Psyllid ID: psy1207

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110---
Protein Sequence
MELTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQLSWATFSMHCWE
Secondary Structure (PSIPRED)
ccHHHHHHcccHHHHHHHHcccccccHHHHHHHHHHHHHHcccEEEccccccccccccccccccHHHHHHHHHHHcccEEEEEccccccccccccHHHHHccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHcccHHHHHHHHHHHEEccHHHHHHHHHHHHHccccEEEEcccccccHHHccEEccccHHHHHHHHHHHccccEEEccccHHHHccccEEEEHcccHHHccccccc
Coil and Loop (DISEMBL)
MELTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLmgipyievsrsprllpnflgvlapcEAEAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQLSWATFSMHCWE
Flexible Loop (DISEMBL)
meltlflltgdaqeidkfnrrlvrvssvhVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQLSWATFSMHCWE
Low Complexity Region (SEG)
MELTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQLSWATFSMHCWE
Disordered region (IsUnstruct)
***TLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQLSWATFSMHCW*
Disordered Region (DISOPRED)
*ELTLFL*********************HVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQLSWATFSMHC**
Disordered Region (DISEMBL)
MELTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQLSWATFSMHCWE
Disordered Region (DISPRO)
MELTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQLSWA********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MELTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQLSWATFSMHCWE
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	113	2.2.26 [Sep-21-2011]
A7RRJ0	377	Flap endonuclease 1 OS=Ne	N/A	N/A	0.672	0.201	0.626	4e-27
B5DUR8	386	Flap endonuclease 1 OS=Dr	yes	N/A	0.663	0.194	0.655	7e-27
B4GIM3	386	Flap endonuclease 1 OS=Dr	N/A	N/A	0.663	0.194	0.655	7e-27
B3MDA3	388	Flap endonuclease 1 OS=Dr	N/A	N/A	0.663	0.193	0.655	8e-27
B4MR84	388	Flap endonuclease 1 OS=Dr	N/A	N/A	0.663	0.193	0.644	2e-26
B4LM90	386	Flap endonuclease 1 OS=Dr	N/A	N/A	0.663	0.194	0.655	2e-26
Q7Q323	383	Flap endonuclease 1 OS=An	yes	N/A	0.672	0.198	0.626	2e-26
Q178M1	380	Flap endonuclease 1 OS=Ae	N/A	N/A	0.672	0.2	0.626	2e-26
D3TQJ5	382	Flap endonuclease 1 OS=Gl	N/A	N/A	0.672	0.198	0.626	4e-26
B3NP61	387	Flap endonuclease 1 OS=Dr	N/A	N/A	0.663	0.193	0.644	5e-26

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

 Score =  119 bits (299), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 57/91 (62%), Positives = 67/91 (73%), Gaps = 15/91 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           GD + IDKF+RRLVRV+  H +ECK+LL LMGIPY+E               APCEAEAQ
Sbjct: 118 GDTENIDKFSRRLVRVTKEHNEECKQLLKLMGIPYVE---------------APCEAEAQ 162

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
           CAA+VK+GKVYAT TEDMDALTFGT ++LR 
Sbjct: 163 CAALVKSGKVYATGTEDMDALTFGTTVMLRH 193

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: 3EC: .EC: 1EC: .EC: -EC: .EC: -

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

 Score =  119 bits (297), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 59/90 (65%), Positives = 67/90 (74%), Gaps = 15/90 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           GD  EI+KFNRRLVRV+  H +E KELLSLMG+PY++               APCEAEAQ
Sbjct: 118 GDDAEIEKFNRRLVRVTKEHAREAKELLSLMGVPYVD---------------APCEAEAQ 162

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLR 99
           CAA+VKAGKVYATATEDMDALTFG+  LLR
Sbjct: 163 CAALVKAGKVYATATEDMDALTFGSTKLLR 192

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

 Score =  119 bits (297), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 59/90 (65%), Positives = 67/90 (74%), Gaps = 15/90 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           GD  EI+KFNRRLVRV+  H +E KELLSLMG+PY++               APCEAEAQ
Sbjct: 118 GDDAEIEKFNRRLVRVTKEHAREAKELLSLMGVPYVD---------------APCEAEAQ 162

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLR 99
           CAA+VKAGKVYATATEDMDALTFG+  LLR
Sbjct: 163 CAALVKAGKVYATATEDMDALTFGSTKLLR 192

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: -

>sp|B3MDA3|FEN1_DROAN Flap endonuclease 1 OS=Drosophila ananassae GN=Fen1 PE=3 SV=1

 Score =  118 bits (296), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 59/90 (65%), Positives = 66/90 (73%), Gaps = 15/90 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           GD  EI+KFNRRLVRV+  H +E KELL LMG+PY+E               APCEAEAQ
Sbjct: 118 GDDAEIEKFNRRLVRVTKEHAREAKELLKLMGVPYVE---------------APCEAEAQ 162

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLR 99
           CAA+VKAGKVYATATEDMDALTFG+  LLR
Sbjct: 163 CAALVKAGKVYATATEDMDALTFGSTKLLR 192

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 ananassae (taxid: 7217)

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 =  117 bits (294), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 58/90 (64%), Positives = 67/90 (74%), Gaps = 15/90 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           GD  EI+KFNRRLVRV+  H +E KELL LMG+PY++               APCEAEAQ
Sbjct: 118 GDEAEIEKFNRRLVRVTKEHAREAKELLKLMGVPYVD---------------APCEAEAQ 162

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLR 99
           CAA+VKAGKVYATATEDMDALTFG++ LLR
Sbjct: 163 CAALVKAGKVYATATEDMDALTFGSSKLLR 192

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|B4LM90|FEN1_DROVI Flap endonuclease 1 OS=Drosophila virilis GN=Fen1 PE=3 SV=1

 Score =  117 bits (294), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 59/90 (65%), Positives = 66/90 (73%), Gaps = 15/90 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           GD  EIDKFNRRLVRV+  H +E KELL LMG+PY++               APCEAEAQ
Sbjct: 118 GDEAEIDKFNRRLVRVTKEHSREAKELLKLMGVPYVD---------------APCEAEAQ 162

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLR 99
           CAA+VKAGKVYATATEDMDALTFG+  LLR
Sbjct: 163 CAALVKAGKVYATATEDMDALTFGSCKLLR 192

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 virilis (taxid: 7244)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

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

 Score =  117 bits (293), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 57/91 (62%), Positives = 67/91 (73%), Gaps = 15/91 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           G  ++I+KFNRRLV+V+  H  E KELL LMG+PY+E               APCEAEAQ
Sbjct: 118 GATEDIEKFNRRLVKVTKHHANEAKELLRLMGVPYVE---------------APCEAEAQ 162

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
           CAA+V+AGKVYATATEDMDALTFG+NILLR 
Sbjct: 163 CAALVRAGKVYATATEDMDALTFGSNILLRH 193

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

 Score =  117 bits (293), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 57/91 (62%), Positives = 66/91 (72%), Gaps = 15/91 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           G  ++IDKFNRRLV+V+  H  E KELL LMG+PY++               APCEAEAQ
Sbjct: 118 GVTEDIDKFNRRLVKVTKQHSNEAKELLKLMGVPYVD---------------APCEAEAQ 162

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
           CAA+VK GKVYATATEDMDALTFG+NILLR 
Sbjct: 163 CAALVKGGKVYATATEDMDALTFGSNILLRH 193

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: 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 =  116 bits (290), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 57/91 (62%), Positives = 66/91 (72%), Gaps = 15/91 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           G+  ++DKFNRRLV+V+  H  E KELL LMG+PY+E               APCEAEAQ
Sbjct: 118 GNEADMDKFNRRLVKVTKEHANEAKELLKLMGVPYVE---------------APCEAEAQ 162

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
           CAA+VKAGKVYATATEDMDALTFG+ ILLR 
Sbjct: 163 CAALVKAGKVYATATEDMDALTFGSGILLRH 193

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|B3NP61|FEN1_DROER Flap endonuclease 1 OS=Drosophila erecta GN=Fen1 PE=3 SV=1

 Score =  116 bits (290), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 58/90 (64%), Positives = 66/90 (73%), Gaps = 15/90 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           GD   I+KFNRRLVRV+  H KE KELL+LMG+PY++               APCEAEAQ
Sbjct: 118 GDDAGIEKFNRRLVRVTKEHAKEAKELLTLMGVPYVD---------------APCEAEAQ 162

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLR 99
           CAA+VKAGKVYATATEDMDALTFG+  LLR
Sbjct: 163 CAALVKAGKVYATATEDMDALTFGSTKLLR 192

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 erecta (taxid: 7220)

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	113
242014497	380	Flap endonuclease 1-B, putative [Pedicul	0.681	0.202	0.663	2e-27
332376861	380	unknown [Dendroctonus ponderosae]	0.672	0.2	0.648	6e-26
193659550	380	PREDICTED: flap endonuclease 1 [Acyrthos	0.672	0.2	0.648	7e-26
307214986	380	Flap endonuclease 1-B [Harpegnathos salt	0.672	0.2	0.648	7e-26
91085979	381	PREDICTED: similar to flap endonuclease-	0.672	0.199	0.648	8e-26
383859686	383	PREDICTED: flap endonuclease 1-like [Meg	0.672	0.198	0.637	1e-25
156398094	377	predicted protein [Nematostella vectensi	0.672	0.201	0.626	2e-25
321473340	374	hypothetical protein DAPPUDRAFT_47502 [D	0.734	0.221	0.602	2e-25
380015033	383	PREDICTED: flap endonuclease 1-like [Api	0.672	0.198	0.648	3e-25
198477405	386	GA27689 [Drosophila pseudoobscura pseudo	0.663	0.194	0.655	3e-25

>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 =  126 bits (316), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 61/92 (66%), Positives = 71/92 (77%), Gaps = 15/92 (16%)

Query: 9   TGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEA 68
           +G+ +E+DKF+RRLV+V+  HV ECKELL LMGIPYIE               APCEAEA
Sbjct: 117 SGNTEEVDKFSRRLVKVTKDHVAECKELLKLMGIPYIE---------------APCEAEA 161

Query: 69  QCAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
           QCAA+VKAGKVYATATEDMDALTFG+NI+LR 
Sbjct: 162 QCAALVKAGKVYATATEDMDALTFGSNIILRH 193

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332376861|gb|AEE63570.1| unknown [Dendroctonus ponderosae]

 Score =  121 bits (303), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 59/91 (64%), Positives = 67/91 (73%), Gaps = 15/91 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           GD  E+DKFNRRLV+V+  H  E KELL LMG+PYIE               APCEAEAQ
Sbjct: 118 GDQAEVDKFNRRLVKVTRHHADEAKELLRLMGVPYIE---------------APCEAEAQ 162

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
           CAAMVKAGK+YATATEDMDALTFG++I+LR 
Sbjct: 163 CAAMVKAGKIYATATEDMDALTFGSDIVLRH 193

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  121 bits (303), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 59/91 (64%), Positives = 68/91 (74%), Gaps = 15/91 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           GDA  IDKF++RLV+V+S H  ECKELL LMG+P++E               APCEAEAQ
Sbjct: 118 GDATGIDKFSKRLVKVTSTHTTECKELLKLMGVPFVE---------------APCEAEAQ 162

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
           CAAMVKAGKVYATATEDMDALTFG+ +LLR 
Sbjct: 163 CAAMVKAGKVYATATEDMDALTFGSPVLLRH 193

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307214986|gb|EFN89831.1| Flap endonuclease 1-B [Harpegnathos saltator]

 Score =  121 bits (303), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 59/91 (64%), Positives = 69/91 (75%), Gaps = 15/91 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           GDA+ IDKFNRRLV+V+  H +E K+LL LMGIPYI+               APCEAEAQ
Sbjct: 118 GDAEAIDKFNRRLVKVTKTHAEEAKQLLKLMGIPYID---------------APCEAEAQ 162

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
           CAA+VKAGKV+ATATEDMDALTFG N+LLR+
Sbjct: 163 CAALVKAGKVFATATEDMDALTFGCNVLLRR 193

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91085979|ref|XP_971921.1| PREDICTED: similar to flap endonuclease-1 [Tribolium castaneum] gi|270009935|gb|EFA06383.1| hypothetical protein TcasGA2_TC009261 [Tribolium castaneum]

 Score =  120 bits (302), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 59/91 (64%), Positives = 67/91 (73%), Gaps = 15/91 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           GDA E+DKFNRRLV+V+  H  E K+LL+LMG+PYIE               APCEAEAQ
Sbjct: 118 GDATEVDKFNRRLVKVTRHHADEAKQLLTLMGVPYIE---------------APCEAEAQ 162

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
           CAAMVK G VYATATEDMDALTFG+N+LLR 
Sbjct: 163 CAAMVKGGLVYATATEDMDALTFGSNVLLRH 193

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383859686|ref|XP_003705323.1| PREDICTED: flap endonuclease 1-like [Megachile rotundata]

 Score =  120 bits (300), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 58/91 (63%), Positives = 70/91 (76%), Gaps = 15/91 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           G+A++I+KFNRRLV+V+ VH  E K+LL LMGIPY+E               APCEAEAQ
Sbjct: 118 GNAEDIEKFNRRLVKVTQVHADEAKQLLKLMGIPYVE---------------APCEAEAQ 162

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
           CAA+VKAGKV+ATATEDMDALTFG N+LLR+
Sbjct: 163 CAALVKAGKVFATATEDMDALTFGCNVLLRR 193

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

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 =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 57/91 (62%), Positives = 67/91 (73%), Gaps = 15/91 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           GD + IDKF+RRLVRV+  H +ECK+LL LMGIPY+E               APCEAEAQ
Sbjct: 118 GDTENIDKFSRRLVRVTKEHNEECKQLLKLMGIPYVE---------------APCEAEAQ 162

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
           CAA+VK+GKVYAT TEDMDALTFGT ++LR 
Sbjct: 163 CAALVKSGKVYATGTEDMDALTFGTTVMLRH 193

Source: Nematostella vectensis

Species: Nematostella vectensis

Genus: Nematostella

Family: Edwardsiidae

Order: Actiniaria

Class: Anthozoa

Phylum: Cnidaria

Superkingdom: Eukaryota

>gi|321473340|gb|EFX84308.1| hypothetical protein DAPPUDRAFT_47502 [Daphnia pulex]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 59/98 (60%), Positives = 72/98 (73%), Gaps = 15/98 (15%)

Query: 2   ELTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVL 61
           +L L    GDA E++K N+RLV+V+  H  ECK+LL+LMGIPY+E               
Sbjct: 110 QLVLATDAGDAVEMEKMNKRLVKVNKGHTDECKQLLTLMGIPYVE--------------- 154

Query: 62  APCEAEAQCAAMVKAGKVYATATEDMDALTFGTNILLR 99
           APCEAEAQCAA+VKAGKVYATATEDMD+LTFG+N+LLR
Sbjct: 155 APCEAEAQCAALVKAGKVYATATEDMDSLTFGSNVLLR 192

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  119 bits (298), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 59/91 (64%), Positives = 70/91 (76%), Gaps = 15/91 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           G+A++I+KFNRRLV+V+  H +E K+LL LMGIPYI+               APCEAEAQ
Sbjct: 118 GNAEDIEKFNRRLVKVTKEHAEEAKQLLKLMGIPYID---------------APCEAEAQ 162

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
           CAAMVKAGKV+ATATEDMDALTFG NILLR+
Sbjct: 163 CAAMVKAGKVFATATEDMDALTFGCNILLRR 193

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198477405|ref|XP_002136633.1| GA27689 [Drosophila pseudoobscura pseudoobscura] gi|317374893|sp|B5DUR8.1|FEN1_DROPS RecName: Full=Flap endonuclease 1; Short=FEN-1; AltName: Full=Flap structure-specific endonuclease 1 gi|198142925|gb|EDY71637.1| GA27689 [Drosophila pseudoobscura pseudoobscura]

 Score =  119 bits (297), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 59/90 (65%), Positives = 67/90 (74%), Gaps = 15/90 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           GD  EI+KFNRRLVRV+  H +E KELLSLMG+PY++               APCEAEAQ
Sbjct: 118 GDDAEIEKFNRRLVRVTKEHAREAKELLSLMGVPYVD---------------APCEAEAQ 162

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLR 99
           CAA+VKAGKVYATATEDMDALTFG+  LLR
Sbjct: 163 CAALVKAGKVYATATEDMDALTFGSTKLLR 192

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

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	113
ZFIN|ZDB-GENE-031112-11	380	fen1 "flap structure-specific	0.663	0.197	0.622	3.8e-23
FB|FBgn0025832	385	Fen1 "Flap endonuclease 1" [Dr	0.663	0.194	0.644	4.8e-23
UNIPROTKB|P70054	382	fen1-b "Flap endonuclease 1-B"	0.663	0.196	0.611	1.3e-22
UNIPROTKB|P70040	382	fen1-a "Flap endonuclease 1-A"	0.663	0.196	0.588	1.3e-21
UNIPROTKB|P39748	380	FEN1 "Flap endonuclease 1" [Ho	0.663	0.197	0.566	1.7e-19
UNIPROTKB|J9PB88	380	FEN1 "Flap endonuclease 1" [Ca	0.663	0.197	0.555	3.7e-19
UNIPROTKB|F1RKS3	380	FEN1 "Flap endonuclease 1" [Su	0.663	0.197	0.544	3.7e-19
UNIPROTKB|Q58DH8	380	FEN1 "Flap endonuclease 1" [Bo	0.663	0.197	0.555	8.3e-19
RGD|621821	380	Fen1 "flap structure-specific	0.663	0.197	0.544	1.1e-18
MGI|MGI:102779	378	Fen1 "flap structure specific	0.663	0.198	0.544	1.4e-18

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

 Score = 267 (99.0 bits), Expect = 3.8e-23, P = 3.8e-23
 Identities = 56/90 (62%), Positives = 67/90 (74%)

Query:    10 GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
             G+ + IDKF++RLV+V+  H +ECK+LLSLMG+PYIE               APCEAEA 
Sbjct:   118 GEQENIDKFSKRLVKVTKQHNEECKKLLSLMGVPYIE---------------APCEAEAS 162

Query:    70 CAAMVKAGKVYATATEDMDALTFGTNILLR 99
             CAA+VKAGKVYATATEDMD LTFGT +LLR
Sbjct:   163 CAALVKAGKVYATATEDMDGLTFGTTVLLR 192

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 = 266 (98.7 bits), Expect = 4.8e-23, P = 4.8e-23
 Identities = 58/90 (64%), Positives = 66/90 (73%)

Query:    10 GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
             GD   I+KFNRRLVRV+  H KE KELL+LMG+PY++               APCEAEAQ
Sbjct:   118 GDDAGIEKFNRRLVRVTKEHAKEAKELLTLMGVPYVD---------------APCEAEAQ 162

Query:    70 CAAMVKAGKVYATATEDMDALTFGTNILLR 99
             CAA+VKAGKVYATATEDMDALTFG+  LLR
Sbjct:   163 CAALVKAGKVYATATEDMDALTFGSTKLLR 192

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 = 262 (97.3 bits), Expect = 1.3e-22, P = 1.3e-22
 Identities = 55/90 (61%), Positives = 67/90 (74%)

Query:    10 GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
             G+ + I+KFN+RLV+V+  H +ECK+LLSLMGIPY++               APCEAEA 
Sbjct:   118 GEVENIEKFNKRLVKVTKQHNEECKKLLSLMGIPYVD---------------APCEAEAT 162

Query:    70 CAAMVKAGKVYATATEDMDALTFGTNILLR 99
             CAA+VKAGKVYA ATEDMDALTFGT +LLR
Sbjct:   163 CAALVKAGKVYAAATEDMDALTFGTPVLLR 192

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 = 253 (94.1 bits), Expect = 1.3e-21, P = 1.3e-21
 Identities = 53/90 (58%), Positives = 66/90 (73%)

Query:    10 GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
             G+ + I+KF +RLV+V+  H +ECK+LL+LMGIPY++               APCEAEA 
Sbjct:   118 GEVENIEKFTKRLVKVTKQHNEECKKLLTLMGIPYVD---------------APCEAEAT 162

Query:    70 CAAMVKAGKVYATATEDMDALTFGTNILLR 99
             CAA+VKAGKVYA ATEDMDALTFGT +LLR
Sbjct:   163 CAALVKAGKVYAAATEDMDALTFGTPVLLR 192

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

 Score = 235 (87.8 bits), Expect = 1.7e-19, P = 1.7e-19
 Identities = 51/90 (56%), Positives = 62/90 (68%)

Query:    10 GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
             G  QE++KF +RLV+V+  H  ECK LLSLMGIPY++               AP EAEA 
Sbjct:   118 GAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLD---------------APSEAEAS 162

Query:    70 CAAMVKAGKVYATATEDMDALTFGTNILLR 99
             CAA+VKAGKVYA ATEDMD LTFG+ +L+R
Sbjct:   163 CAALVKAGKVYAAATEDMDCLTFGSPVLMR 192

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

 Score = 232 (86.7 bits), Expect = 3.7e-19, P = 3.7e-19
 Identities = 50/90 (55%), Positives = 62/90 (68%)

Query:    10 GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
             G  +E++KF +RLV+V+  H  ECK LLSLMGIPY++               AP EAEA 
Sbjct:   118 GAEEEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLD---------------APSEAEAS 162

Query:    70 CAAMVKAGKVYATATEDMDALTFGTNILLR 99
             CAA+VKAGKVYA ATEDMD LTFG+ +L+R
Sbjct:   163 CAALVKAGKVYAAATEDMDCLTFGSPVLMR 192

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

 Score = 232 (86.7 bits), Expect = 3.7e-19, P = 3.7e-19
 Identities = 49/90 (54%), Positives = 62/90 (68%)

Query:    10 GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
             G  +E++KF +RLV+V+  H  ECK LLSLMG+PY++               AP EAEA 
Sbjct:   118 GAGEEVEKFTKRLVKVTKQHNDECKHLLSLMGVPYLD---------------APSEAEAS 162

Query:    70 CAAMVKAGKVYATATEDMDALTFGTNILLR 99
             CAA+VKAGKVYA ATEDMD LTFG+ +L+R
Sbjct:   163 CAALVKAGKVYAAATEDMDCLTFGSPVLMR 192

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

 Score = 229 (85.7 bits), Expect = 8.3e-19, P = 8.3e-19
 Identities = 50/90 (55%), Positives = 61/90 (67%)

Query:    10 GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
             G   E++KF +RLV+V+  H  ECK LLSLMGIPY++               AP EAEA 
Sbjct:   118 GAEAEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLD---------------APSEAEAS 162

Query:    70 CAAMVKAGKVYATATEDMDALTFGTNILLR 99
             CAA+VKAGKVYA ATEDMD LTFG+ +L+R
Sbjct:   163 CAALVKAGKVYAAATEDMDCLTFGSPVLMR 192

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

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

 Score = 228 (85.3 bits), Expect = 1.1e-18, P = 1.1e-18
 Identities = 49/90 (54%), Positives = 61/90 (67%)

Query:    10 GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
             G  +E++KF +RLV+V+  H  ECK LLSLMGIPY++               AP EAEA 
Sbjct:   118 GAEEEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLD---------------APSEAEAS 162

Query:    70 CAAMVKAGKVYATATEDMDALTFGTNILLR 99
             CAA+ KAGKVYA ATEDMD LTFG+ +L+R
Sbjct:   163 CAALAKAGKVYAAATEDMDCLTFGSPVLMR 192

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

MGI|MGI:102779 Fen1 "flap structure specific endonuclease 1" [Mus musculus (taxid:10090)]

 Score = 227 (85.0 bits), Expect = 1.4e-18, P = 1.4e-18
 Identities = 49/90 (54%), Positives = 61/90 (67%)

Query:    10 GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
             G  +E++KF +RLV+V+  H  ECK LLSLMGIPY++               AP EAEA 
Sbjct:   116 GMEEEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLD---------------APSEAEAS 160

Query:    70 CAAMVKAGKVYATATEDMDALTFGTNILLR 99
             CAA+ KAGKVYA ATEDMD LTFG+ +L+R
Sbjct:   161 CAALAKAGKVYAAATEDMDCLTFGSPVLMR 190

GO:0000287 "magnesium ion binding" evidence=IDA

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

GO:0003824 "catalytic activity" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=ISO

GO:0004527 "exonuclease activity" evidence=IDA

GO:0005634 "nucleus" evidence=ISO;TAS

GO:0005739 "mitochondrion" evidence=ISO

GO:0006260 "DNA replication" evidence=IMP

GO:0006281 "DNA repair" evidence=IMP

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

GO:0007613 "memory" evidence=ISO

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

GO:0016787 "hydrolase activity" evidence=IEA

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

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

GO:0030145 "manganese ion binding" evidence=IDA

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0048256 "flap endonuclease activity" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q7K7A9	FEN1_DROME	3, ., 1, ., -, ., -	0.6444	0.6637	0.1948	yes	N/A
Q58DH8	FEN1_BOVIN	3, ., 1, ., -, ., -	0.5714	0.6106	0.1815	yes	N/A
Q5XIP6	FEN1_RAT	3, ., 1, ., -, ., -	0.5384	0.6725	0.2	yes	N/A
C3ZBT0	FEN1_BRAFL	3, ., 1, ., -, ., -	0.5517	0.6371	0.1894	yes	N/A
Q4WWJ1	FEN1_ASPFU	3, ., 1, ., -, ., -	0.5326	0.6814	0.1949	yes	N/A
A5ABU3	FEN1_ASPNC	3, ., 1, ., -, ., -	0.5434	0.6814	0.1949	yes	N/A
B1H158	FEN1_XENTR	3, ., 1, ., -, ., -	0.6046	0.6283	0.1858	yes	N/A
B5DUR8	FEN1_DROPS	3, ., 1, ., -, ., -	0.6555	0.6637	0.1943	yes	N/A
Q9N3T2	FEN1_CAEEL	3, ., 1, ., -, ., -	0.5425	0.6991	0.2068	yes	N/A
Q5ZLN4	FEN1_CHICK	3, ., 1, ., -, ., -	0.5384	0.6725	0.1994	yes	N/A
Q7Q323	FEN1_ANOGA	3, ., 1, ., -, ., -	0.6263	0.6725	0.1984	yes	N/A
Q5B9L6	FEN1_EMENI	3, ., 1, ., -, ., -	0.5326	0.6814	0.1949	yes	N/A
P39749	FEN1_MOUSE	3, ., 1, ., -, ., -	0.5384	0.6725	0.2010	yes	N/A
P39748	FEN1_HUMAN	3, ., 1, ., -, ., -	0.5581	0.6283	0.1868	yes	N/A

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	113
cd09867	261	cd09867, PIN_FEN1, PIN domain of Flap Endonuclease	2e-42
PTZ00217	393	PTZ00217, PTZ00217, flap endonuclease-1; Provision	5e-37
PRK03980	292	PRK03980, PRK03980, flap endonuclease-1; Provision	2e-23
cd00128	209	cd00128, PIN_FEN1_EXO1-like, PIN domains of Flap E	2e-21
TIGR03674	338	TIGR03674, fen_arch, flap structure-specific endon	3e-21
smart00484	73	smart00484, XPGI, Xeroderma pigmentosum G I-region	2e-18
pfam00867	46	pfam00867, XPG_I, XPG I-region	2e-17
cd09853	163	cd09853, PIN_StructSpec-5'-nucleases, PIN domains	3e-17
cd09868	249	cd09868, PIN_XPG, PIN domain of Xeroderma pigmento	1e-15
cd09856	207	cd09856, PIN_FEN1-like, PIN domain of Flap Endonuc	4e-14
cd09870	239	cd09870, PIN_YEN1, PIN domain of Yeast Endonucleas	5e-12
TIGR00600	1034	TIGR00600, rad2, DNA excision repair protein (rad2	2e-10
COG0258	310	COG0258, Exo, 5'-3' exonuclease (including N-termi	2e-09
cd09869	233	cd09869, PIN_GEN1, PIN domain of Gap Endonuclease	5e-09
cd09852	120	cd09852, PIN_SF, PIN (PilT N terminus) domain: Sup	9e-07
cd09857	210	cd09857, PIN_EXO1, PIN domain of Exonuclease-1, a	2e-04

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

 Score =  139 bits (352), Expect = 2e-42
 Identities = 45/91 (49%), Positives = 57/91 (62%), Gaps = 15/91 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           GDA+E  K+ +R VRV+   V+ECK+LL LMGIPY+E               AP EAEAQ
Sbjct: 113 GDAEEARKYAKRTVRVTKEIVEECKKLLRLMGIPYVE---------------APSEAEAQ 157

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
           CA +VK G VYA A++D D+L FG   L+R 
Sbjct: 158 CAYLVKKGDVYAVASQDYDSLLFGAPRLVRN 188

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 =  128 bits (324), Expect = 5e-37
 Identities = 51/91 (56%), Positives = 60/91 (65%), Gaps = 15/91 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           GD +EI K ++R VRV+    ++ K+LL LMGIP IE               APCEAEAQ
Sbjct: 120 GDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIE---------------APCEAEAQ 164

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
           CA +VK GKVYA ATEDMDALTFGT +LLR 
Sbjct: 165 CAELVKKGKVYAVATEDMDALTFGTPVLLRN 195

Length = 393

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

 Score = 90.7 bits (226), Expect = 2e-23
 Identities = 34/91 (37%), Positives = 49/91 (53%), Gaps = 15/91 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           GD +E  K+ +R  R++   V++ K+LL LMGIPY++               AP E EAQ
Sbjct: 65  GDLEEARKYAQRSSRLTDEIVEDSKKLLDLMGIPYVQ---------------APSEGEAQ 109

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
            A M K G  +A  ++D D+L FG   L+R 
Sbjct: 110 AAYMAKKGDAWAVGSQDYDSLLFGAPRLVRN 140

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 = 84.1 bits (208), Expect = 2e-21
 Identities = 34/90 (37%), Positives = 43/90 (47%), Gaps = 15/90 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           G   E  K  +R V ++    + CK LLSL GIPY+                AP EAEAQ
Sbjct: 107 GQFIEAQKPFKRNVTITPKAYQNCKILLSLEGIPYVV---------------APYEAEAQ 151

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLR 99
            A + K+G V A  TED D L +G    +R
Sbjct: 152 LAYLAKSGHVIAAITEDTDCLMYGVPRFIR 181

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|234306 TIGR03674, fen_arch, flap structure-specific endonuclease

 Score = 85.8 bits (213), Expect = 3e-21
 Identities = 35/91 (38%), Positives = 48/91 (52%), Gaps = 15/91 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           GD +E  K+ +R  R++S  V+  K+LL LMGIPY++               AP E EAQ
Sbjct: 112 GDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQ---------------APSEGEAQ 156

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
            A M K G V    ++D D+L FG   L+R 
Sbjct: 157 AAYMAKKGDVDYVGSQDYDSLLFGAPRLVRN 187

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|214689 smart00484, XPGI, Xeroderma pigmentosum G I-region

 Score = 72.6 bits (179), Expect = 2e-18
 Identities = 29/62 (46%), Positives = 31/62 (50%), Gaps = 15/62 (24%)

Query: 38 SLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNIL 97
           LMGIPYI                AP EAEAQCA + K+G V A  TED D L FG   L
Sbjct: 1  RLMGIPYIV---------------APYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRL 45

Query: 98 LR 99
           R
Sbjct: 46 YR 47

domain in nucleases. Length = 73

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

 Score = 69.0 bits (170), Expect = 2e-17
 Identities = 26/55 (47%), Positives = 29/55 (52%), Gaps = 15/55 (27%)

Query: 39 LMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDALTFG 93
          LMGIPY+                AP EAEAQCA +VK G V A  +ED D L FG
Sbjct: 2  LMGIPYVV---------------APYEAEAQCAYLVKTGLVDAVISEDSDLLLFG 41

Length = 46

>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 = 72.3 bits (177), Expect = 3e-17
 Identities = 31/86 (36%), Positives = 41/86 (47%), Gaps = 18/86 (20%)

Query: 13  QEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAA 72
            E  +  +RL   +  ++K+CKELL LMGIPY ++               P EAE   A 
Sbjct: 77  AEATEEEKRLDEQTFEYLKDCKELLKLMGIPYFDIR--------------PSEAEDMAAY 122

Query: 73  MVKAGK----VYATATEDMDALTFGT 94
           +VK G     V A  + D D LT GT
Sbjct: 123 LVKKGGHLYDVVALISTDGDWLTLGT 148

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 = 69.2 bits (170), Expect = 1e-15
 Identities = 29/93 (31%), Positives = 37/93 (39%), Gaps = 19/93 (20%)

Query: 5   LFLLTGDAQEIDKFNRRLVRVSSVH----VKECKELLSLMGIPYIEVSRSPRLLPNFLGV 60
           L         +    ++  R +         EC+ELL L GIPYI               
Sbjct: 109 LLASQLKKSAVKSQQQQQERDADEITQEMYDECQELLRLFGIPYIV-------------- 154

Query: 61  LAPCEAEAQCAAMVKAGKVYATATEDMDALTFG 93
            AP EAEAQCA + + G V    T+D D   FG
Sbjct: 155 -APMEAEAQCAILNQLGLVDGVITDDSDVFLFG 186

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

 Score = 64.8 bits (158), Expect = 4e-14
 Identities = 30/95 (31%), Positives = 44/95 (46%), Gaps = 18/95 (18%)

Query: 5   LFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPC 64
           +F+  G+     K  R+    +   + EC++LL LMGIPY++               AP 
Sbjct: 75  IFVFDGEPP---KLKRKTNPSTPEMISECRKLLDLMGIPYVQ---------------APG 116

Query: 65  EAEAQCAAMVKAGKVYATATEDMDALTFGTNILLR 99
           E EAQCA +  +G V    + D D L FG   + R
Sbjct: 117 EGEAQCAYLQVSGAVDGILSNDSDTLLFGAEKVYR 151

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

 Score = 59.6 bits (145), Expect = 5e-12
 Identities = 31/85 (36%), Positives = 40/85 (47%), Gaps = 17/85 (20%)

Query: 17  KFNRRLVRVSSVH--VKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMV 74
           K  +R+      H  +K  KELL L GIPY                 AP EAEA+CA + 
Sbjct: 97  KRGKRVGLKKKEHWLIKLVKELLDLFGIPYHT---------------APGEAEAECARLQ 141

Query: 75  KAGKVYATATEDMDALTFGTNILLR 99
           + G V A  + D DAL FG   ++R
Sbjct: 142 RLGIVDAVLSNDSDALMFGATRVIR 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|233044 TIGR00600, rad2, DNA excision repair protein (rad2)

 Score = 56.1 bits (135), Expect = 2e-10
 Identities = 26/69 (37%), Positives = 32/69 (46%), Gaps = 15/69 (21%)

Query: 25  VSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATAT 84
           V+   + E +ELL L GIPYI                AP EAEAQCA +    +   T T
Sbjct: 769 VTGQMILESQELLRLFGIPYIV---------------APMEAEAQCAILDLLDQTSGTIT 813

Query: 85  EDMDALTFG 93
           +D D   FG
Sbjct: 814 DDSDIWLFG 822

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

 Score = 52.7 bits (127), Expect = 2e-09
 Identities = 19/81 (23%), Positives = 27/81 (33%), Gaps = 18/81 (22%)

Query: 14  EIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAM 73
             D+   ++  ++ + V     LL LMGI                    P E  AQ A  
Sbjct: 90  MPDELAPQIPILTELLVALGIPLLELMGIE----------------ADDPIETLAQKAY- 132

Query: 74  VKAGKVYATATEDMDALTFGT 94
            K G V    + D D L   +
Sbjct: 133 -KKGDVVLIISGDKDLLQLVS 152

Length = 310

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

 Score = 51.2 bits (123), Expect = 5e-09
 Identities = 24/64 (37%), Positives = 31/64 (48%), Gaps = 15/64 (23%)

Query: 30  VKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDA 89
           +KEC ELL L+GIP ++               A  EAEA CA +   G V    T+D DA
Sbjct: 120 LKECVELLELLGIPCLQ---------------AAGEAEALCAELNSEGLVDGCITQDSDA 164

Query: 90  LTFG 93
             +G
Sbjct: 165 FLYG 168

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 = 43.7 bits (103), Expect = 9e-07
 Identities = 25/82 (30%), Positives = 30/82 (36%), Gaps = 12/82 (14%)

Query: 13  QEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAA 72
            E  K  RR     +  +    ELL LMGIP +                   EA+AQ AA
Sbjct: 44  LEAQKGLRRKKGRVAELLLRDLELLDLMGIPVVHA------------PGDLYEADAQIAA 91

Query: 73  MVKAGKVYATATEDMDALTFGT 94
           + K G V A  T D D      
Sbjct: 92  LAKKGHVVALITNDSDLRQKAK 113

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

 Score = 38.6 bits (91), Expect = 2e-04
 Identities = 26/84 (30%), Positives = 37/84 (44%), Gaps = 15/84 (17%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           G+  E  +  +R V ++     E  + L   G+ YI               +AP EA+AQ
Sbjct: 110 GNRSEARECFQRAVDITPEMAHELIKALRKEGVEYI---------------VAPYEADAQ 154

Query: 70  CAAMVKAGKVYATATEDMDALTFG 93
            A + K G V A  TED D L +G
Sbjct: 155 LAYLAKTGYVDAVITEDSDLLAYG 178

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	113
PRK03980	292	flap endonuclease-1; Provisional	99.93
TIGR03674	338	fen_arch flap structure-specific endonuclease. End	99.92
PTZ00217	393	flap endonuclease-1; Provisional	99.92
KOG2518|consensus	556		99.9
cd00128	316	XPG Xeroderma pigmentosum G N- and I-regions (XPGN	99.9
TIGR00600	1034	rad2 DNA excision repair protein (rad2). All prote	99.89
smart00484	73	XPGI Xeroderma pigmentosum G I-region. domain in n	99.89
PF00867	94	XPG_I: XPG I-region; InterPro: IPR006086 This entr	99.88
KOG2519|consensus	449		99.87
KOG2520|consensus	815		99.84
smart00475	259	53EXOc 5'-3' exonuclease.	98.71
COG0258	310	Exo 5'-3' exonuclease (including N-terminal domain	98.69
cd00008	240	53EXOc 5'-3' exonuclease; T5 type 5'-3' exonucleas	98.61
PF12813	246	XPG_I_2: XPG domain containing	98.45
PRK05755	880	DNA polymerase I; Provisional	98.1
PRK14976	281	5'-3' exonuclease; Provisional	98.06
TIGR00593	887	pola DNA polymerase I. This family is based on the	97.88
PRK09482	256	flap endonuclease-like protein; Provisional	96.27
PHA00439	286	exonuclease	91.13
PHA02567	304	rnh RnaseH; Provisional	91.07
PF02739	169	5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolv	90.36
PRK00124	151	hypothetical protein; Validated	87.93
cd03041	77	GST_N_2GST_N GST_N family, 2 repeats of the N-term	87.1
TIGR00321	301	dhys deoxyhypusine synthase. This family of appare	86.46
PRK00805	329	putative deoxyhypusine synthase; Provisional	86.32
PRK02492	347	deoxyhypusine synthase-like protein; Provisional	85.4
PF03159	237	XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro:	82.88
PRK03971	334	putative deoxyhypusine synthase; Provisional	82.07
PRK02301	316	putative deoxyhypusine synthase; Provisional	81.77

>PRK03980 flap endonuclease-1; Provisional

Probab=99.93  E-value=5.9e-26  Score=183.32  Aligned_cols=89  Identities=38%  Similarity=0.585  Sum_probs=85.5

Q ss_pred             hhhHHHHcCCHHHHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeE
Q psy1207           2 ELTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYA   81 (113)
Q Consensus         2 ~~~~~~~~gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~   81 (113)
                      ++++++++||.++++++++|++++|++|+..++++|+.|||||++               ||+|||||||+|++.|+||+
T Consensus        57 ~~~~~~~~g~~~~a~k~~~~~~~vt~~~~~~~k~lL~~~GIp~i~---------------AP~EAEAq~A~L~~~g~vd~  121 (292)
T PRK03980         57 KYEEAKEEGDLEEARKYAQRSSRLTDEIVEDSKKLLDLMGIPYVQ---------------APSEGEAQAAYMAKKGDAWA  121 (292)
T ss_pred             HHHHHHHcCCHHHHHHHHhccccCCHHHHHHHHHHHHHCCCCEEe---------------cCchHHHHHHHHHHCCCeEE
Confidence            467788999999999999999999999999999999999999999               99999999999999999999


Q ss_pred             EEcCCCceeeecCCeeeeccccCC
Q psy1207          82 TATEDMDALTFGTNILLRQQLSWA  105 (113)
Q Consensus        82 V~SeDsD~l~fGa~~vlr~~~~~~  105 (113)
                      |+|+|+|+|+||++.++|+++..+
T Consensus       122 V~S~D~D~l~fg~~~vir~l~~~~  145 (292)
T PRK03980        122 VGSQDYDSLLFGAPRLVRNLTISG  145 (292)
T ss_pred             EecCCcCeeeecCCEEEEeecccc
Confidence            999999999999999999998764

>TIGR03674 fen_arch flap structure-specific endonuclease

Probab=99.92  E-value=6.3e-25  Score=179.69  Aligned_cols=90  Identities=40%  Similarity=0.566  Sum_probs=85.7

Q ss_pred             hhhHHHHcCCHHHHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeE
Q psy1207           2 ELTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYA   81 (113)
Q Consensus         2 ~~~~~~~~gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~   81 (113)
                      +++++++.||.++++++.+|+.++|++++..++++|+.|||||++               ||+|||||||+|++.|.||+
T Consensus       104 ~~~~~~~~g~~~~a~~~~~r~~~~~~~~~~~~k~lL~~~Gip~i~---------------AP~EAeaq~a~L~~~g~vd~  168 (338)
T TIGR03674       104 KWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQ---------------APSEGEAQAAYMAKKGDVDY  168 (338)
T ss_pred             HHHHHHHcCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCCeEEE---------------CCccHHHHHHHHHHCCCeeE
Confidence            367788999999999999999999999999999999999999999               99999999999999999999


Q ss_pred             EEcCCCceeeecCCeeeeccccCCc
Q psy1207          82 TATEDMDALTFGTNILLRQQLSWAT  106 (113)
Q Consensus        82 V~SeDsD~l~fGa~~vlr~~~~~~~  106 (113)
                      |+|+|+|+|+||++.++|+++..++
T Consensus       169 v~S~D~D~l~fg~~~vi~~~~~~~~  193 (338)
T TIGR03674       169 VGSQDYDSLLFGAPRLVRNLTISGK  193 (338)
T ss_pred             EecCCcCeeeecCCEEEEecccccc
Confidence            9999999999999999999887553

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

>PTZ00217 flap endonuclease-1; Provisional

Probab=99.92  E-value=5.5e-25  Score=183.82  Aligned_cols=87  Identities=61%  Similarity=0.877  Sum_probs=84.1

Q ss_pred             hhhHHHHcCCHHHHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeE
Q psy1207           2 ELTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYA   81 (113)
Q Consensus         2 ~~~~~~~~gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~   81 (113)
                      +++++.+.||.++++++++|++++|++|+..++++|+.||||||+               ||+|||||||+|++.|+||+
T Consensus       112 ~l~~a~~~g~~~~a~k~~~r~~~vt~~~~~~~~~lL~~~Gip~i~---------------AP~EAdaq~A~L~~~g~v~~  176 (393)
T PTZ00217        112 ELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIE---------------APCEAEAQCAELVKKGKVYA  176 (393)
T ss_pred             HHHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCCceEE---------------CCcCHHHHHHHHHHCCCeEE
Confidence            467789999999999999999999999999999999999999999               99999999999999999999


Q ss_pred             EEcCCCceeeecCCeeeecccc
Q psy1207          82 TATEDMDALTFGTNILLRQQLS  103 (113)
Q Consensus        82 V~SeDsD~l~fGa~~vlr~~~~  103 (113)
                      |+|+|+|+|+||++++||+++.
T Consensus       177 ViS~D~D~l~fg~~~vi~~l~~  198 (393)
T PTZ00217        177 VATEDMDALTFGTPVLLRNLNF  198 (393)
T ss_pred             EeCCCcCeeecCCcEEEEcccc
Confidence            9999999999999999999874

>KOG2518|consensus

Probab=99.90  E-value=5.8e-24  Score=183.96  Aligned_cols=91  Identities=27%  Similarity=0.328  Sum_probs=86.1

Q ss_pred             hhhHHHHcCCHHHHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeE
Q psy1207           2 ELTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYA   81 (113)
Q Consensus         2 ~~~~~~~~gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~   81 (113)
                      ..++++..|+..+|+.+++|++.||++|++.++..++.+||+||+               ||||||||+|||++.|+||+
T Consensus       102 ~a~~ll~~G~~~~A~~~fqr~VdIT~~ma~~lI~~~r~~nVe~IV---------------APyEADAQlayL~~~~~i~~  166 (556)
T KOG2518|consen  102 AAEQLLAEGKESNARECFQRCVDITPEMAHKLIQYLRSQNVEYIV---------------APYEADAQLAYLEREGIVDA  166 (556)
T ss_pred             HHHHHHHcCCHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCceEe---------------cCccccchhHHHHhcCcceE
Confidence            356788999999999999999999999999999999999999999               99999999999999999999


Q ss_pred             EEcCCCceeeecCCeeeeccccCCce
Q psy1207          82 TATEDMDALTFGTNILLRQQLSWATF  107 (113)
Q Consensus        82 V~SeDsD~l~fGa~~vlr~~~~~~~~  107 (113)
                      |||||||+|+|||+.+|.++...+.+
T Consensus       167 IITEDSDLl~fGc~~vifK~d~~G~~  192 (556)
T KOG2518|consen  167 IITEDSDLLVFGCKKVIFKMDSFGNG  192 (556)
T ss_pred             EEeccccccccCchhheeeccCCCCc
Confidence            99999999999999999999875544

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

Probab=99.90  E-value=2.9e-23  Score=166.22  Aligned_cols=88  Identities=48%  Similarity=0.631  Sum_probs=83.3

Q ss_pred             hhHHHHcCCHHHHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEE
Q psy1207           3 LTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYAT   82 (113)
Q Consensus         3 ~~~~~~~gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V   82 (113)
                      ...+.++||.+++.++.+++.++|+.++..++++|+.|||||++               ||+|||||||+|+++|.||+|
T Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~gi~~i~---------------ap~EAdaq~a~l~~~g~v~~i  167 (316)
T cd00128         103 AKEALEKGLEEEAKKLERRAVRVTPQMIEEAKELLRLMGIPYIV---------------APYEAEAQCAYLAKKGLVDAI  167 (316)
T ss_pred             HHHHHHhCCHHHHHHHHhccCcCCHHHHHHHHHHHHHcCCCEEE---------------CCcCHHHHHHHHHhCCCeeEE
Confidence            34577889999999999999999999999999999999999999               999999999999999999999


Q ss_pred             EcCCCceeeecCCeeeeccccCC
Q psy1207          83 ATEDMDALTFGTNILLRQQLSWA  105 (113)
Q Consensus        83 ~SeDsD~l~fGa~~vlr~~~~~~  105 (113)
                      +|+|||+|+||++.++++++..+
T Consensus       168 ~S~DsD~l~fg~~~vi~~~~~~~  190 (316)
T cd00128         168 ITEDSDLLLFGAPRVYRNLFDSG  190 (316)
T ss_pred             EecCCCeeeecCceEEEecccCC
Confidence            99999999999999999988654

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=99.89  E-value=2e-23  Score=191.13  Aligned_cols=83  Identities=34%  Similarity=0.518  Sum_probs=75.7

Q ss_pred             HHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEEEcCCCceeeec
Q psy1207          14 EIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDALTFG   93 (113)
Q Consensus        14 ~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V~SeDsD~l~fG   93 (113)
                      +..+..|++.+||++|+.+|++||++||||||+               ||+|||||||+|++.|+||+|+|+|||+|+||
T Consensus       758 ~~~~~~r~~~~vt~~m~~~~~~LL~~~GIP~i~---------------AP~EAEAqcA~L~~~G~vd~V~TeDsD~llFG  822 (1034)
T TIGR00600       758 QKQQQKRIAAEVTGQMILESQELLRLFGIPYIV---------------APMEAEAQCAILDLLDQTSGTITDDSDIWLFG  822 (1034)
T ss_pred             HHHHhccccccCCHHHHHHHHHHHHHCCCCeee---------------CCccHHHHHHHHHhCCCeEEEEccccceeccC
Confidence            344558899999999999999999999999999               99999999999999999999999999999999


Q ss_pred             CCeeeeccccCCceeeccc
Q psy1207          94 TNILLRQQLSWATFSMHCW  112 (113)
Q Consensus        94 a~~vlr~~~~~~~~~~~~~  112 (113)
                      |++|+||+++.+++ +.||
T Consensus       823 a~~v~rn~~~~~~~-ve~~  840 (1034)
T TIGR00600       823 ARHVYKNFFNQNKF-VEYY  840 (1034)
T ss_pred             CceeeecccCCCCc-eEEe
Confidence            99999999876654 4454

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).

>smart00484 XPGI Xeroderma pigmentosum G I-region

Probab=99.89  E-value=1.1e-23  Score=140.96  Aligned_cols=55  Identities=53%  Similarity=0.684  Sum_probs=51.8

Q ss_pred             HhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEEEcCCCceeeecCCeeeeccccCCce
Q psy1207          38 SLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQLSWATF  107 (113)
Q Consensus        38 ~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V~SeDsD~l~fGa~~vlr~~~~~~~~  107 (113)
                      +.|||||++               ||+|||||||+|+++|+||+|+|+|+|+|+||++++||+++..++.
T Consensus         1 ~~~gi~~i~---------------AP~eAeAq~A~L~~~g~vdav~s~D~D~llfG~~~vi~~~~~~~~~   55 (73)
T smart00484        1 RLMGIPYIV---------------APYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKK   55 (73)
T ss_pred             CcCCCeEEE---------------cCCcHHHHHHHHHhCCCeeEEEcCccceEecCCcEEEEecccCCCc
Confidence            368999999               9999999999999999999999999999999999999999877653

domain in nucleases

>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=99.88  E-value=1.2e-23  Score=143.90  Aligned_cols=50  Identities=52%  Similarity=0.767  Sum_probs=43.8

Q ss_pred             HhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEEEcCCCceeeecCCeeeeccc
Q psy1207          38 SLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQL  102 (113)
Q Consensus        38 ~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V~SeDsD~l~fGa~~vlr~~~  102 (113)
                      +.|||||++               ||||||||||||+++|+||+|+|+|||+|+||++++||+++
T Consensus         1 ~~~gv~~i~---------------AP~EAeAq~A~L~~~g~vd~V~t~DsD~l~fG~~~vi~~~~   50 (94)
T PF00867_consen    1 RLMGVPYIV---------------APYEAEAQCAYLERNGLVDAVITEDSDLLLFGAPKVIRKLS   50 (94)
T ss_dssp             HHHT-EEEE----------------SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESST
T ss_pred             CCCCCeEEE---------------cCchHHHHHHHHHHhcceeEEEecCCCEEeeCCCEEEEecc
Confidence            579999999               99999999999999999999999999999999999999998

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 ....

>KOG2519|consensus

Probab=99.87  E-value=5.9e-23  Score=174.89  Aligned_cols=96  Identities=51%  Similarity=0.734  Sum_probs=88.7

Q ss_pred             hhhHHHHcCCHHHHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeE
Q psy1207           2 ELTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYA   81 (113)
Q Consensus         2 ~~~~~~~~gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~   81 (113)
                      +++.+.+.|+.++.+++.+|.+.+|.+++.+|++||..|||||++               ||+|||||||+|+++|.|++
T Consensus       106 ~~~~~~e~~~~~~~~k~~~r~vkvtk~~~dEak~LL~lmGIp~i~---------------ap~EAEAqCA~Lnk~g~V~~  170 (449)
T KOG2519|consen  106 ELKPAKEAGAKENMEKFFSRLVKVTKQHNDEAKRLLSLMGIPVLD---------------APGEAEAQCAALNKAGKVYA  170 (449)
T ss_pred             hhhhHHHhhhHHHHHHHHHHHhhhcchhhHHHHHHHHHcCCeeec---------------CCchHHHHHHHHhhcCceee
Confidence            456788899999999999999999999999999999999999999               99999999999999999999


Q ss_pred             EEcCCCceeeecCCeeeecccc--CCceeeccc
Q psy1207          82 TATEDMDALTFGTNILLRQQLS--WATFSMHCW  112 (113)
Q Consensus        82 V~SeDsD~l~fGa~~vlr~~~~--~~~~~~~~~  112 (113)
                      ++|+|||+|.||++.++|++..  ..+..+.||
T Consensus       171 ~at~DsD~l~fg~~~~lr~l~~s~~~~~pv~e~  203 (449)
T KOG2519|consen  171 VATEDSDALTFGAPVKLRHLIHSLASGLPVSEY  203 (449)
T ss_pred             eeccccchhhccCHHHHHHhccchhcCCCeEEe
Confidence            9999999999999999999984  445555555

>KOG2520|consensus

Probab=99.84  E-value=1.5e-21  Score=175.45  Aligned_cols=76  Identities=39%  Similarity=0.527  Sum_probs=72.1

Q ss_pred             hhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEEEcCCCceeeecCCeee
Q psy1207          19 NRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNILL   98 (113)
Q Consensus        19 ~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V~SeDsD~l~fGa~~vl   98 (113)
                      .+.+-.+|+.|+.+|++||+.||||||+               ||.|||||||.|.+.|+||+|||+|||+|+||++.|+
T Consensus       457 ~r~~~evt~~m~~e~QElL~~fGIPyI~---------------APmEAEAQCa~Le~~~LvdGiITDDSDV~LFGg~~VY  521 (815)
T KOG2520|consen  457 SRGADEVTSDMFKELQELLRLFGIPYII---------------APMEAEAQCAFLEQLNLVDGIITDDSDVFLFGGTRVY  521 (815)
T ss_pred             hccCchhHHHHHHHHHHHHHHcCCceec---------------ccccHHHHHHHHHHcCCcceeecccccceeeccchhh
Confidence            4556779999999999999999999999               9999999999999999999999999999999999999


Q ss_pred             eccccCCceee
Q psy1207          99 RQQLSWATFSM  109 (113)
Q Consensus        99 r~~~~~~~~~~  109 (113)
                      ||+++.+++.+
T Consensus       522 rn~F~knk~ve  532 (815)
T KOG2520|consen  522 RNFFNKNKYVE  532 (815)
T ss_pred             HHHhhcCccce
Confidence            99999998855

>smart00475 53EXOc 5'-3' exonuclease

Probab=98.71  E-value=3.6e-08  Score=78.75  Aligned_cols=55  Identities=29%  Similarity=0.371  Sum_probs=48.7

Q ss_pred             HHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcc-hHHHHHHHHHHC----CCeeEEEcCCCceeeecCCeeee
Q psy1207          30 VKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPC-EAEAQCAAMVKA----GKVYATATEDMDALTFGTNILLR   99 (113)
Q Consensus        30 v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~-EAEAqcA~L~k~----G~vd~V~SeDsD~l~fGa~~vlr   99 (113)
                      ...++++|+.||||++.               +|+ |||.+||.|.++    |....|+|+|.|.+.++++.+..
T Consensus        86 ~~~~~~~l~~~gi~~i~---------------~~g~EADD~iatla~~~~~~g~~~~IvS~DkDl~ql~~~~v~~  145 (259)
T smart00475       86 IPLIKELLDALGIPVLE---------------VEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSV  145 (259)
T ss_pred             HHHHHHHHHHCCCCEEe---------------eCCcCHHHHHHHHHHHHHhCCCeEEEEeCCCcHhhcCCCCEEE
Confidence            46799999999999999               786 999999999885    78899999999999999876543

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

Probab=98.69  E-value=1.6e-08  Score=81.49  Aligned_cols=75  Identities=27%  Similarity=0.266  Sum_probs=66.8

Q ss_pred             HcCCHH-HHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEEEcCC
Q psy1207           8 LTGDAQ-EIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATED   86 (113)
Q Consensus         8 ~~gd~~-~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V~SeD   86 (113)
                      +.+..+ ....+..+...+++.+....+.+++.+|+| +.               +|.|++||+|+  +.|.+++|+|+|
T Consensus        83 K~~R~~~~p~~l~~q~~~i~~~~~~~~~~~l~~~G~e-ad---------------d~i~t~A~~a~--~~g~~~~I~S~D  144 (310)
T COG0258          83 KANREKEMPDELAPQIPILTELLVALGIPLLELMGIE-AD---------------DPIETLAQKAY--KKGDVVLIISGD  144 (310)
T ss_pred             HhCCCccCHHHHHHHHHHHHHHHHHhCcHhhhcCCCC-cc---------------hhHHHHHHHHH--hcCCeEEEEeCC
Confidence            344445 788899999999999999999999999999 77               89999999999  999999999999


Q ss_pred             CceeeecCCeeeec
Q psy1207          87 MDALTFGTNILLRQ  100 (113)
Q Consensus        87 sD~l~fGa~~vlr~  100 (113)
                      +|+|.||++.+...
T Consensus       145 kD~lql~~~~~~~~  158 (310)
T COG0258         145 KDLLQLVSPNVLVI  158 (310)
T ss_pred             cchhhhcCCCcEEE
Confidence            99999999995443

>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=98.61  E-value=1e-07  Score=74.75  Aligned_cols=54  Identities=28%  Similarity=0.372  Sum_probs=47.4

Q ss_pred             HHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcc-hHHHHHHHHHH----CCCeeEEEcCCCceeeecCCe
Q psy1207          28 VHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPC-EAEAQCAAMVK----AGKVYATATEDMDALTFGTNI   96 (113)
Q Consensus        28 ~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~-EAEAqcA~L~k----~G~vd~V~SeDsD~l~fGa~~   96 (113)
                      .++..++++|+.||||++.               +|+ |||.++|.|.+    .|....|+|+|.|.+.+.++.
T Consensus        85 ~q~~~~~~~l~~~gi~~i~---------------~~~~EADD~ia~la~~~~~~g~~~~I~S~DkD~~ql~~~~  143 (240)
T cd00008          85 EQIPLIKELLEALGIPVLE---------------IEGYEADDVIGTLAKKAEAEGYKVVIVSGDKDLLQLVSDN  143 (240)
T ss_pred             HHHHHHHHHHHHCCCCEEe---------------cCCcCHHHHHHHHHHHHHHcCCeEEEEeCCCChhhhCCCC
Confidence            4567899999999999999               875 99999999985    677889999999999996654

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=98.45  E-value=4.2e-07  Score=72.12  Aligned_cols=51  Identities=29%  Similarity=0.417  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHHhh---CCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEEEcCCCceeeecC
Q psy1207          28 VHVKECKELLSLM---GIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGT   94 (113)
Q Consensus        28 ~~v~~~~~lL~~~---Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V~SeDsD~l~fGa   94 (113)
                      -++.-+.+.|+.+   |+++++               .|+|||..||.+.++.-+ .|+|.|||.++|.-
T Consensus         4 f~~~~~~e~L~~~~~~~~~~~~---------------~~~EAD~~~A~~A~~~~~-~VLt~DSDf~I~dl   57 (246)
T PF12813_consen    4 FLVPAFIEALRESWRYGVPVVQ---------------CPGEADRECAALARKWGC-PVLTNDSDFLIHDL   57 (246)
T ss_pred             chHHHHHHHHHHHhhcCCcEEE---------------cCccchHHHHHHHHHcCC-eEEccCCCEEEecc
Confidence            3567788889988   999999               999999999999987766 99999999999988

>PRK05755 DNA polymerase I; Provisional

Probab=98.10  E-value=6.2e-06  Score=74.88  Aligned_cols=55  Identities=27%  Similarity=0.356  Sum_probs=48.7

Q ss_pred             HHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcc-hHHHHHHHHH----HCCCeeEEEcCCCceeeecCCee
Q psy1207          28 VHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPC-EAEAQCAAMV----KAGKVYATATEDMDALTFGTNIL   97 (113)
Q Consensus        28 ~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~-EAEAqcA~L~----k~G~vd~V~SeDsD~l~fGa~~v   97 (113)
                      .....++++|+.||||++.               +|+ |||.++|.|.    +.|....|+|.|.|.+.++++.+
T Consensus        86 ~q~~~~~~~l~~~gi~~~~---------------~~g~EADD~ia~la~~~~~~~~~~~i~S~DkD~~ql~~~~v  145 (880)
T PRK05755         86 EQIPLIRELLRALGIPLLE---------------LEGYEADDVIGTLAKQAEAAGYEVLIVTGDKDLLQLVDDNV  145 (880)
T ss_pred             HHHHHHHHHHHHCCCCEEe---------------eCCccHHHHHHHHHHHHHhCCCcEEEEcCCCChhhhCCCCE
Confidence            3466799999999999999               996 9999999998    46889999999999999998753

>PRK14976 5'-3' exonuclease; Provisional

Probab=98.06  E-value=1.1e-05  Score=65.11  Aligned_cols=55  Identities=24%  Similarity=0.293  Sum_probs=47.1

Q ss_pred             HHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcc-hHHHHHHHHHHC----CCeeEEEcCCCceeeecCCee
Q psy1207          28 VHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPC-EAEAQCAAMVKA----GKVYATATEDMDALTFGTNIL   97 (113)
Q Consensus        28 ~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~-EAEAqcA~L~k~----G~vd~V~SeDsD~l~fGa~~v   97 (113)
                      .....++++|+.||||++.               +|+ |||..+|.|.++    |.--.|+|.|.|.+.+.++.+
T Consensus        90 ~q~~~i~~~l~~~gi~~~~---------------~~g~EADDviatla~~~~~~g~~v~IvS~DkDl~ql~~~~v  149 (281)
T PRK14976         90 SQIPLLKKILKLAGIKWEE---------------QPGYEADDLIGSLAKKLSKQNITVLIYSSDKDLLQLVNENT  149 (281)
T ss_pred             HHHHHHHHHHHHCCCCEEe---------------cCCcCHHHHHHHHHHHHHHCCCeEEEEeCCCCcCccCCCCe
Confidence            3567789999999999999               996 999999999765    555579999999999998754

>TIGR00593 pola DNA polymerase I

Probab=97.88  E-value=2.5e-05  Score=71.88  Aligned_cols=53  Identities=30%  Similarity=0.404  Sum_probs=47.2

Q ss_pred             HHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcc-hHHHHHHHHHHC----CCeeEEEcCCCceeeecCCee
Q psy1207          30 VKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPC-EAEAQCAAMVKA----GKVYATATEDMDALTFGTNIL   97 (113)
Q Consensus        30 v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~-EAEAqcA~L~k~----G~vd~V~SeDsD~l~fGa~~v   97 (113)
                      +..++++|+.||||++.               +|+ |||.++|.|.++    |+...|+|.|.|.+-+.++.+
T Consensus        86 ~~~i~~~l~~~gi~~i~---------------~~g~EADDiIatla~~~~~~g~~v~IvS~DkDllQLv~~~v  143 (887)
T TIGR00593        86 IPLIKELLDALGIPILE---------------VEGYEADDVIATLAKQAEKEGYEVRIISGDKDLLQLVSDNV  143 (887)
T ss_pred             HHHHHHHHHHCCCcEEe---------------eCCccHHHHHHHHHHHHHhCCCcEEEEECCCChhhcCCCCE
Confidence            46689999999999999               886 999999999874    888899999999999988753

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

>PRK09482 flap endonuclease-like protein; Provisional

Probab=96.27  E-value=0.012  Score=47.57  Aligned_cols=47  Identities=17%  Similarity=0.174  Sum_probs=38.3

Q ss_pred             HHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcc-hHHHHHHHHHHC----CCeeEEEcCCCceee
Q psy1207          30 VKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPC-EAEAQCAAMVKA----GKVYATATEDMDALT   91 (113)
Q Consensus        30 v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~-EAEAqcA~L~k~----G~vd~V~SeDsD~l~   91 (113)
                      +..++++++.||||++.               +|+ |||-.+|.|.++    |.==.|+|.|-|.+-
T Consensus        86 ~~~i~~~l~~~gi~~~~---------------~~g~EADDvIatla~~~~~~~~~v~I~S~DKDl~Q  137 (256)
T PRK09482         86 LPAIRAAFEELGIDSWH---------------ADGNEADDLIATLAVKVAQAGHQATIVSTDKGYCQ  137 (256)
T ss_pred             HHHHHHHHHhCCCCEec---------------cCCcCHHHHHHHHHHHHHHCCCeEEEEECCCCccc
Confidence            45689999999999999               887 999999988764    432357999999863

>PHA00439 exonuclease

Probab=91.13  E-value=0.63  Score=38.46  Aligned_cols=52  Identities=19%  Similarity=0.019  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcc-hHHHHHHHHHH----CCC-eeEEEcCCCceeeec
Q psy1207          27 SVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPC-EAEAQCAAMVK----AGK-VYATATEDMDALTFG   93 (113)
Q Consensus        27 ~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~-EAEAqcA~L~k----~G~-vd~V~SeDsD~l~fG   93 (113)
                      ..+..-++++++.+|||++.               .|+ |||--++.|.+    .|. -=.|+|.|-|.+-.-
T Consensus        96 ~~~~~~i~el~~~~gi~~i~---------------~~G~EADDvIgtla~~~~~~g~~~vvIvS~DKDl~QLv  153 (286)
T PHA00439         96 VGYRKFLEELMAREEWKSIL---------------EPGLEGDDVMGIIGTNPSLFGFKKAVLVSCDKDFKTIP  153 (286)
T ss_pred             hhhHHHHHHHHHhCCCCEEe---------------eCCccHHHHHHHHHHHHHHCCCCeEEEEeCCCCHhhcC
Confidence            44556678999999999998               555 99987777764    454 336899999976543

>PHA02567 rnh RnaseH; Provisional

Probab=91.07  E-value=0.62  Score=38.89  Aligned_cols=47  Identities=21%  Similarity=0.192  Sum_probs=34.9

Q ss_pred             HHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcc-hHHHHHHHHHH----CCCeeEEEcCCCceeee
Q psy1207          31 KECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPC-EAEAQCAAMVK----AGKVYATATEDMDALTF   92 (113)
Q Consensus        31 ~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~-EAEAqcA~L~k----~G~vd~V~SeDsD~l~f   92 (113)
                      .-++++++.||||++.               .|+ |||=-.|.|.+    .|.-=.|+|.|.|.+=.
T Consensus       110 ~ii~el~~~~gi~~l~---------------~~g~EADDvIgTLA~k~~~~g~~VvIvS~DKDl~QL  161 (304)
T PHA02567        110 KIVDEIKENMPYKVMK---------------IDKAEADDIIAVLTKKFSAEGRPVLIVSSDGDFTQL  161 (304)
T ss_pred             HHHHHHHHHCCCCEEE---------------eCCccHHHHHHHHHHHHHhCCCcEEEEeCCCChhhc
Confidence            3467888899999999               665 99966555554    55444789999998654

>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=90.36  E-value=0.34  Score=36.38  Aligned_cols=53  Identities=30%  Similarity=0.384  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHH----CCCeeEEEcCCCceeeecCC
Q psy1207          29 HVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVK----AGKVYATATEDMDALTFGTN   95 (113)
Q Consensus        29 ~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k----~G~vd~V~SeDsD~l~fGa~   95 (113)
                      .+..++++++.+|||++.   .           .-+|||=..|.|.+    .|.==.|+|.|.|.+=.=..
T Consensus        87 q~~~i~~~l~~~gi~~~~---~-----------~g~EADDvIatla~~~~~~~~~v~IvS~DkD~~QLv~~  143 (169)
T PF02739_consen   87 QLPYIKELLEALGIPVLE---V-----------PGYEADDVIATLAKKASEEGFEVIIVSGDKDLLQLVDE  143 (169)
T ss_dssp             HHHHHHHHHHHTTSEEEE---E-----------TTB-HHHHHHHHHHHHHHTTCEEEEE-SSGGGGGGTCS
T ss_pred             HHHHHHHHHHHCCCCEec---C-----------CCCcHHHHHHHHHhhhccCCCEEEEEcCCCCHHHhcCC
Confidence            355689999999999998   1           34799966666654    44434778999998765555

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 ....

>PRK00124 hypothetical protein; Validated

Probab=87.93  E-value=1.7  Score=32.88  Aligned_cols=57  Identities=16%  Similarity=0.077  Sum_probs=42.9

Q ss_pred             HHHHHHHHHHhhCCcEEEec--CCCCCCCC------ccCCCCcchHHHHHHHHHHCCCeeEEEcCCC
Q psy1207          29 HVKECKELLSLMGIPYIEVS--RSPRLLPN------FLGVLAPCEAEAQCAAMVKAGKVYATATEDM   87 (113)
Q Consensus        29 ~v~~~~~lL~~~Gip~i~~~--~~~~~~~~------~~~~~AP~EAEAqcA~L~k~G~vd~V~SeDs   87 (113)
                      ..+++.++-+..|+|++.|.  ..+.-.|.      ..+-..|..||-..+.+.+.|  |.|+|.|-
T Consensus        12 Vk~~i~r~a~r~~i~v~~Vas~n~~~~~~~~~~v~~v~V~~g~D~AD~~Iv~~~~~g--DiVIT~Di   76 (151)
T PRK00124         12 VKDIIIRVAERHGIPVTLVASFNHFLRVPYSPFIRTVYVDAGFDAADNEIVQLAEKG--DIVITQDY   76 (151)
T ss_pred             HHHHHHHHHHHHCCeEEEEEeCCcccCCCCCCceEEEEeCCCCChHHHHHHHhCCCC--CEEEeCCH
Confidence            45667788889999999877  44433333      233457889999999999998  99999994

>cd03041 GST_N_2GST_N GST_N family, 2 repeats of the N-terminal domain of soluble GSTs (2 GST_N) subfamily; composed of uncharacterized proteins

Probab=87.10  E-value=1.2  Score=28.29  Aligned_cols=62  Identities=8%  Similarity=0.038  Sum_probs=44.9

Q ss_pred             HHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcch-HHHHHHHHHHCCCeeEEEcCCCceeeecCCeeeeccc
Q psy1207          29 HVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCE-AEAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQL  102 (113)
Q Consensus        29 ~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~E-AEAqcA~L~k~G~vd~V~SeDsD~l~fGa~~vlr~~~  102 (113)
                      ....++.+|+..||||-.+.-            .+++ +......++-.|.|..++.+|.|..+|++..+++.+.
T Consensus        12 ~~~kv~~~L~~~gi~y~~~~v------------~~~~~~~~~~~~~~p~~~vP~l~~~~~~~~l~es~~I~~yL~   74 (77)
T cd03041          12 FCRLVREVLTELELDVILYPC------------PKGSPKRDKFLEKGGKVQVPYLVDPNTGVQMFESADIVKYLF   74 (77)
T ss_pred             hHHHHHHHHHHcCCcEEEEEC------------CCChHHHHHHHHhCCCCcccEEEeCCCCeEEEcHHHHHHHHH
Confidence            456788899999999966322            3444 2344556777788999887777899999887776553

GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains.

>TIGR00321 dhys deoxyhypusine synthase

Probab=86.46  E-value=5.4  Score=33.22  Aligned_cols=69  Identities=14%  Similarity=0.104  Sum_probs=52.7

Q ss_pred             CHHHHHHHhhhccCCCHHHHHHHHHHHHhh----CCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEEEcCC
Q psy1207          11 DAQEIDKFNRRLVRVSSVHVKECKELLSLM----GIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATED   86 (113)
Q Consensus        11 d~~~a~~~~~r~~~vt~~~v~~~~~lL~~~----Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V~SeD   86 (113)
                      +..+.-+-+.++ ......+.++.++++.|    +..++....|+-         .|..---..++|.++|+||+|+|.-
T Consensus        12 ~v~~lv~~~~~~-gF~a~~l~~A~~i~~~m~~~~~~~ifLt~tg~m---------vsaGlr~ii~~Li~~g~Vd~ivtTg   81 (301)
T TIGR00321        12 TVCELIDSMGRT-GFQGRRIGEADKIWKEMCFDEEITIFMGYAGNL---------VPSGMREIIAYLIQHGMIDALVTTG   81 (301)
T ss_pred             cHHHHHHHHHhc-CccHHHHHHHHHHHHHHHhCCCCeEEEEecccc---------chhhHHHHHHHHHHcCCeeEEEeCC
Confidence            445555555565 77888888888888877    577777666655         7888888899999999999999987


Q ss_pred             Cce
Q psy1207          87 MDA   89 (113)
Q Consensus        87 sD~   89 (113)
                      .-+
T Consensus        82 anl   84 (301)
T TIGR00321        82 ANL   84 (301)
T ss_pred             Cch
Confidence            643

This family of apparent orthologs has an unusual UPGMA difference tree, in which the members from the archaea M. jannaschii and P. horikoshii cluster with the known eukaryotic deoxyhypusine synthases. Separated by a fairly deep branch, although still strongly related, is a small cluster of proteins from Methanobacterium thermoautotrophicum and Archeoglobus fulgidus, the latter of which has two.

>PRK00805 putative deoxyhypusine synthase; Provisional

Probab=86.32  E-value=4.2  Score=34.28  Aligned_cols=78  Identities=8%  Similarity=0.002  Sum_probs=56.7

Q ss_pred             cCCHHHHHHHhhhccCCCHHHHHHHHHHHHhh----CCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEEEc
Q psy1207           9 TGDAQEIDKFNRRLVRVSSVHVKECKELLSLM----GIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATAT   84 (113)
Q Consensus         9 ~gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~----Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V~S   84 (113)
                      .++..+.-+-+.++ ......+.++.++++.|    +..++....|+-         .|..---..++|.++|+||+|+|
T Consensus        11 ~~~~~~lv~~~~~~-gF~A~~l~~A~~i~~~Ml~d~~~~ifL~~tg~m---------vsaGlr~~i~~Li~~g~VD~iVT   80 (329)
T PRK00805         11 ERSISELLDAMADT-GFQGRKLGESVRVWTEMLKDPDNTIFMGLSGAM---------VPAGMRKIIKWLIRNRYVDVLVS   80 (329)
T ss_pred             CCCHHHHHHHHHHh-CccHHHHHHHHHHHHHHHhCCCCeEEEEeccch---------HHHHHHHHHHHHHHcCCeeEEEe
Confidence            34566666666666 77777777777777766    666666555544         77777789999999999999999


Q ss_pred             CCCce----e-eecCCe
Q psy1207          85 EDMDA----L-TFGTNI   96 (113)
Q Consensus        85 eDsD~----l-~fGa~~   96 (113)
                      .-.-+    + ++|.+.
T Consensus        81 Tgani~hD~~~~lg~~~   97 (329)
T PRK00805         81 TGANIFHDIHEALGFKH   97 (329)
T ss_pred             CCCchHHHHHHHcCCCe
Confidence            87643    3 566554

>PRK02492 deoxyhypusine synthase-like protein; Provisional

Probab=85.40  E-value=4.9  Score=34.14  Aligned_cols=77  Identities=14%  Similarity=0.118  Sum_probs=56.3

Q ss_pred             CCHHHHHHHhhhccCCCHHHHHHHHHHHHhh----CCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEEEcC
Q psy1207          10 GDAQEIDKFNRRLVRVSSVHVKECKELLSLM----GIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATE   85 (113)
Q Consensus        10 gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~----Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V~Se   85 (113)
                      .+..+.-+-+.++ -.....+.++.++++.|    +..++....|+-         .|..---..++|.++|+||+++|.
T Consensus        24 ~~v~~Lv~~~~~~-gF~A~~L~~A~~i~~~Ml~~~~~~ifL~~tgam---------vsaGlr~~i~~Li~~~~VD~iVTT   93 (347)
T PRK02492         24 FDAVPIIDAMGKM-AFQSRDLARAADIYDMMLQDKECAVILTLAGSL---------SSAGCMQVYIDLVRNNMVDAIVAT   93 (347)
T ss_pred             CCHHHHHHHHHHh-CccHHHHHHHHHHHHHHHhCCCCeEEEEeccch---------HHHHHHHHHHHHHHcCCeeEEEEC
Confidence            3556666666666 77777777777777766    566666444444         777778899999999999999999


Q ss_pred             CC-----cee-eecCCe
Q psy1207          86 DM-----DAL-TFGTNI   96 (113)
Q Consensus        86 Ds-----D~l-~fGa~~   96 (113)
                      -.     |++ ++|.+.
T Consensus        94 ganl~eeD~~k~~g~~~  110 (347)
T PRK02492         94 GANIVDQDFFEALGFKH  110 (347)
T ss_pred             CCCchHHHHHHHcCCCe
Confidence            77     555 777665

>PF03159 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: IPR004859 Signatures of this entry align residues towards the N terminus of several proteins with multiple functions

Probab=82.88  E-value=0.96  Score=36.13  Aligned_cols=33  Identities=15%  Similarity=0.251  Sum_probs=23.3

Q ss_pred             CcchHHHHHHHHHHC---------CCeeEEEcCCCceeeecC
Q psy1207          62 APCEAEAQCAAMVKA---------GKVYATATEDMDALTFGT   94 (113)
Q Consensus        62 AP~EAEAqcA~L~k~---------G~vd~V~SeDsD~l~fGa   94 (113)
                      -|||+|-.+....+.         +...+|.+.|+|++++|=
T Consensus       182 vpGEGE~KI~~~IR~~~~~~~~~~n~~h~i~g~DaDlIll~L  223 (237)
T PF03159_consen  182 VPGEGEHKIMDFIRSQRSQPDYDPNTSHCIYGSDADLILLSL  223 (237)
T ss_dssp             SSS-HHHHHHHHHHHHHHSTTS-TT--EEEE-SSTHHHHHHH
T ss_pred             CCCccHHHHHHHHHHhhhcCCCCCCceEEEEecCHhHHHHHH
Confidence            599999877665543         678999999999998873

The members of this family all appear to possess 5'-3' exonuclease activity 3.1.11 from EC. Thus, the aligned region may be necessary for 5'-3' exonuclease function.; GO: 0003676 nucleic acid binding, 0004527 exonuclease activity, 0005622 intracellular; PDB: 2Y35_A 3PIE_B 3PIF_C 3FQD_A.

>PRK03971 putative deoxyhypusine synthase; Provisional

Probab=82.07  E-value=11  Score=31.94  Aligned_cols=68  Identities=15%  Similarity=0.116  Sum_probs=50.3

Q ss_pred             CHHHHHHHhhhccCCCHHHHHHHHHHHHhh-------CCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEEE
Q psy1207          11 DAQEIDKFNRRLVRVSSVHVKECKELLSLM-------GIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATA   83 (113)
Q Consensus        11 d~~~a~~~~~r~~~vt~~~v~~~~~lL~~~-------Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V~   83 (113)
                      +..+.-+.+.++ ......+.++.++++.|       +..++....|+-         .|..---..++|.++|+||+|+
T Consensus        30 ~~~~l~~~~~~~-gF~A~~l~~A~~i~~~M~~~~~~~~~~ifL~~tg~m---------isaGlr~~i~~Li~~~~Vd~iV   99 (334)
T PRK03971         30 DLEEVLDYYAKI-GFQATHLGKAIKIWKKIEEKRKKEEATVFLGYTSNI---------VSSGLREIIAYLVKEKKVDVIV   99 (334)
T ss_pred             CHHHHHHHHHHc-CccHHHHHHHHHHHHHHHhhcccCCCeEEEEccccc---------cchhHHHHHHHHHHcCCeeEEE
Confidence            345555555555 77777777777777766       566666455444         7888889999999999999999


Q ss_pred             cCCCc
Q psy1207          84 TEDMD   88 (113)
Q Consensus        84 SeDsD   88 (113)
                      |.-.-
T Consensus       100 tTgan  104 (334)
T PRK03971        100 TTAGG  104 (334)
T ss_pred             eCCCc
Confidence            98763

>PRK02301 putative deoxyhypusine synthase; Provisional

Probab=81.77  E-value=9.8  Score=31.94  Aligned_cols=76  Identities=9%  Similarity=0.133  Sum_probs=54.0

Q ss_pred             CHHHHHHHhhhccCCCHHHHHHHHHHHHhh----CCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEEEcCC
Q psy1207          11 DAQEIDKFNRRLVRVSSVHVKECKELLSLM----GIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATED   86 (113)
Q Consensus        11 d~~~a~~~~~r~~~vt~~~v~~~~~lL~~~----Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V~SeD   86 (113)
                      +..+.-+-+.++ ......+.++.++++.|    +..++....|+-         .|..---..++|.++|+||+|+|.-
T Consensus        24 ~v~~l~~~~~~~-gF~A~~l~~A~~i~~~ml~~~~~~ifL~~tg~m---------vsaGlr~ii~~Li~~~~VD~iVtTg   93 (316)
T PRK02301         24 TVGELVREYGGA-GFGAGRLAEAVDIYEEMLADDDVTKFFGLAGAM---------VPAGMRGIVSDLIRDGHIDVLVTTG   93 (316)
T ss_pred             cHHHHHHHHHhc-CccHHHHHHHHHHHHHHHhCCCCeEEEEcccch---------hHHHHHHHHHHHHHcCCeeEEEcCC
Confidence            345555555555 67777777777776665    566666555554         7888889999999999999999987


Q ss_pred             Cce----e-eecCCe
Q psy1207          87 MDA----L-TFGTNI   96 (113)
Q Consensus        87 sD~----l-~fGa~~   96 (113)
                      .-+    + ++|.+.
T Consensus        94 aniehD~~~~lg~~~  108 (316)
T PRK02301         94 ANLTHDVIEAIGGHH  108 (316)
T ss_pred             CchHHHHHHHcCCCe
Confidence            643    3 666554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	113
1ul1_X	379	Crystal Structure Of The Human Fen1-Pcna Complex Le		1e-21
3q8k_A	341	Crystal Structure Of Human Flap Endonuclease Fen1 (		1e-21
3q8m_A	341	Crystal Structure Of Human Flap Endonuclease Fen1 (		1e-20
1b43_A	340	Fen-1 From P. Furiosus Length = 340		7e-12
1mc8_A	343	Crystal Structure Of Flap Endonuclease-1 R42e Mutan		7e-12
1a76_A	326	Flap Endonuclease-1 From Methanococcus Jannaschii L		3e-11
2izo_A	346	Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex L		4e-10
3ory_A	363	Crystal Structure Of Flap Endonuclease 1 From Hyper		2e-09
1rxv_A	336	Crystal Structure Of A. Fulgidus Fen-1 Bound To Dna		1e-07

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

Iteration: 1
 Score = 98.2 bits (243), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 48/86 (55%), Positives = 59/86 (68%), Gaps = 15/86 (17%)
Query: 15  IDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMV 74
           ++KF +RLV+V+  H  ECK LLSLMGIPY++               AP EAEA CAA+V
Sbjct: 122 VEKFTKRLVKVTKQHNDECKHLLSLMGIPYLD---------------APSEAEASCAALV 166
Query: 75  KAGKVYATATEDMDALTFGTNILLRQ 100
           KAGKVYA ATEDMD LTFG+ +L+R 
Sbjct: 167 KAGKVYAAATEDMDCLTFGSPVLMRH 192

>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 = 97.8 bits (242), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 48/86 (55%), Positives = 59/86 (68%), Gaps = 15/86 (17%)
Query: 15  IDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMV 74
           ++KF +RLV+V+  H  ECK LLSLMGIPY++               AP EAEA CAA+V
Sbjct: 122 VEKFTKRLVKVTKQHNDECKHLLSLMGIPYLD---------------APSEAEASCAALV 166
Query: 75  KAGKVYATATEDMDALTFGTNILLRQ 100
           KAGKVYA ATEDMD LTFG+ +L+R 
Sbjct: 167 KAGKVYAAATEDMDCLTFGSPVLMRH 192

>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 = 94.4 bits (233), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 47/86 (54%), Positives = 58/86 (67%), Gaps = 15/86 (17%)
Query: 15  IDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMV 74
           ++KF +RLV+V+  H  ECK LLSLMGIPY++               AP EAEA CAA+V
Sbjct: 122 VEKFTKRLVKVTKQHNDECKHLLSLMGIPYLD---------------APSEAEASCAALV 166
Query: 75  KAGKVYATATEDMDALTFGTNILLRQ 100
           KAGKVYA ATEDM  LTFG+ +L+R 
Sbjct: 167 KAGKVYAAATEDMACLTFGSPVLMRH 192

>pdb|1B43|A Chain A, Fen-1 From P. Furiosus Length = 340

Iteration: 1
 Score = 65.5 bits (158), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 52/93 (55%), Gaps = 15/93 (16%)
Query: 7   LLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEA 66
           L  G+ +E  K+ +R  RV+ + +++ K+LL LMGIP ++               AP E 
Sbjct: 109 LEKGEIEEARKYAQRATRVNEMLIEDAKKLLELMGIPIVQ---------------APSEG 153
Query: 67  EAQCAAMVKAGKVYATATEDMDALTFGTNILLR 99
           EAQ A M   G VYA+A++D D+L FG   L+R
Sbjct: 154 EAQAAYMAAKGSVYASASQDYDSLLFGAPRLVR 186

>pdb|1MC8|A Chain A, Crystal Structure Of Flap Endonuclease-1 R42e Mutant From Pyrococcus Horikoshii Length = 343

Iteration: 1
 Score = 65.5 bits (158), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 52/93 (55%), Gaps = 15/93 (16%)
Query: 7   LLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEA 66
           L  G+ +E  K+ +R  +V+ + +++ K+LL LMGIP I+               AP E 
Sbjct: 109 LAKGNLEEARKYAQRATKVNEMLIEDAKKLLQLMGIPIIQ---------------APSEG 153
Query: 67  EAQCAAMVKAGKVYATATEDMDALTFGTNILLR 99
           EAQ A M   G VYA+A++D D+L FG   L+R
Sbjct: 154 EAQAAYMASKGDVYASASQDYDSLLFGAPRLIR 186

>pdb|1A76|A Chain A, Flap Endonuclease-1 From Methanococcus Jannaschii Length = 326

Iteration: 1
 Score = 63.5 bits (153), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 34/90 (37%), Positives = 49/90 (54%), Gaps = 15/90 (16%)
Query: 11  DAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQC 70
           D +E  K+ +R+  ++   V+ CK LLSLMGIPY+E               AP E EAQ 
Sbjct: 113 DFEEAAKYAKRVSYLTPKMVENCKYLLSLMGIPYVE---------------APSEGEAQA 157
Query: 71  AAMVKAGKVYATATEDMDALTFGTNILLRQ 100
           + M K G V+A  ++D DAL +G   ++R 
Sbjct: 158 SYMAKKGDVWAVVSQDYDALLYGAPRVVRN 187

>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex Length = 346

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 31/90 (34%), Positives = 52/90 (57%), Gaps = 15/90 (16%)
Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           G  +E+ K+++ ++R+S++ V+E K+LL  MGIP ++               AP E EA+
Sbjct: 109 GKIEELRKYSQAILRLSNIMVEESKKLLRAMGIPIVQ---------------APSEGEAE 153
Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLR 99
            A + K G  +A A++D DA+ FG   L+R
Sbjct: 154 AAYLNKLGLSWAAASQDYDAILFGAKRLVR 183

>pdb|3ORY|A Chain A, Crystal Structure Of Flap Endonuclease 1 From Hyperthermophilic Archaeon Desulfurococcus Amylolyticus Length = 363

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 30/91 (32%), Positives = 49/91 (53%), Gaps = 15/91 (16%)
Query: 9   TGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEA 68
           +GD +   ++     +++   V++ K LL  MGIP+++               AP E EA
Sbjct: 125 SGDLELARRYAMMSAKLTEEMVRDAKSLLDAMGIPWVQ---------------APAEGEA 169
Query: 69  QCAAMVKAGKVYATATEDMDALTFGTNILLR 99
           Q A +VK G  YA+A++D D+L FG+  L+R
Sbjct: 170 QAAYIVKKGDAYASASQDYDSLLFGSPKLVR 200

>pdb|1RXV|A Chain A, Crystal Structure Of A. Fulgidus Fen-1 Bound To Dna Length = 336

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 44/94 (46%), Gaps = 16/94 (17%)
Query: 7   LLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEA 66
           L  GD ++  K+ +   RV    V   K LLS MGIP+++               AP E 
Sbjct: 109 LQAGD-KDAKKYAQAAGRVDEYIVDSAKTLLSYMGIPFVD---------------APSEG 152
Query: 67  EAQCAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
           EAQ A M   G V  T ++D D+L FG+  L R 
Sbjct: 153 EAQAAYMAAKGDVEYTGSQDYDSLLFGSPRLARN 186

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	113
1rxw_A	336	Flap structure-specific endonuclease; helical clam	2e-28
3q8k_A	341	Flap endonuclease 1; helix-3 turn-helix, hydrophob	3e-28
1a76_A	326	Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea	5e-28
1ul1_X	379	Flap endonuclease-1; protein complex, DNA-binding	2e-27
2izo_A	346	FEN1, flap structure-specific endonuclease; hydrol	3e-27
3ory_A	363	Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco	9e-27
1b43_A	340	Protein (FEN-1); nuclease, DNA repair, DNA replica	2e-26
3qe9_Y	352	Exonuclease 1; exonuclease, hydrolase-DNA complex;	1e-21

>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 =  104 bits (260), Expect = 2e-28
 Identities = 30/87 (34%), Positives = 41/87 (47%), Gaps = 15/87 (17%)

Query: 13  QEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAA 72
           ++  K+ +   RV    V   K LLS MGIP+++               AP E EAQ A 
Sbjct: 114 KDAKKYAQAAGRVDEYIVDSAKTLLSYMGIPFVD---------------APSEGEAQAAY 158

Query: 73  MVKAGKVYATATEDMDALTFGTNILLR 99
           M   G V  T ++D D+L FG+  L R
Sbjct: 159 MAAKGDVEYTGSQDYDSLLFGSPRLAR 185

>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 =  103 bits (259), Expect = 3e-28
 Identities = 51/90 (56%), Positives = 62/90 (68%), Gaps = 15/90 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           G  QE++KF +RLV+V+  H  ECK LLSLMGIPY++               AP EAEA 
Sbjct: 117 GAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLD---------------APSEAEAS 161

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLR 99
           CAA+VKAGKVYA ATEDMD LTFG+ +L+R
Sbjct: 162 CAALVKAGKVYAAATEDMDCLTFGSPVLMR 191

>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 =  102 bits (257), Expect = 5e-28
 Identities = 34/94 (36%), Positives = 50/94 (53%), Gaps = 15/94 (15%)

Query: 6   FLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCE 65
            +   D +E  K+ +R+  ++   V+ CK LLSLMGIPY+E               AP E
Sbjct: 108 AIKKEDFEEAAKYAKRVSYLTPKMVENCKYLLSLMGIPYVE---------------APSE 152

Query: 66  AEAQCAAMVKAGKVYATATEDMDALTFGTNILLR 99
            EAQ + M K G V+A  ++D DAL +G   ++R
Sbjct: 153 GEAQASYMAKKGDVWAVVSQDYDALLYGAPRVVR 186

>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 =  101 bits (254), Expect = 2e-27
 Identities = 51/90 (56%), Positives = 62/90 (68%), Gaps = 15/90 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           G  QE++KF +RLV+V+  H  ECK LLSLMGIPY++               AP EAEA 
Sbjct: 117 GAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLD---------------APSEAEAS 161

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLR 99
           CAA+VKAGKVYA ATEDMD LTFG+ +L+R
Sbjct: 162 CAALVKAGKVYAAATEDMDCLTFGSPVLMR 191

>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 =  101 bits (253), Expect = 3e-27
 Identities = 31/91 (34%), Positives = 52/91 (57%), Gaps = 15/91 (16%)

Query: 9   TGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEA 68
            G  +E+ K+++ ++R+S++ V+E K+LL  MGIP ++               AP E EA
Sbjct: 108 EGKIEELRKYSQAILRLSNIMVEESKKLLRAMGIPIVQ---------------APSEGEA 152

Query: 69  QCAAMVKAGKVYATATEDMDALTFGTNILLR 99
           + A + K G  +A A++D DA+ FG   L+R
Sbjct: 153 EAAYLNKLGLSWAAASQDYDAILFGAKRLVR 183

>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus amylolyticus} Length = 363

 Score =  100 bits (250), Expect = 9e-27
 Identities = 30/91 (32%), Positives = 49/91 (53%), Gaps = 15/91 (16%)

Query: 9   TGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEA 68
           +GD +   ++     +++   V++ K LL  MGIP+++               AP E EA
Sbjct: 125 SGDLELARRYAMMSAKLTEEMVRDAKSLLDAMGIPWVQ---------------APAEGEA 169

Query: 69  QCAAMVKAGKVYATATEDMDALTFGTNILLR 99
           Q A +VK G  YA+A++D D+L FG+  L+R
Sbjct: 170 QAAYIVKKGDAYASASQDYDSLLFGSPKLVR 200

>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 = 98.8 bits (246), Expect = 2e-26
 Identities = 34/91 (37%), Positives = 51/91 (56%), Gaps = 15/91 (16%)

Query: 9   TGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEA 68
            G+ +E  K+ +R  RV+ + +++ K+LL LMGIP ++               AP E EA
Sbjct: 111 KGEIEEARKYAQRATRVNEMLIEDAKKLLELMGIPIVQ---------------APSEGEA 155

Query: 69  QCAAMVKAGKVYATATEDMDALTFGTNILLR 99
           Q A M   G VYA+A++D D+L FG   L+R
Sbjct: 156 QAAYMAAKGSVYASASQDYDSLLFGAPRLVR 186

>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A {Homo sapiens} PDB: 3qeb_Z* 3qea_Z* Length = 352

 Score = 86.6 bits (214), Expect = 1e-21
 Identities = 22/95 (23%), Positives = 35/95 (36%), Gaps = 15/95 (15%)

Query: 9   TGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEA 68
            G   E  +   R + ++     +  +     G+  +                AP EA+A
Sbjct: 109 EGKVSEARECFTRSINITHAMAHKVIKAARSQGVDCLV---------------APYEADA 153

Query: 69  QCAAMVKAGKVYATATEDMDALTFGTNILLRQQLS 103
           Q A + KAG V A  TED   L FG   ++ +   
Sbjct: 154 QLAYLNKAGIVQAIITEDSALLAFGCKKVILKMDQ 188

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	113
3ory_A	363	Flap endonuclease 1; hydrolase; 2.00A {Desulfuroco	99.88
3qe9_Y	352	Exonuclease 1; exonuclease, hydrolase-DNA complex;	99.87
1b43_A	340	Protein (FEN-1); nuclease, DNA repair, DNA replica	99.86
2izo_A	346	FEN1, flap structure-specific endonuclease; hydrol	99.86
3q8k_A	341	Flap endonuclease 1; helix-3 turn-helix, hydrophob	99.85
1a76_A	326	Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea	99.84
1rxw_A	336	Flap structure-specific endonuclease; helical clam	99.83
1ul1_X	379	Flap endonuclease-1; protein complex, DNA-binding	99.83
1bgx_T	832	TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhi	98.87
1exn_A	290	5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent	98.77
3h7i_A	305	Ribonuclease H, RNAse H; BPT4 RNAse H, 5'-3' exonu	95.28

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

Probab=99.88  E-value=5.7e-23  Score=168.34  Aligned_cols=89  Identities=34%  Similarity=0.555  Sum_probs=84.5

Q ss_pred             hhhHHHHcCCHHHHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeE
Q psy1207           2 ELTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYA   81 (113)
Q Consensus         2 ~~~~~~~~gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~   81 (113)
                      ++.+++++|+.+++.++++|++++|++|+..++++|+.|||||++               ||+|||||||+|+++|++|+
T Consensus       118 ~l~~~~~~g~~~~a~~~~~~~~~vt~~~~~~i~~lL~~~GIp~i~---------------apgEADaqiA~La~~g~~~~  182 (363)
T 3ory_A          118 KYEEAVQSGDLELARRYAMMSAKLTEEMVRDAKSLLDAMGIPWVQ---------------APAEGEAQAAYIVKKGDAYA  182 (363)
T ss_dssp             HHHHHHHHTCHHHHHHHTCCCCCCCHHHHHHHHHHHHHHTCCEEE---------------CSSCHHHHHHHHHHTTSCSE
T ss_pred             HHHHHHHcCCHHHHHHHHhccccCCHHHHHHHHHHHHHCCCCEEE---------------eCccHHHHHHHHHHCCCeEE
Confidence            456678899999999999999999999999999999999999999               99999999999999999999


Q ss_pred             EEcCCCceeeecCCeeeeccccCC
Q psy1207          82 TATEDMDALTFGTNILLRQQLSWA  105 (113)
Q Consensus        82 V~SeDsD~l~fGa~~vlr~~~~~~  105 (113)
                      |+|+|+|+|.||++.++++++..+
T Consensus       183 I~S~D~D~l~fg~~~v~~~l~~~~  206 (363)
T 3ory_A          183 SASQDYDSLLFGSPKLVRNLTISG  206 (363)
T ss_dssp             EECSSSHHHHTTCSEEEESTTTCE
T ss_pred             EECCCcCccccCCCeEEEEeeccc
Confidence            999999999999999999988654

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

Probab=99.87  E-value=1.9e-22  Score=164.46  Aligned_cols=89  Identities=26%  Similarity=0.309  Sum_probs=83.0

Q ss_pred             hhHHHHcCCHHHHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEE
Q psy1207           3 LTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYAT   82 (113)
Q Consensus         3 ~~~~~~~gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V   82 (113)
                      ..++.++|+.+++.++++|++++|+.|+..++++|+.|||||++               ||+|||||||+|.++|++|+|
T Consensus       103 ~~~~~~~g~~~~a~~~f~~~~~vt~~~~~~i~~~L~~~gIp~i~---------------ap~EADaqiA~La~~g~~~~I  167 (352)
T 3qe9_Y          103 GKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGVDCLV---------------APYEADAQLAYLNKAGIVQAI  167 (352)
T ss_dssp             HHHHTTSSCCHHHHHHHGGGCCCCHHHHHHHHHHHHHTTCEEEE---------------CSSCHHHHHHHHHHTTSCSEE
T ss_pred             HHHHHHhCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCCcEEE---------------CCcchHHHHHHHHHCCCeEEE
Confidence            34567789999999999999999999999999999999999999               999999999999999999999


Q ss_pred             EcCCCceeeecCCeeeeccccCCc
Q psy1207          83 ATEDMDALTFGTNILLRQQLSWAT  106 (113)
Q Consensus        83 ~SeDsD~l~fGa~~vlr~~~~~~~  106 (113)
                      +|+|+|+|.||++.++++++..+.
T Consensus       168 ~S~D~Dll~~~~~~v~~~~~~~~~  191 (352)
T 3qe9_Y          168 ITEDSALLAFGCKKVILKMDQFGN  191 (352)
T ss_dssp             ECSCGGGGGGTCSEEEESCCTTSE
T ss_pred             EeCCcCcccccCCeEEEeccCCCC
Confidence            999999999999999998876543

>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=99.86  E-value=5.3e-22  Score=159.40  Aligned_cols=88  Identities=40%  Similarity=0.619  Sum_probs=83.3

Q ss_pred             hHHHHcCCHHHHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEEE
Q psy1207           4 TLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATA   83 (113)
Q Consensus         4 ~~~~~~gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V~   83 (113)
                      .++.+.|+.+++.+++++++.+|+.++..++++|+.|||||++               ||+|||||||+|+++|++|+|+
T Consensus       106 ~~~yk~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~gip~i~---------------ap~EADa~iA~La~~g~~~~i~  170 (340)
T 1b43_A          106 REALEKGEIEEARKYAQRATRVNEMLIEDAKKLLELMGIPIVQ---------------APSEGEAQAAYMAAKGSVYASA  170 (340)
T ss_dssp             HHHHHHSCHHHHHHHHHTSGGGTHHHHHHHHHHHHHHTCCEEE---------------CSSCHHHHHHHHHHHTSSSEEE
T ss_pred             HHHHHcCCHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCcEEE---------------cChhHHHHHHHHHHcCCEEEEE
Confidence            4477899999999999999999999999999999999999999               9999999999999999999999


Q ss_pred             cCCCceeeecCCeeeeccccCCc
Q psy1207          84 TEDMDALTFGTNILLRQQLSWAT  106 (113)
Q Consensus        84 SeDsD~l~fGa~~vlr~~~~~~~  106 (113)
                      |+|+|+|+||++.++++++..+.
T Consensus       171 S~D~D~l~~g~~~v~~~~~~~~~  193 (340)
T 1b43_A          171 SQDYDSLLFGAPRLVRNLTITGK  193 (340)
T ss_dssp             CSSSHHHHTTCSEEEESTTTCEE
T ss_pred             ccCCCcceecCcEEEEEeccCCC
Confidence            99999999999999999886643

>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=99.86  E-value=3e-22  Score=161.60  Aligned_cols=87  Identities=37%  Similarity=0.580  Sum_probs=61.7

Q ss_pred             hhHHHHcCCHHHHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEE
Q psy1207           3 LTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYAT   82 (113)
Q Consensus         3 ~~~~~~~gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V   82 (113)
                      +.++.+.|+.+++.+|+++++.+|+.++..++++|+.|||||++               ||+|||||||+|++.|++|+|
T Consensus       102 l~~~~~~g~~~~a~~~~~~~~~vt~~~~~~~~~lL~~~gi~~i~---------------ap~EADa~ia~La~~g~~~~I  166 (346)
T 2izo_A          102 LERAKSEGKIEELRKYSQAILRLSNIMVEESKKLLRAMGIPIVQ---------------APSEGEAEAAYLNKLGLSWAA  166 (346)
T ss_dssp             -----------------------CHHHHHHHHHHHHHHTCCEEE---------------CSSCHHHHHHHHHHTTSSSEE
T ss_pred             HHHHHhcCCHHHHHHHHhhccCCCHHHHHHHHHHHHHCCCCEEE---------------cCCcHHHHHHHHHhCCCeEEE
Confidence            55677899999999999999999999999999999999999999               999999999999999999999


Q ss_pred             EcCCCceeeecCCeeeeccccC
Q psy1207          83 ATEDMDALTFGTNILLRQQLSW  104 (113)
Q Consensus        83 ~SeDsD~l~fGa~~vlr~~~~~  104 (113)
                      +|+|+|+|.||++.++++++..
T Consensus       167 ~S~D~D~l~~~~~~v~~~~~~~  188 (346)
T 2izo_A          167 ASQDYDAILFGAKRLVRNLTIT  188 (346)
T ss_dssp             ECSSSHHHHTTCSEEEESSCC-
T ss_pred             ECCCCCcceecCCeEEEEeccc
Confidence            9999999999999999998654

>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=99.85  E-value=2.6e-21  Score=157.04  Aligned_cols=86  Identities=60%  Similarity=0.979  Sum_probs=82.0

Q ss_pred             hhHHHHcCCHHHHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEE
Q psy1207           3 LTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYAT   82 (113)
Q Consensus         3 ~~~~~~~gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V   82 (113)
                      ++++.+.|+.+++.+|++|++++|+.++..++++|+.|||||++               ||+|||||||+|.++|.+++|
T Consensus       110 ~~~a~r~~~pe~l~~~~~~~~~vt~~q~~~~~~lL~~~gip~i~---------------ap~EADd~ia~La~~g~v~~i  174 (341)
T 3q8k_A          110 LQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLD---------------APSEAEASCAALVKAGKVYAA  174 (341)
T ss_dssp             HHHHHTTCCHHHHHHHHHHTCCCCHHHHHHHHHHHHHHTCCEEE---------------CSSCHHHHHHHHHHTTSSSEE
T ss_pred             HHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCCCEEE---------------CCccHHHHHHHHHhcCCeEEE
Confidence            45677889999999999999999999999999999999999999               999999999999999999999


Q ss_pred             EcCCCceeeecCCeeeecccc
Q psy1207          83 ATEDMDALTFGTNILLRQQLS  103 (113)
Q Consensus        83 ~SeDsD~l~fGa~~vlr~~~~  103 (113)
                      +|+|+|+|.||++.++++++.
T Consensus       175 ~s~D~D~l~~~~~~v~~~~~~  195 (341)
T 3q8k_A          175 ATEDMDCLTFGSPVLMRHLTA  195 (341)
T ss_dssp             ECSCTHHHHTTCSEEEESCCC
T ss_pred             EcCCccccccCCcEEEEcccc
Confidence            999999999999999999853

>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=99.84  E-value=4.5e-22  Score=158.99  Aligned_cols=88  Identities=39%  Similarity=0.625  Sum_probs=82.1

Q ss_pred             hhHHHHcCCHHHHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEE
Q psy1207           3 LTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYAT   82 (113)
Q Consensus         3 ~~~~~~~gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V   82 (113)
                      +.++.+.|+.+++.+++++++++|+.++..++++|+.|||||++               ||+|||||||+|.++|++++|
T Consensus       105 l~~~~~~g~~~~a~~~~~~~~~vt~~~~~~~~~lL~~~gi~~i~---------------apgEAD~~ia~La~~g~~~~I  169 (326)
T 1a76_A          105 MKEAIKKEDFEEAAKYAKRVSYLTPKMVENCKYLLSLMGIPYVE---------------APSEGEAQASYMAKKGDVWAV  169 (326)
T ss_dssp             CCCCCSHHHHHTTSTTGGGGCSSCHHHHHHHHHHHHHHTCCEEE---------------CSSCHHHHHHHHHHTTSSSEE
T ss_pred             HHHHHHcCCHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCCeEE---------------CCccHHHHHHHHHHCCCEEEE
Confidence            33456678899999999999999999999999999999999999               999999999999999999999


Q ss_pred             EcCCCceeeecCCeeeeccccCC
Q psy1207          83 ATEDMDALTFGTNILLRQQLSWA  105 (113)
Q Consensus        83 ~SeDsD~l~fGa~~vlr~~~~~~  105 (113)
                      +|+|+|+|.||++.++++++..+
T Consensus       170 ~S~D~Dll~~~~~~v~~~~~~~~  192 (326)
T 1a76_A          170 VSQDYDALLYGAPRVVRNLTTTK  192 (326)
T ss_dssp             ECSSSGGGGGTCSEEEESSSSCS
T ss_pred             ecCCcccceecCCEEEEeecCCC
Confidence            99999999999999999987653

>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=99.83  E-value=5.4e-21  Score=153.29  Aligned_cols=87  Identities=38%  Similarity=0.533  Sum_probs=80.9

Q ss_pred             hhHHHHcCCHHHHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEE
Q psy1207           3 LTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYAT   82 (113)
Q Consensus         3 ~~~~~~~gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V   82 (113)
                      +.++.+.|+ +++.++.++++.+|+.++..++++|+.|||||++               ||+|||||||+|.++|++++|
T Consensus       105 ~~~~~~~g~-~~l~~~~~~~~~vt~~~~~~~~~lL~~~gi~~i~---------------apgeAEA~lA~la~~g~~~~I  168 (336)
T 1rxw_A          105 WIAALQAGD-KDAKKYAQAAGRVDEYIVDSAKTLLSYMGIPFVD---------------APSEGEAQAAYMAAKGDVEYT  168 (336)
T ss_dssp             HHHHHHHTC-TTHHHHHHHHCCCCHHHHHHHHHHHHHTTCCEEE---------------CSSCHHHHHHHHHHTTSSSEE
T ss_pred             HHHHHHhch-HHHHHHHHhhccCCHHHHHHHHHHHHhCCCCEEE---------------cCchHHHHHHHHHHcCCeeEE
Confidence            456678888 8899999999999999999999999999999999               999999999999999999999


Q ss_pred             EcCCCceeeecCCeeeeccccCC
Q psy1207          83 ATEDMDALTFGTNILLRQQLSWA  105 (113)
Q Consensus        83 ~SeDsD~l~fGa~~vlr~~~~~~  105 (113)
                      +|+|+|+|.||++.++|+++.++
T Consensus       169 ~S~D~Dllql~~~~v~~~l~~~~  191 (336)
T 1rxw_A          169 GSQDYDSLLFGSPRLARNLAITG  191 (336)
T ss_dssp             ECSSSHHHHTTCSEEEESCCC--
T ss_pred             EcCCCCcceecCCeEEEeccccc
Confidence            99999999999999999987664

>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=99.83  E-value=2e-21  Score=158.82  Aligned_cols=86  Identities=60%  Similarity=0.979  Sum_probs=65.5

Q ss_pred             hhHHHHcCCHHHHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEE
Q psy1207           3 LTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYAT   82 (113)
Q Consensus         3 ~~~~~~~gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V   82 (113)
                      +.++.+.|+.+++++|+++++++|+.++..++++|+.|||||++               ||+|||||||+|+++|.+|+|
T Consensus       110 ~~~~~~~g~~~~~~~~~~~~~~vt~~~~~~~~~lL~~~Gi~~i~---------------apgEADd~iA~La~~g~~~~i  174 (379)
T 1ul1_X          110 LQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLD---------------APSEAEASCAALVKAGKVYAA  174 (379)
T ss_dssp             -------------------CCCCCCSCHHHHHHHHHHHTCCEEE---------------CSSCHHHHHHHHHHHTSSSEE
T ss_pred             HHHHHHcCCHHHHHHHHhhccCCCHHHHHHHHHHHHHcCCCeec---------------CCCcHHHHHHHHHhcCCeEEE
Confidence            45677889999999999999999999999999999999999999               999999999999999999999


Q ss_pred             EcCCCceeeecCCeeeecccc
Q psy1207          83 ATEDMDALTFGTNILLRQQLS  103 (113)
Q Consensus        83 ~SeDsD~l~fGa~~vlr~~~~  103 (113)
                      +|+|+|+|+||++.++++++.
T Consensus       175 iS~D~Dll~~g~~~v~~~~~~  195 (379)
T 1ul1_X          175 ATEDMDCLTFGSPVLMRHLTA  195 (379)
T ss_dssp             ECSCTHHHHTTCSEEEECSSC
T ss_pred             EecCcCccccccceEEEEecc
Confidence            999999999999999999864

>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=98.87  E-value=3.9e-10  Score=100.60  Aligned_cols=60  Identities=25%  Similarity=0.308  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcc-hHHHHHHHHHH----CCCeeEEEcCCCceeeecCCeeeeccc
Q psy1207          28 VHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPC-EAEAQCAAMVK----AGKVYATATEDMDALTFGTNILLRQQL  102 (113)
Q Consensus        28 ~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~-EAEAqcA~L~k----~G~vd~V~SeDsD~l~fGa~~vlr~~~  102 (113)
                      .++..++++|+.||||++.               +|+ |||+|||+|.+    .|..++|+|+|+|++.|+++.|.+..+
T Consensus        94 ~q~~~i~~~l~~~gi~~i~---------------~pg~EADD~iatLa~~~~~~G~~v~IvS~DkDllql~~~~v~~~~~  158 (832)
T 1bgx_T           94 RQLALIKELVDLLGLARLE---------------VPGYEADDVLASLAKKAEKEGYEVRILTADKDLYQLLSDRIHVLHP  158 (832)
T ss_dssp             TGGGTHHHHHHHTTCCCCC---------------CSSSCHHHHHHHHHHHHHHHTCCBCCCCSSTTCCTTCCTTBCBCCS
T ss_pred             HHHHHHHHHHHHCCCCEEE---------------eCCccHHHHHHHHHHHHHHcCCeEEEEeCCCChhhcCcCCEEEEeC
Confidence            4577899999999999999               996 99999999988    799999999999999999999887765

>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=98.77  E-value=6.5e-09  Score=83.36  Aligned_cols=56  Identities=21%  Similarity=0.102  Sum_probs=50.7

Q ss_pred             HHHHHHHHHHHHh--hCCcEEEecCCCCCCCCccCCCCcc-hHHHHHHHHHHC----CCeeEEEcCCCceeeecCCee
Q psy1207          27 SVHVKECKELLSL--MGIPYIEVSRSPRLLPNFLGVLAPC-EAEAQCAAMVKA----GKVYATATEDMDALTFGTNIL   97 (113)
Q Consensus        27 ~~~v~~~~~lL~~--~Gip~i~~~~~~~~~~~~~~~~AP~-EAEAqcA~L~k~----G~vd~V~SeDsD~l~fGa~~v   97 (113)
                      ++++..++++|+.  ||||++.               +|+ |||++||.|.++    |....|+|.|.|.+.++++.+
T Consensus       101 ~q~~~~ikell~~~~~gip~i~---------------~~g~EADDviatLa~~~~~~G~~v~IvS~DkDl~Qlv~~~v  163 (290)
T 1exn_A          101 EQFFEYLKDAFELCKTTFPTFT---------------IRGVEADDMAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKV  163 (290)
T ss_dssp             HHHHHHHHHHHHHHTTTSCEEC---------------CTTBCHHHHHHHHHHHHGGGSSCEEEECSCGGGGGGCCSSE
T ss_pred             HhhHHHHHHHHHhhCCCCcEEE---------------ECCcCHHHHHHHHHHHHHHCCCcEEEEeCCCChhhcCCCCE
Confidence            3447789999999  9999999               997 999999999987    777789999999999999875

>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=95.28  E-value=0.03  Score=45.45  Aligned_cols=49  Identities=24%  Similarity=0.219  Sum_probs=39.6

Q ss_pred             HHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcc-hHHHHHHHHHH----CCCeeEEEcCCCceeeecC
Q psy1207          31 KECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPC-EAEAQCAAMVK----AGKVYATATEDMDALTFGT   94 (113)
Q Consensus        31 ~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~-EAEAqcA~L~k----~G~vd~V~SeDsD~l~fGa   94 (113)
                      .-++++|+.||||++.               .|+ |||-.+|-|.+    .|.==.|+|.|.|.+=.-.
T Consensus       110 p~ike~l~a~gi~~l~---------------~~G~EADDiIgTLA~~a~~~g~~V~IvSgDKDl~QLv~  163 (305)
T 3h7i_A          110 KVIDELKAYMPYIVMD---------------IDKYEANDHIAVLVKKFSLEGHKILIISSDGDFTQLHK  163 (305)
T ss_dssp             HHHHHHHHHSSSEEEC---------------CTTCCHHHHHHHHHHHHHHTTCCEEEECSSCCCGGGGG
T ss_pred             HHHHHHHHHCCCCEEc---------------cCCccHHHHHHHHHHHHHHCCCcEEEEeCCCCcccccc
Confidence            5689999999999999               777 99988877765    4554579999999985543

---

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	113
d1rxwa2	217	c.120.1.2 (A:3-219) Flap endonuclease-1 (Fen-1 nuc	6e-16
d1b43a2	219	c.120.1.2 (A:1-219) Flap endonuclease-1 (Fen-1 nuc	7e-16
d1a77a2	207	c.120.1.2 (A:2-208) Flap endonuclease-1 (Fen-1 nuc	7e-16
d1ul1x2	216	c.120.1.2 (X:2-217) Flap endonuclease-1 (Fen-1 nuc	8e-15

>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 = 68.2 bits (166), Expect = 6e-16
 Identities = 29/83 (34%), Positives = 38/83 (45%), Gaps = 15/83 (18%)

Query: 17  KFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKA 76
           K+ +   RV    V   K LLS MGIP+++                P E EAQ A M   
Sbjct: 116 KYAQAAGRVDEYIVDSAKTLLSYMGIPFVDA---------------PSEGEAQAAYMAAK 160

Query: 77  GKVYATATEDMDALTFGTNILLR 99
           G V  T ++D D+L FG+  L R
Sbjct: 161 GDVEYTGSQDYDSLLFGSPRLAR 183

>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 = 67.9 bits (165), Expect = 7e-16
 Identities = 34/94 (36%), Positives = 51/94 (54%), Gaps = 15/94 (15%)

Query: 6   FLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCE 65
            L  G+ +E  K+ +R  RV+ + +++ K+LL LMGIP ++                P E
Sbjct: 107 ALEKGEIEEARKYAQRATRVNEMLIEDAKKLLELMGIPIVQA---------------PSE 151

Query: 66  AEAQCAAMVKAGKVYATATEDMDALTFGTNILLR 99
            EAQ A M   G VYA+A++D D+L FG   L+R
Sbjct: 152 GEAQAAYMAAKGSVYASASQDYDSLLFGAPRLVR 185

>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 = 67.8 bits (165), Expect = 7e-16
 Identities = 33/91 (36%), Positives = 48/91 (52%), Gaps = 15/91 (16%)

Query: 9   TGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEA 68
             D +E  K+ +R+  ++   V+ CK LLSLMGIPY+E                P E EA
Sbjct: 110 KEDFEEAAKYAKRVSYLTPKMVENCKYLLSLMGIPYVEA---------------PSEGEA 154

Query: 69  QCAAMVKAGKVYATATEDMDALTFGTNILLR 99
           Q + M K G V+A  ++D DAL +G   ++R
Sbjct: 155 QASYMAKKGDVWAVVSQDYDALLYGAPRVVR 185

>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 = 65.2 bits (158), Expect = 8e-15
 Identities = 50/91 (54%), Positives = 61/91 (67%), Gaps = 15/91 (16%)

Query: 9   TGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEA 68
            G  QE++KF +RLV+V+  H  ECK LLSLMGIPY++                P EAEA
Sbjct: 116 AGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDA---------------PSEAEA 160

Query: 69  QCAAMVKAGKVYATATEDMDALTFGTNILLR 99
            CAA+VKAGKVYA ATEDMD LTFG+ +L+R
Sbjct: 161 SCAALVKAGKVYAAATEDMDCLTFGSPVLMR 191

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	113
d1b43a2	219	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr	99.95
d1rxwa2	217	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc	99.94
d1a77a2	207	Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met	99.94
d1ul1x2	216	Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo	99.94
d1cmwa2	164	5' to 3' exonuclease domain of DNA polymerase Taq	95.05
d1ufma_	84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	84.02

>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=99.95  E-value=1.4e-28  Score=185.82  Aligned_cols=92  Identities=38%  Similarity=0.589  Sum_probs=86.3

Q ss_pred             hhHHHHcCCHHHHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEE
Q psy1207           3 LTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYAT   82 (113)
Q Consensus         3 ~~~~~~~gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V   82 (113)
                      +.++.++|+.+++.++.++.+.+|+.++..++++|+.+|||||+               ||||||||||+|+++|+||+|
T Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~~~lL~~~gv~~i~---------------Ap~EAdaqcA~L~~~g~vd~v  168 (219)
T d1b43a2         104 WREALEKGEIEEARKYAQRATRVNEMLIEDAKKLLELMGIPIVQ---------------APSEGEAQAAYMAAKGSVYAS  168 (219)
T ss_dssp             HHHHHHHSCHHHHHHHHHTSGGGTHHHHHHHHHHHHHHTCCEEE---------------CSSCHHHHHHHHHHHTSSSEE
T ss_pred             hhhhhhccchhhhhhhhcccccCCHHHHHHHHHHHHHcCCceee---------------CchHHHHHHHHHHhcCCeEEE
Confidence            45677899999999999999999999999999999999999999               999999999999999999999


Q ss_pred             EcCCCceeeecCCeeeeccccCCceee
Q psy1207          83 ATEDMDALTFGTNILLRQQLSWATFSM  109 (113)
Q Consensus        83 ~SeDsD~l~fGa~~vlr~~~~~~~~~~  109 (113)
                      +|||||+|+|||+++||+++..++..+
T Consensus       169 ~SeDsD~L~fG~~~vl~~l~~~~~~~~  195 (219)
T d1b43a2         169 ASQDYDSLLFGAPRLVRNLTITGKRKL  195 (219)
T ss_dssp             ECSSSHHHHTTCSEEEESTTTCEEEEC
T ss_pred             EecccceeeeCCCEEEEecccccCccc
Confidence            999999999999999999987765443

>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=99.94  E-value=3.6e-28  Score=183.01  Aligned_cols=90  Identities=37%  Similarity=0.510  Sum_probs=77.7

Q ss_pred             hHHHHcCCHHHHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEEE
Q psy1207           4 TLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATA   83 (113)
Q Consensus         4 ~~~~~~gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V~   83 (113)
                      ..+.+.++. ++.++.+++.++|++++..++++|+.+|||||+               ||||||||||+|+++|+||+|+
T Consensus       104 ~~~~~~~~~-~~~~~~~~~~~vt~~~~~~~~~lL~~~gi~~i~---------------Ap~EAeaqcA~L~~~g~vd~v~  167 (217)
T d1rxwa2         104 IAALQAGDK-DAKKYAQAAGRVDEYIVDSAKTLLSYMGIPFVD---------------APSEGEAQAAYMAAKGDVEYTG  167 (217)
T ss_dssp             HHHHHHTCT-THHHHHHHHCCCCHHHHHHHHHHHHHTTCCEEE---------------CSSCHHHHHHHHHHTTSSSEEE
T ss_pred             hhhhhhhhH-HHHHHHHhhccCCHHHHHHHHHHHHHcCceEEe---------------cCchHHHHHHHHHhCCCeEEEE
Confidence            344555654 578888999999999999999999999999999               9999999999999999999999


Q ss_pred             cCCCceeeecCCeeeeccccCCceee
Q psy1207          84 TEDMDALTFGTNILLRQQLSWATFSM  109 (113)
Q Consensus        84 SeDsD~l~fGa~~vlr~~~~~~~~~~  109 (113)
                      |+|||+|+|||++|||+++..++...
T Consensus       168 seDsD~l~fG~~~vir~l~~~~~~~~  193 (217)
T d1rxwa2         168 SQDYDSLLFGSPRLARNLAITGKRKL  193 (217)
T ss_dssp             CSSSHHHHTTCSEEEESCCC------
T ss_pred             ecccceeeeCCCEEEEecccccCccC
Confidence            99999999999999999997665433

>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=99.94  E-value=1.8e-28  Score=183.92  Aligned_cols=85  Identities=40%  Similarity=0.656  Sum_probs=78.9

Q ss_pred             HHcCCHHHHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEEEcCC
Q psy1207           7 LLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYATATED   86 (113)
Q Consensus         7 ~~~gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V~SeD   86 (113)
                      .+.++.+++.++.++++++|+.++++++++|+.+|||||+               ||||||||||+|+++|+||+|+|+|
T Consensus       108 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~ll~~~gi~yi~---------------Ap~EAeaqcA~L~~~g~vd~v~seD  172 (207)
T d1a77a2         108 IKKEDFEEAAKYAKRVSYLTPKMVENCKYLLSLMGIPYVE---------------APSEGEAQASYMAKKGDVWAVVSQD  172 (207)
T ss_dssp             CSHHHHSSTTSSSSTTCSCCHHHHHHHHHHHHHHTCCEEE---------------CSSCHHHHHHHHHHHTSSSEEECSS
T ss_pred             hccccHHHHhhhcccceecCHHHHHHHHHHHHHcCCceEe---------------cCccHHHHHHHHHHcCCeEEEEecc
Confidence            3446667888899999999999999999999999999999               9999999999999999999999999


Q ss_pred             CceeeecCCeeeeccccCCc
Q psy1207          87 MDALTFGTNILLRQQLSWAT  106 (113)
Q Consensus        87 sD~l~fGa~~vlr~~~~~~~  106 (113)
                      ||+|+|||++|||+++..++
T Consensus       173 sD~l~yG~~~vir~l~~~~~  192 (207)
T d1a77a2         173 YDALLYGAPRVVRNLTTTKE  192 (207)
T ss_dssp             SGGGGGTCSEEEESSSCCSS
T ss_pred             cceeccCCCEEEEecccCCC
Confidence            99999999999999986544

>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=99.94  E-value=7.8e-28  Score=179.21  Aligned_cols=89  Identities=58%  Similarity=0.936  Sum_probs=67.3

Q ss_pred             hhHHHHcCCHHHHHHHhhhccCCCHHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcchHHHHHHHHHHCCCeeEE
Q psy1207           3 LTLFLLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMVKAGKVYAT   82 (113)
Q Consensus         3 ~~~~~~~gd~~~a~~~~~r~~~vt~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~EAEAqcA~L~k~G~vd~V   82 (113)
                      +..+.+.++.+++.++.++.+.+|+.++..++++|+.+|||||+               ||||||||||+|+++|.||+|
T Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~ll~~~gv~~i~---------------Ap~EAdaq~A~L~~~g~vd~v  174 (216)
T d1ul1x2         110 LQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLD---------------APSEAEASCAALVKAGKVYAA  174 (216)
T ss_dssp             -------------------CCCCCCSCHHHHHHHHHHHTCCEEE---------------CSSCHHHHHHHHHHHTSSSEE
T ss_pred             HHhhhhcchHHHHHHhhccCeeccHHHHHHHHHHHHhcCeeeEe---------------ccchHHHHHHHHHhcCceEEE
Confidence            45667788999999999999999999999999999999999999               999999999999999999999


Q ss_pred             EcCCCceeeecCCeeeeccccCCc
Q psy1207          83 ATEDMDALTFGTNILLRQQLSWAT  106 (113)
Q Consensus        83 ~SeDsD~l~fGa~~vlr~~~~~~~  106 (113)
                      +|+|||+|+|||++|||+++..+.
T Consensus       175 ~S~DsD~l~fG~~~vi~~~~~~~~  198 (216)
T d1ul1x2         175 ATEDMDCLTFGSPVLMRHLTASEA  198 (216)
T ss_dssp             ECSCTHHHHTTCSEEEECSSCCC-
T ss_pred             EccccceeccCCcEEEEecccccC
Confidence            999999999999999999986643

>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=95.05  E-value=0.0075  Score=41.67  Aligned_cols=51  Identities=29%  Similarity=0.409  Sum_probs=38.8

Q ss_pred             HHHHHHHHHHHHhhCCcEEEecCCCCCCCCccCCCCcc-hHHHHHHHHHH----CCCeeEEEcCCCceeee
Q psy1207          27 SVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPC-EAEAQCAAMVK----AGKVYATATEDMDALTF   92 (113)
Q Consensus        27 ~~~v~~~~~lL~~~Gip~i~~~~~~~~~~~~~~~~AP~-EAEAqcA~L~k----~G~vd~V~SeDsD~l~f   92 (113)
                      ......++++++.+|++++.               .|+ |||=..|.|++    .|.==.|+|.|.|.+=.
T Consensus        84 ~~~~~~~~~~~~~~g~~~~~---------------~~~~EADDvIa~la~~~~~~~~~v~IvS~DkD~~QL  139 (164)
T d1cmwa2          84 PRQLALIKELVDLLGLARLE---------------VPGYEADDVLASLAKKAEKEGYEVRILTADKDLYQL  139 (164)
T ss_dssp             HHHHHHHHHHHHHTTCEEEC---------------CTTSCHHHHHHHHHHHHHHTTEEEEEECSSGGGGGS
T ss_pred             HHHHHHHHHHHhhcCceEEE---------------ecCcchHHHHHHHHHHhccccceEEEecCCCChHHh
Confidence            44566789999999999998               665 99988888765    34322588999997643

>d1ufma_ a.4.5.47 (A:) COP9 signalosome complex subunit 4, GSN4 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: COP9 signalosome complex subunit 4, GSN4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.02  E-value=0.54  Score=29.23  Aligned_cols=35  Identities=17%  Similarity=0.229  Sum_probs=31.8

Q ss_pred             CcchHHHHHHHHHHCCCeeEEEcCCCceeeecCCe
Q psy1207          62 APCEAEAQCAAMVKAGKVYATATEDMDALTFGTNI   96 (113)
Q Consensus        62 AP~EAEAqcA~L~k~G~vd~V~SeDsD~l~fGa~~   96 (113)
                      .+.|+|..++.|...|.+++-|..-..++.|..+.
T Consensus        43 ~~~evE~~l~~mI~~~~i~akIDq~~g~V~F~~~e   77 (84)
T d1ufma_          43 PAAKAEKIASQMITEGRMNGFIDQIDGIVHFETRE   77 (84)
T ss_dssp             CHHHHHHHHHHHHHTTSSCEEEETTTTEEEECCSS
T ss_pred             CHHHHHHHHHHHHhcCeEEEEEeCCCCEEEECCCC
Confidence            47799999999999999999999999999998763