGLFYRTINILEEGVIPIYVFDGKPPEQKSEELERRRKAKE   96 (346)
T ss_dssp             TTEEEEEEHHHHHHHHHHSCCCC---CCBCSSSCBCHHHHHHHHHHHHHHHHTEEEEEEECC------------------
T ss_pred             CCCEEEEEhHHHHHHHHHhccccccccccccCCCccHHHHHHHHHHHHHHHCCCcEEEEECCCCcchhhhHHHHHHHHHH
Confidence            3799999999999999999987 788999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhc
Q psy1206         395 DAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARS  446 (531)
Q Consensus       395 ~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~  446 (531)
                      ++.++|+++.+.|+.+       ++++|.++ +..+++.+++.++++|++||
T Consensus        97 ~~~~~l~~~~~~g~~~-------~a~~~~~~-~~~vt~~~~~~~~~lL~~~g  140 (346)
T 2izo_A           97 EAERKLERAKSEGKIE-------ELRKYSQA-ILRLSNIMVEESKKLLRAMG  140 (346)
T ss_dssp             ------------------------------------CHHHHHHHHHHHHHHT
T ss_pred             HhHHHHHHHHhcCCHH-------HHHHHHhh-ccCCCHHHHHHHHHHHHHCC
Confidence            9999999999999987       89999998 99999999999999999998

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

Probab=99.85  E-value=3.2e-22  Score=207.05  Aligned_cols=125  Identities=44%  Similarity=0.695  Sum_probs=119.0

Q ss_pred             ccccceeeecccchHHHHHHHHhh-cCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHHH
Q psy1206         314 IRESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEK  392 (531)
Q Consensus       314 i~~gk~iAIDa~~~lyqfl~~ir~-~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~~  392 (531)
                      -..|++||||||+|||++++++++ +|.+++++.|++|+|+.|+|+|+++|+++||+|||||||++|++|.++.++|+++
T Consensus        18 ~l~g~~l~ID~~~~l~r~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~l~~ll~~~i~pv~VFDG~~~~~K~~~~~~R~~~   97 (340)
T 1b43_A           18 NLYGKKIAIDALNAIYQFLSTIRQKDGTPLMDSKGRITSHLSGLFYRTINLMEAGIKPVYVFDGEPPEFKKKELEKRREA   97 (340)
T ss_dssp             GGTTCEEEEEHHHHHHHHHHHSBCTTSCBCBCTTSCBCHHHHHHHHHHHHHHHTTCEEEEEECCSCCCCSSCSSTTCCCC
T ss_pred             HhCCCEEEEEhHHHHHHHHHHhccccCCccccccCCchHHHHHHHHHHHHHHhCCCEEEEEecCCCchhhhhhHHHHHHH
Confidence            345999999999999999999986 7889999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhc
Q psy1206         393 REDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARS  446 (531)
Q Consensus       393 r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~  446 (531)
                      |+++.++|+++.++|+.+       .+.+|.++ +..+++.+++.++++|++||
T Consensus        98 r~~~~~~~~~~yk~g~~~-------~~~~~~~~-~~~vt~~~~~~~~~lL~~~g  143 (340)
T 1b43_A           98 REEAEEKWREALEKGEIE-------EARKYAQR-ATRVNEMLIEDAKKLLELMG  143 (340)
T ss_dssp             TTHHHHHHHHHHHHSCHH-------HHHHHHHT-SGGGTHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcCCHH-------HHHHHHHh-cCCCCHHHHHHHHHHHHHcC
Confidence            999999999999999876       88999988 88999999999999999998

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

Probab=99.85  E-value=3.7e-21  Score=198.84  Aligned_cols=125  Identities=35%  Similarity=0.618  Sum_probs=119.2

Q ss_pred             cccccceeeecccchHHHHHHHHhh-cCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHH
Q psy1206         313 SIRESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRME  391 (531)
Q Consensus       313 ~i~~gk~iAIDa~~~lyqfl~~ir~-~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~  391 (531)
                      ....|++|||||++|||++++++++ +|.+++++.|++|+|+.|+++|+++|+++||+|||||||.+|.+|.++..+|+.
T Consensus        17 ~~l~~~~l~IDg~~~l~r~~~a~~~~~~~~l~~~~G~~t~a~~g~~~~l~~ll~~~i~Pv~vFDg~~~~~R~~~~~~yk~   96 (336)
T 1rxw_A           17 EYFSGKKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSHLSGILYRVSNMVEVGIRPVFVFDGEPPEFKKAEIEERKK   96 (336)
T ss_dssp             GGGTTCEEEEEHHHHHHHHHHHSBCTTSCBCBCTTSCBCHHHHHHHHHHHHHHHHTCEEEEEECCSCCGGGHHHHHHHHH
T ss_pred             HHhCCCEEEEEhHHHHHHHHHhhccccCCcccccCCCccHHHHHHHHHHHHHHHCCCEEEEEEcCCCCcccccchHHHHH
Confidence            4456899999999999999999987 788999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhc
Q psy1206         392 KREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARS  446 (531)
Q Consensus       392 ~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~  446 (531)
                      +|+++.+.+.++.++|+ +       ++++|+++ +..+++.++..++++|++||
T Consensus        97 ~R~~~~~~~~~~~~~g~-~-------~l~~~~~~-~~~vt~~~~~~~~~lL~~~g  142 (336)
T 1rxw_A           97 RRAEAEEMWIAALQAGD-K-------DAKKYAQA-AGRVDEYIVDSAKTLLSYMG  142 (336)
T ss_dssp             HHHHHHHHHHHHHHHTC-T-------THHHHHHH-HCCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHhch-H-------HHHHHHHh-hccCCHHHHHHHHHHHHhCC
Confidence            99999999999999998 6       89999998 99999999999999999998

>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=99.84  E-value=1.7e-22  Score=212.20  Aligned_cols=124  Identities=52%  Similarity=0.794  Sum_probs=79.3

Q ss_pred             ccceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHHHHHH
Q psy1206         316 ESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKRED  395 (531)
Q Consensus       316 ~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~~r~~  395 (531)
                      .|++|||||++|||+++++++.+|.+|+++.|++|+|+.|+|+|+++|+++||+|||||||.+|.+|.++..+|+.+|++
T Consensus        26 ~g~~l~IDg~~~lyr~~~a~~~~~~~l~~~~G~~t~~l~g~~~~~~~ll~~~i~P~~VFDG~~~~~K~~~~~~yk~~R~~  105 (379)
T 1ul1_X           26 FGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAE  105 (379)
T ss_dssp             TTCCEEEEHHHHHHHHHSCC-------------CCHHHHHHHHHHHHHHHTTCCEEEEECCSCCSCCCCCCCCC------
T ss_pred             CCCEEEEEchHHHHHHHHhCCCcccccCcCCCCCchHHHHHHHHHHHHHHCCCCeEEEEeCCCcccccchHHHHHhhhhH
Confidence            48999999999999999999877889999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhcc
Q psy1206         396 AQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARST  447 (531)
Q Consensus       396 a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~  447 (531)
                      +.+++.+|.++|+.+       ++.+|.++ +..++..++..++++|++||=
T Consensus       106 ~~~~~~~~~~~g~~~-------~~~~~~~~-~~~vt~~~~~~~~~lL~~~Gi  149 (379)
T 1ul1_X          106 AEKQLQQAQAAGAEQ-------EVEKFTKR-LVKVTKQHNDECKHLLSLMGI  149 (379)
T ss_dssp             -------------------------------CCCCCCSCHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHcCCHH-------HHHHHHhh-ccCCCHHHHHHHHHHHHHcCC
Confidence            999999999999876       89999998 899999999999999999983

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

Probab=99.80  E-value=1.1e-21  Score=201.92  Aligned_cols=125  Identities=34%  Similarity=0.555  Sum_probs=117.8

Q ss_pred             ccccceeeecccchHHHHHHHHhh-cCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHHH
Q psy1206         314 IRESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEK  392 (531)
Q Consensus       314 i~~gk~iAIDa~~~lyqfl~~ir~-~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~~  392 (531)
                      -..|++|||||++|||++++++++ +|.+++++.|++|+|+.|+|+|+++|+.+||+|||||||.+|.+|.++..+|+.+
T Consensus        18 ~l~~~~l~IDg~~~l~r~~~a~~~~~~~~l~~~~G~~t~~l~g~~~~l~~ll~~~i~Pv~vFDG~~~~~k~~~~~~yk~~   97 (326)
T 1a76_A           18 DLKGKKVAIDGMNALYQFLTSIRLRDGSPLRNRKGEITSAYNGVFYKTIHLLENDITPIWVFDGEPPKLKEKTRKVRREM   97 (326)
T ss_dssp             GGTTCEEEEEHHHHHHHHHHHSBCTTSCBCBCTTSCBCHHHHHHHHHHHHHHHTTCEEEEEECCCSSCCCCSSCCSSCSS
T ss_pred             HhCCCEEEEEhHHHHHHHHHhhccccccccccccCCccHHHHHHHHHHHHHHHCCCeEEEEEeCcCcccchhhHHHHHHH
Confidence            346899999999999999999986 7889999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhc
Q psy1206         393 REDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARS  446 (531)
Q Consensus       393 r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~  446 (531)
                      |+++.+++.+|.+.|+.+       ++.+|.++ +..+++.+++.++++|++||
T Consensus        98 R~~~~~~l~~~~~~g~~~-------~a~~~~~~-~~~vt~~~~~~~~~lL~~~g  143 (326)
T 1a76_A           98 KEKAELKMKEAIKKEDFE-------EAAKYAKR-VSYLTPKMVENCKYLLSLMG  143 (326)
T ss_dssp             SCSSCSCCCCCCSHHHHH-------TTSTTGGG-GCSSCHHHHHHHHHHHHHHT
T ss_pred             HHhhHHHHHHHHHcCCHH-------HHHHHHHh-cCCCCHHHHHHHHHHHHHcC
Confidence            999999998888889876       88999888 89999999999999999998

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

Probab=99.78  E-value=5.4e-20  Score=186.63  Aligned_cols=125  Identities=14%  Similarity=-0.030  Sum_probs=103.1

Q ss_pred             CCCccceeecccCC-CCCcchhHHhHHHHHHhhccCCCH---------------HHHHHHHhhcCCccccCC-CchhHHH
Q psy1206           7 DPDEDGLVKYLCGD-KNFAEDRIRNGAKKLLKARSSTTQ---------------GRLDSFFTIRREEKRKAP-CEAEAQC   69 (531)
Q Consensus         7 ~~d~~~~~a~~~~~-~~f~~~~~R~~~~~~~k~~~~~t~---------------~~i~~lL~~~gIp~vvAP-yEADAq~   69 (531)
                      .|+| ++|+||.+. ++     +|++.++.||++|..+|               +.|+++|+++|||++..| |||||.|
T Consensus        62 ~P~~-iavaFD~~~~~t-----fR~elyp~YKanR~~~PeeL~~Q~~~l~~Qi~p~ike~l~a~gi~~l~~~G~EADDiI  135 (305)
T 3h7i_A           62 GYTK-IVLCIDNAKSGY-----WRRDFAYYYKKNRGKAREESTWDWEGYFESSHKVIDELKAYMPYIVMDIDKYEANDHI  135 (305)
T ss_dssp             TCCE-EEEECCCCTTCC-----HHHHHSTTTTHHHHHHHHHCSSCHHHHHHHHHHHHHHHHHHSSSEEECCTTCCHHHHH
T ss_pred             CCCE-EEEEecCCCCcc-----hHhhhCHHhccCCCCCCHHHHHHHHHhhhhhHHHHHHHHHHCCCCEEccCCccHHHHH
Confidence            8999 999999763 44     56667888899987776               258899999999999888 6999999


Q ss_pred             HHHHH----cCCEEEEEcCCCccccccC-CeE-EEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcC--CCCC
Q psy1206          70 AAMVK----AGKVYATATEDMDALTFGS-NIL-LRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLG--CDYC  141 (531)
Q Consensus        70 A~L~r----~G~vd~ViSeDsDlL~fg~-~~V-i~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G--~DY~  141 (531)
                      |+|++    .|.-..|+|+|+|++|+.. +.| +++. ..           .+.|.+++|+ |+|++|+.+|+|  +|++
T Consensus       136 gTLA~~a~~~g~~V~IvSgDKDl~QLv~~~~V~~~~~-~~-----------~~~V~ek~Gv-P~q~iD~~aL~GDsSDNI  202 (305)
T 3h7i_A          136 AVLVKKFSLEGHKILIISSDGDFTQLHKYPNVKQWSP-MH-----------KKWVKIKSGS-AEIDCMTKILKGDKKDNV  202 (305)
T ss_dssp             HHHHHHHHHTTCCEEEECSSCCCGGGGGSSSEEEEET-TT-----------TEEECSSCSC-HHHHHHHHHHHCBGGGTB
T ss_pred             HHHHHHHHHCCCcEEEEeCCCCccccccCCCeEEEec-CC-----------HHHHHHHhCC-HHHHhhHHheeCccccCC
Confidence            99986    4777789999999999998 565 3322 11           1335678998 999999999999  9999


Q ss_pred             CCCCCccHH
Q psy1206         142 DSIRGIGPK  150 (531)
Q Consensus       142 pGIpGIG~k  150 (531)
                      |||||||+.
T Consensus       203 PGVpGIG~~  211 (305)
T 3h7i_A          203 ASVKVRSDF  211 (305)
T ss_dssp             CCTTSCTTH
T ss_pred             CCCCcCCcc
Confidence            999999985

>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=98.87  E-value=1.1e-09  Score=111.21  Aligned_cols=81  Identities=10%  Similarity=0.134  Sum_probs=60.5

Q ss_pred             ccccccCCCcccccceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCee---EEeecCCCCC
Q psy1206         304 ELVADVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKP---IYVFDGKPPT  380 (531)
Q Consensus       304 ~Lv~~~aP~~i~~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkP---VfVFDG~pp~  380 (531)
                      +++..++++--..++.++||++++||++.+          +++|++  |++|+++++.+|++. ++|   |+||||++|.
T Consensus         6 ~~~~~~~~~~~~~~~lllIDg~~llyRa~~----------~~~G~p--av~Gf~~~l~~ll~~-~~p~~~vvvFD~~~~t   72 (290)
T 1exn_A            6 KFIEEEEAEMASRRNLMIVDGTNLGFRFKH----------NNSKKP--FASSYVSTIQSLAKS-YSARTTIVLGDKGKSV   72 (290)
T ss_dssp             -------------CEEEEEEHHHHHHHHHH----------HCSSSC--CHHHHHHHHHHHHHH-TTEEEEEEECCBSCCH
T ss_pred             HHhhhcccccccCCCEEEEECcHHHHHHHh----------CCCCch--HHHHHHHHHHHHHHH-cCCCeEEEEEcCCCch
Confidence            445444443222578999999999999987          356766  999999999999987 777   9999999999


Q ss_pred             cchHHHHHHHHHHHHHH
Q psy1206         381 LKSGELNKRMEKREDAQ  397 (531)
Q Consensus       381 lK~~~~~kR~~~r~~a~  397 (531)
                      ++.+...+++..|.++-
T Consensus        73 fR~~~~~~YKa~R~~~p   89 (290)
T 1exn_A           73 FRLEHLPEYKGNRDEKY   89 (290)
T ss_dssp             HHHHHCTTTTHHHHHHH
T ss_pred             hhhhCcHHHHcCCCCCC
Confidence            99888888888888765

>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=98.68  E-value=1.2e-09  Score=124.95  Aligned_cols=82  Identities=22%  Similarity=0.346  Sum_probs=72.1

Q ss_pred             CCcccccceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHc-CCeeEEeecCCCCCcchHHHHHH
Q psy1206         311 PSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEH-GLKPIYVFDGKPPTLKSGELNKR  389 (531)
Q Consensus       311 P~~i~~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~-gIkPVfVFDG~pp~lK~~~~~kR  389 (531)
                      |-.-..|+.|+||+++|||+++.+++    ++++++|.+|+|+.|+++++.+|++. +++|||||||++|.+|.++..++
T Consensus         6 ~l~~~~~~~llIDg~~~l~ra~~a~~----~l~~~~G~~t~av~gf~~~l~~ll~~~~~~~v~vFDg~~~tfR~~~~~~Y   81 (832)
T 1bgx_T            6 PLFEPKGRVLLVDGHHLAYRTFHALK----GLTTSRGEPVQAVYGFAKSLLKALKEDGDAVIVVFDAKAPSFRHEAYGGY   81 (832)
T ss_dssp             CCCCCCTTSCCCCCSTHHHHTTSSCT----TCBCSSSCBCSSSTTHHHHHHHGGGTCCSCCCCCCCCSSSCSSSGGGGTT
T ss_pred             CHHHhCCCEEEEEChHHHHHHHhcCC----ccccCCCcEehHHHHHHHHHHHHHHHcCCeEEEEEcCCCccccccchHHH
Confidence            44555689999999999999999884    58999999999999999999999877 69999999999999999988888


Q ss_pred             HHHHHHH
Q psy1206         390 MEKREDA  396 (531)
Q Consensus       390 ~~~r~~a  396 (531)
                      +..|.++
T Consensus        82 Ka~R~~~   88 (832)
T 1bgx_T           82 KAGRAPT   88 (832)
T ss_dssp             TSCCCCC
T ss_pred             HhccccC
Confidence            7776653

>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA BIND oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A

Probab=95.57  E-value=0.0081  Score=58.22  Aligned_cols=49  Identities=20%  Similarity=0.332  Sum_probs=32.9

Q ss_pred             HHHHHHhCCCCHHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHh
Q psy1206         115 LEKVLEGMELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENI  169 (531)
Q Consensus       115 ~~~i~~~lglt~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l  169 (531)
                      .++-...|||....-.++..++.+     |+|||||+|.+++..|+. +.+...+
T Consensus        69 RED~~~LyGF~~~~Er~lf~~L~s-----v~GIGpk~A~~Ils~~~~-~~l~~aI  117 (212)
T 2ztd_A           69 REDSMTLYGFPDGETRDLFLTLLS-----VSGVGPRLAMAALAVHDA-PALRQVL  117 (212)
T ss_dssp             ETTEEEEEEESSHHHHHHHHHHHT-----STTCCHHHHHHHHHHSCH-HHHHHHH
T ss_pred             ecCCcceEecCcHHHHHHHHHhcC-----cCCcCHHHHHHHHHhCCH-HHHHHHH
Confidence            344455678765555555554333     999999999999999875 4444433

>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} SCOP: a.60.2.1 b.40.4.2

Probab=95.50  E-value=0.011  Score=56.34  Aligned_cols=25  Identities=24%  Similarity=0.541  Sum_probs=21.3

Q ss_pred             CCCccHHHHHHHHHHcCCHHHHHHHh
Q psy1206         144 IRGIGPKRAIELIKEHRSIEKILENI  169 (531)
Q Consensus       144 IpGIG~ktA~kLI~~~~sle~il~~l  169 (531)
                      |||||||+|.+|++.|++ +.+.+.+
T Consensus        77 v~GIGpk~A~~iL~~f~~-~~l~~aI  101 (191)
T 1ixr_A           77 VSGVGPKVALALLSALPP-RLLARAL  101 (191)
T ss_dssp             SSCCCHHHHHHHHHHSCH-HHHHHHH
T ss_pred             CCCcCHHHHHHHHHhCCh-HHHHHHH
Confidence            999999999999999988 5555554

>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A*

Probab=95.08  E-value=0.013  Score=45.94  Aligned_cols=26  Identities=15%  Similarity=0.332  Sum_probs=23.6

Q ss_pred             CCCCCccHHHHHHHHHHcCCHHHHHH
Q psy1206         142 DSIRGIGPKRAIELIKEHRSIEKILE  167 (531)
Q Consensus       142 pGIpGIG~ktA~kLI~~~~sle~il~  167 (531)
                      ..|||||++++..|+++|||+++|.+
T Consensus         7 ~~IpGIG~kr~~~LL~~Fgs~~~i~~   32 (63)
T 2a1j_A            7 LKMPGVNAKNCRSLMHHVKNIAELAA   32 (63)
T ss_dssp             HTSTTCCHHHHHHHHHHCSSHHHHHT
T ss_pred             HcCCCCCHHHHHHHHHHcCCHHHHHH
Confidence            47999999999999999999988864

>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A

Probab=94.79  E-value=0.017  Score=55.47  Aligned_cols=25  Identities=20%  Similarity=0.587  Sum_probs=21.0

Q ss_pred             CCCccHHHHHHHHHHcCCHHHHHHHh
Q psy1206         144 IRGIGPKRAIELIKEHRSIEKILENI  169 (531)
Q Consensus       144 IpGIG~ktA~kLI~~~~sle~il~~l  169 (531)
                      |||||||+|.+|++.|++ +.+.+.+
T Consensus        78 V~GIGpk~A~~iL~~f~~-~~l~~aI  102 (203)
T 1cuk_A           78 TNGVGPKLALAILSGMSA-QQFVNAV  102 (203)
T ss_dssp             SSSCCHHHHHHHHHHSCH-HHHHHHH
T ss_pred             CCCcCHHHHHHHHhhCCh-HHHHHHH
Confidence            999999999999999988 5555544

>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A*

Probab=94.25  E-value=0.03  Score=46.58  Aligned_cols=26  Identities=15%  Similarity=0.345  Sum_probs=23.7

Q ss_pred             CCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206         143 SIRGIGPKRAIELIKEHRSIEKILEN  168 (531)
Q Consensus       143 GIpGIG~ktA~kLI~~~~sle~il~~  168 (531)
                      .|||||+|++..|+++|+|+++|.+.
T Consensus        22 ~IpGIG~kr~~~LL~~FgSl~~i~~A   47 (84)
T 1z00_B           22 KMPGVNAKNCRSLMHHVKNIAELAAL   47 (84)
T ss_dssp             TCSSCCHHHHHHHHHHSSCHHHHHHS
T ss_pred             hCCCCCHHHHHHHHHHcCCHHHHHHC
Confidence            69999999999999999999988653

>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A*

Probab=94.12  E-value=0.018  Score=45.10  Aligned_cols=28  Identities=14%  Similarity=0.351  Sum_probs=24.9

Q ss_pred             cccCCCCCchHHHHHHHHhhccHHHHHH
Q psy1206         243 YCDSIRGIGPKRAIELIKEHRSIEKILE  270 (531)
Q Consensus       243 Y~~~i~giG~k~A~kli~k~~s~~~vi~  270 (531)
                      -+.+|||||+|++.+|+++++|+++|..
T Consensus         5 ~L~~IpGIG~kr~~~LL~~Fgs~~~i~~   32 (63)
T 2a1j_A            5 FLLKMPGVNAKNCRSLMHHVKNIAELAA   32 (63)
T ss_dssp             HHHTSTTCCHHHHHHHHHHCSSHHHHHT
T ss_pred             HHHcCCCCCHHHHHHHHHHcCCHHHHHH
Confidence            3568999999999999999999988764

>2y35_A LD22664P; hydrolase-DNA complex, RNA degradation, exonuclease 5'-3', R interference; 3.20A {Drosophila melanogaster}

Probab=93.37  E-value=0.062  Score=63.42  Aligned_cols=102  Identities=18%  Similarity=0.227  Sum_probs=65.7

Q ss_pred             CCccccC----CCchhHHHHHHHHc---------CCEEEEEcCCCccccccC----Ce--EEEec-cccCc-c-----cC
Q psy1206          55 REEKRKA----PCEAEAQCAAMVKA---------GKVYATATEDMDALTFGS----NI--LLRHM-TFSEA-R-----KL  108 (531)
Q Consensus        55 gIp~vvA----PyEADAq~A~L~r~---------G~vd~ViSeDsDlL~fg~----~~--Vi~~l-~~~~~-~-----~~  108 (531)
                      ++.++.+    |+|+|.-|-...|.         ....+|++.|+|++++|=    ++  |+|.- .+... +     ..
T Consensus       162 ~~~Vi~S~~~vPGEGEhKIm~~IR~~~~~p~~~pn~~HciyG~DADLImL~L~the~~f~ilRe~v~f~~~~~~~~~~~~  241 (1140)
T 2y35_A          162 RCTVILSGQEAPGEGEHKIMDYIRYMKTQPDYDPNTRHCLYGLDAALIILGLCTHELHFVVLREEVKFGRNVKRTSVEET  241 (1140)
T ss_dssp             SSEEEEECSSSCSCHHHHHHHHHHHHHHSTTCCTTCCEEEECCSHHHHHHHHHTTCSSEEEEEESSCTTCCTTCCCGGGC
T ss_pred             ceEEEEeCCCCCCchHHHHHHHHHHHhhCCCCCCCCeEEEEccCHhHHHHHHccCCCcEEEeeccccccccccccccccc
Confidence            5777753    89999888776652         356889999999999882    33  45542 12110 0     11


Q ss_pred             CcEEecHHHHHHh------------CCCC----HHHHHHHHhHcCCCCCCCCCCccHHH-HHHHH
Q psy1206         109 PVQEFHLEKVLEG------------MELS----HEEFIDLCILLGCDYCDSIRGIGPKR-AIELI  156 (531)
Q Consensus       109 ~v~~~~~~~i~~~------------lglt----~eqfid~~iL~G~DY~pGIpGIG~kt-A~kLI  156 (531)
                      .+..+++..+.+.            ..++    .+.|+.+|.|+|.||+|++|++.+.. |+.++
T Consensus       242 ~f~~l~i~~lReyL~~ef~~~~~~~~~~d~eriidDfVfl~fl~GNDFLP~lp~l~I~~gai~~L  306 (1140)
T 2y35_A          242 RFFLLHLGLLREYLELEFDALRTDEHKLDIAQLIDDWVLMGFLVGNDFIPHLPCLHISSNALPLL  306 (1140)
T ss_dssp             EEEEEEHHHHHHHHHHHGGGGCCSSSCCCHHHHHHHHHHHHHHHCCTTSCCCTTCCTTTTHHHHH
T ss_pred             ceEEEEehHHHHHHHHHhhhhccccccccHHHHHHHHHHHHHHhCCccCCCCCccccCCCHHHHH
Confidence            3445665544332            1234    55778899999999999999987543 44443

>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5

Probab=93.15  E-value=0.063  Score=42.26  Aligned_cols=26  Identities=19%  Similarity=0.406  Sum_probs=23.4

Q ss_pred             CCCCCccHHHHHHHHHHcCCHHHHHH
Q psy1206         142 DSIRGIGPKRAIELIKEHRSIEKILE  167 (531)
Q Consensus       142 pGIpGIG~ktA~kLI~~~~sle~il~  167 (531)
                      .+|||||+++|.+|+..|+|++++..
T Consensus        17 ~~i~giG~~~a~~Ll~~fgs~~~l~~   42 (75)
T 1x2i_A           17 EGLPHVSATLARRLLKHFGSVERVFT   42 (75)
T ss_dssp             TTSTTCCHHHHHHHHHHHCSHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHcCCHHHHHh
Confidence            48999999999999999999888764

>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A*

Probab=93.14  E-value=0.036  Score=46.10  Aligned_cols=29  Identities=14%  Similarity=0.305  Sum_probs=25.5

Q ss_pred             cccCCCCCchHHHHHHHHhhccHHHHHHH
Q psy1206         243 YCDSIRGIGPKRAIELIKEHRSIEKILEN  271 (531)
Q Consensus       243 Y~~~i~giG~k~A~kli~k~~s~~~vi~~  271 (531)
                      -+..|||||+|++.+|+++++|++.|..+
T Consensus        19 ~L~~IpGIG~kr~~~LL~~FgSl~~i~~A   47 (84)
T 1z00_B           19 FLLKMPGVNAKNCRSLMHHVKNIAELAAL   47 (84)
T ss_dssp             HHHTCSSCCHHHHHHHHHHSSCHHHHHHS
T ss_pred             HHHhCCCCCHHHHHHHHHHcCCHHHHHHC
Confidence            35689999999999999999999887654

>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli}

Probab=92.80  E-value=0.16  Score=56.10  Aligned_cols=93  Identities=16%  Similarity=0.245  Sum_probs=60.0

Q ss_pred             CCCCccHHHHHHHHHHc-----CCHHHHHHHhhhcCCCCCCCCcHHHHHHHhcCCCcCCCCCcccccccccccccccccc
Q psy1206         143 SIRGIGPKRAIELIKEH-----RSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFIDLCILLGCDYCDSI  217 (531)
Q Consensus       143 GIpGIG~ktA~kLI~~~-----~sle~il~~l~~~~~~ip~~f~~~~A~~~f~~p~V~d~~~~~~v~Ls~~~~~d~cesl  217 (531)
                      .++|+|.|+|.+|+...     .++..++-.|.     |                                         
T Consensus       484 ~l~g~geKsa~nL~~aIe~sk~~~l~r~l~aLG-----I-----------------------------------------  517 (586)
T 4glx_A          484 GLERMGPKSAQNVVNALEKAKETTFARFLYALG-----I-----------------------------------------  517 (586)
T ss_dssp             TSTTCCHHHHHHHHHHHHHHTBCCHHHHHHHTT-----C-----------------------------------------
T ss_pred             cccCccHHHHHHHHHHHHHHcCCCHHHHHHHcC-----C-----------------------------------------
Confidence            89999999999999763     45666665552     1                                         


Q ss_pred             cCCChhhhHhHHhhhhhhhhhccC--ccccCCCCCchHHHHHHHHhhccHH--HHHHHHhhCCCCCCC
Q psy1206         218 RGIGPKRAIELLYSFIDLCILLGC--DYCDSIRGIGPKRAIELIKEHRSIE--KILENIDTKKYTVPE  281 (531)
Q Consensus       218 ~~~Gp~~~~el~e~F~~~CiLsGC--DY~~~i~giG~k~A~kli~k~~s~~--~vi~~l~~~~~~vP~  281 (531)
                      ++.|+..+..|...|.+|=-|..-  +-+..|+|||+++|..++.=+...+  .++..|...|+..|+
T Consensus       518 ~~vG~~~a~~La~~f~sl~~l~~a~~e~l~~i~giG~~~A~si~~ff~~~~n~~~i~~L~~~Gv~~~~  585 (586)
T 4glx_A          518 REVGEATAAGLAAYFGTLEALEAASIEELQKVPDVGIVVASHVHNFFAEESNRNVISELLAEGVHWPA  585 (586)
T ss_dssp             TTCCHHHHHHHHHHHCSHHHHHHCCHHHHTTSTTCCHHHHHHHHHHHHSHHHHHHHHHHHHTTCBCCC
T ss_pred             CchhHHHHHHHHHHcCCHHHHHccCHHHHhcCCCccHHHHHHHHHHHcCHHHHHHHHHHHHcCCCCCC
Confidence            122333332223333333222221  2245899999999999999887754  688999888876653

>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3

Probab=92.80  E-value=0.043  Score=44.24  Aligned_cols=28  Identities=29%  Similarity=0.529  Sum_probs=24.3

Q ss_pred             CCCCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206         141 CDSIRGIGPKRAIELIKEHRSIEKILEN  168 (531)
Q Consensus       141 ~pGIpGIG~ktA~kLI~~~~sle~il~~  168 (531)
                      +.+|||||+++|.+|+..|++++++.+.
T Consensus        26 L~~I~gIG~~~A~~Ll~~fgsl~~l~~a   53 (78)
T 1kft_A           26 LETIEGVGPKRRQMLLKYMGGLQGLRNA   53 (78)
T ss_dssp             GGGCTTCSSSHHHHHHHHHSCHHHHHHC
T ss_pred             HhcCCCCCHHHHHHHHHHcCCHHHHHHC
Confidence            3489999999999999999998887643

>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5

Probab=92.65  E-value=0.077  Score=43.75  Aligned_cols=26  Identities=12%  Similarity=0.397  Sum_probs=23.4

Q ss_pred             CCCCCccHHHHHHHHHHcCCHHHHHH
Q psy1206         142 DSIRGIGPKRAIELIKEHRSIEKILE  167 (531)
Q Consensus       142 pGIpGIG~ktA~kLI~~~~sle~il~  167 (531)
                      .+|||||+++|.+|+..|+|++++..
T Consensus        22 ~~IpgIG~~~A~~Ll~~fgsl~~l~~   47 (89)
T 1z00_A           22 TTVKSVNKTDSQTLLTTFGSLEQLIA   47 (89)
T ss_dssp             TTSSSCCHHHHHHHHHHTCBHHHHHH
T ss_pred             HcCCCCCHHHHHHHHHHCCCHHHHHh
Confidence            47999999999999999999888764

>3fqd_A Protein DHP1, 5'-3' exoribonuclease 2; protein-protein complex, exonuclease, hydrolase, mRNA proces nuclease, nucleus, rRNA processing, transcription; 2.20A {Schizosaccharomyces pombe}

Probab=92.47  E-value=0.18  Score=57.68  Aligned_cols=95  Identities=15%  Similarity=0.229  Sum_probs=63.0

Q ss_pred             CCccccC----CCchhHHHHHHHHc---------CCEEEEEcCCCccccccC----C--eEEEec-cccCc---------
Q psy1206          55 REEKRKA----PCEAEAQCAAMVKA---------GKVYATATEDMDALTFGS----N--ILLRHM-TFSEA---------  105 (531)
Q Consensus        55 gIp~vvA----PyEADAq~A~L~r~---------G~vd~ViSeDsDlL~fg~----~--~Vi~~l-~~~~~---------  105 (531)
                      ++.+|.+    |+|+|.-|....|.         ....+|.+.|+|++++|-    +  .|+|.- .+.++         
T Consensus       195 ~~~VIlSd~~vPGEGEHKIm~fIR~~r~~p~ydpN~~HcIyGlDADLImL~LatHep~f~ILRE~v~~~~~q~~~~~~~~  274 (899)
T 3fqd_A          195 NVRFILSDASVPGEGEHKIMEFIRSQRVKPEYDPNTHHVVYGLDADLIMLGLATHEPHFRVLREDVFFQQGSTKKTKEER  274 (899)
T ss_dssp             TCEEEEECTTSCSCHHHHHHHHHHHHHTSTTSCTTCCEEEECCCTTHHHHHHHTTCSSEEEEEECCC---------CTTT
T ss_pred             cceEEEeCCCCCCccHHHHHHHHHHHhcCCCCCCCCeEEEEccCccHhHHhhhccCCceEEEeeecccCcCccccchhhh
Confidence            5677753    89999998877653         356899999999999983    3  346532 11100         


Q ss_pred             ----------------ccCCcEEecHHHHHHh----C-------CCC----HHHHHHHHhHcCCCCCCCCCCccH
Q psy1206         106 ----------------RKLPVQEFHLEKVLEG----M-------ELS----HEEFIDLCILLGCDYCDSIRGIGP  149 (531)
Q Consensus       106 ----------------~~~~v~~~~~~~i~~~----l-------glt----~eqfid~~iL~G~DY~pGIpGIG~  149 (531)
                                      ...++..+++.-+++-    +       .++    .+.||.+|.|+|.||+|++|.+.+
T Consensus       275 ~~~~k~~~~~~~~~~~~~~~f~~l~i~iLREYL~~E~~~~~~~f~~d~ERiIDDfVfmcFfvGNDFLPhlP~l~I  349 (899)
T 3fqd_A          275 LGIKRLDDVSETNKVPVKKPFIWLNVSILREYLEVELYVPNLPFPFDLERAIDDWVFFIFFVGNDFLPHLPSLDI  349 (899)
T ss_dssp             TTCCBTTC----------CCEEEEEHHHHHHHHHHHHCCTTCSSCCCHHHHHHHHHHHGGGGCCSSSCCCTTCCG
T ss_pred             ccccccccccccccccccCceEEEeHHHHHHHHHHHhcccCCCCCchhhhhhhhhhhhhHhhCcccCCCCCccCc
Confidence                            0023456666655442    2       233    458888999999999999998765

>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5

Probab=91.67  E-value=0.11  Score=43.12  Aligned_cols=25  Identities=12%  Similarity=0.413  Sum_probs=22.4

Q ss_pred             CCCCCccHHHHHHHHHHcCCHHHHH
Q psy1206         142 DSIRGIGPKRAIELIKEHRSIEKIL  166 (531)
Q Consensus       142 pGIpGIG~ktA~kLI~~~~sle~il  166 (531)
                      .+|||||+++|.+|+..|+++++++
T Consensus        35 ~~IpgIG~~~A~~Ll~~fgs~~~l~   59 (91)
T 2a1j_B           35 TTVKSVNKTDSQTLLTTFGSLEQLI   59 (91)
T ss_dssp             TTSTTCCHHHHHHHHHHHSSHHHHH
T ss_pred             HcCCCCCHHHHHHHHHHCCCHHHHH
Confidence            4789999999999999999987765

>3b0x_A DNA polymerase beta family (X family); structural genomics, riken structural genomics/proteomics in RSGI, polxc, PHP, DRP lyase; HET: DNA DGT; 1.36A {Thermus thermophilus} PDB: 3au2_A* 3au6_A* 3auo_A* 3b0y_A*

Probab=91.17  E-value=0.24  Score=54.28  Aligned_cols=27  Identities=33%  Similarity=0.528  Sum_probs=23.1

Q ss_pred             CCCCccHHHHHHHHHH--cCCHHHHHHHh
Q psy1206         143 SIRGIGPKRAIELIKE--HRSIEKILENI  169 (531)
Q Consensus       143 GIpGIG~ktA~kLI~~--~~sle~il~~l  169 (531)
                      +|+|||||+|.+++..  ..|++++...+
T Consensus        97 ~v~GvGpk~A~~~~~~lg~~~~~~l~~a~  125 (575)
T 3b0x_A           97 EVPGVGPKTARLLYEGLGIDSLEKLKAAL  125 (575)
T ss_dssp             TSTTTCHHHHHHHHHTSCCCSHHHHHHHH
T ss_pred             cCCCcCHHHHHHHHHhcCCCCHHHHHHHH
Confidence            6899999999999996  57888887765

>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans}

Probab=91.08  E-value=0.23  Score=54.49  Aligned_cols=28  Identities=32%  Similarity=0.509  Sum_probs=23.9

Q ss_pred             CCCCCccHHHHHHHHHH-cCCHHHHHHHh
Q psy1206         142 DSIRGIGPKRAIELIKE-HRSIEKILENI  169 (531)
Q Consensus       142 pGIpGIG~ktA~kLI~~-~~sle~il~~l  169 (531)
                      -+|||||+|+|.+|+.. +.|++++.+.+
T Consensus       100 ~~v~GVGpk~A~~i~~~G~~s~edL~~a~  128 (578)
T 2w9m_A          100 LGVRGLGPKKIRSLWLAGIDSLERLREAA  128 (578)
T ss_dssp             TTSTTCCHHHHHHHHHTTCCSHHHHHHHH
T ss_pred             hCCCCcCHHHHHHHHHcCCCCHHHHHHHH
Confidence            47999999999999986 67888887765

>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli}

Probab=89.89  E-value=0.36  Score=54.08  Aligned_cols=60  Identities=13%  Similarity=0.092  Sum_probs=36.1

Q ss_pred             CCChhhhHhHHhhhhhhhhhc--cCccccCCCCCchHHHHHHHHhhccHH--HHHHHHhhCCCC
Q psy1206         219 GIGPKRAIELLYSFIDLCILL--GCDYCDSIRGIGPKRAIELIKEHRSIE--KILENIDTKKYT  278 (531)
Q Consensus       219 ~~Gp~~~~el~e~F~~~CiLs--GCDY~~~i~giG~k~A~kli~k~~s~~--~vi~~l~~~~~~  278 (531)
                      +.|+..+..|.+.|-.+--|.  .-+-+..++|||+++|..++.-+...+  .+++.|...|+.
T Consensus       519 ~VG~~~Ak~La~~Fgsl~~l~~As~eeL~~i~GIG~~~A~sI~~ff~~~~~~~~i~~L~~~gv~  582 (671)
T 2owo_A          519 EVGEATAAGLAAYFGTLEALEAASIEELQKVPDVGIVVASHVHNFFAEESNRNVISELLAEGVH  582 (671)
T ss_dssp             TCCHHHHHHHHHHHCSHHHHHTCCHHHHTTSTTCCHHHHHHHHHHHTCHHHHHHHHHHHHHTCB
T ss_pred             CccHHHHHHHHHHcCCHHHHHhCCHHHHhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHHcCCc
Confidence            444444444444443332221  113356899999999999998877643  577777655554

>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis}

Probab=89.86  E-value=0.06  Score=59.66  Aligned_cols=36  Identities=14%  Similarity=0.207  Sum_probs=0.0

Q ss_pred             ccCCCCCchHHHHHHHHhhccHH--HHHHHHhhCCCCC
Q psy1206         244 CDSIRGIGPKRAIELIKEHRSIE--KILENIDTKKYTV  279 (531)
Q Consensus       244 ~~~i~giG~k~A~kli~k~~s~~--~vi~~l~~~~~~v  279 (531)
                      +..|+|||+++|-.++.-+...+  .+++.|...|+.+
T Consensus       563 L~~I~GIG~~~A~sI~~ff~~~~n~~~i~~L~~~Gv~~  600 (615)
T 3sgi_A          563 LAAVEGVGPTIAAAVTEWFAVDWHREIVDKWRAAGVRM  600 (615)
T ss_dssp             --------------------------------------
T ss_pred             HhhCCCCCHHHHHHHHHHHcCHHHHHHHHHHHHcCCCc
Confidence            45789999999999887777654  4777776555443

>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3

Probab=89.73  E-value=0.16  Score=40.82  Aligned_cols=28  Identities=29%  Similarity=0.529  Sum_probs=24.4

Q ss_pred             ccCCCCCchHHHHHHHHhhccHHHHHHH
Q psy1206         244 CDSIRGIGPKRAIELIKEHRSIEKILEN  271 (531)
Q Consensus       244 ~~~i~giG~k~A~kli~k~~s~~~vi~~  271 (531)
                      +..|||||+++|.+|+..+++++.+..+
T Consensus        26 L~~I~gIG~~~A~~Ll~~fgsl~~l~~a   53 (78)
T 1kft_A           26 LETIEGVGPKRRQMLLKYMGGLQGLRNA   53 (78)
T ss_dssp             GGGCTTCSSSHHHHHHHHHSCHHHHHHC
T ss_pred             HhcCCCCCHHHHHHHHHHcCCHHHHHHC
Confidence            4579999999999999999999887654

>3pie_A 5'->3' exoribonuclease (XRN1); beta berrel, tudor domain, chromo domain, mRNA turnover, RRN processing, RNA binding, DNA binding; 2.90A {Kluyveromyces lactis} PDB: 3pif_A

Probab=89.56  E-value=0.27  Score=57.85  Aligned_cols=96  Identities=21%  Similarity=0.269  Sum_probs=62.7

Q ss_pred             CCccccC----CCchhHHHHHHHHc---------CCEEEEEcCCCccccccC----Ce--EEEec-cccCcc-------c
Q psy1206          55 REEKRKA----PCEAEAQCAAMVKA---------GKVYATATEDMDALTFGS----NI--LLRHM-TFSEAR-------K  107 (531)
Q Consensus        55 gIp~vvA----PyEADAq~A~L~r~---------G~vd~ViSeDsDlL~fg~----~~--Vi~~l-~~~~~~-------~  107 (531)
                      ++.++.+    |+|+|.-|....|.         ....+|.+.|+|++++|-    ++  |+|.- .+....       .
T Consensus       163 ~~~vi~S~~~vPGEGEhKIm~~IR~~r~~p~y~pn~~H~IyG~DADLImL~L~thep~f~iLRe~v~f~~~~~~~~~~~~  242 (1155)
T 3pie_A          163 NVKVIFSGHEVPGEGQHKIMDYIRAIRAQEDYNPNTRHCIYGLDADLIILGLSTHDHHFCLLREEVTFGKRSSSVKTLET  242 (1155)
T ss_pred             ccEEEEeCCCCCCccHHHHHHHHHHhccCCCCCCCCeEEEeccChhHHHhhhccCCCcEEEEeeccccCccccccccccc
Confidence            4666643    89999988877653         246899999999999983    22  45542 121110       1


Q ss_pred             CCcEEecHHHHHHhC-------------CCC----HHHHHHHHhHcCCCCCCCCCCccHH
Q psy1206         108 LPVQEFHLEKVLEGM-------------ELS----HEEFIDLCILLGCDYCDSIRGIGPK  150 (531)
Q Consensus       108 ~~v~~~~~~~i~~~l-------------glt----~eqfid~~iL~G~DY~pGIpGIG~k  150 (531)
                      .++..+++.-+++.+             .++    .+.|+.+|.|+|.||+|++|.+.+.
T Consensus       243 ~~f~~l~i~~LREyL~~ef~~~~~~~~~~~d~ERiiDDfVflcf~vGNDFLPhlP~l~I~  302 (1155)
T 3pie_A          243 QNFFLLHLSILREYLALEFEEITDSVQFEYDFERVLDDFIFVLFTIGNDFLPNLPDLHLK  302 (1155)
T ss_pred             CCeEEEEHHHHHHHHHHHHHhhccccCCCccHhHhhcceeeehhhhCcccCCCCCccCcC
Confidence            234556665443321             233    3467778999999999999998654

>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A

Probab=89.39  E-value=0.17  Score=49.31  Aligned_cols=26  Identities=42%  Similarity=0.690  Sum_probs=23.9

Q ss_pred             CCCCCccHHHHHHHHHHcCCHHHHHH
Q psy1206         142 DSIRGIGPKRAIELIKEHRSIEKILE  167 (531)
Q Consensus       142 pGIpGIG~ktA~kLI~~~~sle~il~  167 (531)
                      .||||||+++|.+|+++|+|++++.+
T Consensus       171 dgIpGIG~k~ak~Ll~~FgSl~~i~~  196 (220)
T 2nrt_A          171 DNVPGIGPIRKKKLIEHFGSLENIRS  196 (220)
T ss_dssp             TTSTTCCHHHHHHHHHHHCSHHHHHT
T ss_pred             cCCCCcCHHHHHHHHHHcCCHHHHHh
Confidence            68999999999999999999988754

>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A*

Probab=88.24  E-value=0.4  Score=53.66  Aligned_cols=35  Identities=6%  Similarity=0.172  Sum_probs=26.9

Q ss_pred             ccCCCCCchHHHHHHHHhhccHH--HHHHHHhhCCCC
Q psy1206         244 CDSIRGIGPKRAIELIKEHRSIE--KILENIDTKKYT  278 (531)
Q Consensus       244 ~~~i~giG~k~A~kli~k~~s~~--~vi~~l~~~~~~  278 (531)
                      +..++|||+++|-.++.-+...+  .+++.|...|+.
T Consensus       541 L~~I~GIG~~~A~sI~~ff~~~~~~~~i~~L~~~gv~  577 (667)
T 1dgs_A          541 LIEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVS  577 (667)
T ss_dssp             HHTSTTCCHHHHHHHHHHHHCHHHHHHHHHHHHTTCC
T ss_pred             HHhccCcCHHHHHHHHHHHhhHHHHHHHHHHHHcCCc
Confidence            45799999999999998887653  577777655554

>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5

Probab=87.70  E-value=0.3  Score=40.12  Aligned_cols=28  Identities=11%  Similarity=0.348  Sum_probs=24.5

Q ss_pred             ccCCCCCchHHHHHHHHhhccHHHHHHH
Q psy1206         244 CDSIRGIGPKRAIELIKEHRSIEKILEN  271 (531)
Q Consensus       244 ~~~i~giG~k~A~kli~k~~s~~~vi~~  271 (531)
                      +.+|||||+++|.+|+..+++++.++..
T Consensus        21 L~~IpgIG~~~A~~Ll~~fgsl~~l~~a   48 (89)
T 1z00_A           21 LTTVKSVNKTDSQTLLTTFGSLEQLIAA   48 (89)
T ss_dssp             HTTSSSCCHHHHHHHHHHTCBHHHHHHC
T ss_pred             HHcCCCCCHHHHHHHHHHCCCHHHHHhC
Confidence            4579999999999999999999887654

>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5

Probab=87.56  E-value=0.32  Score=38.05  Aligned_cols=28  Identities=18%  Similarity=0.374  Sum_probs=24.3

Q ss_pred             ccCCCCCchHHHHHHHHhhccHHHHHHH
Q psy1206         244 CDSIRGIGPKRAIELIKEHRSIEKILEN  271 (531)
Q Consensus       244 ~~~i~giG~k~A~kli~k~~s~~~vi~~  271 (531)
                      +.+|||||+++|.+|+..+++++.++.+
T Consensus        16 L~~i~giG~~~a~~Ll~~fgs~~~l~~a   43 (75)
T 1x2i_A           16 VEGLPHVSATLARRLLKHFGSVERVFTA   43 (75)
T ss_dssp             HTTSTTCCHHHHHHHHHHHCSHHHHHHC
T ss_pred             HcCCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence            3579999999999999999999887654

>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5

Probab=85.02  E-value=0.54  Score=38.84  Aligned_cols=27  Identities=11%  Similarity=0.364  Sum_probs=23.7

Q ss_pred             ccCCCCCchHHHHHHHHhhccHHHHHH
Q psy1206         244 CDSIRGIGPKRAIELIKEHRSIEKILE  270 (531)
Q Consensus       244 ~~~i~giG~k~A~kli~k~~s~~~vi~  270 (531)
                      +..|||||+++|.+|+..+++++.++.
T Consensus        34 L~~IpgIG~~~A~~Ll~~fgs~~~l~~   60 (91)
T 2a1j_B           34 LTTVKSVNKTDSQTLLTTFGSLEQLIA   60 (91)
T ss_dssp             HTTSTTCCHHHHHHHHHHHSSHHHHHS
T ss_pred             HHcCCCCCHHHHHHHHHHCCCHHHHHh
Confidence            457999999999999999999987764

>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus}

Probab=84.29  E-value=0.2  Score=48.99  Aligned_cols=28  Identities=36%  Similarity=0.539  Sum_probs=0.0

Q ss_pred             CCCCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206         141 CDSIRGIGPKRAIELIKEHRSIEKILEN  168 (531)
Q Consensus       141 ~pGIpGIG~ktA~kLI~~~~sle~il~~  168 (531)
                      +.+|||||+++|.+|++.|+|++++.+.
T Consensus       175 L~~IpGIG~k~ak~Ll~~FGSl~~i~~A  202 (226)
T 3c65_A          175 LDDIPGVGEKRKKALLNYFGSVKKMKEA  202 (226)
T ss_dssp             ----------------------------
T ss_pred             ccccCCCCHHHHHHHHHHhCCHHHHHhC
Confidence            3689999999999999999999887543

>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A

Probab=83.87  E-value=0.42  Score=45.64  Aligned_cols=25  Identities=28%  Similarity=0.567  Sum_probs=22.5

Q ss_pred             CCCCCccHHHHHHHHHHcCCHHHHH
Q psy1206         142 DSIRGIGPKRAIELIKEHRSIEKIL  166 (531)
Q Consensus       142 pGIpGIG~ktA~kLI~~~~sle~il  166 (531)
                      .+|||||+++|..|+..|+|+++++
T Consensus       165 ~~i~gVg~~~a~~Ll~~fgs~~~l~  189 (219)
T 2bgw_A          165 QSFPGIGRRTAERILERFGSLERFF  189 (219)
T ss_dssp             HTSTTCCHHHHHHHHHHHSSHHHHT
T ss_pred             hcCCCCCHHHHHHHHHHcCCHHHHH
Confidence            3799999999999999999987764

>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A*

Probab=80.89  E-value=0.81  Score=51.20  Aligned_cols=24  Identities=21%  Similarity=0.508  Sum_probs=22.2

Q ss_pred             CCCCCchHHHHHHHHhhccHHHHH
Q psy1206         246 SIRGIGPKRAIELIKEHRSIEKIL  269 (531)
Q Consensus       246 ~i~giG~k~A~kli~k~~s~~~vi  269 (531)
                      +|||||.++|.+|.+.|+|++++.
T Consensus       511 GI~~VG~~~Ak~La~~Fgsl~~l~  534 (667)
T 1dgs_A          511 GLPGVGEVLARNLARRFGTMDRLL  534 (667)
T ss_dssp             TCSSCCHHHHHHHHHTTSBHHHHT
T ss_pred             ccCCccHHHHHHHHHHcCCHHHHH
Confidence            699999999999999999998864

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	531
d1ul1x1	140	a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nu	2e-25
d1ul1x1	140	a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nu	9e-23
d1ul1x1	140	a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nu	6e-14
d1ul1x1	140	a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nu	2e-13
d1ul1x2	216	c.120.1.2 (X:2-217) Flap endonuclease-1 (Fen-1 nuc	3e-20
d1ul1x2	216	c.120.1.2 (X:2-217) Flap endonuclease-1 (Fen-1 nuc	2e-17
d1a77a2	207	c.120.1.2 (A:2-208) Flap endonuclease-1 (Fen-1 nuc	5e-20
d1a77a2	207	c.120.1.2 (A:2-208) Flap endonuclease-1 (Fen-1 nuc	1e-12
d1b43a1	120	a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nu	1e-19
d1b43a1	120	a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nu	7e-17
d1b43a1	120	a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nu	9e-16
d1b43a1	120	a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nu	2e-15
d1rxwa1	105	a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nu	2e-19
d1rxwa1	105	a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nu	5e-17
d1rxwa1	105	a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nu	2e-06
d1rxwa1	105	a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nu	3e-06
d1a77a1	108	a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nu	1e-18
d1a77a1	108	a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nu	3e-16
d1a77a1	108	a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nu	4e-09
d1a77a1	108	a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nu	5e-09
d1rxwa2	217	c.120.1.2 (A:3-219) Flap endonuclease-1 (Fen-1 nuc	1e-17
d1rxwa2	217	c.120.1.2 (A:3-219) Flap endonuclease-1 (Fen-1 nuc	3e-17
d1b43a2	219	c.120.1.2 (A:1-219) Flap endonuclease-1 (Fen-1 nuc	2e-17
d1b43a2	219	c.120.1.2 (A:1-219) Flap endonuclease-1 (Fen-1 nuc	5e-17
d1xo1a1	105	a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacterioph	1e-06
d1xo1a1	105	a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacterioph	4e-06
d1xo1a1	105	a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacterioph	2e-04
d1kfta_	56	a.60.2.3 (A:) Excinuclease UvrC C-terminal domain	1e-05
d1kfta_	56	a.60.2.3 (A:) Excinuclease UvrC C-terminal domain	0.001
d1kfta_	56	a.60.2.3 (A:) Excinuclease UvrC C-terminal domain	0.001
d2bgwa1	70	a.60.2.5 (A:160-229) DNA repair endonuclease XPF {	7e-05
d1n8yc3	157	g.3.9.1 (C:166-322) Protooncoprotein Her2 extracel	2e-04
d1n8yc3	157	g.3.9.1 (C:166-322) Protooncoprotein Her2 extracel	7e-04
d1n8yc3	157	g.3.9.1 (C:166-322) Protooncoprotein Her2 extracel	0.001
d1n8yc3	157	g.3.9.1 (C:166-322) Protooncoprotein Her2 extracel	0.004
d1x2ia1	68	a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF201	2e-04
d1ky8a_	499	c.82.1.1 (A:) Non-phosphorylating glyceraldehyde-3	0.004

>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]} Length = 140

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 99.3 bits (247), Expect = 2e-25
 Identities = 50/79 (63%), Positives = 66/79 (83%)

Query: 124 LSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYK 183
           L+ E+F+DLCILLG DYC+SIRGIGPKRA++LI++H+SIE+I+  +D  KY VPE WL+K
Sbjct: 1   LNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHK 60

Query: 184 EARELFRHPEVADPETIEF 202
           EA +LF  PEV DPE++E 
Sbjct: 61  EAHQLFLEPEVLDPESVEL 79

>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]} Length = 140

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 92.0 bits (228), Expect = 9e-23
 Identities = 48/75 (64%), Positives = 63/75 (84%)

Query: 232 FIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAREL 291
           F+DLCILLG DYC+SIRGIGPKRA++LI++H+SIE+I+  +D  KY VPE WL+KEA +L
Sbjct: 6   FVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQL 65

Query: 292 FRHPEIADPETIELV 306
           F  PE+ DPE++EL 
Sbjct: 66  FLEPEVLDPESVELK 80

>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]} Length = 140

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.6 bits (162), Expect = 6e-14
 Identities = 32/79 (40%), Positives = 49/79 (62%)

Query: 390 MEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTT 449
            E  +   +      E  +LKWS+P+E+ L+K++CG+K F+E+RIR+G K+L K+R  +T
Sbjct: 60  KEAHQLFLEPEVLDPESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGST 119

Query: 450 QGRLDSFFTIRREEKRKSR 468
           QGRLD FF +        R
Sbjct: 120 QGRLDDFFKVTGSLSSAKR 138

>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]} Length = 140

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.4 bits (159), Expect = 2e-13
 Identities = 32/61 (52%), Positives = 46/61 (75%), Gaps = 3/61 (4%)

Query: 3   LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFFTIR---REEKR 59
           LKWS+P+E+ L+K++CG+K F+E+RIR+G K+L K+R  +TQGRLD FF +       KR
Sbjct: 79  LKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTQGRLDDFFKVTGSLSSAKR 138

Query: 60  K 60
           K
Sbjct: 139 K 139

>d1ul1x2 c.120.1.2 (X:2-217) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]} Length = 216

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]

 Score = 87.2 bits (215), Expect = 3e-20
 Identities = 70/114 (61%), Positives = 89/114 (78%), Gaps = 7/114 (6%)

Query: 304 ELVADVAPSSIRES-------RKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGT 356
           +L+ADVAPS+IRE+       RK+ IDASMS+YQFLIAVR  G+ L + +GE TSHLMG 
Sbjct: 7   KLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGM 66

Query: 357 FYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKREDAQKALAKAQEQGKLK 410
           FYRTIR++E+G+KP+YVFDGKPP LKSGEL KR E+R +A+K L +AQ  G  +
Sbjct: 67  FYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQ 120

>d1ul1x2 c.120.1.2 (X:2-217) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]} Length = 216

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]

 Score = 79.1 bits (194), Expect = 2e-17
 Identities = 48/94 (51%), Positives = 61/94 (64%), Gaps = 3/94 (3%)

Query: 32  AKKLLKARSSTTQGRLDSFFTIRREEKRK---APCEAEAQCAAMVKAGKVYATATEDMDA 88
            +K  K     T+   D    +          AP EAEA CAA+VKAGKVYA ATEDMD 
Sbjct: 122 VEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDC 181

Query: 89  LTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGM 122
           LTFGS +L+RH+T SEA+KLP+QEFHL ++L+ +
Sbjct: 182 LTFGSPVLMRHLTASEAKKLPIQEFHLSRILQEL 215

>d1a77a2 c.120.1.2 (A:2-208) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 207

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

 Score = 86.3 bits (213), Expect = 5e-20
 Identities = 37/94 (39%), Positives = 58/94 (61%), Gaps = 1/94 (1%)

Query: 318 RKICIDASMSLYQFLIAVR-SEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDG 376
           +K+ ID   +LYQFL ++R  +G+ L +  GE TS   G FY+TI L+E+ + PI+VFDG
Sbjct: 21  KKVAIDGMNALYQFLTSIRLRDGSPLRNRKGEITSAYNGVFYKTIHLLENDITPIWVFDG 80

Query: 377 KPPTLKSGELNKRMEKREDAQKALAKAQEQGKLK 410
           +PP LK      R E +E A+  + +A ++   +
Sbjct: 81  EPPKLKEKTRKVRREMKEKAELKMKEAIKKEDFE 114

>d1a77a2 c.120.1.2 (A:2-208) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 207

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

 Score = 65.1 bits (158), Expect = 1e-12
 Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 3/63 (4%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           AP E EAQ + M K G V+A  ++D DAL +G+  ++R++T +   K   +   L +VLE
Sbjct: 148 APSEGEAQASYMAKKGDVWAVVSQDYDALLYGAPRVVRNLTTT---KEMPELIELNEVLE 204

Query: 121 GME 123
            + 
Sbjct: 205 DLR 207

>d1b43a1 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 120

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score = 82.2 bits (203), Expect = 1e-19
 Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 9/80 (11%)

Query: 124 LSHEEFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLY 182
           L+ E+ I+L IL+G DY    I+GIG K+A+E+++  +      +               
Sbjct: 1   LTREKLIELAILVGTDYNPGGIKGIGLKKALEIVRHSKDPLAKFQ--------KQSDVDL 52

Query: 183 KEARELFRHPEVADPETIEF 202
              +E F +P V D   + +
Sbjct: 53  YAIKEFFLNPPVTDNYNLVW 72

>d1b43a1 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 120

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score = 74.5 bits (183), Expect = 7e-17
 Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 9/74 (12%)

Query: 232 FIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARE 290
            I+L IL+G DY    I+GIG K+A+E+++  +      +                  +E
Sbjct: 6   LIELAILVGTDYNPGGIKGIGLKKALEIVRHSKDPLAKFQ--------KQSDVDLYAIKE 57

Query: 291 LFRHPEIADPETIE 304
            F +P + D   + 
Sbjct: 58  FFLNPPVTDNYNLV 71

>d1b43a1 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 120

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score = 71.5 bits (175), Expect = 9e-16
 Identities = 22/51 (43%), Positives = 37/51 (72%)

Query: 408 KLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFT 458
            L W DPDE+G++K+LC + +F+E+R++NG ++L KA  +  Q  L+S+F 
Sbjct: 69  NLVWRDPDEEGILKFLCDEHDFSEERVKNGLERLKKAIKSGKQSTLESWFK 119

>d1b43a1 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 120

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score = 70.7 bits (173), Expect = 2e-15
 Identities = 23/50 (46%), Positives = 37/50 (74%)

Query: 3   LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQGRLDSFFT 52
           L W DPDE+G++K+LC + +F+E+R++NG ++L KA  S  Q  L+S+F 
Sbjct: 70  LVWRDPDEEGILKFLCDEHDFSEERVKNGLERLKKAIKSGKQSTLESWFK 119

>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 105

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 81.1 bits (200), Expect = 2e-19
 Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 6/79 (7%)

Query: 124 LSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYK 183
           L+ E+ ID+ IL+G DY + ++G+G K+A+  IK +  I + L+ +             +
Sbjct: 1   LTREQLIDIAILVGTDYNEGVKGVGVKKALNYIKTYGDIFRALKALKVNI------DHVE 54

Query: 184 EARELFRHPEVADPETIEF 202
           E R  F +P V D   IEF
Sbjct: 55  EIRNFFLNPPVTDDYRIEF 73

>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 105

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 74.6 bits (183), Expect = 5e-17
 Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 232 FIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAREL 291
            ID+ IL+G DY + ++G+G K+A+  IK +  I + L+ +             +E R  
Sbjct: 6   LIDIAILVGTDYNEGVKGVGVKKALNYIKTYGDIFRALKALKVNI------DHVEEIRNF 59

Query: 292 FRHPEIADPETIEL 305
           F +P + D   IE 
Sbjct: 60  FLNPPVTDDYRIEF 73

>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 105

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 44.5 bits (105), Expect = 2e-06
 Identities = 8/34 (23%), Positives = 23/34 (67%)

Query: 408 KLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKL 441
           ++++ +PD +  +++LC + +F+ +R+    +KL
Sbjct: 70  RIEFREPDFEKAIEFLCEEHDFSRERVEKALEKL 103

>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 105

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 43.7 bits (103), Expect = 3e-06
 Identities = 8/33 (24%), Positives = 22/33 (66%)

Query: 3   LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKL 35
           +++ +PD +  +++LC + +F+ +R+    +KL
Sbjct: 71  IEFREPDFEKAIEFLCEEHDFSRERVEKALEKL 103

>d1a77a1 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 108

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 79.1 bits (195), Expect = 1e-18
 Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 11/80 (13%)

Query: 124 LSHEEFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLY 182
           +S ++ ID+ I +G DY    ++GIG KRA EL++   + + + + +            Y
Sbjct: 1   ISLDDLIDIAIFMGTDYNPGGVKGIGFKRAYELVRSGVAKDVLKKEV----------EYY 50

Query: 183 KEARELFRHPEVADPETIEF 202
            E + +F+ P+V D  ++  
Sbjct: 51  DEIKRIFKEPKVTDNYSLSL 70

>d1a77a1 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 108

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 72.6 bits (178), Expect = 3e-16
 Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 11/75 (14%)

Query: 232 FIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARE 290
            ID+ I +G DY    ++GIG KRA EL++   + + + + +            Y E + 
Sbjct: 6   LIDIAIFMGTDYNPGGVKGIGFKRAYELVRSGVAKDVLKKEV----------EYYDEIKR 55

Query: 291 LFRHPEIADPETIEL 305
           +F+ P++ D  ++ L
Sbjct: 56  IFKEPKVTDNYSLSL 70

>d1a77a1 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 108

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 52.2 bits (125), Expect = 4e-09
 Identities = 12/41 (29%), Positives = 23/41 (56%)

Query: 3   LKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTT 43
           L    PD++G++K+L  + +F  DR++    KL    ++ T
Sbjct: 68  LSLKLPDKEGIIKFLVDENDFNYDRVKKHVDKLYNLIANKT 108

>d1a77a1 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 108

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 51.8 bits (124), Expect = 5e-09
 Identities = 12/45 (26%), Positives = 23/45 (51%)

Query: 405 EQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTT 449
           +   L    PD++G++K+L  + +F  DR++    KL    +  T
Sbjct: 64  DNYSLSLKLPDKEGIIKFLVDENDFNYDRVKKHVDKLYNLIANKT 108

>d1rxwa2 c.120.1.2 (A:3-219) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 217

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

 Score = 79.4 bits (195), Expect = 1e-17
 Identities = 26/72 (36%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           AP E EAQ A M   G V  T ++D D+L FGS  L R++  +  RKLP +  +++   E
Sbjct: 146 APSEGEAQAAYMAAKGDVEYTGSQDYDSLLFGSPRLARNLAITGKRKLPGKNVYVDVKPE 205

Query: 121 GMELSHEEFIDL 132
            + L       L
Sbjct: 206 IIILE-SNLKRL 216

>d1rxwa2 c.120.1.2 (A:3-219) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 217

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

 Score = 78.2 bits (192), Expect = 3e-17
 Identities = 34/81 (41%), Positives = 52/81 (64%), Gaps = 1/81 (1%)

Query: 318 RKICIDASMSLYQFLIAVR-SEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDG 376
           +KI +DA  +LYQF+  +R  +G  L    G  TSHL G  YR   +VE G++P++VFDG
Sbjct: 20  KKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSHLSGILYRVSNMVEVGIRPVFVFDG 79

Query: 377 KPPTLKSGELNKRMEKREDAQ 397
           +PP  K  E+ +R ++R +A+
Sbjct: 80  EPPEFKKAEIEERKKRRAEAE 100

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

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

 Score = 79.5 bits (195), Expect = 2e-17
 Identities = 30/72 (41%), Positives = 44/72 (61%), Gaps = 1/72 (1%)

Query: 61  APCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLE 120
           AP E EAQ A M   G VYA+A++D D+L FG+  L+R++T +  RKLP +  ++E   E
Sbjct: 148 APSEGEAQAAYMAAKGSVYASASQDYDSLLFGAPRLVRNLTITGKRKLPGKNVYVEIKPE 207

Query: 121 GMELSHEEFIDL 132
            + L  E   +L
Sbjct: 208 LIILE-EVLKEL 218

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

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

 Score = 77.9 bits (191), Expect = 5e-17
 Identities = 48/94 (51%), Positives = 65/94 (69%), Gaps = 1/94 (1%)

Query: 318 RKICIDASMSLYQFLIAVR-SEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDG 376
           +KI IDA  ++YQFL  +R  +G  LM   G  TSHL G FYRTI L+E G+KP+YVFDG
Sbjct: 21  KKIAIDALNAIYQFLSTIRQKDGTPLMDSKGRITSHLSGLFYRTINLMEAGIKPVYVFDG 80

Query: 377 KPPTLKSGELNKRMEKREDAQKALAKAQEQGKLK 410
           +PP  K  EL KR E RE+A++   +A E+G+++
Sbjct: 81  EPPEFKKKELEKRREAREEAEEKWREALEKGEIE 114

>d1xo1a1 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]} Length = 105

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: T5 5'-exonuclease
species: Bacteriophage T5 [TaxId: 10726]

 Score = 44.6 bits (105), Expect = 1e-06
 Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 127 EEFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKE 184
           E+FI L  ++G   D    + GIG KR   +I+E  ++  I++ +           L   
Sbjct: 5   EQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNAS 64

Query: 185 ARELFRHPEVADPETI 200
              LFR+  + D  T 
Sbjct: 65  EELLFRNLILVDLPTY 80

>d1xo1a1 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]} Length = 105

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: T5 5'-exonuclease
species: Bacteriophage T5 [TaxId: 10726]

 Score = 43.4 bits (102), Expect = 4e-06
 Identities = 20/80 (25%), Positives = 33/80 (41%), Gaps = 2/80 (2%)

Query: 232 FIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEAR 289
           FI L  ++G   D    + GIG KR   +I+E  ++  I++ +           L     
Sbjct: 7   FISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEE 66

Query: 290 ELFRHPEIADPETIELVADV 309
            LFR+  + D  T  + A  
Sbjct: 67  LLFRNLILVDLPTYCVDAIA 86

>d1xo1a1 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]} Length = 105

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: T5 5'-exonuclease
species: Bacteriophage T5 [TaxId: 10726]

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 12/92 (13%)

Query: 194 VADPETIEFIDLCILLG--CDYCDSIRGIGPKRAIELLYSFIDLCILLGCDYCDSIRGIG 251
           V D E  +FI L  ++G   D    + GIG KR   ++  F ++      D  D +   G
Sbjct: 1   VDDVE--QFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNV-----LDIIDQLPLPG 53

Query: 252 PKRAIELIKEHR---SIEKILENIDTKKYTVP 280
            ++ I+ +           IL ++ T      
Sbjct: 54  KQKYIQNLNASEELLFRNLILVDLPTYCVDAI 85

>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]} Length = 56

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Excinuclease UvrC C-terminal domain
domain: Excinuclease UvrC C-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 40.5 bits (95), Expect = 1e-05
 Identities = 15/50 (30%), Positives = 20/50 (40%), Gaps = 3/50 (6%)

Query: 215 DSIRGIGPKRAIELLYSFIDLCILLGCDYCD--SIRGIGPKRAIELIKEH 262
           ++I G+GPKR   LL     L  L      +   + GI    A E I   
Sbjct: 5   ETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLA-EKIFWS 53

>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]} Length = 56

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Excinuclease UvrC C-terminal domain
domain: Excinuclease UvrC C-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 35.5 bits (82), Expect = 0.001
 Identities = 8/27 (29%), Positives = 15/27 (55%)

Query: 142 DSIRGIGPKRAIELIKEHRSIEKILEN 168
           ++I G+GPKR   L+K    ++ +   
Sbjct: 5   ETIEGVGPKRRQMLLKYMGGLQGLRNA 31

>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]} Length = 56

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Excinuclease UvrC C-terminal domain
domain: Excinuclease UvrC C-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 35.5 bits (82), Expect = 0.001
 Identities = 8/27 (29%), Positives = 15/27 (55%)

Query: 245 DSIRGIGPKRAIELIKEHRSIEKILEN 271
           ++I G+GPKR   L+K    ++ +   
Sbjct: 5   ETIEGVGPKRRQMLLKYMGGLQGLRNA 31

>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} Length = 70

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Aeropyrum pernix [TaxId: 56636]

 Score = 39.0 bits (91), Expect = 7e-05
 Identities = 17/50 (34%), Positives = 22/50 (44%), Gaps = 3/50 (6%)

Query: 215 DSIRGIGPKRAIELLYSFIDLCILLGCDYCD--SIRGIGPKRAIELIKEH 262
            S  GIG + A  +L  F  L         +   + GIG KRA E IK+ 
Sbjct: 16  QSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRA-EEIKKI 64

>d1n8yc3 g.3.9.1 (C:166-322) Protooncoprotein Her2 extracellular domain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 157

class: Small proteins
fold: Knottins (small inhibitors, toxins, lectins)
superfamily: Growth factor receptor domain
family: Growth factor receptor domain
domain: Protooncoprotein Her2 extracellular domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 39.4 bits (90), Expect = 2e-04
 Identities = 5/64 (7%), Positives = 14/64 (21%)

Query: 468 RCQYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQYQYQYQCQCQCQCQC 527
           RC+ +    C ++         +      C           +            +     
Sbjct: 40  RCKGRLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMHNP 99

Query: 528 QYQY 531
           + +Y
Sbjct: 100 EGRY 103

>d1n8yc3 g.3.9.1 (C:166-322) Protooncoprotein Her2 extracellular domain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 157

class: Small proteins
fold: Knottins (small inhibitors, toxins, lectins)
superfamily: Growth factor receptor domain
family: Growth factor receptor domain
domain: Protooncoprotein Her2 extracellular domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 38.3 bits (87), Expect = 7e-04
 Identities = 5/66 (7%), Positives = 9/66 (13%)

Query: 466 KSRCQYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQYQYQYQCQCQCQC 525
                                   +     + +  +         Y Y       C   C
Sbjct: 70  LHFNHSGICELHCPALVTYNTDTFESMHNPEGRYTFGASCVTTCPYNYLSTEVGSCTLVC 129

Query: 526 QCQYQY 531
               Q 
Sbjct: 130 PPNNQE 135

>d1n8yc3 g.3.9.1 (C:166-322) Protooncoprotein Her2 extracellular domain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 157

class: Small proteins
fold: Knottins (small inhibitors, toxins, lectins)
superfamily: Growth factor receptor domain
family: Growth factor receptor domain
domain: Protooncoprotein Her2 extracellular domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 37.1 bits (84), Expect = 0.001
 Identities = 5/63 (7%), Positives = 9/63 (14%)

Query: 469 CQYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQYQYQYQCQCQCQCQCQ 528
                 +            +     + +            Y Y       C   C    Q
Sbjct: 75  SGICELHCPALVTYNTDTFESMHNPEGRYTFGASCVTTCPYNYLSTEVGSCTLVCPPNNQ 134

Query: 529 YQY 531
              
Sbjct: 135 EVT 137

>d1n8yc3 g.3.9.1 (C:166-322) Protooncoprotein Her2 extracellular domain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 157

class: Small proteins
fold: Knottins (small inhibitors, toxins, lectins)
superfamily: Growth factor receptor domain
family: Growth factor receptor domain
domain: Protooncoprotein Her2 extracellular domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 36.0 bits (81), Expect = 0.004
 Identities = 2/61 (3%), Positives = 11/61 (18%)

Query: 469 CQYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQYQYQYQCQCQCQCQCQ 528
               C ++         +      C           +           ++     + +  
Sbjct: 45  LPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMHNPEGRYT 104

Query: 529 Y 529
           +
Sbjct: 105 F 105

>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 68

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 37.1 bits (86), Expect = 2e-04
 Identities = 10/50 (20%), Positives = 19/50 (38%), Gaps = 3/50 (6%)

Query: 215 DSIRGIGPKRAIELLYSFIDLCILLGCDYCD--SIRGIGPKRAIELIKEH 262
           + +  +    A  LL  F  +  +      +   + GIG K A + I+  
Sbjct: 13  EGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIA-KEIRRV 61

>d1ky8a_ c.82.1.1 (A:) Non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase GapN {Archaeon Thermoproteus tenax [TaxId: 2271]} Length = 499

class: Alpha and beta proteins (a/b)
fold: ALDH-like
superfamily: ALDH-like
family: ALDH-like
domain: Non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase GapN
species: Archaeon Thermoproteus tenax [TaxId: 2271]

 Score = 37.2 bits (85), Expect = 0.004
 Identities = 12/139 (8%), Positives = 33/139 (23%), Gaps = 19/139 (13%)

Query: 393 REDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGR 452
           RE+ ++ L    ++G+    D                  +R+      +L+  +   +  
Sbjct: 51  REEVERTLDVLFKRGRWSARDMP--------------GTERLA-----VLRKAADIIERN 91

Query: 453 LDSFFTIRREEKRKSRCQYQCQYQCQYQCQYQCQCQCQCQCQCQCQCQYQYQYQYQYQYQ 512
           LD F  +      K +     + +         +   +          + Y         
Sbjct: 92  LDVFAEVLVMNAGKPKSAAVGEVKAAVDRLRLAELDLKKIGGDYIPGDWTYDTLETEGLV 151

Query: 513 YQYQYQCQCQCQCQCQYQY 531
            +                +
Sbjct: 152 RREPLGVVAAITPFNYPLF 170

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	531
d1rxwa2	217	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc	99.92
d1b43a2	219	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr	99.91
d1a77a2	207	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met	99.9
d1ul1x1	140	Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo	99.88
d1ul1x2	216	Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo	99.87
d1b43a1	120	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr	99.87
d1ul1x1	140	Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo	99.76
d1rxwa1	105	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc	99.73
d1ul1x2	216	Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo	99.72
d1a77a1	108	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met	99.72
d1a77a1	108	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met	99.71
d1b43a1	120	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr	99.7
d1a77a2	207	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met	99.68
d1rxwa2	217	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc	99.67
d1rxwa1	105	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc	99.66
d1b43a2	219	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr	99.65
d1xo1a1	105	T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]	99.23
d1cmwa1	116	5' to 3' exonuclease domain of DNA polymerase Taq	99.06
d1cmwa2	164	5' to 3' exonuclease domain of DNA polymerase Taq	98.93
d1tfra2	169	T4 RNase H {Bacteriophage T4 [TaxId: 10665]}	98.63
d1xo1a1	105	T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]	98.54
d1xo1a2	167	T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]	98.46
d1cmwa1	116	5' to 3' exonuclease domain of DNA polymerase Taq	97.71
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	97.23
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	97.12
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	97.11
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	97.06
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	96.7
d1dgsa1	181	NAD+-dependent DNA ligase, domain 3 {Thermus filif	95.75
d2a1ja1	62	DNA repair endonuclease XPF {Human (Homo sapiens)	95.6
d1kfta_	56	Excinuclease UvrC C-terminal domain {Escherichia c	95.28
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	95.2
d2a1ja1	62	DNA repair endonuclease XPF {Human (Homo sapiens)	95.08
d1x2ia1	68	ATP-dependent RNA helicase PF2015 {Pyrococcus furi	94.08
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	93.4
d2bgwa1	70	DNA repair endonuclease XPF {Aeropyrum pernix [Tax	92.77
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	92.31
d2bcqa2	57	DNA polymerase lambda {Human (Homo sapiens) [TaxId	90.46
d2a1jb1	78	DNA excision repair protein ERCC-1 {Human (Homo sa	90.33
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	90.11
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	90.01
d1jmsa3	60	Terminal deoxynucleotidyl transferase {Mouse (Mus	89.96
d2fmpa2	57	DNA polymerase beta {Human (Homo sapiens) [TaxId:	88.85
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	88.36
d1bvsa2	71	DNA helicase RuvA subunit, middle domain {Mycobact	86.16
d1ixra1	73	DNA helicase RuvA subunit, middle domain {Thermus	85.82
d1cuka2	78	DNA helicase RuvA subunit, middle domain {Escheric	84.13
d1cmwa2	164	5' to 3' exonuclease domain of DNA polymerase Taq	82.56

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

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

Probab=99.92  E-value=9.6e-26  Score=217.48  Aligned_cols=125  Identities=34%  Similarity=0.603  Sum_probs=117.5

Q ss_pred             cccccceeeecccchHHHHHHHHhh-cCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHH
Q psy1206         313 SIRESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRME  391 (531)
Q Consensus       313 ~i~~gk~iAIDa~~~lyqfl~~ir~-~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~  391 (531)
                      ....||+||||||+|||||+.++|. +|.++.+..|++++|+.++++|+..|+.+||+|||||||.||+.|..|+++|++
T Consensus        15 ~~l~Gk~vAIDas~wL~k~l~~~~~~~~~~l~~~~~~~~~~l~~~~~ri~~l~~~~I~pifVFDG~~p~~K~~~~~~R~~   94 (217)
T d1rxwa2          15 EYFSGKKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSHLSGILYRVSNMVEVGIRPVFVFDGEPPEFKKAEIEERKK   94 (217)
T ss_dssp             GGGTTCEEEEEHHHHHHHHHHHSBCTTSCBCBCTTSCBCHHHHHHHHHHHHHHHHTCEEEEEECCSCCGGGHHHHHHHHH
T ss_pred             HHhCCCEEEEECHHHHHHHHHHhccccCCchhhccCCccHHHHHHHHHHHHHHHcCCeEEEEECCCCCcchhhHHHHHHH
Confidence            4456999999999999999999999 799999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhc
Q psy1206         392 KREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARS  446 (531)
Q Consensus       392 ~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~  446 (531)
                      +|+++.+.++++.++|+.        ++.++..+ ...+++++++.+++||+.+|
T Consensus        95 ~r~~~~~~~~~~~~~~~~--------~~~~~~~~-~~~vt~~~~~~~~~lL~~~g  140 (217)
T d1rxwa2          95 RRAEAEEMWIAALQAGDK--------DAKKYAQA-AGRVDEYIVDSAKTLLSYMG  140 (217)
T ss_dssp             HHHHHHHHHHHHHHHTCT--------THHHHHHH-HCCCCHHHHHHHHHHHHHTT
T ss_pred             HHHhhhhhhhhhhhhhhH--------HHHHHHHh-hccCCHHHHHHHHHHHHHcC
Confidence            999999999999998774        47778777 88999999999999999997

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

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

Probab=99.91  E-value=7.4e-26  Score=218.69  Aligned_cols=125  Identities=44%  Similarity=0.695  Sum_probs=119.6

Q ss_pred             ccccceeeecccchHHHHHHHHhh-cCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHHH
Q psy1206         314 IRESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEK  392 (531)
Q Consensus       314 i~~gk~iAIDa~~~lyqfl~~ir~-~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~~  392 (531)
                      -..|++||||||+|||||+++++. .|.++++..|++++||.++|+|+..|+.+||+|||||||.||+.|..|+.+|+++
T Consensus        17 ~l~gk~iaIDas~~L~k~l~~~~~~~~~~l~~~~~~~~~~l~~~~~r~~~Ll~~~I~pVFVFDG~~~~~K~~~~~~R~~~   96 (219)
T d1b43a2          17 NLYGKKIAIDALNAIYQFLSTIRQKDGTPLMDSKGRITSHLSGLFYRTINLMEAGIKPVYVFDGEPPEFKKKELEKRREA   96 (219)
T ss_dssp             GGTTCEEEEEHHHHHHHHHHHSBCTTSCBCBCTTSCBCHHHHHHHHHHHHHHHTTCEEEEEECCSCCCCSSCSSTTCCCC
T ss_pred             HcCCCEEEEEChHHHHHHHHHhcccccchhhhccCCCchHHHHHHHHHHHHHHcCCeEEEEeCCCCCHHHhhhHHhhhhh
Confidence            345999999999999999999999 7999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhc
Q psy1206         393 REDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARS  446 (531)
Q Consensus       393 r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~  446 (531)
                      |.++.+++.++.++|+.+       ++.++..+ ...+++.+++.+++||+.+|
T Consensus        97 r~~~~~~~~~~~~~~~~~-------~~~~~~~~-~~~~t~~~~~~~~~lL~~~g  142 (219)
T d1b43a2          97 REEAEEKWREALEKGEIE-------EARKYAQR-ATRVNEMLIEDAKKLLELMG  142 (219)
T ss_dssp             TTHHHHHHHHHHHHSCHH-------HHHHHHHT-SGGGTHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhhhhhhccchh-------hhhhhhcc-cccCCHHHHHHHHHHHHHcC
Confidence            999999999999999877       89999887 99999999999999999997

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

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

Probab=99.90  E-value=2e-26  Score=220.86  Aligned_cols=127  Identities=33%  Similarity=0.545  Sum_probs=117.0

Q ss_pred             cccccceeeecccchHHHHHHHHhh-cCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHH
Q psy1206         313 SIRESRKICIDASMSLYQFLIAVRS-EGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRME  391 (531)
Q Consensus       313 ~i~~gk~iAIDa~~~lyqfl~~ir~-~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~  391 (531)
                      ....|++||||||+|||||+++++. +|.++.+..|.+|+|+.++|+|+++|+.+||+|||||||.||+.|..|..+|++
T Consensus        16 ~~l~gk~vaIDas~~L~~~l~~~~~~~~~~l~~~~g~~~~~l~~~~~~~~~ll~~~I~pifVFDG~~~~~K~~~~~~R~~   95 (207)
T d1a77a2          16 EDLKGKKVAIDGMNALYQFLTSIRLRDGSPLRNRKGEITSAYNGVFYKTIHLLENDITPIWVFDGEPPKLKEKTRKVRRE   95 (207)
T ss_dssp             GGGTTCEEEEEHHHHHHHHHHHSBCTTSCBCBCTTSCBCHHHHHHHHHHHHHHHTTCEEEEEECCCTTCCCCSSCCSSCS
T ss_pred             HHhCCCEEEEEChHHHHHHHHHhhcccCchhhhccCCcCHHHHHHHHHHHHHHHcCCeEEEEECCCCchhhhhhHHHhHH
Confidence            4567999999999999999999998 799999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhcc
Q psy1206         392 KREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARST  447 (531)
Q Consensus       392 ~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~  447 (531)
                      +|+++...+.++.+.|+.+       ++.++.++ ...+++++++.+++||+.+|-
T Consensus        96 ~~~~~~~~~~~~~~~~~~~-------~~~~~~~~-~~~i~~~~~~~~~~ll~~~gi  143 (207)
T d1a77a2          96 MKEKAELKMKEAIKKEDFE-------EAAKYAKR-VSYLTPKMVENCKYLLSLMGI  143 (207)
T ss_dssp             SSSSSSCCCCCCCSHHHHS-------STTSSSST-TCSCCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHhhhccccHH-------HHhhhccc-ceecCHHHHHHHHHHHHHcCC
Confidence            9998888777777777665       77888887 899999999999999999984

>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=5.7e-23  Score=185.16  Aligned_cols=130  Identities=58%  Similarity=1.141  Sum_probs=118.4

Q ss_pred             HhhhhhhhhhccCccccCCCCCchHHHHHHHHhhccHHHHHHHHhhCCCCCCCcchHHHHHHHhcCCcccCccccccccc
Q psy1206         229 LYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIADPETIELVAD  308 (531)
Q Consensus       229 ~e~F~~~CiLsGCDY~~~i~giG~k~A~kli~k~~s~~~vi~~l~~~~~~vP~~y~~~~A~~~F~~~~V~dP~~~~Lv~~  308 (531)
                      .|+|++||||+||||+|+|||||+|||++||++|+++++|++++...+..+|+++.+..|+.+|+|+.|+||...     
T Consensus         3 ~~q~id~~~L~GsD~~pgv~gIG~ktA~kli~~~~~le~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~-----   77 (140)
T d1ul1x1           3 QEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESV-----   77 (140)
T ss_dssp             HHHHHHHHHHHHCSSSCCCTTCCHHHHHHHHHHSSSHHHHHTTCCCTTSCCCSSCCHHHHHHHHHSCCCCCGGGC-----
T ss_pred             HHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHhCCHHHHHHHHHHhccccchhhhhHHHHHHHcCCccCCCCCC-----
Confidence            589999999999999999999999999999999999999999998778889999999999999999999998432     


Q ss_pred             cCCCcccccceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHH
Q psy1206         309 VAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNK  388 (531)
Q Consensus       309 ~aP~~i~~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~k  388 (531)
                                                                                                      
T Consensus        78 --------------------------------------------------------------------------------   77 (140)
T d1ul1x1          78 --------------------------------------------------------------------------------   77 (140)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             HHHHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhccCCcCccccccccchh
Q psy1206         389 RMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFTIRRE  462 (531)
Q Consensus       389 R~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~rld~ff~~~~~  462 (531)
                                         +++|..|+.+++.+++..+..+...++.+...+|.++....+|+|||+||++...
T Consensus        78 -------------------~l~~~~~d~~~l~~~l~~~~~f~~~~~~~~l~~l~~~~~~~~q~~L~~ff~~~~~  132 (140)
T d1ul1x1          78 -------------------ELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTQGRLDDFFKVTGS  132 (140)
T ss_dssp             -------------------CCCCCCCCHHHHHHHTTTTSCCCHHHHHHHHHHHHHHHSCCSBCCHHHHSEEEEE
T ss_pred             -------------------CCCcCCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccccHHHhcCCCCC
Confidence                               2467888888999998877888889999999999999999999999999998653

>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=99.87  E-value=2.9e-24  Score=206.02  Aligned_cols=123  Identities=52%  Similarity=0.803  Sum_probs=78.6

Q ss_pred             ccceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHHHHHHHHHH
Q psy1206         316 ESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELNKRMEKRED  395 (531)
Q Consensus       316 ~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~kR~~~r~~  395 (531)
                      .|++||||||+||||++.+++..+.++.+..|++++|+.++|.|+.+|+.+||+|||||||.||+.|..|..+|+++|++
T Consensus        26 ~gk~vaIDas~~l~~~l~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~l~~~~I~pifVFDG~~~~~K~~~~~~R~~~r~~  105 (216)
T d1ul1x2          26 FGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAE  105 (216)
T ss_dssp             TTCCEEEEHHHHHHHHHSCC-------------CCHHHHHHHHHHHHHHHTTCCEEEEECCSCCSCCCCCCCCC------
T ss_pred             CCCEEEEEeHHHHHHHHHHhccccchhhccCCCCcHHHHHHHHHHHHHHHcCCeEEEEEcCCCCccccchhhhhhhhHHH
Confidence            48999999999999999999888889999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhc
Q psy1206         396 AQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARS  446 (531)
Q Consensus       396 a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~  446 (531)
                      +.++++.+.+.++..       ++.++..+ ...+++++++.+++||+.+|
T Consensus       106 ~~~~~~~~~~~~~~~-------~~~~~~~~-~~~i~~~~~~~~~~ll~~~g  148 (216)
T d1ul1x2         106 AEKQLQQAQAAGAEQ-------EVEKFTKR-LVKVTKQHNDECKHLLSLMG  148 (216)
T ss_dssp             -------------------------------CCCCCCSCHHHHHHHHHHHT
T ss_pred             hhhhHHhhhhcchHH-------HHHHhhcc-CeeccHHHHHHHHHHHHhcC
Confidence            999999999988876       89999887 88999999999999999986

>d1b43a1 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=99.87  E-value=7.5e-23  Score=180.71  Aligned_cols=116  Identities=34%  Similarity=0.696  Sum_probs=105.0

Q ss_pred             HhhhhhhhhhccCccc-cCCCCCchHHHHHHHHhhccHHHHHHHHhhCCCCCCCcchHHHHHHHhcCCcccCcccccccc
Q psy1206         229 LYSFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIADPETIELVA  307 (531)
Q Consensus       229 ~e~F~~~CiLsGCDY~-~~i~giG~k~A~kli~k~~s~~~vi~~l~~~~~~vP~~y~~~~A~~~F~~~~V~dP~~~~Lv~  307 (531)
                      .|+|++||||+||||+ ++||||||+||+++|++|++++.+        +..|++|.+..++.+|++|.|-|-       
T Consensus         3 ~eqfIdl~iL~G~DY~~~gI~GIGpktAlklikk~~~~~~~--------~~~~~~~~~~~~~~~f~~p~v~d~-------   67 (120)
T d1b43a1           3 REKLIELAILVGTDYNPGGIKGIGLKKALEIVRHSKDPLAK--------FQKQSDVDLYAIKEFFLNPPVTDN-------   67 (120)
T ss_dssp             HHHHHHHHHHHCCTTSTTCSTTCCHHHHHHHHHTCSSGGGG--------TGGGCSSCHHHHHHHHHSCCCCCC-------
T ss_pred             HHHHHHHHHHhCCCCCcccCCCcCHHHHHHHHHHhCCHHHH--------HHhccccchHHHHHHhcCCCCCCC-------
Confidence            6899999999999999 599999999999999999998643        456888999999999999887432       


Q ss_pred             ccCCCcccccceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHH
Q psy1206         308 DVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELN  387 (531)
Q Consensus       308 ~~aP~~i~~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~  387 (531)
                                                                                                      
T Consensus        68 --------------------------------------------------------------------------------   67 (120)
T d1b43a1          68 --------------------------------------------------------------------------------   67 (120)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             HHHHHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhccCCcCccccccc
Q psy1206         388 KRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTTQGRLDSFFT  458 (531)
Q Consensus       388 kR~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~rld~ff~  458 (531)
                                         -+++|+.||.+++++|++.+..+..++|.+..++|.+++.+.+|+|||+||+
T Consensus        68 -------------------~~~~~~~pd~~~l~~fL~~e~~f~~~rv~~~l~kl~k~~~~~~Q~~L~~fFk  119 (120)
T d1b43a1          68 -------------------YNLVWRDPDEEGILKFLCDEHDFSEERVKNGLERLKKAIKSGKQSTLESWFK  119 (120)
T ss_dssp             -------------------CCCCCCCCCHHHHHHHHTTTTCCCHHHHHHHHHHHHHHHHHTTGGGCCSSCC
T ss_pred             -------------------CCcCCCCCCHHHHHHHHHHccCCCHHHHHHHHHHHHHHHccCCCCCHHHHhC
Confidence                               1367999999999999999999999999999999999999999999999996

>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=3.6e-19  Score=160.05  Aligned_cols=83  Identities=60%  Similarity=1.100  Sum_probs=75.9

Q ss_pred             CCHHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhhcCCCCCCCCcHHHHHHHhcCCCcCCCCCcccc
Q psy1206         124 LSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFI  203 (531)
Q Consensus       124 lt~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~~~~~ip~~f~~~~A~~~f~~p~V~d~~~~~~v  203 (531)
                      ++++||+|+|+|+||||+|||||||+|||++||++|+|+|+|+++++..+..++.++.+..++.+|.++.|+++....+.
T Consensus         1 l~~~q~id~~~L~GsD~~pgv~gIG~ktA~kli~~~~~le~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~l~   80 (140)
T d1ul1x1           1 LNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVELK   80 (140)
T ss_dssp             CCHHHHHHHHHHHHCSSSCCCTTCCHHHHHHHHHHSSSHHHHHTTCCCTTSCCCSSCCHHHHHHHHHSCCCCCGGGCCCC
T ss_pred             CCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHhCCHHHHHHHHHHhccccchhhhhHHHHHHHcCCccCCCCCCCCC
Confidence            68999999999999999999999999999999999999999999998888888889999999999999999987766654


Q ss_pred             ccc
Q psy1206         204 DLC  206 (531)
Q Consensus       204 ~Ls  206 (531)
                      +..
T Consensus        81 ~~~   83 (140)
T d1ul1x1          81 WSE   83 (140)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            443

>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.73  E-value=2.2e-18  Score=148.32  Aligned_cols=76  Identities=34%  Similarity=0.592  Sum_probs=65.4

Q ss_pred             CCHHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhhcCCCCCCCCcHHHHHHHhcCCCcCCCCCcccc
Q psy1206         124 LSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFI  203 (531)
Q Consensus       124 lt~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~~~~~ip~~f~~~~A~~~f~~p~V~d~~~~~~v  203 (531)
                      +|++||+|+|+|+||||+|||||||||||++||++|+|+|+++++++...      .....++..|.++.|.++....|.
T Consensus         1 lt~eq~iD~~~L~GsDn~pGV~GIG~ktA~kli~~~gsle~i~~~~~~~~------~~~~~~r~l~~~~~v~~~~~l~~~   74 (105)
T d1rxwa1           1 LTREQLIDIAILVGTDYNEGVKGVGVKKALNYIKTYGDIFRALKALKVNI------DHVEEIRNFFLNPPVTDDYRIEFR   74 (105)
T ss_dssp             CCHHHHHHHHHHHCBTTBCCCTTCCHHHHHHHHHHHSSHHHHHHHHTC----------CHHHHHHHHSCCCCCCCCCCCC
T ss_pred             CCHHHHHHHHHHhCCCCCCCCCCcCHHHHHHHHHHhCCHHHHHHHHHhhH------HHHHHHHHHhcCCCCCChHhhccC
Confidence            68999999999999999999999999999999999999999999986532      246789999999999887766665


Q ss_pred             cc
Q psy1206         204 DL  205 (531)
Q Consensus       204 ~L  205 (531)
                      ..
T Consensus        75 ~~   76 (105)
T d1rxwa1          75 EP   76 (105)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.72  E-value=2.1e-18  Score=164.79  Aligned_cols=79  Identities=56%  Similarity=0.865  Sum_probs=73.4

Q ss_pred             HHHHHHHhhcCCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCC
Q psy1206          45 GRLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGME  123 (531)
Q Consensus        45 ~~i~~lL~~~gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lg  123 (531)
                      ..++++|+.+||||++||||||||||+|+++|++|+|+|+|||+|+||+++||++++..+.++.+++.+++++|++.+|
T Consensus       138 ~~~~~ll~~~gv~~i~Ap~EAdaq~A~L~~~g~vd~v~S~DsD~l~fG~~~vi~~~~~~~~~~~~~~~~~~~~il~~LG  216 (216)
T d1ul1x2         138 DECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELG  216 (216)
T ss_dssp             HHHHHHHHHHTCCEEECSSCHHHHHHHHHHHTSSSEEECSCTHHHHTTCSEEEECSSCCC-CCCCEEEEEHHHHHHHHT
T ss_pred             HHHHHHHHhcCeeeEeccchHHHHHHHHHhcCceEEEEccccceeccCCcEEEEecccccCCCCcEEEEEHHHHHHhcC
Confidence            4678999999999999999999999999999999999999999999999999999987776667899999999999876

>d1a77a1 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.72  E-value=5.3e-18  Score=146.48  Aligned_cols=99  Identities=22%  Similarity=0.377  Sum_probs=75.7

Q ss_pred             CCHHHHHHHHhHcCCCCC-CCCCCccHHHHHHHHHHcCCHHHHHHHhhhcCCCCCCCCcHHHHHHHhcCCCcCCCCCccc
Q psy1206         124 LSHEEFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEF  202 (531)
Q Consensus       124 lt~eqfid~~iL~G~DY~-pGIpGIG~ktA~kLI~~~~sle~il~~l~~~~~~ip~~f~~~~A~~~f~~p~V~d~~~~~~  202 (531)
                      +|++||+|+|+|+||||+ |||||||||||++||++|+|+|.++++.          +++..++..|++|.|.+....+|
T Consensus         1 lt~~q~IDl~iL~G~dyn~pGV~GIGpktA~klIk~~g~ie~l~~~~----------~~~~~~~~~fl~~~v~~~~~~~~   70 (108)
T d1a77a1           1 ISLDDLIDIAIFMGTDYNPGGVKGIGFKRAYELVRSGVAKDVLKKEV----------EYYDEIKRIFKEPKVTDNYSLSL   70 (108)
T ss_dssp             CCHHHHHHHHHHHCCTTSTTCSTTCCHHHHHHHHHTTCHHHHHHHHC----------TTHHHHHHHHHSCCCCCCCCCCC
T ss_pred             CCHHHHHHHHHHhCCcCCCCCCCCcCHHHHHHHHHHcCCHHHHHHhh----------hhhHHHHHHHcCCCCCChhhccC
Confidence            689999999999999998 6999999999999999999999999874          35789999999999998877777


Q ss_pred             ccccccccccccccccCCChhhhHhHHhhh
Q psy1206         203 IDLCILLGCDYCDSIRGIGPKRAIELLYSF  232 (531)
Q Consensus       203 v~Ls~~~~~d~cesl~~~Gp~~~~el~e~F  232 (531)
                      ..........+......+++.+....++++
T Consensus        71 ~~~d~~~l~~fL~~e~~f~~~rv~~~l~kl  100 (108)
T d1a77a1          71 KLPDKEGIIKFLVDENDFNYDRVKKHVDKL  100 (108)
T ss_dssp             CCCCHHHHHHHHTTTTCCCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence            654443323333233445554544433333

>d1a77a1 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.71  E-value=1.4e-17  Score=143.75  Aligned_cols=105  Identities=30%  Similarity=0.623  Sum_probs=92.7

Q ss_pred             HhhhhhhhhhccCccc-cCCCCCchHHHHHHHHhhccHHHHHHHHhhCCCCCCCcchHHHHHHHhcCCcccCcccccccc
Q psy1206         229 LYSFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIADPETIELVA  307 (531)
Q Consensus       229 ~e~F~~~CiLsGCDY~-~~i~giG~k~A~kli~k~~s~~~vi~~l~~~~~~vP~~y~~~~A~~~F~~~~V~dP~~~~Lv~  307 (531)
                      .|+|+|+|||+||||+ |+|||||||||+++|++|++++.++++.          +.++.++..|+++.|.++       
T Consensus         3 ~~q~IDl~iL~G~dyn~pGV~GIGpktA~klIk~~g~ie~l~~~~----------~~~~~~~~~fl~~~v~~~-------   65 (108)
T d1a77a1           3 LDDLIDIAIFMGTDYNPGGVKGIGFKRAYELVRSGVAKDVLKKEV----------EYYDEIKRIFKEPKVTDN-------   65 (108)
T ss_dssp             HHHHHHHHHHHCCTTSTTCSTTCCHHHHHHHHHTTCHHHHHHHHC----------TTHHHHHHHHHSCCCCCC-------
T ss_pred             HHHHHHHHHHhCCcCCCCCCCCcCHHHHHHHHHHcCCHHHHHHhh----------hhhHHHHHHHcCCCCCCh-------
Confidence            5899999999999999 6999999999999999999999998864          238899999999887543       


Q ss_pred             ccCCCcccccceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHcCCeeEEeecCCCCCcchHHHH
Q psy1206         308 DVAPSSIRESRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEHGLKPIYVFDGKPPTLKSGELN  387 (531)
Q Consensus       308 ~~aP~~i~~gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~gIkPVfVFDG~pp~lK~~~~~  387 (531)
                                                                                                      
T Consensus        66 --------------------------------------------------------------------------------   65 (108)
T d1a77a1          66 --------------------------------------------------------------------------------   65 (108)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             HHHHHHHHHHHHHHHHHHcccccCCCCChhHHHHHHhhccccchHHHHHHHHHHHHHhccCC
Q psy1206         388 KRMEKREDAQKALAKAQEQGKLKWSDPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSTTT  449 (531)
Q Consensus       388 kR~~~r~~a~~~~~~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~  449 (531)
                                         -+++|+.|+.+.+++|+..+..|..++|.+..++|.++++++|
T Consensus        66 -------------------~~~~~~~~d~~~l~~fL~~e~~f~~~rv~~~l~kl~~~~~~kt  108 (108)
T d1a77a1          66 -------------------YSLSLKLPDKEGIIKFLVDENDFNYDRVKKHVDKLYNLIANKT  108 (108)
T ss_dssp             -------------------CCCCCCCCCHHHHHHHHTTTTCCCHHHHHHHHHHHHHHHHHHC
T ss_pred             -------------------hhccCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHccCC
Confidence                               1357899999999999998899999999999999999987653

>d1b43a1 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=99.70  E-value=6.3e-18  Score=148.82  Aligned_cols=96  Identities=24%  Similarity=0.354  Sum_probs=75.4

Q ss_pred             CCHHHHHHHHhHcCCCCC-CCCCCccHHHHHHHHHHcCCHHHHHHHhhhcCCCCCCCCcHHHHHHHhcCCCcCCCCCccc
Q psy1206         124 LSHEEFIDLCILLGCDYC-DSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEF  202 (531)
Q Consensus       124 lt~eqfid~~iL~G~DY~-pGIpGIG~ktA~kLI~~~~sle~il~~l~~~~~~ip~~f~~~~A~~~f~~p~V~d~~~~~~  202 (531)
                      +|++||+|+|+|+||||+ +|||||||+||++||++|++++.+++        .|.+|++..++.+|.+|.|.+.....|
T Consensus         1 lt~eqfIdl~iL~G~DY~~~gI~GIGpktAlklikk~~~~~~~~~--------~~~~~~~~~~~~~f~~p~v~d~~~~~~   72 (120)
T d1b43a1           1 LTREKLIELAILVGTDYNPGGIKGIGLKKALEIVRHSKDPLAKFQ--------KQSDVDLYAIKEFFLNPPVTDNYNLVW   72 (120)
T ss_dssp             CCHHHHHHHHHHHCCTTSTTCSTTCCHHHHHHHHHTCSSGGGGTG--------GGCSSCHHHHHHHHHSCCCCCCCCCCC
T ss_pred             CCHHHHHHHHHHhCCCCCcccCCCcCHHHHHHHHHHhCCHHHHHH--------hccccchHHHHHHhcCCCCCCCCCcCC
Confidence            689999999999999999 59999999999999999999876543        367899999999999999987666666


Q ss_pred             ccccccccccccccccCCChhhhHh
Q psy1206         203 IDLCILLGCDYCDSIRGIGPKRAIE  227 (531)
Q Consensus       203 v~Ls~~~~~d~cesl~~~Gp~~~~e  227 (531)
                      ..........++....+|+..+...
T Consensus        73 ~~pd~~~l~~fL~~e~~f~~~rv~~   97 (120)
T d1b43a1          73 RDPDEEGILKFLCDEHDFSEERVKN   97 (120)
T ss_dssp             CCCCHHHHHHHHTTTTCCCHHHHHH
T ss_pred             CCCCHHHHHHHHHHccCCCHHHHHH
Confidence            5444333344455555566555544

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

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

Probab=99.68  E-value=1.6e-17  Score=158.43  Aligned_cols=84  Identities=30%  Similarity=0.404  Sum_probs=72.8

Q ss_pred             HhhccCCCHH---HHHHHHhhcCCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEE
Q psy1206          36 LKARSSTTQG---RLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQE  112 (531)
Q Consensus        36 ~k~~~~~t~~---~i~~lL~~~gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~  112 (531)
                      .+....+++.   .++++|+.+||||++||||||||||+|+++|+||+|+|+|||+|+||+++||++++++++   .+..
T Consensus       120 ~~~~~~i~~~~~~~~~~ll~~~gi~yi~Ap~EAeaqcA~L~~~g~vd~v~seDsD~l~yG~~~vir~l~~~~~---~~~~  196 (207)
T d1a77a2         120 AKRVSYLTPKMVENCKYLLSLMGIPYVEAPSEGEAQASYMAKKGDVWAVVSQDYDALLYGAPRVVRNLTTTKE---MPEL  196 (207)
T ss_dssp             SSTTCSCCHHHHHHHHHHHHHHTCCEEECSSCHHHHHHHHHHHTSSSEEECSSSGGGGGTCSEEEESSSCCSS---CCEE
T ss_pred             cccceecCHHHHHHHHHHHHHcCCceEecCccHHHHHHHHHHcCCeEEEEecccceeccCCCEEEEecccCCC---cEEE
Confidence            3444456664   467889999999999999999999999999999999999999999999999999987653   4689


Q ss_pred             ecHHHHHHhC
Q psy1206         113 FHLEKVLEGM  122 (531)
Q Consensus       113 ~~~~~i~~~l  122 (531)
                      +++++|++.|
T Consensus       197 ~~~~~iL~~L  206 (207)
T d1a77a2         197 IELNEVLEDL  206 (207)
T ss_dssp             EEHHHHHHHH
T ss_pred             EEHHHHHHhh
Confidence            9999998765

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

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

Probab=99.67  E-value=4.7e-17  Score=156.09  Aligned_cols=97  Identities=27%  Similarity=0.331  Sum_probs=73.4

Q ss_pred             ccceeecccCCCCCcchhHHhH------H---------------HHHHhhccCCCH---HHHHHHHhhcCCccccCCCch
Q psy1206          10 EDGLVKYLCGDKNFAEDRIRNG------A---------------KKLLKARSSTTQ---GRLDSFFTIRREEKRKAPCEA   65 (531)
Q Consensus        10 ~~~~~a~~~~~~~f~~~~~R~~------~---------------~~~~k~~~~~t~---~~i~~lL~~~gIp~vvAPyEA   65 (531)
                      ...++=||+..+..++++....      +               ..+.+....+++   ..++++|+.+||||++|||||
T Consensus        71 I~pifVFDG~~p~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~gi~~i~Ap~EA  150 (217)
T d1rxwa2          71 IRPVFVFDGEPPEFKKAEIEERKKRRAEAEEMWIAALQAGDKDAKKYAQAAGRVDEYIVDSAKTLLSYMGIPFVDAPSEG  150 (217)
T ss_dssp             CEEEEEECCSCCGGGHHHHHHHHHHHHHHHHHHHHHHHHTCTTHHHHHHHHCCCCHHHHHHHHHHHHHTTCCEEECSSCH
T ss_pred             CeEEEEECCCCCcchhhHHHHHHHHHHhhhhhhhhhhhhhhHHHHHHHHhhccCCHHHHHHHHHHHHHcCceEEecCchH
Confidence            4567789987777665442222      1               112333334555   346788999999999999999


Q ss_pred             hHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcc
Q psy1206          66 EAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEAR  106 (531)
Q Consensus        66 DAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~  106 (531)
                      |||||+|++.|+||+|+|+|||+|+||+++|||+++.++..
T Consensus       151 eaqcA~L~~~g~vd~v~seDsD~l~fG~~~vir~l~~~~~~  191 (217)
T d1rxwa2         151 EAQAAYMAAKGDVEYTGSQDYDSLLFGSPRLARNLAITGKR  191 (217)
T ss_dssp             HHHHHHHHHTTSSSEEECSSSHHHHTTCSEEEESCCC----
T ss_pred             HHHHHHHHhCCCeEEEEecccceeeeCCCEEEEecccccCc
Confidence            99999999999999999999999999999999999877644

>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.66  E-value=8.4e-17  Score=138.26  Aligned_cols=66  Identities=30%  Similarity=0.550  Sum_probs=55.9

Q ss_pred             HhhhhhhhhhccCccccCCCCCchHHHHHHHHhhccHHHHHHHHhhCCCCCCCcchHHHHHHHhcCCcccCc
Q psy1206         229 LYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEIADP  300 (531)
Q Consensus       229 ~e~F~~~CiLsGCDY~~~i~giG~k~A~kli~k~~s~~~vi~~l~~~~~~vP~~y~~~~A~~~F~~~~V~dP  300 (531)
                      .|+|+|+|+|+||||+|+|||||||||+++|++|+|+++|++++...+      ..+.+++.+|+++.|.++
T Consensus         3 ~eq~iD~~~L~GsDn~pGV~GIG~ktA~kli~~~gsle~i~~~~~~~~------~~~~~~r~l~~~~~v~~~   68 (105)
T d1rxwa1           3 REQLIDIAILVGTDYNEGVKGVGVKKALNYIKTYGDIFRALKALKVNI------DHVEEIRNFFLNPPVTDD   68 (105)
T ss_dssp             HHHHHHHHHHHCBTTBCCCTTCCHHHHHHHHHHHSSHHHHHHHHTC----------CHHHHHHHHSCCCCCC
T ss_pred             HHHHHHHHHHhCCCCCCCCCCcCHHHHHHHHHHhCCHHHHHHHHHhhH------HHHHHHHHHhcCCCCCCh
Confidence            589999999999999999999999999999999999999999996432      126788889987766543

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

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

Probab=99.65  E-value=6.4e-17  Score=155.45  Aligned_cols=73  Identities=32%  Similarity=0.465  Sum_probs=63.7

Q ss_pred             HHhhccCCCHH---HHHHHHhhcCCccccCCCchhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCccc
Q psy1206          35 LLKARSSTTQG---RLDSFFTIRREEKRKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARK  107 (531)
Q Consensus        35 ~~k~~~~~t~~---~i~~lL~~~gIp~vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~  107 (531)
                      +.+....+++.   .++++|+.+||||++||||||||||+|++.|+||+|+|+|||+|+||+++|+++++.+|.++
T Consensus       119 ~~~~~~~~t~~~~~~~~~lL~~~gv~~i~Ap~EAdaqcA~L~~~g~vd~v~SeDsD~L~fG~~~vl~~l~~~~~~~  194 (219)
T d1b43a2         119 YAQRATRVNEMLIEDAKKLLELMGIPIVQAPSEGEAQAAYMAAKGSVYASASQDYDSLLFGAPRLVRNLTITGKRK  194 (219)
T ss_dssp             HHHTSGGGTHHHHHHHHHHHHHHTCCEEECSSCHHHHHHHHHHHTSSSEEECSSSHHHHTTCSEEEESTTTCEEEE
T ss_pred             hhcccccCCHHHHHHHHHHHHHcCCceeeCchHHHHHHHHHHhcCCeEEEEecccceeeeCCCEEEEecccccCcc
Confidence            34455556664   47888999999999999999999999999999999999999999999999999998776543

>d1xo1a1 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: T5 5'-exonuclease
species: Bacteriophage T5 [TaxId: 10726]

Probab=99.23  E-value=2.5e-12  Score=110.13  Aligned_cols=47  Identities=30%  Similarity=0.586  Sum_probs=44.8

Q ss_pred             CHHHHHHHHhHcC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206         125 SHEEFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDT  171 (531)
Q Consensus       125 t~eqfid~~iL~G--~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~  171 (531)
                      .++||+|+++|+|  |||+|||||||+|||.+||++|+|++++++++..
T Consensus         3 ~~eq~~d~~aL~GD~sDnipGV~GiG~KtA~kli~~~gsle~i~~~~~~   51 (105)
T d1xo1a1           3 DVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPL   51 (105)
T ss_dssp             SHHHHHHHHHHHCBGGGTBCCCTTCCHHHHHHHHHHHCSHHHHHHHCSC
T ss_pred             cHHHHHHHHHHhCCcccCCcCcCCcCHHHHHHHHHHcchhHHHHHhHHH
Confidence            4899999999999  9999999999999999999999999999999864

>d1cmwa1 a.60.7.1 (A:174-289) 5' to 3' exonuclease domain of DNA polymerase Taq {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: 5' to 3' exonuclease domain of DNA polymerase Taq
species: Thermus aquaticus [TaxId: 271]

Probab=99.06  E-value=2.2e-12  Score=111.58  Aligned_cols=49  Identities=35%  Similarity=0.573  Sum_probs=46.0

Q ss_pred             CCHHHHHHHHhHcC--CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhhc
Q psy1206         124 LSHEEFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENIDTK  172 (531)
Q Consensus       124 lt~eqfid~~iL~G--~DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~~  172 (531)
                      +.|++++|+.+|+|  |||+|||||||+|||.+|+++|+|+|++++++++.
T Consensus         1 ~~P~~~~~~~~l~GD~sDnipGv~GiG~KtA~kll~~~gsle~i~~~~~~i   51 (116)
T d1cmwa1           1 LRPDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRL   51 (116)
T ss_dssp             CCGGGHHHHHHTTCCSSSCCCCCCCSTTCTTTTTGGGGGTTCSSSSSCCCC
T ss_pred             CCHHHHHHHHHHhCccccCcccccccCchhHHHHHHhcchHHHHHHHHhhh
Confidence            57999999999999  99999999999999999999999999999887653

>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=98.93  E-value=8.5e-10  Score=100.55  Aligned_cols=104  Identities=18%  Similarity=0.135  Sum_probs=81.9

Q ss_pred             CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCH-------HHHHHHHhhcCCccccCC-CchhHHHHHHHH----
Q psy1206           7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ-------GRLDSFFTIRREEKRKAP-CEAEAQCAAMVK----   74 (531)
Q Consensus         7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~-------~~i~~lL~~~gIp~vvAP-yEADAq~A~L~r----   74 (531)
                      .|++ .+++||.+.++|+     ++.++.||+++..++       +.+.+++..+|++++..| +||||.+|+|++    
T Consensus        49 ~~~~-~~v~~d~~~~~~R-----~~l~p~YK~~R~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~EADDvIa~la~~~~~  122 (164)
T d1cmwa2          49 DGDA-VIVVFDAKAPSFR-----HEAYGGYKAGRAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDVLASLAKKAEK  122 (164)
T ss_dssp             CCSE-EEEECCCSSSCTT-----GGGGSTTTSCCCCCCSSHHHHHHHHHHHHHHTTCEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCce-EEEEEecccccch-----hhhhhhhhhccccCchhHHHHHHHHHHHHhhcCceEEEecCcchHHHHHHHHHHhcc
Confidence            6888 8899998877763     334677788888777       367888999999999888 699999999986    


Q ss_pred             cCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCC
Q psy1206          75 AGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGME  123 (531)
Q Consensus        75 ~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lg  123 (531)
                      .|.-..|+|.|+|++|+..++|.. ++.+.      ..++.+.+.+++|
T Consensus       123 ~~~~v~IvS~DkD~~QLv~~~v~i-~~~~~------~~~~~~~v~ek~G  164 (164)
T d1cmwa2         123 EGYEVRILTADKDLYQLLSDRIHV-LHPEG------YLITPAWLWEKYG  164 (164)
T ss_dssp             TTEEEEEECSSGGGGGSCCSSCEE-ECSSS------SEECHHHHHHSSC
T ss_pred             ccceEEEecCCCChHHheeCCEEE-EeCCC------EEECHHHHHhhhC
Confidence            355567899999999999988733 22221      3588999998887

>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=98.63  E-value=9e-09  Score=94.49  Aligned_cols=88  Identities=11%  Similarity=0.017  Sum_probs=65.4

Q ss_pred             CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCH---------------HHHHHHHhhcCCccccCC-CchhHHHH
Q psy1206           7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQ---------------GRLDSFFTIRREEKRKAP-CEAEAQCA   70 (531)
Q Consensus         7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~---------------~~i~~lL~~~gIp~vvAP-yEADAq~A   70 (531)
                      +|++ .+++||.+.+++.|..    .++.||++|..++               +.+.++++.+|++.+..| +||||.+|
T Consensus        51 ~p~~-viv~~D~~~~~~~R~~----l~p~YKanR~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~EADDvIa  125 (169)
T d1tfra2          51 GYTK-IVLCIDNAKSGYWRRD----FAYYYKKNRGKAREESTWDWEGYFESSHKVIDELKAYMPYIVMDIDKYEADDHIA  125 (169)
T ss_dssp             TEEE-EEEECCCCTTCCGGGG----TCTTTTC---------CCCHHHHHHHHHHHHHHHHHHSSSEEECCTTCCHHHHHH
T ss_pred             CCCe-EEEEEeCCCCCchhhh----hHHHHhhCCCCCcccchhhhhHHHHHHHHHHHHHHHHhhhhccccCCcccccHHH
Confidence            6888 9999998888876544    4566788887655               235667889999999877 79999999


Q ss_pred             HHHH----cCCEEEEEcCCCccccccC-CeE-EEe
Q psy1206          71 AMVK----AGKVYATATEDMDALTFGS-NIL-LRH   99 (531)
Q Consensus        71 ~L~r----~G~vd~ViSeDsDlL~fg~-~~V-i~~   99 (531)
                      +|++    .|.-..|+|.|+|++|+.. ++| +++
T Consensus       126 ~la~~~~~~~~~vvIvS~DkD~~QLv~~~~V~~~~  160 (169)
T d1tfra2         126 VLVKKFSLEGHKILIISSDGDFTQLHKYPNVKQWS  160 (169)
T ss_dssp             HHHHHHHHTTCCEEEECCCGGGGGGTTSTTEEEEE
T ss_pred             HHHHHHHHCCCcEEEEeCCCCHHHhCcCCCeEEee
Confidence            9985    4666678999999999987 776 443

>d1xo1a1 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: T5 5'-exonuclease
species: Bacteriophage T5 [TaxId: 10726]

Probab=98.54  E-value=2.2e-08  Score=85.13  Aligned_cols=45  Identities=29%  Similarity=0.588  Sum_probs=43.3

Q ss_pred             Hhhhhhhhhhcc--CccccCCCCCchHHHHHHHHhhccHHHHHHHHh
Q psy1206         229 LYSFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENID  273 (531)
Q Consensus       229 ~e~F~~~CiLsG--CDY~~~i~giG~k~A~kli~k~~s~~~vi~~l~  273 (531)
                      .++|+++++|.|  +|++|++||||+|||.+++++|+|++.++.++.
T Consensus         4 ~eq~~d~~aL~GD~sDnipGV~GiG~KtA~kli~~~gsle~i~~~~~   50 (105)
T d1xo1a1           4 VEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLP   50 (105)
T ss_dssp             HHHHHHHHHHHCBGGGTBCCCTTCCHHHHHHHHHHHCSHHHHHHHCS
T ss_pred             HHHHHHHHHHhCCcccCCcCcCCcCHHHHHHHHHHcchhHHHHHhHH
Confidence            579999999999  999999999999999999999999999999985

>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=98.46  E-value=7e-08  Score=87.98  Aligned_cols=104  Identities=17%  Similarity=0.059  Sum_probs=68.3

Q ss_pred             CCCccceeecccCCCCCcchhHHhHHHHHHhhccCCCHH---------------HHHHHH--hhcCCccccCC-CchhHH
Q psy1206           7 DPDEDGLVKYLCGDKNFAEDRIRNGAKKLLKARSSTTQG---------------RLDSFF--TIRREEKRKAP-CEAEAQ   68 (531)
Q Consensus         7 ~~d~~~~~a~~~~~~~f~~~~~R~~~~~~~k~~~~~t~~---------------~i~~lL--~~~gIp~vvAP-yEADAq   68 (531)
                      +|++ .+|++|.+.++     +|+..++.||++|...++               .+..++  ...|++++..| +||||.
T Consensus        41 ~~~~-iiv~~d~~~~~-----~R~~l~p~YKanR~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~EADDi  114 (167)
T d1xo1a2          41 SART-TIVLGDKGKSV-----FRLEHLPEYAGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDM  114 (167)
T ss_dssp             TEEE-EEEECCBSCCH-----HHHTTCTTCC--------------------CHHHHHHHHHHHHTTSCEECCTTBCHHHH
T ss_pred             CCCE-EEEEEeCCCCC-----cccccchhhhhcCCCCchhcccchhHHHHHHHHHHHHHHHHhhccccEEEeccccchhH
Confidence            7888 89999976444     455667778888864431               233332  24589999887 799999


Q ss_pred             HHHHHH----cCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhC
Q psy1206          69 CAAMVK----AGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGM  122 (531)
Q Consensus        69 ~A~L~r----~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~l  122 (531)
                      +|+|++    .|.-..|+|.|+|++|+..++|..--...+      ..++.+.+.+++
T Consensus       115 Ia~l~~~~~~~~~~v~IvS~DkD~~QLv~~~v~~~~~~~k------k~~~~~~~~e~~  166 (167)
T d1xo1a2         115 AAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSFTTR------REYHLRDMYEHH  166 (167)
T ss_dssp             HHHHHHHHGGGSSCEEEECSCGGGGGGCBTTEEEECTTTC------CEECGGGHHHHH
T ss_pred             HHHHHHHhhcCCCEEEEEeCCccHHHheeCCEEEEeCCCC------EEEchhhhhhcC
Confidence            999985    466567899999999999988744211111      357777777654

>d1cmwa1 a.60.7.1 (A:174-289) 5' to 3' exonuclease domain of DNA polymerase Taq {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: SAM domain-like
superfamily: 5' to 3' exonuclease, C-terminal subdomain
family: 5' to 3' exonuclease, C-terminal subdomain
domain: 5' to 3' exonuclease domain of DNA polymerase Taq
species: Thermus aquaticus [TaxId: 271]

Probab=97.71  E-value=6.9e-07  Score=76.27  Aligned_cols=45  Identities=36%  Similarity=0.553  Sum_probs=41.6

Q ss_pred             Hhhhhhhhhhcc--CccccCCCCCchHHHHHHHHhhccHHHHHHHHh
Q psy1206         229 LYSFIDLCILLG--CDYCDSIRGIGPKRAIELIKEHRSIEKILENID  273 (531)
Q Consensus       229 ~e~F~~~CiLsG--CDY~~~i~giG~k~A~kli~k~~s~~~vi~~l~  273 (531)
                      .++|.+...|.|  .|.+|+|||||+|||.+|+.+|+|++.|++++.
T Consensus         3 P~~~~~~~~l~GD~sDnipGv~GiG~KtA~kll~~~gsle~i~~~~~   49 (116)
T d1cmwa1           3 PDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLD   49 (116)
T ss_dssp             GGGHHHHHHTTCCSSSCCCCCCCSTTCTTTTTGGGGGTTCSSSSSCC
T ss_pred             HHHHHHHHHHhCccccCcccccccCchhHHHHHHhcchHHHHHHHHh
Confidence            368999999999  999999999999999999999999998888764

>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Excinuclease UvrC C-terminal domain
domain: Excinuclease UvrC C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=97.23  E-value=8.6e-05  Score=55.48  Aligned_cols=28  Identities=29%  Similarity=0.529  Sum_probs=24.9

Q ss_pred             CCCCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206         141 CDSIRGIGPKRAIELIKEHRSIEKILEN  168 (531)
Q Consensus       141 ~pGIpGIG~ktA~kLI~~~~sle~il~~  168 (531)
                      +..|||||+++|.+|+++|+|+++|.+.
T Consensus         4 L~~I~gVG~~~a~~L~~~F~s~~~i~~A   31 (56)
T d1kfta_           4 LETIEGVGPKRRQMLLKYMGGLQGLRNA   31 (56)
T ss_dssp             GGGCTTCSSSHHHHHHHHHSCHHHHHHC
T ss_pred             cccCCCccHHHHHHHHHHhCCHHHHHHh
Confidence            4579999999999999999999988763

>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Mycobacterium leprae [TaxId: 1769]

Probab=97.12  E-value=0.00023  Score=55.72  Aligned_cols=28  Identities=21%  Similarity=0.517  Sum_probs=23.5

Q ss_pred             CCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206         143 SIRGIGPKRAIELIKEHRSIEKILENIDT  171 (531)
Q Consensus       143 GIpGIG~ktA~kLI~~~~sle~il~~l~~  171 (531)
                      +|+|||||+|+.++..+ +++++.+.+..
T Consensus        13 ~V~GIGpK~Al~iLs~~-~~~~l~~aI~~   40 (71)
T d1bvsa2          13 SVSGVGPRLAMATLAVH-DAAALRQALAD   40 (71)
T ss_dssp             TSSSCCHHHHHHHHHHS-CHHHHHHHTTT
T ss_pred             ccCCcCHHHHHHHHHhC-CHHHHHHHHHc
Confidence            68999999999999887 66888877643

>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=97.11  E-value=0.00029  Score=55.44  Aligned_cols=28  Identities=25%  Similarity=0.425  Sum_probs=23.3

Q ss_pred             CCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206         143 SIRGIGPKRAIELIKEHRSIEKILENIDT  171 (531)
Q Consensus       143 GIpGIG~ktA~kLI~~~~sle~il~~l~~  171 (531)
                      +|+|||||+|+.+++.++ .+++.+.+..
T Consensus        14 ~V~GIGpk~Al~iLs~~~-~~~l~~aI~~   41 (73)
T d1ixra1          14 SVSGVGPKVALALLSALP-PRLLARALLE   41 (73)
T ss_dssp             SSSCCCHHHHHHHHHHSC-HHHHHHHHHT
T ss_pred             ccCCcCHHHHHHHHHHcc-HHHHHHHHHh
Confidence            689999999999998765 5788877744

>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=97.06  E-value=0.00028  Score=54.53  Aligned_cols=27  Identities=19%  Similarity=0.388  Sum_probs=24.6

Q ss_pred             CCCCCccHHHHHHHHHHcCCHHHHHHH
Q psy1206         142 DSIRGIGPKRAIELIKEHRSIEKILEN  168 (531)
Q Consensus       142 pGIpGIG~ktA~kLI~~~~sle~il~~  168 (531)
                      .||||||+++|.+|+++|+|++++.+.
T Consensus        13 ~~I~gIG~~~a~~L~~~f~s~~~i~~A   39 (68)
T d1x2ia1          13 EGLPHVSATLARRLLKHFGSVERVFTA   39 (68)
T ss_dssp             TTSTTCCHHHHHHHHHHHCSHHHHHHC
T ss_pred             cCCCCcCHHHHHHHHHHcCCHHHHHHh
Confidence            489999999999999999999988754

>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Escherichia coli [TaxId: 562]

Probab=96.70  E-value=0.00054  Score=54.50  Aligned_cols=28  Identities=21%  Similarity=0.561  Sum_probs=23.2

Q ss_pred             CCCCccHHHHHHHHHHcCCHHHHHHHhhh
Q psy1206         143 SIRGIGPKRAIELIKEHRSIEKILENIDT  171 (531)
Q Consensus       143 GIpGIG~ktA~kLI~~~~sle~il~~l~~  171 (531)
                      +|+|||||+|+.++..+ +.+++.+.+..
T Consensus        13 ~V~GIGpK~Al~iLs~~-~~~~l~~aI~~   40 (78)
T d1cuka2          13 KTNGVGPKLALAILSGM-SAQQFVNAVER   40 (78)
T ss_dssp             HSSSCCHHHHHHHHHHS-CHHHHHHHHHT
T ss_pred             ccCCccHHHHHHHHHhC-CHHHHHHHHHc
Confidence            58999999999999887 46888877744

>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: NAD+-dependent DNA ligase, domain 3
domain: NAD+-dependent DNA ligase, domain 3
species: Thermus filiformis [TaxId: 276]

Probab=95.75  E-value=0.0043  Score=56.38  Aligned_cols=133  Identities=13%  Similarity=0.199  Sum_probs=85.3

Q ss_pred             ccCCCchhHHHHHHHHcCCEEEEEcCCCccccccCCeEEEeccccCcccCCcEEecHHHHHHhCCCCHHHHHHHHhHcCC
Q psy1206          59 RKAPCEAEAQCAAMVKAGKVYATATEDMDALTFGSNILLRHMTFSEARKLPVQEFHLEKVLEGMELSHEEFIDLCILLGC  138 (531)
Q Consensus        59 vvAPyEADAq~A~L~r~G~vd~ViSeDsDlL~fg~~~Vi~~l~~~~~~~~~v~~~~~~~i~~~lglt~eqfid~~iL~G~  138 (531)
                      +.-.+=++..+..|...|++    .+-.|++-+-.+. +..++.-|.+.  . .--.+.|...-..+.+.|+        
T Consensus        44 mdI~GlG~~~i~~L~~~g~i----~~~~Dly~L~~~~-l~~l~~~g~ks--a-~nl~~~Ie~sk~~~l~r~l--------  107 (181)
T d1dgsa1          44 MDIEGLGEKLIERLLEKGLV----RDVADLYHLRKED-LLGLERMGEKS--A-QNLLRQIEESKHRGLERLL--------  107 (181)
T ss_dssp             SCCTTCCHHHHHHHHHTTSC----SSGGGGGGGCCHH-HHTTSSCCSTT--H-HHHHHHHHHGGGCCHHHHH--------
T ss_pred             HHHHHHHHHHHHHHhhcCCc----chhhhhhhhhhHH-HhcccccchHH--H-HHHHHHHHhhcchhHHHHH--------
Confidence            33356677889999999986    4456777554433 22232222110  0 0012334444456666665        


Q ss_pred             CCCCCCCCccHHHHHHHHHHcCCHHHHHHHhhhcCCCCCCCCcHHHHHHHhcCCCcCCCCCccccccccccccccccccc
Q psy1206         139 DYCDSIRGIGPKRAIELIKEHRSIEKILENIDTKKYTVPEGWLYKEARELFRHPEVADPETIEFIDLCILLGCDYCDSIR  218 (531)
Q Consensus       139 DY~pGIpGIG~ktA~kLI~~~~sle~il~~l~~~~~~ip~~f~~~~A~~~f~~p~V~d~~~~~~v~Ls~~~~~d~cesl~  218 (531)
                       |-=||||||+++|..|+++|+|++++.+.-                                                 
T Consensus       108 -~aLGI~~vG~~~Ak~La~~f~sl~~l~~as-------------------------------------------------  137 (181)
T d1dgsa1         108 -YALGLPGVGEVLARNLARRFGTMDRLLEAS-------------------------------------------------  137 (181)
T ss_dssp             -HHTTCSSCCHHHHHHHHHTTSBHHHHTTCC-------------------------------------------------
T ss_pred             -HHHHhhhhhHHHHHHHHHHhhhhhhhhhhH-------------------------------------------------
Confidence             224899999999999999999998775310                                                 


Q ss_pred             CCChhhhHhHHhhhhhhhhhccCccccCCCCCchHHHHHHHHhhccHH--HHHHHHhhCCCCC
Q psy1206         219 GIGPKRAIELLYSFIDLCILLGCDYCDSIRGIGPKRAIELIKEHRSIE--KILENIDTKKYTV  279 (531)
Q Consensus       219 ~~Gp~~~~el~e~F~~~CiLsGCDY~~~i~giG~k~A~kli~k~~s~~--~vi~~l~~~~~~v  279 (531)
                            .                +-+.+|+|||+++|-.++.=+.+.+  .+++.|...|+.+
T Consensus       138 ------~----------------eeL~~I~GIG~~~A~si~~ff~~~~n~~~i~~L~~~Gv~~  178 (181)
T d1dgsa1         138 ------L----------------EELIEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVSM  178 (181)
T ss_dssp             ------H----------------HHHHTSTTCCHHHHHHHHHHHHCHHHHHHHHHHHHTTCCC
T ss_pred             ------H----------------HHHhhcCCcCHHHHHHHHHHHCCHHHHHHHHHHHHcCCCc
Confidence                  0                0124689999999999999888764  5788887666553

>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.60  E-value=0.0014  Score=49.40  Aligned_cols=28  Identities=14%  Similarity=0.351  Sum_probs=24.8

Q ss_pred             CCCCCCCccHHHHHHHHHHcCCHHHHHH
Q psy1206         140 YCDSIRGIGPKRAIELIKEHRSIEKILE  167 (531)
Q Consensus       140 Y~pGIpGIG~ktA~kLI~~~~sle~il~  167 (531)
                      .+.+|||||++++..|+++|+|++++.+
T Consensus         4 ~L~~iPGIg~~~~~~Ll~~f~Si~~l~~   31 (62)
T d2a1ja1           4 FLLKMPGVNAKNCRSLMHHVKNIAELAA   31 (62)
T ss_dssp             HHHTSTTCCHHHHHHHHHHCSSHHHHHT
T ss_pred             HHhcCCCCCHHHHHHHHHHhccHHHHHh
Confidence            3458999999999999999999998864

>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Excinuclease UvrC C-terminal domain
domain: Excinuclease UvrC C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.28  E-value=0.0038  Score=46.14  Aligned_cols=28  Identities=29%  Similarity=0.529  Sum_probs=25.6

Q ss_pred             ccCCCCCchHHHHHHHHhhccHHHHHHH
Q psy1206         244 CDSIRGIGPKRAIELIKEHRSIEKILEN  271 (531)
Q Consensus       244 ~~~i~giG~k~A~kli~k~~s~~~vi~~  271 (531)
                      |.+|||||+++|-+|++.|+|+++|..+
T Consensus         4 L~~I~gVG~~~a~~L~~~F~s~~~i~~A   31 (56)
T d1kfta_           4 LETIEGVGPKRRQMLLKYMGGLQGLRNA   31 (56)
T ss_dssp             GGGCTTCSSSHHHHHHHHHSCHHHHHHC
T ss_pred             cccCCCccHHHHHHHHHHhCCHHHHHHh
Confidence            5789999999999999999999998863

>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Aeropyrum pernix [TaxId: 56636]

Probab=95.20  E-value=0.0051  Score=47.22  Aligned_cols=26  Identities=27%  Similarity=0.544  Sum_probs=23.2

Q ss_pred             CCCCCccHHHHHHHHHHcCCHHHHHH
Q psy1206         142 DSIRGIGPKRAIELIKEHRSIEKILE  167 (531)
Q Consensus       142 pGIpGIG~ktA~kLI~~~~sle~il~  167 (531)
                      .+|||||+++|..|+++|+|++++..
T Consensus        16 ~~IpgIG~~~a~~L~~~F~s~~~l~~   41 (70)
T d2bgwa1          16 QSFPGIGRRTAERILERFGSLERFFT   41 (70)
T ss_dssp             HTSTTCCHHHHHHHHHHHSSHHHHTT
T ss_pred             cCCCCcCHHHHHHHHHHhCCHHHHHH
Confidence            47999999999999999999887753

>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.08  E-value=0.0032  Score=47.39  Aligned_cols=29  Identities=17%  Similarity=0.393  Sum_probs=26.1

Q ss_pred             ccccCCCCCchHHHHHHHHhhccHHHHHH
Q psy1206         242 DYCDSIRGIGPKRAIELIKEHRSIEKILE  270 (531)
Q Consensus       242 DY~~~i~giG~k~A~kli~k~~s~~~vi~  270 (531)
                      |.+.+|||||++++..|+++++|+++|..
T Consensus         3 d~L~~iPGIg~~~~~~Ll~~f~Si~~l~~   31 (62)
T d2a1ja1           3 DFLLKMPGVNAKNCRSLMHHVKNIAELAA   31 (62)
T ss_dssp             HHHHTSTTCCHHHHHHHHHHCSSHHHHHT
T ss_pred             hHHhcCCCCCHHHHHHHHHHhccHHHHHh
Confidence            55779999999999999999999988764

>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=94.08  E-value=0.013  Score=44.72  Aligned_cols=28  Identities=18%  Similarity=0.374  Sum_probs=25.0

Q ss_pred             ccCCCCCchHHHHHHHHhhccHHHHHHH
Q psy1206         244 CDSIRGIGPKRAIELIKEHRSIEKILEN  271 (531)
Q Consensus       244 ~~~i~giG~k~A~kli~k~~s~~~vi~~  271 (531)
                      +.+|||||+++|.+|++.|+|+++++.+
T Consensus        12 L~~I~gIG~~~a~~L~~~f~s~~~i~~A   39 (68)
T d1x2ia1          12 VEGLPHVSATLARRLLKHFGSVERVFTA   39 (68)
T ss_dssp             HTTSTTCCHHHHHHHHHHHCSHHHHHHC
T ss_pred             HcCCCCcCHHHHHHHHHHcCCHHHHHHh
Confidence            3479999999999999999999998864

>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA excision repair protein ERCC-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.40  E-value=0.023  Score=44.36  Aligned_cols=26  Identities=12%  Similarity=0.397  Sum_probs=23.7

Q ss_pred             CCCCCccHHHHHHHHHHcCCHHHHHH
Q psy1206         142 DSIRGIGPKRAIELIKEHRSIEKILE  167 (531)
Q Consensus       142 pGIpGIG~ktA~kLI~~~~sle~il~  167 (531)
                      .+|||||+++|..|+++|+|+++++.
T Consensus        22 ~~I~gIg~~~a~~L~~~F~s~~~i~~   47 (78)
T d2a1jb1          22 TTVKSVNKTDSQTLLTTFGSLEQLIA   47 (78)
T ss_dssp             TTSTTCCHHHHHHHHHHHSSHHHHHS
T ss_pred             cCCCCcCHHHHHHHHHHhCCcHHHHh
Confidence            46999999999999999999998864

>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Aeropyrum pernix [TaxId: 56636]

Probab=92.77  E-value=0.016  Score=44.25  Aligned_cols=27  Identities=26%  Similarity=0.506  Sum_probs=23.9

Q ss_pred             ccCCCCCchHHHHHHHHhhccHHHHHH
Q psy1206         244 CDSIRGIGPKRAIELIKEHRSIEKILE  270 (531)
Q Consensus       244 ~~~i~giG~k~A~kli~k~~s~~~vi~  270 (531)
                      +.+|||||+++|.+|++.++|++.+..
T Consensus        15 L~~IpgIG~~~a~~L~~~F~s~~~l~~   41 (70)
T d2bgwa1          15 LQSFPGIGRRTAERILERFGSLERFFT   41 (70)
T ss_dssp             HHTSTTCCHHHHHHHHHHHSSHHHHTT
T ss_pred             HcCCCCcCHHHHHHHHHHhCCHHHHHH
Confidence            456999999999999999999988764

>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=92.31  E-value=0.045  Score=40.61  Aligned_cols=26  Identities=27%  Similarity=0.465  Sum_probs=23.2

Q ss_pred             CCCCCccHHHHHHHHHH-cCCHHHHHH
Q psy1206         142 DSIRGIGPKRAIELIKE-HRSIEKILE  167 (531)
Q Consensus       142 pGIpGIG~ktA~kLI~~-~~sle~il~  167 (531)
                      ..|||||+++|-+|... |+|+++|..
T Consensus         2 ~~IpGIG~~~a~~L~~~G~~tv~~l~~   28 (60)
T d2i1qa1           2 TDLPGVGPSTAEKLVEAGYIDFMKIAT   28 (60)
T ss_dssp             TTSTTCCHHHHHHHHHHTCCSHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHccCCCHHHHHh
Confidence            46999999999999997 999988864

>d2bcqa2 a.60.12.1 (A:329-385) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: DNA polymerase beta-like, second domain
domain: DNA polymerase lambda
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.46  E-value=0.098  Score=38.65  Aligned_cols=26  Identities=35%  Similarity=0.456  Sum_probs=23.1

Q ss_pred             CCCCccHHHHHHHHHH-cCCHHHHHHH
Q psy1206         143 SIRGIGPKRAIELIKE-HRSIEKILEN  168 (531)
Q Consensus       143 GIpGIG~ktA~kLI~~-~~sle~il~~  168 (531)
                      +|.||||++|.+|+.+ +.|++++.++
T Consensus        12 ~I~GvGp~~A~~l~~~Gi~ti~dLr~~   38 (57)
T d2bcqa2          12 NIWGAGTKTAQMWYQQGFRSLEDIRSQ   38 (57)
T ss_dssp             TSTTCCHHHHHHHHHTTCCSHHHHHHH
T ss_pred             ccccccHHHHHHHHHhCCCCHHHHHhc
Confidence            7899999999999986 6899998764

>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA excision repair protein ERCC-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.33  E-value=0.055  Score=42.05  Aligned_cols=27  Identities=11%  Similarity=0.364  Sum_probs=24.7

Q ss_pred             ccCCCCCchHHHHHHHHhhccHHHHHH
Q psy1206         244 CDSIRGIGPKRAIELIKEHRSIEKILE  270 (531)
Q Consensus       244 ~~~i~giG~k~A~kli~k~~s~~~vi~  270 (531)
                      +.+|||||.++|..|+++|+|+++++.
T Consensus        21 L~~I~gIg~~~a~~L~~~F~s~~~i~~   47 (78)
T d2a1jb1          21 LTTVKSVNKTDSQTLLTTFGSLEQLIA   47 (78)
T ss_dssp             HTTSTTCCHHHHHHHHHHHSSHHHHHS
T ss_pred             hcCCCCcCHHHHHHHHHHhCCcHHHHh
Confidence            567999999999999999999999874

>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=90.11  E-value=0.075  Score=39.43  Aligned_cols=27  Identities=26%  Similarity=0.457  Sum_probs=23.0

Q ss_pred             CCCCCCccHHHHHHHHHH-cCCHHHHHH
Q psy1206         141 CDSIRGIGPKRAIELIKE-HRSIEKILE  167 (531)
Q Consensus       141 ~pGIpGIG~ktA~kLI~~-~~sle~il~  167 (531)
                      +..|||||+++|-+|+.. |+|+++|..
T Consensus         3 L~~i~GIG~~~a~~L~~~g~~sv~~l~~   30 (61)
T d1pzna1           3 IEDLPGVGPATAEKLREAGYDTLEAIAV   30 (61)
T ss_dssp             SSCCTTCCHHHHHHHHTTTCCSHHHHHT
T ss_pred             cccCCCCCHHHHHHHHHhcCCCHHHHHh
Confidence            457999999999999985 799888764

>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=90.01  E-value=0.099  Score=38.67  Aligned_cols=27  Identities=26%  Similarity=0.429  Sum_probs=23.9

Q ss_pred             ccCCCCCchHHHHHHHHh-hccHHHHHH
Q psy1206         244 CDSIRGIGPKRAIELIKE-HRSIEKILE  270 (531)
Q Consensus       244 ~~~i~giG~k~A~kli~k-~~s~~~vi~  270 (531)
                      +..|||||+++|-+|... ++|++.|..
T Consensus         1 L~~IpGIG~~~a~~L~~~G~~tv~~l~~   28 (60)
T d2i1qa1           1 LTDLPGVGPSTAEKLVEAGYIDFMKIAT   28 (60)
T ss_dssp             CTTSTTCCHHHHHHHHHHTCCSHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHccCCCHHHHHh
Confidence            457999999999999998 999988774

>d1jmsa3 a.60.12.1 (A:243-302) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: DNA polymerase beta-like, second domain
domain: Terminal deoxynucleotidyl transferase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.96  E-value=0.095  Score=39.07  Aligned_cols=25  Identities=32%  Similarity=0.480  Sum_probs=22.3

Q ss_pred             CCCCccHHHHHHHHHH-cCCHHHHHH
Q psy1206         143 SIRGIGPKRAIELIKE-HRSIEKILE  167 (531)
Q Consensus       143 GIpGIG~ktA~kLI~~-~~sle~il~  167 (531)
                      +|.||||++|.+++.+ +.|++++.+
T Consensus        12 ~I~GvGp~~A~~l~~~Gi~ti~dL~~   37 (60)
T d1jmsa3          12 SVFGVGLKTAEKWFRMGFRTLSKIQS   37 (60)
T ss_dssp             TSTTCCHHHHHHHHHTTCCSHHHHHH
T ss_pred             ccccccHHHHHHHHHhCCCCHHHHHh
Confidence            7899999999999986 689998874

>d2fmpa2 a.60.12.1 (A:92-148) DNA polymerase beta {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: PsbU/PolX domain-like
family: DNA polymerase beta-like, second domain
domain: DNA polymerase beta
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.85  E-value=0.13  Score=38.01  Aligned_cols=26  Identities=27%  Similarity=0.617  Sum_probs=22.1

Q ss_pred             CCCCCccHHHHHHHHHH-cCCHHHHHH
Q psy1206         142 DSIRGIGPKRAIELIKE-HRSIEKILE  167 (531)
Q Consensus       142 pGIpGIG~ktA~kLI~~-~~sle~il~  167 (531)
                      -+|.||||++|.+|+.+ +.|++++.+
T Consensus        10 ~~I~GvGp~~A~~l~~~Gi~ti~dLr~   36 (57)
T d2fmpa2          10 TRVSGIGPSAARKFVDEGIKTLEDLRK   36 (57)
T ss_dssp             TTSTTCCHHHHHHHHHTTCCSHHHHHT
T ss_pred             hccccccHHHHHHHHHhCCCCHHHHHh
Confidence            47999999999999986 679988853

>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=88.36  E-value=0.09  Score=38.97  Aligned_cols=27  Identities=26%  Similarity=0.457  Sum_probs=23.0

Q ss_pred             ccCCCCCchHHHHHHHHh-hccHHHHHH
Q psy1206         244 CDSIRGIGPKRAIELIKE-HRSIEKILE  270 (531)
Q Consensus       244 ~~~i~giG~k~A~kli~k-~~s~~~vi~  270 (531)
                      +.+|||||+++|-+|... ++|++.|..
T Consensus         3 L~~i~GIG~~~a~~L~~~g~~sv~~l~~   30 (61)
T d1pzna1           3 IEDLPGVGPATAEKLREAGYDTLEAIAV   30 (61)
T ss_dssp             SSCCTTCCHHHHHHHHTTTCCSHHHHHT
T ss_pred             cccCCCCCHHHHHHHHHhcCCCHHHHHh
Confidence            568999999999999987 699887763

>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Mycobacterium leprae [TaxId: 1769]

Probab=86.16  E-value=0.27  Score=37.73  Aligned_cols=28  Identities=21%  Similarity=0.517  Sum_probs=19.1

Q ss_pred             CCCCCchHHHHHHHHhhccHHHHHHHHhh
Q psy1206         246 SIRGIGPKRAIELIKEHRSIEKILENIDT  274 (531)
Q Consensus       246 ~i~giG~k~A~kli~k~~s~~~vi~~l~~  274 (531)
                      +++|||||+|+.++..+ +++.+..++..
T Consensus        13 ~V~GIGpK~Al~iLs~~-~~~~l~~aI~~   40 (71)
T d1bvsa2          13 SVSGVGPRLAMATLAVH-DAAALRQALAD   40 (71)
T ss_dssp             TSSSCCHHHHHHHHHHS-CHHHHHHHTTT
T ss_pred             ccCCcCHHHHHHHHHhC-CHHHHHHHHHc
Confidence            56778888888777666 45666666643

>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=85.82  E-value=0.17  Score=39.06  Aligned_cols=37  Identities=22%  Similarity=0.246  Sum_probs=26.7

Q ss_pred             CCCHHHHHHHHhHcC-CCCCCCCCCccHHHHHHHHHHcC
Q psy1206         123 ELSHEEFIDLCILLG-CDYCDSIRGIGPKRAIELIKEHR  160 (531)
Q Consensus       123 glt~eqfid~~iL~G-~DY~pGIpGIG~ktA~kLI~~~~  160 (531)
                      .+++++|+..- ..| .+.+..|||||+|||-+++.+..
T Consensus        29 ~~~~~~l~~aI-~~~D~~~L~~vpGIG~KtA~rIi~eLk   66 (73)
T d1ixra1          29 ALPPRLLARAL-LEGDARLLTSASGVGRRLAERIALELK   66 (73)
T ss_dssp             HSCHHHHHHHH-HTTCHHHHTTSTTCCHHHHHHHHHHHT
T ss_pred             HccHHHHHHHH-HhcCHHHhhcCCCCCHHHHHHHHHHHH
Confidence            35677766543 333 45667999999999999998653

>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Escherichia coli [TaxId: 562]

Probab=84.13  E-value=0.17  Score=39.62  Aligned_cols=37  Identities=27%  Similarity=0.301  Sum_probs=26.6

Q ss_pred             CCCHHHHHHHHhHcCCCCCCCCCCccHHHHHHHHHHc
Q psy1206         123 ELSHEEFIDLCILLGCDYCDSIRGIGPKRAIELIKEH  159 (531)
Q Consensus       123 glt~eqfid~~iL~G~DY~pGIpGIG~ktA~kLI~~~  159 (531)
                      .+++++|+..-.----+.+..|||||+|||-++|.+.
T Consensus        28 ~~~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~eL   64 (78)
T d1cuka2          28 GMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEM   64 (78)
T ss_dssp             HSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHccCHHHhhcCCCCCHHHHHHHHHHH
Confidence            3677777765433224555699999999999999753

>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=82.56  E-value=0.8  Score=39.67  Aligned_cols=60  Identities=27%  Similarity=0.451  Sum_probs=44.7

Q ss_pred             cceeeecccchHHHHHHHHhhcCccccCCCCCCcchhhhHHHHHHHHHHc-CCeeEEeecCCCCC
Q psy1206         317 SRKICIDASMSLYQFLIAVRSEGNQLMSVDGEPTSHLMGTFYRTIRLVEH-GLKPIYVFDGKPPT  380 (531)
Q Consensus       317 gk~iAIDa~~~lyqfl~~ir~~g~~l~~~~g~~tshl~g~~~R~~~ll~~-gIkPVfVFDG~pp~  380 (531)
                      ++.+-||+++.+|....+..    .+.+++|..|.-+.|+..-+.+++.. .=.-+.|||+.-+.
T Consensus         3 ~~~lLIDg~~l~~R~~~a~~----~~~~~~g~~~~~i~gf~~~l~~~~~~~~~~~~v~~d~~~~~   63 (164)
T d1cmwa2           3 GRVLLVDGHHLAYRTFHALK----GLTTSRGEPVQAVYGFAKSLLKALKEDGDAVIVVFDAKAPS   63 (164)
T ss_dssp             EEEEEEETTHHHHHHHTSST----TCBCTTSCBCHHHHHHHHHHHHHHHHCCSEEEEECCCSSSC
T ss_pred             CeEEEEeChHHHHHHHHcCC----cccCCCCCeeHHHHHHHHHHHHHHhcCCceEEEEEeccccc
Confidence            57889999999998777653    46688999999998988877777544 33456677665443